From 0e9640f65e822f1b2e1a3cc0744011d64778058c Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 19 Mar 2024 11:44:14 +0000 Subject: [PATCH 001/574] Module test data uses paths rather than config map This makes tests reusable in pipeline repos Closes #2858 --- CHANGELOG.md | 1 + nf_core/module-template/tests/main.nf.test | 12 ++++++------ 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a47fda7270..51cdfa947a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846)) - Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848)) - Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849)) +- Module test data uses paths rather than config map ### Linting diff --git a/nf_core/module-template/tests/main.nf.test b/nf_core/module-template/tests/main.nf.test index e1b1dadf12..a53131ca20 100644 --- a/nf_core/module-template/tests/main.nf.test +++ b/nf_core/module-template/tests/main.nf.test @@ -28,10 +28,10 @@ nextflow_process { {% if has_meta %} input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] {%- else %} - input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), {%- endif %} """ } @@ -60,10 +60,10 @@ nextflow_process { {% if has_meta %} input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] {%- else %} - input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), {%- endif %} """ } From bb53c9dc8e5db0e3258839dfc0bb1d54ae12c3d2 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 19 Mar 2024 11:46:45 +0000 Subject: [PATCH 002/574] Update subworkflow test data --- CHANGELOG.md | 2 +- nf_core/subworkflow-template/tests/main.nf.test | 14 ++++++++------ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 51cdfa947a..33b9827bd9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ - Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846)) - Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848)) - Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849)) -- Module test data uses paths rather than config map +- Module and subworkflow test data uses paths rather than config map ([#]()) ### Linting diff --git a/nf_core/subworkflow-template/tests/main.nf.test b/nf_core/subworkflow-template/tests/main.nf.test index c44e19a4e4..897888369b 100644 --- a/nf_core/subworkflow-template/tests/main.nf.test +++ b/nf_core/subworkflow-template/tests/main.nf.test @@ -22,12 +22,14 @@ nextflow_workflow { workflow { """ // TODO nf-core: define inputs of the workflow here. Example: - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] """ } } From f6bd633a55c3bd586ac8cfe607c19ad4abd30859 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 19 Mar 2024 11:47:51 +0000 Subject: [PATCH 003/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 33b9827bd9..25c854beb2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ - Strip out mention of "Nextflow Tower" and replace with "Seqera Platform" wherever possible - Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.3 ([#2850](https://github.com/nf-core/tools/pull/2850)) - Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862)) +- 2858 Test data uses paths instead of config map ([#2877](https://github.com/nf-core/tools/pull/2877)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From 065d1c34dffe9bbc45b9eae66e4090ca3426742e Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 19 Mar 2024 11:48:12 +0000 Subject: [PATCH 004/574] CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 25c854beb2..10d2b42799 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ - Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846)) - Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848)) - Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849)) -- Module and subworkflow test data uses paths rather than config map ([#]()) +- Module and subworkflow test data uses paths rather than config map ([#2877](https://github.com/nf-core/tools/pull/2877)) ### Linting From 6bf5389f6c20c55e071d6255e8960146393fb244 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Tue, 19 Mar 2024 11:49:08 +0000 Subject: [PATCH 005/574] Auto changelog did it all for me --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10d2b42799..bd3e253bec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,6 @@ - Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846)) - Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848)) - Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849)) -- Module and subworkflow test data uses paths rather than config map ([#2877](https://github.com/nf-core/tools/pull/2877)) ### Linting @@ -38,7 +37,7 @@ - Strip out mention of "Nextflow Tower" and replace with "Seqera Platform" wherever possible - Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.3 ([#2850](https://github.com/nf-core/tools/pull/2850)) - Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862)) -- 2858 Test data uses paths instead of config map ([#2877](https://github.com/nf-core/tools/pull/2877)) +- Test data uses paths instead of config map ([#2877](https://github.com/nf-core/tools/pull/2877)) ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29] From 33179ea81b05862fcdd2fca844d96fdaf91ca241 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 22 May 2024 11:06:20 -0400 Subject: [PATCH 006/574] Removes tags.yml from module and subworkflow template tags.yml is no longer needed with newer testing workflows. This PR removes the file from the module and subworkflow templates and updates the linting tests to reflect this. Related to #2881 --- .prettierignore | 2 - nf_core/components/create.py | 46 ++- nf_core/components/nfcore_component.py | 10 +- nf_core/module-template/tests/tags.yml | 2 - nf_core/modules/lint/module_tests.py | 103 +++-- nf_core/subworkflow-template/tests/tags.yml | 2 - .../subworkflows/lint/subworkflow_tests.py | 124 +++--- tests/modules/lint.py | 381 +++++++++++++----- tests/subworkflows/lint.py | 211 ++++++---- 9 files changed, 599 insertions(+), 282 deletions(-) delete mode 100644 nf_core/module-template/tests/tags.yml delete mode 100644 nf_core/subworkflow-template/tests/tags.yml diff --git a/.prettierignore b/.prettierignore index b923532bd7..2a445d487f 100644 --- a/.prettierignore +++ b/.prettierignore @@ -4,8 +4,6 @@ slackreport.json docs/api/_build testing nf_core/module-template/meta.yml -nf_core/module-template/tests/tags.yml -nf_core/subworkflow-template/tests/tags.yml nf_core/pipeline-template/nextflow_schema.json # don't run on things handled by ruff *.py diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 6c9c01b496..f2ffa3caf5 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -88,8 +88,7 @@ def create(self): ├── meta.yml ├── environment.yml └── tests - ├── main.nf.test - └── tags.yml + └── main.nf.test ``` The function will attempt to automatically find a Bioconda package called @@ -102,8 +101,7 @@ def create(self): ├── main.nf ├── meta.yml └── tests - ├── main.nf.test - └── tags.yml + └── main.nf.test ``` """ @@ -228,7 +226,13 @@ def _get_bioconda_tool(self): log.info(f"Could not find a Docker/Singularity container ({e})") def _get_module_structure_components(self): - process_label_defaults = ["process_single", "process_low", "process_medium", "process_high", "process_long"] + process_label_defaults = [ + "process_single", + "process_low", + "process_medium", + "process_high", + "process_long", + ] if self.process_label is None: log.info( "Provide an appropriate resource label for the process, taken from the " @@ -252,7 +256,8 @@ def _get_module_structure_components(self): ) while self.has_meta is None: self.has_meta = rich.prompt.Confirm.ask( - "[violet]Will the module require a meta map of sample information?", default=True + "[violet]Will the module require a meta map of sample information?", + default=True, ) def _render_template(self): @@ -262,7 +267,8 @@ def _render_template(self): object_attrs = vars(self) # Run jinja2 for each file in the template folder env = jinja2.Environment( - loader=jinja2.PackageLoader("nf_core", f"{self.component_type[:-1]}-template"), keep_trailing_newline=True + loader=jinja2.PackageLoader("nf_core", f"{self.component_type[:-1]}-template"), + keep_trailing_newline=True, ) for template_fn, dest_fn in self.file_paths.items(): log.debug(f"Rendering template file: '{template_fn}'") @@ -372,7 +378,13 @@ def _get_component_dirs(self): if self.component_type == "modules": # If a subtool, check if there is a module called the base tool name already - parent_tool_main_nf = Path(self.directory, self.component_type, self.org, self.component, "main.nf") + parent_tool_main_nf = Path( + self.directory, + self.component_type, + self.org, + self.component, + "main.nf", + ) if self.subtool and parent_tool_main_nf.exists() and not self.migrate_pytest: raise UserWarning( f"Module '{parent_tool_main_nf}' exists already, cannot make subtool '{self.component_name}'" @@ -393,7 +405,6 @@ def _get_component_dirs(self): file_paths["meta.yml"] = component_dir / "meta.yml" if self.component_type == "modules": file_paths["environment.yml"] = component_dir / "environment.yml" - file_paths["tests/tags.yml"] = component_dir / "tests" / "tags.yml" file_paths["tests/main.nf.test.j2"] = component_dir / "tests" / "main.nf.test" return file_paths @@ -428,11 +439,15 @@ def _copy_old_files(self, component_old_path): shutil.copyfile(component_old_path / "meta.yml", self.file_paths["meta.yml"]) if self.component_type == "modules": log.debug("Copying original environment.yml file") - shutil.copyfile(component_old_path / "environment.yml", self.file_paths["environment.yml"]) + shutil.copyfile( + component_old_path / "environment.yml", + self.file_paths["environment.yml"], + ) if (component_old_path / "templates").is_dir(): log.debug("Copying original templates directory") shutil.copytree( - component_old_path / "templates", self.file_paths["environment.yml"].parent / "templates" + component_old_path / "templates", + self.file_paths["environment.yml"].parent / "templates", ) # Create a nextflow.config file if it contains information other than publishDir pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir) @@ -447,7 +462,14 @@ def _copy_old_files(self, component_old_path): if len(config_lines) > 11: log.debug("Copying nextflow.config file from pytest tests") with open( - Path(self.directory, self.component_type, self.org, self.component_dir, "tests", "nextflow.config"), + Path( + self.directory, + self.component_type, + self.org, + self.component_dir, + "tests", + "nextflow.config", + ), "w+", ) as ofh: ofh.write(config_lines) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index bcba068afe..5d0baf63dd 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -17,7 +17,14 @@ class NFCoreComponent: """ def __init__( - self, component_name, repo_url, component_dir, repo_type, base_dir, component_type, remote_component=True + self, + component_name, + repo_url, + component_dir, + repo_type, + base_dir, + component_type, + remote_component=True, ): """ Initialize the object @@ -59,7 +66,6 @@ def __init__( self.org = repo_dir self.nftest_testdir = Path(self.component_dir, "tests") self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test") - self.tags_yml = Path(self.nftest_testdir, "tags.yml") if self.repo_type == "pipeline": patch_fn = f"{self.component_name.replace('/', '-')}.diff" diff --git a/nf_core/module-template/tests/tags.yml b/nf_core/module-template/tests/tags.yml deleted file mode 100644 index e7fac9f5b9..0000000000 --- a/nf_core/module-template/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -{{ component_dir }}: - - "modules/{{ org }}/{{ component_dir }}/**" diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index b2b6c2221f..694aee9c17 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -18,7 +18,7 @@ def module_tests(_, module: NFCoreComponent): Lint the tests of a module in ``nf-core/modules`` It verifies that the test directory exists - and contains a ``main.nf.test`` a ``main.nf.test.snap`` and ``tags.yml``. + and contains a ``main.nf.test`` and a ``main.nf.test.snap`` """ repo_dir = module.component_dir.parts[: module.component_dir.parts.index(module.component_name.split("/")[0])][-1] @@ -29,9 +29,21 @@ def module_tests(_, module: NFCoreComponent): module.passed.append(("test_dir_exists", "nf-test test directory exists", module.nftest_testdir)) else: if is_pytest: - module.warned.append(("test_dir_exists", "nf-test directory is missing", module.nftest_testdir)) + module.warned.append( + ( + "test_dir_exists", + "nf-test directory is missing", + module.nftest_testdir, + ) + ) else: - module.failed.append(("test_dir_exists", "nf-test directory is missing", module.nftest_testdir)) + module.failed.append( + ( + "test_dir_exists", + "nf-test directory is missing", + module.nftest_testdir, + ) + ) return # Lint the test main.nf file @@ -39,9 +51,21 @@ def module_tests(_, module: NFCoreComponent): module.passed.append(("test_main_nf_exists", "test `main.nf.test` exists", module.nftest_main_nf)) else: if is_pytest: - module.warned.append(("test_main_nf_exists", "test `main.nf.test` does not exist", module.nftest_main_nf)) + module.warned.append( + ( + "test_main_nf_exists", + "test `main.nf.test` does not exist", + module.nftest_main_nf, + ) + ) else: - module.failed.append(("test_main_nf_exists", "test `main.nf.test` does not exist", module.nftest_main_nf)) + module.failed.append( + ( + "test_main_nf_exists", + "test `main.nf.test` does not exist", + module.nftest_main_nf, + ) + ) if module.nftest_main_nf.is_file(): # Check if main.nf.test.snap file exists, if 'snap(' is inside main.nf.test @@ -50,7 +74,11 @@ def module_tests(_, module: NFCoreComponent): snap_file = module.nftest_testdir / "main.nf.test.snap" if snap_file.is_file(): module.passed.append( - ("test_snapshot_exists", "snapshot file `main.nf.test.snap` exists", snap_file) + ( + "test_snapshot_exists", + "snapshot file `main.nf.test.snap` exists", + snap_file, + ) ) # Validate no empty files with open(snap_file) as snap_fh: @@ -133,7 +161,11 @@ def module_tests(_, module: NFCoreComponent): ) else: module.failed.append( - ("test_snapshot_exists", "snapshot file `main.nf.test.snap` does not exist", snap_file) + ( + "test_snapshot_exists", + "snapshot file `main.nf.test.snap` does not exist", + snap_file, + ) ) # Verify that tags are correct. main_nf_tags = module._get_main_nf_tags(module.nftest_main_nf) @@ -148,7 +180,13 @@ def module_tests(_, module: NFCoreComponent): if tag not in main_nf_tags: missing_tags.append(tag) if len(missing_tags) == 0: - module.passed.append(("test_main_tags", "Tags adhere to guidelines", module.nftest_main_nf)) + module.passed.append( + ( + "test_main_tags", + "Tags adhere to guidelines", + module.nftest_main_nf, + ) + ) else: module.failed.append( ( @@ -174,41 +212,20 @@ def module_tests(_, module: NFCoreComponent): ) else: module.passed.append( - ("test_pytest_yml", "module with nf-test not in pytest_modules.yml", pytest_yml_path) - ) - except FileNotFoundError: - module.warned.append(("test_pytest_yml", "Could not open pytest_modules.yml file", pytest_yml_path)) - - if module.tags_yml.is_file(): - # Check that tags.yml exists and it has the correct entry - module.passed.append(("test_tags_yml_exists", "file `tags.yml` exists", module.tags_yml)) - with open(module.tags_yml) as fh: - tags_yml = yaml.safe_load(fh) - if module.component_name in tags_yml.keys(): - module.passed.append(("test_tags_yml", "correct entry in tags.yml", module.tags_yml)) - if f"modules/{module.org}/{module.component_name}/**" in tags_yml[module.component_name]: - module.passed.append(("test_tags_yml", "correct path in tags.yml", module.tags_yml)) - else: - module.failed.append( ( - "test_tags_yml", - f"incorrect path in tags.yml, expected `modules/{module.org}/{module.component_name}/**`, got `{tags_yml[module.component_name][0]}`", - module.tags_yml, + "test_pytest_yml", + "module with nf-test not in pytest_modules.yml", + pytest_yml_path, ) ) - else: - module.failed.append( - ( - "test_tags_yml", - f"incorrect key in tags.yml, should be `{module.component_name}`, got `{list(tags_yml.keys())[0]}`.", - module.tags_yml, - ) + except FileNotFoundError: + module.warned.append( + ( + "test_pytest_yml", + "Could not open pytest_modules.yml file", + pytest_yml_path, ) - else: - if is_pytest: - module.warned.append(("test_tags_yml_exists", "file `tags.yml` does not exist", module.tags_yml)) - else: - module.failed.append(("test_tags_yml_exists", "file `tags.yml` does not exist", module.tags_yml)) + ) # Check that the old test directory does not exist if not is_pytest: @@ -222,4 +239,10 @@ def module_tests(_, module: NFCoreComponent): ) ) else: - module.passed.append(("test_old_test_dir", "Old pytests don't exist for this module", old_test_dir)) + module.passed.append( + ( + "test_old_test_dir", + "Old pytests don't exist for this module", + old_test_dir, + ) + ) diff --git a/nf_core/subworkflow-template/tests/tags.yml b/nf_core/subworkflow-template/tests/tags.yml deleted file mode 100644 index 35cad36785..0000000000 --- a/nf_core/subworkflow-template/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/{{ component_name_underscore }}: - - subworkflows/{{ org }}/{{ component_dir }}/** diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index cfae2d553c..b7ab685095 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -18,7 +18,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): Lint the tests of a subworkflow in ``nf-core/modules`` It verifies that the test directory exists - and contains a ``main.nf.test`` a ``main.nf.test.snap`` and ``tags.yml``. + and contains a ``main.nf.test`` and a ``main.nf.test.snap`` Additionally, checks that all included components in test ``main.nf`` are specified in ``test.yml`` """ @@ -26,30 +26,68 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): repo_dir = subworkflow.component_dir.parts[ : subworkflow.component_dir.parts.index(subworkflow.component_name.split("/")[0]) ][-1] - test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", repo_dir, subworkflow.component_name) + test_dir = Path( + subworkflow.base_dir, + "tests", + "subworkflows", + repo_dir, + subworkflow.component_name, + ) pytest_main_nf = Path(test_dir, "main.nf") is_pytest = pytest_main_nf.is_file() log.debug(f"{pytest_main_nf} is pytest: {is_pytest}") if subworkflow.nftest_testdir.is_dir(): - subworkflow.passed.append(("test_dir_exists", "nf-test test directory exists", subworkflow.nftest_testdir)) + subworkflow.passed.append( + ( + "test_dir_exists", + "nf-test test directory exists", + subworkflow.nftest_testdir, + ) + ) else: if is_pytest: - subworkflow.warned.append(("test_dir_exists", "nf-test directory is missing", subworkflow.nftest_testdir)) + subworkflow.warned.append( + ( + "test_dir_exists", + "nf-test directory is missing", + subworkflow.nftest_testdir, + ) + ) else: - subworkflow.failed.append(("test_dir_exists", "nf-test directory is missing", subworkflow.nftest_testdir)) + subworkflow.failed.append( + ( + "test_dir_exists", + "nf-test directory is missing", + subworkflow.nftest_testdir, + ) + ) return # Lint the test main.nf file if subworkflow.nftest_main_nf.is_file(): - subworkflow.passed.append(("test_main_nf_exists", "test `main.nf.test` exists", subworkflow.nftest_main_nf)) + subworkflow.passed.append( + ( + "test_main_nf_exists", + "test `main.nf.test` exists", + subworkflow.nftest_main_nf, + ) + ) else: if is_pytest: subworkflow.warned.append( - ("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf) + ( + "test_main_nf_exists", + "test `main.nf.test` does not exist", + subworkflow.nftest_main_nf, + ) ) else: subworkflow.failed.append( - ("test_main_nf_exists", "test `main.nf.test` does not exist", subworkflow.nftest_main_nf) + ( + "test_main_nf_exists", + "test `main.nf.test` does not exist", + subworkflow.nftest_main_nf, + ) ) if subworkflow.nftest_main_nf.is_file(): @@ -58,7 +96,13 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): if "snapshot(" in fh.read(): snap_file = subworkflow.nftest_testdir / "main.nf.test.snap" if snap_file.is_file(): - subworkflow.passed.append(("test_snapshot_exists", "test `main.nf.test.snap` exists", snap_file)) + subworkflow.passed.append( + ( + "test_snapshot_exists", + "test `main.nf.test.snap` exists", + snap_file, + ) + ) # Validate no empty files with open(snap_file) as snap_fh: try: @@ -140,7 +184,11 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): ) else: subworkflow.failed.append( - ("test_snapshot_exists", "test `main.nf.test.snap` does not exist", snap_file) + ( + "test_snapshot_exists", + "test `main.nf.test.snap` does not exist", + snap_file, + ) ) # Verify that tags are correct. main_nf_tags = subworkflow._get_main_nf_tags(subworkflow.nftest_main_nf) @@ -161,7 +209,13 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): if tag not in main_nf_tags: missing_tags.append(tag) if len(missing_tags) == 0: - subworkflow.passed.append(("test_main_tags", "Tags adhere to guidelines", subworkflow.nftest_main_nf)) + subworkflow.passed.append( + ( + "test_main_tags", + "Tags adhere to guidelines", + subworkflow.nftest_main_nf, + ) + ) else: subworkflow.failed.append( ( @@ -187,43 +241,17 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): ) else: subworkflow.passed.append( - ("test_pytest_yml", "subworkflow with nf-test not in pytest_modules.yml", pytest_yml_path) + ( + "test_pytest_yml", + "subworkflow with nf-test not in pytest_modules.yml", + pytest_yml_path, + ) ) except FileNotFoundError: - subworkflow.warned.append(("test_pytest_yml", "Could not open pytest_modules.yml file", pytest_yml_path)) - - if subworkflow.tags_yml.is_file(): - # Check tags.yml exists and it has the correct entry - subworkflow.passed.append(("test_tags_yml_exists", "file `tags.yml` exists", subworkflow.tags_yml)) - with open(subworkflow.tags_yml) as fh: - tags_yml = yaml.safe_load(fh) - if "subworkflows/" + subworkflow.component_name in tags_yml.keys(): - subworkflow.passed.append(("test_tags_yml", "correct entry in tags.yml", subworkflow.tags_yml)) - if ( - f"subworkflows/{subworkflow.org}/{subworkflow.component_name}/**" - in tags_yml["subworkflows/" + subworkflow.component_name] - ): - subworkflow.passed.append(("test_tags_yml", "correct path in tags.yml", subworkflow.tags_yml)) - else: - subworkflow.failed.append(("test_tags_yml", "incorrect path in tags.yml", subworkflow.tags_yml)) - else: - subworkflow.failed.append( - ( - "test_tags_yml", - "incorrect entry in tags.yml, should be 'subworkflows/'", - subworkflow.tags_yml, - ) + subworkflow.warned.append( + ( + "test_pytest_yml", + "Could not open pytest_modules.yml file", + pytest_yml_path, ) - else: - if is_pytest: - subworkflow.warned.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml)) - else: - subworkflow.failed.append(("test_tags_yml_exists", "file `tags.yml` does not exist", subworkflow.tags_yml)) - - # Check that the old test directory does not exist - if not is_pytest: - old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name) - if old_test_dir.is_dir(): - subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir)) - else: - subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir)) + ) diff --git a/tests/modules/lint.py b/tests/modules/lint.py index 595509de4e..6bb74d34ed 100644 --- a/tests/modules/lint.py +++ b/tests/modules/lint.py @@ -15,7 +15,12 @@ def setup_patch(pipeline_dir: str, modify_module: bool): install_obj = nf_core.modules.ModuleInstall( - pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=CORRECT_SHA + pipeline_dir, + prompt=False, + force=False, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + sha=CORRECT_SHA, ) # Install the module @@ -112,7 +117,10 @@ def test_modules_lint_patched_modules(self): # to avoid error from try_apply_patch() during linting with set_wd(self.pipeline_dir): module_lint = nf_core.modules.ModuleLint( - dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=PATCH_BRANCH, hide_progress=True + dir=self.pipeline_dir, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + hide_progress=True, ) module_lint.lint( print_results=False, @@ -320,10 +328,26 @@ def test_modules_lint_snapshot_file(self): def test_modules_lint_snapshot_file_missing_fail(self): """Test linting a module with a snapshot file missing, which should fail""" - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap").unlink() + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).unlink() module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap").touch() + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).touch() assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -332,10 +356,31 @@ def test_modules_lint_snapshot_file_missing_fail(self): def test_modules_lint_snapshot_file_not_needed(self): """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ) + ) as fh: content = fh.read() new_content = content.replace("snapshot(", "snap (") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ), + "w", + ) as fh: fh.write(new_content) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") @@ -347,12 +392,33 @@ def test_modules_lint_snapshot_file_not_needed(self): def test_modules_environment_yml_file_doesnt_exists(self): """Test linting a module with an environment.yml file""" Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml.bak") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml.bak", + ) ) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml.bak").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml.bak", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) ) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -371,13 +437,32 @@ def test_modules_environment_yml_file_sorted_correctly(self): def test_modules_environment_yml_file_sorted_incorrectly(self): """Test linting a module with an incorrectly sorted environment.yml file""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: yaml_content = yaml.safe_load(fh) # Add a new dependency to the environment.yml file and reverse the order yaml_content["dependencies"].append("z") yaml_content["dependencies"].reverse() yaml_content = yaml.dump(yaml_content) - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml_content) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") @@ -389,10 +474,29 @@ def test_modules_environment_yml_file_sorted_incorrectly(self): def test_modules_environment_yml_file_not_array(self): """Test linting a module with an incorrectly formatted environment.yml file""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: yaml_content = yaml.safe_load(fh) yaml_content["dependencies"] = "z" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml.dump(yaml_content)) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") @@ -404,16 +508,45 @@ def test_modules_environment_yml_file_not_array(self): def test_modules_environment_yml_file_name_mismatch(self): """Test linting a module with a different name in the environment.yml file""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: yaml_content = yaml.safe_load(fh) yaml_content["name"] = "bpipe-test" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml.dump(yaml_content)) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes yaml_content["name"] = "bpipe_test" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml.dump(yaml_content)) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -427,14 +560,20 @@ def test_modules_meta_yml_incorrect_licence_field(self): with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: meta_yml = yaml.safe_load(fh) meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh: + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: fh.write(yaml.dump(meta_yml)) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh: + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: fh.write(yaml.dump(meta_yml)) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -489,22 +628,57 @@ def test_modules_meta_yml_incorrect_name(self): meta_yml = yaml.safe_load(fh) meta_yml["name"] = "bpipe/test" # need to make the same change to the environment.yml file - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: environment_yml = yaml.safe_load(fh) environment_yml["name"] = "bpipe/test" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh: + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: fh.write(yaml.dump(meta_yml)) - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml.dump(environment_yml)) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes meta_yml["name"] = "bpipe_test" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), "w") as fh: + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: fh.write(yaml.dump(meta_yml)) environment_yml["name"] = "bpipe_test" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml"), "w") as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: fh.write(yaml.dump(environment_yml)) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -531,13 +705,45 @@ def test_modules_missing_test_dir(self): def test_modules_missing_test_main_nf(self): """Test linting a module with a missing test/main.nf file""" - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.bak") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.bak", + ) ) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.bak").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.bak", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ) ) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 @@ -545,73 +751,6 @@ def test_modules_missing_test_main_nf(self): assert module_lint.failed[0].lint_test == "test_main_nf_exists" -def test_modules_missing_required_tag(self): - """Test linting a module with a missing required tag""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test")) as fh: - content = fh.read() - new_content = content.replace("modules_nfcore", "foo") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh: - fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test"), "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_main_tags" - - -def test_modules_missing_tags_yml(self): - """Test linting a module with a missing tags.yml file""" - tags_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml") - tags_path.rename(tags_path.parent / "tags.yml.bak") - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_tags_yml_exists" - # cleanup - Path(tags_path.parent / "tags.yml.bak").rename(tags_path.parent / "tags.yml") - - -def test_modules_incorrect_tags_yml_key(self): - """Test linting a module with an incorrect key in tags.yml file""" - tags_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml") - with open(tags_path) as fh: - content = fh.read() - new_content = content.replace("bpipe/test:", "bpipe_test:") - with open(tags_path, "w") as fh: - fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=True, module="bpipe/test") - with open(tags_path, "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_tags_yml" - - -def test_modules_incorrect_tags_yml_values(self): - """Test linting a module with an incorrect path in tags.yml file""" - tags_path = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "tags.yml") - with open(tags_path) as fh: - content = fh.read() - new_content = content.replace("modules/nf-core/bpipe/test/**", "foo") - with open(tags_path, "w") as fh: - fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(tags_path, "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_tags_yml" - - def test_modules_unused_pytest_files(self): """Test linting a nf-test module with files still present in `tests/modules/`""" Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) @@ -647,17 +786,45 @@ def test_nftest_failing_linting(self): def test_modules_absent_version(self): """Test linting a nf-test module if the versions is absent in the snapshot file `""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap")) as fh: + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) + ) as fh: content = fh.read() new_content = content.replace("versions", "foo") with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap"), "w" + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ), + "w", ) as fh: fh.write(new_content) module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap"), "w" + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ), + "w", ) as fh: fh.write(content) assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -668,7 +835,15 @@ def test_modules_absent_version(self): def test_modules_empty_file_in_snapshot(self): """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" - snap_file = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap") + snap_file = Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) snap = json.load(snap_file.open()) content = snap_file.read_text() snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -690,7 +865,15 @@ def test_modules_empty_file_in_snapshot(self): def test_modules_empty_file_in_stub_snapshot(self): """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" - snap_file = Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap") + snap_file = Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) snap = json.load(snap_file.open()) content = snap_file.read_text() snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py index 73d2452b37..540f421ad2 100644 --- a/tests/subworkflows/lint.py +++ b/tests/subworkflows/lint.py @@ -80,10 +80,24 @@ def test_subworkflows_lint_snapshot_file(self): def test_subworkflows_lint_snapshot_file_missing_fail(self): """Test linting a subworkflow with a snapshot file missing, which should fail""" - Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink() + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).unlink() subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch() + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).touch() assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 assert len(subworkflow_lint.warned) >= 0 @@ -91,18 +105,49 @@ def test_subworkflows_lint_snapshot_file_missing_fail(self): def test_subworkflows_lint_snapshot_file_not_needed(self): """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" - with open(Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test")) as fh: + with open( + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test", + ) + ) as fh: content = fh.read() new_content = content.replace("snapshot(", "snap (") with open( - Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"), "w" + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test", + ), + "w", ) as fh: fh.write(new_content) - Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink() + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).unlink() subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch() + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).touch() assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 assert len(subworkflow_lint.warned) >= 0 @@ -112,15 +157,34 @@ def test_subworkflows_lint_less_than_two_modules_warning(self): """Test linting a subworkflow with less than two modules""" self.subworkflow_install.install("bam_stats_samtools") # Remove two modules - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf")) as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: content = fh.read() new_content = content.replace( - "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'", "" + "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'", + "", ) new_content = new_content.replace( - "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'", "" + "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'", + "", ) - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf"), "w") as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: fh.write(new_content) subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") @@ -135,14 +199,31 @@ def test_subworkflows_lint_less_than_two_modules_warning(self): def test_subworkflows_lint_include_multiple_alias(self): """Test linting a subworkflow with multiple include methods""" self.subworkflow_install.install("bam_stats_samtools") - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf")) as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: content = fh.read() new_content = content.replace("SAMTOOLS_STATS", "SAMTOOLS_STATS_1") new_content = new_content.replace( "include { SAMTOOLS_STATS_1 ", "include { SAMTOOLS_STATS as SAMTOOLS_STATS_1; SAMTOOLS_STATS as SAMTOOLS_STATS_2 ", ) - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf"), "w") as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: fh.write(new_content) subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) @@ -169,10 +250,27 @@ def test_subworkflows_lint_capitalization_fail(self): """Test linting a subworkflow with a capitalization fail""" self.subworkflow_install.install("bam_stats_samtools") # change workflow name to lowercase - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf")) as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: content = fh.read() new_content = content.replace("workflow BAM_STATS_SAMTOOLS {", "workflow bam_stats_samtools {") - with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_stats_samtools", "main.nf"), "w") as fh: + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: fh.write(new_content) subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") @@ -187,7 +285,14 @@ def test_subworkflows_lint_capitalization_fail(self): def test_subworkflows_absent_version(self): """Test linting a nf-test module if the versions is absent in the snapshot file `""" - snap_file = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap") + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) with open(snap_file) as fh: content = fh.read() new_content = content.replace("versions", "foo") @@ -242,7 +347,14 @@ def test_subworkflows_missing_main_nf(self): def test_subworkflows_empty_file_in_snapshot(self): """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" - snap_file = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap") + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) snap = json.load(snap_file.open()) content = snap_file.read_text() snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -264,7 +376,14 @@ def test_subworkflows_empty_file_in_snapshot(self): def test_subworkflows_empty_file_in_stub_snapshot(self): """Test linting a nf-test subworkflow with an empty file sha sum in the stub test snapshot, which should make it not fail""" - snap_file = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap") + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) snap = json.load(snap_file.open()) content = snap_file.read_text() snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} @@ -282,61 +401,3 @@ def test_subworkflows_empty_file_in_stub_snapshot(self): # reset the file with open(snap_file, "w") as fh: fh.write(content) - - -def test_subworkflows_missing_tags_yml(self): - """Test linting a subworkflow with a missing tags.yml file""" - tags_path = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "tags.yml") - tags_path.rename(tags_path.parent / "tags.yml.bak") - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - - assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) >= 0 - assert len(subworkflow_lint.warned) >= 0 - assert subworkflow_lint.failed[0].lint_test == "test_tags_yml_exists" - - # cleanup - Path(tags_path.parent / "tags.yml.bak").rename(tags_path.parent / "tags.yml") - - -def test_subworkflows_incorrect_tags_yml_key(self): - """Test linting a subworkflow with an incorrect key in tags.yml file""" - tags_path = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "tags.yml") - with open(tags_path) as fh: - content = fh.read() - new_content = content.replace("test_subworkflow:", "subworkflow:") - with open(tags_path, "w") as fh: - fh.write(new_content) - module_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - module_lint.lint(print_results=True, subworkflow="test_subworkflow") - with open(tags_path, "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_tags_yml" - # cleanup - with open(tags_path, "w") as fh: - fh.write(content) - - -def test_subworkflows_incorrect_tags_yml_values(self): - """Test linting a subworkflow with an incorrect path in tags.yml file""" - tags_path = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "tags.yml") - with open(tags_path) as fh: - content = fh.read() - new_content = content.replace("subworkflows/nf-core/test_subworkflow/**", "foo") - with open(tags_path, "w") as fh: - fh.write(new_content) - module_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, subworkflow="test_subworkflow") - with open(tags_path, "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_tags_yml" - # cleanup - with open(tags_path, "w") as fh: - fh.write(content) From 4cb6fd14910050438de7845cb9a0781519a9f7e2 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 22 May 2024 11:37:37 -0400 Subject: [PATCH 007/574] mypy fixes --- tests/test_modules.py | 4 ---- tests/test_subworkflows.py | 18 +++++++++++++----- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/tests/test_modules.py b/tests/test_modules.py index a122f16b69..f353a7edfe 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -202,8 +202,6 @@ def test_modulesrepo_class(self): test_modules_environment_yml_file_not_array, test_modules_environment_yml_file_sorted_correctly, test_modules_environment_yml_file_sorted_incorrectly, - test_modules_incorrect_tags_yml_key, - test_modules_incorrect_tags_yml_values, test_modules_lint_check_process_labels, test_modules_lint_check_url, test_modules_lint_empty, @@ -220,8 +218,6 @@ def test_modulesrepo_class(self): test_modules_meta_yml_incorrect_name, test_modules_meta_yml_input_mismatch, test_modules_meta_yml_output_mismatch, - test_modules_missing_required_tag, - test_modules_missing_tags_yml, test_modules_missing_test_dir, test_modules_missing_test_main_nf, test_modules_unused_pytest_files, diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 59de1967e4..786ba53836 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -33,7 +33,14 @@ def create_modules_repo_dummy(tmp_dir): subworkflow_create.create() # Add dummy content to main.nf.test.snap - test_snap_path = Path(root_dir, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap") + test_snap_path = Path( + root_dir, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) test_snap_path.parent.mkdir(parents=True, exist_ok=True) with open(test_snap_path, "w") as fh: json.dump( @@ -70,7 +77,11 @@ def setUp(self): # Set up install objects self.subworkflow_install = nf_core.subworkflows.SubworkflowInstall(self.pipeline_dir, prompt=False, force=False) self.subworkflow_install_gitlab = nf_core.subworkflows.SubworkflowInstall( - self.pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + self.pipeline_dir, + prompt=False, + force=False, + remote_url=GITLAB_URL, + branch=GITLAB_SUBWORKFLOWS_BRANCH, ) self.subworkflow_install_gitlab_same_org_path = nf_core.subworkflows.SubworkflowInstall( self.pipeline_dir, @@ -136,8 +147,6 @@ def tearDown(self): test_subworkflows_absent_version, test_subworkflows_empty_file_in_snapshot, test_subworkflows_empty_file_in_stub_snapshot, - test_subworkflows_incorrect_tags_yml_key, - test_subworkflows_incorrect_tags_yml_values, test_subworkflows_lint, test_subworkflows_lint_capitalization_fail, test_subworkflows_lint_empty, @@ -150,7 +159,6 @@ def tearDown(self): test_subworkflows_lint_snapshot_file, test_subworkflows_lint_snapshot_file_missing_fail, test_subworkflows_lint_snapshot_file_not_needed, - test_subworkflows_missing_tags_yml, ) from .subworkflows.list import ( # type: ignore[misc] test_subworkflows_install_and_list_subworkflows, From 8eb4f417d09540ab0703751de8d8dbbdbeecc5ed Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Wed, 22 May 2024 11:39:51 -0400 Subject: [PATCH 008/574] re-add checks for pytest dirs existing --- nf_core/subworkflows/lint/subworkflow_tests.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index b7ab685095..335789cb7a 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -255,3 +255,11 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): pytest_yml_path, ) ) + + # Check that the old test directory does not exist + if not is_pytest: + old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name) + if old_test_dir.is_dir(): + subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir)) + else: + subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir)) From 95976e5cf2c9ba5757a51574773c18c16bcc708a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 22 May 2024 16:51:57 +0000 Subject: [PATCH 009/574] remove test_tags_yml from pytest test --- tests/modules/lint.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/modules/lint.py b/tests/modules/lint.py index 6bb74d34ed..e1a4e27ff8 100644 --- a/tests/modules/lint.py +++ b/tests/modules/lint.py @@ -774,14 +774,13 @@ def test_nftest_failing_linting(self): module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) module_lint.lint(print_results=False, module="kallisto/quant") - assert len(module_lint.failed) == 4, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 assert len(module_lint.warned) >= 0 assert module_lint.failed[0].lint_test == "environment_yml_valid" assert module_lint.failed[1].lint_test == "meta_yml_valid" assert module_lint.failed[2].lint_test == "test_main_tags" assert "kallisto/index" in module_lint.failed[2].message - assert module_lint.failed[3].lint_test == "test_tags_yml" def test_modules_absent_version(self): From 33177912b000658d38479136f315b1e268dc647b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 15 May 2024 10:12:55 +0200 Subject: [PATCH 010/574] move pipeline subcommands for v3.0 --- docs/api/make_lint_md.py | 6 +- nf_core/__main__.py | 268 ++++++++++++++---- nf_core/components/create.py | 2 +- nf_core/components/lint/__init__.py | 2 +- nf_core/launch.py | 2 +- nf_core/modules/lint/__init__.py | 2 +- nf_core/modules/lint/module_todos.py | 2 +- nf_core/modules/modules_json.py | 2 +- .../bump_version}/bump_version.py | 2 +- nf_core/pipelines/create/create.py | 2 +- nf_core/{ => pipelines}/lint/__init__.py | 8 +- .../lint/actions_awsfulltest.py | 0 .../{ => pipelines}/lint/actions_awstest.py | 0 nf_core/{ => pipelines}/lint/actions_ci.py | 0 .../lint/actions_schema_validation.py | 0 nf_core/{ => pipelines}/lint/configs.py | 2 +- nf_core/{ => pipelines}/lint/files_exist.py | 0 .../{ => pipelines}/lint/files_unchanged.py | 0 nf_core/{ => pipelines}/lint/merge_markers.py | 0 nf_core/{ => pipelines}/lint/modules_json.py | 0 .../{ => pipelines}/lint/modules_structure.py | 0 .../{ => pipelines}/lint/multiqc_config.py | 2 +- .../{ => pipelines}/lint/nextflow_config.py | 0 nf_core/{ => pipelines}/lint/nfcore_yml.py | 0 .../lint/pipeline_name_conventions.py | 0 .../{ => pipelines}/lint/pipeline_todos.py | 0 nf_core/{ => pipelines}/lint/readme.py | 0 .../lint/schema_description.py | 0 nf_core/{ => pipelines}/lint/schema_lint.py | 0 nf_core/{ => pipelines}/lint/schema_params.py | 0 nf_core/{ => pipelines}/lint/system_exit.py | 0 .../{ => pipelines}/lint/template_strings.py | 0 .../lint/version_consistency.py | 0 nf_core/{ => pipelines}/lint_utils.py | 0 nf_core/{ => pipelines/sync}/sync.py | 0 nf_core/schema.py | 2 +- nf_core/subworkflows/lint/__init__.py | 2 +- .../subworkflows/lint/subworkflow_todos.py | 2 +- tests/lint/actions_awsfulltest.py | 6 +- tests/lint/actions_awstest.py | 4 +- tests/lint/actions_ci.py | 4 +- tests/lint/actions_schema_validation.py | 8 +- tests/lint/configs.py | 12 +- tests/lint/files_exist.py | 16 +- tests/lint/files_unchanged.py | 4 +- tests/lint/merge_markers.py | 4 +- tests/lint/multiqc_config.py | 20 +- tests/lint/nextflow_config.py | 22 +- tests/lint/nfcore_yml.py | 6 +- tests/lint/template_strings.py | 8 +- tests/lint/version_consistency.py | 4 +- tests/test_bump_version.py | 8 +- tests/test_cli.py | 6 +- tests/test_lint.py | 82 +++--- tests/test_lint_utils.py | 8 +- tests/test_sync.py | 64 ++--- 56 files changed, 382 insertions(+), 212 deletions(-) rename nf_core/{ => pipelines/bump_version}/bump_version.py (98%) rename nf_core/{ => pipelines}/lint/__init__.py (99%) rename nf_core/{ => pipelines}/lint/actions_awsfulltest.py (100%) rename nf_core/{ => pipelines}/lint/actions_awstest.py (100%) rename nf_core/{ => pipelines}/lint/actions_ci.py (100%) rename nf_core/{ => pipelines}/lint/actions_schema_validation.py (100%) rename nf_core/{ => pipelines}/lint/configs.py (98%) rename nf_core/{ => pipelines}/lint/files_exist.py (100%) rename nf_core/{ => pipelines}/lint/files_unchanged.py (100%) rename nf_core/{ => pipelines}/lint/merge_markers.py (100%) rename nf_core/{ => pipelines}/lint/modules_json.py (100%) rename nf_core/{ => pipelines}/lint/modules_structure.py (100%) rename nf_core/{ => pipelines}/lint/multiqc_config.py (99%) rename nf_core/{ => pipelines}/lint/nextflow_config.py (100%) rename nf_core/{ => pipelines}/lint/nfcore_yml.py (100%) rename nf_core/{ => pipelines}/lint/pipeline_name_conventions.py (100%) rename nf_core/{ => pipelines}/lint/pipeline_todos.py (100%) rename nf_core/{ => pipelines}/lint/readme.py (100%) rename nf_core/{ => pipelines}/lint/schema_description.py (100%) rename nf_core/{ => pipelines}/lint/schema_lint.py (100%) rename nf_core/{ => pipelines}/lint/schema_params.py (100%) rename nf_core/{ => pipelines}/lint/system_exit.py (100%) rename nf_core/{ => pipelines}/lint/template_strings.py (100%) rename nf_core/{ => pipelines}/lint/version_consistency.py (100%) rename nf_core/{ => pipelines}/lint_utils.py (100%) rename nf_core/{ => pipelines/sync}/sync.py (100%) diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py index 35e38a55ca..48393094b3 100644 --- a/docs/api/make_lint_md.py +++ b/docs/api/make_lint_md.py @@ -3,8 +3,8 @@ import fnmatch import os -import nf_core.lint import nf_core.modules.lint +import nf_core.pipelines.lint import nf_core.subworkflows.lint @@ -31,11 +31,11 @@ def make_docs(docs_basedir, lint_tests, md_template): pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests") make_docs( pipeline_docs_basedir, - nf_core.lint.PipelineLint._get_all_lint_tests(True), + nf_core.pipelines.lint.PipelineLint._get_all_lint_tests(True), """# {0} ```{{eval-rst}} -.. automethod:: nf_core.lint.PipelineLint.{0} +.. automethod:: nf_core.pipelines.lint.PipelineLint.{0} ``` """, ) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 67af238b5c..c2423ef1fc 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -46,20 +46,17 @@ "name": "Commands for developers", "commands": [ "pipelines", - "lint", "modules", "subworkflows", "schema", "create-logo", - "bump-version", - "sync", ], }, ], "nf-core pipelines": [ { "name": "Pipeline commands", - "commands": ["create"], + "commands": ["create", "lint", "bump-version", "sync"], }, ], "nf-core modules": [ @@ -486,8 +483,8 @@ def licences(pipeline, json): sys.exit(1) -# nf-core lint -@nf_core_cli.command() +# nf-core lint (deprecated) +@nf_core_cli.command(hidden=True, deprecated=True) @click.option( "-d", "--dir", @@ -556,6 +553,7 @@ def lint( sort_by, ): """ + DEPRECATED Check pipeline code against nf-core guidelines. Runs a large number of automated tests to ensure that the supplied pipeline @@ -565,42 +563,8 @@ def lint( You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. See the documentation for details. """ - from nf_core.lint import run_linting - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory is a pipeline - try: - is_pipeline_directory(dir) - except UserWarning as e: - log.error(e) - sys.exit(1) - - # Run the lint tests! - try: - lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - sort_by, - markdown, - json, - ctx.obj["hide_progress"], - ) - swf_failed = 0 - if subworkflow_lint_obj is not None: - swf_failed = len(subworkflow_lint_obj.failed) - if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: - sys.exit(1) - except AssertionError as e: - log.critical(e) - sys.exit(1) - except UserWarning as e: - log.error(e) - sys.exit(1) + log.error("The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead.") + sys.exit(0) # nf-core pipelines subcommands @@ -679,6 +643,124 @@ def create_pipeline(ctx, name, description, author, version, force, outdir, temp sys.exit(app.return_code or 0) +# nf-core pipelines lint +@pipelines.command("lint") +@click.pass_context +@click.option( + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory [dim]\[default: current working directory][/]", +) +@click.option( + "--release", + is_flag=True, + default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" + and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") + and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", + help="Execute additional checks for release-ready workflows.", +) +@click.option( + "-f", + "--fix", + type=str, + metavar="", + multiple=True, + help="Attempt to automatically fix specified lint test", +) +@click.option( + "-k", + "--key", + type=str, + metavar="", + multiple=True, + help="Run only these lint tests", +) +@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") +@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") +@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") +@click.option( + "--markdown", + type=str, + metavar="", + help="File to write linting results to (Markdown)", +) +@click.option( + "--json", + type=str, + metavar="", + help="File to write linting results to (JSON)", +) +@click.option( + "--sort-by", + type=click.Choice(["module", "test"]), + default="test", + help="Sort lint output by module or test name.", + show_default=True, +) +@click.pass_context +def lint_pipeline( + ctx, + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + markdown, + json, + sort_by, +): + """ + Check pipeline code against nf-core guidelines. + + Runs a large number of automated tests to ensure that the supplied pipeline + meets the nf-core guidelines. Documentation of all lint tests can be found + on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] + + You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. + See the documentation for details. + """ + from nf_core.pipelines.lint import run_linting + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory is a pipeline + try: + is_pipeline_directory(dir) + except UserWarning as e: + log.error(e) + sys.exit(1) + + # Run the lint tests! + try: + lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + sort_by, + markdown, + json, + ctx.obj["hide_progress"], + ) + swf_failed = 0 + if subworkflow_lint_obj is not None: + swf_failed = len(subworkflow_lint_obj.failed) + if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: + sys.exit(1) + except AssertionError as e: + log.critical(e) + sys.exit(1) + except UserWarning as e: + log.error(e) + sys.exit(1) + + # nf-core create (deprecated) @nf_core_cli.command(hidden=True, deprecated=True) @click.option( @@ -2063,9 +2145,9 @@ def docs(schema_path, output, format, force, columns): schema_obj.print_documentation(output, format, force, columns.split(",")) -# nf-core bump-version -@nf_core_cli.command("bump-version") -@click.argument("new_version", required=True, metavar="") +# nf-core bump-version (deprecated) +@nf_core_cli.command(hidden=True, deprecated=True) +@click.argument("new_version", default="") @click.option( "-d", "--dir", @@ -2081,6 +2163,44 @@ def docs(schema_path, output, format, force, columns): help="Bump required nextflow version instead of pipeline version", ) def bump_version(new_version, dir, nextflow): + """ + DEPRECATED + Update nf-core pipeline version number. + + The pipeline version number is mentioned in a lot of different places + in nf-core pipelines. This tool updates the version for you automatically, + so that you don't accidentally miss any. + + Should be used for each pipeline release, and again for the next + development version after release. + + As well as the pipeline version, you can also change the required version of Nextflow. + """ + log.error( + "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead." + ) + sys.exit(0) + + +# nf-core pipelines bump-version +@pipelines.command("bump-version") +@click.pass_context +@click.argument("new_version", required=True, metavar="") +@click.option( + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", +) +@click.option( + "-n", + "--nextflow", + is_flag=True, + default=False, + help="Bump required nextflow version instead of pipeline version", +) +def bump_version_pipeline(new_version, dir, nextflow): """ Update nf-core pipeline version number. @@ -2093,7 +2213,7 @@ def bump_version(new_version, dir, nextflow): As well as the pipeline version, you can also change the required version of Nextflow. """ - from nf_core.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.pipelines.bump_version.bump_version import bump_nextflow_version, bump_pipeline_version from nf_core.utils import Pipeline, is_pipeline_directory try: @@ -2175,8 +2295,8 @@ def logo(logo_text, dir, name, theme, width, format, force): sys.exit(1) -# nf-core sync -@nf_core_cli.command("sync") +# nf-core sync (deprecated) +@nf_core_cli.command(hidden=True, deprecated=True) @click.option( "-d", "--dir", @@ -2207,6 +2327,56 @@ def logo(logo_text, dir, name, theme, width, format, force): @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") def sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): + """ + DEPRECATED + Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. + + To keep nf-core pipelines up to date with improvements in the main + template, we use a method of synchronisation that uses a special + git branch called [cyan i]TEMPLATE[/]. + + This command updates the [cyan i]TEMPLATE[/] branch with the latest version of + the nf-core template, so that these updates can be synchronised with + the pipeline. It is run automatically for all pipelines when ever a + new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + """ + log.error("The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead.") + sys.exit(0) + + +# nf-core pipelines sync +@pipelines.command("sync") +@click.pass_context +@click.option( + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", +) +@click.option( + "-b", + "--from-branch", + type=str, + help="The git branch to use to fetch workflow variables.", +) +@click.option( + "-p", + "--pull-request", + is_flag=True, + default=False, + help="Make a GitHub pull-request with the changes.", +) +@click.option( + "--force_pr", + is_flag=True, + default=False, + help="Force the creation of a pull-request, even if there are no changes.", +) +@click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") +@click.option("-u", "--username", type=str, help="GitHub PR: auth username.") +@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") +def sync_pipeline(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. @@ -2219,7 +2389,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y the pipeline. It is run automatically for all pipelines when ever a new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ - from nf_core.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.pipelines.sync.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError from nf_core.utils import is_pipeline_directory # Check if pipeline directory contains necessary files diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 6c9c01b496..c9afb390d8 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -20,7 +20,7 @@ import nf_core import nf_core.utils from nf_core.components.components_command import ComponentCommand -from nf_core.lint_utils import run_prettier_on_file +from nf_core.pipelines.lint_utils import run_prettier_on_file log = logging.getLogger(__name__) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 564dcfaf6b..499d31e71e 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -19,8 +19,8 @@ import nf_core.utils from nf_core.components.components_command import ComponentCommand from nf_core.components.nfcore_component import NFCoreComponent -from nf_core.lint_utils import console from nf_core.modules.modules_json import ModulesJson +from nf_core.pipelines.lint_utils import console from nf_core.utils import plural_s as _s log = logging.getLogger(__name__) diff --git a/nf_core/launch.py b/nf_core/launch.py index bc0cd58aec..423f0728ed 100644 --- a/nf_core/launch.py +++ b/nf_core/launch.py @@ -15,7 +15,7 @@ import nf_core.schema import nf_core.utils -from nf_core.lint_utils import dump_json_with_prettier +from nf_core.pipelines.lint_utils import dump_json_with_prettier log = logging.getLogger(__name__) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index f96683089c..b780144ef7 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -15,7 +15,7 @@ import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult -from nf_core.lint_utils import console +from nf_core.pipelines.lint_utils import console log = logging.getLogger(__name__) diff --git a/nf_core/modules/lint/module_todos.py b/nf_core/modules/lint/module_todos.py index c9c90ec3dc..a07005df03 100644 --- a/nf_core/modules/lint/module_todos.py +++ b/nf_core/modules/lint/module_todos.py @@ -1,6 +1,6 @@ import logging -from nf_core.lint.pipeline_todos import pipeline_todos +from nf_core.pipelines.lint.pipeline_todos import pipeline_todos log = logging.getLogger(__name__) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 7d78268e92..b0a4fa661f 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -14,12 +14,12 @@ import nf_core.utils from nf_core.components.components_utils import get_components_to_install -from nf_core.lint_utils import dump_json_with_prettier from nf_core.modules.modules_repo import ( NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, ModulesRepo, ) +from nf_core.pipelines.lint_utils import dump_json_with_prettier from .modules_differ import ModulesDiffer diff --git a/nf_core/bump_version.py b/nf_core/pipelines/bump_version/bump_version.py similarity index 98% rename from nf_core/bump_version.py rename to nf_core/pipelines/bump_version/bump_version.py index c5e8931fbc..18aa869328 100644 --- a/nf_core/bump_version.py +++ b/nf_core/pipelines/bump_version/bump_version.py @@ -176,7 +176,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt Args: filename (str): File to scan. - pipeline_obj (nf_core.lint.PipelineLint): A PipelineLint object that holds information + pipeline_obj (nf_core.pipelines.lint.PipelineLint): A PipelineLint object that holds information about the pipeline contents and build files. pattern (str): Regex pattern to apply. diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 381e2f07ab..763165da6f 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -18,8 +18,8 @@ import nf_core.schema import nf_core.utils from nf_core.create_logo import create_logo -from nf_core.lint_utils import run_prettier_on_file from nf_core.pipelines.create.utils import CreateConfig +from nf_core.pipelines.lint_utils import run_prettier_on_file log = logging.getLogger(__name__) diff --git a/nf_core/lint/__init__.py b/nf_core/pipelines/lint/__init__.py similarity index 99% rename from nf_core/lint/__init__.py rename to nf_core/pipelines/lint/__init__.py index 9292a07fd8..4ec62ddb0d 100644 --- a/nf_core/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -20,13 +20,13 @@ from rich.panel import Panel from rich.table import Table -import nf_core.lint_utils import nf_core.modules.lint +import nf_core.pipelines.lint_utils import nf_core.subworkflows.lint import nf_core.utils from nf_core import __version__ from nf_core.components.lint import ComponentLint -from nf_core.lint_utils import console +from nf_core.pipelines.lint_utils import console from nf_core.utils import plural_s as _s from nf_core.utils import strip_ansi_codes @@ -623,8 +623,8 @@ def run_linting( module_lint_obj._print_results(show_passed, sort_by=sort_by) if subworkflow_lint_obj is not None: subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by) - nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj) - nf_core.lint_utils.print_fixes(lint_obj) + nf_core.pipelines.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj) + nf_core.pipelines.lint_utils.print_fixes(lint_obj) # Save results to Markdown file if md_fn is not None: diff --git a/nf_core/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py similarity index 100% rename from nf_core/lint/actions_awsfulltest.py rename to nf_core/pipelines/lint/actions_awsfulltest.py diff --git a/nf_core/lint/actions_awstest.py b/nf_core/pipelines/lint/actions_awstest.py similarity index 100% rename from nf_core/lint/actions_awstest.py rename to nf_core/pipelines/lint/actions_awstest.py diff --git a/nf_core/lint/actions_ci.py b/nf_core/pipelines/lint/actions_ci.py similarity index 100% rename from nf_core/lint/actions_ci.py rename to nf_core/pipelines/lint/actions_ci.py diff --git a/nf_core/lint/actions_schema_validation.py b/nf_core/pipelines/lint/actions_schema_validation.py similarity index 100% rename from nf_core/lint/actions_schema_validation.py rename to nf_core/pipelines/lint/actions_schema_validation.py diff --git a/nf_core/lint/configs.py b/nf_core/pipelines/lint/configs.py similarity index 98% rename from nf_core/lint/configs.py rename to nf_core/pipelines/lint/configs.py index 2741529198..f0fa1170c2 100644 --- a/nf_core/lint/configs.py +++ b/nf_core/pipelines/lint/configs.py @@ -3,7 +3,7 @@ from pathlib import Path from typing import Dict, List -from nf_core.lint_utils import ignore_file +from nf_core.pipelines.lint_utils import ignore_file log = logging.getLogger(__name__) diff --git a/nf_core/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py similarity index 100% rename from nf_core/lint/files_exist.py rename to nf_core/pipelines/lint/files_exist.py diff --git a/nf_core/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py similarity index 100% rename from nf_core/lint/files_unchanged.py rename to nf_core/pipelines/lint/files_unchanged.py diff --git a/nf_core/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py similarity index 100% rename from nf_core/lint/merge_markers.py rename to nf_core/pipelines/lint/merge_markers.py diff --git a/nf_core/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py similarity index 100% rename from nf_core/lint/modules_json.py rename to nf_core/pipelines/lint/modules_json.py diff --git a/nf_core/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py similarity index 100% rename from nf_core/lint/modules_structure.py rename to nf_core/pipelines/lint/modules_structure.py diff --git a/nf_core/lint/multiqc_config.py b/nf_core/pipelines/lint/multiqc_config.py similarity index 99% rename from nf_core/lint/multiqc_config.py rename to nf_core/pipelines/lint/multiqc_config.py index 8b4fa2120f..2b0fc7902e 100644 --- a/nf_core/lint/multiqc_config.py +++ b/nf_core/pipelines/lint/multiqc_config.py @@ -3,7 +3,7 @@ import yaml -from nf_core.lint_utils import ignore_file +from nf_core.pipelines.lint_utils import ignore_file def multiqc_config(self) -> Dict[str, List[str]]: diff --git a/nf_core/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py similarity index 100% rename from nf_core/lint/nextflow_config.py rename to nf_core/pipelines/lint/nextflow_config.py diff --git a/nf_core/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py similarity index 100% rename from nf_core/lint/nfcore_yml.py rename to nf_core/pipelines/lint/nfcore_yml.py diff --git a/nf_core/lint/pipeline_name_conventions.py b/nf_core/pipelines/lint/pipeline_name_conventions.py similarity index 100% rename from nf_core/lint/pipeline_name_conventions.py rename to nf_core/pipelines/lint/pipeline_name_conventions.py diff --git a/nf_core/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py similarity index 100% rename from nf_core/lint/pipeline_todos.py rename to nf_core/pipelines/lint/pipeline_todos.py diff --git a/nf_core/lint/readme.py b/nf_core/pipelines/lint/readme.py similarity index 100% rename from nf_core/lint/readme.py rename to nf_core/pipelines/lint/readme.py diff --git a/nf_core/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py similarity index 100% rename from nf_core/lint/schema_description.py rename to nf_core/pipelines/lint/schema_description.py diff --git a/nf_core/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py similarity index 100% rename from nf_core/lint/schema_lint.py rename to nf_core/pipelines/lint/schema_lint.py diff --git a/nf_core/lint/schema_params.py b/nf_core/pipelines/lint/schema_params.py similarity index 100% rename from nf_core/lint/schema_params.py rename to nf_core/pipelines/lint/schema_params.py diff --git a/nf_core/lint/system_exit.py b/nf_core/pipelines/lint/system_exit.py similarity index 100% rename from nf_core/lint/system_exit.py rename to nf_core/pipelines/lint/system_exit.py diff --git a/nf_core/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py similarity index 100% rename from nf_core/lint/template_strings.py rename to nf_core/pipelines/lint/template_strings.py diff --git a/nf_core/lint/version_consistency.py b/nf_core/pipelines/lint/version_consistency.py similarity index 100% rename from nf_core/lint/version_consistency.py rename to nf_core/pipelines/lint/version_consistency.py diff --git a/nf_core/lint_utils.py b/nf_core/pipelines/lint_utils.py similarity index 100% rename from nf_core/lint_utils.py rename to nf_core/pipelines/lint_utils.py diff --git a/nf_core/sync.py b/nf_core/pipelines/sync/sync.py similarity index 100% rename from nf_core/sync.py rename to nf_core/pipelines/sync/sync.py diff --git a/nf_core/schema.py b/nf_core/schema.py index 4f5acfa0af..eee9f9978d 100644 --- a/nf_core/schema.py +++ b/nf_core/schema.py @@ -18,7 +18,7 @@ import nf_core.list import nf_core.utils -from nf_core.lint_utils import dump_json_with_prettier, run_prettier_on_file +from nf_core.pipelines.lint_utils import dump_json_with_prettier, run_prettier_on_file log = logging.getLogger(__name__) diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index cc79ed8639..a3cacf2952 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -15,7 +15,7 @@ import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult -from nf_core.lint_utils import console +from nf_core.pipelines.lint_utils import console log = logging.getLogger(__name__) diff --git a/nf_core/subworkflows/lint/subworkflow_todos.py b/nf_core/subworkflows/lint/subworkflow_todos.py index 91f9f55b0b..3417215db9 100644 --- a/nf_core/subworkflows/lint/subworkflow_todos.py +++ b/nf_core/subworkflows/lint/subworkflow_todos.py @@ -1,6 +1,6 @@ import logging -from nf_core.lint.pipeline_todos import pipeline_todos +from nf_core.pipelines.lint.pipeline_todos import pipeline_todos log = logging.getLogger(__name__) diff --git a/tests/lint/actions_awsfulltest.py b/tests/lint/actions_awsfulltest.py index bbda92a4d1..caf7bbf366 100644 --- a/tests/lint/actions_awsfulltest.py +++ b/tests/lint/actions_awsfulltest.py @@ -2,7 +2,7 @@ import yaml -import nf_core.lint +import nf_core.pipelines.lint def test_actions_awsfulltest_warn(self): @@ -26,7 +26,7 @@ def test_actions_awsfulltest_pass(self): fh.write(awsfulltest_yml) # Make lint object - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_awsfulltest() @@ -51,7 +51,7 @@ def test_actions_awsfulltest_fail(self): yaml.dump(awsfulltest_yml, fh) # Make lint object - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_awsfulltest() diff --git a/tests/lint/actions_awstest.py b/tests/lint/actions_awstest.py index 7bfa6052f8..259bf866bf 100644 --- a/tests/lint/actions_awstest.py +++ b/tests/lint/actions_awstest.py @@ -2,7 +2,7 @@ import yaml -import nf_core.lint +import nf_core.pipelines.lint def test_actions_awstest_pass(self): @@ -27,7 +27,7 @@ def test_actions_awstest_fail(self): yaml.dump(awstest_yml, fh) # Make lint object - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_awstest() diff --git a/tests/lint/actions_ci.py b/tests/lint/actions_ci.py index 8734b2f78b..eb438b881d 100644 --- a/tests/lint/actions_ci.py +++ b/tests/lint/actions_ci.py @@ -2,7 +2,7 @@ import yaml -import nf_core.lint +import nf_core.pipelines.lint def test_actions_ci_pass(self): @@ -39,7 +39,7 @@ def test_actions_ci_fail_wrong_trigger(self): yaml.dump(ci_yml, fh) # Make lint object - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_ci() diff --git a/tests/lint/actions_schema_validation.py b/tests/lint/actions_schema_validation.py index e202b3b1ce..4b00e7bf40 100644 --- a/tests/lint/actions_schema_validation.py +++ b/tests/lint/actions_schema_validation.py @@ -2,7 +2,7 @@ import yaml -import nf_core.lint +import nf_core.pipelines.lint def test_actions_schema_validation_missing_jobs(self): @@ -16,7 +16,7 @@ def test_actions_schema_validation_missing_jobs(self): with open(awstest_yml_path, "w") as fh: yaml.dump(awstest_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_schema_validation() @@ -35,7 +35,7 @@ def test_actions_schema_validation_missing_on(self): with open(awstest_yml_path, "w") as fh: yaml.dump(awstest_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_schema_validation() @@ -55,7 +55,7 @@ def test_actions_schema_validation_fails_for_additional_property(self): with open(awstest_yml_path, "w") as fh: yaml.dump(awstest_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.actions_schema_validation() diff --git a/tests/lint/configs.py b/tests/lint/configs.py index 8610910cd8..3ca35cab8c 100644 --- a/tests/lint/configs.py +++ b/tests/lint/configs.py @@ -2,15 +2,15 @@ import yaml -import nf_core.lint import nf_core.pipelines.create +import nf_core.pipelines.lint def test_withname_in_modules_config(self): """Tests finding withName in modules.config passes linting.""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.modules_config() assert len(result["failed"]) == 0 @@ -26,7 +26,7 @@ def test_superfluous_withname_in_modules_config_fails(self): modules_config = Path(new_pipeline) / "conf" / "modules.config" with open(modules_config, "a") as f: f.write("\nwithName: 'BPIPE' {\n cache = false \n}") - lint_obj = nf_core.lint.PipelineLint(new_pipeline, hide_progress=False) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline, hide_progress=False) lint_obj._load() result = lint_obj.modules_config() assert len(result["failed"]) == 1 @@ -44,7 +44,7 @@ def test_ignore_modules_config(self): with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: yaml.dump(content, f) Path(new_pipeline, "conf", "modules.config").unlink() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.modules_config() assert len(result["ignored"]) == 1 @@ -61,7 +61,7 @@ def test_superfluous_withname_in_base_config_fails(self): base_config = Path(new_pipeline) / "conf" / "base.config" with open(base_config, "a") as f: f.write("\nwithName:CUSTOM_DUMPSOFTWAREVERSIONS {\n cache = false \n}") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.base_config() assert len(result["failed"]) == 1 @@ -79,7 +79,7 @@ def test_ignore_base_config(self): with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: yaml.dump(content, f) Path(new_pipeline, "conf", "base.config").unlink() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.base_config() assert len(result["ignored"]) == 1 diff --git a/tests/lint/files_exist.py b/tests/lint/files_exist.py index 08da7f14db..679d209876 100644 --- a/tests/lint/files_exist.py +++ b/tests/lint/files_exist.py @@ -1,7 +1,7 @@ import os from pathlib import Path -import nf_core.lint +import nf_core.pipelines.lint def test_files_exist_missing_config(self): @@ -10,7 +10,7 @@ def test_files_exist_missing_config(self): Path(new_pipeline, "CHANGELOG.md").unlink() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline" @@ -24,7 +24,7 @@ def test_files_exist_missing_main(self): Path(new_pipeline, "main.nf").unlink() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.files_exist() @@ -38,7 +38,7 @@ def test_files_exist_depreciated_file(self): nf = Path(new_pipeline, "parameters.settings.json") os.system(f"touch {nf}") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.files_exist() @@ -49,7 +49,7 @@ def test_files_exist_pass(self): """Lint check should pass if all files are there""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.files_exist() @@ -58,7 +58,7 @@ def test_files_exist_pass(self): def test_files_exist_pass_conditional(self): new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() lint_obj.nf_config["plugins"] = [] lib_dir = Path(new_pipeline, "lib") @@ -71,7 +71,7 @@ def test_files_exist_pass_conditional(self): def test_files_exist_fail_conditional(self): new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() lib_dir = Path(new_pipeline, "lib") lib_dir.mkdir() @@ -90,7 +90,7 @@ def test_files_exist_pass_conditional_nfschema(self): with open(Path(new_pipeline, "nextflow.config"), "w") as f: f.write(config) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() lint_obj.nf_config["manifest.schema"] = "nf-core" results = lint_obj.files_exist() diff --git a/tests/lint/files_unchanged.py b/tests/lint/files_unchanged.py index 601f09b9df..07a7229191 100644 --- a/tests/lint/files_unchanged.py +++ b/tests/lint/files_unchanged.py @@ -1,6 +1,6 @@ from pathlib import Path -import nf_core.lint +import nf_core.pipelines.lint def test_files_unchanged_pass(self): @@ -18,7 +18,7 @@ def test_files_unchanged_fail(self): with open(Path(new_pipeline, failing_file), "a") as fh: fh.write("THIS SHOULD NOT BE HERE") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.files_unchanged() assert len(results["failed"]) > 0 diff --git a/tests/lint/merge_markers.py b/tests/lint/merge_markers.py index 64a62e25c3..0e3699e190 100644 --- a/tests/lint/merge_markers.py +++ b/tests/lint/merge_markers.py @@ -1,6 +1,6 @@ import os -import nf_core.lint +import nf_core.pipelines.lint def test_merge_markers_found(self): @@ -13,7 +13,7 @@ def test_merge_markers_found(self): with open(os.path.join(new_pipeline, "main.nf"), "w") as fh: fh.write(main_nf_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.merge_markers() diff --git a/tests/lint/multiqc_config.py b/tests/lint/multiqc_config.py index 463d5e7654..70c09ae543 100644 --- a/tests/lint/multiqc_config.py +++ b/tests/lint/multiqc_config.py @@ -2,7 +2,7 @@ import yaml -import nf_core.lint +import nf_core.pipelines.lint def test_multiqc_config_exists(self): @@ -10,7 +10,7 @@ def test_multiqc_config_exists(self): # Delete the file new_pipeline = self._make_pipeline_copy() Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.multiqc_config() assert result["failed"] == ["`assets/multiqc_config.yml` not found."] @@ -28,7 +28,7 @@ def test_multiqc_config_ignore(self): with open(Path(new_pipeline, ".nf-core.yml"), "w") as f: yaml.dump(content, f) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.multiqc_config() assert result["ignored"] == ["`assets/multiqc_config.yml` not found, but it is ignored."] @@ -47,7 +47,7 @@ def test_multiqc_config_missing_report_section_order(self): mqc_yml.pop("report_section_order") with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.multiqc_config() # Reset the file @@ -65,7 +65,7 @@ def test_multiqc_incorrect_export_plots(self): mqc_yml["export_plots"] = False with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.multiqc_config() # Reset the file @@ -83,7 +83,7 @@ def test_multiqc_config_report_comment_fail(self): mqc_yml["report_comment"] = "This is a test" with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.multiqc_config() # Reset the file @@ -101,7 +101,7 @@ def test_multiqc_config_report_comment_release_fail(self): mqc_yml_tmp = mqc_yml.copy() with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() # bump version lint_obj.nf_config["manifest.version"] = "1.0" @@ -116,13 +116,13 @@ def test_multiqc_config_report_comment_release_fail(self): def test_multiqc_config_report_comment_release_succeed(self): """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version""" - import nf_core.bump_version + import nf_core.pipelines.bump_version.bump_version new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() # bump version using the bump_version function - nf_core.bump_version.bump_pipeline_version(lint_obj, "1.0") + nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(lint_obj, "1.0") # lint again lint_obj._load() result = lint_obj.multiqc_config() diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py index 4bd7959448..b90298f542 100644 --- a/tests/lint/nextflow_config.py +++ b/tests/lint/nextflow_config.py @@ -2,8 +2,8 @@ import re from pathlib import Path -import nf_core.lint import nf_core.pipelines.create.create +import nf_core.pipelines.lint def test_nextflow_config_example_pass(self): @@ -17,7 +17,7 @@ def test_nextflow_config_example_pass(self): def test_nextflow_config_bad_name_fail(self): """Tests that config variable existence test fails with bad pipeline name""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() lint_obj.nf_config["manifest.name"] = "bad_name" @@ -29,7 +29,7 @@ def test_nextflow_config_bad_name_fail(self): def test_nextflow_config_dev_in_release_mode_failed(self): """Tests that config variable existence test fails with dev version in release mode""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() lint_obj.release_mode = True @@ -49,7 +49,7 @@ def test_nextflow_config_missing_test_profile_failed(self): fail_content = re.sub(r"\btest\b", "testfail", content) with open(nf_conf_file, "w") as f: f.write(fail_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) > 0 @@ -59,7 +59,7 @@ def test_nextflow_config_missing_test_profile_failed(self): def test_default_values_match(self): """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json.""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 @@ -85,7 +85,7 @@ def test_default_values_fail(self): fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content) with open(nf_schema_file, "w") as f: f.write(fail_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 2 @@ -106,7 +106,7 @@ def test_catch_params_assignment_in_main_nf(self): main_nf_file = Path(new_pipeline) / "main.nf" with open(main_nf_file, "a") as f: f.write("params.max_time = 42") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 1 @@ -123,7 +123,7 @@ def test_allow_params_reference_in_main_nf(self): main_nf_file = Path(new_pipeline) / "main.nf" with open(main_nf_file, "a") as f: f.write("params.max_time == 42") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 @@ -138,7 +138,7 @@ def test_default_values_ignored(self): f.write( "repository_type: pipeline\nlint:\n nextflow_config:\n - config_defaults:\n - params.max_cpus\n" ) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() lint_obj._load_lint_config() result = lint_obj.nextflow_config() @@ -172,7 +172,7 @@ def test_default_values_float(self): with open(nf_schema_file, "w") as f: f.write(fail_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 @@ -202,7 +202,7 @@ def test_default_values_float_fail(self): with open(nf_schema_file, "w") as f: f.write(fail_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() result = lint_obj.nextflow_config() diff --git a/tests/lint/nfcore_yml.py b/tests/lint/nfcore_yml.py index 9d745a6346..94d2870e11 100644 --- a/tests/lint/nfcore_yml.py +++ b/tests/lint/nfcore_yml.py @@ -1,8 +1,8 @@ import re from pathlib import Path -import nf_core.lint import nf_core.pipelines.create +import nf_core.pipelines.lint def test_nfcore_yml_pass(self): @@ -26,7 +26,7 @@ def test_nfcore_yml_fail_repo_type(self): new_content = content.replace("repository_type: pipeline", "repository_type: foo") with open(nf_core_yml, "w") as fh: fh.write(new_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.nfcore_yml() assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"]) @@ -44,7 +44,7 @@ def test_nfcore_yml_fail_nfcore_version(self): new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content) with open(nf_core_yml, "w") as fh: fh.write(new_content) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() results = lint_obj.nfcore_yml() assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"]) diff --git a/tests/lint/template_strings.py b/tests/lint/template_strings.py index 50c956b217..2db9e20a3f 100644 --- a/tests/lint/template_strings.py +++ b/tests/lint/template_strings.py @@ -1,8 +1,8 @@ import subprocess from pathlib import Path -import nf_core.lint import nf_core.pipelines.create +import nf_core.pipelines.lint def test_template_strings(self): @@ -13,7 +13,7 @@ def test_template_strings(self): with open(txt_file, "w") as f: f.write("my {{ template_string }}") subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline) - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.template_strings() assert len(result["failed"]) == 1 @@ -27,7 +27,7 @@ def test_template_strings_ignored(self): nf_core_yml = Path(new_pipeline) / ".nf-core.yml" with open(nf_core_yml, "w") as f: f.write("repository_type: pipeline\nlint:\n template_strings: False") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() lint_obj._lint_pipeline() assert len(lint_obj.failed) == 0 @@ -46,7 +46,7 @@ def test_template_strings_ignore_file(self): nf_core_yml = Path(new_pipeline) / ".nf-core.yml" with open(nf_core_yml, "w") as f: f.write("repository_type: pipeline\nlint:\n template_strings:\n - docs/test.txt") - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() result = lint_obj.template_strings() assert len(result["failed"]) == 0 diff --git a/tests/lint/version_consistency.py b/tests/lint/version_consistency.py index 4763020fb9..1be57969f1 100644 --- a/tests/lint/version_consistency.py +++ b/tests/lint/version_consistency.py @@ -1,11 +1,11 @@ -import nf_core.lint import nf_core.pipelines.create.create +import nf_core.pipelines.lint def test_version_consistency(self): """Tests that config variable existence test fails with bad pipeline name""" new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load_pipeline_config() lint_obj.nextflow_config() diff --git a/tests/test_bump_version.py b/tests/test_bump_version.py index 059e18e92e..ad7efcd1fd 100644 --- a/tests/test_bump_version.py +++ b/tests/test_bump_version.py @@ -4,7 +4,7 @@ import yaml -import nf_core.bump_version +import nf_core.pipelines.bump_version.bump_version import nf_core.pipelines.create.create import nf_core.utils @@ -24,7 +24,7 @@ def test_bump_pipeline_version(datafiles, tmp_path): pipeline_obj._load() # Bump the version number - nf_core.bump_version.bump_pipeline_version(pipeline_obj, "1.1") + nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(pipeline_obj, "1.1") new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check nextflow.config @@ -44,7 +44,7 @@ def test_dev_bump_pipeline_version(datafiles, tmp_path): pipeline_obj._load() # Bump the version number - nf_core.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev") + nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev") new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check the pipeline config @@ -65,7 +65,7 @@ def test_bump_nextflow_version(datafiles, tmp_path): # Bump the version number to a specific version, preferably one # we're not already on version = "22.04.3" - nf_core.bump_version.bump_nextflow_version(pipeline_obj, version) + nf_core.pipelines.bump_version.bump_version.bump_nextflow_version(pipeline_obj, version) new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check nextflow.config diff --git a/tests/test_cli.py b/tests/test_cli.py index 76d167101a..95a3d6ab66 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -283,7 +283,7 @@ def test_create_app(self, mock_create): mock_create.return_value.run.assert_called_once() @mock.patch("nf_core.utils.is_pipeline_directory") - @mock.patch("nf_core.lint.run_linting") + @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint(self, mock_lint, mock_is_pipeline): """Test nf-core lint""" mock_lint_results = (mock.MagicMock, mock.MagicMock, mock.MagicMock) @@ -353,7 +353,7 @@ def test_lint_dir_is_not_pipeline(self, mock_is_pipeline): assert captured_logs.records[-1].levelname == "ERROR" @mock.patch("nf_core.utils.is_pipeline_directory") - @mock.patch("nf_core.lint.run_linting") + @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint_log_assert_error(self, mock_lint, mock_is_pipeline): """Test nf-core lint logs assertion errors""" error_txt = "AssertionError has been raised" @@ -368,7 +368,7 @@ def test_lint_log_assert_error(self, mock_lint, mock_is_pipeline): assert captured_logs.records[-1].levelname == "CRITICAL" @mock.patch("nf_core.utils.is_pipeline_directory") - @mock.patch("nf_core.lint.run_linting") + @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint_log_user_warning(self, mock_lint, mock_is_pipeline): """Test nf-core lint logs assertion errors""" error_txt = "AssertionError has been raised" diff --git a/tests/test_lint.py b/tests/test_lint.py index aaf8330800..c3a03c5795 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -9,8 +9,8 @@ import yaml -import nf_core.lint import nf_core.pipelines.create.create +import nf_core.pipelines.lint from .utils import with_temporary_folder @@ -32,7 +32,7 @@ def setUp(self): self.create_obj.init_pipeline() # Base lint object on this directory - self.lint_obj = nf_core.lint.PipelineLint(self.test_pipeline_dir) + self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir) def tearDown(self): """Clean up temporary files and folders""" @@ -56,7 +56,7 @@ def test_run_linting_function(self): We don't really check any of this code as it's just a series of function calls and we're testing each of those individually. This is mostly to check for syntax errors.""" - nf_core.lint.run_linting(self.test_pipeline_dir, False) + nf_core.pipelines.lint.run_linting(self.test_pipeline_dir, False) def test_init_pipeline_lint(self): """Simply create a PipelineLint object. @@ -64,7 +64,7 @@ def test_init_pipeline_lint(self): This checks that all of the lint test imports are working properly, we also check that the git sha was found and that the release flag works properly """ - lint_obj = nf_core.lint.PipelineLint(self.test_pipeline_dir, True) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir, True) # Tests that extra test is added for release mode assert "version_consistency" in lint_obj.lint_tests @@ -82,7 +82,7 @@ def test_load_lint_config_ignore_all_tests(self): # Make a copy of the test pipeline and create a lint object new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.lint.PipelineLint(new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) # Make a config file listing all test names config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} @@ -167,7 +167,7 @@ def test_sphinx_md_files(self): existing_docs.append(os.path.join(docs_basedir, fn)) # Check .md files against each test name - lint_obj = nf_core.lint.PipelineLint("", True) + lint_obj = nf_core.pipelines.lint.PipelineLint("", True) for test_name in lint_obj.lint_tests: fn = os.path.join(docs_basedir, f"{test_name}.md") assert os.path.exists(fn), f"Could not find lint docs .md file: {fn}" @@ -259,40 +259,40 @@ def test_sphinx_md_files(self): # def test_critical_missingfiles_example(self): # """Tests for missing nextflow config and main.nf files""" -# lint_obj = nf_core.lint.run_linting(PATH_CRITICAL_EXAMPLE, False) +# lint_obj = nf_core.pipelines.lint.run_linting(PATH_CRITICAL_EXAMPLE, False) # assert len(lint_obj.failed) > 0 # # def test_failing_missingfiles_example(self): # """Tests for missing files like Dockerfile or LICENSE""" -# lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_FAILING_EXAMPLE) # lint_obj.check_files_exist() # expectations = {"failed": 6, "warned": 2, "passed": 14} # self.assess_lint_status(lint_obj, **expectations) # # def test_mit_licence_example_pass(self): # """Tests that MIT test works with good MIT licences""" -# good_lint_obj = nf_core.lint.PipelineLint(PATH_CRITICAL_EXAMPLE) +# good_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_CRITICAL_EXAMPLE) # good_lint_obj.check_licence() # expectations = {"failed": 0, "warned": 0, "passed": 1} # self.assess_lint_status(good_lint_obj, **expectations) # # def test_mit_license_example_with_failed(self): # """Tests that MIT test works with bad MIT licences""" -# bad_lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) +# bad_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_FAILING_EXAMPLE) # bad_lint_obj.check_licence() # expectations = {"failed": 1, "warned": 0, "passed": 0} # self.assess_lint_status(bad_lint_obj, **expectations) # # def test_config_variable_example_pass(self): # """Tests that config variable existence test works with good pipeline example""" -# good_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# good_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # good_lint_obj.check_nextflow_config() # expectations = {"failed": 0, "warned": 1, "passed": 34} # self.assess_lint_status(good_lint_obj, **expectations) # # def test_config_variable_example_with_failed(self): # """Tests that config variable existence test fails with bad pipeline example""" -# bad_lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) +# bad_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_FAILING_EXAMPLE) # bad_lint_obj.check_nextflow_config() # expectations = {"failed": 19, "warned": 6, "passed": 10} # self.assess_lint_status(bad_lint_obj, **expectations) @@ -300,28 +300,28 @@ def test_sphinx_md_files(self): # @pytest.mark.xfail(raises=AssertionError, strict=True) # def test_config_variable_error(self): # """Tests that config variable existence test falls over nicely with nextflow can't run""" -# bad_lint_obj = nf_core.lint.PipelineLint("/non/existant/path") +# bad_lint_obj = nf_core.pipelines.lint.PipelineLint("/non/existant/path") # bad_lint_obj.check_nextflow_config() # # # def test_wrong_license_examples_with_failed(self): # """Tests for checking the license test behavior""" # for example in PATHS_WRONG_LICENSE_EXAMPLE: -# lint_obj = nf_core.lint.PipelineLint(example) +# lint_obj = nf_core.pipelines.lint.PipelineLint(example) # lint_obj.check_licence() # expectations = {"failed": 1, "warned": 0, "passed": 0} # self.assess_lint_status(lint_obj, **expectations) # # def test_missing_license_example(self): # """Tests for missing license behavior""" -# lint_obj = nf_core.lint.PipelineLint(PATH_MISSING_LICENSE_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_MISSING_LICENSE_EXAMPLE) # lint_obj.check_licence() # expectations = {"failed": 1, "warned": 0, "passed": 0} # self.assess_lint_status(lint_obj, **expectations) # # def test_readme_pass(self): # """Tests that the pipeline README file checks work with a good example""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.minNextflowVersion = "20.04.0" # lint_obj.files = ["environment.yml"] # lint_obj.check_readme() @@ -330,7 +330,7 @@ def test_sphinx_md_files(self): # # def test_readme_warn(self): # """Tests that the pipeline README file checks fail """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.minNextflowVersion = "0.28.0" # lint_obj.check_readme() # expectations = {"failed": 1, "warned": 0, "passed": 0} @@ -338,7 +338,7 @@ def test_sphinx_md_files(self): # # def test_readme_fail(self): # """Tests that the pipeline README file checks give warnings with a bad example""" -# lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_FAILING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.check_readme() # expectations = {"failed": 0, "warned": 2, "passed": 0} @@ -346,7 +346,7 @@ def test_sphinx_md_files(self): # # def test_dockerfile_pass(self): # """Tests if a valid Dockerfile passes the lint checks""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["Dockerfile"] # lint_obj.check_docker() # expectations = {"failed": 0, "warned": 0, "passed": 1} @@ -354,7 +354,7 @@ def test_sphinx_md_files(self): # # def test_version_consistency_pass(self): # """Tests the workflow version and container version sucessfully""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.config["manifest.version"] = "0.4" # lint_obj.config["process.container"] = "nfcore/tools:0.4" # lint_obj.check_version_consistency() @@ -366,7 +366,7 @@ def test_sphinx_md_files(self): # and simulate wrong release tag""" # os.environ["GITHUB_REF"] = "refs/tags/0.5" # os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.config["manifest.version"] = "0.4" # lint_obj.config["process.container"] = "nfcore/tools:0.4" # lint_obj.check_version_consistency() @@ -378,7 +378,7 @@ def test_sphinx_md_files(self): # and simulate wrong release tag""" # os.environ["GITHUB_REF"] = "refs/tags/0.5dev" # os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.config["manifest.version"] = "0.4" # lint_obj.config["process.container"] = "nfcore/tools:0.4" # lint_obj.check_version_consistency() @@ -390,7 +390,7 @@ def test_sphinx_md_files(self): # and simulate wrong missing docker version tag""" # os.environ["GITHUB_REF"] = "refs/tags/0.4" # os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.config["manifest.version"] = "0.4" # lint_obj.config["process.container"] = "nfcore/tools" # lint_obj.check_version_consistency() @@ -402,7 +402,7 @@ def test_sphinx_md_files(self): # and simulate correct release tag""" # os.environ["GITHUB_REF"] = "refs/tags/0.4" # os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.config["manifest.version"] = "0.4" # lint_obj.config["process.container"] = "nfcore/tools:0.4" # lint_obj.check_version_consistency() @@ -411,7 +411,7 @@ def test_sphinx_md_files(self): # # def test_conda_env_pass(self): # """ Tests the conda environment config checks with a working example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # with open(os.path.join(PATH_WORKING_EXAMPLE, "environment.yml"), "r") as fh: # lint_obj.conda_config = yaml.safe_load(fh) @@ -423,7 +423,7 @@ def test_sphinx_md_files(self): # # def test_conda_env_fail(self): # """ Tests the conda environment config fails with a bad example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # with open(os.path.join(PATH_WORKING_EXAMPLE, "environment.yml"), "r") as fh: # lint_obj.conda_config = yaml.safe_load(fh) @@ -441,20 +441,20 @@ def test_sphinx_md_files(self): # # Define the behaviour of the request get mock # mock_get.side_effect = requests.exceptions.Timeout() # # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.conda_config["channels"] = ["bioconda"] # lint_obj.check_anaconda_package("multiqc=1.6") # # def test_conda_env_skip(self): # """ Tests the conda environment config is skipped when not needed """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.check_conda_env_yaml() # expectations = {"failed": 0, "warned": 0, "passed": 0} # self.assess_lint_status(lint_obj, **expectations) # # def test_conda_dockerfile_pass(self): # """ Tests the conda Dockerfile test works with a working example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.version = "1.11" # lint_obj.files = ["environment.yml", "Dockerfile"] # with open(os.path.join(PATH_WORKING_EXAMPLE, "Dockerfile"), "r") as fh: @@ -466,7 +466,7 @@ def test_sphinx_md_files(self): # # def test_conda_dockerfile_fail(self): # """ Tests the conda Dockerfile test fails with a bad example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.version = "1.11" # lint_obj.files = ["environment.yml", "Dockerfile"] # lint_obj.conda_config["name"] = "nf-core-tools-0.4" @@ -477,14 +477,14 @@ def test_sphinx_md_files(self): # # def test_conda_dockerfile_skip(self): # """ Tests the conda Dockerfile test is skipped when not needed """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.check_conda_dockerfile() # expectations = {"failed": 0, "warned": 0, "passed": 0} # self.assess_lint_status(lint_obj, **expectations) # # def test_pip_no_version_fail(self): # """ Tests the pip dependency version definition is present """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -495,7 +495,7 @@ def test_sphinx_md_files(self): # # def test_pip_package_not_latest_warn(self): # """ Tests the pip dependency version definition is present """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -511,7 +511,7 @@ def test_sphinx_md_files(self): # # Define the behaviour of the request get mock # mock_get.side_effect = requests.exceptions.Timeout() # # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -527,7 +527,7 @@ def test_sphinx_md_files(self): # # Define the behaviour of the request get mock # mock_get.side_effect = requests.exceptions.ConnectionError() # # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -538,7 +538,7 @@ def test_sphinx_md_files(self): # # def test_pip_dependency_fail(self): # """ Tests the PyPi API package information query """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -551,7 +551,7 @@ def test_sphinx_md_files(self): # """Tests that linting fails, if conda dependency # package version is not available on Anaconda. # """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -564,7 +564,7 @@ def test_sphinx_md_files(self): # """Tests that linting fails, if conda dependency # package version is not available on Anaconda. # """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # lint_obj.files = ["environment.yml"] # lint_obj.pipeline_name = "tools" # lint_obj.config["manifest.version"] = "0.4" @@ -575,8 +575,8 @@ def test_sphinx_md_files(self): # # def test_pipeline_name_pass(self): # """Tests pipeline name good pipeline example: lower case, no punctuation""" -# # good_lint_obj = nf_core.lint.run_linting(PATH_WORKING_EXAMPLE) -# good_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# # good_lint_obj = nf_core.pipelines.lint.run_linting(PATH_WORKING_EXAMPLE) +# good_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # good_lint_obj.pipeline_name = "tools" # good_lint_obj.check_pipeline_name() # expectations = {"failed": 0, "warned": 0, "passed": 1} @@ -584,7 +584,7 @@ def test_sphinx_md_files(self): # # def test_pipeline_name_critical(self): # """Tests that warning is returned for pipeline not adhering to naming convention""" -# critical_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) +# critical_lint_obj = nf_core.pipelines.lint.PipelineLint(PATH_WORKING_EXAMPLE) # critical_lint_obj.pipeline_name = "Tools123" # critical_lint_obj.check_pipeline_name() # expectations = {"failed": 0, "warned": 1, "passed": 0} diff --git a/tests/test_lint_utils.py b/tests/test_lint_utils.py index 2b624a3ecf..a4b7caf307 100644 --- a/tests/test_lint_utils.py +++ b/tests/test_lint_utils.py @@ -3,7 +3,7 @@ import git import pytest -import nf_core.lint_utils +import nf_core.pipelines.lint_utils JSON_WITH_SYNTAX_ERROR = "{'a':1, 1}" JSON_MALFORMED = "{'a':1}" @@ -50,16 +50,16 @@ def git_dir_with_json_syntax_error(temp_git_repo): def test_run_prettier_on_formatted_file(formatted_json): - nf_core.lint_utils.run_prettier_on_file(formatted_json) + nf_core.pipelines.lint_utils.run_prettier_on_file(formatted_json) assert formatted_json.read_text() == JSON_FORMATTED def test_run_prettier_on_malformed_file(malformed_json): - nf_core.lint_utils.run_prettier_on_file(malformed_json) + nf_core.pipelines.lint_utils.run_prettier_on_file(malformed_json) assert malformed_json.read_text() == JSON_FORMATTED def test_run_prettier_on_syntax_error_file(syntax_error_json, caplog): - nf_core.lint_utils.run_prettier_on_file(syntax_error_json) + nf_core.pipelines.lint_utils.run_prettier_on_file(syntax_error_json) expected_critical_log = "SyntaxError: Unexpected token (1:10)" assert expected_critical_log in caplog.text diff --git a/tests/test_sync.py b/tests/test_sync.py index 40e68dc7dc..0cacbf544e 100644 --- a/tests/test_sync.py +++ b/tests/test_sync.py @@ -12,7 +12,7 @@ import pytest import nf_core.pipelines.create.create -import nf_core.sync +import nf_core.pipelines.sync.sync from .utils import with_temporary_folder @@ -46,8 +46,8 @@ def tearDown(self): @with_temporary_folder def test_inspect_sync_dir_notgit(self, tmp_dir): """Try syncing an empty directory""" - psync = nf_core.sync.PipelineSync(tmp_dir) - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + psync = nf_core.pipelines.sync.sync.PipelineSync(tmp_dir) + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() assert "does not appear to be a git repository" in exc_info.value.args[0] @@ -57,9 +57,9 @@ def test_inspect_sync_dir_dirty(self): test_fn = Path(self.pipeline_dir) / "uncommitted" test_fn.touch() # Try to sync, check we halt with the right error - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) try: - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() assert exc_info.value.args[0].startswith("Uncommitted changes found in pipeline directory!") finally: @@ -68,8 +68,8 @@ def test_inspect_sync_dir_dirty(self): def test_get_wf_config_no_branch(self): """Try getting a workflow config when the branch doesn't exist""" # Try to sync, check we halt with the right error - psync = nf_core.sync.PipelineSync(self.pipeline_dir, from_branch="foo") - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir, from_branch="foo") + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() psync.get_wf_config() assert exc_info.value.args[0] == "Branch `foo` not found!" @@ -77,9 +77,9 @@ def test_get_wf_config_no_branch(self): def test_get_wf_config_missing_required_config(self): """Try getting a workflow config, then make it miss a required config option""" # Try to sync, check we halt with the right error - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.required_config_vars = ["fakethisdoesnotexist"] - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() psync.get_wf_config() # Check that we did actually get some config back @@ -89,26 +89,26 @@ def test_get_wf_config_missing_required_config(self): def test_checkout_template_branch(self): """Try checking out the TEMPLATE branch of the pipeline""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() def test_checkout_template_branch_no_template(self): """Try checking out the TEMPLATE branch of the pipeline when it does not exist""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.delete_head("TEMPLATE") - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.checkout_template_branch() assert exc_info.value.args[0] == "Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'" def test_delete_template_branch_files(self): """Confirm that we can delete all files in the TEMPLATE branch""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -118,7 +118,7 @@ def test_delete_template_branch_files(self): def test_create_template_pipeline(self): """Confirm that we can delete all files in the TEMPLATE branch""" # First, delete all the files - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -132,7 +132,7 @@ def test_create_template_pipeline(self): def test_commit_template_changes_nochanges(self): """Try to commit the TEMPLATE branch, but no changes were made""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -142,7 +142,7 @@ def test_commit_template_changes_nochanges(self): def test_commit_template_changes_changes(self): """Try to commit the TEMPLATE branch, but no changes were made""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -159,7 +159,7 @@ def test_commit_template_changes_changes(self): def test_push_template_branch_error(self): """Try pushing the changes, but without a remote (should fail)""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -168,13 +168,13 @@ def test_push_template_branch_error(self): test_fn.touch() psync.commit_template_changes() # Try to push changes - with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: psync.push_template_branch() assert exc_info.value.args[0].startswith("Could not push TEMPLATE branch") def test_create_merge_base_branch(self): """Try creating a merge base branch""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -193,7 +193,7 @@ def test_create_merge_base_branch_thrice(self): end, so it is needed to call it a third time to make sure this is picked up. """ - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -206,7 +206,7 @@ def test_create_merge_base_branch_thrice(self): def test_push_merge_branch(self): """Try pushing merge branch""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.create_remote("origin", self.remote_path) @@ -218,12 +218,12 @@ def test_push_merge_branch(self): def test_push_merge_branch_without_create_branch(self): """Try pushing merge branch without creating first""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.create_remote("origin", self.remote_path) - with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: psync.push_merge_branch() assert exc_info.value.args[0].startswith(f"Could not push branch '{psync.merge_branch}'") @@ -313,7 +313,7 @@ def json(self): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) def test_make_pull_request_success(self, mock_post, mock_get): """Try making a PR - successful response""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.gh_api.get = mock_get psync.gh_api.post = mock_post psync.gh_username = "no_existing_pr" @@ -326,13 +326,13 @@ def test_make_pull_request_success(self, mock_post, mock_get): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) def test_make_pull_request_bad_response(self, mock_post, mock_get): """Try making a PR and getting a 404 error""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.gh_api.get = mock_get psync.gh_api.post = mock_post psync.gh_username = "bad_url" psync.gh_repo = "bad_url/response" os.environ["GITHUB_AUTH_TOKEN"] = "test" - with pytest.raises(nf_core.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: psync.make_pull_request() assert exc_info.value.args[0].startswith( "Something went badly wrong - GitHub API PR failed - got return code 404" @@ -341,7 +341,7 @@ def test_make_pull_request_bad_response(self, mock_post, mock_get): @mock.patch("nf_core.utils.gh_api.get", side_effect=mocked_requests_get) def test_close_open_template_merge_prs(self, mock_get): """Try closing all open prs""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.get = mock_get @@ -360,7 +360,7 @@ def test_close_open_template_merge_prs(self, mock_get): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch) def test_close_open_pr(self, mock_patch, mock_post): - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.post = mock_post @@ -383,7 +383,7 @@ def test_close_open_pr(self, mock_patch, mock_post): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch) def test_close_open_pr_fail(self, mock_patch, mock_post): - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.post = mock_post @@ -405,7 +405,7 @@ def test_close_open_pr_fail(self, mock_patch, mock_post): def test_reset_target_dir(self): """Try resetting target pipeline directory""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -417,12 +417,12 @@ def test_reset_target_dir(self): def test_reset_target_dir_fake_branch(self): """Try resetting target pipeline directory but original branch does not exist""" - psync = nf_core.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.original_branch = "fake_branch" - with pytest.raises(nf_core.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: psync.reset_target_dir() assert exc_info.value.args[0].startswith("Could not reset to original branch `fake_branch`") From d6799d55b91136ed128d340f4484001e41dbcb9d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 15 May 2024 08:16:22 +0000 Subject: [PATCH 011/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16262bd1c3..60e632bd46 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) +- move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From bc1d3dbebd2f3ce0ae1367227e26d64ac243d81c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 15 May 2024 12:35:32 +0200 Subject: [PATCH 012/574] more pipeline commands path changes to fix tests --- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/actions/create-lint-wf/action.yml | 18 ++++++++--------- .../create-test-lint-wf-template.yml | 16 +++++++-------- CONTRIBUTING.md | 4 ++-- docs/api/_src/index.md | 7 ++++--- nf_core/__main__.py | 1 - .../pipeline-template/.github/CONTRIBUTING.md | 4 ++-- .../.github/PULL_REQUEST_TEMPLATE.md | 2 +- .../.github/workflows/linting.yml | 6 +++--- nf_core/pipelines/lint/__init__.py | 2 +- nf_core/pipelines/lint/files_exist.py | 2 +- nf_core/pipelines/lint/files_unchanged.py | 2 +- nf_core/pipelines/lint/nextflow_config.py | 2 +- nf_core/pipelines/lint/schema_lint.py | 2 +- nf_core/pipelines/lint/version_consistency.py | 2 +- nf_core/pipelines/lint_utils.py | 2 +- nf_core/pipelines/sync/sync.py | 2 +- nf_core/utils.py | 2 +- tests/test_cli.py | 20 +++++++++---------- tests/test_sync.py | 2 +- 20 files changed, 50 insertions(+), 50 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 5043b37acc..5b627a1451 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -24,7 +24,7 @@ body: description: Steps to reproduce the behaviour. Please paste the command and output from your terminal. render: console placeholder: | - $ nf-core lint ... + $ nf-core pipelines lint ... Some output where something broke diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 9052c90ddc..8760901db1 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -30,9 +30,9 @@ runs: nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" # Try syncing it before we change anything - - name: nf-core sync + - name: nf-core pipelines sync shell: bash - run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/ + run: nf-core --log-file log.txt pipelines sync --dir nf-core-testpipeline/ working-directory: create-lint-wf # Run code style linting @@ -59,20 +59,20 @@ runs: run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; working-directory: create-lint-wf - # Run nf-core linting - - name: nf-core lint + # Run nf-core pipelines linting + - name: nf-core pipelines lint shell: bash - run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned + run: nf-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned working-directory: create-lint-wf - - name: nf-core bump-version to release + - name: nf-core pipelines bump-version to release shell: bash - run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1 + run: nf-core --log-file log.txt pipelines bump-version --dir nf-core-testpipeline/ 1.1 working-directory: create-lint-wf - - name: nf-core lint in release mode + - name: nf-core pipelines lint in release mode shell: bash - run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release + run: nf-core --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release working-directory: create-lint-wf - name: Upload log file artifact diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 4ae2714534..b823ca72d8 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -119,8 +119,8 @@ jobs: rm -rf create-test-lint-wf/results # Try syncing it before we change anything - - name: nf-core sync - run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/ + - name: nf-core pipelines sync + run: nf-core --log-file log.txt pipelines sync --dir create-test-lint-wf/my-prefix-testpipeline/ # Run code style linting - name: Run pre-commit @@ -138,18 +138,18 @@ jobs: working-directory: create-test-lint-wf # Run nf-core linting - - name: nf-core lint - run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned + - name: nf-core pipelines lint + run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned working-directory: create-test-lint-wf # Run bump-version - - name: nf-core bump-version - run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1 + - name: nf-core pipelines bump-version + run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1 working-directory: create-test-lint-wf # Run nf-core linting in release mode - - name: nf-core lint in release mode - run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release + - name: nf-core pipelines lint in release mode + run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned --release working-directory: create-test-lint-wf - name: Tar files diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 04d327bd8c..2b2dfc1bed 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -107,8 +107,8 @@ This ensures that any changes we make to either the linting or the template stay You can replicate this process locally with the following commands: ```bash -nf-core create -n testpipeline -d "This pipeline is for testing" -nf-core lint nf-core-testpipeline +nf-core pipelines create -n testpipeline -d "This pipeline is for testing" +nf-core pipelines lint nf-core-testpipeline ``` ## GitHub Codespaces diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md index af3813bc51..037ca95475 100644 --- a/docs/api/_src/index.md +++ b/docs/api/_src/index.md @@ -16,6 +16,7 @@ This documentation is for the `nf-core/tools` package. ## Contents -- [Pipeline code lint tests](pipeline_lint_tests/) (run by `nf-core lint`) -- [Module code lint tests](module_lint_tests/) (run by `nf-core modules lint`) -- [Subworkflow code lint tests](subworkflow_lint_tests/) (run by `nf-core subworkflows lint`) +- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`) +- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`) +- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`) +- [nf-core/tools Python package API reference](api/index.md) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index c2423ef1fc..921b5c8cf2 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -645,7 +645,6 @@ def create_pipeline(ctx, name, description, author, version, force, outdir, temp # nf-core pipelines lint @pipelines.command("lint") -@click.pass_context @click.option( "-d", "--dir", diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index 3f541162d3..dc05d165d1 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -44,7 +44,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -111,7 +111,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md index 9ad257a0b8..dee23ccab1 100644 --- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md +++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md @@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t {%- if is_nfcore %} - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. {%- endif %} -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index b2cde075fe..f681380fde 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. {%- raw %} on: push: @@ -46,12 +46,12 @@ jobs: python -m pip install --upgrade pip pip install nf-core - - name: Run nf-core lint + - name: Run nf-core pipelines lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index 4ec62ddb0d..cf5ba3913f 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -439,7 +439,7 @@ def _get_results_md(self): comment_body_text = f"Posted for pipeline commit {self.git_sha[:7]}" if self.git_sha is not None else "" timestamp = now.strftime("%Y-%m-%d %H:%M:%S") markdown = ( - f"## `nf-core lint` overall result: {overall_result}\n\n" + f"## `nf-core pipelines lint` overall result: {overall_result}\n\n" f"{comment_body_text}\n\n" f"```diff{test_passed_count}{test_ignored_count}{test_fixed_count}{test_warning_count}{test_failure_count}" "\n```\n\n" diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py index 0c87100622..c6f622b3e0 100644 --- a/nf_core/pipelines/lint/files_exist.py +++ b/nf_core/pipelines/lint/files_exist.py @@ -104,7 +104,7 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]: lib/nfcore_external_java_deps.jar # if "nf-validation" is in nextflow.config - .. tip:: You can configure the ``nf-core lint`` tests to ignore any of these checks by setting + .. tip:: You can configure the ``nf-core pipelines lint`` tests to ignore any of these checks by setting the ``files_exist`` key as follows in your ``.nf-core.yml`` config file. For example: .. code-block:: yaml diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py index fc044b6597..bafd8aec78 100644 --- a/nf_core/pipelines/lint/files_unchanged.py +++ b/nf_core/pipelines/lint/files_unchanged.py @@ -49,7 +49,7 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]: .prettierignore - .. tip:: You can configure the ``nf-core lint`` tests to ignore any of these checks by setting + .. tip:: You can configure the ``nf-core pipelines lint`` tests to ignore any of these checks by setting the ``files_unchanged`` key as follows in your ``.nf-core.yml`` config file. For example: .. code-block:: yaml diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 47b7d78f5e..4fa49acbcb 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -26,7 +26,7 @@ def nextflow_config(self): * ``manifest.version`` * The version of this pipeline. This should correspond to a `GitHub release `_. - * If ``--release`` is set when running ``nf-core lint``, the version number must not contain the string ``dev`` + * If ``--release`` is set when running ``nf-core pipelines lint``, the version number must not contain the string ``dev`` * If ``--release`` is _not_ set, the version should end in ``dev`` (warning triggered if not) * ``manifest.nextflowVersion`` diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py index 178063d5dd..3342dc4b9d 100644 --- a/nf_core/pipelines/lint/schema_lint.py +++ b/nf_core/pipelines/lint/schema_lint.py @@ -58,7 +58,7 @@ def schema_lint(self): } .. tip:: You can check your pipeline schema without having to run the entire pipeline lint - by running ``nf-core schema lint`` instead of ``nf-core lint`` + by running ``nf-core schema lint`` instead of ``nf-core pipelines lint`` """ passed = [] warned = [] diff --git a/nf_core/pipelines/lint/version_consistency.py b/nf_core/pipelines/lint/version_consistency.py index e396ca9e7a..5fe24ed723 100644 --- a/nf_core/pipelines/lint/version_consistency.py +++ b/nf_core/pipelines/lint/version_consistency.py @@ -4,7 +4,7 @@ def version_consistency(self): """Pipeline and container version number consistency. - .. note:: This test only runs when the ``--release`` flag is set for ``nf-core lint``, + .. note:: This test only runs when the ``--release`` flag is set for ``nf-core pipelines lint``, or ``$GITHUB_REF`` is equal to ``master``. This lint fetches the pipeline version number from three possible locations: diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py index 167600bfc0..4ccf790076 100644 --- a/nf_core/pipelines/lint_utils.py +++ b/nf_core/pipelines/lint_utils.py @@ -50,7 +50,7 @@ def print_fixes(lint_obj): if lint_obj.could_fix: fix_flags = "".join([f" --fix {fix}" for fix in lint_obj.could_fix]) wf_dir = "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}" - fix_cmd = f"nf-core lint {wf_dir} {fix_flags}" + fix_cmd = f"nf-core pipelines lint {wf_dir} {fix_flags}" console.print( "\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n" f"[blue] {fix_cmd}\n" diff --git a/nf_core/pipelines/sync/sync.py b/nf_core/pipelines/sync/sync.py index 81082c24be..ccee2a9c4f 100644 --- a/nf_core/pipelines/sync/sync.py +++ b/nf_core/pipelines/sync/sync.py @@ -185,7 +185,7 @@ def inspect_sync_dir(self): # Check to see if there are uncommitted changes on current branch if self.repo.is_dirty(untracked_files=True): raise SyncExceptionError( - "Uncommitted changes found in pipeline directory!\nPlease commit these before running nf-core sync" + "Uncommitted changes found in pipeline directory!\nPlease commit these before running nf-core pipelines sync" ) def get_wf_config(self): diff --git a/nf_core/utils.py b/nf_core/utils.py index 8c50f0a49f..9dae4b9e56 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -578,7 +578,7 @@ def request_retry(self, url, post_data=None): """ Try to fetch a URL, keep retrying if we get a certain return code. - Used in nf-core sync code because we get 403 errors: too many simultaneous requests + Used in nf-core pipelines sync code because we get 403 errors: too many simultaneous requests See https://github.com/nf-core/tools/issues/911 """ if not self.has_init: diff --git a/tests/test_cli.py b/tests/test_cli.py index 95a3d6ab66..53780b14e1 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -285,7 +285,7 @@ def test_create_app(self, mock_create): @mock.patch("nf_core.utils.is_pipeline_directory") @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint(self, mock_lint, mock_is_pipeline): - """Test nf-core lint""" + """Test nf-core pipelines lint""" mock_lint_results = (mock.MagicMock, mock.MagicMock, mock.MagicMock) mock_lint_results[0].failed = [] mock_lint_results[1].failed = [] @@ -305,7 +305,7 @@ def test_lint(self, mock_lint, mock_is_pipeline): "json": "output_file.json", } - cmd = ["lint"] + self.assemble_params(params) + cmd = ["pipelines", "lint"] + self.assemble_params(params) result = self.invoke_cli(cmd) assert result.exit_code == 0 @@ -324,12 +324,12 @@ def test_lint(self, mock_lint, mock_is_pipeline): ) def test_lint_no_dir(self): - """Test nf-core lint fails if --dir does not exist""" + """Test nf-core pipelines lint fails if --dir does not exist""" params = { "dir": "/bad/path", } - cmd = ["lint"] + self.assemble_params(params) + cmd = ["pipelines", "lint"] + self.assemble_params(params) result = self.invoke_cli(cmd) assert result.exit_code == 2 @@ -340,11 +340,11 @@ def test_lint_no_dir(self): @mock.patch("nf_core.utils.is_pipeline_directory") def test_lint_dir_is_not_pipeline(self, mock_is_pipeline): - """Test nf-core lint logs an error if not called from a pipeline directory.""" + """Test nf-core pipelines lint logs an error if not called from a pipeline directory.""" error_txt = "UserWarning has been raised" mock_is_pipeline.side_effect = UserWarning(error_txt) - cmd = ["lint"] + cmd = ["pipelines", "lint"] with self.assertLogs() as captured_logs: result = self.invoke_cli(cmd) @@ -355,11 +355,11 @@ def test_lint_dir_is_not_pipeline(self, mock_is_pipeline): @mock.patch("nf_core.utils.is_pipeline_directory") @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint_log_assert_error(self, mock_lint, mock_is_pipeline): - """Test nf-core lint logs assertion errors""" + """Test nf-core pipelines lint logs assertion errors""" error_txt = "AssertionError has been raised" mock_lint.side_effect = AssertionError(error_txt) - cmd = ["lint"] + cmd = ["pipelines", "lint"] with self.assertLogs() as captured_logs: result = self.invoke_cli(cmd) @@ -370,11 +370,11 @@ def test_lint_log_assert_error(self, mock_lint, mock_is_pipeline): @mock.patch("nf_core.utils.is_pipeline_directory") @mock.patch("nf_core.pipelines.lint.run_linting") def test_lint_log_user_warning(self, mock_lint, mock_is_pipeline): - """Test nf-core lint logs assertion errors""" + """Test nf-core pipelines lint logs assertion errors""" error_txt = "AssertionError has been raised" mock_lint.side_effect = UserWarning(error_txt) - cmd = ["lint"] + cmd = ["pipelines", "lint"] with self.assertLogs() as captured_logs: result = self.invoke_cli(cmd) diff --git a/tests/test_sync.py b/tests/test_sync.py index 0cacbf544e..b980335387 100644 --- a/tests/test_sync.py +++ b/tests/test_sync.py @@ -349,7 +349,7 @@ def test_close_open_template_merge_prs(self, mock_get): psync.gh_repo = "list_prs/response" os.environ["GITHUB_AUTH_TOKEN"] = "test" - with mock.patch("nf_core.sync.PipelineSync.close_open_pr") as mock_close_open_pr: + with mock.patch("nf_core.pipelines.sync.sync.PipelineSync.close_open_pr") as mock_close_open_pr: psync.close_open_template_merge_prs() prs = mock_get(f"https://api.github.com/repos/{psync.gh_repo}/pulls").data From 7f197b337d7e84e0be2d6d5ac998d706726ffd42 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 23 May 2024 18:24:08 +0200 Subject: [PATCH 013/574] pass ctx to pipeliens sync command --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 921b5c8cf2..398668d338 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2375,7 +2375,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def sync_pipeline(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. From c14a24a288d7841bad31ae3edab3fcb9b50ad0cb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 24 May 2024 14:08:15 +0200 Subject: [PATCH 014/574] add init files --- nf_core/__main__.py | 2 +- nf_core/pipelines/bump_version/__init__.py | 0 nf_core/pipelines/sync/__init__.py | 0 3 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 nf_core/pipelines/bump_version/__init__.py create mode 100644 nf_core/pipelines/sync/__init__.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 398668d338..3934566845 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2199,7 +2199,7 @@ def bump_version(new_version, dir, nextflow): default=False, help="Bump required nextflow version instead of pipeline version", ) -def bump_version_pipeline(new_version, dir, nextflow): +def bump_version_pipeline(ctx, new_version, dir, nextflow): """ Update nf-core pipeline version number. diff --git a/nf_core/pipelines/bump_version/__init__.py b/nf_core/pipelines/bump_version/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nf_core/pipelines/sync/__init__.py b/nf_core/pipelines/sync/__init__.py new file mode 100644 index 0000000000..e69de29bb2 From 60b79b156ccd77f369ad174997fdb0284db62682 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 29 May 2024 15:35:19 +0200 Subject: [PATCH 015/574] use pydantic validation context on module initialization. use global variable for pipeline type --- nf_core/pipelines/create/__init__.py | 16 +++++----- nf_core/pipelines/create/utils.py | 46 +++++++++++++++++++++++----- 2 files changed, 46 insertions(+), 16 deletions(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index da6a693220..c118d8520d 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -5,6 +5,7 @@ from textual.app import App from textual.widgets import Button +from nf_core.pipelines.create import utils from nf_core.pipelines.create.basicdetails import BasicDetails from nf_core.pipelines.create.custompipeline import CustomPipeline from nf_core.pipelines.create.finaldetails import FinalDetails @@ -14,15 +15,10 @@ from nf_core.pipelines.create.loggingscreen import LoggingScreen from nf_core.pipelines.create.nfcorepipeline import NfcorePipeline from nf_core.pipelines.create.pipelinetype import ChoosePipelineType -from nf_core.pipelines.create.utils import ( - CreateConfig, - CustomLogHandler, - LoggingConsole, -) from nf_core.pipelines.create.welcome import WelcomeScreen -log_handler = CustomLogHandler( - console=LoggingConsole(classes="log_console"), +log_handler = utils.CustomLogHandler( + console=utils.LoggingConsole(classes="log_console"), rich_tracebacks=True, show_time=False, show_path=False, @@ -36,7 +32,7 @@ log_handler.setLevel("INFO") -class PipelineCreateApp(App[CreateConfig]): +class PipelineCreateApp(App[utils.CreateConfig]): """A Textual app to manage stopwatches.""" CSS_PATH = "create.tcss" @@ -60,7 +56,7 @@ class PipelineCreateApp(App[CreateConfig]): } # Initialise config as empty - TEMPLATE_CONFIG = CreateConfig() + TEMPLATE_CONFIG = utils.CreateConfig() # Initialise pipeline type PIPELINE_TYPE = None @@ -79,9 +75,11 @@ def on_button_pressed(self, event: Button.Pressed) -> None: self.push_screen("choose_type") elif event.button.id == "type_nfcore": self.PIPELINE_TYPE = "nfcore" + utils.PIPELINE_TYPE_GLOBAL = "nfcore" self.push_screen("basic_details") elif event.button.id == "type_custom": self.PIPELINE_TYPE = "custom" + utils.PIPELINE_TYPE_GLOBAL = "custom" self.push_screen("basic_details") elif event.button.id == "continue": self.push_screen("final_details") diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 6006452baf..0754c54b54 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -1,9 +1,11 @@ import re +from contextlib import contextmanager +from contextvars import ContextVar from logging import LogRecord from pathlib import Path -from typing import Optional, Union +from typing import Any, Dict, Iterator, Optional, Union -from pydantic import BaseModel, ConfigDict, ValidationError, field_validator +from pydantic import BaseModel, ConfigDict, ValidationError, ValidationInfo, field_validator from rich.logging import RichHandler from textual import on from textual._context import active_app @@ -14,6 +16,22 @@ from textual.widget import Widget from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch +# Use ContextVar to define a context on the model initialization +_init_context_var: ContextVar = ContextVar("_init_context_var", default={}) + + +@contextmanager +def init_context(value: Dict[str, Any]) -> Iterator[None]: + token = _init_context_var.set(value) + try: + yield + finally: + _init_context_var.reset(token) + + +# Define a global variable to store the pipeline type +PIPELINE_TYPE_GLOBAL: str | None = None + class CreateConfig(BaseModel): """Pydantic model for the nf-core create config.""" @@ -30,12 +48,25 @@ class CreateConfig(BaseModel): model_config = ConfigDict(extra="allow") + def __init__(self, /, **data: Any) -> None: + """Custom init method to allow using a context on the model initialization.""" + self.__pydantic_validator__.validate_python( + data, + self_instance=self, + context=_init_context_var.get(), + ) + @field_validator("name") @classmethod - def name_nospecialchars(cls, v: str) -> str: + def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str: """Check that the pipeline name is simple.""" - if not re.match(r"^[a-z]+$", v): - raise ValueError("Must be lowercase without punctuation.") + context = info.context + if context and context["is_nfcore"]: + if not re.match(r"^[a-z]+$", v): + raise ValueError("Must be lowercase without punctuation.") + else: + if not re.match(r"^[a-zA-Z-_]+$", v): + raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.") return v @field_validator("org", "description", "author", "version", "outdir") @@ -117,8 +148,9 @@ def validate(self, value: str) -> ValidationResult: If it fails, return the error messages.""" try: - CreateConfig(**{f"{self.key}": value}) - return self.success() + with init_context({"is_nfcore": PIPELINE_TYPE_GLOBAL == "nfcore"}): + CreateConfig(**{f"{self.key}": value}) + return self.success() except ValidationError as e: return self.failure(", ".join([err["msg"] for err in e.errors()])) From 0186535fe3e6a7c8f79fdd379ebc0d2d20f423d1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 29 May 2024 13:40:21 +0000 Subject: [PATCH 016/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63bef50b84..af62a6ed55 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) +- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 6275553f13f948ad76a6ebd0ec6ad2b73fa07cd1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 29 May 2024 15:51:36 +0200 Subject: [PATCH 017/574] use union for typing --- nf_core/pipelines/create/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 0754c54b54..d70fea1403 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -30,7 +30,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]: # Define a global variable to store the pipeline type -PIPELINE_TYPE_GLOBAL: str | None = None +PIPELINE_TYPE_GLOBAL: Union[str, None] = None class CreateConfig(BaseModel): From 2b724e0e7f98d8f6b5956eda6b776041728885bd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 30 May 2024 13:46:53 +0200 Subject: [PATCH 018/574] use NFCORE_PIPELINE as a boolean instead of a PIPELINE_TYPE string --- nf_core/pipelines/create/__init__.py | 10 +++++----- nf_core/pipelines/create/basicdetails.py | 8 ++++---- nf_core/pipelines/create/utils.py | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index c118d8520d..56e25bf1d5 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -59,7 +59,7 @@ class PipelineCreateApp(App[utils.CreateConfig]): TEMPLATE_CONFIG = utils.CreateConfig() # Initialise pipeline type - PIPELINE_TYPE = None + NFCORE_PIPELINE = True # Log handler LOG_HANDLER = log_handler @@ -74,12 +74,12 @@ def on_button_pressed(self, event: Button.Pressed) -> None: if event.button.id == "start": self.push_screen("choose_type") elif event.button.id == "type_nfcore": - self.PIPELINE_TYPE = "nfcore" - utils.PIPELINE_TYPE_GLOBAL = "nfcore" + self.NFCORE_PIPELINE = True + utils.NFCORE_PIPELINE_GLOBAL = True self.push_screen("basic_details") elif event.button.id == "type_custom": - self.PIPELINE_TYPE = "custom" - utils.PIPELINE_TYPE_GLOBAL = "custom" + self.NFCORE_PIPELINE = False + utils.NFCORE_PIPELINE_GLOBAL = False self.push_screen("basic_details") elif event.button.id == "continue": self.push_screen("final_details") diff --git a/nf_core/pipelines/create/basicdetails.py b/nf_core/pipelines/create/basicdetails.py index b88ede10d0..09484fa2ea 100644 --- a/nf_core/pipelines/create/basicdetails.py +++ b/nf_core/pipelines/create/basicdetails.py @@ -39,7 +39,7 @@ def compose(self) -> ComposeResult: "GitHub organisation", "nf-core", classes="column", - disabled=self.parent.PIPELINE_TYPE == "nfcore", + disabled=self.parent.NFCORE_PIPELINE, ) yield TextInput( "name", @@ -85,7 +85,7 @@ def on_screen_resume(self): add_hide_class(self.parent, "exist_warn") for text_input in self.query("TextInput"): if text_input.field_id == "org": - text_input.disabled = self.parent.PIPELINE_TYPE == "nfcore" + text_input.disabled = self.parent.NFCORE_PIPELINE @on(Button.Pressed) def on_button_pressed(self, event: Button.Pressed) -> None: @@ -102,9 +102,9 @@ def on_button_pressed(self, event: Button.Pressed) -> None: try: self.parent.TEMPLATE_CONFIG = CreateConfig(**config) if event.button.id == "next": - if self.parent.PIPELINE_TYPE == "nfcore": + if self.parent.NFCORE_PIPELINE: self.parent.push_screen("type_nfcore") - elif self.parent.PIPELINE_TYPE == "custom": + else: self.parent.push_screen("type_custom") except ValueError: pass diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index d70fea1403..f1e0bae3ce 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -30,7 +30,7 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]: # Define a global variable to store the pipeline type -PIPELINE_TYPE_GLOBAL: Union[str, None] = None +NFCORE_PIPELINE_GLOBAL: bool = True class CreateConfig(BaseModel): @@ -148,7 +148,7 @@ def validate(self, value: str) -> ValidationResult: If it fails, return the error messages.""" try: - with init_context({"is_nfcore": PIPELINE_TYPE_GLOBAL == "nfcore"}): + with init_context({"is_nfcore": NFCORE_PIPELINE_GLOBAL}): CreateConfig(**{f"{self.key}": value}) return self.success() except ValidationError as e: From 69968b817df2df7063a790db97f56ba39c926fc6 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 30 May 2024 15:27:58 +0200 Subject: [PATCH 019/574] move all commands under pipelines and organise help message --- nf_core/__main__.py | 1818 ++++++++++------- .../{bump_version => }/bump_version.py | 0 nf_core/pipelines/bump_version/__init__.py | 0 nf_core/pipelines/create/create.py | 6 +- nf_core/{ => pipelines}/create_logo.py | 0 nf_core/{ => pipelines}/download.py | 4 +- nf_core/{ => pipelines}/launch.py | 6 +- nf_core/pipelines/lint/nextflow_config.py | 2 +- nf_core/pipelines/lint/schema_description.py | 4 +- nf_core/pipelines/lint/schema_lint.py | 4 +- nf_core/pipelines/lint/schema_params.py | 4 +- nf_core/{ => pipelines}/list.py | 0 nf_core/{ => pipelines}/params_file.py | 6 +- nf_core/{ => pipelines}/refgenie.py | 0 nf_core/{ => pipelines}/schema.py | 4 +- nf_core/pipelines/{sync => }/sync.py | 2 +- nf_core/pipelines/sync/__init__.py | 0 tests/test_create_logo.py | 22 +- tests/test_download.py | 2 +- tests/test_launch.py | 20 +- tests/test_list.py | 44 +- tests/test_params_file.py | 6 +- tests/test_schema.py | 4 +- tests/test_utils.py | 10 +- 24 files changed, 1207 insertions(+), 761 deletions(-) rename nf_core/pipelines/{bump_version => }/bump_version.py (100%) delete mode 100644 nf_core/pipelines/bump_version/__init__.py rename nf_core/{ => pipelines}/create_logo.py (100%) rename nf_core/{ => pipelines}/download.py (99%) rename nf_core/{ => pipelines}/launch.py (99%) rename nf_core/{ => pipelines}/list.py (100%) rename nf_core/{ => pipelines}/params_file.py (98%) rename nf_core/{ => pipelines}/refgenie.py (100%) rename nf_core/{ => pipelines}/schema.py (99%) rename nf_core/pipelines/{sync => }/sync.py (99%) delete mode 100644 nf_core/pipelines/sync/__init__.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 3934566845..4921e15d5f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -14,9 +14,9 @@ from trogon import tui from nf_core import __version__ -from nf_core.download import DownloadError from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE -from nf_core.params_file import ParamsFileBuilder +from nf_core.pipelines.download import DownloadError +from nf_core.pipelines.params_file import ParamsFileBuilder from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir # Set up logging as the root logger @@ -32,31 +32,23 @@ click.rich_click.COMMAND_GROUPS = { "nf-core": [ { - "name": "Commands for users", - "commands": [ - "list", - "launch", - "create-params-file", - "download", - "licences", - "tui", - ], - }, - { - "name": "Commands for developers", + "name": "Commands", "commands": [ "pipelines", "modules", "subworkflows", - "schema", - "create-logo", + "tui", ], }, ], "nf-core pipelines": [ { - "name": "Pipeline commands", - "commands": ["create", "lint", "bump-version", "sync"], + "name": "For users", + "commands": ["list", "launch", "download", "create-params-file", "licences"], + }, + { + "name": "For developers", + "commands": ["create", "lint", "bump-version", "sync", "schema", "create-logo"], }, ], "nf-core modules": [ @@ -66,19 +58,20 @@ }, { "name": "Developing new modules", - "commands": ["create", "lint", "bump-versions", "test"], + "commands": ["create", "lint", "test", "bump-versions"], }, ], "nf-core subworkflows": [ { "name": "For pipelines", - "commands": ["info", "install", "list", "remove", "update"], + "commands": ["list", "info", "install", "update", "remove"], }, { "name": "Developing new subworkflows", - "commands": ["create", "test", "lint"], + "commands": ["create", "lint", "test"], }, ], + "nf-core pipelines schema": [{"name": "Schema commands", "commands": ["validate", "build", "lint", "docs"]}], } click.rich_click.OPTION_GROUPS = { "nf-core modules list local": [{"options": ["--dir", "--json", "--help"]}], @@ -189,195 +182,239 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file): } -# nf-core list -@nf_core_cli.command("list") -@click.argument("keywords", required=False, nargs=-1, metavar="") -@click.option( - "-s", - "--sort", - type=click.Choice(["release", "pulled", "name", "stars"]), - default="release", - help="How to sort listed pipelines", -) -@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") -@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") -def list_pipelines(keywords, sort, json, show_archived): +# nf-core pipelines subcommands +@nf_core_cli.group() +@click.pass_context +def pipelines(ctx): """ - List available nf-core pipelines with local info. - - Checks the web for a list of nf-core pipelines with their latest releases. - Shows which nf-core pipelines you have pulled locally and whether they are up to date. + Commands to manage nf-core pipelines. """ - from nf_core.list import list_workflows - - stdout.print(list_workflows(keywords, sort, json, show_archived)) + # ensure that ctx.obj exists and is a dict (in case `cli()` is called + # by means other than the `if` block below) + ctx.ensure_object(dict) -# nf-core launch -@nf_core_cli.command() -@click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") -@click.option("-i", "--id", help="ID for web-gui launch parameter set") -@click.option( - "-c", - "--command-only", - is_flag=True, - default=False, - help="Create Nextflow command with params (no params file)", -) -@click.option( - "-o", - "--params-out", - type=click.Path(), - default=os.path.join(os.getcwd(), "nf-params.json"), - help="Path to save run parameters file", -) -@click.option( - "-p", - "--params-in", - type=click.Path(exists=True), - help="Set of input run params to use from a previous run", -) -@click.option( - "-a", - "--save-all", - is_flag=True, - default=False, - help="Save all parameters, even if unchanged from default", -) +# nf-core pipelines create +@pipelines.command("create") +@click.pass_context @click.option( - "-x", - "--show-hidden", - is_flag=True, - default=False, - help="Show hidden params which don't normally need changing", + "-n", + "--name", + type=str, + help="The name of your new pipeline", ) +@click.option("-d", "--description", type=str, help="A short description of your pipeline") +@click.option("-a", "--author", type=str, help="Name of the main author(s)") +@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use") +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") +@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") +@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") @click.option( - "-u", - "--url", + "--organisation", type=str, - default="https://nf-co.re/launch", - help="Customise the builder URL (for development work)", + default="nf-core", + help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", ) -def launch( - pipeline, - id, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, -): +def create_pipeline(ctx, name, description, author, version, force, outdir, template_yaml, organisation): """ - Launch a pipeline using a web GUI or command line prompts. - - Uses the pipeline schema file to collect inputs for all available pipeline - parameters. Parameter names, descriptions and help text are shown. - The pipeline schema is used to validate all inputs as they are entered. - - When finished, saves a file with the selected parameters which can be - passed to Nextflow using the -params-file option. + Create a new pipeline using the nf-core template. - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory or an ID from the nf-core web launch tool. + Uses the nf-core template to make a skeleton Nextflow pipeline with all required + files, boilerplate code and best-practices. + \n\n + Run without any command line arguments to use an interactive interface. """ - from nf_core.launch import Launch + from nf_core.pipelines.create import PipelineCreateApp + from nf_core.pipelines.create.create import PipelineCreate - launcher = Launch( - pipeline, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, - id, - ) - if not launcher.launch_pipeline(): + if (name and description and author) or (template_yaml): + # If all command arguments are used, run without the interactive interface + try: + create_obj = PipelineCreate( + name, + description, + author, + version=version, + force=force, + outdir=outdir, + template_config=template_yaml, + organisation=organisation, + ) + create_obj.init_pipeline() + except UserWarning as e: + log.error(e) + sys.exit(1) + elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": + log.error( + "[red]Partial arguments supplied.[/] " + "Run without [i]any[/] arguments for an interactive interface, " + "or with at least name + description + author to use non-interactively." + ) sys.exit(1) + else: + log.info("Launching interactive nf-core pipeline creation tool.") + app = PipelineCreateApp() + app.run() + sys.exit(app.return_code or 0) -# nf-core create-params-file -@nf_core_cli.command() -@click.argument("pipeline", required=False, metavar="") -@click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") +# nf-core pipelines lint +@pipelines.command("lint") @click.option( - "-o", - "--output", - type=str, - default="nf-params.yml", - metavar="", - help="Output filename. Defaults to `nf-params.yml`.", + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory [dim]\[default: current working directory][/]", ) -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") @click.option( - "-x", - "--show-hidden", + "--release", is_flag=True, - default=False, - help="Show hidden params which don't normally need changing", + default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" + and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") + and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", + help="Execute additional checks for release-ready workflows.", ) -def create_params_file(pipeline, revision, output, force, show_hidden): - """ - Build a parameter file for a pipeline. - - Uses the pipeline schema file to generate a YAML parameters file. - Parameters are set to the pipeline defaults and descriptions are shown in comments. - After the output file is generated, it can then be edited as needed before - passing to nextflow using the `-params-file` option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory. - """ - builder = ParamsFileBuilder(pipeline, revision) - - if not builder.write_params_file(output, show_hidden=show_hidden, force=force): - sys.exit(1) - - -# nf-core download -@nf_core_cli.command() -@click.argument("pipeline", required=False, metavar="") @click.option( - "-r", - "--revision", + "-f", + "--fix", + type=str, + metavar="", multiple=True, - help="Pipeline release to download. Multiple invocations are possible, e.g. `-r 1.1 -r 1.2`", + help="Attempt to automatically fix specified lint test", ) -@click.option("-o", "--outdir", type=str, help="Output directory") @click.option( - "-x", - "--compress", - type=click.Choice(["tar.gz", "tar.bz2", "zip", "none"]), - help="Archive compression type", + "-k", + "--key", + type=str, + metavar="", + multiple=True, + help="Run only these lint tests", ) -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") -# TODO: Remove this in a future release. Deprecated in March 2024. +@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") +@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") +@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") @click.option( - "-t", - "--tower", - is_flag=True, - default=False, - hidden=True, - help="Download for Seqera Platform. DEPRECATED: Please use `--platform` instead.", + "--markdown", + type=str, + metavar="", + help="File to write linting results to (Markdown)", ) @click.option( - "--platform", - is_flag=True, - default=False, - help="Download for Seqera Platform (formerly Nextflow Tower)", + "--json", + type=str, + metavar="", + help="File to write linting results to (JSON)", ) @click.option( - "-d", - "--download-configuration", - is_flag=True, - default=False, - help="Include configuration profiles in download. Not available with `--platform`", + "--sort-by", + type=click.Choice(["module", "test"]), + default="test", + help="Sort lint output by module or test name.", + show_default=True, ) -@click.option( +@click.pass_context +def lint_pipeline( + ctx, + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + markdown, + json, + sort_by, +): + """ + Check pipeline code against nf-core guidelines. + + Runs a large number of automated tests to ensure that the supplied pipeline + meets the nf-core guidelines. Documentation of all lint tests can be found + on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] + + You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. + See the documentation for details. + """ + from nf_core.pipelines.lint import run_linting + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory is a pipeline + try: + is_pipeline_directory(dir) + except UserWarning as e: + log.error(e) + sys.exit(1) + + # Run the lint tests! + try: + lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + sort_by, + markdown, + json, + ctx.obj["hide_progress"], + ) + swf_failed = 0 + if subworkflow_lint_obj is not None: + swf_failed = len(subworkflow_lint_obj.failed) + if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: + sys.exit(1) + except AssertionError as e: + log.critical(e) + sys.exit(1) + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines download +@pipelines.command("download") +@click.argument("pipeline", required=False, metavar="") +@click.option( + "-r", + "--revision", + multiple=True, + help="Pipeline release to download. Multiple invocations are possible, e.g. `-r 1.1 -r 1.2`", +) +@click.option("-o", "--outdir", type=str, help="Output directory") +@click.option( + "-x", + "--compress", + type=click.Choice(["tar.gz", "tar.bz2", "zip", "none"]), + help="Archive compression type", +) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") +# TODO: Remove this in a future release. Deprecated in March 2024. +@click.option( + "-t", + "--tower", + is_flag=True, + default=False, + hidden=True, + help="Download for Seqera Platform. DEPRECATED: Please use `--platform` instead.", +) +@click.option( + "--platform", + is_flag=True, + default=False, + help="Download for Seqera Platform (formerly Nextflow Tower)", +) +@click.option( + "-d", + "--download-configuration", + is_flag=True, + default=False, + help="Include configuration profiles in download. Not available with `--platform`", +) +@click.option( "--tag", multiple=True, help="Add custom alias tags to `--platform` downloads. For example, `--tag \"3.10=validated\"` adds the custom 'validated' tag to the 3.10 release.", @@ -415,7 +452,9 @@ def create_params_file(pipeline, revision, output, force, show_hidden): default=4, help="Number of parallel image downloads", ) -def download( +@click.pass_context +def download_pipeline( + ctx, pipeline, revision, outdir, @@ -437,7 +476,7 @@ def download( Collects all files in a single archive and configures the downloaded workflow to use relative paths to the configs and singularity images. """ - from nf_core.download import DownloadWorkflow + from nf_core.pipelines.download import DownloadWorkflow if tower: log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") @@ -460,374 +499,531 @@ def download( dl.download_workflow() -# nf-core licences -@nf_core_cli.command() -@click.argument("pipeline", required=True, metavar="") -@click.option("--json", is_flag=True, default=False, help="Print output in JSON") -def licences(pipeline, json): +# nf-core pipelines create-params-file +@pipelines.command("create-params-file") +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") +@click.option( + "-o", + "--output", + type=str, + default="nf-params.yml", + metavar="", + help="Output filename. Defaults to `nf-params.yml`.", +) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") +@click.option( + "-x", + "--show-hidden", + is_flag=True, + default=False, + help="Show hidden params which don't normally need changing", +) +@click.pass_context +def create_params_file_pipeline(ctx, pipeline, revision, output, force, show_hidden): """ - List software licences for a given workflow (DSL1 only). + Build a parameter file for a pipeline. - Checks the pipeline environment.yml file which lists all conda software packages, which is not available for DSL2 workflows. Therefore, this command only supports DSL1 workflows (for now). - Each of these is queried against the anaconda.org API to find the licence. - Package name, version and licence is printed to the command line. + Uses the pipeline schema file to generate a YAML parameters file. + Parameters are set to the pipeline defaults and descriptions are shown in comments. + After the output file is generated, it can then be edited as needed before + passing to nextflow using the `-params-file` option. + + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory. """ - from nf_core.licences import WorkflowLicences + builder = ParamsFileBuilder(pipeline, revision) - lic = WorkflowLicences(pipeline) - lic.as_json = json - try: - stdout.print(lic.run_licences()) - except LookupError as e: - log.error(e) + if not builder.write_params_file(output, show_hidden=show_hidden, force=force): sys.exit(1) -# nf-core lint (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) -@click.option( - "-d", - "--dir", - type=click.Path(exists=True), - default=".", - help=r"Pipeline directory [dim]\[default: current working directory][/]", -) +# nf-core pipelines launch +@pipelines.command("launch") +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( - "--release", + "-c", + "--command-only", is_flag=True, - default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" - and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") - and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", - help="Execute additional checks for release-ready workflows.", + default=False, + help="Create Nextflow command with params (no params file)", ) @click.option( - "-f", - "--fix", - type=str, - metavar="", - multiple=True, - help="Attempt to automatically fix specified lint test", + "-o", + "--params-out", + type=click.Path(), + default=os.path.join(os.getcwd(), "nf-params.json"), + help="Path to save run parameters file", ) @click.option( - "-k", - "--key", - type=str, - metavar="", - multiple=True, - help="Run only these lint tests", + "-p", + "--params-in", + type=click.Path(exists=True), + help="Set of input run params to use from a previous run", ) -@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") -@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") -@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") @click.option( - "--markdown", - type=str, - metavar="", - help="File to write linting results to (Markdown)", + "-a", + "--save-all", + is_flag=True, + default=False, + help="Save all parameters, even if unchanged from default", ) @click.option( - "--json", - type=str, - metavar="", - help="File to write linting results to (JSON)", + "-x", + "--show-hidden", + is_flag=True, + default=False, + help="Show hidden params which don't normally need changing", ) @click.option( - "--sort-by", - type=click.Choice(["module", "test"]), - default="test", - help="Sort lint output by module or test name.", - show_default=True, + "-u", + "--url", + type=str, + default="https://nf-co.re/launch", + help="Customise the builder URL (for development work)", ) @click.pass_context -def lint( +def launch_pipeline( ctx, - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - markdown, - json, - sort_by, + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, ): """ - DEPRECATED - Check pipeline code against nf-core guidelines. - - Runs a large number of automated tests to ensure that the supplied pipeline - meets the nf-core guidelines. Documentation of all lint tests can be found - on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] + Launch a pipeline using a web GUI or command line prompts. - You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. - See the documentation for details. - """ - log.error("The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead.") - sys.exit(0) + Uses the pipeline schema file to collect inputs for all available pipeline + parameters. Parameter names, descriptions and help text are shown. + The pipeline schema is used to validate all inputs as they are entered. + When finished, saves a file with the selected parameters which can be + passed to Nextflow using the -params-file option. -# nf-core pipelines subcommands -@nf_core_cli.group() + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory or an ID from the nf-core web launch tool. + """ + from nf_core.pipelines.launch import Launch + + launcher = Launch( + pipeline, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, + id, + ) + if not launcher.launch_pipeline(): + sys.exit(1) + + +# nf-core pipelnies list +@pipelines.command("list") +@click.argument("keywords", required=False, nargs=-1, metavar="") +@click.option( + "-s", + "--sort", + type=click.Choice(["release", "pulled", "name", "stars"]), + default="release", + help="How to sort listed pipelines", +) +@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") +@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") @click.pass_context -def pipelines(ctx): +def list_pipelines(ctx, keywords, sort, json, show_archived): """ - Commands to manage nf-core pipelines. + List available nf-core pipelines with local info. + + Checks the web for a list of nf-core pipelines with their latest releases. + Shows which nf-core pipelines you have pulled locally and whether they are up to date. """ - # ensure that ctx.obj exists and is a dict (in case `cli()` is called - # by means other than the `if` block below) - ctx.ensure_object(dict) + from nf_core.pipelines.list import list_workflows + stdout.print(list_workflows(keywords, sort, json, show_archived)) -# nf-core pipelines create -@pipelines.command("create") + +# nf-core pipelines sync +@pipelines.command("sync") @click.pass_context @click.option( - "-n", - "--name", - type=str, - help="The name of your new pipeline", + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -@click.option("-d", "--description", type=str, help="A short description of your pipeline") -@click.option("-a", "--author", type=str, help="Name of the main author(s)") -@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use") -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") -@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") -@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") @click.option( - "--organisation", + "-b", + "--from-branch", type=str, - default="nf-core", - help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", + help="The git branch to use to fetch workflow variables.", ) -def create_pipeline(ctx, name, description, author, version, force, outdir, template_yaml, organisation): +@click.option( + "-p", + "--pull-request", + is_flag=True, + default=False, + help="Make a GitHub pull-request with the changes.", +) +@click.option( + "--force_pr", + is_flag=True, + default=False, + help="Force the creation of a pull-request, even if there are no changes.", +) +@click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") +@click.option("-u", "--username", type=str, help="GitHub PR: auth username.") +@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") +def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ - Create a new pipeline using the nf-core template. + Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - Uses the nf-core template to make a skeleton Nextflow pipeline with all required - files, boilerplate code and best-practices. - \n\n - Run without any command line arguments to use an interactive interface. + To keep nf-core pipelines up to date with improvements in the main + template, we use a method of synchronisation that uses a special + git branch called [cyan i]TEMPLATE[/]. + + This command updates the [cyan i]TEMPLATE[/] branch with the latest version of + the nf-core template, so that these updates can be synchronised with + the pipeline. It is run automatically for all pipelines when ever a + new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ - from nf_core.pipelines.create import PipelineCreateApp - from nf_core.pipelines.create.create import PipelineCreate + from nf_core.pipelines.sync.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.utils import is_pipeline_directory - if (name and description and author) or (template_yaml): - # If all command arguments are used, run without the interactive interface - try: - create_obj = PipelineCreate( - name, - description, - author, - version=version, - force=force, - outdir=outdir, - template_config=template_yaml, - organisation=organisation, - ) - create_obj.init_pipeline() - except UserWarning as e: - log.error(e) - sys.exit(1) - elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": - log.error( - "[red]Partial arguments supplied.[/] " - "Run without [i]any[/] arguments for an interactive interface, " - "or with at least name + description + author to use non-interactively." - ) + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Sync the given pipeline dir + sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + try: + sync_obj.sync() + except (SyncExceptionError, PullRequestExceptionError) as e: + log.error(e) sys.exit(1) - else: - log.info("Launching interactive nf-core pipeline creation tool.") - app = PipelineCreateApp() - app.run() - sys.exit(app.return_code or 0) -# nf-core pipelines lint -@pipelines.command("lint") +# nf-core pipelines bump-version +@pipelines.command("bump-version") +@click.pass_context +@click.argument("new_version", required=True, metavar="") @click.option( "-d", "--dir", type=click.Path(exists=True), default=".", - help=r"Pipeline directory [dim]\[default: current working directory][/]", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) @click.option( - "--release", + "-n", + "--nextflow", is_flag=True, - default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" - and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") - and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", - help="Execute additional checks for release-ready workflows.", + default=False, + help="Bump required nextflow version instead of pipeline version", ) +def bump_version_pipeline(ctx, new_version, dir, nextflow): + """ + Update nf-core pipeline version number. + + The pipeline version number is mentioned in a lot of different places + in nf-core pipelines. This tool updates the version for you automatically, + so that you don't accidentally miss any. + + Should be used for each pipeline release, and again for the next + development version after release. + + As well as the pipeline version, you can also change the required version of Nextflow. + """ + from nf_core.pipelines.bump_version.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.utils import Pipeline, is_pipeline_directory + + try: + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Make a pipeline object and load config etc + pipeline_obj = Pipeline(dir) + pipeline_obj._load() + + # Bump the pipeline version number + if not nextflow: + bump_pipeline_version(pipeline_obj, new_version) + else: + bump_nextflow_version(pipeline_obj, new_version) + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines create-logo +@pipelines.command("create-logo") +@click.argument("logo-text", metavar="") +@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.") @click.option( - "-f", - "--fix", + "-n", + "--name", type=str, - metavar="", - multiple=True, - help="Attempt to automatically fix specified lint test", + help="Name of the output file (with or without '.png' suffix).", ) @click.option( - "-k", - "--key", - type=str, - metavar="", - multiple=True, - help="Run only these lint tests", + "--theme", + type=click.Choice(["light", "dark"]), + default="light", + help="Theme for the logo.", + show_default=True, ) -@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") -@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") -@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") @click.option( - "--markdown", - type=str, - metavar="", - help="File to write linting results to (Markdown)", + "--width", + type=int, + default=2300, + help="Width of the logo in pixels.", + show_default=True, ) @click.option( - "--json", - type=str, - metavar="", - help="File to write linting results to (JSON)", + "--format", + type=click.Choice(["png", "svg"]), + default="png", + help="Image format of the logo, either PNG or SVG.", + show_default=True, ) @click.option( - "--sort-by", - type=click.Choice(["module", "test"]), - default="test", - help="Sort lint output by module or test name.", - show_default=True, + "-f", + "--force", + is_flag=True, + default=False, + help="Overwrite any files if they already exist", ) -@click.pass_context -def lint_pipeline( - ctx, - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - markdown, - json, - sort_by, -): +def logo_pipeline(logo_text, dir, name, theme, width, format, force): """ - Check pipeline code against nf-core guidelines. - - Runs a large number of automated tests to ensure that the supplied pipeline - meets the nf-core guidelines. Documentation of all lint tests can be found - on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] + Generate a logo with the nf-core logo template. - You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. - See the documentation for details. + This command generates an nf-core pipeline logo, using the supplied """ - from nf_core.pipelines.lint import run_linting - from nf_core.utils import is_pipeline_directory + from nf_core.pipelines.create_logo import create_logo - # Check if pipeline directory is a pipeline try: - is_pipeline_directory(dir) + if dir == ".": + dir = Path.cwd() + logo_path = create_logo(logo_text, dir, name, theme, width, format, force) + # Print path to logo relative to current working directory + try: + logo_path = Path(logo_path).relative_to(Path.cwd()) + except ValueError: + logo_path = Path(logo_path) + log.info(f"Created logo: [magenta]{logo_path}[/]") except UserWarning as e: log.error(e) sys.exit(1) - # Run the lint tests! + +# nf-core licences +@nf_core_cli.command() +@click.argument("pipeline", required=True, metavar="") +@click.option("--json", is_flag=True, default=False, help="Print output in JSON") +def licences(pipeline, json): + """ + List software licences for a given workflow (DSL1 only). + + Checks the pipeline environment.yml file which lists all conda software packages, which is not available for DSL2 workflows. Therefore, this command only supports DSL1 workflows (for now). + Each of these is queried against the anaconda.org API to find the licence. + Package name, version and licence is printed to the command line. + """ + from nf_core.licences import WorkflowLicences + + lic = WorkflowLicences(pipeline) + lic.as_json = json try: - lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - sort_by, - markdown, - json, - ctx.obj["hide_progress"], - ) - swf_failed = 0 - if subworkflow_lint_obj is not None: - swf_failed = len(subworkflow_lint_obj.failed) - if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: - sys.exit(1) - except AssertionError as e: - log.critical(e) + stdout.print(lic.run_licences()) + except LookupError as e: + log.error(e) sys.exit(1) - except UserWarning as e: + + +# nf-core pipelines schema subcommands +@pipelines.group("schema") +def pipeline_schema(): + """ + Suite of tools for developers to manage pipeline schema. + + All nf-core pipelines should have a nextflow_schema.json file in their + root directory that describes the different pipeline parameters. + """ + pass + + +# nf-core pipelines schema validate +@pipeline_schema.command("validate") +@click.argument("pipeline", required=True, metavar="") +@click.argument("params", type=click.Path(exists=True), required=True, metavar="") +def validate_schema(pipeline, params): + """ + Validate a set of parameters against a pipeline schema. + + Nextflow can be run using the -params-file flag, which loads + script parameters from a JSON file. + + This command takes such a file and validates it against the pipeline + schema, checking whether all schema rules are satisfied. + """ + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(pipeline) + # Load and check schema + schema_obj.load_lint_schema() + except AssertionError as e: log.error(e) sys.exit(1) + schema_obj.load_input_params(params) + try: + schema_obj.validate_params() + except AssertionError: + sys.exit(1) -# nf-core create (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) +# nf-core pipelines schema build +@pipeline_schema.command("build") @click.option( - "-n", - "--name", + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", +) +@click.option( + "--no-prompts", + is_flag=True, + help="Do not confirm changes, just update parameters and exit", +) +@click.option( + "--web-only", + is_flag=True, + help="Skip building using Nextflow config, just launch the web tool", +) +@click.option( + "--url", type=str, - help="The name of your new pipeline", + default="https://nf-co.re/pipeline_schema_builder", + help="Customise the builder URL (for development work)", ) -@click.option("-d", "--description", type=str, help="A short description of your pipeline") -@click.option("-a", "--author", type=str, help="Name of the main author(s)") -@click.option("--version", type=str, help="The initial version number to use") -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") -@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") -@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -@click.option("--plain", is_flag=True, help="Use the standard nf-core template") -def create(name, description, author, version, force, outdir, template_yaml, plain): +def build_schema(dir, no_prompts, web_only, url): """ - DEPRECATED - Create a new pipeline using the nf-core template. + Interactively build a pipeline schema from Nextflow params. + + Automatically detects parameters from the pipeline config and main.nf and + compares these to the pipeline schema. Prompts to add or remove parameters + if the two do not match one another. + + Once all parameters are accounted for, can launch a web GUI tool on the + https://nf-co.re website where you can annotate and organise parameters. + Listens for this to be completed and saves the updated schema. + """ + from nf_core.pipelines.schema import PipelineSchema + + try: + schema_obj = PipelineSchema() + if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: + sys.exit(1) + except (UserWarning, AssertionError) as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines schema lint +@pipeline_schema.command("lint") +@click.argument( + "schema_path", + type=click.Path(exists=True), + default="nextflow_schema.json", + metavar="", +) +def lint_schema(schema_path): + """ + Check that a given pipeline schema is valid. - Uses the nf-core template to make a skeleton Nextflow pipeline with all required - files, boilerplate code and best-practices. + Checks whether the pipeline schema validates as JSON Schema Draft 7 + and adheres to the additional nf-core schema requirements. + + This function runs as part of the nf-core lint command, this is a convenience + command that does just the schema linting nice and quickly. + + If no schema path is provided, "nextflow_schema.json" will be used (if it exists). """ - log.error( - "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." - ) - sys.exit(0) + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(schema_path) + schema_obj.load_lint_schema() + # Validate title and description - just warnings as schema should still work fine + try: + schema_obj.validate_schema_title_description() + except AssertionError as e: + log.warning(e) + except AssertionError: + sys.exit(1) -# nf-core modules subcommands -@nf_core_cli.group() +# nf-core pipelines schema docs +@pipeline_schema.command("docs") +@click.argument( + "schema_path", + type=click.Path(exists=True), + default="nextflow_schema.json", + required=False, + metavar="", +) @click.option( - "-g", - "--git-remote", + "-o", + "--output", type=str, - default=NF_CORE_MODULES_REMOTE, - help="Remote git repo to fetch files from", + metavar="", + help="Output filename. Defaults to standard out.", ) @click.option( - "-b", - "--branch", - type=str, - default=None, - help="Branch of git repository hosting modules.", + "-x", + "--format", + type=click.Choice(["markdown", "html"]), + default="markdown", + help="Format to output docs in.", ) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") @click.option( - "-N", - "--no-pull", - is_flag=True, - default=False, - help="Do not pull in latest changes to local clone of modules repository.", + "-c", + "--columns", + type=str, + metavar="", + help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)", + default="parameter,description,type,default,required,hidden", ) -@click.pass_context -def modules(ctx, git_remote, branch, no_pull): +def docs_schema(schema_path, output, format, force, columns): """ - Commands to manage Nextflow DSL2 modules (tool wrappers). + Outputs parameter documentation for a pipeline schema. """ - # ensure that ctx.obj exists and is a dict (in case `cli()` is called - # by means other than the `if` block below) - ctx.ensure_object(dict) + if not os.path.exists(schema_path): + log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") + sys.exit(1) - # Place the arguments in a context object - ctx.obj["modules_repo_url"] = git_remote - ctx.obj["modules_repo_branch"] = branch - ctx.obj["modules_repo_no_pull"] = no_pull + from nf_core.pipelines.schema import PipelineSchema + schema_obj = PipelineSchema() + # Assume we're in a pipeline dir root if schema path not set + schema_obj.get_schema_path(schema_path) + schema_obj.load_schema() + schema_obj.print_documentation(output, format, force, columns.split(",")) -# nf-core subworkflows click command + +# nf-core modules subcommands @nf_core_cli.group() @click.option( "-g", @@ -851,9 +1047,9 @@ def modules(ctx, git_remote, branch, no_pull): help="Do not pull in latest changes to local clone of modules repository.", ) @click.pass_context -def subworkflows(ctx, git_remote, branch, no_pull): +def modules(ctx, git_remote, branch, no_pull): """ - Commands to manage Nextflow DSL2 subworkflows (tool wrappers). + Commands to manage Nextflow DSL2 modules (tool wrappers). """ # ensure that ctx.obj exists and is a dict (in case `cli()` is called # by means other than the `if` block below) @@ -1489,6 +1685,44 @@ def bump_versions(ctx, tool, dir, all, show_all): sys.exit(1) +# nf-core subworkflows click command +@nf_core_cli.group() +@click.option( + "-g", + "--git-remote", + type=str, + default=NF_CORE_MODULES_REMOTE, + help="Remote git repo to fetch files from", +) +@click.option( + "-b", + "--branch", + type=str, + default=None, + help="Branch of git repository hosting modules.", +) +@click.option( + "-N", + "--no-pull", + is_flag=True, + default=False, + help="Do not pull in latest changes to local clone of modules repository.", +) +@click.pass_context +def subworkflows(ctx, git_remote, branch, no_pull): + """ + Commands to manage Nextflow DSL2 subworkflows (tool wrappers). + """ + # ensure that ctx.obj exists and is a dict (in case `cli()` is called + # by means other than the `if` block below) + ctx.ensure_object(dict) + + # Place the arguments in a context object + ctx.obj["modules_repo_url"] = git_remote + ctx.obj["modules_repo_branch"] = branch + ctx.obj["modules_repo_no_pull"] = no_pull + + # nf-core subworkflows create @subworkflows.command("create") @click.pass_context @@ -1970,8 +2204,11 @@ def subworkflows_update( sys.exit(1) -# nf-core schema subcommands -@nf_core_cli.group() +## DEPRECATED commands since v3.0.0 + + +# nf-core schema subcommands (deprecated) +@nf_core_cli.group(deprecated=True, hidden=True) def schema(): """ Suite of tools for developers to manage pipeline schema. @@ -1982,12 +2219,13 @@ def schema(): pass -# nf-core schema validate -@schema.command() +# nf-core schema validate (deprecated) +@schema.command("validate", deprecated=True) @click.argument("pipeline", required=True, metavar="") @click.argument("params", type=click.Path(exists=True), required=True, metavar="") def validate(pipeline, params): """ + DEPRECATED Validate a set of parameters against a pipeline schema. Nextflow can be run using the -params-file flag, which loads @@ -1996,25 +2234,14 @@ def validate(pipeline, params): This command takes such a file and validates it against the pipeline schema, checking whether all schema rules are satisfied. """ - from nf_core.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(pipeline) - # Load and check schema - schema_obj.load_lint_schema() - except AssertionError as e: - log.error(e) - sys.exit(1) - schema_obj.load_input_params(params) - try: - schema_obj.validate_params() - except AssertionError: - sys.exit(1) + log.error( + "The `[magenta]nf-core schema validate[/]` command is deprecated. Use `[magenta]nf-core pipelines schema validate[/]` instead." + ) + sys.exit(0) -# nf-core schema build -@schema.command() +# nf-core schema build (deprecated) +@schema.command("build", deprecated=True) @click.option( "-d", "--dir", @@ -2040,6 +2267,7 @@ def validate(pipeline, params): ) def build(dir, no_prompts, web_only, url): """ + DEPRECATED Interactively build a pipeline schema from Nextflow params. Automatically detects parameters from the pipeline config and main.nf and @@ -2050,19 +2278,14 @@ def build(dir, no_prompts, web_only, url): https://nf-co.re website where you can annotate and organise parameters. Listens for this to be completed and saves the updated schema. """ - from nf_core.schema import PipelineSchema - - try: - schema_obj = PipelineSchema() - if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: - sys.exit(1) - except (UserWarning, AssertionError) as e: - log.error(e) - sys.exit(1) + log.error( + "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead." + ) + sys.exit(0) -# nf-core schema lint -@schema.command("lint") +# nf-core schema lint (deprecated) +@schema.command("lint", deprecated=True) @click.argument( "schema_path", type=click.Path(exists=True), @@ -2071,6 +2294,7 @@ def build(dir, no_prompts, web_only, url): ) def schema_lint(schema_path): """ + DEPRECATED Check that a given pipeline schema is valid. Checks whether the pipeline schema validates as JSON Schema Draft 7 @@ -2081,67 +2305,153 @@ def schema_lint(schema_path): If no schema path is provided, "nextflow_schema.json" will be used (if it exists). """ - from nf_core.schema import PipelineSchema + log.error( + "The `[magenta]nf-core schema lint[/]` command is deprecated. Use `[magenta]nf-core pipelines schema lint[/]` instead." + ) + sys.exit(0) - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(schema_path) - schema_obj.load_lint_schema() - # Validate title and description - just warnings as schema should still work fine - try: - schema_obj.validate_schema_title_description() - except AssertionError as e: - log.warning(e) - except AssertionError: - sys.exit(1) + +# nf-core schema docs (deprecated) +@schema.command("docs", deprecated=True) +@click.argument( + "schema_path", + type=click.Path(exists=True), + default="nextflow_schema.json", + required=False, + metavar="", +) +@click.option( + "-o", + "--output", + type=str, + metavar="", + help="Output filename. Defaults to standard out.", +) +@click.option( + "-x", + "--format", + type=click.Choice(["markdown", "html"]), + default="markdown", + help="Format to output docs in.", +) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") +@click.option( + "-c", + "--columns", + type=str, + metavar="", + help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)", + default="parameter,description,type,default,required,hidden", +) +def docs(schema_path, output, format, force, columns): + """ + DEPRECATED + Outputs parameter documentation for a pipeline schema. + """ + log.error( + "The `[magenta]nf-core schema docs[/]` command is deprecated. Use `[magenta]nf-core pipelines schema docs[/]` instead." + ) + sys.exit(0) + + +# nf-core create-logo (deprecated) +@nf_core_cli.command("create-logo", deprecated=True, hidden=True) +@click.argument("logo-text", metavar="") +@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.") +@click.option( + "-n", + "--name", + type=str, + help="Name of the output file (with or without '.png' suffix).", +) +@click.option( + "--theme", + type=click.Choice(["light", "dark"]), + default="light", + help="Theme for the logo.", + show_default=True, +) +@click.option( + "--width", + type=int, + default=2300, + help="Width of the logo in pixels.", + show_default=True, +) +@click.option( + "--format", + type=click.Choice(["png", "svg"]), + default="png", + help="Image format of the logo, either PNG or SVG.", + show_default=True, +) +@click.option( + "-f", + "--force", + is_flag=True, + default=False, + help="Overwrite any files if they already exist", +) +def logo(logo_text, dir, name, theme, width, format, force): + """ + DEPRECATED + Generate a logo with the nf-core logo template. + + This command generates an nf-core pipeline logo, using the supplied + """ + log.error( + "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead." + ) + sys.exit(0) -@schema.command() -@click.argument( - "schema_path", +# nf-core sync (deprecated) +@nf_core_cli.command(hidden=True, deprecated=True) +@click.option( + "-d", + "--dir", type=click.Path(exists=True), - default="nextflow_schema.json", - required=False, - metavar="", + default=".", + help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) @click.option( - "-o", - "--output", + "-b", + "--from-branch", type=str, - metavar="", - help="Output filename. Defaults to standard out.", + help="The git branch to use to fetch workflow variables.", ) @click.option( - "-x", - "--format", - type=click.Choice(["markdown", "html"]), - default="markdown", - help="Format to output docs in.", + "-p", + "--pull-request", + is_flag=True, + default=False, + help="Make a GitHub pull-request with the changes.", ) -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") @click.option( - "-c", - "--columns", - type=str, - metavar="", - help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)", - default="parameter,description,type,default,required,hidden", + "--force_pr", + is_flag=True, + default=False, + help="Force the creation of a pull-request, even if there are no changes.", ) -def docs(schema_path, output, format, force, columns): - """ - Outputs parameter documentation for a pipeline schema. +@click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") +@click.option("-u", "--username", type=str, help="GitHub PR: auth username.") +@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") +def sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ - if not os.path.exists(schema_path): - log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") - sys.exit(1) + DEPRECATED + Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - from nf_core.schema import PipelineSchema + To keep nf-core pipelines up to date with improvements in the main + template, we use a method of synchronisation that uses a special + git branch called [cyan i]TEMPLATE[/]. - schema_obj = PipelineSchema() - # Assume we're in a pipeline dir root if schema path not set - schema_obj.get_schema_path(schema_path) - schema_obj.load_schema() - schema_obj.print_documentation(output, format, force, columns.split(",")) + This command updates the [cyan i]TEMPLATE[/] branch with the latest version of + the nf-core template, so that these updates can be synchronised with + the pipeline. It is run automatically for all pipelines when ever a + new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + """ + log.error("The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead.") + sys.exit(0) # nf-core bump-version (deprecated) @@ -2181,226 +2491,360 @@ def bump_version(new_version, dir, nextflow): sys.exit(0) -# nf-core pipelines bump-version -@pipelines.command("bump-version") -@click.pass_context -@click.argument("new_version", required=True, metavar="") +# nf-core list (deprecated) +@nf_core_cli.command("list", deprecated=True, hidden=True) +@click.argument("keywords", required=False, nargs=-1, metavar="") @click.option( - "-d", - "--dir", + "-s", + "--sort", + type=click.Choice(["release", "pulled", "name", "stars"]), + default="release", + help="How to sort listed pipelines", +) +@click.option("--json", is_flag=True, default=False, help="Print full output as JSON") +@click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") +def list(keywords, sort, json, show_archived): + """ + DEPRECATED + List available nf-core pipelines with local info. + + Checks the web for a list of nf-core pipelines with their latest releases. + Shows which nf-core pipelines you have pulled locally and whether they are up to date. + """ + log.error("The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead.") + sys.exit(0) + + +# nf-core launch (deprecated) +@nf_core_cli.command(deprecated=True, hidden=True) +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") +@click.option("-i", "--id", help="ID for web-gui launch parameter set") +@click.option( + "-c", + "--command-only", + is_flag=True, + default=False, + help="Create Nextflow command with params (no params file)", +) +@click.option( + "-o", + "--params-out", + type=click.Path(), + default=os.path.join(os.getcwd(), "nf-params.json"), + help="Path to save run parameters file", +) +@click.option( + "-p", + "--params-in", type=click.Path(exists=True), - default=".", - help=r"Pipeline directory. [dim]\[default: current working directory][/]", + help="Set of input run params to use from a previous run", ) @click.option( - "-n", - "--nextflow", + "-a", + "--save-all", is_flag=True, default=False, - help="Bump required nextflow version instead of pipeline version", + help="Save all parameters, even if unchanged from default", ) -def bump_version_pipeline(ctx, new_version, dir, nextflow): +@click.option( + "-x", + "--show-hidden", + is_flag=True, + default=False, + help="Show hidden params which don't normally need changing", +) +@click.option( + "-u", + "--url", + type=str, + default="https://nf-co.re/launch", + help="Customise the builder URL (for development work)", +) +def launch( + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): """ - Update nf-core pipeline version number. + DEPRECATED + Launch a pipeline using a web GUI or command line prompts. - The pipeline version number is mentioned in a lot of different places - in nf-core pipelines. This tool updates the version for you automatically, - so that you don't accidentally miss any. + Uses the pipeline schema file to collect inputs for all available pipeline + parameters. Parameter names, descriptions and help text are shown. + The pipeline schema is used to validate all inputs as they are entered. - Should be used for each pipeline release, and again for the next - development version after release. + When finished, saves a file with the selected parameters which can be + passed to Nextflow using the -params-file option. - As well as the pipeline version, you can also change the required version of Nextflow. + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory or an ID from the nf-core web launch tool. """ - from nf_core.pipelines.bump_version.bump_version import bump_nextflow_version, bump_pipeline_version - from nf_core.utils import Pipeline, is_pipeline_directory + log.error( + "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead." + ) + sys.exit(0) - try: - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - # Make a pipeline object and load config etc - pipeline_obj = Pipeline(dir) - pipeline_obj._load() +# nf-core create-params-file (deprecated) +@nf_core_cli.command(deprecated=True, hidden=True) +@click.argument("pipeline", required=False, metavar="") +@click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") +@click.option( + "-o", + "--output", + type=str, + default="nf-params.yml", + metavar="", + help="Output filename. Defaults to `nf-params.yml`.", +) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") +@click.option( + "-x", + "--show-hidden", + is_flag=True, + default=False, + help="Show hidden params which don't normally need changing", +) +def create_params_file(pipeline, revision, output, force, show_hidden): + """ + DEPRECATED + Build a parameter file for a pipeline. - # Bump the pipeline version number - if not nextflow: - bump_pipeline_version(pipeline_obj, new_version) - else: - bump_nextflow_version(pipeline_obj, new_version) - except UserWarning as e: - log.error(e) - sys.exit(1) + Uses the pipeline schema file to generate a YAML parameters file. + Parameters are set to the pipeline defaults and descriptions are shown in comments. + After the output file is generated, it can then be edited as needed before + passing to nextflow using the `-params-file` option. + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory. + """ + log.error( + "The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead." + ) + sys.exit(0) -# nf-core create-logo -@nf_core_cli.command("create-logo") -@click.argument("logo-text", metavar="") -@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.") + +# nf-core download (deprecated) +@nf_core_cli.command(deprecated=True, hidden=True) +@click.argument("pipeline", required=False, metavar="") +@click.option( + "-r", + "--revision", + multiple=True, + help="Pipeline release to download. Multiple invocations are possible, e.g. `-r 1.1 -r 1.2`", +) +@click.option("-o", "--outdir", type=str, help="Output directory") +@click.option( + "-x", + "--compress", + type=click.Choice(["tar.gz", "tar.bz2", "zip", "none"]), + help="Archive compression type", +) +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") +@click.option( + "-t", + "--tower", + is_flag=True, + default=False, + hidden=True, + help="Download for Seqera Platform. DEPRECATED: Please use `--platform` instead.", +) +@click.option( + "--platform", + is_flag=True, + default=False, + help="Download for Seqera Platform (formerly Nextflow Tower)", +) +@click.option( + "-d", + "--download-configuration", + is_flag=True, + default=False, + help="Include configuration profiles in download. Not available with `--platform`", +) @click.option( - "-n", - "--name", - type=str, - help="Name of the output file (with or without '.png' suffix).", + "--tag", + multiple=True, + help="Add custom alias tags to `--platform` downloads. For example, `--tag \"3.10=validated\"` adds the custom 'validated' tag to the 3.10 release.", ) @click.option( - "--theme", - type=click.Choice(["light", "dark"]), - default="light", - help="Theme for the logo.", - show_default=True, + "-s", + "--container-system", + type=click.Choice(["none", "singularity"]), + help="Download container images of required software.", ) @click.option( - "--width", - type=int, - default=2300, - help="Width of the logo in pixels.", - show_default=True, + "-l", + "--container-library", + multiple=True, + help="Container registry/library or mirror to pull images from.", ) @click.option( - "--format", - type=click.Choice(["png", "svg"]), - default="png", - help="Image format of the logo, either PNG or SVG.", - show_default=True, + "-u", + "--container-cache-utilisation", + type=click.Choice(["amend", "copy", "remote"]), + help="Utilise a `singularity.cacheDir` in the download process, if applicable.", ) @click.option( - "-f", - "--force", - is_flag=True, - default=False, - help="Overwrite any files if they already exist", + "-i", + "--container-cache-index", + type=str, + help="List of images already available in a remote `singularity.cacheDir`.", ) -def logo(logo_text, dir, name, theme, width, format, force): +@click.option( + "-p", + "--parallel-downloads", + type=int, + default=4, + help="Number of parallel image downloads", +) +def download( + pipeline, + revision, + outdir, + compress, + force, + tower, + platform, + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, +): """ - Generate a logo with the nf-core logo template. + DEPRECATED + Download a pipeline, nf-core/configs and pipeline singularity images. - This command generates an nf-core pipeline logo, using the supplied + Collects all files in a single archive and configures the downloaded + workflow to use relative paths to the configs and singularity images. """ - from nf_core.create_logo import create_logo - - try: - if dir == ".": - dir = Path.cwd() - logo_path = create_logo(logo_text, dir, name, theme, width, format, force) - # Print path to logo relative to current working directory - try: - logo_path = Path(logo_path).relative_to(Path.cwd()) - except ValueError: - logo_path = Path(logo_path) - log.info(f"Created logo: [magenta]{logo_path}[/]") - except UserWarning as e: - log.error(e) - sys.exit(1) + log.error( + "The `[magenta]nf-core download[/]` command is deprecated. Use `[magenta]nf-core pipelines download[/]` instead." + ) + sys.exit(0) -# nf-core sync (deprecated) +# nf-core lint (deprecated) @nf_core_cli.command(hidden=True, deprecated=True) @click.option( "-d", "--dir", type=click.Path(exists=True), default=".", - help=r"Pipeline directory. [dim]\[default: current working directory][/]", + help=r"Pipeline directory [dim]\[default: current working directory][/]", ) @click.option( - "-b", - "--from-branch", + "--release", + is_flag=True, + default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" + and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") + and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", + help="Execute additional checks for release-ready workflows.", +) +@click.option( + "-f", + "--fix", type=str, - help="The git branch to use to fetch workflow variables.", + metavar="", + multiple=True, + help="Attempt to automatically fix specified lint test", ) @click.option( - "-p", - "--pull-request", - is_flag=True, - default=False, - help="Make a GitHub pull-request with the changes.", + "-k", + "--key", + type=str, + metavar="", + multiple=True, + help="Run only these lint tests", +) +@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") +@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") +@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") +@click.option( + "--markdown", + type=str, + metavar="", + help="File to write linting results to (Markdown)", ) @click.option( - "--force_pr", - is_flag=True, - default=False, - help="Force the creation of a pull-request, even if there are no changes.", + "--json", + type=str, + metavar="", + help="File to write linting results to (JSON)", ) -@click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") -@click.option("-u", "--username", type=str, help="GitHub PR: auth username.") -@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +@click.option( + "--sort-by", + type=click.Choice(["module", "test"]), + default="test", + help="Sort lint output by module or test name.", + show_default=True, +) +@click.pass_context +def lint( + ctx, + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + markdown, + json, + sort_by, +): """ DEPRECATED - Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. + Check pipeline code against nf-core guidelines. - To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special - git branch called [cyan i]TEMPLATE[/]. + Runs a large number of automated tests to ensure that the supplied pipeline + meets the nf-core guidelines. Documentation of all lint tests can be found + on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] - This command updates the [cyan i]TEMPLATE[/] branch with the latest version of - the nf-core template, so that these updates can be synchronised with - the pipeline. It is run automatically for all pipelines when ever a - new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. + See the documentation for details. """ - log.error("The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead.") + log.error("The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead.") sys.exit(0) -# nf-core pipelines sync -@pipelines.command("sync") -@click.pass_context -@click.option( - "-d", - "--dir", - type=click.Path(exists=True), - default=".", - help=r"Pipeline directory. [dim]\[default: current working directory][/]", -) +# nf-core create (deprecated) +@nf_core_cli.command(hidden=True, deprecated=True) @click.option( - "-b", - "--from-branch", + "-n", + "--name", type=str, - help="The git branch to use to fetch workflow variables.", -) -@click.option( - "-p", - "--pull-request", - is_flag=True, - default=False, - help="Make a GitHub pull-request with the changes.", -) -@click.option( - "--force_pr", - is_flag=True, - default=False, - help="Force the creation of a pull-request, even if there are no changes.", + help="The name of your new pipeline", ) -@click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") -@click.option("-u", "--username", type=str, help="GitHub PR: auth username.") +@click.option("-d", "--description", type=str, help="A short description of your pipeline") +@click.option("-a", "--author", type=str, help="Name of the main author(s)") +@click.option("--version", type=str, help="The initial version number to use") +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") +@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +@click.option("--plain", is_flag=True, help="Use the standard nf-core template") +def create(name, description, author, version, force, outdir, template_yaml, plain): """ - Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - - To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special - git branch called [cyan i]TEMPLATE[/]. + DEPRECATED + Create a new pipeline using the nf-core template. - This command updates the [cyan i]TEMPLATE[/] branch with the latest version of - the nf-core template, so that these updates can be synchronised with - the pipeline. It is run automatically for all pipelines when ever a - new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + Uses the nf-core template to make a skeleton Nextflow pipeline with all required + files, boilerplate code and best-practices. """ - from nf_core.pipelines.sync.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Sync the given pipeline dir - sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) - try: - sync_obj.sync() - except (SyncExceptionError, PullRequestExceptionError) as e: - log.error(e) - sys.exit(1) + log.error( + "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." + ) + sys.exit(0) # Main script is being run - launch the CLI diff --git a/nf_core/pipelines/bump_version/bump_version.py b/nf_core/pipelines/bump_version.py similarity index 100% rename from nf_core/pipelines/bump_version/bump_version.py rename to nf_core/pipelines/bump_version.py diff --git a/nf_core/pipelines/bump_version/__init__.py b/nf_core/pipelines/bump_version/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 763165da6f..bdbbca646f 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -15,10 +15,10 @@ import yaml import nf_core -import nf_core.schema +import nf_core.pipelines.schema import nf_core.utils -from nf_core.create_logo import create_logo from nf_core.pipelines.create.utils import CreateConfig +from nf_core.pipelines.create_logo import create_logo from nf_core.pipelines.lint_utils import run_prettier_on_file log = logging.getLogger(__name__) @@ -382,7 +382,7 @@ def update_nextflow_schema(self): """ schema_path = self.outdir / "nextflow_schema.json" - schema = nf_core.schema.PipelineSchema() + schema = nf_core.pipelines.schema.PipelineSchema() schema.schema_filename = schema_path schema.no_prompts = True schema.load_schema() diff --git a/nf_core/create_logo.py b/nf_core/pipelines/create_logo.py similarity index 100% rename from nf_core/create_logo.py rename to nf_core/pipelines/create_logo.py diff --git a/nf_core/download.py b/nf_core/pipelines/download.py similarity index 99% rename from nf_core/download.py rename to nf_core/pipelines/download.py index f5ab3a0f58..5a2acf4896 100644 --- a/nf_core/download.py +++ b/nf_core/pipelines/download.py @@ -23,7 +23,7 @@ from pkg_resources import parse_version as version_parser import nf_core -import nf_core.list +import nf_core.pipelines.list import nf_core.utils from nf_core.synced_repo import RemoteProgressbar, SyncedRepo from nf_core.utils import ( @@ -169,7 +169,7 @@ def __init__( self.containers_remote = [] # stores the remote images provided in the file. # Fetch remote workflows - self.wfs = nf_core.list.Workflows() + self.wfs = nf_core.pipelines.list.Workflows() self.wfs.get_remote_workflows() def download_workflow(self): diff --git a/nf_core/launch.py b/nf_core/pipelines/launch.py similarity index 99% rename from nf_core/launch.py rename to nf_core/pipelines/launch.py index 423f0728ed..77a7948eaf 100644 --- a/nf_core/launch.py +++ b/nf_core/pipelines/launch.py @@ -13,7 +13,7 @@ from rich.markdown import Markdown from rich.prompt import Confirm -import nf_core.schema +import nf_core.pipelines.schema import nf_core.utils from nf_core.pipelines.lint_utils import dump_json_with_prettier @@ -138,7 +138,7 @@ def launch_pipeline(self): # Check if we have a web ID if self.web_id is not None: - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() try: if not self.get_web_launch_response(): log.info( @@ -191,7 +191,7 @@ def get_pipeline_schema(self): """Load and validate the schema from the supplied pipeline""" # Set up the schema - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() # Check if this is a local directory localpath = os.path.abspath(os.path.expanduser(self.pipeline)) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 4fa49acbcb..f62100a70a 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -3,7 +3,7 @@ import re from pathlib import Path -from nf_core.schema import PipelineSchema +from nf_core.pipelines.schema import PipelineSchema log = logging.getLogger(__name__) diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py index 90735f609a..82165b6e7d 100644 --- a/nf_core/pipelines/lint/schema_description.py +++ b/nf_core/pipelines/lint/schema_description.py @@ -1,4 +1,4 @@ -import nf_core.schema +import nf_core.pipelines.schema def schema_description(self): @@ -17,7 +17,7 @@ def schema_description(self): # First, get the top-level config options for the pipeline # Schema object already created in the `schema_lint` test - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() self.schema_obj.get_schema_path(self.wf_path) self.schema_obj.get_wf_params() self.schema_obj.no_prompts = True diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py index 3342dc4b9d..21858a0f49 100644 --- a/nf_core/pipelines/lint/schema_lint.py +++ b/nf_core/pipelines/lint/schema_lint.py @@ -1,6 +1,6 @@ import logging -import nf_core.schema +import nf_core.pipelines.schema def schema_lint(self): @@ -68,7 +68,7 @@ def schema_lint(self): logging.getLogger("nf_core.schema").setLevel(logging.ERROR) # Lint the schema - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() self.schema_obj.get_schema_path(self.wf_path) try: diff --git a/nf_core/pipelines/lint/schema_params.py b/nf_core/pipelines/lint/schema_params.py index 9280fe4703..4c569defdb 100644 --- a/nf_core/pipelines/lint/schema_params.py +++ b/nf_core/pipelines/lint/schema_params.py @@ -1,4 +1,4 @@ -import nf_core.schema +import nf_core.pipelines.schema def schema_params(self): @@ -15,7 +15,7 @@ def schema_params(self): failed = [] # First, get the top-level config options for the pipeline - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() self.schema_obj.get_schema_path(self.wf_path) self.schema_obj.get_wf_params() self.schema_obj.no_prompts = True diff --git a/nf_core/list.py b/nf_core/pipelines/list.py similarity index 100% rename from nf_core/list.py rename to nf_core/pipelines/list.py diff --git a/nf_core/params_file.py b/nf_core/pipelines/params_file.py similarity index 98% rename from nf_core/params_file.py rename to nf_core/pipelines/params_file.py index 78798b065e..0384521c74 100644 --- a/nf_core/params_file.py +++ b/nf_core/pipelines/params_file.py @@ -8,9 +8,9 @@ import questionary -import nf_core.list +import nf_core.pipelines.list import nf_core.utils -from nf_core.schema import PipelineSchema +from nf_core.pipelines.schema import PipelineSchema log = logging.getLogger(__name__) @@ -97,7 +97,7 @@ def __init__( self.schema_obj: Optional[PipelineSchema] = None # Fetch remote workflows - self.wfs = nf_core.list.Workflows() + self.wfs = nf_core.pipelines.list.Workflows() self.wfs.get_remote_workflows() def get_pipeline(self): diff --git a/nf_core/refgenie.py b/nf_core/pipelines/refgenie.py similarity index 100% rename from nf_core/refgenie.py rename to nf_core/pipelines/refgenie.py diff --git a/nf_core/schema.py b/nf_core/pipelines/schema.py similarity index 99% rename from nf_core/schema.py rename to nf_core/pipelines/schema.py index eee9f9978d..28a7d0b4ff 100644 --- a/nf_core/schema.py +++ b/nf_core/pipelines/schema.py @@ -16,7 +16,7 @@ from rich.prompt import Confirm from rich.syntax import Syntax -import nf_core.list +import nf_core.pipelines.list import nf_core.utils from nf_core.pipelines.lint_utils import dump_json_with_prettier, run_prettier_on_file @@ -66,7 +66,7 @@ def get_schema_path( # Path does not exist - assume a name of a remote workflow elif not local_only: - self.pipeline_dir = nf_core.list.get_local_wf(path, revision=revision) + self.pipeline_dir = nf_core.pipelines.list.get_local_wf(path, revision=revision) self.schema_filename = Path(self.pipeline_dir or "", "nextflow_schema.json") # check if the schema file exists if not self.schema_filename.exists(): diff --git a/nf_core/pipelines/sync/sync.py b/nf_core/pipelines/sync.py similarity index 99% rename from nf_core/pipelines/sync/sync.py rename to nf_core/pipelines/sync.py index ccee2a9c4f..f9a874c7e4 100644 --- a/nf_core/pipelines/sync/sync.py +++ b/nf_core/pipelines/sync.py @@ -15,8 +15,8 @@ from git import GitCommandError, InvalidGitRepositoryError import nf_core -import nf_core.list import nf_core.pipelines.create.create +import nf_core.pipelines.list import nf_core.utils log = logging.getLogger(__name__) diff --git a/nf_core/pipelines/sync/__init__.py b/nf_core/pipelines/sync/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/tests/test_create_logo.py b/tests/test_create_logo.py index b3c01638e1..8942894ce2 100644 --- a/tests/test_create_logo.py +++ b/tests/test_create_logo.py @@ -4,7 +4,7 @@ import unittest from pathlib import Path -import nf_core.create_logo +import nf_core.pipelines.create_logo class TestCreateLogo(unittest.TestCase): @@ -23,7 +23,7 @@ def test_create_logo_png(self): """Test that the create-logo command works for PNGs""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG @@ -37,7 +37,7 @@ def test_create_logo_png_dark(self): """Test that the create-logo command works for dark PNGs""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path, theme="dark") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, theme="dark") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG @@ -51,7 +51,7 @@ def test_create_log_png_width(self): """Test that the create-logo command works for PNGs with a custom width""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path, width=100) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, width=100) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG @@ -65,12 +65,12 @@ def test_create_logo_twice(self): """Test that the create-logo command returns an info message when run twice""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Create the logo again and capture the log output with self.assertLogs(level="INFO") as log: - nf_core.create_logo.create_logo("pipes", self.tempdir_path) + nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) # Check that the log message is correct self.assertIn("Logo already exists", log.output[0]) @@ -79,13 +79,15 @@ def test_create_logo_without_text_fail(self): # Create a logo with self.assertRaises(UserWarning): - nf_core.create_logo.create_logo("", self.tempdir_path) + nf_core.pipelines.create_logo.create_logo("", self.tempdir_path) def test_create_logo_with_filename(self): """Test that the create-logo command works with a custom filename""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", Path(self.tempdir_path / "custom_dir"), filename="custom") + logo_fn = nf_core.pipelines.create_logo.create_logo( + "pipes", Path(self.tempdir_path / "custom_dir"), filename="custom" + ) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the parent directory name @@ -97,7 +99,7 @@ def test_create_logo_svg(self): """Test that the create-logo command works for SVGs""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path, format="svg") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a SVG @@ -113,7 +115,7 @@ def test_create_logo_svg_dark(self): """Test that the create-logo command works for svgs and dark theme""" # Create a logo - logo_fn = nf_core.create_logo.create_logo("pipes", self.tempdir_path, format="svg", theme="dark") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg", theme="dark") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a SVG diff --git a/tests/test_download.py b/tests/test_download.py index e090885bb4..2d4231c7d1 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -14,7 +14,7 @@ import nf_core.pipelines.create.create import nf_core.utils -from nf_core.download import ContainerError, DownloadWorkflow, WorkflowRepo +from nf_core.pipelines.download import ContainerError, DownloadWorkflow, WorkflowRepo from nf_core.synced_repo import SyncedRepo from nf_core.utils import run_cmd diff --git a/tests/test_launch.py b/tests/test_launch.py index 043055a2d5..9774853419 100644 --- a/tests/test_launch.py +++ b/tests/test_launch.py @@ -8,8 +8,8 @@ import pytest -import nf_core.launch import nf_core.pipelines.create.create +import nf_core.pipelines.launch from .utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder @@ -21,7 +21,7 @@ def setUp(self): """Create a new PipelineSchema and Launch objects""" self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline() self.nf_params_fn = os.path.join(self.tmp_dir, "nf-params.json") - self.launcher = nf_core.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) + self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) def tearDown(self): """Clean up temporary files and folders""" @@ -32,13 +32,13 @@ def tearDown(self): if Path(self.tmp_dir).exists(): shutil.rmtree(self.tmp_dir) - @mock.patch.object(nf_core.launch.Launch, "prompt_web_gui", side_effect=[True]) - @mock.patch.object(nf_core.launch.Launch, "launch_web_gui") + @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]) + @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui") def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui): """Test the main launch function""" self.launcher.launch_pipeline() - @mock.patch.object(nf_core.launch.Confirm, "ask", side_effect=[False]) + @mock.patch.object(nf_core.pipelines.launch.Confirm, "ask", side_effect=[False]) def test_launch_file_exists(self, mock_confirm): """Test that we detect an existing params file and return""" # Make an empty params file to be overwritten @@ -46,9 +46,9 @@ def test_launch_file_exists(self, mock_confirm): # Try and to launch, return with error assert self.launcher.launch_pipeline() is False - @mock.patch.object(nf_core.launch.Launch, "prompt_web_gui", side_effect=[True]) - @mock.patch.object(nf_core.launch.Launch, "launch_web_gui") - @mock.patch.object(nf_core.launch.Confirm, "ask", side_effect=[False]) + @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]) + @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui") + @mock.patch.object(nf_core.pipelines.launch.Confirm, "ask", side_effect=[False]) def test_launch_file_exists_overwrite(self, mock_webbrowser, mock_lauch_web_gui, mock_confirm): """Test that we detect an existing params file and we overwrite it""" # Make an empty params file to be overwritten @@ -70,7 +70,7 @@ def test_make_pipeline_schema(self, tmp_path): ) create_obj.init_pipeline() os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json")) - self.launcher = nf_core.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn) + self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn) self.launcher.get_pipeline_schema() assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2 assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == { @@ -186,7 +186,7 @@ def test_get_web_launch_response_missing_keys(self, mock_poll_nfcore_web_api): } ], ) - @mock.patch.object(nf_core.launch.Launch, "sanitise_web_response") + @mock.patch.object(nf_core.pipelines.launch.Launch, "sanitise_web_response") def test_get_web_launch_response_valid(self, mock_poll_nfcore_web_api, mock_sanitise): """Test polling the website for a launch response - complete, valid response""" self.launcher.get_pipeline_schema() diff --git a/tests/test_list.py b/tests/test_list.py index c78276b41d..e11dbb12e1 100644 --- a/tests/test_list.py +++ b/tests/test_list.py @@ -12,7 +12,7 @@ import pytest from rich.console import Console -import nf_core.list +import nf_core.pipelines.list # create a temporary directory that can be used by the tests in this file tmp = Path(tempfile.mkdtemp()) @@ -26,7 +26,7 @@ class TestList(unittest.TestCase): @mock.patch("subprocess.check_output") def test_working_listcall(self, mock_subprocess): """Test that listing pipelines works""" - wf_table = nf_core.list.list_workflows() + wf_table = nf_core.pipelines.list.list_workflows() console = Console(record=True) console.print(wf_table) output = console.export_text() @@ -36,7 +36,7 @@ def test_working_listcall(self, mock_subprocess): @mock.patch("subprocess.check_output") def test_working_listcall_archived(self, mock_subprocess): """Test that listing pipelines works, showing archived pipelines""" - wf_table = nf_core.list.list_workflows(show_archived=True) + wf_table = nf_core.pipelines.list.list_workflows(show_archived=True) console = Console(record=True) console.print(wf_table) output = console.export_text() @@ -45,7 +45,7 @@ def test_working_listcall_archived(self, mock_subprocess): @mock.patch("subprocess.check_output") def test_working_listcall_json(self, mock_subprocess): """Test that listing pipelines with JSON works""" - wf_json_str = nf_core.list.list_workflows(as_json=True) + wf_json_str = nf_core.pipelines.list.list_workflows(as_json=True) wf_json = json.loads(wf_json_str) for wf in wf_json["remote_workflows"]: if wf["name"] == "ampliseq": @@ -56,22 +56,22 @@ def test_working_listcall_json(self, mock_subprocess): def test_pretty_datetime(self): """Test that the pretty datetime function works""" now = datetime.now() - nf_core.list.pretty_date(now) + nf_core.pipelines.list.pretty_date(now) now_ts = time.mktime(now.timetuple()) - nf_core.list.pretty_date(now_ts) + nf_core.pipelines.list.pretty_date(now_ts) def test_local_workflows_and_fail(self): """Test the local workflow class and try to get local Nextflow workflow information""" - loc_wf = nf_core.list.LocalWorkflow("myWF") + loc_wf = nf_core.pipelines.list.LocalWorkflow("myWF") with pytest.raises(RuntimeError): loc_wf.get_local_nf_workflow_details() def test_local_workflows_compare_and_fail_silently(self): """Test the workflow class and try to compare local and remote workflows""" - wfs = nf_core.list.Workflows() - lwf_ex = nf_core.list.LocalWorkflow("myWF") + wfs = nf_core.pipelines.list.Workflows() + lwf_ex = nf_core.pipelines.list.LocalWorkflow("myWF") lwf_ex.full_name = "my Workflow" lwf_ex.commit_sha = "aw3s0meh1sh" @@ -86,7 +86,7 @@ def test_local_workflows_compare_and_fail_silently(self): "releases": [], } - rwf_ex = nf_core.list.RemoteWorkflow(remote) + rwf_ex = nf_core.pipelines.list.RemoteWorkflow(remote) rwf_ex.commit_sha = "aw3s0meh1sh" rwf_ex.releases = [{"tag_sha": "aw3s0meh1sh"}] @@ -114,7 +114,7 @@ def test_parse_local_workflow_and_succeed(self, mock_local_wf): assert os.environ["NXF_ASSETS"] == tmp_nxf_str with open(tmp_nxf / "nf-core/dummy-wf", "w") as f: f.write("dummy") - workflows_obj = nf_core.list.Workflows() + workflows_obj = nf_core.pipelines.list.Workflows() workflows_obj.get_local_nf_workflows() assert len(workflows_obj.local_workflows) == 1 @@ -128,20 +128,20 @@ def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess): assert os.environ["NXF_ASSETS"] == tmp_nxf_str with open(tmp_nxf / "nf-core/dummy-wf", "w") as f: f.write("dummy") - workflows_obj = nf_core.list.Workflows() + workflows_obj = nf_core.pipelines.list.Workflows() workflows_obj.get_local_nf_workflows() @mock.patch("os.stat") @mock.patch("git.Repo") def test_local_workflow_investigation(self, mock_repo, mock_stat): - local_wf = nf_core.list.LocalWorkflow("dummy") + local_wf = nf_core.pipelines.list.LocalWorkflow("dummy") local_wf.local_path = tmp mock_repo.head.commit.hexsha = "h00r4y" mock_stat.st_mode = 1 local_wf.get_local_nf_workflow_details() def test_worflow_filter(self): - workflows_obj = nf_core.list.Workflows(["rna", "myWF"]) + workflows_obj = nf_core.pipelines.list.Workflows(["rna", "myWF"]) remote = { "name": "myWF", @@ -154,7 +154,7 @@ def test_worflow_filter(self): "releases": [], } - rwf_ex = nf_core.list.RemoteWorkflow(remote) + rwf_ex = nf_core.pipelines.list.RemoteWorkflow(remote) rwf_ex.commit_sha = "aw3s0meh1sh" rwf_ex.releases = [{"tag_sha": "aw3s0meh1sh"}] @@ -169,7 +169,7 @@ def test_worflow_filter(self): "releases": [], } - rwf_ex2 = nf_core.list.RemoteWorkflow(remote2) + rwf_ex2 = nf_core.pipelines.list.RemoteWorkflow(remote2) rwf_ex2.commit_sha = "aw3s0meh1sh" rwf_ex2.releases = [{"tag_sha": "aw3s0meh1sh"}] @@ -182,11 +182,11 @@ def test_filter_archived_workflows(self): """ Test that archived workflows are not shown by default """ - workflows_obj = nf_core.list.Workflows() + workflows_obj = nf_core.pipelines.list.Workflows() remote1 = {"name": "myWF", "full_name": "my Workflow", "archived": True, "releases": []} - rwf_ex1 = nf_core.list.RemoteWorkflow(remote1) + rwf_ex1 = nf_core.pipelines.list.RemoteWorkflow(remote1) remote2 = {"name": "myWF", "full_name": "my Workflow", "archived": False, "releases": []} - rwf_ex2 = nf_core.list.RemoteWorkflow(remote2) + rwf_ex2 = nf_core.pipelines.list.RemoteWorkflow(remote2) workflows_obj.remote_workflows.append(rwf_ex1) workflows_obj.remote_workflows.append(rwf_ex2) @@ -200,11 +200,11 @@ def test_show_archived_workflows(self): """ Test that archived workflows can be shown optionally """ - workflows_obj = nf_core.list.Workflows(show_archived=True) + workflows_obj = nf_core.pipelines.list.Workflows(show_archived=True) remote1 = {"name": "myWF", "full_name": "my Workflow", "archived": True, "releases": []} - rwf_ex1 = nf_core.list.RemoteWorkflow(remote1) + rwf_ex1 = nf_core.pipelines.list.RemoteWorkflow(remote1) remote2 = {"name": "myWF", "full_name": "my Workflow", "archived": False, "releases": []} - rwf_ex2 = nf_core.list.RemoteWorkflow(remote2) + rwf_ex2 = nf_core.pipelines.list.RemoteWorkflow(remote2) workflows_obj.remote_workflows.append(rwf_ex1) workflows_obj.remote_workflows.append(rwf_ex2) diff --git a/tests/test_params_file.py b/tests/test_params_file.py index 673139c3b2..7e3e4b4f42 100644 --- a/tests/test_params_file.py +++ b/tests/test_params_file.py @@ -5,8 +5,8 @@ from pathlib import Path import nf_core.pipelines.create.create -import nf_core.schema -from nf_core.params_file import ParamsFileBuilder +import nf_core.pipelines.schema +from nf_core.pipelines.params_file import ParamsFileBuilder class TestParamsFileBuilder: @@ -15,7 +15,7 @@ class TestParamsFileBuilder: @classmethod def setup_class(cls): """Create a new PipelineSchema object""" - cls.schema_obj = nf_core.schema.PipelineSchema() + cls.schema_obj = nf_core.pipelines.schema.PipelineSchema() cls.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) # Create a test pipeline in temp directory diff --git a/tests/test_schema.py b/tests/test_schema.py index b4be7ae455..4cb157c087 100644 --- a/tests/test_schema.py +++ b/tests/test_schema.py @@ -13,7 +13,7 @@ import yaml import nf_core.pipelines.create.create -import nf_core.schema +import nf_core.pipelines.schema from .utils import with_temporary_file, with_temporary_folder @@ -23,7 +23,7 @@ class TestSchema(unittest.TestCase): def setUp(self): """Create a new PipelineSchema object""" - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() self.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) # Create a test pipeline in temp directory diff --git a/tests/test_utils.py b/tests/test_utils.py index 85f4e3c548..89ba0444ff 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -10,8 +10,8 @@ import pytest import requests -import nf_core.list import nf_core.pipelines.create.create +import nf_core.pipelines.list import nf_core.utils from .utils import with_temporary_folder @@ -160,7 +160,7 @@ def test_pip_erroneous_package(self): nf_core.utils.pip_package("not_a_package=1.0") def test_get_repo_releases_branches_nf_core(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("methylseq", wfs) for r in wf_releases: @@ -171,7 +171,7 @@ def test_get_repo_releases_branches_nf_core(self): assert "dev" in wf_branches.keys() def test_get_repo_releases_branches_not_nf_core(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("MultiQC/MultiQC", wfs) for r in wf_releases: @@ -182,13 +182,13 @@ def test_get_repo_releases_branches_not_nf_core(self): assert "main" in wf_branches.keys() def test_get_repo_releases_branches_not_exists(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() with pytest.raises(AssertionError): nf_core.utils.get_repo_releases_branches("made_up_pipeline", wfs) def test_get_repo_releases_branches_not_exists_slash(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() with pytest.raises(AssertionError): nf_core.utils.get_repo_releases_branches("made-up/pipeline", wfs) From 033eaa074cd3314c206d8dc948de7e830dacfba6 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 31 May 2024 09:29:56 +0200 Subject: [PATCH 020/574] fix commands imports and mentions --- .github/workflows/create-lint-wf.yml | 8 +-- nf_core/__main__.py | 8 +-- .../pipeline-template/.github/CONTRIBUTING.md | 6 +- .../.github/workflows/download_pipeline.yml | 6 +- nf_core/pipelines/download.py | 12 ++-- nf_core/pipelines/launch.py | 6 +- .../lint/actions_schema_validation.py | 2 +- nf_core/pipelines/lint/schema_lint.py | 6 +- nf_core/pipelines/params_file.py | 2 +- nf_core/pipelines/schema.py | 2 +- nf_core/utils.py | 6 +- setup.py | 2 +- tests/lint/multiqc_config.py | 4 +- tests/test_bump_version.py | 8 +-- tests/test_cli.py | 36 +++++----- tests/test_download.py | 18 ++--- tests/test_list.py | 4 +- tests/test_sync.py | 66 +++++++++---------- 18 files changed, 102 insertions(+), 100 deletions(-) diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 03b9aa2411..7e90febb74 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -79,12 +79,12 @@ jobs: working-directory: create-lint-wf # Run the other nf-core commands - - name: nf-core list - run: nf-core --log-file log.txt list + - name: nf-core pipelines list + run: nf-core --log-file log.txt pipelines list working-directory: create-lint-wf - - name: nf-core schema - run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts + - name: nf-core pipelines schema + run: nf-core --log-file log.txt pipelines schema build --dir nf-core-testpipeline/ --no-prompts working-directory: create-lint-wf - name: Cleanup work directory diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 4921e15d5f..2d34b8e883 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -697,7 +697,7 @@ def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, userna the pipeline. It is run automatically for all pipelines when ever a new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ - from nf_core.pipelines.sync.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError from nf_core.utils import is_pipeline_directory # Check if pipeline directory contains necessary files @@ -743,7 +743,7 @@ def bump_version_pipeline(ctx, new_version, dir, nextflow): As well as the pipeline version, you can also change the required version of Nextflow. """ - from nf_core.pipelines.bump_version.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version from nf_core.utils import Pipeline, is_pipeline_directory try: @@ -952,9 +952,9 @@ def lint_schema(schema_path): Check that a given pipeline schema is valid. Checks whether the pipeline schema validates as JSON Schema Draft 7 - and adheres to the additional nf-core schema requirements. + and adheres to the additional nf-core pipelines schema requirements. - This function runs as part of the nf-core lint command, this is a convenience + This function runs as part of the nf-core pipelines lint command, this is a convenience command that does just the schema linting nice and quickly. If no schema path is provided, "nextflow_schema.json" will be used (if it exists). diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index dc05d165d1..e22a664250 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -23,7 +23,7 @@ If you'd like to write some code for {{ name }}, the standard workflow is as fol 1. Check that there isn't already an issue about your idea in the [{{ name }} issues](https://github.com/{{ name }}/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [{{ name }} repository](https://github.com/{{ name }}) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -83,7 +83,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -94,7 +94,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index ebea16c5cb..99a42d86d2 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -58,7 +58,7 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 5a2acf4896..8454f894a2 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -42,7 +42,7 @@ class DownloadError(RuntimeError): - """A custom exception that is raised when nf-core download encounters a problem that we already took into consideration. + """A custom exception that is raised when nf-core pipelines download encounters a problem that we already took into consideration. In this case, we do not want to print the traceback, but give the user some concise, helpful feedback instead. """ @@ -505,7 +505,7 @@ def prompt_singularity_cachedir_creation(self): with open(os.path.expanduser(shellprofile_path), "a") as f: f.write( "\n\n#######################################\n" - f"## Added by `nf-core download` v{nf_core.__version__} ##\n" + f"## Added by `nf-core pipelines download` v{nf_core.__version__} ##\n" + f'export NXF_SINGULARITY_CACHEDIR="{cachedir_path}"' + "\n#######################################\n" ) @@ -687,7 +687,7 @@ def wf_use_local_configs(self, revision_dirname): # Append the singularity.cacheDir to the end if we need it if self.container_system == "singularity" and self.container_cache_utilisation == "copy": nfconfig += ( - f"\n\n// Added by `nf-core download` v{nf_core.__version__} //\n" + f"\n\n// Added by `nf-core pipelines download` v{nf_core.__version__} //\n" + 'singularity.cacheDir = "${projectDir}/../singularity-images/"' + "\n///////////////////////////////////////" ) @@ -1730,7 +1730,7 @@ def __add_additional_tags(self) -> None: # Although "dev-null" is a syntactically-valid local-part that is equally valid for delivery, # and only the receiving MTA can decide whether to accept it, it is to my best knowledge configured with # a Postfix discard mail delivery agent (https://www.postfix.org/discard.8.html), so incoming mails should be sinkholed. - self.ensure_git_user_config(f"nf-core download v{nf_core.__version__}", "dev-null@example.com") + self.ensure_git_user_config(f"nf-core pipelines download v{nf_core.__version__}", "dev-null@example.com") for additional_tag in self.additional_tags: # A valid git branch or tag name can contain alphanumeric characters, underscores, hyphens, and dots. @@ -1740,7 +1740,9 @@ def __add_additional_tags(self) -> None: if self.repo.is_valid_object(anchor) and not self.repo.is_valid_object(tag): try: self.repo.create_tag( - tag, ref=anchor, message=f"Synonynmous tag to {anchor}; added by `nf-core download`." + tag, + ref=anchor, + message=f"Synonynmous tag to {anchor}; added by `nf-core pipelines download`.", ) except (GitCommandError, InvalidGitRepositoryError) as e: log.error(f"[red]Additional tag(s) could not be applied:[/]\n{e}\n") diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py index 77a7948eaf..3a5f97e78f 100644 --- a/nf_core/pipelines/launch.py +++ b/nf_core/pipelines/launch.py @@ -38,7 +38,7 @@ def __init__( """Initialise the Launcher class Args: - schema: An nf_core.schema.PipelineSchema() object + schema: An nf_core.pipelines.schema.PipelineSchema() object """ self.pipeline = pipeline @@ -59,7 +59,7 @@ def __init__( self.nextflow_cmd = None # Fetch remote workflows - self.wfs = nf_core.list.Workflows() + self.wfs = nf_core.pipelines.list.Workflows() self.wfs.get_remote_workflows() # Prepend property names with a single hyphen in case we have parameters with the same ID @@ -340,7 +340,7 @@ def get_web_launch_response(self): elif web_response["status"] == "waiting_for_user": return False elif web_response["status"] == "launch_params_complete": - log.info("Found completed parameters from nf-core launch GUI") + log.info("Found completed parameters from nf-core pipelines launch GUI") try: # Set everything that we can with the cache results # NB: If using web builder, may have only run with --id and nothing else diff --git a/nf_core/pipelines/lint/actions_schema_validation.py b/nf_core/pipelines/lint/actions_schema_validation.py index 7e878a1af8..b4be42b54c 100644 --- a/nf_core/pipelines/lint/actions_schema_validation.py +++ b/nf_core/pipelines/lint/actions_schema_validation.py @@ -23,7 +23,7 @@ def actions_schema_validation(self) -> Dict[str, List[str]]: warned: List[str] = [] # Only show error messages from schema - logging.getLogger("nf_core.schema").setLevel(logging.ERROR) + logging.getLogger("nf_core.pipelines.schema").setLevel(logging.ERROR) # Get all workflow files action_workflows = glob.glob(os.path.join(self.wf_path, ".github/workflows/*.y*ml")) diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py index 21858a0f49..6786c5012d 100644 --- a/nf_core/pipelines/lint/schema_lint.py +++ b/nf_core/pipelines/lint/schema_lint.py @@ -10,7 +10,7 @@ def schema_lint(self): pipeline parameters (eg. ``params.something``, ``--something``). .. tip:: Reminder: you should generally never need to edit this JSON file by hand. - The ``nf-core schema build`` command can create *and edit* the file for you + The ``nf-core pipelines schema build`` command can create *and edit* the file for you to keep it up to date, with a friendly user-interface for customisation. The lint test checks the schema for the following: @@ -58,14 +58,14 @@ def schema_lint(self): } .. tip:: You can check your pipeline schema without having to run the entire pipeline lint - by running ``nf-core schema lint`` instead of ``nf-core pipelines lint`` + by running ``nf-core pipelines schema lint`` instead of ``nf-core pipelines lint`` """ passed = [] warned = [] failed = [] # Only show error messages from schema - logging.getLogger("nf_core.schema").setLevel(logging.ERROR) + logging.getLogger("nf_core.pipelines.schema").setLevel(logging.ERROR) # Lint the schema self.schema_obj = nf_core.pipelines.schema.PipelineSchema() diff --git a/nf_core/pipelines/params_file.py b/nf_core/pipelines/params_file.py index 0384521c74..d61b7cfbc8 100644 --- a/nf_core/pipelines/params_file.py +++ b/nf_core/pipelines/params_file.py @@ -124,7 +124,7 @@ def get_pipeline(self): ).unsafe_ask() # Get the schema - self.schema_obj = nf_core.schema.PipelineSchema() + self.schema_obj = nf_core.pipelines.schema.PipelineSchema() self.schema_obj.get_schema_path(self.pipeline, local_only=False, revision=self.pipeline_revision) self.schema_obj.get_wf_params() diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 28a7d0b4ff..7f562bff38 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -912,7 +912,7 @@ def get_web_builder_response(self): if web_response["status"] == "waiting_for_user": return False if web_response["status"] == "web_builder_edited": - log.info("Found saved status from nf-core schema builder") + log.info("Found saved status from nf-core pipelines schema builder") try: self.schema = web_response["schema"] self.remove_schema_empty_definitions() diff --git a/nf_core/utils.py b/nf_core/utils.py index 9dae4b9e56..29f026c842 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -854,7 +854,7 @@ def prompt_remote_pipeline_name(wfs): """Prompt for the pipeline name with questionary Args: - wfs: A nf_core.list.Workflows() object, where get_remote_workflows() has been called. + wfs: A nf_core.pipelines.list.Workflows() object, where get_remote_workflows() has been called. Returns: pipeline (str): GitHub repo - username/repo @@ -934,7 +934,7 @@ def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False): class SingularityCacheFilePathValidator(questionary.Validator): """ - Validator for file path specified as --singularity-cache-index argument in nf-core download + Validator for file path specified as --singularity-cache-index argument in nf-core pipelines download """ def validate(self, value): @@ -954,7 +954,7 @@ def get_repo_releases_branches(pipeline, wfs): Args: pipeline (str): GitHub repo username/repo - wfs: A nf_core.list.Workflows() object, where get_remote_workflows() has been called. + wfs: A nf_core.pipelines.list.Workflows() object, where get_remote_workflows() has been called. Returns: wf_releases, wf_branches (tuple): Array of releases, Array of branches diff --git a/setup.py b/setup.py index 013c863b9a..8f32daa904 100644 --- a/setup.py +++ b/setup.py @@ -33,7 +33,7 @@ license="MIT", entry_points={ "console_scripts": ["nf-core=nf_core.__main__:run_nf_core"], - "refgenie.hooks.post_update": ["nf-core-refgenie=nf_core.refgenie:update_config"], + "refgenie.hooks.post_update": ["nf-core-refgenie=nf_core.pipelines.refgenie:update_config"], }, python_requires=">=3.8, <4", install_requires=required, diff --git a/tests/lint/multiqc_config.py b/tests/lint/multiqc_config.py index 70c09ae543..7f1fdbd67c 100644 --- a/tests/lint/multiqc_config.py +++ b/tests/lint/multiqc_config.py @@ -116,13 +116,13 @@ def test_multiqc_config_report_comment_release_fail(self): def test_multiqc_config_report_comment_release_succeed(self): """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version""" - import nf_core.pipelines.bump_version.bump_version + import nf_core.pipelines.bump_version new_pipeline = self._make_pipeline_copy() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() # bump version using the bump_version function - nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(lint_obj, "1.0") + nf_core.pipelines.bump_version.bump_pipeline_version(lint_obj, "1.0") # lint again lint_obj._load() result = lint_obj.multiqc_config() diff --git a/tests/test_bump_version.py b/tests/test_bump_version.py index ad7efcd1fd..260637c064 100644 --- a/tests/test_bump_version.py +++ b/tests/test_bump_version.py @@ -4,7 +4,7 @@ import yaml -import nf_core.pipelines.bump_version.bump_version +import nf_core.pipelines.bump_version import nf_core.pipelines.create.create import nf_core.utils @@ -24,7 +24,7 @@ def test_bump_pipeline_version(datafiles, tmp_path): pipeline_obj._load() # Bump the version number - nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(pipeline_obj, "1.1") + nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "1.1") new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check nextflow.config @@ -44,7 +44,7 @@ def test_dev_bump_pipeline_version(datafiles, tmp_path): pipeline_obj._load() # Bump the version number - nf_core.pipelines.bump_version.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev") + nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev") new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check the pipeline config @@ -65,7 +65,7 @@ def test_bump_nextflow_version(datafiles, tmp_path): # Bump the version number to a specific version, preferably one # we're not already on version = "22.04.3" - nf_core.pipelines.bump_version.bump_version.bump_nextflow_version(pipeline_obj, version) + nf_core.pipelines.bump_version.bump_nextflow_version(pipeline_obj, version) new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) # Check nextflow.config diff --git a/tests/test_cli.py b/tests/test_cli.py index 53780b14e1..8142caa211 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -79,7 +79,7 @@ def test_cli_verbose(self): # Checks that -v was considered valid assert "No such option: -v" not in nf_core.utils.strip_ansi_codes(result.output) - @mock.patch("nf_core.list.list_workflows", return_value="pipeline test list") + @mock.patch("nf_core.pipelines.list.list_workflows", return_value="pipeline test list") def test_cli_list(self, mock_list_workflows): """Test nf-core pipelines are listed and cli parameters are passed on.""" params = { @@ -87,7 +87,7 @@ def test_cli_list(self, mock_list_workflows): "json": None, "show-archived": None, } - cmd = ["list"] + self.assemble_params(params) + ["kw1", "kw2"] + cmd = ["pipelines", "list"] + self.assemble_params(params) + ["kw1", "kw2"] result = self.invoke_cli(cmd) mock_list_workflows.assert_called_once_with( @@ -96,7 +96,7 @@ def test_cli_list(self, mock_list_workflows): assert result.exit_code == 0 assert "pipeline test list" in result.output - @mock.patch("nf_core.launch.Launch") + @mock.patch("nf_core.pipelines.launch.Launch") def test_cli_launch(self, mock_launcher): """Test nf-core pipeline is launched and cli parameters are passed on.""" mock_launcher.return_value.launch_pipeline.return_value = True @@ -112,7 +112,7 @@ def test_cli_launch(self, mock_launcher): "show-hidden": None, "url": "builder_url", } - cmd = ["launch"] + self.assemble_params(params) + ["pipeline_name"] + cmd = ["pipelines", "launch"] + self.assemble_params(params) + ["pipeline_name"] result = self.invoke_cli(cmd) assert result.exit_code == 0 @@ -131,7 +131,7 @@ def test_cli_launch(self, mock_launcher): mock_launcher.return_value.launch_pipeline.assert_called_once() - @mock.patch("nf_core.launch.Launch") + @mock.patch("nf_core.pipelines.launch.Launch") def test_cli_launch_no_params_in(self, mock_launcher): """Test nf-core pipeline fails when params-in does not exist""" mock_launcher.return_value.launch_pipeline.return_value = True @@ -139,7 +139,7 @@ def test_cli_launch_no_params_in(self, mock_launcher): params = { "params-in": "/fake/path", } - cmd = ["launch"] + self.assemble_params(params) + ["pipeline_name"] + cmd = ["pipelines", "launch"] + self.assemble_params(params) + ["pipeline_name"] result = self.invoke_cli(cmd) assert result.exit_code == 2 @@ -150,15 +150,15 @@ def test_cli_launch_no_params_in(self, mock_launcher): mock_launcher.assert_not_called() - @mock.patch("nf_core.launch.Launch") + @mock.patch("nf_core.pipelines.launch.Launch") def test_cli_launch_fail(self, mock_launcher): """Test nf-core pipeline fails with exit code 1 when pipeline fails.""" mock_launcher.return_value.launch_pipeline.return_value = False - cmd = ["launch", "pipeline_name"] + cmd = ["pipelines", "launch", "pipeline_name"] result = self.invoke_cli(cmd) assert result.exit_code == 1 - @mock.patch("nf_core.download.DownloadWorkflow") + @mock.patch("nf_core.pipelines.download.DownloadWorkflow") def test_cli_download(self, mock_dl): """Test nf-core pipeline is downloaded and cli parameters are passed on.""" params = { @@ -176,7 +176,7 @@ def test_cli_download(self, mock_dl): "parallel-downloads": 2, } - cmd = ["download"] + self.assemble_params(params) + ["pipeline_name"] + cmd = ["pipelines", "download"] + self.assemble_params(params) + ["pipeline_name"] result = self.invoke_cli(cmd) assert result.exit_code == 0 @@ -382,31 +382,31 @@ def test_lint_log_user_warning(self, mock_lint, mock_is_pipeline): assert error_txt in captured_logs.output[-1] assert captured_logs.records[-1].levelname == "ERROR" - @mock.patch("nf_core.schema.PipelineSchema.get_schema_path") + @mock.patch("nf_core.pipelines.schema.PipelineSchema.get_schema_path") def test_schema_lint(self, mock_get_schema_path): - """Test nf-core schema lint defaults to nextflow_schema.json""" - cmd = ["schema", "lint"] + """Test nf-core pipelines schema lint defaults to nextflow_schema.json""" + cmd = ["pipelines", "schema", "lint"] with self.runner.isolated_filesystem(): with open("nextflow_schema.json", "w") as f: f.write("{}") self.invoke_cli(cmd) mock_get_schema_path.assert_called_with("nextflow_schema.json") - @mock.patch("nf_core.schema.PipelineSchema.get_schema_path") + @mock.patch("nf_core.pipelines.schema.PipelineSchema.get_schema_path") def test_schema_lint_filename(self, mock_get_schema_path): - """Test nf-core schema lint accepts a filename""" - cmd = ["schema", "lint", "some_other_filename"] + """Test nf-core pipelines schema lint accepts a filename""" + cmd = ["pipelines", "schema", "lint", "some_other_filename"] with self.runner.isolated_filesystem(): with open("some_other_filename", "w") as f: f.write("{}") self.invoke_cli(cmd) mock_get_schema_path.assert_called_with("some_other_filename") - @mock.patch("nf_core.create_logo.create_logo") + @mock.patch("nf_core.pipelines.create_logo.create_logo") def test_create_logo(self, mock_create_logo): # Set up the mock to return a specific value - cmd = ["create-logo", "test"] + cmd = ["pipelines", "create-logo", "test"] result = self.invoke_cli(cmd) mock_create_logo.assert_called_with("test", Path.cwd(), None, "light", 2300, "png", False) diff --git a/tests/test_download.py b/tests/test_download.py index 2d4231c7d1..c3a8c5546a 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -44,7 +44,7 @@ def __contains__(self, item: str) -> bool: # Tests for 'get_release_hash' # def test_get_release_hash_release(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() pipeline = "methylseq" download_obj = DownloadWorkflow(pipeline=pipeline, revision="1.6") @@ -62,7 +62,7 @@ def test_get_release_hash_release(self): ) def test_get_release_hash_branch(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() # Exoseq pipeline is archived, so `dev` branch should be stable pipeline = "exoseq" @@ -81,7 +81,7 @@ def test_get_release_hash_branch(self): ) def test_get_release_hash_non_existent_release(self): - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() pipeline = "methylseq" download_obj = DownloadWorkflow(pipeline=pipeline, revision="thisisfake") @@ -564,7 +564,7 @@ def test_remote_container_functionality(self, tmp_dir): # Tests for the main entry method 'download_workflow' # @with_temporary_folder - @mock.patch("nf_core.download.DownloadWorkflow.singularity_pull_image") + @mock.patch("nf_core.pipelines.download.DownloadWorkflow.singularity_pull_image") @mock.patch("shutil.which") def test_download_workflow_with_success(self, tmp_dir, mock_download_image, mock_singularity_installed): os.environ["NXF_SINGULARITY_CACHEDIR"] = "foo" @@ -585,7 +585,7 @@ def test_download_workflow_with_success(self, tmp_dir, mock_download_image, mock # Test Download for Seqera Platform # @with_temporary_folder - @mock.patch("nf_core.download.DownloadWorkflow.get_singularity_images") + @mock.patch("nf_core.pipelines.download.DownloadWorkflow.get_singularity_images") def test_download_workflow_for_platform(self, tmp_dir, _): download_obj = DownloadWorkflow( pipeline="nf-core/rnaseq", @@ -601,7 +601,7 @@ def test_download_workflow_for_platform(self, tmp_dir, _): assert isinstance(download_obj.wf_sha, dict) and len(download_obj.wf_sha) == 0 assert isinstance(download_obj.wf_download_url, dict) and len(download_obj.wf_download_url) == 0 - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() ( download_obj.pipeline, @@ -646,7 +646,7 @@ def test_download_workflow_for_platform(self, tmp_dir, _): # # Brief test adding a single custom tag to Seqera Platform download # - @mock.patch("nf_core.download.DownloadWorkflow.get_singularity_images") + @mock.patch("nf_core.pipelines.download.DownloadWorkflow.get_singularity_images") @with_temporary_folder def test_download_workflow_for_platform_with_one_custom_tag(self, _, tmp_dir): download_obj = DownloadWorkflow( @@ -662,7 +662,7 @@ def test_download_workflow_for_platform_with_one_custom_tag(self, _, tmp_dir): # # Test adding custom tags to Seqera Platform download (full test) # - @mock.patch("nf_core.download.DownloadWorkflow.get_singularity_images") + @mock.patch("nf_core.pipelines.download.DownloadWorkflow.get_singularity_images") @with_temporary_folder def test_download_workflow_for_platform_with_custom_tags(self, _, tmp_dir): with self._caplog.at_level(logging.INFO): @@ -690,7 +690,7 @@ def test_download_workflow_for_platform_with_custom_tags(self, _, tmp_dir): assert isinstance(download_obj.wf_download_url, dict) and len(download_obj.wf_download_url) == 0 assert isinstance(download_obj.additional_tags, list) and len(download_obj.additional_tags) == 5 - wfs = nf_core.list.Workflows() + wfs = nf_core.pipelines.list.Workflows() wfs.get_remote_workflows() ( download_obj.pipeline, diff --git a/tests/test_list.py b/tests/test_list.py index e11dbb12e1..21d239287d 100644 --- a/tests/test_list.py +++ b/tests/test_list.py @@ -106,7 +106,7 @@ def test_local_workflows_compare_and_fail_silently(self): rwf_ex.releases = None @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str}) - @mock.patch("nf_core.list.LocalWorkflow") + @mock.patch("nf_core.pipelines.list.LocalWorkflow") def test_parse_local_workflow_and_succeed(self, mock_local_wf): test_path = tmp_nxf / "nf-core" if not os.path.isdir(test_path): @@ -119,7 +119,7 @@ def test_parse_local_workflow_and_succeed(self, mock_local_wf): assert len(workflows_obj.local_workflows) == 1 @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str}) - @mock.patch("nf_core.list.LocalWorkflow") + @mock.patch("nf_core.pipelines.list.LocalWorkflow") @mock.patch("subprocess.check_output") def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess): test_path = tmp_nxf / "nf-core" diff --git a/tests/test_sync.py b/tests/test_sync.py index b980335387..ca90071d95 100644 --- a/tests/test_sync.py +++ b/tests/test_sync.py @@ -12,7 +12,7 @@ import pytest import nf_core.pipelines.create.create -import nf_core.pipelines.sync.sync +import nf_core.pipelines.sync from .utils import with_temporary_folder @@ -46,8 +46,8 @@ def tearDown(self): @with_temporary_folder def test_inspect_sync_dir_notgit(self, tmp_dir): """Try syncing an empty directory""" - psync = nf_core.pipelines.sync.sync.PipelineSync(tmp_dir) - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + psync = nf_core.pipelines.sync.PipelineSync(tmp_dir) + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() assert "does not appear to be a git repository" in exc_info.value.args[0] @@ -57,9 +57,9 @@ def test_inspect_sync_dir_dirty(self): test_fn = Path(self.pipeline_dir) / "uncommitted" test_fn.touch() # Try to sync, check we halt with the right error - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) try: - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() assert exc_info.value.args[0].startswith("Uncommitted changes found in pipeline directory!") finally: @@ -68,8 +68,8 @@ def test_inspect_sync_dir_dirty(self): def test_get_wf_config_no_branch(self): """Try getting a workflow config when the branch doesn't exist""" # Try to sync, check we halt with the right error - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir, from_branch="foo") - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir, from_branch="foo") + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() psync.get_wf_config() assert exc_info.value.args[0] == "Branch `foo` not found!" @@ -77,9 +77,9 @@ def test_get_wf_config_no_branch(self): def test_get_wf_config_missing_required_config(self): """Try getting a workflow config, then make it miss a required config option""" # Try to sync, check we halt with the right error - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.required_config_vars = ["fakethisdoesnotexist"] - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() psync.get_wf_config() # Check that we did actually get some config back @@ -89,26 +89,26 @@ def test_get_wf_config_missing_required_config(self): def test_checkout_template_branch(self): """Try checking out the TEMPLATE branch of the pipeline""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() def test_checkout_template_branch_no_template(self): """Try checking out the TEMPLATE branch of the pipeline when it does not exist""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.delete_head("TEMPLATE") - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.checkout_template_branch() assert exc_info.value.args[0] == "Could not check out branch 'origin/TEMPLATE' or 'TEMPLATE'" def test_delete_template_branch_files(self): """Confirm that we can delete all files in the TEMPLATE branch""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -118,7 +118,7 @@ def test_delete_template_branch_files(self): def test_create_template_pipeline(self): """Confirm that we can delete all files in the TEMPLATE branch""" # First, delete all the files - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -132,7 +132,7 @@ def test_create_template_pipeline(self): def test_commit_template_changes_nochanges(self): """Try to commit the TEMPLATE branch, but no changes were made""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -142,7 +142,7 @@ def test_commit_template_changes_nochanges(self): def test_commit_template_changes_changes(self): """Try to commit the TEMPLATE branch, but no changes were made""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -159,7 +159,7 @@ def test_commit_template_changes_changes(self): def test_push_template_branch_error(self): """Try pushing the changes, but without a remote (should fail)""" # Check out the TEMPLATE branch but skip making the new template etc. - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.checkout_template_branch() @@ -168,13 +168,13 @@ def test_push_template_branch_error(self): test_fn.touch() psync.commit_template_changes() # Try to push changes - with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.PullRequestExceptionError) as exc_info: psync.push_template_branch() assert exc_info.value.args[0].startswith("Could not push TEMPLATE branch") def test_create_merge_base_branch(self): """Try creating a merge base branch""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -193,7 +193,7 @@ def test_create_merge_base_branch_thrice(self): end, so it is needed to call it a third time to make sure this is picked up. """ - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -206,7 +206,7 @@ def test_create_merge_base_branch_thrice(self): def test_push_merge_branch(self): """Try pushing merge branch""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.create_remote("origin", self.remote_path) @@ -218,12 +218,12 @@ def test_push_merge_branch(self): def test_push_merge_branch_without_create_branch(self): """Try pushing merge branch without creating first""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.repo.create_remote("origin", self.remote_path) - with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.PullRequestExceptionError) as exc_info: psync.push_merge_branch() assert exc_info.value.args[0].startswith(f"Could not push branch '{psync.merge_branch}'") @@ -313,7 +313,7 @@ def json(self): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) def test_make_pull_request_success(self, mock_post, mock_get): """Try making a PR - successful response""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.gh_api.get = mock_get psync.gh_api.post = mock_post psync.gh_username = "no_existing_pr" @@ -326,13 +326,13 @@ def test_make_pull_request_success(self, mock_post, mock_get): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) def test_make_pull_request_bad_response(self, mock_post, mock_get): """Try making a PR and getting a 404 error""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.gh_api.get = mock_get psync.gh_api.post = mock_post psync.gh_username = "bad_url" psync.gh_repo = "bad_url/response" os.environ["GITHUB_AUTH_TOKEN"] = "test" - with pytest.raises(nf_core.pipelines.sync.sync.PullRequestExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.PullRequestExceptionError) as exc_info: psync.make_pull_request() assert exc_info.value.args[0].startswith( "Something went badly wrong - GitHub API PR failed - got return code 404" @@ -341,7 +341,7 @@ def test_make_pull_request_bad_response(self, mock_post, mock_get): @mock.patch("nf_core.utils.gh_api.get", side_effect=mocked_requests_get) def test_close_open_template_merge_prs(self, mock_get): """Try closing all open prs""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.get = mock_get @@ -349,7 +349,7 @@ def test_close_open_template_merge_prs(self, mock_get): psync.gh_repo = "list_prs/response" os.environ["GITHUB_AUTH_TOKEN"] = "test" - with mock.patch("nf_core.pipelines.sync.sync.PipelineSync.close_open_pr") as mock_close_open_pr: + with mock.patch("nf_core.pipelines.sync.PipelineSync.close_open_pr") as mock_close_open_pr: psync.close_open_template_merge_prs() prs = mock_get(f"https://api.github.com/repos/{psync.gh_repo}/pulls").data @@ -360,7 +360,7 @@ def test_close_open_template_merge_prs(self, mock_get): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch) def test_close_open_pr(self, mock_patch, mock_post): - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.post = mock_post @@ -383,7 +383,7 @@ def test_close_open_pr(self, mock_patch, mock_post): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch) def test_close_open_pr_fail(self, mock_patch, mock_post): - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.gh_api.post = mock_post @@ -405,7 +405,7 @@ def test_close_open_pr_fail(self, mock_patch, mock_post): def test_reset_target_dir(self): """Try resetting target pipeline directory""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() @@ -417,12 +417,12 @@ def test_reset_target_dir(self): def test_reset_target_dir_fake_branch(self): """Try resetting target pipeline directory but original branch does not exist""" - psync = nf_core.pipelines.sync.sync.PipelineSync(self.pipeline_dir) + psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() psync.original_branch = "fake_branch" - with pytest.raises(nf_core.pipelines.sync.sync.SyncExceptionError) as exc_info: + with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.reset_target_dir() assert exc_info.value.args[0].startswith("Could not reset to original branch `fake_branch`") From 7fb360d72c2a1c3dab77dba84e222afc565fd553 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 31 May 2024 10:01:41 +0200 Subject: [PATCH 021/574] show options after commands on help message. Thanks @dwreeves for the suggestion --- nf_core/__main__.py | 13 ++++++++++++- requirements.txt | 2 +- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 2d34b8e883..a263139b4a 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -107,6 +107,17 @@ def normalize_case(ctx, param, component_name): return component_name.casefold() +# Define a custom click group class to sort options and commands in the help message +# TODO: Remove this class and use COMMANDS_BEFORE_OPTIONS when rich-click is updated +# See https://github.com/ewels/rich-click/issues/200 for more information +class CustomRichGroup(click.RichGroup): + def format_options(self, ctx, formatter) -> None: + from rich_click.rich_help_rendering import get_rich_options + + self.format_commands(ctx, formatter) + get_rich_options(self, ctx, formatter) + + def run_nf_core(): # print nf-core header if environment variable is not set if os.environ.get("_NF_CORE_COMPLETE") is None: @@ -133,7 +144,7 @@ def run_nf_core(): @tui() -@click.group(context_settings=dict(help_option_names=["-h", "--help"])) +@click.group(context_settings=dict(help_option_names=["-h", "--help"]), cls=CustomRichGroup) @click.version_option(__version__) @click.option( "-v", diff --git a/requirements.txt b/requirements.txt index 44241e0d95..0574083fd0 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,7 +18,7 @@ questionary>=1.8.0 refgenie requests requests_cache -rich-click>=1.6.1 +rich-click==1.8.* rich>=13.3.1 tabulate textual>=0.63.1 From 63c4c061564a1854a6144fea0c70beda608311a1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 31 May 2024 10:07:23 +0200 Subject: [PATCH 022/574] rename command tui to interface --- nf_core/__main__.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index a263139b4a..c21aee30a7 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -37,7 +37,7 @@ "pipelines", "modules", "subworkflows", - "tui", + "interface", ], }, ], @@ -143,7 +143,10 @@ def run_nf_core(): nf_core_cli(auto_envvar_prefix="NFCORE") -@tui() +@tui( + command="interface", + help="Launch the nf-core interface", +) @click.group(context_settings=dict(help_option_names=["-h", "--help"]), cls=CustomRichGroup) @click.version_option(__version__) @click.option( From 7191f98562abfa9072f1e4d987c97169a8730155 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 31 May 2024 10:13:15 +0200 Subject: [PATCH 023/574] remove nf-core licences command --- nf_core/__main__.py | 24 --- nf_core/licences.py | 115 -------------- tests/test_cli.py | 32 ---- tests/test_licenses.py | 57 ------- tests/test_lint.py | 337 ----------------------------------------- 5 files changed, 565 deletions(-) delete mode 100644 nf_core/licences.py delete mode 100644 tests/test_licenses.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 67af238b5c..3a3c35e275 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -38,7 +38,6 @@ "launch", "create-params-file", "download", - "licences", "tui", ], }, @@ -463,29 +462,6 @@ def download( dl.download_workflow() -# nf-core licences -@nf_core_cli.command() -@click.argument("pipeline", required=True, metavar="") -@click.option("--json", is_flag=True, default=False, help="Print output in JSON") -def licences(pipeline, json): - """ - List software licences for a given workflow (DSL1 only). - - Checks the pipeline environment.yml file which lists all conda software packages, which is not available for DSL2 workflows. Therefore, this command only supports DSL1 workflows (for now). - Each of these is queried against the anaconda.org API to find the licence. - Package name, version and licence is printed to the command line. - """ - from nf_core.licences import WorkflowLicences - - lic = WorkflowLicences(pipeline) - lic.as_json = json - try: - stdout.print(lic.run_licences()) - except LookupError as e: - log.error(e) - sys.exit(1) - - # nf-core lint @nf_core_cli.command() @click.option( diff --git a/nf_core/licences.py b/nf_core/licences.py deleted file mode 100644 index be737280f8..0000000000 --- a/nf_core/licences.py +++ /dev/null @@ -1,115 +0,0 @@ -"""Lists software licences for a given workflow.""" - -import json -import logging -import os - -import requests -import rich.console -import rich.table -import yaml - -import nf_core.utils - -log = logging.getLogger(__name__) - - -class WorkflowLicences: - """A nf-core workflow licenses collection. - - Tries to retrieve the license information from all dependencies - of a given nf-core pipeline. - - A condensed overview with license per dependency can be printed out. - - Args: - pipeline (str): An existing nf-core pipeline name, like `nf-core/hlatyping` - or short `hlatyping`. - """ - - def __init__(self, pipeline): - self.pipeline = pipeline - self.conda_config = None - if self.pipeline.startswith("nf-core/"): - self.pipeline = self.pipeline[8:] - self.conda_packages = {} - self.conda_package_licences = {} - self.as_json = False - - def run_licences(self): - """ - Run the nf-core licences action - """ - self.get_environment_file() - self.fetch_conda_licences() - return self.print_licences() - - def get_environment_file(self): - """Get the conda environment file for the pipeline""" - if os.path.exists(self.pipeline): - pipeline_obj = nf_core.utils.Pipeline(self.pipeline) - pipeline_obj._load() - if pipeline_obj._fp("environment.yml") not in pipeline_obj.files: - raise LookupError( - "No `environment.yml` file found. (Note: DSL2 pipelines are currently not supported by this command.)" - ) - self.conda_config = pipeline_obj.conda_config - else: - env_url = f"https://raw.githubusercontent.com/nf-core/{self.pipeline}/master/environment.yml" - log.debug(f"Fetching environment.yml file: {env_url}") - response = requests.get(env_url) - # Check that the pipeline exists - if response.status_code == 404: - raise LookupError( - f"Couldn't find pipeline conda file: {env_url}. (Note: DSL2 pipelines are currently not supported by this command.)" - ) - self.conda_config = yaml.safe_load(response.text) - - def fetch_conda_licences(self): - """Fetch package licences from Anaconda and PyPi.""" - - # Check conda dependency list - deps = self.conda_config.get("dependencies", []) - deps_data = {} - log.info(f"Fetching licence information for {len(deps)} tools") - for dep in deps: - try: - if isinstance(dep, str): - dep_channels = self.conda_config.get("channels", []) - deps_data[dep] = nf_core.utils.anaconda_package(dep, dep_channels) - elif isinstance(dep, dict): - deps_data[dep] = nf_core.utils.pip_package(dep) - except ValueError: - log.error(f"Couldn't get licence information for {dep}") - - for dep, data in deps_data.items(): - _, depver = dep.split("=", 1) - self.conda_package_licences[dep] = nf_core.utils.parse_anaconda_licence(data, depver) - - def print_licences(self): - """Prints the fetched license information. - - Args: - as_json (boolean): Prints the information in JSON. Defaults to False. - """ - log.info("Warning: This tool only prints licence information for the software tools packaged using conda.") - log.info("The pipeline may use other software and dependencies not described here. ") - - if self.as_json: - return json.dumps(self.conda_package_licences, indent=4) - else: - table = rich.table.Table("Package Name", "Version", "Licence") - licence_list = [] - for dep, licences in self.conda_package_licences.items(): - depname, depver = dep.split("=", 1) - try: - depname = depname.split("::")[1] - except IndexError: - pass - licence_list.append([depname, depver, ", ".join(licences)]) - # Sort by licence, then package name - licence_list = sorted(sorted(licence_list), key=lambda x: x[2]) - # Add table rows - for lic in licence_list: - table.add_row(*lic) - return table diff --git a/tests/test_cli.py b/tests/test_cli.py index 76d167101a..dd19097e5d 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -199,38 +199,6 @@ def test_cli_download(self, mock_dl): mock_dl.return_value.download_workflow.assert_called_once() - @mock.patch("nf_core.licences.WorkflowLicences") - def test_licences(self, mock_lic): - """Test nf-core pipeline licence is printed out and cli parameters are passed on.""" - licence_text = "dummy licence text" - mock_lic.return_value.run_licences.return_value = licence_text - - params = { - "json": None, - } - - cmd = ["licences"] + self.assemble_params(params) + ["pipeline_name"] - result = self.invoke_cli(cmd) - - assert result.exit_code == 0 - assert licence_text in result.output - - mock_lic.assert_called_once_with(cmd[-1]) - - @mock.patch("nf_core.licences.WorkflowLicences") - def test_licences_log_error(self, mock_lic): - """Test LookupError is logged""" - error_txt = "LookupError has been raised" - mock_lic.return_value.run_licences.side_effect = LookupError(error_txt) - - cmd = ["licences", "pipeline_name"] - with self.assertLogs() as captured_logs: - result = self.invoke_cli(cmd) - - assert result.exit_code == 1 - assert error_txt in captured_logs.output[-1] - assert captured_logs.records[-1].levelname == "ERROR" - @mock.patch("nf_core.pipelines.create.create.PipelineCreate") def test_create(self, mock_create): """Test nf-core pipeline is created and cli parameters are passed on.""" diff --git a/tests/test_licenses.py b/tests/test_licenses.py deleted file mode 100644 index 8023c9e891..0000000000 --- a/tests/test_licenses.py +++ /dev/null @@ -1,57 +0,0 @@ -"""Some tests covering the pipeline creation sub command.""" -# import json -# import os -# import tempfile -# import unittest -# -# import pytest -# from rich.console import Console -# -# import nf_core.create -# import nf_core.licences - -# TODO nf-core: Assess and strip out if no longer required for DSL2 - -# class WorkflowLicensesTest(unittest.TestCase): -# """A class that performs tests on the workflow license -# retrieval functionality of nf-core tools.""" - -# def setUp(self): -# """ Create a new pipeline, then make a Licence object """ -# # Set up the schema -# self.pipeline_dir = os.path.join(tempfile.mkdtemp(), "test_pipeline") -# self.create_obj = nf_core.create.PipelineCreate("testing", "test pipeline", "tester", outdir=self.pipeline_dir) -# self.create_obj.init_pipeline() -# self.license_obj = nf_core.licences.WorkflowLicences(self.pipeline_dir) - -# def test_run_licences_successful(self): -# console = Console(record=True) -# console.print(self.license_obj.run_licences()) -# output = console.export_text() -# assert "GPL v3" in output - -# def test_run_licences_successful_json(self): -# self.license_obj.as_json = True -# console = Console(record=True) -# console.print(self.license_obj.run_licences()) -# output = json.loads(console.export_text()) -# for package in output: -# if "multiqc" in package: -# assert output[package][0] == "GPL v3" -# break -# else: -# raise LookupError("Could not find MultiQC") - -# def test_get_environment_file_local(self): -# self.license_obj.get_environment_file() -# assert any(["multiqc" in k for k in self.license_obj.conda_config["dependencies"]]) - -# def test_get_environment_file_remote(self): -# self.license_obj = nf_core.licences.WorkflowLicences("methylseq") -# self.license_obj.get_environment_file() -# assert any(["multiqc" in k for k in self.license_obj.conda_config["dependencies"]]) - -# @pytest.mark.xfail(raises=LookupError, strict=True) -# def test_get_environment_file_nonexistent(self): -# self.license_obj = nf_core.licences.WorkflowLicences("fubarnotreal") -# self.license_obj.get_environment_file() diff --git a/tests/test_lint.py b/tests/test_lint.py index aaf8330800..183af64626 100644 --- a/tests/test_lint.py +++ b/tests/test_lint.py @@ -253,340 +253,3 @@ def test_sphinx_md_files(self): test_template_strings_ignored, ) from .lint.version_consistency import test_version_consistency # type: ignore[misc] - - -# TODO nf-core: Assess and strip out if no longer required for DSL2 - -# def test_critical_missingfiles_example(self): -# """Tests for missing nextflow config and main.nf files""" -# lint_obj = nf_core.lint.run_linting(PATH_CRITICAL_EXAMPLE, False) -# assert len(lint_obj.failed) > 0 -# -# def test_failing_missingfiles_example(self): -# """Tests for missing files like Dockerfile or LICENSE""" -# lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) -# lint_obj.check_files_exist() -# expectations = {"failed": 6, "warned": 2, "passed": 14} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_mit_licence_example_pass(self): -# """Tests that MIT test works with good MIT licences""" -# good_lint_obj = nf_core.lint.PipelineLint(PATH_CRITICAL_EXAMPLE) -# good_lint_obj.check_licence() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(good_lint_obj, **expectations) -# -# def test_mit_license_example_with_failed(self): -# """Tests that MIT test works with bad MIT licences""" -# bad_lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) -# bad_lint_obj.check_licence() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(bad_lint_obj, **expectations) -# -# def test_config_variable_example_pass(self): -# """Tests that config variable existence test works with good pipeline example""" -# good_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# good_lint_obj.check_nextflow_config() -# expectations = {"failed": 0, "warned": 1, "passed": 34} -# self.assess_lint_status(good_lint_obj, **expectations) -# -# def test_config_variable_example_with_failed(self): -# """Tests that config variable existence test fails with bad pipeline example""" -# bad_lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) -# bad_lint_obj.check_nextflow_config() -# expectations = {"failed": 19, "warned": 6, "passed": 10} -# self.assess_lint_status(bad_lint_obj, **expectations) -# -# @pytest.mark.xfail(raises=AssertionError, strict=True) -# def test_config_variable_error(self): -# """Tests that config variable existence test falls over nicely with nextflow can't run""" -# bad_lint_obj = nf_core.lint.PipelineLint("/non/existant/path") -# bad_lint_obj.check_nextflow_config() -# -# -# def test_wrong_license_examples_with_failed(self): -# """Tests for checking the license test behavior""" -# for example in PATHS_WRONG_LICENSE_EXAMPLE: -# lint_obj = nf_core.lint.PipelineLint(example) -# lint_obj.check_licence() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_missing_license_example(self): -# """Tests for missing license behavior""" -# lint_obj = nf_core.lint.PipelineLint(PATH_MISSING_LICENSE_EXAMPLE) -# lint_obj.check_licence() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_readme_pass(self): -# """Tests that the pipeline README file checks work with a good example""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.minNextflowVersion = "20.04.0" -# lint_obj.files = ["environment.yml"] -# lint_obj.check_readme() -# expectations = {"failed": 0, "warned": 0, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_readme_warn(self): -# """Tests that the pipeline README file checks fail """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.minNextflowVersion = "0.28.0" -# lint_obj.check_readme() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_readme_fail(self): -# """Tests that the pipeline README file checks give warnings with a bad example""" -# lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.check_readme() -# expectations = {"failed": 0, "warned": 2, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_dockerfile_pass(self): -# """Tests if a valid Dockerfile passes the lint checks""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["Dockerfile"] -# lint_obj.check_docker() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_version_consistency_pass(self): -# """Tests the workflow version and container version sucessfully""" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.config["process.container"] = "nfcore/tools:0.4" -# lint_obj.check_version_consistency() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_version_consistency_with_env_fail(self): -# """Tests the behaviour, when a git activity is a release -# and simulate wrong release tag""" -# os.environ["GITHUB_REF"] = "refs/tags/0.5" -# os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.config["process.container"] = "nfcore/tools:0.4" -# lint_obj.check_version_consistency() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_version_consistency_with_numeric_fail(self): -# """Tests the behaviour, when a git activity is a release -# and simulate wrong release tag""" -# os.environ["GITHUB_REF"] = "refs/tags/0.5dev" -# os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.config["process.container"] = "nfcore/tools:0.4" -# lint_obj.check_version_consistency() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_version_consistency_with_no_docker_version_fail(self): -# """Tests the behaviour, when a git activity is a release -# and simulate wrong missing docker version tag""" -# os.environ["GITHUB_REF"] = "refs/tags/0.4" -# os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.config["process.container"] = "nfcore/tools" -# lint_obj.check_version_consistency() -# expectations = {"failed": 1, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_version_consistency_with_env_pass(self): -# """Tests the behaviour, when a git activity is a release -# and simulate correct release tag""" -# os.environ["GITHUB_REF"] = "refs/tags/0.4" -# os.environ["GITHUB_REPOSITORY"] = "nf-core/testpipeline" -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.config["process.container"] = "nfcore/tools:0.4" -# lint_obj.check_version_consistency() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_env_pass(self): -# """ Tests the conda environment config checks with a working example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# with open(os.path.join(PATH_WORKING_EXAMPLE, "environment.yml"), "r") as fh: -# lint_obj.conda_config = yaml.safe_load(fh) -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 0, "warned": 4, "passed": 5} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_env_fail(self): -# """ Tests the conda environment config fails with a bad example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# with open(os.path.join(PATH_WORKING_EXAMPLE, "environment.yml"), "r") as fh: -# lint_obj.conda_config = yaml.safe_load(fh) -# lint_obj.conda_config["dependencies"] = ["fastqc", "multiqc=0.9", "notapackaage=0.4"] -# lint_obj.pipeline_name = "not_tools" -# lint_obj.config["manifest.version"] = "0.23" -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 3, "warned": 1, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# @mock.patch("requests.get") -# @pytest.mark.xfail(raises=ValueError, strict=True) -# def test_conda_env_timeout(self, mock_get): -# """ Tests the conda environment handles API timeouts """ -# # Define the behaviour of the request get mock -# mock_get.side_effect = requests.exceptions.Timeout() -# # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.conda_config["channels"] = ["bioconda"] -# lint_obj.check_anaconda_package("multiqc=1.6") -# -# def test_conda_env_skip(self): -# """ Tests the conda environment config is skipped when not needed """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 0, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_dockerfile_pass(self): -# """ Tests the conda Dockerfile test works with a working example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.version = "1.11" -# lint_obj.files = ["environment.yml", "Dockerfile"] -# with open(os.path.join(PATH_WORKING_EXAMPLE, "Dockerfile"), "r") as fh: -# lint_obj.dockerfile = fh.read().splitlines() -# lint_obj.conda_config["name"] = "nf-core-tools-0.4" -# lint_obj.check_conda_dockerfile() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_dockerfile_fail(self): -# """ Tests the conda Dockerfile test fails with a bad example """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.version = "1.11" -# lint_obj.files = ["environment.yml", "Dockerfile"] -# lint_obj.conda_config["name"] = "nf-core-tools-0.4" -# lint_obj.dockerfile = ["fubar"] -# lint_obj.check_conda_dockerfile() -# expectations = {"failed": 5, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_dockerfile_skip(self): -# """ Tests the conda Dockerfile test is skipped when not needed """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.check_conda_dockerfile() -# expectations = {"failed": 0, "warned": 0, "passed": 0} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_pip_no_version_fail(self): -# """ Tests the pip dependency version definition is present """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["multiqc"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 1, "warned": 0, "passed": 1} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_pip_package_not_latest_warn(self): -# """ Tests the pip dependency version definition is present """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["multiqc==1.4"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 0, "warned": 1, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# @mock.patch("requests.get") -# def test_pypi_timeout_warn(self, mock_get): -# """Tests the PyPi connection and simulates a request timeout, which should -# return in an addiional warning in the linting""" -# # Define the behaviour of the request get mock -# mock_get.side_effect = requests.exceptions.Timeout() -# # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["multiqc==1.5"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 0, "warned": 1, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# @mock.patch("requests.get") -# def test_pypi_connection_error_warn(self, mock_get): -# """Tests the PyPi connection and simulates a connection error, which should -# result in an additional warning, as we cannot test if dependent module is latest""" -# # Define the behaviour of the request get mock -# mock_get.side_effect = requests.exceptions.ConnectionError() -# # Now do the test -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["multiqc==1.5"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 0, "warned": 1, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_pip_dependency_fail(self): -# """ Tests the PyPi API package information query """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["notpresent==1.5"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 1, "warned": 0, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_conda_dependency_fails(self): -# """Tests that linting fails, if conda dependency -# package version is not available on Anaconda. -# """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": ["openjdk=0.0.0"]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 1, "warned": 0, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_pip_dependency_fails(self): -# """Tests that linting fails, if conda dependency -# package version is not available on Anaconda. -# """ -# lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# lint_obj.files = ["environment.yml"] -# lint_obj.pipeline_name = "tools" -# lint_obj.config["manifest.version"] = "0.4" -# lint_obj.conda_config = {"name": "nf-core-tools-0.4", "dependencies": [{"pip": ["multiqc==0.0"]}]} -# lint_obj.check_conda_env_yaml() -# expectations = {"failed": 1, "warned": 0, "passed": 2} -# self.assess_lint_status(lint_obj, **expectations) -# -# def test_pipeline_name_pass(self): -# """Tests pipeline name good pipeline example: lower case, no punctuation""" -# # good_lint_obj = nf_core.lint.run_linting(PATH_WORKING_EXAMPLE) -# good_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# good_lint_obj.pipeline_name = "tools" -# good_lint_obj.check_pipeline_name() -# expectations = {"failed": 0, "warned": 0, "passed": 1} -# self.assess_lint_status(good_lint_obj, **expectations) -# -# def test_pipeline_name_critical(self): -# """Tests that warning is returned for pipeline not adhering to naming convention""" -# critical_lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE) -# critical_lint_obj.pipeline_name = "Tools123" -# critical_lint_obj.check_pipeline_name() -# expectations = {"failed": 0, "warned": 1, "passed": 0} -# self.assess_lint_status(critical_lint_obj, **expectations) -# From aed32a9f90169680a1c45c144845c3f215746e98 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 31 May 2024 08:16:09 +0000 Subject: [PATCH 024/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1d7678c45..bb116c9a40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- Remove nf-core licenses command ([#3012](https://github.com/nf-core/tools/pull/3012)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 02017aac324b790d7afedfbaa2edc9ca8fb7fb9f Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 31 May 2024 23:13:04 +0200 Subject: [PATCH 025/574] README - absolute image paths Make the logo render on PyPI --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 85b608bf77..58fb708a0d 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@

- - nf-core/tools + + nf-core/tools

From 089264292c7f1430c2e17f0978c1169dfc369ff7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 31 May 2024 21:13:59 +0000 Subject: [PATCH 026/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1d7678c45..e8a8d1fbf6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From b96f56b15d24431fb97382bed7715bccfafd21df Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 31 May 2024 23:35:39 +0200 Subject: [PATCH 027/574] Conda module linting: Include package name in log file MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Tried to do this with GitHub Copilot Workspaces but it failed 😅 As I was looking at the code anyway I could see the fix so figured I would put it manually. Closes https://github.com/nf-core/tools/issues/3009 Untested, done in web browser only. --- nf_core/modules/lint/main_nf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index fd4d81f7f2..81308ba5c5 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -367,14 +367,14 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): # response = _bioconda_package(bp) response = nf_core.utils.anaconda_package(bp) except LookupError: - self.warned.append(("bioconda_version", "Conda version not specified correctly", self.main_nf)) + self.warned.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)) except ValueError: - self.failed.append(("bioconda_version", "Conda version not specified correctly", self.main_nf)) + self.failed.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf)) else: # Check that required version is available at all if bioconda_version not in response.get("versions"): self.failed.append( - ("bioconda_version", f"Conda package had unknown version: `{bioconda_version}`", self.main_nf) + ("bioconda_version", f"Conda package {bp} had unknown version: `{bioconda_version}`", self.main_nf) ) continue # No need to test for latest version, continue linting # Check version is latest available From 93acb91abe8c418ac9a8b9f06b237e2ec2d980e2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 31 May 2024 22:20:54 +0000 Subject: [PATCH 028/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8521c44100..0bfe44f870 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.6 + rev: v0.4.7 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From d4a91832343df619927ed1fdcc776c0daffb5e5a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 31 May 2024 22:21:50 +0000 Subject: [PATCH 029/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1d7678c45..515189e300 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 847a3763d1b67a9e75432bf0c74a0c531891d687 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 3 Jun 2024 08:40:07 +0000 Subject: [PATCH 030/574] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1d7678c45..6b421ba4de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ ### Linting - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) +- Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) ### Download From 005972e33d0d5808791fbcc18a6af914b249babc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 5 Jun 2024 19:58:25 +0000 Subject: [PATCH 031/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0bfe44f870..2e1373904f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.7 + rev: v0.4.8 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From ee5a22b263ffe926fc4e437adcc45831d13ab4e8 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 5 Jun 2024 19:59:12 +0000 Subject: [PATCH 032/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 996650e00a..1d82830b71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 8ee2040007c222825dc8356a731a024424cc1397 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 8 Jun 2024 01:11:09 +0000 Subject: [PATCH 033/574] Update python:3.12-slim Docker digest to e3ae8cf --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index fe4162b4fe..6fe79d2eba 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:afc139a0a640942491ec481ad8dda10f2c5b753f5c969393b12480155fe15a63 +FROM python:3.12-slim@sha256:e3ae8cf03c4f0abbfef13a8147478a7cd92798a94fa729a36a185d9106cbae32 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From a63a653ab230e6b576d3e1cd952a51433a852ea4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Sun, 9 Jun 2024 03:35:11 +0000 Subject: [PATCH 034/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d82830b71..715bc2dc12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) +- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 05f60b440aa3a2b5125ed3cc65ae8b86dc979ef2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 12 Jun 2024 13:30:29 +0000 Subject: [PATCH 035/574] Update dawidd6/action-download-artifact action to v6 --- nf_core/pipeline-template/.github/workflows/linting_comment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml index ea408fd6f8..908dcea159 100644 --- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed From 90f7e344d7e8d07060701bca0cedd36ce7866bf9 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 13 Jun 2024 18:31:15 +0000 Subject: [PATCH 036/574] Update python:3.12-slim Docker digest to 2fba8e7 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 6fe79d2eba..9ebc7e9853 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:e3ae8cf03c4f0abbfef13a8147478a7cd92798a94fa729a36a185d9106cbae32 +FROM python:3.12-slim@sha256:2fba8e70a87bcc9f6edd20dda0a1d4adb32046d2acbca7361bc61da5a106a914 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 6f444c96d3292dd3fd9fd4863ec7716de6ed4c1d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 14 Jun 2024 23:01:49 +0000 Subject: [PATCH 037/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 715bc2dc12..9da8c1ab24 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) - Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) +- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From a15a6f0e7f94a6d57e4d35a349b96bd29e7f886e Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 15 Jun 2024 04:47:47 +0000 Subject: [PATCH 038/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.9 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2e1373904f..6d8e34e0b4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.8 + rev: v0.4.9 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 1e47693b295eea4c2a5f7b6b0351305c10133a31 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 19 Jun 2024 15:03:44 +0200 Subject: [PATCH 039/574] Linting: Remove 'defaults' from conda environment.yml file. See nf-core/modules#5829 --- nf_core/module-template/environment.yml | 1 - .../pipeline-template/modules/nf-core/fastqc/environment.yml | 1 - .../pipeline-template/modules/nf-core/multiqc/environment.yml | 1 - nf_core/pipeline-template/nextflow.config | 2 +- .../subworkflows/nf-core/utils_nextflow_pipeline/main.nf | 2 +- tests/test_utils.py | 2 +- 6 files changed, 3 insertions(+), 6 deletions(-) diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml index dcf510affb..f234f85422 100644 --- a/nf_core/module-template/environment.yml +++ b/nf_core/module-template/environment.yml @@ -4,6 +4,5 @@ name: "{{ component_name_underscore }}" channels: - conda-forge - bioconda - - defaults dependencies: - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml index 1787b38a9a..0d5be45f26 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml @@ -2,6 +2,5 @@ name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml index ca39fb67e2..329ddb4870 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml @@ -2,6 +2,5 @@ name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.21 diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..6202aa8319 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -98,7 +98,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f66..e770d91b97 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -102,7 +102,7 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order diff --git a/tests/test_utils.py b/tests/test_utils.py index 85f4e3c548..48288be817 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -105,7 +105,7 @@ def test_load_pipeline_config(self): # def test_load_conda_env(self): # """Load the pipeline Conda environment.yml file""" # self.pipeline_obj._load_conda_environment() - # assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda", "defaults"] + # assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda"] def test_list_files_git(self): """Test listing pipeline files using `git ls`""" From d6191cce7843918cf256da0f9b0fe0940e813288 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 19 Jun 2024 13:05:27 +0000 Subject: [PATCH 040/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9da8c1ab24..3e2be8fd91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) +- Remove defaults from conda environment.yml file. ([#3029](https://github.com/nf-core/tools/pull/3029)) ### Download From e7d034ee664d8111fc22f8e38e8f501868046c1a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 20 Jun 2024 18:21:07 +0000 Subject: [PATCH 041/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6d8e34e0b4..4360c7fd7a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.9 + rev: v0.4.10 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From eff71e6b847dfa7e813d82ab8abbf91f6efd394b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 20 Jun 2024 18:21:52 +0000 Subject: [PATCH 042/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9da8c1ab24..60207e1a41 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) - Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) - Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From b3dc8c3319582300b9f007a5097fd7d322da4c8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 25 Jun 2024 10:40:18 +0200 Subject: [PATCH 043/574] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb116c9a40..18bd70062f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,7 @@ - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) -- Remove nf-core licenses command ([#3012](https://github.com/nf-core/tools/pull/3012)) +- Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 324cef26f2f2687e5935e611d42f8e871781a2d4 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 25 Jun 2024 12:56:10 +0200 Subject: [PATCH 044/574] make top-level commands work with a warning deprecation message --- nf_core/__main__.py | 261 +++++++++++++++++++++++++++++++++++++++----- 1 file changed, 233 insertions(+), 28 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index c21aee30a7..341382f647 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -641,7 +641,7 @@ def launch_pipeline( sys.exit(1) -# nf-core pipelnies list +# nf-core pipelines list @pipelines.command("list") @click.argument("keywords", required=False, nargs=-1, metavar="") @click.option( @@ -2248,10 +2248,24 @@ def validate(pipeline, params): This command takes such a file and validates it against the pipeline schema, checking whether all schema rules are satisfied. """ - log.error( + log.warning( "The `[magenta]nf-core schema validate[/]` command is deprecated. Use `[magenta]nf-core pipelines schema validate[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(pipeline) + # Load and check schema + schema_obj.load_lint_schema() + except AssertionError as e: + log.error(e) + sys.exit(1) + schema_obj.load_input_params(params) + try: + schema_obj.validate_params() + except AssertionError: + sys.exit(1) # nf-core schema build (deprecated) @@ -2292,10 +2306,18 @@ def build(dir, no_prompts, web_only, url): https://nf-co.re website where you can annotate and organise parameters. Listens for this to be completed and saves the updated schema. """ - log.error( + log.warning( "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.schema import PipelineSchema + + try: + schema_obj = PipelineSchema() + if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: + sys.exit(1) + except (UserWarning, AssertionError) as e: + log.error(e) + sys.exit(1) # nf-core schema lint (deprecated) @@ -2319,10 +2341,22 @@ def schema_lint(schema_path): If no schema path is provided, "nextflow_schema.json" will be used (if it exists). """ - log.error( + log.warning( "The `[magenta]nf-core schema lint[/]` command is deprecated. Use `[magenta]nf-core pipelines schema lint[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(schema_path) + schema_obj.load_lint_schema() + # Validate title and description - just warnings as schema should still work fine + try: + schema_obj.validate_schema_title_description() + except AssertionError as e: + log.warning(e) + except AssertionError: + sys.exit(1) # nf-core schema docs (deprecated) @@ -2362,10 +2396,20 @@ def docs(schema_path, output, format, force, columns): DEPRECATED Outputs parameter documentation for a pipeline schema. """ - log.error( + log.warning( "The `[magenta]nf-core schema docs[/]` command is deprecated. Use `[magenta]nf-core pipelines schema docs[/]` instead." ) - sys.exit(0) + if not os.path.exists(schema_path): + log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") + sys.exit(1) + + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + # Assume we're in a pipeline dir root if schema path not set + schema_obj.get_schema_path(schema_path) + schema_obj.load_schema() + schema_obj.print_documentation(output, format, force, columns.split(",")) # nf-core create-logo (deprecated) @@ -2413,10 +2457,24 @@ def logo(logo_text, dir, name, theme, width, format, force): This command generates an nf-core pipeline logo, using the supplied """ - log.error( + log.warning( "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.create_logo import create_logo + + try: + if dir == ".": + dir = Path.cwd() + logo_path = create_logo(logo_text, dir, name, theme, width, format, force) + # Print path to logo relative to current working directory + try: + logo_path = Path(logo_path).relative_to(Path.cwd()) + except ValueError: + logo_path = Path(logo_path) + log.info(f"Created logo: [magenta]{logo_path}[/]") + except UserWarning as e: + log.error(e) + sys.exit(1) # nf-core sync (deprecated) @@ -2464,8 +2522,22 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y the pipeline. It is run automatically for all pipelines when ever a new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ - log.error("The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead.") - sys.exit(0) + log.warning( + "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead." + ) + from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Sync the given pipeline dir + sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + try: + sync_obj.sync() + except (SyncExceptionError, PullRequestExceptionError) as e: + log.error(e) + sys.exit(1) # nf-core bump-version (deprecated) @@ -2499,10 +2571,28 @@ def bump_version(new_version, dir, nextflow): As well as the pipeline version, you can also change the required version of Nextflow. """ - log.error( + log.warning( "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.utils import Pipeline, is_pipeline_directory + + try: + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Make a pipeline object and load config etc + pipeline_obj = Pipeline(dir) + pipeline_obj._load() + + # Bump the pipeline version number + if not nextflow: + bump_pipeline_version(pipeline_obj, new_version) + else: + bump_nextflow_version(pipeline_obj, new_version) + except UserWarning as e: + log.error(e) + sys.exit(1) # nf-core list (deprecated) @@ -2525,8 +2615,12 @@ def list(keywords, sort, json, show_archived): Checks the web for a list of nf-core pipelines with their latest releases. Shows which nf-core pipelines you have pulled locally and whether they are up to date. """ - log.error("The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead.") - sys.exit(0) + log.warning( + "The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead." + ) + from nf_core.pipelines.list import list_workflows + + stdout.print(list_workflows(keywords, sort, json, show_archived)) # nf-core launch (deprecated) @@ -2600,10 +2694,24 @@ def launch( Run using a remote pipeline name (such as GitHub `user/repo` or a URL), a local pipeline directory or an ID from the nf-core web launch tool. """ - log.error( + log.warning( "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.launch import Launch + + launcher = Launch( + pipeline, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, + id, + ) + if not launcher.launch_pipeline(): + sys.exit(1) # nf-core create-params-file (deprecated) @@ -2639,10 +2747,13 @@ def create_params_file(pipeline, revision, output, force, show_hidden): Run using a remote pipeline name (such as GitHub `user/repo` or a URL), a local pipeline directory. """ - log.error( + log.warning( "The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead." ) - sys.exit(0) + builder = ParamsFileBuilder(pipeline, revision) + + if not builder.write_params_file(output, show_hidden=show_hidden, force=force): + sys.exit(1) # nf-core download (deprecated) @@ -2742,10 +2853,30 @@ def download( Collects all files in a single archive and configures the downloaded workflow to use relative paths to the configs and singularity images. """ - log.error( + log.warning( "The `[magenta]nf-core download[/]` command is deprecated. Use `[magenta]nf-core pipelines download[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.download import DownloadWorkflow + + if tower: + log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") + + dl = DownloadWorkflow( + pipeline, + revision, + outdir, + compress, + force, + tower or platform, # True if either specified + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, + ) + dl.download_workflow() # nf-core lint (deprecated) @@ -2828,8 +2959,45 @@ def lint( You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. See the documentation for details. """ - log.error("The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead.") - sys.exit(0) + log.warning( + "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead." + ) + from nf_core.pipelines.lint import run_linting + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory is a pipeline + try: + is_pipeline_directory(dir) + except UserWarning as e: + log.error(e) + sys.exit(1) + + # Run the lint tests! + try: + lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + sort_by, + markdown, + json, + ctx.obj["hide_progress"], + ) + swf_failed = 0 + if subworkflow_lint_obj is not None: + swf_failed = len(subworkflow_lint_obj.failed) + if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: + sys.exit(1) + except AssertionError as e: + log.critical(e) + sys.exit(1) + except UserWarning as e: + log.error(e) + sys.exit(1) # nf-core create (deprecated) @@ -2847,7 +3015,13 @@ def lint( @click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") @click.option("--plain", is_flag=True, help="Use the standard nf-core template") -def create(name, description, author, version, force, outdir, template_yaml, plain): +@click.option( + "--organisation", + type=str, + default="nf-core", + help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", +) +def create(name, description, author, version, force, outdir, template_yaml, plain, organisation): """ DEPRECATED Create a new pipeline using the nf-core template. @@ -2855,10 +3029,41 @@ def create(name, description, author, version, force, outdir, template_yaml, pla Uses the nf-core template to make a skeleton Nextflow pipeline with all required files, boilerplate code and best-practices. """ - log.error( + log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - sys.exit(0) + from nf_core.pipelines.create import PipelineCreateApp + from nf_core.pipelines.create.create import PipelineCreate + + if (name and description and author) or (template_yaml): + # If all command arguments are used, run without the interactive interface + try: + create_obj = PipelineCreate( + name, + description, + author, + version=version, + force=force, + outdir=outdir, + template_config=template_yaml, + organisation=organisation, + ) + create_obj.init_pipeline() + except UserWarning as e: + log.error(e) + sys.exit(1) + elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": + log.error( + "[red]Partial arguments supplied.[/] " + "Run without [i]any[/] arguments for an interactive interface, " + "or with at least name + description + author to use non-interactively." + ) + sys.exit(1) + else: + log.info("Launching interactive nf-core pipeline creation tool.") + app = PipelineCreateApp() + app.run() + sys.exit(app.return_code or 0) # Main script is being run - launch the CLI From 31b3663e2137b849c53f646190052efdb08000f7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 25 Jun 2024 10:57:35 +0000 Subject: [PATCH 045/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c06d6017df..008c755848 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,6 +34,7 @@ - Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) - Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) +- Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 44f8b213d0194259553ed12daa6d90f2e8fed203 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 25 Jun 2024 11:14:15 +0000 Subject: [PATCH 046/574] Update pre-commit hook pre-commit/mirrors-mypy to v1.10.1 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4360c7fd7a..34856956c5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: alias: ec - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.10.0" + rev: "v1.10.1" hooks: - id: mypy additional_dependencies: From ee2241a4e763239c3d45f343f7d5e930c8f1561f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 25 Jun 2024 14:52:57 +0200 Subject: [PATCH 047/574] Replace check_max with resourceLimits --- CHANGELOG.md | 1 + nf_core/pipeline-template/conf/base.config | 40 +++++++++++++--------- nf_core/pipeline-template/nextflow.config | 33 ------------------ 3 files changed, 24 insertions(+), 50 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 008c755848..c65b999a5a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,6 +42,7 @@ - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961)) - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978)) +- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([]()) ### General diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config index 9c62bf0634..72a912fe47 100644 --- a/nf_core/pipeline-template/conf/base.config +++ b/nf_core/pipeline-template/conf/base.config @@ -11,9 +11,15 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + + resourceLimits = [ + cpus: params.max_cpus, + memory: params.max_memory, + time: params.max_time + ] errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +33,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..0316c2e0c5 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -265,36 +265,3 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } - } -} From ce49baddf0a39478d1d5483d5cfeac56c32e1e77 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 25 Jun 2024 14:55:43 +0200 Subject: [PATCH 048/574] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c65b999a5a..60808610d0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,7 +42,7 @@ - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961)) - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978)) -- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([]()) +- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037)) ### General From c8abbef61080458001fe8eb590a26a05c627cea1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 25 Jun 2024 15:13:28 +0200 Subject: [PATCH 049/574] Code alignment, and try to get test to run on GHA Actions runner --- .github/workflows/create-test-wf.yml | 2 +- nf_core/pipeline-template/conf/base.config | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index a95a477459..cb2aad2675 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -75,7 +75,7 @@ jobs: pwd # echo content of current directory ls -la - nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results + nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results --max_cpus 4 - name: Upload log file artifact if: ${{ always() }} diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config index 72a912fe47..fb3a8456bd 100644 --- a/nf_core/pipeline-template/conf/base.config +++ b/nf_core/pipeline-template/conf/base.config @@ -16,9 +16,9 @@ process { time = { 4.h * task.attempt } resourceLimits = [ - cpus: params.max_cpus, + cpus: params.max_cpus, memory: params.max_memory, - time: params.max_time + time: params.max_time ] errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } From fc4de3324111f2000afbc5ac4827f61388600453 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 29 May 2024 11:42:57 +0200 Subject: [PATCH 050/574] mock github cretentials for snapshot tests --- tests/__snapshots__/test_create_app.ambr | 263 +++++++++++------------ tests/test_create_app.py | 14 +- 2 files changed, 139 insertions(+), 138 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index ed7bf8b256..4036695bb4 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -1408,260 +1408,259 @@ font-weight: 700; } - .terminal-3893066652-matrix { + .terminal-2925039714-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3893066652-title { + .terminal-2925039714-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3893066652-r1 { fill: #c5c8c6 } - .terminal-3893066652-r2 { fill: #e3e3e3 } - .terminal-3893066652-r3 { fill: #989898 } - .terminal-3893066652-r4 { fill: #e1e1e1 } - .terminal-3893066652-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3893066652-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-3893066652-r7 { fill: #1e1e1e } - .terminal-3893066652-r8 { fill: #008139 } - .terminal-3893066652-r9 { fill: #454a50 } - .terminal-3893066652-r10 { fill: #787878 } - .terminal-3893066652-r11 { fill: #e2e2e2 } - .terminal-3893066652-r12 { fill: #e2e3e3;font-weight: bold } - .terminal-3893066652-r13 { fill: #000000 } - .terminal-3893066652-r14 { fill: #b93c5b } - .terminal-3893066652-r15 { fill: #18954b } - .terminal-3893066652-r16 { fill: #e2e2e2;font-weight: bold } - .terminal-3893066652-r17 { fill: #969696;font-weight: bold } - .terminal-3893066652-r18 { fill: #808080 } - .terminal-3893066652-r19 { fill: #7ae998 } - .terminal-3893066652-r20 { fill: #507bb3 } - .terminal-3893066652-r21 { fill: #0a180e;font-weight: bold } - .terminal-3893066652-r22 { fill: #dde6ed;font-weight: bold } - .terminal-3893066652-r23 { fill: #001541 } - .terminal-3893066652-r24 { fill: #fea62b;font-weight: bold } - .terminal-3893066652-r25 { fill: #a7a9ab } - .terminal-3893066652-r26 { fill: #e2e3e3 } + .terminal-2925039714-r1 { fill: #c5c8c6 } + .terminal-2925039714-r2 { fill: #e3e3e3 } + .terminal-2925039714-r3 { fill: #989898 } + .terminal-2925039714-r4 { fill: #e1e1e1 } + .terminal-2925039714-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2925039714-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-2925039714-r7 { fill: #1e1e1e } + .terminal-2925039714-r8 { fill: #008139 } + .terminal-2925039714-r9 { fill: #454a50 } + .terminal-2925039714-r10 { fill: #e2e2e2 } + .terminal-2925039714-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-2925039714-r12 { fill: #000000 } + .terminal-2925039714-r13 { fill: #b93c5b } + .terminal-2925039714-r14 { fill: #18954b } + .terminal-2925039714-r15 { fill: #e2e2e2;font-weight: bold } + .terminal-2925039714-r16 { fill: #969696;font-weight: bold } + .terminal-2925039714-r17 { fill: #808080 } + .terminal-2925039714-r18 { fill: #7ae998 } + .terminal-2925039714-r19 { fill: #507bb3 } + .terminal-2925039714-r20 { fill: #0a180e;font-weight: bold } + .terminal-2925039714-r21 { fill: #dde6ed;font-weight: bold } + .terminal-2925039714-r22 { fill: #001541 } + .terminal-2925039714-r23 { fill: #fea62b;font-weight: bold } + .terminal-2925039714-r24 { fill: #a7a9ab } + .terminal-2925039714-r25 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ + ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + +  d Toggle dark mode q Quit diff --git a/tests/test_create_app.py b/tests/test_create_app.py index f01ea5b6bd..980939f483 100644 --- a/tests/test_create_app.py +++ b/tests/test_create_app.py @@ -1,5 +1,7 @@ """Test Pipeline Create App""" +from unittest import mock + from nf_core.pipelines.create import PipelineCreateApp @@ -216,7 +218,8 @@ async def run_before(pilot) -> None: assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) -def test_github_details(tmpdir, snap_compare): +@mock.patch("nf_core.pipelines.create.githubrepo.GithubRepo._get_github_credentials") +def test_github_details(mock_get_github_credentials, tmpdir, snap_compare): """Test snapshot for the github_repo screen. Steps to get to this screen: screen welcome > press start > @@ -229,7 +232,10 @@ def test_github_details(tmpdir, snap_compare): """ async def run_before(pilot) -> None: - delete = ["backspace"] * 50 + mock_get_github_credentials.return_value = ( + None, + None, + ) # mock the github credentials to have consistent snapshots await pilot.click("#start") await pilot.click("#type_nfcore") await pilot.click("#name") @@ -247,10 +253,6 @@ async def run_before(pilot) -> None: await pilot.app.workers.wait_for_complete() await pilot.click("#close_screen") await pilot.click("#github_repo") - await pilot.click("#gh_username") - await pilot.press(*delete) # delete field automatically filled using github CLI - await pilot.press("tab") - await pilot.press(*delete) assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) From 997c1725e8e05ae5358f8db9f987fc0373e0a772 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 29 May 2024 09:45:37 +0000 Subject: [PATCH 051/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 008c755848..5cf0c79305 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,6 +35,7 @@ - Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) +- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 75a42480df66d891b3e58ef966d4506ca88a807d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 25 Jun 2024 09:59:01 +0000 Subject: [PATCH 052/574] update snapshot --- tests/__snapshots__/test_create_app.ambr | 1272 ++++++++--------- .../pytest-0/test_github_details0 | 2 +- .../pytest-0/test_github_exit_message0 | 2 +- .../pytest-0/test_github_question0 | 2 +- .../pytest-1/test_github_details0 | 1 + .../pytest-1/test_github_exit_message0 | 1 + .../pytest-1/test_github_question0 | 1 + 7 files changed, 640 insertions(+), 641 deletions(-) create mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_details0 create mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 create mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_question0 diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 4036695bb4..9aa2da2a19 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -22,254 +22,253 @@ font-weight: 700; } - .terminal-3833894853-matrix { + .terminal-2299698092-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3833894853-title { + .terminal-2299698092-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3833894853-r1 { fill: #c5c8c6 } - .terminal-3833894853-r2 { fill: #e3e3e3 } - .terminal-3833894853-r3 { fill: #989898 } - .terminal-3833894853-r4 { fill: #e1e1e1 } - .terminal-3833894853-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3833894853-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-3833894853-r7 { fill: #1e1e1e } - .terminal-3833894853-r8 { fill: #008139 } - .terminal-3833894853-r9 { fill: #121212 } - .terminal-3833894853-r10 { fill: #e2e2e2 } - .terminal-3833894853-r11 { fill: #787878 } - .terminal-3833894853-r12 { fill: #b93c5b } - .terminal-3833894853-r13 { fill: #454a50 } - .terminal-3833894853-r14 { fill: #7ae998 } - .terminal-3833894853-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-3833894853-r16 { fill: #0a180e;font-weight: bold } - .terminal-3833894853-r17 { fill: #000000 } - .terminal-3833894853-r18 { fill: #fea62b;font-weight: bold } - .terminal-3833894853-r19 { fill: #a7a9ab } - .terminal-3833894853-r20 { fill: #e2e3e3 } + .terminal-2299698092-r1 { fill: #c5c8c6 } + .terminal-2299698092-r2 { fill: #e3e3e3 } + .terminal-2299698092-r3 { fill: #989898 } + .terminal-2299698092-r4 { fill: #e1e1e1 } + .terminal-2299698092-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2299698092-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-2299698092-r7 { fill: #1e1e1e } + .terminal-2299698092-r8 { fill: #008139 } + .terminal-2299698092-r9 { fill: #121212 } + .terminal-2299698092-r10 { fill: #e2e2e2 } + .terminal-2299698092-r11 { fill: #787878 } + .terminal-2299698092-r12 { fill: #454a50 } + .terminal-2299698092-r13 { fill: #7ae998 } + .terminal-2299698092-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-2299698092-r15 { fill: #0a180e;font-weight: bold } + .terminal-2299698092-r16 { fill: #000000 } + .terminal-2299698092-r17 { fill: #fea62b;font-weight: bold } + .terminal-2299698092-r18 { fill: #a7a9ab } + .terminal-2299698092-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -299,257 +298,256 @@ font-weight: 700; } - .terminal-170499771-matrix { + .terminal-4102136482-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-170499771-title { + .terminal-4102136482-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-170499771-r1 { fill: #c5c8c6 } - .terminal-170499771-r2 { fill: #e3e3e3 } - .terminal-170499771-r3 { fill: #989898 } - .terminal-170499771-r4 { fill: #e1e1e1 } - .terminal-170499771-r5 { fill: #4ebf71;font-weight: bold } - .terminal-170499771-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-170499771-r7 { fill: #1e1e1e } - .terminal-170499771-r8 { fill: #0f4e2a } - .terminal-170499771-r9 { fill: #0178d4 } - .terminal-170499771-r10 { fill: #a7a7a7 } - .terminal-170499771-r11 { fill: #787878 } - .terminal-170499771-r12 { fill: #e2e2e2 } - .terminal-170499771-r13 { fill: #b93c5b } - .terminal-170499771-r14 { fill: #121212 } - .terminal-170499771-r15 { fill: #454a50 } - .terminal-170499771-r16 { fill: #7ae998 } - .terminal-170499771-r17 { fill: #e2e3e3;font-weight: bold } - .terminal-170499771-r18 { fill: #0a180e;font-weight: bold } - .terminal-170499771-r19 { fill: #000000 } - .terminal-170499771-r20 { fill: #008139 } - .terminal-170499771-r21 { fill: #fea62b;font-weight: bold } - .terminal-170499771-r22 { fill: #a7a9ab } - .terminal-170499771-r23 { fill: #e2e3e3 } + .terminal-4102136482-r1 { fill: #c5c8c6 } + .terminal-4102136482-r2 { fill: #e3e3e3 } + .terminal-4102136482-r3 { fill: #989898 } + .terminal-4102136482-r4 { fill: #e1e1e1 } + .terminal-4102136482-r5 { fill: #4ebf71;font-weight: bold } + .terminal-4102136482-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-4102136482-r7 { fill: #1e1e1e } + .terminal-4102136482-r8 { fill: #0f4e2a } + .terminal-4102136482-r9 { fill: #0178d4 } + .terminal-4102136482-r10 { fill: #a7a7a7 } + .terminal-4102136482-r11 { fill: #787878 } + .terminal-4102136482-r12 { fill: #e2e2e2 } + .terminal-4102136482-r13 { fill: #121212 } + .terminal-4102136482-r14 { fill: #454a50 } + .terminal-4102136482-r15 { fill: #7ae998 } + .terminal-4102136482-r16 { fill: #e2e3e3;font-weight: bold } + .terminal-4102136482-r17 { fill: #0a180e;font-weight: bold } + .terminal-4102136482-r18 { fill: #000000 } + .terminal-4102136482-r19 { fill: #008139 } + .terminal-4102136482-r20 { fill: #fea62b;font-weight: bold } + .terminal-4102136482-r21 { fill: #a7a9ab } + .terminal-4102136482-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1133,252 +1131,251 @@ font-weight: 700; } - .terminal-1869771697-matrix { + .terminal-1422742483-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1869771697-title { + .terminal-1422742483-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1869771697-r1 { fill: #c5c8c6 } - .terminal-1869771697-r2 { fill: #e3e3e3 } - .terminal-1869771697-r3 { fill: #989898 } - .terminal-1869771697-r4 { fill: #e1e1e1 } - .terminal-1869771697-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1869771697-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-1869771697-r7 { fill: #1e1e1e } - .terminal-1869771697-r8 { fill: #008139 } - .terminal-1869771697-r9 { fill: #e2e2e2 } - .terminal-1869771697-r10 { fill: #b93c5b } - .terminal-1869771697-r11 { fill: #454a50 } - .terminal-1869771697-r12 { fill: #7ae998 } - .terminal-1869771697-r13 { fill: #e2e3e3;font-weight: bold } - .terminal-1869771697-r14 { fill: #0a180e;font-weight: bold } - .terminal-1869771697-r15 { fill: #000000 } - .terminal-1869771697-r16 { fill: #fea62b;font-weight: bold } - .terminal-1869771697-r17 { fill: #a7a9ab } - .terminal-1869771697-r18 { fill: #e2e3e3 } + .terminal-1422742483-r1 { fill: #c5c8c6 } + .terminal-1422742483-r2 { fill: #e3e3e3 } + .terminal-1422742483-r3 { fill: #989898 } + .terminal-1422742483-r4 { fill: #e1e1e1 } + .terminal-1422742483-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1422742483-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-1422742483-r7 { fill: #1e1e1e } + .terminal-1422742483-r8 { fill: #008139 } + .terminal-1422742483-r9 { fill: #e2e2e2 } + .terminal-1422742483-r10 { fill: #454a50 } + .terminal-1422742483-r11 { fill: #7ae998 } + .terminal-1422742483-r12 { fill: #e2e3e3;font-weight: bold } + .terminal-1422742483-r13 { fill: #0a180e;font-weight: bold } + .terminal-1422742483-r14 { fill: #000000 } + .terminal-1422742483-r15 { fill: #fea62b;font-weight: bold } + .terminal-1422742483-r16 { fill: #a7a9ab } + .terminal-1422742483-r17 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Final details - - - - First version of the pipelinePath to the output directory where the pipeline  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created - ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackFinish - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Final details + + + + First version of the pipelinePath to the output directory where the pipeline  + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created + ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackFinish + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1408,259 +1405,258 @@ font-weight: 700; } - .terminal-2925039714-matrix { + .terminal-4244045401-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2925039714-title { + .terminal-4244045401-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2925039714-r1 { fill: #c5c8c6 } - .terminal-2925039714-r2 { fill: #e3e3e3 } - .terminal-2925039714-r3 { fill: #989898 } - .terminal-2925039714-r4 { fill: #e1e1e1 } - .terminal-2925039714-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2925039714-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-2925039714-r7 { fill: #1e1e1e } - .terminal-2925039714-r8 { fill: #008139 } - .terminal-2925039714-r9 { fill: #454a50 } - .terminal-2925039714-r10 { fill: #e2e2e2 } - .terminal-2925039714-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2925039714-r12 { fill: #000000 } - .terminal-2925039714-r13 { fill: #b93c5b } - .terminal-2925039714-r14 { fill: #18954b } - .terminal-2925039714-r15 { fill: #e2e2e2;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ + ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -2791,256 +2787,256 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Must be lowercase without  + punctuation. + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 index 19fc648c4a..ee82f320cb 160000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 @@ -1 +1 @@ -Subproject commit 19fc648c4a1fc31b474b13cbfebd322ce9538b95 +Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 index 75465e6bd7..f7fe48cf9d 160000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 @@ -1 +1 @@ -Subproject commit 75465e6bd715b1bf9075c7efbce1f2dd38c4df37 +Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 index 07281e3aa6..dce3324acb 160000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 +++ b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 @@ -1 +1 @@ -Subproject commit 07281e3aa6aef6d8a282c1cafaf7defaef745565 +Subproject commit dce3324acbbe32f905afae8553e042f39404b37e diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0 new file mode 160000 index 0000000000..e2638dca91 --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-1/test_github_details0 @@ -0,0 +1 @@ +Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 new file mode 160000 index 0000000000..74cda800a8 --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 @@ -0,0 +1 @@ +Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0 new file mode 160000 index 0000000000..444ebc5370 --- /dev/null +++ b/tmp/pytest-of-gitpod/pytest-1/test_github_question0 @@ -0,0 +1 @@ +Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045 From 7c8260010aac15e844c9776d4a2a13c40f8e0834 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 26 Jun 2024 09:58:04 +0000 Subject: [PATCH 053/574] pause after clicking a button on snapshot test --- tests/__snapshots__/test_create_app.ambr | 255 +++++++++++------------ tests/test_create_app.py | 1 + 2 files changed, 128 insertions(+), 128 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 9aa2da2a19..89a5699f4d 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -2787,256 +2787,255 @@ font-weight: 700; } - 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.terminal-496814773-r17 { fill: #3c8b54;font-weight: bold } - .terminal-496814773-r18 { fill: #000000 } - .terminal-496814773-r19 { fill: #5aa86f } - .terminal-496814773-r20 { fill: #fea62b;font-weight: bold } - .terminal-496814773-r21 { fill: #a7a9ab } - .terminal-496814773-r22 { fill: #e2e3e3 } + .terminal-3046427883-r1 { fill: #c5c8c6 } + .terminal-3046427883-r2 { fill: #e3e3e3 } + .terminal-3046427883-r3 { fill: #989898 } + .terminal-3046427883-r4 { fill: #e1e1e1 } + .terminal-3046427883-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3046427883-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-3046427883-r7 { fill: #1e1e1e } + .terminal-3046427883-r8 { fill: #0f4e2a } + .terminal-3046427883-r9 { fill: #7b3042 } + .terminal-3046427883-r10 { fill: #a7a7a7 } + .terminal-3046427883-r11 { fill: #787878 } + .terminal-3046427883-r12 { fill: #e2e2e2 } + .terminal-3046427883-r13 { fill: #b93c5b } + .terminal-3046427883-r14 { fill: #454a50 } + .terminal-3046427883-r15 { fill: #7ae998 } + .terminal-3046427883-r16 { fill: #e2e3e3;font-weight: bold } + .terminal-3046427883-r17 { fill: #000000 } + .terminal-3046427883-r18 { fill: #008139 } + .terminal-3046427883-r19 { fill: #fea62b;font-weight: bold } + .terminal-3046427883-r20 { fill: #a7a9ab } + .terminal-3046427883-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Must be lowercase without  + punctuation. + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit diff --git a/tests/test_create_app.py b/tests/test_create_app.py index 980939f483..8c89b92cba 100644 --- a/tests/test_create_app.py +++ b/tests/test_create_app.py @@ -106,6 +106,7 @@ async def run_before(pilot) -> None: await pilot.click("#start") await pilot.click("#type_nfcore") await pilot.click("#next") + await pilot.pause() assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) From aec56ce5281154d6ced36ba6d4c2ce88a5c454e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 26 Jun 2024 11:03:40 +0000 Subject: [PATCH 054/574] fix pytests --- nf_core/modules/bump_versions.py | 4 +++- .../.github/workflows/template_version_comment.yml | 3 ++- tests/test_modules.py | 4 ++-- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 9b54174d5a..6556dcf0f4 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -241,7 +241,9 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: # change version in environment.yml with open(module.environment_yml) as fh: env_yml = yaml.safe_load(fh) - re.sub(bioconda_packages[0], f"'bioconda::{bioconda_tool_name}={last_ver}'", env_yml["dependencies"]) + env_yml["dependencies"][0] = re.sub( + bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0] + ) with open(module.environment_yml, "w") as fh: yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper()) diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml index e21283309d..58db2eb63a 100644 --- a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml @@ -1,6 +1,6 @@ name: nf-core template version comment # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. -# It posts a comment to the PR, even if it comes from a fork. +# It posts a comment to the PR, even if it comes from a fork.{%- raw %} on: pull_request_target @@ -40,3 +40,4 @@ jobs: Please update your pipeline to the latest version. For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + #{%- endraw %} diff --git a/tests/test_modules.py b/tests/test_modules.py index f353a7edfe..107b245663 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -37,8 +37,8 @@ def create_modules_repo_dummy(tmp_dir): fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"]) # mock biocontainers and anaconda response with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "bpipe", "0.9.11--hdfd78af_0") - mock_biocontainers_api_calls(rsps, "bpipe", "0.9.11--hdfd78af_0") + mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") + mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False) with requests_cache.disabled(): From 5d570cddde472951b569ac906f38d6ee6a32b334 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 26 Jun 2024 15:44:23 +0200 Subject: [PATCH 055/574] display input textbox with grid --- nf_core/pipelines/create/create.tcss | 6 + nf_core/pipelines/create/utils.py | 19 +- tests/__snapshots__/test_create_app.ambr | 1271 +++++++++++----------- 3 files changed, 655 insertions(+), 641 deletions(-) diff --git a/nf_core/pipelines/create/create.tcss b/nf_core/pipelines/create/create.tcss index 67394a9de3..747be3f75e 100644 --- a/nf_core/pipelines/create/create.tcss +++ b/nf_core/pipelines/create/create.tcss @@ -30,6 +30,12 @@ width: auto; } +.text-input-grid { + padding: 1 1 1 1; + grid-size: 1 3; + grid-rows: 3 3 auto; + height: auto; +} .field_help { padding: 1 1 0 1; color: $text-muted; diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index f1e0bae3ce..c15d61e266 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -10,7 +10,7 @@ from textual import on from textual._context import active_app from textual.app import ComposeResult -from textual.containers import HorizontalScroll +from textual.containers import Grid, HorizontalScroll from textual.message import Message from textual.validation import ValidationResult, Validator from textual.widget import Widget @@ -116,14 +116,17 @@ def __init__(self, field_id, placeholder, description, default=None, password=No self.password: bool = password def compose(self) -> ComposeResult: - yield Static(self.description, classes="field_help") - yield Input( - placeholder=self.placeholder, - validators=[ValidateConfig(self.field_id)], - value=self.default, - password=self.password, + yield Grid( + Static(self.description, classes="field_help"), + Input( + placeholder=self.placeholder, + validators=[ValidateConfig(self.field_id)], + value=self.default, + password=self.password, + ), + Static(classes="validation_msg"), + classes="text-input-grid", ) - yield Static(classes="validation_msg") @on(Input.Changed) @on(Input.Submitted) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 89a5699f4d..7133bb0983 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -22,253 +22,254 @@ font-weight: 700; } - .terminal-2299698092-matrix { + .terminal-207444902-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2299698092-title { + .terminal-207444902-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2299698092-r1 { fill: #c5c8c6 } - .terminal-2299698092-r2 { fill: #e3e3e3 } - .terminal-2299698092-r3 { fill: #989898 } - .terminal-2299698092-r4 { fill: #e1e1e1 } - .terminal-2299698092-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2299698092-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-2299698092-r7 { fill: #1e1e1e } - .terminal-2299698092-r8 { fill: #008139 } - .terminal-2299698092-r9 { fill: #121212 } - .terminal-2299698092-r10 { fill: #e2e2e2 } - .terminal-2299698092-r11 { fill: #787878 } - .terminal-2299698092-r12 { fill: #454a50 } - .terminal-2299698092-r13 { fill: #7ae998 } - .terminal-2299698092-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-2299698092-r15 { fill: #0a180e;font-weight: bold } - .terminal-2299698092-r16 { fill: #000000 } - .terminal-2299698092-r17 { fill: #fea62b;font-weight: bold } - .terminal-2299698092-r18 { fill: #a7a9ab } - .terminal-2299698092-r19 { fill: #e2e3e3 } + .terminal-207444902-r1 { fill: #c5c8c6 } + .terminal-207444902-r2 { fill: #e3e3e3 } + .terminal-207444902-r3 { fill: #989898 } + .terminal-207444902-r4 { fill: #e1e1e1 } + .terminal-207444902-r5 { fill: #4ebf71;font-weight: bold } + .terminal-207444902-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-207444902-r7 { fill: #1e1e1e } + .terminal-207444902-r8 { fill: #008139 } + .terminal-207444902-r9 { fill: #121212 } + .terminal-207444902-r10 { fill: #e2e2e2 } + .terminal-207444902-r11 { fill: #787878 } + .terminal-207444902-r12 { fill: #b93c5b } + .terminal-207444902-r13 { fill: #454a50 } + .terminal-207444902-r14 { fill: #7ae998 } + .terminal-207444902-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-207444902-r16 { fill: #0a180e;font-weight: bold } + .terminal-207444902-r17 { fill: #000000 } + .terminal-207444902-r18 { fill: #fea62b;font-weight: bold } + .terminal-207444902-r19 { fill: #a7a9ab } + .terminal-207444902-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + + GitHub organisationWorkflow name + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + + A short description of your pipeline. + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + + Name of the main author / authors + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -298,256 +299,257 @@ font-weight: 700; } - .terminal-4102136482-matrix { + .terminal-813458076-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4102136482-title { + .terminal-813458076-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4102136482-r1 { fill: #c5c8c6 } - .terminal-4102136482-r2 { fill: #e3e3e3 } - .terminal-4102136482-r3 { fill: #989898 } - .terminal-4102136482-r4 { fill: #e1e1e1 } - .terminal-4102136482-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4102136482-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-4102136482-r7 { fill: #1e1e1e } - .terminal-4102136482-r8 { fill: #0f4e2a } - .terminal-4102136482-r9 { fill: #0178d4 } - .terminal-4102136482-r10 { fill: #a7a7a7 } - .terminal-4102136482-r11 { fill: #787878 } - .terminal-4102136482-r12 { fill: #e2e2e2 } - .terminal-4102136482-r13 { fill: #121212 } - .terminal-4102136482-r14 { fill: #454a50 } - .terminal-4102136482-r15 { fill: #7ae998 } - .terminal-4102136482-r16 { fill: #e2e3e3;font-weight: bold } - .terminal-4102136482-r17 { fill: #0a180e;font-weight: bold } - .terminal-4102136482-r18 { fill: #000000 } - .terminal-4102136482-r19 { fill: #008139 } - .terminal-4102136482-r20 { fill: #fea62b;font-weight: bold } - .terminal-4102136482-r21 { fill: #a7a9ab } - .terminal-4102136482-r22 { fill: #e2e3e3 } + .terminal-813458076-r1 { fill: #c5c8c6 } + .terminal-813458076-r2 { fill: #e3e3e3 } + .terminal-813458076-r3 { fill: #989898 } + .terminal-813458076-r4 { fill: #e1e1e1 } + .terminal-813458076-r5 { fill: #4ebf71;font-weight: bold } + .terminal-813458076-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-813458076-r7 { fill: #1e1e1e } + .terminal-813458076-r8 { fill: #0f4e2a } + .terminal-813458076-r9 { fill: #0178d4 } + .terminal-813458076-r10 { fill: #a7a7a7 } + .terminal-813458076-r11 { fill: #787878 } + .terminal-813458076-r12 { fill: #e2e2e2 } + .terminal-813458076-r13 { fill: #b93c5b } + .terminal-813458076-r14 { fill: #121212 } + .terminal-813458076-r15 { fill: #454a50 } + .terminal-813458076-r16 { fill: #7ae998 } + .terminal-813458076-r17 { fill: #e2e3e3;font-weight: bold } + .terminal-813458076-r18 { fill: #0a180e;font-weight: bold } + .terminal-813458076-r19 { fill: #000000 } + .terminal-813458076-r20 { fill: #008139 } + .terminal-813458076-r21 { fill: #fea62b;font-weight: bold } + .terminal-813458076-r22 { fill: #a7a9ab } + .terminal-813458076-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + + GitHub organisationWorkflow name + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + + A short description of your pipeline. + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + + Name of the main author / authors + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1131,251 +1133,252 @@ font-weight: 700; } - .terminal-1422742483-matrix { + .terminal-1204198466-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1422742483-title { + .terminal-1204198466-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1422742483-r1 { fill: #c5c8c6 } - .terminal-1422742483-r2 { fill: #e3e3e3 } - .terminal-1422742483-r3 { fill: #989898 } - .terminal-1422742483-r4 { fill: #e1e1e1 } - .terminal-1422742483-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1422742483-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-1422742483-r7 { fill: #1e1e1e } - .terminal-1422742483-r8 { fill: #008139 } - .terminal-1422742483-r9 { fill: #e2e2e2 } - .terminal-1422742483-r10 { fill: #454a50 } - .terminal-1422742483-r11 { fill: #7ae998 } - .terminal-1422742483-r12 { fill: #e2e3e3;font-weight: bold } - .terminal-1422742483-r13 { fill: #0a180e;font-weight: bold } - .terminal-1422742483-r14 { fill: #000000 } - .terminal-1422742483-r15 { fill: #fea62b;font-weight: bold } - .terminal-1422742483-r16 { fill: #a7a9ab } - .terminal-1422742483-r17 { fill: #e2e3e3 } + .terminal-1204198466-r1 { fill: #c5c8c6 } + .terminal-1204198466-r2 { fill: #e3e3e3 } + .terminal-1204198466-r3 { fill: #989898 } + .terminal-1204198466-r4 { fill: #e1e1e1 } + .terminal-1204198466-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1204198466-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-1204198466-r7 { fill: #1e1e1e } + .terminal-1204198466-r8 { fill: #008139 } + .terminal-1204198466-r9 { fill: #e2e2e2 } + .terminal-1204198466-r10 { fill: #b93c5b } + .terminal-1204198466-r11 { fill: #454a50 } + .terminal-1204198466-r12 { fill: #7ae998 } + .terminal-1204198466-r13 { fill: #e2e3e3;font-weight: bold } + .terminal-1204198466-r14 { fill: #0a180e;font-weight: bold } + .terminal-1204198466-r15 { fill: #000000 } + .terminal-1204198466-r16 { fill: #fea62b;font-weight: bold } + .terminal-1204198466-r17 { fill: #a7a9ab } + .terminal-1204198466-r18 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Final details - - - - First version of the pipelinePath to the output directory where the pipeline  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created - ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackFinish - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Final details + + + + + First version of the pipelinePath to the output directory where the  + pipeline will be created + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊1.0.0dev▎▊.▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackFinish + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode q Quit @@ -1405,258 +1408,259 @@ font-weight: 700; } - .terminal-4244045401-matrix { + .terminal-3078297506-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4244045401-title { + .terminal-3078297506-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4244045401-r1 { fill: #c5c8c6 } - .terminal-4244045401-r2 { fill: #e3e3e3 } - .terminal-4244045401-r3 { fill: #989898 } - .terminal-4244045401-r4 { fill: #e1e1e1 } - .terminal-4244045401-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4244045401-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-4244045401-r7 { fill: #1e1e1e } - .terminal-4244045401-r8 { fill: #008139 } - .terminal-4244045401-r9 { fill: #454a50 } - .terminal-4244045401-r10 { fill: #e2e2e2 } - .terminal-4244045401-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-4244045401-r12 { fill: #000000 } - .terminal-4244045401-r13 { fill: #18954b } - .terminal-4244045401-r14 { fill: #e2e2e2;font-weight: bold } - .terminal-4244045401-r15 { fill: #969696;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + + + + Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + for login.Show + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊GitHub username▎▊••••••••••••▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊mypipeline▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + +  d Toggle dark mode q Quit @@ -2787,255 +2791,256 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + + GitHub organisationWorkflow name + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Must be lowercase without  + punctuation. + + + + A short description of your pipeline. + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + + + Name of the main author / authors + + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackNext + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + +  d Toggle dark mode q Quit From cbd9791dc53a671cacc8b41e1f7c08df0fb81c4a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 26 Jun 2024 13:55:45 +0000 Subject: [PATCH 056/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d1628fd918..73cd98af1b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 4937fc5abd520606a54cd7b988016c53e24a7503 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 06:48:22 +0000 Subject: [PATCH 057/574] Update python:3.12-slim Docker digest to da2d7af --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 9ebc7e9853..66ee3ab2f2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:2fba8e70a87bcc9f6edd20dda0a1d4adb32046d2acbca7361bc61da5a106a914 +FROM python:3.12-slim@sha256:da2d7af143dab7cd5b0d5a5c9545fe14e67fc24c394fcf1cf15e8ea16cbd8637 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From fb984e4e19a68bc900d56f386e0d3fcff86b002e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Jun 2024 09:40:08 +0000 Subject: [PATCH 058/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d1628fd918..6d3f4f088c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From a2b226fd8e6c3a476f59b56523bb643775352550 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 28 Jun 2024 13:20:05 +0000 Subject: [PATCH 059/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 34856956c5..6cefa7fc0f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.4.10 + rev: v0.5.0 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 4f7139953d11cfacd4844ae1d96c6fdd440a6323 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 28 Jun 2024 16:39:51 +0200 Subject: [PATCH 060/574] Template: Run awsfulltest on PRs to `master` with two PR approvals --- .../.github/workflows/awsfulltest.yml | 23 +++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index 56ecb60302..f0d0724424 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -1,18 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == '{{ name }}' + if: github.repository == '{{ name }}' && github.event.review.state == 'approved' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required From 407075741219497441444beba9bad62604844732 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Jun 2024 14:42:04 +0000 Subject: [PATCH 061/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6d3f4f088c..d417b9d57a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ ### Template - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985)) +- Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042)) ### Linting From 044fc1d6750f4cf9d3ccf87bcb6ed9f3e61760b8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 1 Jul 2024 14:30:55 +0200 Subject: [PATCH 062/574] Remove default basic resource limits in template (should be set by users) --- nf_core/pipeline-template/conf/base.config | 6 ------ 1 file changed, 6 deletions(-) diff --git a/nf_core/pipeline-template/conf/base.config b/nf_core/pipeline-template/conf/base.config index fb3a8456bd..fa292339e3 100644 --- a/nf_core/pipeline-template/conf/base.config +++ b/nf_core/pipeline-template/conf/base.config @@ -15,12 +15,6 @@ process { memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } - resourceLimits = [ - cpus: params.max_cpus, - memory: params.max_memory, - time: params.max_time - ] - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' From 528a207ca8e2e5169140876b5d7cdbf5c5845d5f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 1 Jul 2024 14:31:31 +0200 Subject: [PATCH 063/574] Add a basic set of resource limits in test configs, matching GithubActions runner limits --- nf_core/pipeline-template/conf/test.config | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config index 827e21b7b7..2b9715efb6 100644 --- a/nf_core/pipeline-template/conf/test.config +++ b/nf_core/pipeline-template/conf/test.config @@ -10,6 +10,14 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '16.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' From 936802fbfc553dde07a2acb9df134c995f5ab2d3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 1 Jul 2024 14:37:13 +0200 Subject: [PATCH 064/574] Bump minimum NXF version to allow resourceLimits --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 0316c2e0c5..d575c6186f 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -258,7 +258,7 @@ manifest { homePage = 'https://github.com/{{ name }}' description = """{{ description }}""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=24.04.2' version = '{{ version }}' doi = '' } From 06a1dbe41203c284b92d34912d14f12d77aebb72 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 1 Jul 2024 14:43:23 +0200 Subject: [PATCH 065/574] Add linting check for now deprecated params --- nf_core/pipelines/lint/nextflow_config.py | 89 ++++++++++++++++++----- 1 file changed, 69 insertions(+), 20 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index f62100a70a..f1c4c536c5 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -87,6 +87,9 @@ def nextflow_config(self): * ``params.nf_required_version``: The old method for specifying the minimum Nextflow version. Replaced by ``manifest.nextflowVersion`` * ``params.container``: The old method for specifying the dockerhub container address. Replaced by ``process.container`` * ``igenomesIgnore``: Changed to ``igenomes_ignore`` + * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive. + * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits`directive. + * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits`directive. .. tip:: The ``snake_case`` convention should now be used when defining pipeline parameters @@ -170,6 +173,9 @@ def nextflow_config(self): "params.igenomesIgnore", "params.name", "params.enable_conda", + "params.max_cpus", + "params.max_memory", + "params.max_time", ] # Remove field that should be ignored according to the linting config @@ -200,9 +206,13 @@ def nextflow_config(self): ignored.append(f"Config variable ignored: {self._wrap_quotes(cf)}") break if cf not in self.nf_config.keys(): - passed.append(f"Config variable (correctly) not found: {self._wrap_quotes(cf)}") + passed.append( + f"Config variable (correctly) not found: {self._wrap_quotes(cf)}" + ) else: - failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}") + failed.append( + f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}" + ) # Check and warn if the process configuration is done with deprecated syntax process_with_deprecated_syntax = list( @@ -222,9 +232,13 @@ def nextflow_config(self): if k in ignore_configs: continue if self.nf_config.get(k) == "true": - passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``") + passed.append( + f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``" + ) else: - failed.append(f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``") + failed.append( + f"Config ``{k}`` did not have correct value: ``{self.nf_config.get(k)}``" + ) if "manifest.name" not in ignore_configs: # Check that the pipeline name starts with nf-core @@ -233,7 +247,9 @@ def nextflow_config(self): if not manifest_name.startswith("nf-core/"): raise AssertionError() except (AssertionError, IndexError): - failed.append(f"Config ``manifest.name`` did not begin with ``nf-core/``:\n {manifest_name}") + failed.append( + f"Config ``manifest.name`` did not begin with ``nf-core/``:\n {manifest_name}" + ) else: passed.append("Config ``manifest.name`` began with ``nf-core/``") @@ -249,7 +265,9 @@ def nextflow_config(self): ) else: - passed.append("Config variable ``manifest.homePage`` began with https://github.com/nf-core/") + passed.append( + "Config variable ``manifest.homePage`` began with https://github.com/nf-core/" + ) # Check that the DAG filename ends in ``.svg`` if "dag.file" in self.nf_config: @@ -257,12 +275,21 @@ def nextflow_config(self): if self.nf_config["dag.file"].strip("'\"").endswith(default_dag_format): passed.append(f"Config ``dag.file`` ended with ``{default_dag_format}``") else: - failed.append(f"Config ``dag.file`` did not end with ``{default_dag_format}``") + failed.append( + f"Config ``dag.file`` did not end with ``{default_dag_format}``" + ) # Check that the minimum nextflowVersion is set properly if "manifest.nextflowVersion" in self.nf_config: - if self.nf_config.get("manifest.nextflowVersion", "").strip("\"'").lstrip("!").startswith(">="): - passed.append("Config variable ``manifest.nextflowVersion`` started with >= or !>=") + if ( + self.nf_config.get("manifest.nextflowVersion", "") + .strip("\"'") + .lstrip("!") + .startswith(">=") + ): + passed.append( + "Config variable ``manifest.nextflowVersion`` started with >= or !>=" + ) else: failed.append( "Config ``manifest.nextflowVersion`` did not start with ``>=`` or ``!>=`` : " @@ -272,7 +299,9 @@ def nextflow_config(self): # Check that the pipeline version contains ``dev`` if not self.release_mode and "manifest.version" in self.nf_config: if self.nf_config["manifest.version"].strip(" '\"").endswith("dev"): - passed.append(f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``") + passed.append( + f"Config ``manifest.version`` ends in ``dev``: ``{self.nf_config['manifest.version']}``" + ) else: warned.append( f"Config ``manifest.version`` should end in ``dev``: ``{self.nf_config['manifest.version']}``" @@ -291,18 +320,32 @@ def nextflow_config(self): if "custom_config" not in ignore_configs: # Check if custom profile params are set correctly - if self.nf_config.get("params.custom_config_version", "").strip("'") == "master": + if ( + self.nf_config.get("params.custom_config_version", "").strip("'") + == "master" + ): passed.append("Config `params.custom_config_version` is set to `master`") else: - failed.append("Config `params.custom_config_version` is not set to `master`") + failed.append( + "Config `params.custom_config_version` is not set to `master`" + ) - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/{}".format( - self.nf_config.get("params.custom_config_version", "").strip("'") + custom_config_base = ( + "https://raw.githubusercontent.com/nf-core/configs/{}".format( + self.nf_config.get("params.custom_config_version", "").strip("'") + ) ) - if self.nf_config.get("params.custom_config_base", "").strip("'") == custom_config_base: - passed.append(f"Config `params.custom_config_base` is set to `{custom_config_base}`") + if ( + self.nf_config.get("params.custom_config_base", "").strip("'") + == custom_config_base + ): + passed.append( + f"Config `params.custom_config_base` is set to `{custom_config_base}`" + ) else: - failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`") + failed.append( + f"Config `params.custom_config_base` is not set to `{custom_config_base}`" + ) # Check that lines for loading custom profiles exist lines = [ @@ -344,7 +387,9 @@ def nextflow_config(self): match = re.search(r"\bprofiles\s*{", cleaned_content) if not match: - failed.append("nextflow.config does not contain `profiles` scope, but `test` profile is required") + failed.append( + "nextflow.config does not contain `profiles` scope, but `test` profile is required" + ) else: # Extract profiles scope content and check for test profile start = match.end() @@ -360,7 +405,9 @@ def nextflow_config(self): if re.search(r"\btest\s*{", profiles_content): passed.append("nextflow.config contains configuration profile `test`") else: - failed.append("nextflow.config does not contain configuration profile `test`") + failed.append( + "nextflow.config does not contain configuration profile `test`" + ) # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json ignore_defaults = [] @@ -404,7 +451,9 @@ def nextflow_config(self): schema_default = str(schema.schema_defaults[param_name]) config_default = str(self.nf_config[param]) if config_default is not None and config_default == schema_default: - passed.append(f"Config default value correct: {param}= {schema_default}") + passed.append( + f"Config default value correct: {param}= {schema_default}" + ) else: failed.append( f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." From 47abfc2a2dbf9f8ae42a70bc5b833e1836fdb121 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 1 Jul 2024 14:44:55 +0200 Subject: [PATCH 066/574] Add linting check for check_ params and continue removing from everywhere (not finished) --- nf_core/pipeline-template/conf/test.config | 5 --- nf_core/pipeline-template/nextflow.config | 6 ---- .../pipeline-template/nextflow_schema.json | 35 ------------------- 3 files changed, 46 deletions(-) diff --git a/nf_core/pipeline-template/conf/test.config b/nf_core/pipeline-template/conf/test.config index 2b9715efb6..0f1d974101 100644 --- a/nf_core/pipeline-template/conf/test.config +++ b/nf_core/pipeline-template/conf/test.config @@ -22,11 +22,6 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index d575c6186f..7d9040104c 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -50,12 +50,6 @@ params { config_profile_url = null {%- endif %} - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 18bad71b76..07a90f6259 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -124,41 +124,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", From 2e1dc9650ebe24935ff1545627f579e46e6a967f Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 3 Jul 2024 09:47:39 +0200 Subject: [PATCH 067/574] Remove deprecated syntax --- nf_core/pipeline-template/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index 1fd6a5b275..c13a0d24e1 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -11,8 +11,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS From 20089357e17aa5c850476a61fe67a8e6033ce17a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 3 Jul 2024 07:48:32 +0000 Subject: [PATCH 068/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6d3f4f088c..63f4bdc43b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) +- Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 034ae05e7db07fcef41a711464ecea65bfdf5e6c Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 3 Jul 2024 09:57:33 +0200 Subject: [PATCH 069/574] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63f4bdc43b..a13ccc2291 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ ### Template - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985)) +- Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) ### Linting @@ -38,7 +39,6 @@ - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) -- Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From d863c4d8fcbe3ef41ae8f0d16f1c314e0c45a6d9 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 08:29:04 +0000 Subject: [PATCH 070/574] add default limit_output argument for write_diff_file & print_diff --- nf_core/modules/modules_differ.py | 24 +++++++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index dc2b163dd4..fb1fc31dc1 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -133,6 +133,7 @@ def write_diff_file( for_git=True, dsp_from_dir=None, dsp_to_dir=None, + limit_output=False, ): """ Writes the diffs of a module to the diff file. @@ -174,8 +175,14 @@ def write_diff_file( else: fh.write(f"Changes in module '{Path(repo_path, module)}'\n") - for _, (diff_status, diff) in diffs.items(): - if diff_status != ModulesDiffer.DiffEnum.UNCHANGED: + for file, (diff_status, diff) in diffs.items(): + if diff_status == ModulesDiffer.DiffEnum.UNCHANGED: + # The files are identical + fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") + elif limit_output and file != "main.nf": + # Skip printing the diff for files other than main.nf + fh.write(f"Changes in '{Path(module, file)}' not shown\n") + else: # The file has changed write the diff lines to the file for line in diff: fh.write(line) @@ -219,7 +226,15 @@ def append_modules_json_diff(diff_path, old_modules_json, new_modules_json, modu @staticmethod def print_diff( - module, repo_path, from_dir, to_dir, current_version=None, new_version=None, dsp_from_dir=None, dsp_to_dir=None + module, + repo_path, + from_dir, + to_dir, + current_version=None, + new_version=None, + dsp_from_dir=None, + dsp_to_dir=None, + limit_output=False, ): """ Prints the diffs between two module versions to the terminal @@ -261,6 +276,9 @@ def print_diff( elif diff_status == ModulesDiffer.DiffEnum.REMOVED: # The file was removed between the commits log.info(f"'{Path(dsp_from_dir, file)}' was removed") + elif limit_output and file != "main.nf": + # Skip printing the diff for files other than main.nf + log.info(f"Changes in '{Path(module, file)}' not shown") else: # The file has changed log.info(f"Changes in '{Path(module, file)}':") From 5b9d3f54eb206b835035ccdc349130026c42eb9d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 3 Jul 2024 08:33:07 +0000 Subject: [PATCH 071/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6d3f4f088c..fc4a233491 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) +- add default limit_output argument for write_diff_file & print_diff ([#3047](https://github.com/nf-core/tools/pull/3047)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 1997ee41a974e26dd6e9de7e30e91ff0240fe49f Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 09:38:23 +0000 Subject: [PATCH 072/574] adding limit_output to click --- nf_core/__main__.py | 10 ++++++++++ nf_core/components/update.py | 17 +++++++++++++---- nf_core/modules/update.py | 2 ++ 3 files changed, 25 insertions(+), 4 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index ea0018e2af..86bcde86e3 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1214,6 +1214,14 @@ def modules_install(ctx, tool, dir, prompt, force, sha): default=False, help="Prompt for the version of the module", ) +@click.option( + "-l", + "--limit-output", + "limit_output", + is_flag=True, + default=False, + help="Limit ouput to only the difference in main.nf", +) @click.option("-s", "--sha", type=str, metavar="", help="Install module at commit SHA") @click.option( "-a", @@ -1256,6 +1264,7 @@ def modules_update( preview, save_diff, update_deps, + limit_output, ): """ Update DSL2 modules within a pipeline. @@ -1277,6 +1286,7 @@ def modules_update( ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], + limit_output, ) exit_status = module_install.update(tool) if not exit_status and install_all: diff --git a/nf_core/components/update.py b/nf_core/components/update.py index a54c47232e..3c3cdca6c9 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -38,6 +38,7 @@ def __init__( remote_url=None, branch=None, no_pull=False, + limit_output=False, ): super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.force = force @@ -76,7 +77,7 @@ def _parameter_checks(self): if not self.has_valid_directory(): raise UserWarning("The command was not run in a valid pipeline directory.") - def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool: + def update(self, component=None, silent=False, updated=None, check_diff_exist=True, limit_output=False) -> bool: """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline. If updating a subworkflow: updates all modules used in that subworkflow. @@ -231,6 +232,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr version, dsp_from_dir=component_dir, dsp_to_dir=component_dir, + limit_output=limit_output, ) updated.append(component) except UserWarning as e: @@ -271,6 +273,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr version, dsp_from_dir=component_dir, dsp_to_dir=component_dir, + limit_output=limit_output, ) # Ask the user if they want to install the component @@ -875,7 +878,9 @@ def get_components_to_update(self, component): return modules_to_update, subworkflows_to_update - def update_linked_components(self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True): + def update_linked_components( + self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True, limit_output=False + ): """ Update modules and subworkflows linked to the component being updated. """ @@ -883,7 +888,9 @@ def update_linked_components(self, modules_to_update, subworkflows_to_update, up if s_update in updated: continue original_component_type, original_update_all = self._change_component_type("subworkflows") - self.update(s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist) + self.update( + s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output + ) self._reset_component_type(original_component_type, original_update_all) for m_update in modules_to_update: @@ -891,7 +898,9 @@ def update_linked_components(self, modules_to_update, subworkflows_to_update, up continue original_component_type, original_update_all = self._change_component_type("modules") try: - self.update(m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist) + self.update( + m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output + ) except LookupError as e: # If the module to be updated is not available, check if there has been a name change if "not found in list of available" in str(e): diff --git a/nf_core/modules/update.py b/nf_core/modules/update.py index 9d53bf2017..f6cf5235a4 100644 --- a/nf_core/modules/update.py +++ b/nf_core/modules/update.py @@ -15,6 +15,7 @@ def __init__( remote_url=None, branch=None, no_pull=False, + limit_output=False, ): super().__init__( pipeline_dir, @@ -29,4 +30,5 @@ def __init__( remote_url, branch, no_pull, + limit_output, ) From 6dd57dfb8c2052a851ec0bae220aecf33ba95f37 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 3 Jul 2024 11:32:23 +0200 Subject: [PATCH 073/574] pin all textual versions --- requirements-dev.txt | 4 +- requirements.txt | 2 +- tests/__snapshots__/test_create_app.ambr | 3014 +++++++++++----------- 3 files changed, 1510 insertions(+), 1510 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index fa98655aed..ebfbb530d3 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -6,7 +6,7 @@ responses ruff Sphinx sphinx-rtd-theme -textual-dev>=1.2.1 +textual-dev==1.5.1 mypy types-PyYAML types-requests @@ -15,5 +15,5 @@ types-Markdown types-PyYAML types-requests types-setuptools -pytest-textual-snapshot +pytest-textual-snapshot==0.4.0 ruff diff --git a/requirements.txt b/requirements.txt index 0574083fd0..ccfc1bc9c1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -21,6 +21,6 @@ requests_cache rich-click==1.8.* rich>=13.3.1 tabulate -textual>=0.63.1 +textual==0.71.0 trogon pdiff diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 89a5699f4d..aa1d36f97a 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -22,253 +22,253 @@ font-weight: 700; } - .terminal-2299698092-matrix { + .terminal-3554683094-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2299698092-title { + .terminal-3554683094-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2299698092-r1 { fill: #c5c8c6 } - .terminal-2299698092-r2 { fill: #e3e3e3 } - .terminal-2299698092-r3 { fill: #989898 } - .terminal-2299698092-r4 { fill: #e1e1e1 } - .terminal-2299698092-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2299698092-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-2299698092-r7 { fill: #1e1e1e } - .terminal-2299698092-r8 { fill: #008139 } - .terminal-2299698092-r9 { fill: #121212 } - .terminal-2299698092-r10 { fill: #e2e2e2 } - .terminal-2299698092-r11 { fill: #787878 } - .terminal-2299698092-r12 { fill: #454a50 } - .terminal-2299698092-r13 { fill: #7ae998 } - .terminal-2299698092-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-2299698092-r15 { fill: #0a180e;font-weight: bold } - .terminal-2299698092-r16 { fill: #000000 } - .terminal-2299698092-r17 { fill: #fea62b;font-weight: bold } - .terminal-2299698092-r18 { fill: #a7a9ab } - .terminal-2299698092-r19 { fill: #e2e3e3 } + .terminal-3554683094-r1 { fill: #c5c8c6 } + .terminal-3554683094-r2 { fill: #e3e3e3 } + .terminal-3554683094-r3 { fill: #989898 } + .terminal-3554683094-r4 { fill: #e1e1e1 } + .terminal-3554683094-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3554683094-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-3554683094-r7 { fill: #1e1e1e } + .terminal-3554683094-r8 { fill: #008139 } + .terminal-3554683094-r9 { fill: #121212 } + .terminal-3554683094-r10 { fill: #e2e2e2 } + .terminal-3554683094-r11 { fill: #787878 } + .terminal-3554683094-r12 { fill: #454a50 } + .terminal-3554683094-r13 { fill: #7ae998 } + .terminal-3554683094-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-3554683094-r15 { fill: #0a180e;font-weight: bold } + .terminal-3554683094-r16 { fill: #000000 } + .terminal-3554683094-r17 { fill: #fea62b;font-weight: bold } + .terminal-3554683094-r18 { fill: #a7a9ab } + .terminal-3554683094-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Next  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -298,256 +298,256 @@ font-weight: 700; } - .terminal-4102136482-matrix { + .terminal-2636639375-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4102136482-title { + .terminal-2636639375-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4102136482-r1 { fill: #c5c8c6 } - .terminal-4102136482-r2 { fill: #e3e3e3 } - .terminal-4102136482-r3 { fill: #989898 } - .terminal-4102136482-r4 { fill: #e1e1e1 } - .terminal-4102136482-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4102136482-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-4102136482-r7 { fill: #1e1e1e } - .terminal-4102136482-r8 { fill: #0f4e2a } - .terminal-4102136482-r9 { fill: #0178d4 } - .terminal-4102136482-r10 { fill: #a7a7a7 } - .terminal-4102136482-r11 { fill: #787878 } - .terminal-4102136482-r12 { fill: #e2e2e2 } - .terminal-4102136482-r13 { fill: #121212 } - .terminal-4102136482-r14 { fill: #454a50 } - .terminal-4102136482-r15 { fill: #7ae998 } - .terminal-4102136482-r16 { fill: #e2e3e3;font-weight: bold } - .terminal-4102136482-r17 { fill: #0a180e;font-weight: bold } - .terminal-4102136482-r18 { fill: #000000 } - .terminal-4102136482-r19 { fill: #008139 } - .terminal-4102136482-r20 { fill: #fea62b;font-weight: bold } - .terminal-4102136482-r21 { fill: #a7a9ab } - .terminal-4102136482-r22 { fill: #e2e3e3 } + .terminal-2636639375-r1 { fill: #c5c8c6 } + .terminal-2636639375-r2 { fill: #e3e3e3 } + .terminal-2636639375-r3 { fill: #989898 } + .terminal-2636639375-r4 { fill: #e1e1e1 } + .terminal-2636639375-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2636639375-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-2636639375-r7 { fill: #1e1e1e } + .terminal-2636639375-r8 { fill: #0f4e2a } + .terminal-2636639375-r9 { fill: #0178d4 } + .terminal-2636639375-r10 { fill: #a7a7a7 } + .terminal-2636639375-r11 { fill: #787878 } + .terminal-2636639375-r12 { fill: #e2e2e2 } + .terminal-2636639375-r13 { fill: #121212 } + .terminal-2636639375-r14 { fill: #454a50 } + .terminal-2636639375-r15 { fill: #7ae998 } + .terminal-2636639375-r16 { fill: #e2e3e3;font-weight: bold } + .terminal-2636639375-r17 { fill: #0a180e;font-weight: bold } + .terminal-2636639375-r18 { fill: #000000 } + .terminal-2636639375-r19 { fill: #008139 } + .terminal-2636639375-r20 { fill: #fea62b;font-weight: bold } + .terminal-2636639375-r21 { fill: #a7a9ab } + .terminal-2636639375-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core                                     ▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Next  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -577,251 +577,251 @@ font-weight: 700; } - .terminal-2364166316-matrix { + .terminal-1889064188-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2364166316-title { + .terminal-1889064188-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2364166316-r1 { fill: #c5c8c6 } - .terminal-2364166316-r2 { fill: #e3e3e3 } - .terminal-2364166316-r3 { fill: #989898 } - .terminal-2364166316-r4 { fill: #e1e1e1 } - .terminal-2364166316-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2364166316-r6 { fill: #4ebf71;text-decoration: underline; } - .terminal-2364166316-r7 { fill: #4ebf71;font-style: italic;;text-decoration: underline; } - .terminal-2364166316-r8 { fill: #e1e1e1;font-style: italic; } - .terminal-2364166316-r9 { fill: #7ae998 } - .terminal-2364166316-r10 { fill: #008139 } - .terminal-2364166316-r11 { fill: #507bb3 } - .terminal-2364166316-r12 { fill: #dde6ed;font-weight: bold } - .terminal-2364166316-r13 { fill: #001541 } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Choose pipeline type - - - - - Choose "nf-core" if:Choose "Custom" if: - - ● You want your pipeline to be part of the ● Your pipeline will never be part of  - nf-core communitynf-core - ● You think that there's an outside chance ● You want full control over all features  - that it ever could be part of nf-corethat are included from the template  - (including those that are mandatory for  - nf-core). - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Custom - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - What's the difference? - - Choosing "nf-core" effectively pre-selects the following template features: - - ● GitHub Actions continuous-integration configuration files: - ▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) - ▪ Code formatting checks with Prettier - ▪ Auto-fix linting functionality using @nf-core-bot - ▪ Marking old issues as stale - ● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Choose pipeline type + + + + + Choose "nf-core" if:Choose "Custom" if: + + ● You want your pipeline to be part of the ● Your pipeline will never be part of  + nf-core communitynf-core + ● You think that there's an outside chance ● You want full control over all features  + that it ever could be part of nf-corethat are included from the template  + (including those that are mandatory for  + nf-core). + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  nf-core  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Custom  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + What's the difference? + +   Choosing "nf-core" effectively pre-selects the following template features: + + ● GitHub Actions continuous-integration configuration files: + ▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) + ▪ Code formatting checks with Prettier + ▪ Auto-fix linting functionality using @nf-core-bot + ▪ Marking old issues as stale + ● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -851,257 +851,257 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline will Hide help - ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github CI The pipeline will Show help - ▊▁▁▁▁▁▁▁▁▎testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing▄▄ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github badgesThe README.md fileShow help - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing▄▄ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -1131,251 +1131,251 @@ font-weight: 700; } - .terminal-1422742483-matrix { + .terminal-3764053845-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1422742483-title { + .terminal-3764053845-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1422742483-r1 { fill: #c5c8c6 } - .terminal-1422742483-r2 { fill: #e3e3e3 } - .terminal-1422742483-r3 { fill: #989898 } - .terminal-1422742483-r4 { fill: #e1e1e1 } - .terminal-1422742483-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1422742483-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-1422742483-r7 { fill: #1e1e1e } - .terminal-1422742483-r8 { fill: #008139 } - .terminal-1422742483-r9 { fill: #e2e2e2 } - .terminal-1422742483-r10 { fill: #454a50 } - .terminal-1422742483-r11 { fill: #7ae998 } - .terminal-1422742483-r12 { fill: #e2e3e3;font-weight: bold } - .terminal-1422742483-r13 { fill: #0a180e;font-weight: bold } - .terminal-1422742483-r14 { fill: #000000 } - .terminal-1422742483-r15 { fill: #fea62b;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Final details - - - - First version of the pipelinePath to the output directory where the pipeline  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created - ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackFinish - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Final details + + + + First version of the pipelinePath to the output directory where the pipeline  + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎will be created + ▊1.0.0dev▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊.                                           ▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Finish  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -1405,258 +1405,258 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + +   Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +   the code to it. + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ Show  + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊••••••••••••                    ▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline                              ▎ + ▊nf-core                                 ▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Create GitHub repo  Finish without creating a repo  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -1686,254 +1686,254 @@ font-weight: 700; } - .terminal-396289429-matrix { + .terminal-1078212293-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-396289429-title { + .terminal-1078212293-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-396289429-r1 { fill: #c5c8c6 } - .terminal-396289429-r2 { fill: #e3e3e3 } - .terminal-396289429-r3 { fill: #989898 } - .terminal-396289429-r4 { fill: #e1e1e1 } - .terminal-396289429-r5 { fill: #4ebf71;font-weight: bold } - .terminal-396289429-r6 { fill: #98e024 } - .terminal-396289429-r7 { fill: #626262 } - .terminal-396289429-r8 { fill: #9d65ff } - .terminal-396289429-r9 { fill: #fd971f } - .terminal-396289429-r10 { fill: #d2d2d2 } - .terminal-396289429-r11 { fill: #82aaff } - .terminal-396289429-r12 { fill: #eeffff } - .terminal-396289429-r13 { fill: #18954b } - .terminal-396289429-r14 { fill: #e2e2e2 } - .terminal-396289429-r15 { fill: #969696;font-weight: bold } - .terminal-396289429-r16 { fill: #7ae998 } - .terminal-396289429-r17 { fill: #008139 } - .terminal-396289429-r18 { fill: #fea62b;font-weight: bold } - .terminal-396289429-r19 { fill: #a7a9ab } - .terminal-396289429-r20 { fill: #e2e3e3 } + .terminal-1078212293-r1 { fill: #c5c8c6 } + .terminal-1078212293-r2 { fill: #e3e3e3 } + .terminal-1078212293-r3 { fill: #989898 } + .terminal-1078212293-r4 { fill: #e1e1e1 } + .terminal-1078212293-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1078212293-r6 { fill: #98e024 } + .terminal-1078212293-r7 { fill: #626262 } + .terminal-1078212293-r8 { fill: #9d65ff } + .terminal-1078212293-r9 { fill: #fd971f } + .terminal-1078212293-r10 { fill: #d2d2d2 } + .terminal-1078212293-r11 { fill: #82aaff } + .terminal-1078212293-r12 { fill: #eeffff } + .terminal-1078212293-r13 { fill: #18954b } + .terminal-1078212293-r14 { fill: #e2e2e2 } + .terminal-1078212293-r15 { fill: #969696;font-weight: bold } + .terminal-1078212293-r16 { fill: #7ae998 } + .terminal-1078212293-r17 { fill: #008139 } + .terminal-1078212293-r18 { fill: #fea62b;font-weight: bold } + .terminal-1078212293-r19 { fill: #a7a9ab } + .terminal-1078212293-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - HowTo create a GitHub repository - - - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - - If you would like to create the GitHub repository later, you can do it manually by following  - these steps: - -  1. Create a new GitHub repository -  2. Add the remote to your local repository: - - - cd<pipeline_directory> - gitremoteaddorigingit@github.com:<username>/<repo_name>.git - - -  3. Push the code to the remote: - - - gitpush--allorigin - - - ▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + HowTo create a GitHub repository + + + +                                           ,--./,-. +           ___     __   __   __   ___     /,-._.--~\  +     |\ | |__  __ /  ` /  \ |__) |__         }  { +     | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                           `._,._,' + +   If you would like to create the GitHub repository later, you can do it manually by following  +   these steps: + +  1. Create a new GitHub repository +  2. Add the remote to your local repository: + + + cd <pipeline_directory> + git remote add origin git@github.com:<username>/<repo_name>.git + + +  3. Push the code to the remote: + + + git push --all origin + + + ▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Close  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -1963,247 +1963,247 @@ font-weight: 700; } - .terminal-3492397142-matrix { + .terminal-2285979206-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3492397142-title { + .terminal-2285979206-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3492397142-r1 { fill: #c5c8c6 } - .terminal-3492397142-r2 { fill: #e3e3e3 } - .terminal-3492397142-r3 { fill: #989898 } - .terminal-3492397142-r4 { fill: #e1e1e1 } - .terminal-3492397142-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3492397142-r6 { fill: #7ae998 } - .terminal-3492397142-r7 { fill: #507bb3 } - .terminal-3492397142-r8 { fill: #dde6ed;font-weight: bold } - .terminal-3492397142-r9 { fill: #008139 } - .terminal-3492397142-r10 { fill: #001541 } - .terminal-3492397142-r11 { fill: #fea62b;font-weight: bold } - .terminal-3492397142-r12 { fill: #a7a9ab } - .terminal-3492397142-r13 { fill: #e2e3e3 } + .terminal-2285979206-r1 { fill: #c5c8c6 } + .terminal-2285979206-r2 { fill: #e3e3e3 } + .terminal-2285979206-r3 { fill: #989898 } + .terminal-2285979206-r4 { fill: #e1e1e1 } + .terminal-2285979206-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2285979206-r6 { fill: #7ae998 } + .terminal-2285979206-r7 { fill: #507bb3 } + .terminal-2285979206-r8 { fill: #dde6ed;font-weight: bold } + .terminal-2285979206-r9 { fill: #008139 } + .terminal-2285979206-r10 { fill: #001541 } + .terminal-2285979206-r11 { fill: #fea62b;font-weight: bold } + .terminal-2285979206-r12 { fill: #a7a9ab } + .terminal-2285979206-r13 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - - After creating the pipeline template locally, we can create a GitHub repository and push the  - code to it. - - Do you want to create a GitHub repository? - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + +   After creating the pipeline template locally, we can create a GitHub repository and push the  +   code to it. + +   Do you want to create a GitHub repository? + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Create GitHub repo  Finish without creating a repo  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,254 @@ font-weight: 700; } - .terminal-4082092032-matrix { + .terminal-1445899181-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4082092032-title { + .terminal-1445899181-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4082092032-r1 { fill: #c5c8c6 } - .terminal-4082092032-r2 { fill: #e3e3e3 } - .terminal-4082092032-r3 { fill: #989898 } - .terminal-4082092032-r4 { fill: #e1e1e1 } - .terminal-4082092032-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4082092032-r6 { fill: #1e1e1e } - .terminal-4082092032-r7 { fill: #507bb3 } - .terminal-4082092032-r8 { fill: #e2e2e2 } - .terminal-4082092032-r9 { fill: #808080 } - .terminal-4082092032-r10 { fill: #dde6ed;font-weight: bold } - .terminal-4082092032-r11 { fill: #001541 } - .terminal-4082092032-r12 { fill: #454a50 } - .terminal-4082092032-r13 { fill: #7ae998 } - .terminal-4082092032-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-4082092032-r15 { fill: #0a180e;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline will Show help - ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github CI testsThe pipeline will Show help - ▊▁▁▁▁▁▁▁▁▎include several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for  - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add Github badgesThe README.md file Show help - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include GitHub - badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Add configuration The pipeline will Show help - ▊▁▁▁▁▁▁▁▁▎filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles containing - custom parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI tests        The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for  + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file  Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include GitHub + badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles containing + custom parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2510,254 +2510,254 @@ font-weight: 700; } - .terminal-1639960877-matrix { + .terminal-388991162-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1639960877-title { + .terminal-388991162-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1639960877-r1 { fill: #c5c8c6 } - .terminal-1639960877-r2 { fill: #e3e3e3 } - .terminal-1639960877-r3 { fill: #989898 } - .terminal-1639960877-r4 { fill: #e1e1e1 } - .terminal-1639960877-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1639960877-r6 { fill: #1e1e1e } - .terminal-1639960877-r7 { fill: #507bb3 } - .terminal-1639960877-r8 { fill: #e2e2e2 } - .terminal-1639960877-r9 { fill: #808080 } - .terminal-1639960877-r10 { fill: #dde6ed;font-weight: bold } - .terminal-1639960877-r11 { fill: #001541 } - .terminal-1639960877-r12 { fill: #454a50 } - .terminal-1639960877-r13 { fill: #7ae998 } - .terminal-1639960877-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-1639960877-r15 { fill: #0a180e;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎Use reference The pipeline will Show help - ▊▁▁▁▁▁▁▁▁▎genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from iGenomes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackContinue - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from iGenomes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2787,255 +2787,255 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - GitHub organisationWorkflow name - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - A short description of your pipeline. - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - Name of the main author / authors - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackNext - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Basic details + + + + GitHub organisationWorkflow name + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core                                     ▎▊Pipeline Name▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Must be lowercase without  + punctuation. + + A short description of your pipeline. + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Description▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + + Name of the main author / authors + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊Author(s)▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + Value error, Cannot be left empty. + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Next  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  @@ -3065,253 +3065,253 @@ font-weight: 700; } - .terminal-3787732750-matrix { + .terminal-3972722241-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3787732750-title { + .terminal-3972722241-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3787732750-r1 { fill: #c5c8c6 } - .terminal-3787732750-r2 { fill: #e3e3e3 } - .terminal-3787732750-r3 { fill: #989898 } - .terminal-3787732750-r4 { fill: #98e024 } - .terminal-3787732750-r5 { fill: #626262 } - .terminal-3787732750-r6 { fill: #9d65ff } - .terminal-3787732750-r7 { fill: #fd971f } - .terminal-3787732750-r8 { fill: #e1e1e1 } - .terminal-3787732750-r9 { fill: #4ebf71;font-weight: bold } - .terminal-3787732750-r10 { fill: #e1e1e1;text-decoration: underline; } - .terminal-3787732750-r11 { fill: #18954b } - .terminal-3787732750-r12 { fill: #e2e2e2 } - .terminal-3787732750-r13 { fill: #e2e2e2;text-decoration: underline; } - .terminal-3787732750-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - - - - Welcome to the nf-core pipeline creation wizard - - This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - - The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core  - pipelines. - - ▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with - ▌the community as early as possible; ideally before you start on your pipeline! See the  - ▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go! - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + +                                           ,--./,-. +           ___     __   __   __   ___     /,-._.--~\  +     |\ | |__  __ /  ` /  \ |__) |__         }  { +     | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                           `._,._,' + + + + Welcome to the nf-core pipeline creation wizard + +   This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +   The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    +   pipelines. + + ▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with + ▌the community as early as possible; ideally before you start on your pipeline! See the  + ▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Let's go!  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + +  d Toggle dark mode  q Quit  From 27475f73ccb5dd4529f4e1b6a5f80841ee802b00 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:16:29 +0000 Subject: [PATCH 074/574] add to subworkflow as well --- nf_core/__main__.py | 10 ++++++++++ nf_core/components/update.py | 2 +- nf_core/subworkflows/update.py | 2 ++ 3 files changed, 13 insertions(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 86bcde86e3..815c98c1eb 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2157,6 +2157,14 @@ def subworkflows_remove(ctx, dir, subworkflow): metavar="", help="Install subworkflow at commit SHA", ) +@click.option( + "-l", + "--limit-output", + "limit_output", + is_flag=True, + default=False, + help="Limit ouput to only the difference in main.nf", +) @click.option( "-a", "--all", @@ -2198,6 +2206,7 @@ def subworkflows_update( preview, save_diff, update_deps, + limit_output, ): """ Update DSL2 subworkflow within a pipeline. @@ -2219,6 +2228,7 @@ def subworkflows_update( ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], + limit_output, ) exit_status = subworkflow_install.update(subworkflow) if not exit_status and install_all: diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 3c3cdca6c9..8beab7a925 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -40,7 +40,7 @@ def __init__( no_pull=False, limit_output=False, ): - super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) + super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull, limit_output) self.force = force self.prompt = prompt self.sha = sha diff --git a/nf_core/subworkflows/update.py b/nf_core/subworkflows/update.py index 3cd4ad59fd..9b6bf16928 100644 --- a/nf_core/subworkflows/update.py +++ b/nf_core/subworkflows/update.py @@ -15,6 +15,7 @@ def __init__( remote_url=None, branch=None, no_pull=False, + limit_output=False, ): super().__init__( pipeline_dir, @@ -29,4 +30,5 @@ def __init__( remote_url, branch, no_pull, + limit_output, ) From 2cb6946d100c0b61e238668b0b2b889decd64a28 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:18:49 +0000 Subject: [PATCH 075/574] better changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9355b3ca12..b01e13ce83 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,7 +39,7 @@ - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) -- add default limit_output argument for write_diff_file & print_diff ([#3047](https://github.com/nf-core/tools/pull/3047)) +- Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From f35b1f0f840b8324e0cf6c795538cd372cc5c99c Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:40:16 +0000 Subject: [PATCH 076/574] debug prints --- nf_core/components/update.py | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 8beab7a925..72c053cfd8 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -40,18 +40,20 @@ def __init__( no_pull=False, limit_output=False, ): - super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull, limit_output) + super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.force = force self.prompt = prompt self.sha = sha self.update_all = update_all self.show_diff = show_diff self.save_diff_fn = save_diff_fn + self.limit_output = limit_output self.update_deps = update_deps self.component = None self.update_config = None self.modules_json = ModulesJson(self.dir) self.branch = branch + log.info(f"init component limit_output ={self.limit_output}") def _parameter_checks(self): """Checks the compatibilty of the supplied parameters. @@ -77,7 +79,7 @@ def _parameter_checks(self): if not self.has_valid_directory(): raise UserWarning("The command was not run in a valid pipeline directory.") - def update(self, component=None, silent=False, updated=None, check_diff_exist=True, limit_output=False) -> bool: + def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool: """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline. If updating a subworkflow: updates all modules used in that subworkflow. @@ -232,7 +234,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr version, dsp_from_dir=component_dir, dsp_to_dir=component_dir, - limit_output=limit_output, + limit_output=self.limit_output, ) updated.append(component) except UserWarning as e: @@ -264,6 +266,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr self.manage_changes_in_linked_components(component, modules_to_update, subworkflows_to_update) elif self.show_diff: + log.info(f"limit_output ModulesDiffer: {self.limit_output}") ModulesDiffer.print_diff( component, modules_repo.repo_path, @@ -273,7 +276,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr version, dsp_from_dir=component_dir, dsp_to_dir=component_dir, - limit_output=limit_output, + limit_output=self.limit_output, ) # Ask the user if they want to install the component @@ -879,7 +882,11 @@ def get_components_to_update(self, component): return modules_to_update, subworkflows_to_update def update_linked_components( - self, modules_to_update, subworkflows_to_update, updated=None, check_diff_exist=True, limit_output=False + self, + modules_to_update, + subworkflows_to_update, + updated=None, + check_diff_exist=True, ): """ Update modules and subworkflows linked to the component being updated. @@ -889,7 +896,10 @@ def update_linked_components( continue original_component_type, original_update_all = self._change_component_type("subworkflows") self.update( - s_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output + s_update, + silent=True, + updated=updated, + check_diff_exist=check_diff_exist, ) self._reset_component_type(original_component_type, original_update_all) @@ -899,7 +909,10 @@ def update_linked_components( original_component_type, original_update_all = self._change_component_type("modules") try: self.update( - m_update, silent=True, updated=updated, check_diff_exist=check_diff_exist, limit_output=limit_output + m_update, + silent=True, + updated=updated, + check_diff_exist=check_diff_exist, ) except LookupError as e: # If the module to be updated is not available, check if there has been a name change From f7e830381e6e22e2c08083c1c3bb29df79c0841c Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:47:52 +0000 Subject: [PATCH 077/574] fix file suffix checking --- nf_core/components/update.py | 2 -- nf_core/modules/modules_differ.py | 4 ++-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 72c053cfd8..37e3f62126 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -53,7 +53,6 @@ def __init__( self.update_config = None self.modules_json = ModulesJson(self.dir) self.branch = branch - log.info(f"init component limit_output ={self.limit_output}") def _parameter_checks(self): """Checks the compatibilty of the supplied parameters. @@ -266,7 +265,6 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr self.manage_changes_in_linked_components(component, modules_to_update, subworkflows_to_update) elif self.show_diff: - log.info(f"limit_output ModulesDiffer: {self.limit_output}") ModulesDiffer.print_diff( component, modules_repo.repo_path, diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index fb1fc31dc1..5273857705 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -179,7 +179,7 @@ def write_diff_file( if diff_status == ModulesDiffer.DiffEnum.UNCHANGED: # The files are identical fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") - elif limit_output and file != "main.nf": + elif limit_output and not (file.endswith(".nf")): # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(module, file)}' not shown\n") else: @@ -276,7 +276,7 @@ def print_diff( elif diff_status == ModulesDiffer.DiffEnum.REMOVED: # The file was removed between the commits log.info(f"'{Path(dsp_from_dir, file)}' was removed") - elif limit_output and file != "main.nf": + elif limit_output and not (file.endswith(".nf")): # Skip printing the diff for files other than main.nf log.info(f"Changes in '{Path(module, file)}' not shown") else: From bc8d096e71cebeb22d7e9ac7a10455901e715e5f Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:49:21 +0000 Subject: [PATCH 078/574] remove unnecessary() --- nf_core/modules/modules_differ.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index 5273857705..7de68b9cc5 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -179,7 +179,7 @@ def write_diff_file( if diff_status == ModulesDiffer.DiffEnum.UNCHANGED: # The files are identical fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") - elif limit_output and not (file.endswith(".nf")): + elif limit_output and not file.endswith(".nf"): # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(module, file)}' not shown\n") else: @@ -276,7 +276,7 @@ def print_diff( elif diff_status == ModulesDiffer.DiffEnum.REMOVED: # The file was removed between the commits log.info(f"'{Path(dsp_from_dir, file)}' was removed") - elif limit_output and not (file.endswith(".nf")): + elif limit_output and not file.endswith(".nf"): # Skip printing the diff for files other than main.nf log.info(f"Changes in '{Path(module, file)}' not shown") else: From e5e34aacbe20b77df6c9f178cbe220a8161b45a5 Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 11:55:25 +0000 Subject: [PATCH 079/574] use suffix instead --- nf_core/modules/modules_differ.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index 7de68b9cc5..f97c7dce5b 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -179,7 +179,7 @@ def write_diff_file( if diff_status == ModulesDiffer.DiffEnum.UNCHANGED: # The files are identical fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") - elif limit_output and not file.endswith(".nf"): + elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(module, file)}' not shown\n") else: @@ -276,7 +276,7 @@ def print_diff( elif diff_status == ModulesDiffer.DiffEnum.REMOVED: # The file was removed between the commits log.info(f"'{Path(dsp_from_dir, file)}' was removed") - elif limit_output and not file.endswith(".nf"): + elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf log.info(f"Changes in '{Path(module, file)}' not shown") else: From a61da2d98f1c24905d09a87e7e4efb83c6fbb35c Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 12:02:26 +0000 Subject: [PATCH 080/574] add method argument docs --- nf_core/modules/modules_differ.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index f97c7dce5b..34966b2ffd 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -155,6 +155,7 @@ def write_diff_file( adds a/ and b/ prefixes to the file paths dsp_from_dir (str | Path): The 'from' directory displayed in the diff dsp_to_dir (str | Path): The 'to' directory displayed in the diff + limit_output (bool): If true, don't write the diff for files other than main.nf """ if dsp_from_dir is None: dsp_from_dir = from_dir @@ -181,7 +182,7 @@ def write_diff_file( fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf - fh.write(f"Changes in '{Path(module, file)}' not shown\n") + fh.write(f"Changes in '{Path(module, file)}' but not shown\n") else: # The file has changed write the diff lines to the file for line in diff: @@ -249,6 +250,7 @@ def print_diff( new_version (str): The version of the module the diff is computed against dsp_from_dir (str | Path): The 'from' directory displayed in the diff dsp_to_dir (str | Path): The 'to' directory displayed in the diff + limit_output (bool): If true, don't print the diff for files other than main.nf """ if dsp_from_dir is None: dsp_from_dir = from_dir @@ -278,7 +280,7 @@ def print_diff( log.info(f"'{Path(dsp_from_dir, file)}' was removed") elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf - log.info(f"Changes in '{Path(module, file)}' not shown") + log.info(f"Changes in '{Path(module, file)}' but not shown") else: # The file has changed log.info(f"Changes in '{Path(module, file)}':") From 5a2c09e67cfc814659f258ddd32bd842d4967d93 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 27 Jun 2024 12:02:43 +0200 Subject: [PATCH 081/574] move pipeline commands to functions to avoid duplication --- nf_core/__main__.py | 1111 +++++++++++++++++++------------------------ 1 file changed, 494 insertions(+), 617 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index ea0018e2af..06712acb78 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -196,40 +196,46 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file): } -# nf-core pipelines subcommands -@nf_core_cli.group() -@click.pass_context -def pipelines(ctx): +## nf-core pipelines command functions ## + + +# nf-core pipelines bump-version +def pipelines_bump_version(ctx, new_version, dir, nextflow): """ - Commands to manage nf-core pipelines. + Update nf-core pipeline version number. + + The pipeline version number is mentioned in a lot of different places + in nf-core pipelines. This tool updates the version for you automatically, + so that you don't accidentally miss any. + + Should be used for each pipeline release, and again for the next + development version after release. + + As well as the pipeline version, you can also change the required version of Nextflow. """ - # ensure that ctx.obj exists and is a dict (in case `cli()` is called - # by means other than the `if` block below) - ctx.ensure_object(dict) + from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.utils import Pipeline, is_pipeline_directory + + try: + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Make a pipeline object and load config etc + pipeline_obj = Pipeline(dir) + pipeline_obj._load() + + # Bump the pipeline version number + if not nextflow: + bump_pipeline_version(pipeline_obj, new_version) + else: + bump_nextflow_version(pipeline_obj, new_version) + except UserWarning as e: + log.error(e) + sys.exit(1) # nf-core pipelines create -@pipelines.command("create") -@click.pass_context -@click.option( - "-n", - "--name", - type=str, - help="The name of your new pipeline", -) -@click.option("-d", "--description", type=str, help="A short description of your pipeline") -@click.option("-a", "--author", type=str, help="Name of the main author(s)") -@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use") -@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") -@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") -@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -@click.option( - "--organisation", - type=str, - default="nf-core", - help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", -) -def create_pipeline(ctx, name, description, author, version, force, outdir, template_yaml, organisation): +def pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): """ Create a new pipeline using the nf-core template. @@ -273,62 +279,7 @@ def create_pipeline(ctx, name, description, author, version, force, outdir, temp # nf-core pipelines lint -@pipelines.command("lint") -@click.option( - "-d", - "--dir", - type=click.Path(exists=True), - default=".", - help=r"Pipeline directory [dim]\[default: current working directory][/]", -) -@click.option( - "--release", - is_flag=True, - default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" - and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") - and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", - help="Execute additional checks for release-ready workflows.", -) -@click.option( - "-f", - "--fix", - type=str, - metavar="", - multiple=True, - help="Attempt to automatically fix specified lint test", -) -@click.option( - "-k", - "--key", - type=str, - metavar="", - multiple=True, - help="Run only these lint tests", -) -@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") -@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") -@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") -@click.option( - "--markdown", - type=str, - metavar="", - help="File to write linting results to (Markdown)", -) -@click.option( - "--json", - type=str, - metavar="", - help="File to write linting results to (JSON)", -) -@click.option( - "--sort-by", - type=click.Choice(["module", "test"]), - default="test", - help="Sort lint output by module or test name.", - show_default=True, -) -@click.pass_context -def lint_pipeline( +def pipelines_lint( ctx, dir, release, @@ -389,6 +340,394 @@ def lint_pipeline( sys.exit(1) +# nf-core pipelines download +def pipelines_download( + ctx, + pipeline, + revision, + outdir, + compress, + force, + tower, + platform, + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, +): + """ + Download a pipeline, nf-core/configs and pipeline singularity images. + + Collects all files in a single archive and configures the downloaded + workflow to use relative paths to the configs and singularity images. + """ + from nf_core.pipelines.download import DownloadWorkflow + + if tower: + log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") + + dl = DownloadWorkflow( + pipeline, + revision, + outdir, + compress, + force, + tower or platform, # True if either specified + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, + ) + dl.download_workflow() + + +# nf-core pipelines create-params-file +def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden): + """ + Build a parameter file for a pipeline. + + Uses the pipeline schema file to generate a YAML parameters file. + Parameters are set to the pipeline defaults and descriptions are shown in comments. + After the output file is generated, it can then be edited as needed before + passing to nextflow using the `-params-file` option. + + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory. + """ + builder = ParamsFileBuilder(pipeline, revision) + + if not builder.write_params_file(output, show_hidden=show_hidden, force=force): + sys.exit(1) + + +# nf-core pipelines launch +def pipelines_launch( + ctx, + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ + Launch a pipeline using a web GUI or command line prompts. + + Uses the pipeline schema file to collect inputs for all available pipeline + parameters. Parameter names, descriptions and help text are shown. + The pipeline schema is used to validate all inputs as they are entered. + + When finished, saves a file with the selected parameters which can be + passed to Nextflow using the -params-file option. + + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory or an ID from the nf-core web launch tool. + """ + from nf_core.pipelines.launch import Launch + + launcher = Launch( + pipeline, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, + id, + ) + if not launcher.launch_pipeline(): + sys.exit(1) + + +# nf-core pipelines list +def pipelines_list(ctx, keywords, sort, json, show_archived): + """ + List available nf-core pipelines with local info. + + Checks the web for a list of nf-core pipelines with their latest releases. + Shows which nf-core pipelines you have pulled locally and whether they are up to date. + """ + from nf_core.pipelines.list import list_workflows + + stdout.print(list_workflows(keywords, sort, json, show_archived)) + + +# nf-core pipelines sync +def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): + """ + Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. + + To keep nf-core pipelines up to date with improvements in the main + template, we use a method of synchronisation that uses a special + git branch called [cyan i]TEMPLATE[/]. + + This command updates the [cyan i]TEMPLATE[/] branch with the latest version of + the nf-core template, so that these updates can be synchronised with + the pipeline. It is run automatically for all pipelines when ever a + new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + """ + from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Sync the given pipeline dir + sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + try: + sync_obj.sync() + except (SyncExceptionError, PullRequestExceptionError) as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines create-logo +def pipelines_create_logo(logo_text, dir, name, theme, width, format, force): + """ + Generate a logo with the nf-core logo template. + + This command generates an nf-core pipeline logo, using the supplied + """ + from nf_core.pipelines.create_logo import create_logo + + try: + if dir == ".": + dir = Path.cwd() + logo_path = create_logo(logo_text, dir, name, theme, width, format, force) + # Print path to logo relative to current working directory + try: + logo_path = Path(logo_path).relative_to(Path.cwd()) + except ValueError: + logo_path = Path(logo_path) + log.info(f"Created logo: [magenta]{logo_path}[/]") + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines schema validate +def pipelines_schema_validate(pipeline, params): + """ + Validate a set of parameters against a pipeline schema. + + Nextflow can be run using the -params-file flag, which loads + script parameters from a JSON file. + + This command takes such a file and validates it against the pipeline + schema, checking whether all schema rules are satisfied. + """ + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(pipeline) + # Load and check schema + schema_obj.load_lint_schema() + except AssertionError as e: + log.error(e) + sys.exit(1) + schema_obj.load_input_params(params) + try: + schema_obj.validate_params() + except AssertionError: + sys.exit(1) + + +# nf-core pipelines schema build +def pipelines_schema_build(dir, no_prompts, web_only, url): + """ + Interactively build a pipeline schema from Nextflow params. + + Automatically detects parameters from the pipeline config and main.nf and + compares these to the pipeline schema. Prompts to add or remove parameters + if the two do not match one another. + + Once all parameters are accounted for, can launch a web GUI tool on the + https://nf-co.re website where you can annotate and organise parameters. + Listens for this to be completed and saves the updated schema. + """ + from nf_core.pipelines.schema import PipelineSchema + + try: + schema_obj = PipelineSchema() + if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: + sys.exit(1) + except (UserWarning, AssertionError) as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines schema lint +def pipelines_schema_lint(schema_path): + """ + Check that a given pipeline schema is valid. + + Checks whether the pipeline schema validates as JSON Schema Draft 7 + and adheres to the additional nf-core pipelines schema requirements. + + This function runs as part of the nf-core pipelines lint command, this is a convenience + command that does just the schema linting nice and quickly. + + If no schema path is provided, "nextflow_schema.json" will be used (if it exists). + """ + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(schema_path) + schema_obj.load_lint_schema() + # Validate title and description - just warnings as schema should still work fine + try: + schema_obj.validate_schema_title_description() + except AssertionError as e: + log.warning(e) + except AssertionError: + sys.exit(1) + + +# nf-core pipelines schema docs +def pipelines_schema_docs(schema_path, output, format, force, columns): + """ + Outputs parameter documentation for a pipeline schema. + """ + if not os.path.exists(schema_path): + log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") + sys.exit(1) + + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + # Assume we're in a pipeline dir root if schema path not set + schema_obj.get_schema_path(schema_path) + schema_obj.load_schema() + schema_obj.print_documentation(output, format, force, columns.split(",")) + + +# nf-core pipelines subcommands +@nf_core_cli.group() +@click.pass_context +def pipelines(ctx): + """ + Commands to manage nf-core pipelines. + """ + # ensure that ctx.obj exists and is a dict (in case `cli()` is called + # by means other than the `if` block below) + ctx.ensure_object(dict) + + +# nf-core pipelines create +@pipelines.command("create") +@click.pass_context +@click.option( + "-n", + "--name", + type=str, + help="The name of your new pipeline", +) +@click.option("-d", "--description", type=str, help="A short description of your pipeline") +@click.option("-a", "--author", type=str, help="Name of the main author(s)") +@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use") +@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") +@click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") +@click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") +@click.option( + "--organisation", + type=str, + default="nf-core", + help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", +) +def command_pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): + """ + Create a new pipeline using the nf-core template. + """ + pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation) + + +# nf-core pipelines lint +@pipelines.command("lint") +@click.option( + "-d", + "--dir", + type=click.Path(exists=True), + default=".", + help=r"Pipeline directory [dim]\[default: current working directory][/]", +) +@click.option( + "--release", + is_flag=True, + default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master" + and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/") + and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools", + help="Execute additional checks for release-ready workflows.", +) +@click.option( + "-f", + "--fix", + type=str, + metavar="", + multiple=True, + help="Attempt to automatically fix specified lint test", +) +@click.option( + "-k", + "--key", + type=str, + metavar="", + multiple=True, + help="Run only these lint tests", +) +@click.option("-p", "--show-passed", is_flag=True, help="Show passing tests on the command line") +@click.option("-i", "--fail-ignored", is_flag=True, help="Convert ignored tests to failures") +@click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures") +@click.option( + "--markdown", + type=str, + metavar="", + help="File to write linting results to (Markdown)", +) +@click.option( + "--json", + type=str, + metavar="", + help="File to write linting results to (JSON)", +) +@click.option( + "--sort-by", + type=click.Choice(["module", "test"]), + default="test", + help="Sort lint output by module or test name.", + show_default=True, +) +@click.pass_context +def command_pipelines_lint( + ctx, + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + markdown, + json, + sort_by, +): + """ + Check pipeline code against nf-core guidelines. + """ + pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) + + # nf-core pipelines download @pipelines.command("download") @click.argument("pipeline", required=False, metavar="") @@ -467,7 +806,7 @@ def lint_pipeline( help="Number of parallel image downloads", ) @click.pass_context -def download_pipeline( +def command_pipelines_download( ctx, pipeline, revision, @@ -486,22 +825,16 @@ def download_pipeline( ): """ Download a pipeline, nf-core/configs and pipeline singularity images. - - Collects all files in a single archive and configures the downloaded - workflow to use relative paths to the configs and singularity images. """ - from nf_core.pipelines.download import DownloadWorkflow - - if tower: - log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") - - dl = DownloadWorkflow( + pipelines_download( + ctx, pipeline, revision, outdir, compress, force, - tower or platform, # True if either specified + tower, + platform, download_configuration, tag, container_system, @@ -510,7 +843,6 @@ def download_pipeline( container_cache_index, parallel_downloads, ) - dl.download_workflow() # nf-core pipelines create-params-file @@ -534,22 +866,11 @@ def download_pipeline( help="Show hidden params which don't normally need changing", ) @click.pass_context -def create_params_file_pipeline(ctx, pipeline, revision, output, force, show_hidden): +def command_pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden): """ Build a parameter file for a pipeline. - - Uses the pipeline schema file to generate a YAML parameters file. - Parameters are set to the pipeline defaults and descriptions are shown in comments. - After the output file is generated, it can then be edited as needed before - passing to nextflow using the `-params-file` option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory. """ - builder = ParamsFileBuilder(pipeline, revision) - - if not builder.write_params_file(output, show_hidden=show_hidden, force=force): - sys.exit(1) + pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden) # nf-core pipelines launch @@ -599,7 +920,7 @@ def create_params_file_pipeline(ctx, pipeline, revision, output, force, show_hid help="Customise the builder URL (for development work)", ) @click.pass_context -def launch_pipeline( +def command_pipelines_launch( ctx, pipeline, id, @@ -613,32 +934,8 @@ def launch_pipeline( ): """ Launch a pipeline using a web GUI or command line prompts. - - Uses the pipeline schema file to collect inputs for all available pipeline - parameters. Parameter names, descriptions and help text are shown. - The pipeline schema is used to validate all inputs as they are entered. - - When finished, saves a file with the selected parameters which can be - passed to Nextflow using the -params-file option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory or an ID from the nf-core web launch tool. """ - from nf_core.pipelines.launch import Launch - - launcher = Launch( - pipeline, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, - id, - ) - if not launcher.launch_pipeline(): - sys.exit(1) + pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url) # nf-core pipelines list @@ -654,16 +951,11 @@ def launch_pipeline( @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") @click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") @click.pass_context -def list_pipelines(ctx, keywords, sort, json, show_archived): +def command_pipelines_list(ctx, keywords, sort, json, show_archived): """ List available nf-core pipelines with local info. - - Checks the web for a list of nf-core pipelines with their latest releases. - Shows which nf-core pipelines you have pulled locally and whether they are up to date. """ - from nf_core.pipelines.list import list_workflows - - stdout.print(list_workflows(keywords, sort, json, show_archived)) + pipelines_list(ctx, keywords, sort, json, show_archived) # nf-core pipelines sync @@ -698,32 +990,11 @@ def list_pipelines(ctx, keywords, sort, json, show_archived): @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - - To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special - git branch called [cyan i]TEMPLATE[/]. - - This command updates the [cyan i]TEMPLATE[/] branch with the latest version of - the nf-core template, so that these updates can be synchronised with - the pipeline. It is run automatically for all pipelines when ever a - new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ - from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Sync the given pipeline dir - sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) - try: - sync_obj.sync() - except (SyncExceptionError, PullRequestExceptionError) as e: - log.error(e) - sys.exit(1) + pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) # nf-core pipelines bump-version @@ -744,38 +1015,11 @@ def sync_pipeline(ctx, dir, from_branch, pull_request, github_repository, userna default=False, help="Bump required nextflow version instead of pipeline version", ) -def bump_version_pipeline(ctx, new_version, dir, nextflow): +def command_pipelines_bump_version(ctx, new_version, dir, nextflow): """ - Update nf-core pipeline version number. - - The pipeline version number is mentioned in a lot of different places - in nf-core pipelines. This tool updates the version for you automatically, - so that you don't accidentally miss any. - - Should be used for each pipeline release, and again for the next - development version after release. - - As well as the pipeline version, you can also change the required version of Nextflow. + Update nf-core pipeline version number with `nf-core pipelines bump-version`. """ - from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version - from nf_core.utils import Pipeline, is_pipeline_directory - - try: - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Make a pipeline object and load config etc - pipeline_obj = Pipeline(dir) - pipeline_obj._load() - - # Bump the pipeline version number - if not nextflow: - bump_pipeline_version(pipeline_obj, new_version) - else: - bump_nextflow_version(pipeline_obj, new_version) - except UserWarning as e: - log.error(e) - sys.exit(1) + pipelines_bump_version(ctx, new_version, dir, nextflow) # nf-core pipelines create-logo @@ -816,50 +1060,11 @@ def bump_version_pipeline(ctx, new_version, dir, nextflow): default=False, help="Overwrite any files if they already exist", ) -def logo_pipeline(logo_text, dir, name, theme, width, format, force): +def command_pipelines_create_logo(logo_text, dir, name, theme, width, format, force): """ Generate a logo with the nf-core logo template. - - This command generates an nf-core pipeline logo, using the supplied - """ - from nf_core.pipelines.create_logo import create_logo - - try: - if dir == ".": - dir = Path.cwd() - logo_path = create_logo(logo_text, dir, name, theme, width, format, force) - # Print path to logo relative to current working directory - try: - logo_path = Path(logo_path).relative_to(Path.cwd()) - except ValueError: - logo_path = Path(logo_path) - log.info(f"Created logo: [magenta]{logo_path}[/]") - except UserWarning as e: - log.error(e) - sys.exit(1) - - -# nf-core licences -@nf_core_cli.command() -@click.argument("pipeline", required=True, metavar="") -@click.option("--json", is_flag=True, default=False, help="Print output in JSON") -def licences(pipeline, json): - """ - List software licences for a given workflow (DSL1 only). - - Checks the pipeline environment.yml file which lists all conda software packages, which is not available for DSL2 workflows. Therefore, this command only supports DSL1 workflows (for now). - Each of these is queried against the anaconda.org API to find the licence. - Package name, version and licence is printed to the command line. """ - from nf_core.licences import WorkflowLicences - - lic = WorkflowLicences(pipeline) - lic.as_json = json - try: - stdout.print(lic.run_licences()) - except LookupError as e: - log.error(e) - sys.exit(1) + pipelines_create_logo(logo_text, dir, name, theme, width, format, force) # nf-core pipelines schema subcommands @@ -878,31 +1083,11 @@ def pipeline_schema(): @pipeline_schema.command("validate") @click.argument("pipeline", required=True, metavar="") @click.argument("params", type=click.Path(exists=True), required=True, metavar="") -def validate_schema(pipeline, params): +def command_pipelines_schema_validate(pipeline, params): """ Validate a set of parameters against a pipeline schema. - - Nextflow can be run using the -params-file flag, which loads - script parameters from a JSON file. - - This command takes such a file and validates it against the pipeline - schema, checking whether all schema rules are satisfied. """ - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(pipeline) - # Load and check schema - schema_obj.load_lint_schema() - except AssertionError as e: - log.error(e) - sys.exit(1) - schema_obj.load_input_params(params) - try: - schema_obj.validate_params() - except AssertionError: - sys.exit(1) + pipelines_schema_validate(pipeline, params) # nf-core pipelines schema build @@ -930,27 +1115,11 @@ def validate_schema(pipeline, params): default="https://nf-co.re/pipeline_schema_builder", help="Customise the builder URL (for development work)", ) -def build_schema(dir, no_prompts, web_only, url): +def command_pipelines_schema_build(dir, no_prompts, web_only, url): """ Interactively build a pipeline schema from Nextflow params. - - Automatically detects parameters from the pipeline config and main.nf and - compares these to the pipeline schema. Prompts to add or remove parameters - if the two do not match one another. - - Once all parameters are accounted for, can launch a web GUI tool on the - https://nf-co.re website where you can annotate and organise parameters. - Listens for this to be completed and saves the updated schema. """ - from nf_core.pipelines.schema import PipelineSchema - - try: - schema_obj = PipelineSchema() - if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: - sys.exit(1) - except (UserWarning, AssertionError) as e: - log.error(e) - sys.exit(1) + pipelines_schema_build(dir, no_prompts, web_only, url) # nf-core pipelines schema lint @@ -961,31 +1130,11 @@ def build_schema(dir, no_prompts, web_only, url): default="nextflow_schema.json", metavar="", ) -def lint_schema(schema_path): +def command_pipelines_schema_lint(schema_path): """ Check that a given pipeline schema is valid. - - Checks whether the pipeline schema validates as JSON Schema Draft 7 - and adheres to the additional nf-core pipelines schema requirements. - - This function runs as part of the nf-core pipelines lint command, this is a convenience - command that does just the schema linting nice and quickly. - - If no schema path is provided, "nextflow_schema.json" will be used (if it exists). """ - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(schema_path) - schema_obj.load_lint_schema() - # Validate title and description - just warnings as schema should still work fine - try: - schema_obj.validate_schema_title_description() - except AssertionError as e: - log.warning(e) - except AssertionError: - sys.exit(1) + pipelines_schema_lint(schema_path) # nf-core pipelines schema docs @@ -1020,21 +1169,11 @@ def lint_schema(schema_path): help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)", default="parameter,description,type,default,required,hidden", ) -def docs_schema(schema_path, output, format, force, columns): +def command_pipelines_schema_docs(schema_path, output, format, force, columns): """ Outputs parameter documentation for a pipeline schema. """ - if not os.path.exists(schema_path): - log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") - sys.exit(1) - - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - # Assume we're in a pipeline dir root if schema path not set - schema_obj.get_schema_path(schema_path) - schema_obj.load_schema() - schema_obj.print_documentation(output, format, force, columns.split(",")) + pipelines_schema_docs(schema_path, output, format, force, columns) # nf-core modules subcommands @@ -2225,10 +2364,7 @@ def subworkflows_update( @nf_core_cli.group(deprecated=True, hidden=True) def schema(): """ - Suite of tools for developers to manage pipeline schema. - - All nf-core pipelines should have a nextflow_schema.json file in their - root directory that describes the different pipeline parameters. + DEPRECATED """ pass @@ -2237,35 +2373,14 @@ def schema(): @schema.command("validate", deprecated=True) @click.argument("pipeline", required=True, metavar="") @click.argument("params", type=click.Path(exists=True), required=True, metavar="") -def validate(pipeline, params): +def command_schema_validate(pipeline, params): """ DEPRECATED - Validate a set of parameters against a pipeline schema. - - Nextflow can be run using the -params-file flag, which loads - script parameters from a JSON file. - - This command takes such a file and validates it against the pipeline - schema, checking whether all schema rules are satisfied. """ log.warning( "The `[magenta]nf-core schema validate[/]` command is deprecated. Use `[magenta]nf-core pipelines schema validate[/]` instead." ) - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(pipeline) - # Load and check schema - schema_obj.load_lint_schema() - except AssertionError as e: - log.error(e) - sys.exit(1) - schema_obj.load_input_params(params) - try: - schema_obj.validate_params() - except AssertionError: - sys.exit(1) + pipelines_schema_validate(pipeline, params) # nf-core schema build (deprecated) @@ -2293,31 +2408,14 @@ def validate(pipeline, params): default="https://nf-co.re/pipeline_schema_builder", help="Customise the builder URL (for development work)", ) -def build(dir, no_prompts, web_only, url): +def command_schema_build(dir, no_prompts, web_only, url): """ DEPRECATED - Interactively build a pipeline schema from Nextflow params. - - Automatically detects parameters from the pipeline config and main.nf and - compares these to the pipeline schema. Prompts to add or remove parameters - if the two do not match one another. - - Once all parameters are accounted for, can launch a web GUI tool on the - https://nf-co.re website where you can annotate and organise parameters. - Listens for this to be completed and saves the updated schema. """ log.warning( "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead." ) - from nf_core.pipelines.schema import PipelineSchema - - try: - schema_obj = PipelineSchema() - if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: - sys.exit(1) - except (UserWarning, AssertionError) as e: - log.error(e) - sys.exit(1) + pipelines_schema_build(dir, no_prompts, web_only, url) # nf-core schema lint (deprecated) @@ -2328,35 +2426,14 @@ def build(dir, no_prompts, web_only, url): default="nextflow_schema.json", metavar="", ) -def schema_lint(schema_path): +def command_schema_lint(schema_path): """ DEPRECATED - Check that a given pipeline schema is valid. - - Checks whether the pipeline schema validates as JSON Schema Draft 7 - and adheres to the additional nf-core schema requirements. - - This function runs as part of the nf-core lint command, this is a convenience - command that does just the schema linting nice and quickly. - - If no schema path is provided, "nextflow_schema.json" will be used (if it exists). """ log.warning( "The `[magenta]nf-core schema lint[/]` command is deprecated. Use `[magenta]nf-core pipelines schema lint[/]` instead." ) - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(schema_path) - schema_obj.load_lint_schema() - # Validate title and description - just warnings as schema should still work fine - try: - schema_obj.validate_schema_title_description() - except AssertionError as e: - log.warning(e) - except AssertionError: - sys.exit(1) + pipelines_schema_lint(schema_path) # nf-core schema docs (deprecated) @@ -2391,25 +2468,14 @@ def schema_lint(schema_path): help="CSV list of columns to include in the parameter tables (parameter,description,type,default,required,hidden)", default="parameter,description,type,default,required,hidden", ) -def docs(schema_path, output, format, force, columns): +def command_schema_docs(schema_path, output, format, force, columns): """ DEPRECATED - Outputs parameter documentation for a pipeline schema. """ log.warning( "The `[magenta]nf-core schema docs[/]` command is deprecated. Use `[magenta]nf-core pipelines schema docs[/]` instead." ) - if not os.path.exists(schema_path): - log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") - sys.exit(1) - - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - # Assume we're in a pipeline dir root if schema path not set - schema_obj.get_schema_path(schema_path) - schema_obj.load_schema() - schema_obj.print_documentation(output, format, force, columns.split(",")) + pipelines_schema_docs(schema_path, output, format, force, columns) # nf-core create-logo (deprecated) @@ -2450,35 +2516,18 @@ def docs(schema_path, output, format, force, columns): default=False, help="Overwrite any files if they already exist", ) -def logo(logo_text, dir, name, theme, width, format, force): +def command_create_logo(logo_text, dir, name, theme, width, format, force): """ DEPRECATED - Generate a logo with the nf-core logo template. - - This command generates an nf-core pipeline logo, using the supplied """ log.warning( "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead." ) - from nf_core.pipelines.create_logo import create_logo - - try: - if dir == ".": - dir = Path.cwd() - logo_path = create_logo(logo_text, dir, name, theme, width, format, force) - # Print path to logo relative to current working directory - try: - logo_path = Path(logo_path).relative_to(Path.cwd()) - except ValueError: - logo_path = Path(logo_path) - log.info(f"Created logo: [magenta]{logo_path}[/]") - except UserWarning as e: - log.error(e) - sys.exit(1) + pipelines_create_logo(logo_text, dir, name, theme, width, format, force) # nf-core sync (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) +@nf_core_cli.command("sync", hidden=True, deprecated=True) @click.option( "-d", "--dir", @@ -2508,40 +2557,19 @@ def logo(logo_text, dir, name, theme, width, format, force): @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def command_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ DEPRECATED - Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - - To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special - git branch called [cyan i]TEMPLATE[/]. - - This command updates the [cyan i]TEMPLATE[/] branch with the latest version of - the nf-core template, so that these updates can be synchronised with - the pipeline. It is run automatically for all pipelines when ever a - new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. """ log.warning( "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead." ) - from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Sync the given pipeline dir - sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) - try: - sync_obj.sync() - except (SyncExceptionError, PullRequestExceptionError) as e: - log.error(e) - sys.exit(1) + pipelines_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) # nf-core bump-version (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) +@nf_core_cli.command("bump-version", hidden=True, deprecated=True) +@click.pass_context @click.argument("new_version", default="") @click.option( "-d", @@ -2557,42 +2585,14 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y default=False, help="Bump required nextflow version instead of pipeline version", ) -def bump_version(new_version, dir, nextflow): +def command_bump_version(ctx, new_version, dir, nextflow): """ DEPRECATED - Update nf-core pipeline version number. - - The pipeline version number is mentioned in a lot of different places - in nf-core pipelines. This tool updates the version for you automatically, - so that you don't accidentally miss any. - - Should be used for each pipeline release, and again for the next - development version after release. - - As well as the pipeline version, you can also change the required version of Nextflow. """ log.warning( "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead." ) - from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version - from nf_core.utils import Pipeline, is_pipeline_directory - - try: - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Make a pipeline object and load config etc - pipeline_obj = Pipeline(dir) - pipeline_obj._load() - - # Bump the pipeline version number - if not nextflow: - bump_pipeline_version(pipeline_obj, new_version) - else: - bump_nextflow_version(pipeline_obj, new_version) - except UserWarning as e: - log.error(e) - sys.exit(1) + pipelines_bump_version(ctx, new_version, dir, nextflow) # nf-core list (deprecated) @@ -2607,24 +2607,19 @@ def bump_version(new_version, dir, nextflow): ) @click.option("--json", is_flag=True, default=False, help="Print full output as JSON") @click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows") -def list(keywords, sort, json, show_archived): +@click.pass_context +def command_list(ctx, keywords, sort, json, show_archived): """ DEPRECATED - List available nf-core pipelines with local info. - - Checks the web for a list of nf-core pipelines with their latest releases. - Shows which nf-core pipelines you have pulled locally and whether they are up to date. """ log.warning( "The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead." ) - from nf_core.pipelines.list import list_workflows - - stdout.print(list_workflows(keywords, sort, json, show_archived)) + pipelines_list(ctx, keywords, sort, json, show_archived) # nf-core launch (deprecated) -@nf_core_cli.command(deprecated=True, hidden=True) +@nf_core_cli.command("launch", deprecated=True, hidden=True) @click.argument("pipeline", required=False, metavar="") @click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") @click.option("-i", "--id", help="ID for web-gui launch parameter set") @@ -2669,7 +2664,9 @@ def list(keywords, sort, json, show_archived): default="https://nf-co.re/launch", help="Customise the builder URL (for development work)", ) -def launch( +@click.pass_context +def command_launch( + ctx, pipeline, id, revision, @@ -2682,40 +2679,15 @@ def launch( ): """ DEPRECATED - Launch a pipeline using a web GUI or command line prompts. - - Uses the pipeline schema file to collect inputs for all available pipeline - parameters. Parameter names, descriptions and help text are shown. - The pipeline schema is used to validate all inputs as they are entered. - - When finished, saves a file with the selected parameters which can be - passed to Nextflow using the -params-file option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory or an ID from the nf-core web launch tool. """ log.warning( "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead." ) - from nf_core.pipelines.launch import Launch - - launcher = Launch( - pipeline, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, - id, - ) - if not launcher.launch_pipeline(): - sys.exit(1) + pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url) # nf-core create-params-file (deprecated) -@nf_core_cli.command(deprecated=True, hidden=True) +@nf_core_cli.command("create-params-file", deprecated=True, hidden=True) @click.argument("pipeline", required=False, metavar="") @click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") @click.option( @@ -2734,30 +2706,18 @@ def launch( default=False, help="Show hidden params which don't normally need changing", ) -def create_params_file(pipeline, revision, output, force, show_hidden): +def command_create_params_file(pipeline, revision, output, force, show_hidden): """ DEPRECATED - Build a parameter file for a pipeline. - - Uses the pipeline schema file to generate a YAML parameters file. - Parameters are set to the pipeline defaults and descriptions are shown in comments. - After the output file is generated, it can then be edited as needed before - passing to nextflow using the `-params-file` option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory. """ log.warning( "The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead." ) - builder = ParamsFileBuilder(pipeline, revision) - - if not builder.write_params_file(output, show_hidden=show_hidden, force=force): - sys.exit(1) + pipelines_create_params_file(pipeline, revision, output, force, show_hidden) # nf-core download (deprecated) -@nf_core_cli.command(deprecated=True, hidden=True) +@nf_core_cli.command("download", deprecated=True, hidden=True) @click.argument("pipeline", required=False, metavar="") @click.option( "-r", @@ -2830,7 +2790,9 @@ def create_params_file(pipeline, revision, output, force, show_hidden): default=4, help="Number of parallel image downloads", ) -def download( +@click.pass_context +def command_download( + ctx, pipeline, revision, outdir, @@ -2848,26 +2810,19 @@ def download( ): """ DEPRECATED - Download a pipeline, nf-core/configs and pipeline singularity images. - - Collects all files in a single archive and configures the downloaded - workflow to use relative paths to the configs and singularity images. """ log.warning( "The `[magenta]nf-core download[/]` command is deprecated. Use `[magenta]nf-core pipelines download[/]` instead." ) - from nf_core.pipelines.download import DownloadWorkflow - - if tower: - log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") - - dl = DownloadWorkflow( + pipelines_download( + ctx, pipeline, revision, outdir, compress, force, - tower or platform, # True if either specified + tower, + platform, download_configuration, tag, container_system, @@ -2876,11 +2831,10 @@ def download( container_cache_index, parallel_downloads, ) - dl.download_workflow() # nf-core lint (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) +@nf_core_cli.command("lint", hidden=True, deprecated=True) @click.option( "-d", "--dir", @@ -2935,7 +2889,7 @@ def download( show_default=True, ) @click.pass_context -def lint( +def command_lint( ctx, dir, release, @@ -2950,58 +2904,15 @@ def lint( ): """ DEPRECATED - Check pipeline code against nf-core guidelines. - - Runs a large number of automated tests to ensure that the supplied pipeline - meets the nf-core guidelines. Documentation of all lint tests can be found - on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] - - You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. - See the documentation for details. """ log.warning( "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead." ) - from nf_core.pipelines.lint import run_linting - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory is a pipeline - try: - is_pipeline_directory(dir) - except UserWarning as e: - log.error(e) - sys.exit(1) - - # Run the lint tests! - try: - lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - sort_by, - markdown, - json, - ctx.obj["hide_progress"], - ) - swf_failed = 0 - if subworkflow_lint_obj is not None: - swf_failed = len(subworkflow_lint_obj.failed) - if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: - sys.exit(1) - except AssertionError as e: - log.critical(e) - sys.exit(1) - except UserWarning as e: - log.error(e) - sys.exit(1) + pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) # nf-core create (deprecated) -@nf_core_cli.command(hidden=True, deprecated=True) +@nf_core_cli.command("create", hidden=True, deprecated=True) @click.option( "-n", "--name", @@ -3021,49 +2932,15 @@ def lint( default="nf-core", help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", ) -def create(name, description, author, version, force, outdir, template_yaml, plain, organisation): +@click.pass_context +def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation): """ DEPRECATED - Create a new pipeline using the nf-core template. - - Uses the nf-core template to make a skeleton Nextflow pipeline with all required - files, boilerplate code and best-practices. """ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - from nf_core.pipelines.create import PipelineCreateApp - from nf_core.pipelines.create.create import PipelineCreate - - if (name and description and author) or (template_yaml): - # If all command arguments are used, run without the interactive interface - try: - create_obj = PipelineCreate( - name, - description, - author, - version=version, - force=force, - outdir=outdir, - template_config=template_yaml, - organisation=organisation, - ) - create_obj.init_pipeline() - except UserWarning as e: - log.error(e) - sys.exit(1) - elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": - log.error( - "[red]Partial arguments supplied.[/] " - "Run without [i]any[/] arguments for an interactive interface, " - "or with at least name + description + author to use non-interactively." - ) - sys.exit(1) - else: - log.info("Launching interactive nf-core pipeline creation tool.") - app = PipelineCreateApp() - app.run() - sys.exit(app.return_code or 0) + pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation) # Main script is being run - launch the CLI From d52c1afe959a9dcd50c20bddf9a17cef3d146426 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 27 Jun 2024 15:16:51 +0000 Subject: [PATCH 082/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa079aaa85..170ee8511c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- move pipeline commands to functions to avoid duplication ([#3039](https://github.com/nf-core/tools/pull/3039)) - Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) From 9b965e1981309e46b336fdb927b321c702dbc536 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 3 Jul 2024 16:22:22 +0200 Subject: [PATCH 083/574] move command functions to separate files --- nf_core/__main__.py | 969 ++++--------------------------- nf_core/commands_modules.py | 340 +++++++++++ nf_core/commands_pipelines.py | 429 ++++++++++++++ nf_core/commands_subworkflows.py | 259 +++++++++ 4 files changed, 1127 insertions(+), 870 deletions(-) create mode 100644 nf_core/commands_modules.py create mode 100644 nf_core/commands_pipelines.py create mode 100644 nf_core/commands_subworkflows.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 06712acb78..f9d6a6aebb 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -4,7 +4,6 @@ import logging import os import sys -from pathlib import Path import rich import rich.console @@ -14,9 +13,47 @@ from trogon import tui from nf_core import __version__ +from nf_core.commands_modules import ( + modules_bump_versions, + modules_create, + modules_info, + modules_install, + modules_lint, + modules_list_local, + modules_list_remote, + modules_patch, + modules_remove, + modules_test, + modules_update, +) +from nf_core.commands_pipelines import ( + pipelines_bump_version, + pipelines_create, + pipelines_create_logo, + pipelines_create_params_file, + pipelines_download, + pipelines_launch, + pipelines_lint, + pipelines_list, + pipelines_schema_build, + pipelines_schema_docs, + pipelines_schema_lint, + pipelines_schema_validate, + pipelines_sync, +) +from nf_core.commands_subworkflows import ( + subworkflows_create, + subworkflows_info, + subworkflows_install, + subworkflows_lint, + subworkflows_list_local, + subworkflows_list_remote, + subworkflows_remove, + subworkflows_test, + subworkflows_update, +) from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE from nf_core.pipelines.download import DownloadError -from nf_core.pipelines.params_file import ParamsFileBuilder from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir # Set up logging as the root logger @@ -196,423 +233,6 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file): } -## nf-core pipelines command functions ## - - -# nf-core pipelines bump-version -def pipelines_bump_version(ctx, new_version, dir, nextflow): - """ - Update nf-core pipeline version number. - - The pipeline version number is mentioned in a lot of different places - in nf-core pipelines. This tool updates the version for you automatically, - so that you don't accidentally miss any. - - Should be used for each pipeline release, and again for the next - development version after release. - - As well as the pipeline version, you can also change the required version of Nextflow. - """ - from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version - from nf_core.utils import Pipeline, is_pipeline_directory - - try: - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Make a pipeline object and load config etc - pipeline_obj = Pipeline(dir) - pipeline_obj._load() - - # Bump the pipeline version number - if not nextflow: - bump_pipeline_version(pipeline_obj, new_version) - else: - bump_nextflow_version(pipeline_obj, new_version) - except UserWarning as e: - log.error(e) - sys.exit(1) - - -# nf-core pipelines create -def pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): - """ - Create a new pipeline using the nf-core template. - - Uses the nf-core template to make a skeleton Nextflow pipeline with all required - files, boilerplate code and best-practices. - \n\n - Run without any command line arguments to use an interactive interface. - """ - from nf_core.pipelines.create import PipelineCreateApp - from nf_core.pipelines.create.create import PipelineCreate - - if (name and description and author) or (template_yaml): - # If all command arguments are used, run without the interactive interface - try: - create_obj = PipelineCreate( - name, - description, - author, - version=version, - force=force, - outdir=outdir, - template_config=template_yaml, - organisation=organisation, - ) - create_obj.init_pipeline() - except UserWarning as e: - log.error(e) - sys.exit(1) - elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": - log.error( - "[red]Partial arguments supplied.[/] " - "Run without [i]any[/] arguments for an interactive interface, " - "or with at least name + description + author to use non-interactively." - ) - sys.exit(1) - else: - log.info("Launching interactive nf-core pipeline creation tool.") - app = PipelineCreateApp() - app.run() - sys.exit(app.return_code or 0) - - -# nf-core pipelines lint -def pipelines_lint( - ctx, - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - markdown, - json, - sort_by, -): - """ - Check pipeline code against nf-core guidelines. - - Runs a large number of automated tests to ensure that the supplied pipeline - meets the nf-core guidelines. Documentation of all lint tests can be found - on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] - - You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. - See the documentation for details. - """ - from nf_core.pipelines.lint import run_linting - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory is a pipeline - try: - is_pipeline_directory(dir) - except UserWarning as e: - log.error(e) - sys.exit(1) - - # Run the lint tests! - try: - lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( - dir, - release, - fix, - key, - show_passed, - fail_ignored, - fail_warned, - sort_by, - markdown, - json, - ctx.obj["hide_progress"], - ) - swf_failed = 0 - if subworkflow_lint_obj is not None: - swf_failed = len(subworkflow_lint_obj.failed) - if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: - sys.exit(1) - except AssertionError as e: - log.critical(e) - sys.exit(1) - except UserWarning as e: - log.error(e) - sys.exit(1) - - -# nf-core pipelines download -def pipelines_download( - ctx, - pipeline, - revision, - outdir, - compress, - force, - tower, - platform, - download_configuration, - tag, - container_system, - container_library, - container_cache_utilisation, - container_cache_index, - parallel_downloads, -): - """ - Download a pipeline, nf-core/configs and pipeline singularity images. - - Collects all files in a single archive and configures the downloaded - workflow to use relative paths to the configs and singularity images. - """ - from nf_core.pipelines.download import DownloadWorkflow - - if tower: - log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") - - dl = DownloadWorkflow( - pipeline, - revision, - outdir, - compress, - force, - tower or platform, # True if either specified - download_configuration, - tag, - container_system, - container_library, - container_cache_utilisation, - container_cache_index, - parallel_downloads, - ) - dl.download_workflow() - - -# nf-core pipelines create-params-file -def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden): - """ - Build a parameter file for a pipeline. - - Uses the pipeline schema file to generate a YAML parameters file. - Parameters are set to the pipeline defaults and descriptions are shown in comments. - After the output file is generated, it can then be edited as needed before - passing to nextflow using the `-params-file` option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory. - """ - builder = ParamsFileBuilder(pipeline, revision) - - if not builder.write_params_file(output, show_hidden=show_hidden, force=force): - sys.exit(1) - - -# nf-core pipelines launch -def pipelines_launch( - ctx, - pipeline, - id, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, -): - """ - Launch a pipeline using a web GUI or command line prompts. - - Uses the pipeline schema file to collect inputs for all available pipeline - parameters. Parameter names, descriptions and help text are shown. - The pipeline schema is used to validate all inputs as they are entered. - - When finished, saves a file with the selected parameters which can be - passed to Nextflow using the -params-file option. - - Run using a remote pipeline name (such as GitHub `user/repo` or a URL), - a local pipeline directory or an ID from the nf-core web launch tool. - """ - from nf_core.pipelines.launch import Launch - - launcher = Launch( - pipeline, - revision, - command_only, - params_in, - params_out, - save_all, - show_hidden, - url, - id, - ) - if not launcher.launch_pipeline(): - sys.exit(1) - - -# nf-core pipelines list -def pipelines_list(ctx, keywords, sort, json, show_archived): - """ - List available nf-core pipelines with local info. - - Checks the web for a list of nf-core pipelines with their latest releases. - Shows which nf-core pipelines you have pulled locally and whether they are up to date. - """ - from nf_core.pipelines.list import list_workflows - - stdout.print(list_workflows(keywords, sort, json, show_archived)) - - -# nf-core pipelines sync -def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): - """ - Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. - - To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special - git branch called [cyan i]TEMPLATE[/]. - - This command updates the [cyan i]TEMPLATE[/] branch with the latest version of - the nf-core template, so that these updates can be synchronised with - the pipeline. It is run automatically for all pipelines when ever a - new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. - """ - from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError - from nf_core.utils import is_pipeline_directory - - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Sync the given pipeline dir - sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) - try: - sync_obj.sync() - except (SyncExceptionError, PullRequestExceptionError) as e: - log.error(e) - sys.exit(1) - - -# nf-core pipelines create-logo -def pipelines_create_logo(logo_text, dir, name, theme, width, format, force): - """ - Generate a logo with the nf-core logo template. - - This command generates an nf-core pipeline logo, using the supplied - """ - from nf_core.pipelines.create_logo import create_logo - - try: - if dir == ".": - dir = Path.cwd() - logo_path = create_logo(logo_text, dir, name, theme, width, format, force) - # Print path to logo relative to current working directory - try: - logo_path = Path(logo_path).relative_to(Path.cwd()) - except ValueError: - logo_path = Path(logo_path) - log.info(f"Created logo: [magenta]{logo_path}[/]") - except UserWarning as e: - log.error(e) - sys.exit(1) - - -# nf-core pipelines schema validate -def pipelines_schema_validate(pipeline, params): - """ - Validate a set of parameters against a pipeline schema. - - Nextflow can be run using the -params-file flag, which loads - script parameters from a JSON file. - - This command takes such a file and validates it against the pipeline - schema, checking whether all schema rules are satisfied. - """ - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(pipeline) - # Load and check schema - schema_obj.load_lint_schema() - except AssertionError as e: - log.error(e) - sys.exit(1) - schema_obj.load_input_params(params) - try: - schema_obj.validate_params() - except AssertionError: - sys.exit(1) - - -# nf-core pipelines schema build -def pipelines_schema_build(dir, no_prompts, web_only, url): - """ - Interactively build a pipeline schema from Nextflow params. - - Automatically detects parameters from the pipeline config and main.nf and - compares these to the pipeline schema. Prompts to add or remove parameters - if the two do not match one another. - - Once all parameters are accounted for, can launch a web GUI tool on the - https://nf-co.re website where you can annotate and organise parameters. - Listens for this to be completed and saves the updated schema. - """ - from nf_core.pipelines.schema import PipelineSchema - - try: - schema_obj = PipelineSchema() - if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: - sys.exit(1) - except (UserWarning, AssertionError) as e: - log.error(e) - sys.exit(1) - - -# nf-core pipelines schema lint -def pipelines_schema_lint(schema_path): - """ - Check that a given pipeline schema is valid. - - Checks whether the pipeline schema validates as JSON Schema Draft 7 - and adheres to the additional nf-core pipelines schema requirements. - - This function runs as part of the nf-core pipelines lint command, this is a convenience - command that does just the schema linting nice and quickly. - - If no schema path is provided, "nextflow_schema.json" will be used (if it exists). - """ - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - try: - schema_obj.get_schema_path(schema_path) - schema_obj.load_lint_schema() - # Validate title and description - just warnings as schema should still work fine - try: - schema_obj.validate_schema_title_description() - except AssertionError as e: - log.warning(e) - except AssertionError: - sys.exit(1) - - -# nf-core pipelines schema docs -def pipelines_schema_docs(schema_path, output, format, force, columns): - """ - Outputs parameter documentation for a pipeline schema. - """ - if not os.path.exists(schema_path): - log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") - sys.exit(1) - - from nf_core.pipelines.schema import PipelineSchema - - schema_obj = PipelineSchema() - # Assume we're in a pipeline dir root if schema path not set - schema_obj.get_schema_path(schema_path) - schema_obj.load_schema() - schema_obj.print_documentation(output, format, force, columns.split(",")) - - # nf-core pipelines subcommands @nf_core_cli.group() @click.pass_context @@ -1229,24 +849,11 @@ def modules_list(ctx): @click.pass_context @click.argument("keywords", required=False, nargs=-1, metavar="") @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout") -def modules_list_remote(ctx, keywords, json): +def command_modules_list_remote(ctx, keywords, json): """ List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/]. """ - from nf_core.modules import ModuleList - - try: - module_list = ModuleList( - None, - True, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - stdout.print(module_list.list_components(keywords, json)) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + modules_list_remote(ctx, keywords, json) # nf-core modules list local @@ -1261,24 +868,11 @@ def modules_list_remote(ctx, keywords, json): default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def command_modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin """ List modules installed locally in a pipeline """ - from nf_core.modules import ModuleList - - try: - module_list = ModuleList( - dir, - False, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - stdout.print(module_list.list_components(keywords, json)) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + modules_list_local(ctx, keywords, json, dir) # nf-core modules install @@ -1307,30 +901,11 @@ def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-b help="Force reinstallation of module if it already exists", ) @click.option("-s", "--sha", type=str, metavar="", help="Install module at commit SHA") -def modules_install(ctx, tool, dir, prompt, force, sha): +def command_modules_install(ctx, tool, dir, prompt, force, sha): """ Install DSL2 modules within a pipeline. - - Fetches and installs module files from a remote repo e.g. nf-core/modules. """ - from nf_core.modules import ModuleInstall - - try: - module_install = ModuleInstall( - dir, - force, - prompt, - sha, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - exit_status = module_install.install(tool) - if not exit_status: - sys.exit(1) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + modules_install(ctx, tool, dir, prompt, force, sha) # nf-core modules update @@ -1384,7 +959,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha): default=False, help="Automatically update all linked modules and subworkflows without asking for confirmation", ) -def modules_update( +def command_modules_update( ctx, tool, directory, @@ -1398,35 +973,12 @@ def modules_update( ): """ Update DSL2 modules within a pipeline. - - Fetches and updates module files from a remote repo e.g. nf-core/modules. - """ - from nf_core.modules import ModuleUpdate - - try: - module_install = ModuleUpdate( - directory, - force, - prompt, - sha, - install_all, - preview, - save_diff, - update_deps, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - exit_status = module_install.update(tool) - if not exit_status and install_all: - sys.exit(1) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + """ + modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps) # nf-core modules patch -@modules.command() +@modules.command("patch") @click.pass_context @click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") @click.option( @@ -1437,29 +989,11 @@ def modules_update( help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) @click.option("-r", "--remove", is_flag=True, default=False) -def patch(ctx, tool, dir, remove): +def command_modules_patch(ctx, tool, dir, remove): """ Create a patch file for minor changes in a module - - Checks if a module has been modified locally and creates a patch file - describing how the module has changed from the remote version """ - from nf_core.modules import ModulePatch - - try: - module_patch = ModulePatch( - dir, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - if remove: - module_patch.remove(tool) - else: - module_patch.patch(tool) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + modules_patch(ctx, tool, dir, remove) # nf-core modules remove @@ -1473,23 +1007,11 @@ def patch(ctx, tool, dir, remove): default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -def modules_remove(ctx, dir, tool): +def command_modules_remove(ctx, dir, tool): """ Remove a module from a pipeline. """ - from nf_core.modules import ModuleRemove - - try: - module_remove = ModuleRemove( - dir, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - module_remove.remove(tool) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + modules_remove(ctx, dir, tool) # nf-core modules create @@ -1559,7 +1081,7 @@ def modules_remove(ctx, dir, tool): default=False, help="Migrate a module with pytest tests to nf-test", ) -def create_module( +def command_modules_create( ctx, tool, dir, @@ -1575,45 +1097,21 @@ def create_module( ): """ Create a new DSL2 module from the nf-core template. - - If the specified directory is a pipeline, this function creates a file called - 'modules/local/tool_subtool.nf' - - If the specified directory is a clone of nf-core/modules, it creates or modifies files - in 'modules/', 'tests/modules' and 'tests/config/pytest_modules.yml' - """ - # Combine two bool flags into one variable - has_meta = None - if meta and no_meta: - log.critical("Both arguments '--meta' and '--no-meta' given. Please pick one.") - elif meta: - has_meta = True - elif no_meta: - has_meta = False - - from nf_core.modules import ModuleCreate - - # Run function - try: - module_create = ModuleCreate( - dir, - tool, - author, - label, - has_meta, - force, - conda_name, - conda_package_version, - empty_template, - migrate_pytest, - ) - module_create.create() - except UserWarning as e: - log.critical(e) - sys.exit(1) - except LookupError as e: - log.error(e) - sys.exit(1) + """ + modules_create( + ctx, + tool, + dir, + author, + label, + meta, + no_meta, + force, + conda_name, + conda_package_version, + empty_template, + migrate_pytest, + ) # nf-core modules test @@ -1648,31 +1146,11 @@ def create_module( default=None, help="Run tests with a specific profile", ) -def test_module(ctx, tool, dir, no_prompts, update, once, profile): +def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): """ Run nf-test for a module. - - Given the name of a module, runs the nf-test command to test the module and generate snapshots. - """ - from nf_core.components.components_test import ComponentsTest - - try: - module_tester = ComponentsTest( - component_type="modules", - component_name=tool, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, - ) - module_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + """ + modules_test(ctx, tool, dir, no_prompts, update, once, profile) # nf-core modules lint @@ -1718,48 +1196,11 @@ def test_module(ctx, tool, dir, no_prompts, update, once, profile): is_flag=True, help="Fix the module version if a newer version is available", ) -def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): +def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): """ Lint one or more modules in a directory. - - Checks DSL2 module code against nf-core guidelines to ensure - that all modules follow the same standards. - - Test modules within a pipeline or a clone of the - nf-core/modules repository. """ - from nf_core.components.lint import LintExceptionError - from nf_core.modules import ModuleLint - - try: - module_lint = ModuleLint( - dir, - fail_warned=fail_warned, - registry=ctx.params["registry"], - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - no_pull=ctx.obj["modules_repo_no_pull"], - hide_progress=ctx.obj["hide_progress"], - ) - module_lint.lint( - module=tool, - registry=registry, - key=key, - all_modules=all, - print_results=True, - local=local, - show_passed=passed, - sort_by=sort_by, - fix_version=fix_version, - ) - if len(module_lint.failed) > 0: - sys.exit(1) - except LintExceptionError as e: - log.error(e) - sys.exit(1) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version) # nf-core modules info @@ -1773,36 +1214,15 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def modules_info(ctx, tool, dir): +def command_modules_info(ctx, tool, dir): """ Show developer usage information about a given module. - - Parses information from a module's [i]meta.yml[/] and renders help - on the command line. A handy equivalent to searching the - [link=https://nf-co.re/modules]nf-core website[/]. - - If run from a pipeline and a local copy of the module is found, the command - will print this usage info. - If not, usage from the remote modules repo will be shown. """ - from nf_core.modules import ModuleInfo - - try: - module_info = ModuleInfo( - dir, - tool, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - stdout.print(module_info.get_component_info()) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + modules_info(ctx, tool, dir) # nf-core modules bump-versions -@modules.command() +@modules.command("bump-versions") @click.pass_context @click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") @click.option( @@ -1814,28 +1234,12 @@ def modules_info(ctx, tool, dir): ) @click.option("-a", "--all", is_flag=True, help="Run on all modules") @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too") -def bump_versions(ctx, tool, dir, all, show_all): +def command_modules_bump_versions(ctx, tool, dir, all, show_all): """ Bump versions for one or more modules in a clone of the nf-core/modules repo. """ - from nf_core.modules.bump_versions import ModuleVersionBumper - from nf_core.modules.modules_utils import ModuleExceptionError - - try: - version_bumper = ModuleVersionBumper( - dir, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all) - except ModuleExceptionError as e: - log.error(e) - sys.exit(1) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + modules_bump_versions(ctx, tool, dir, all, show_all) # nf-core subworkflows click command @@ -1901,28 +1305,11 @@ def subworkflows(ctx, git_remote, branch, no_pull): default=False, help="Migrate a module with pytest tests to nf-test", ) -def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest): +def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): """ Create a new subworkflow from the nf-core template. - - If the specified directory is a pipeline, this function creates a file called - 'subworkflows/local/.nf' - - If the specified directory is a clone of nf-core/modules, it creates or modifies files - in 'subworkflows/', 'tests/subworkflows' and 'tests/config/pytest_modules.yml' """ - from nf_core.subworkflows import SubworkflowCreate - - # Run function - try: - subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force, migrate_pytest) - subworkflow_create.create() - except UserWarning as e: - log.critical(e) - sys.exit(1) - except LookupError as e: - log.error(e) - sys.exit(1) + subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest) # nf-core subworkflows test @@ -1957,31 +1344,11 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest): default=None, help="Run tests with a specific profile", ) -def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once, profile): +def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): """ Run nf-test for a subworkflow. - - Given the name of a subworkflow, runs the nf-test command to test the subworkflow and generate snapshots. - """ - from nf_core.components.components_test import ComponentsTest - - try: - sw_tester = ComponentsTest( - component_type="subworkflows", - component_name=subworkflow, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, - ) - sw_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + """ + subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile) # nf-core subworkflows list subcommands @@ -1999,25 +1366,11 @@ def subworkflows_list(ctx): @click.pass_context @click.argument("keywords", required=False, nargs=-1, metavar="") @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout") -def subworkflows_list_remote(ctx, keywords, json): +def command_subworkflows_list_remote(ctx, keywords, json): """ List subworkflows in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/]. """ - from nf_core.subworkflows import SubworkflowList - - try: - subworkflow_list = SubworkflowList( - None, - True, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - - stdout.print(subworkflow_list.list_components(keywords, json)) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + subworkflows_list_remote(ctx, keywords, json) # nf-core subworkflows list local @@ -2032,24 +1385,11 @@ def subworkflows_list_remote(ctx, keywords, json): default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin """ List subworkflows installed locally in a pipeline """ - from nf_core.subworkflows import SubworkflowList - - try: - subworkflow_list = SubworkflowList( - dir, - False, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - stdout.print(subworkflow_list.list_components(keywords, json)) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + subworkflows_list_local(ctx, keywords, json, dir) # nf-core subworkflows lint @@ -2090,47 +1430,11 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi help="Sort lint output by subworkflow or test name.", show_default=True, ) -def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): """ Lint one or more subworkflows in a directory. - - Checks DSL2 subworkflow code against nf-core guidelines to ensure - that all subworkflows follow the same standards. - - Test subworkflows within a pipeline or a clone of the - nf-core/modules repository. """ - from nf_core.components.lint import LintExceptionError - from nf_core.subworkflows import SubworkflowLint - - try: - subworkflow_lint = SubworkflowLint( - dir, - fail_warned=fail_warned, - registry=ctx.params["registry"], - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - no_pull=ctx.obj["modules_repo_no_pull"], - hide_progress=ctx.obj["hide_progress"], - ) - subworkflow_lint.lint( - subworkflow=subworkflow, - registry=registry, - key=key, - all_subworkflows=all, - print_results=True, - local=local, - show_passed=passed, - sort_by=sort_by, - ) - if len(subworkflow_lint.failed) > 0: - sys.exit(1) - except LintExceptionError as e: - log.error(e) - sys.exit(1) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by) # nf-core subworkflows info @@ -2144,32 +1448,11 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def subworkflows_info(ctx, subworkflow, dir): +def command_subworkflows_info(ctx, subworkflow, dir): """ Show developer usage information about a given subworkflow. - - Parses information from a subworkflow's [i]meta.yml[/] and renders help - on the command line. A handy equivalent to searching the - [link=https://nf-co.re/modules]nf-core website[/]. - - If run from a pipeline and a local copy of the subworkflow is found, the command - will print this usage info. - If not, usage from the remote subworkflows repo will be shown. """ - from nf_core.subworkflows import SubworkflowInfo - - try: - subworkflow_info = SubworkflowInfo( - dir, - subworkflow, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - stdout.print(subworkflow_info.get_component_info()) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + subworkflows_info(ctx, subworkflow, dir) # nf-core subworkflows install @@ -2204,30 +1487,11 @@ def subworkflows_info(ctx, subworkflow, dir): metavar="", help="Install subworkflow at commit SHA", ) -def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): +def command_subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): """ Install DSL2 subworkflow within a pipeline. - - Fetches and installs subworkflow files from a remote repo e.g. nf-core/modules. """ - from nf_core.subworkflows import SubworkflowInstall - - try: - subworkflow_install = SubworkflowInstall( - dir, - force, - prompt, - sha, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - exit_status = subworkflow_install.install(subworkflow) - if not exit_status: - sys.exit(1) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + subworkflows_install(ctx, subworkflow, dir, prompt, force, sha) # nf-core subworkflows remove @@ -2241,23 +1505,11 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -def subworkflows_remove(ctx, dir, subworkflow): +def command_subworkflows_remove(ctx, dir, subworkflow): """ Remove a subworkflow from a pipeline. """ - from nf_core.subworkflows import SubworkflowRemove - - try: - module_remove = SubworkflowRemove( - dir, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - module_remove.remove(subworkflow) - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + subworkflows_remove(ctx, dir, subworkflow) # nf-core subworkflows update @@ -2316,7 +1568,7 @@ def subworkflows_remove(ctx, dir, subworkflow): default=False, help="Automatically update all linked modules and subworkflows without asking for confirmation", ) -def subworkflows_update( +def command_subworkflows_update( ctx, subworkflow, dir, @@ -2330,31 +1582,8 @@ def subworkflows_update( ): """ Update DSL2 subworkflow within a pipeline. - - Fetches and updates subworkflow files from a remote repo e.g. nf-core/modules. - """ - from nf_core.subworkflows import SubworkflowUpdate - - try: - subworkflow_install = SubworkflowUpdate( - dir, - force, - prompt, - sha, - install_all, - preview, - save_diff, - update_deps, - ctx.obj["modules_repo_url"], - ctx.obj["modules_repo_branch"], - ctx.obj["modules_repo_no_pull"], - ) - exit_status = subworkflow_install.update(subworkflow) - if not exit_status and install_all: - sys.exit(1) - except (UserWarning, LookupError) as e: - log.error(e) - sys.exit(1) + """ + subworkflows_update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps) ## DEPRECATED commands since v3.0.0 diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py new file mode 100644 index 0000000000..5f7191436c --- /dev/null +++ b/nf_core/commands_modules.py @@ -0,0 +1,340 @@ +import logging +import sys + +import rich + +from nf_core.utils import rich_force_colors + +log = logging.getLogger(__name__) +stdout = rich.console.Console(force_terminal=rich_force_colors()) + + +def modules_list_remote(ctx, keywords, json): + """ + List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/]. + """ + from nf_core.modules import ModuleList + + try: + module_list = ModuleList( + None, + True, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + stdout.print(module_list.list_components(keywords, json)) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin + """ + List modules installed locally in a pipeline + """ + from nf_core.modules import ModuleList + + try: + module_list = ModuleList( + dir, + False, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + stdout.print(module_list.list_components(keywords, json)) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def modules_install(ctx, tool, dir, prompt, force, sha): + """ + Install DSL2 modules within a pipeline. + + Fetches and installs module files from a remote repo e.g. nf-core/modules. + """ + from nf_core.modules import ModuleInstall + + try: + module_install = ModuleInstall( + dir, + force, + prompt, + sha, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + exit_status = module_install.install(tool) + if not exit_status: + sys.exit(1) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def modules_update( + ctx, + tool, + directory, + force, + prompt, + sha, + install_all, + preview, + save_diff, + update_deps, +): + """ + Update DSL2 modules within a pipeline. + + Fetches and updates module files from a remote repo e.g. nf-core/modules. + """ + from nf_core.modules import ModuleUpdate + + try: + module_install = ModuleUpdate( + directory, + force, + prompt, + sha, + install_all, + preview, + save_diff, + update_deps, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + exit_status = module_install.update(tool) + if not exit_status and install_all: + sys.exit(1) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def modules_patch(ctx, tool, dir, remove): + """ + Create a patch file for minor changes in a module + + Checks if a module has been modified locally and creates a patch file + describing how the module has changed from the remote version + """ + from nf_core.modules import ModulePatch + + try: + module_patch = ModulePatch( + dir, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + if remove: + module_patch.remove(tool) + else: + module_patch.patch(tool) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def modules_remove(ctx, dir, tool): + """ + Remove a module from a pipeline. + """ + from nf_core.modules import ModuleRemove + + try: + module_remove = ModuleRemove( + dir, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + module_remove.remove(tool) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def modules_create( + ctx, + tool, + dir, + author, + label, + meta, + no_meta, + force, + conda_name, + conda_package_version, + empty_template, + migrate_pytest, +): + """ + Create a new DSL2 module from the nf-core template. + + If the specified directory is a pipeline, this function creates a file called + 'modules/local/tool_subtool.nf' + + If the specified directory is a clone of nf-core/modules, it creates or modifies files + in 'modules/', 'tests/modules' and 'tests/config/pytest_modules.yml' + """ + # Combine two bool flags into one variable + has_meta = None + if meta and no_meta: + log.critical("Both arguments '--meta' and '--no-meta' given. Please pick one.") + elif meta: + has_meta = True + elif no_meta: + has_meta = False + + from nf_core.modules import ModuleCreate + + # Run function + try: + module_create = ModuleCreate( + dir, + tool, + author, + label, + has_meta, + force, + conda_name, + conda_package_version, + empty_template, + migrate_pytest, + ) + module_create.create() + except UserWarning as e: + log.critical(e) + sys.exit(1) + except LookupError as e: + log.error(e) + sys.exit(1) + + +def modules_test(ctx, tool, dir, no_prompts, update, once, profile): + """ + Run nf-test for a module. + + Given the name of a module, runs the nf-test command to test the module and generate snapshots. + """ + from nf_core.components.components_test import ComponentsTest + + try: + module_tester = ComponentsTest( + component_type="modules", + component_name=tool, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + module_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): + """ + Lint one or more modules in a directory. + + Checks DSL2 module code against nf-core guidelines to ensure + that all modules follow the same standards. + + Test modules within a pipeline or a clone of the + nf-core/modules repository. + """ + from nf_core.components.lint import LintExceptionError + from nf_core.modules import ModuleLint + + try: + module_lint = ModuleLint( + dir, + fail_warned=fail_warned, + registry=ctx.params["registry"], + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + no_pull=ctx.obj["modules_repo_no_pull"], + hide_progress=ctx.obj["hide_progress"], + ) + module_lint.lint( + module=tool, + registry=registry, + key=key, + all_modules=all, + print_results=True, + local=local, + show_passed=passed, + sort_by=sort_by, + fix_version=fix_version, + ) + if len(module_lint.failed) > 0: + sys.exit(1) + except LintExceptionError as e: + log.error(e) + sys.exit(1) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def modules_info(ctx, tool, dir): + """ + Show developer usage information about a given module. + + Parses information from a module's [i]meta.yml[/] and renders help + on the command line. A handy equivalent to searching the + [link=https://nf-co.re/modules]nf-core website[/]. + + If run from a pipeline and a local copy of the module is found, the command + will print this usage info. + If not, usage from the remote modules repo will be shown. + """ + from nf_core.modules import ModuleInfo + + try: + module_info = ModuleInfo( + dir, + tool, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + stdout.print(module_info.get_component_info()) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def modules_bump_versions(ctx, tool, dir, all, show_all): + """ + Bump versions for one or more modules in a clone of + the nf-core/modules repo. + """ + from nf_core.modules.bump_versions import ModuleVersionBumper + from nf_core.modules.modules_utils import ModuleExceptionError + + try: + version_bumper = ModuleVersionBumper( + dir, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all) + except ModuleExceptionError as e: + log.error(e) + sys.exit(1) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py new file mode 100644 index 0000000000..3f569bfe35 --- /dev/null +++ b/nf_core/commands_pipelines.py @@ -0,0 +1,429 @@ +import logging +import os +import sys +from pathlib import Path + +import rich + +from nf_core.pipelines.params_file import ParamsFileBuilder +from nf_core.utils import rich_force_colors + +log = logging.getLogger(__name__) + +stdout = rich.console.Console(force_terminal=rich_force_colors()) + +## nf-core pipelines command functions ## + + +# nf-core pipelines create +def pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): + """ + Create a new pipeline using the nf-core template. + + Uses the nf-core template to make a skeleton Nextflow pipeline with all required + files, boilerplate code and best-practices. + \n\n + Run without any command line arguments to use an interactive interface. + """ + from nf_core.pipelines.create import PipelineCreateApp + from nf_core.pipelines.create.create import PipelineCreate + + if (name and description and author) or (template_yaml): + # If all command arguments are used, run without the interactive interface + try: + create_obj = PipelineCreate( + name, + description, + author, + version=version, + force=force, + outdir=outdir, + template_config=template_yaml, + organisation=organisation, + ) + create_obj.init_pipeline() + except UserWarning as e: + log.error(e) + sys.exit(1) + elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core": + log.error( + "[red]Partial arguments supplied.[/] " + "Run without [i]any[/] arguments for an interactive interface, " + "or with at least name + description + author to use non-interactively." + ) + sys.exit(1) + else: + log.info("Launching interactive nf-core pipeline creation tool.") + app = PipelineCreateApp() + app.run() + sys.exit(app.return_code or 0) + + +# nf-core pipelines bump-version +def pipelines_bump_version(ctx, new_version, dir, nextflow): + """ + Update nf-core pipeline version number. + + The pipeline version number is mentioned in a lot of different places + in nf-core pipelines. This tool updates the version for you automatically, + so that you don't accidentally miss any. + + Should be used for each pipeline release, and again for the next + development version after release. + + As well as the pipeline version, you can also change the required version of Nextflow. + """ + from nf_core.pipelines.bump_version import bump_nextflow_version, bump_pipeline_version + from nf_core.utils import Pipeline, is_pipeline_directory + + try: + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Make a pipeline object and load config etc + pipeline_obj = Pipeline(dir) + pipeline_obj._load() + + # Bump the pipeline version number + if not nextflow: + bump_pipeline_version(pipeline_obj, new_version) + else: + bump_nextflow_version(pipeline_obj, new_version) + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines lint +def pipelines_lint( + ctx, + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + markdown, + json, + sort_by, +): + """ + Check pipeline code against nf-core guidelines. + + Runs a large number of automated tests to ensure that the supplied pipeline + meets the nf-core guidelines. Documentation of all lint tests can be found + on the nf-core website: [link=https://nf-co.re/tools/docs/]https://nf-co.re/tools/docs/[/] + + You can ignore tests using a file called [blue].nf-core.yml[/] [i](if you have a good reason!)[/]. + See the documentation for details. + """ + from nf_core.pipelines.lint import run_linting + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory is a pipeline + try: + is_pipeline_directory(dir) + except UserWarning as e: + log.error(e) + sys.exit(1) + + # Run the lint tests! + try: + lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( + dir, + release, + fix, + key, + show_passed, + fail_ignored, + fail_warned, + sort_by, + markdown, + json, + ctx.obj["hide_progress"], + ) + swf_failed = 0 + if subworkflow_lint_obj is not None: + swf_failed = len(subworkflow_lint_obj.failed) + if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0: + sys.exit(1) + except AssertionError as e: + log.critical(e) + sys.exit(1) + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines download +def pipelines_download( + ctx, + pipeline, + revision, + outdir, + compress, + force, + tower, + platform, + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, +): + """ + Download a pipeline, nf-core/configs and pipeline singularity images. + + Collects all files in a single archive and configures the downloaded + workflow to use relative paths to the configs and singularity images. + """ + from nf_core.pipelines.download import DownloadWorkflow + + if tower: + log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") + + dl = DownloadWorkflow( + pipeline, + revision, + outdir, + compress, + force, + tower or platform, # True if either specified + download_configuration, + tag, + container_system, + container_library, + container_cache_utilisation, + container_cache_index, + parallel_downloads, + ) + dl.download_workflow() + + +# nf-core pipelines create-params-file +def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden): + """ + Build a parameter file for a pipeline. + + Uses the pipeline schema file to generate a YAML parameters file. + Parameters are set to the pipeline defaults and descriptions are shown in comments. + After the output file is generated, it can then be edited as needed before + passing to nextflow using the `-params-file` option. + + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory. + """ + builder = ParamsFileBuilder(pipeline, revision) + + if not builder.write_params_file(output, show_hidden=show_hidden, force=force): + sys.exit(1) + + +# nf-core pipelines launch +def pipelines_launch( + ctx, + pipeline, + id, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, +): + """ + Launch a pipeline using a web GUI or command line prompts. + + Uses the pipeline schema file to collect inputs for all available pipeline + parameters. Parameter names, descriptions and help text are shown. + The pipeline schema is used to validate all inputs as they are entered. + + When finished, saves a file with the selected parameters which can be + passed to Nextflow using the -params-file option. + + Run using a remote pipeline name (such as GitHub `user/repo` or a URL), + a local pipeline directory or an ID from the nf-core web launch tool. + """ + from nf_core.pipelines.launch import Launch + + launcher = Launch( + pipeline, + revision, + command_only, + params_in, + params_out, + save_all, + show_hidden, + url, + id, + ) + if not launcher.launch_pipeline(): + sys.exit(1) + + +# nf-core pipelines list +def pipelines_list(ctx, keywords, sort, json, show_archived): + """ + List available nf-core pipelines with local info. + + Checks the web for a list of nf-core pipelines with their latest releases. + Shows which nf-core pipelines you have pulled locally and whether they are up to date. + """ + from nf_core.pipelines.list import list_workflows + + stdout.print(list_workflows(keywords, sort, json, show_archived)) + + +# nf-core pipelines sync +def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): + """ + Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. + + To keep nf-core pipelines up to date with improvements in the main + template, we use a method of synchronisation that uses a special + git branch called [cyan i]TEMPLATE[/]. + + This command updates the [cyan i]TEMPLATE[/] branch with the latest version of + the nf-core template, so that these updates can be synchronised with + the pipeline. It is run automatically for all pipelines when ever a + new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made. + """ + from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError + from nf_core.utils import is_pipeline_directory + + # Check if pipeline directory contains necessary files + is_pipeline_directory(dir) + + # Sync the given pipeline dir + sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + try: + sync_obj.sync() + except (SyncExceptionError, PullRequestExceptionError) as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines create-logo +def pipelines_create_logo(logo_text, dir, name, theme, width, format, force): + """ + Generate a logo with the nf-core logo template. + + This command generates an nf-core pipeline logo, using the supplied + """ + from nf_core.pipelines.create_logo import create_logo + + try: + if dir == ".": + dir = Path.cwd() + logo_path = create_logo(logo_text, dir, name, theme, width, format, force) + # Print path to logo relative to current working directory + try: + logo_path = Path(logo_path).relative_to(Path.cwd()) + except ValueError: + logo_path = Path(logo_path) + log.info(f"Created logo: [magenta]{logo_path}[/]") + except UserWarning as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines schema validate +def pipelines_schema_validate(pipeline, params): + """ + Validate a set of parameters against a pipeline schema. + + Nextflow can be run using the -params-file flag, which loads + script parameters from a JSON file. + + This command takes such a file and validates it against the pipeline + schema, checking whether all schema rules are satisfied. + """ + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(pipeline) + # Load and check schema + schema_obj.load_lint_schema() + except AssertionError as e: + log.error(e) + sys.exit(1) + schema_obj.load_input_params(params) + try: + schema_obj.validate_params() + except AssertionError: + sys.exit(1) + + +# nf-core pipelines schema build +def pipelines_schema_build(dir, no_prompts, web_only, url): + """ + Interactively build a pipeline schema from Nextflow params. + + Automatically detects parameters from the pipeline config and main.nf and + compares these to the pipeline schema. Prompts to add or remove parameters + if the two do not match one another. + + Once all parameters are accounted for, can launch a web GUI tool on the + https://nf-co.re website where you can annotate and organise parameters. + Listens for this to be completed and saves the updated schema. + """ + from nf_core.pipelines.schema import PipelineSchema + + try: + schema_obj = PipelineSchema() + if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: + sys.exit(1) + except (UserWarning, AssertionError) as e: + log.error(e) + sys.exit(1) + + +# nf-core pipelines schema lint +def pipelines_schema_lint(schema_path): + """ + Check that a given pipeline schema is valid. + + Checks whether the pipeline schema validates as JSON Schema Draft 7 + and adheres to the additional nf-core pipelines schema requirements. + + This function runs as part of the nf-core pipelines lint command, this is a convenience + command that does just the schema linting nice and quickly. + + If no schema path is provided, "nextflow_schema.json" will be used (if it exists). + """ + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + try: + schema_obj.get_schema_path(schema_path) + schema_obj.load_lint_schema() + # Validate title and description - just warnings as schema should still work fine + try: + schema_obj.validate_schema_title_description() + except AssertionError as e: + log.warning(e) + except AssertionError: + sys.exit(1) + + +# nf-core pipelines schema docs +def pipelines_schema_docs(schema_path, output, format, force, columns): + """ + Outputs parameter documentation for a pipeline schema. + """ + if not os.path.exists(schema_path): + log.error("Could not find 'nextflow_schema.json' in current directory. Please specify a path.") + sys.exit(1) + + from nf_core.pipelines.schema import PipelineSchema + + schema_obj = PipelineSchema() + # Assume we're in a pipeline dir root if schema path not set + schema_obj.get_schema_path(schema_path) + schema_obj.load_schema() + schema_obj.print_documentation(output, format, force, columns.split(",")) diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py new file mode 100644 index 0000000000..cc1a544eca --- /dev/null +++ b/nf_core/commands_subworkflows.py @@ -0,0 +1,259 @@ +import logging +import sys + +import rich + +from nf_core.utils import rich_force_colors + +log = logging.getLogger(__name__) + +stdout = rich.console.Console(force_terminal=rich_force_colors()) + + +def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): + """ + Create a new subworkflow from the nf-core template. + + If the specified directory is a pipeline, this function creates a file called + 'subworkflows/local/.nf' + + If the specified directory is a clone of nf-core/modules, it creates or modifies files + in 'subworkflows/', 'tests/subworkflows' and 'tests/config/pytest_modules.yml' + """ + from nf_core.subworkflows import SubworkflowCreate + + # Run function + try: + subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force, migrate_pytest) + subworkflow_create.create() + except UserWarning as e: + log.critical(e) + sys.exit(1) + except LookupError as e: + log.error(e) + sys.exit(1) + + +def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): + """ + Run nf-test for a subworkflow. + + Given the name of a subworkflow, runs the nf-test command to test the subworkflow and generate snapshots. + """ + from nf_core.components.components_test import ComponentsTest + + try: + sw_tester = ComponentsTest( + component_type="subworkflows", + component_name=subworkflow, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + sw_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def subworkflows_list_remote(ctx, keywords, json): + """ + List subworkflows in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/]. + """ + from nf_core.subworkflows import SubworkflowList + + try: + subworkflow_list = SubworkflowList( + None, + True, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + + stdout.print(subworkflow_list.list_components(keywords, json)) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin + """ + List subworkflows installed locally in a pipeline + """ + from nf_core.subworkflows import SubworkflowList + + try: + subworkflow_list = SubworkflowList( + dir, + False, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + stdout.print(subworkflow_list.list_components(keywords, json)) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): + """ + Lint one or more subworkflows in a directory. + + Checks DSL2 subworkflow code against nf-core guidelines to ensure + that all subworkflows follow the same standards. + + Test subworkflows within a pipeline or a clone of the + nf-core/modules repository. + """ + from nf_core.components.lint import LintExceptionError + from nf_core.subworkflows import SubworkflowLint + + try: + subworkflow_lint = SubworkflowLint( + dir, + fail_warned=fail_warned, + registry=ctx.params["registry"], + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + no_pull=ctx.obj["modules_repo_no_pull"], + hide_progress=ctx.obj["hide_progress"], + ) + subworkflow_lint.lint( + subworkflow=subworkflow, + registry=registry, + key=key, + all_subworkflows=all, + print_results=True, + local=local, + show_passed=passed, + sort_by=sort_by, + ) + if len(subworkflow_lint.failed) > 0: + sys.exit(1) + except LintExceptionError as e: + log.error(e) + sys.exit(1) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def subworkflows_info(ctx, subworkflow, dir): + """ + Show developer usage information about a given subworkflow. + + Parses information from a subworkflow's [i]meta.yml[/] and renders help + on the command line. A handy equivalent to searching the + [link=https://nf-co.re/modules]nf-core website[/]. + + If run from a pipeline and a local copy of the subworkflow is found, the command + will print this usage info. + If not, usage from the remote subworkflows repo will be shown. + """ + from nf_core.subworkflows import SubworkflowInfo + + try: + subworkflow_info = SubworkflowInfo( + dir, + subworkflow, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + stdout.print(subworkflow_info.get_component_info()) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): + """ + Install DSL2 subworkflow within a pipeline. + + Fetches and installs subworkflow files from a remote repo e.g. nf-core/modules. + """ + from nf_core.subworkflows import SubworkflowInstall + + try: + subworkflow_install = SubworkflowInstall( + dir, + force, + prompt, + sha, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + exit_status = subworkflow_install.install(subworkflow) + if not exit_status: + sys.exit(1) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) + + +def subworkflows_remove(ctx, dir, subworkflow): + """ + Remove a subworkflow from a pipeline. + """ + from nf_core.subworkflows import SubworkflowRemove + + try: + module_remove = SubworkflowRemove( + dir, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + module_remove.remove(subworkflow) + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) + + +def subworkflows_update( + ctx, + subworkflow, + dir, + force, + prompt, + sha, + install_all, + preview, + save_diff, + update_deps, +): + """ + Update DSL2 subworkflow within a pipeline. + + Fetches and updates subworkflow files from a remote repo e.g. nf-core/modules. + """ + from nf_core.subworkflows import SubworkflowUpdate + + try: + subworkflow_install = SubworkflowUpdate( + dir, + force, + prompt, + sha, + install_all, + preview, + save_diff, + update_deps, + ctx.obj["modules_repo_url"], + ctx.obj["modules_repo_branch"], + ctx.obj["modules_repo_no_pull"], + ) + exit_status = subworkflow_install.update(subworkflow) + if not exit_status and install_all: + sys.exit(1) + except (UserWarning, LookupError) as e: + log.error(e) + sys.exit(1) From 667c53f95b54b3ceb54671d22f72bc312be0ae9b Mon Sep 17 00:00:00 2001 From: Joon-Klaps Date: Wed, 3 Jul 2024 14:24:02 +0000 Subject: [PATCH 084/574] add tests --- tests/modules/update.py | 113 +++++++++++++++++++++++++++++++++ tests/subworkflows/update.py | 120 +++++++++++++++++++++++++++++++++++ tests/test_modules.py | 2 + tests/test_subworkflows.py | 2 + 4 files changed, 237 insertions(+) diff --git a/tests/modules/update.py b/tests/modules/update.py index 81eb85716e..0fddcc8ba8 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -1,5 +1,8 @@ import filecmp +import io +import logging import os +import re import shutil import tempfile from pathlib import Path @@ -67,6 +70,71 @@ def test_install_at_hash_and_update(self): assert correct_git_sha == current_git_sha +def test_install_at_hash_and_update_limit_output(self): + """Installs an old version of a module in the pipeline and updates it with limited output reporting""" + assert self.mods_install_old.install("trimgalore") + + # Capture the logger output + log_capture = io.StringIO() + ch = logging.StreamHandler(log_capture) + logger = logging.getLogger() + logger.addHandler(ch) + + update_obj = ModuleUpdate( + self.pipeline_dir, + show_diff=False, + update_deps=True, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + limit_output=True, + ) + + # Copy the module files and check that they are affected by the update + tmpdir = tempfile.mkdtemp() + trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") + trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + shutil.copytree(trimgalore_path, trimgalore_tmpdir) + + assert update_obj.update("trimgalore") is True + assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False + + # Check that the modules.json is correctly updated + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + # Get the up-to-date git_sha for the module from the ModuleRepo object + correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules") + current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] + assert correct_git_sha == current_git_sha + + # Get the captured log output + log_output = log_capture.getvalue() + log_lines = log_output.split("\n") + + # Check for various scenarios + for line in log_lines: + if re.match(r"'.+' is unchanged", line): + # Unchanged files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"'.+' was created", line): + # Created files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"'.+' was removed", line): + # Removed files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"Changes in '.+' but not shown", line): + # Changes not shown should only be for non-.nf files + file_path = re.search(r"'(.+)'", line).group(1) + assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" + elif re.match(r"Changes in '.+':$", line): + # Changes shown should only be for .nf files + file_path = re.search(r"'(.+)'", line).group(1) + assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" + + # Clean up + logger.removeHandler(ch) + log_capture.close() + + def test_install_at_hash_and_update_and_save_diff_to_file(self): """Installs an old version of a module in the pipeline and updates it""" self.mods_install_old.install("trimgalore") @@ -91,6 +159,51 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): # TODO: Apply the patch to the module +def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): + """Installs an old version of a module in the pipeline and updates it""" + self.mods_install_old.install("trimgalore") + patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch") + update_obj = ModuleUpdate( + self.pipeline_dir, + save_diff_fn=patch_path, + sha=OLD_TRIMGALORE_SHA, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + limit_output=True, + ) + + # Copy the module files and check that they are affected by the update + tmpdir = tempfile.mkdtemp() + trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") + trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + shutil.copytree(trimgalore_path, trimgalore_tmpdir) + + assert update_obj.update("trimgalore") is True + assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True + + # Check that the patch file was created + assert os.path.exists(patch_path), f"Patch file was not created at {patch_path}" + + # Read the contents of the patch file + with open(patch_path) as f: + patch_content = f.read() + + # Check the content of the patch file + patch_lines = patch_content.split("\n") + for line in patch_lines: + if re.match(r"'.+' is unchanged", line): + # Unchanged files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"Changes in '.+' but not shown", line): + # Changes not shown should only be for non-.nf files + file_path = re.search(r"'(.+)'", line).group(1) + assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" + elif re.match("diff --git", line): + # Diff should only be shown for .nf files + file_path = re.search(r"b/(.+)$", line).group(1) + assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}" + + def test_update_all(self): """Updates all modules present in the pipeline""" update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False) diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 9ddc9bec0c..7d1a3808dc 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -1,4 +1,7 @@ import filecmp +import io +import logging +import re import shutil import tempfile from pathlib import Path @@ -57,6 +60,73 @@ def test_install_at_hash_and_update(self): ) +def test_install_at_hash_and_update_limit_output(self): + """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True""" + assert self.subworkflow_install_old.install("fastq_align_bowtie2") + + # Capture the logger output + log_capture = io.StringIO() + ch = logging.StreamHandler(log_capture) + logger = logging.getLogger() + logger.addHandler(ch) + + update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True) + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Copy the subworkflow files and check that they are affected by the update + tmpdir = tempfile.mkdtemp() + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") + shutil.copytree(sw_path, tmpdir) + + assert update_obj.update("fastq_align_bowtie2") is True + assert cmp_component(tmpdir, sw_path) is False + + # Check that the modules.json is correctly updated + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + ) + + # Get the captured log output + log_output = log_capture.getvalue() + log_lines = log_output.split("\n") + + # Check for various scenarios + nf_changes_shown = False + for line in log_lines: + if re.match(r"'.+' is unchanged", line): + # Unchanged files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"'.+' was created", line): + # Created files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"'.+' was removed", line): + # Removed files should be reported for both .nf and non-.nf files + assert True + elif re.match(r"Changes in '.+' but not shown", line): + # Changes not shown should only be for non-.nf files + file_path = re.search(r"'(.+)'", line).group(1) + assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" + elif re.match(r"Changes in '.+':$", line): + # Changes shown should only be for .nf files + file_path = re.search(r"'(.+)'", line).group(1) + assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" + nf_changes_shown = True + + # Ensure that changes in at least one .nf file were shown + assert nf_changes_shown, "No changes in .nf files were shown" + + # Clean up + logger.removeHandler(ch) + log_capture.close() + shutil.rmtree(tmpdir) + + def test_install_at_hash_and_update_and_save_diff_to_file(self): """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" assert self.subworkflow_install_old.install("fastq_align_bowtie2") @@ -79,6 +149,56 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): ) +def test_install_at_hash_and_update_and_save_diff_limit_output(self): + """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" + assert self.subworkflow_install_old.install("fastq_align_bowtie2") + patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") + update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True) + + # Copy the sw files and check that they are affected by the update + tmpdir = tempfile.mkdtemp() + shutil.rmtree(tmpdir) + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") + shutil.copytree(sw_path, tmpdir) + + assert update_obj.update("fastq_align_bowtie2") is True + assert cmp_component(tmpdir, sw_path) is True + + # Check that the patch file was created + assert patch_path.exists(), f"Patch file was not created at {patch_path}" + + nf_changes_shown = False + non_nf_changes_not_shown = False + + with open(patch_path) as fh: + content = fh.read() + + # Check the first line + assert re.match( + r"Changes in module 'nf-core/fastq_align_bowtie2' between \([a-f0-9]+\) and \([a-f0-9]+\)", + content.split("\n")[0], + ), "Unexpected first line in patch file" + + # Check for .nf file changes shown + nf_changes_shown = bool(re.search(r"Changes in '.*\.nf':\n", content)) + + # Check for non-.nf file changes not shown + non_nf_changes_not_shown = bool(re.search(r"Changes in '.*[^.nf]' but not shown", content)) + + # Check that diff content is only for .nf files + diff_lines = re.findall(r"diff --git.*", content) + for line in diff_lines: + assert re.search(r"\.nf$", line), f"Diff shown for non-.nf file: {line}" + + # Ensure that changes in .nf files were shown and non-.nf files were not shown + assert nf_changes_shown, "No changes in .nf files were shown in the patch file" + assert non_nf_changes_not_shown, "Changes in non-.nf files were not properly limited in the patch file" + + # Clean up + patch_path.unlink() + shutil.rmtree(tmpdir) + + def test_update_all(self): """Updates all subworkflows present in the pipeline""" # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools diff --git a/tests/test_modules.py b/tests/test_modules.py index 107b245663..7dd3132d33 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -269,6 +269,8 @@ def test_modulesrepo_class(self): test_install_and_update, test_install_at_hash_and_update, test_install_at_hash_and_update_and_save_diff_to_file, + test_install_at_hash_and_update_and_save_diff_to_file_limit_output, + test_install_at_hash_and_update_limit_output, test_update_all, test_update_different_branch_mix_modules_branch_test, test_update_different_branch_mixed_modules_main, diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 786ba53836..b7ebe952db 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -175,7 +175,9 @@ def tearDown(self): from .subworkflows.update import ( # type: ignore[misc] test_install_and_update, test_install_at_hash_and_update, + test_install_at_hash_and_update_and_save_diff_limit_output, test_install_at_hash_and_update_and_save_diff_to_file, + test_install_at_hash_and_update_limit_output, test_update_all, test_update_all_linked_components_from_subworkflow, test_update_all_subworkflows_from_module, From b04093484e6cf19f82fe670c3a400187162ae9b1 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 2 Jul 2024 19:11:11 +0000 Subject: [PATCH 085/574] Update gitpod/workspace-base Docker digest to 0f38224 --- nf_core/gitpod/gitpod.Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 628421607f..2f458dfc2a 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -1,7 +1,7 @@ # Test build locally before making a PR # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile . -FROM gitpod/workspace-base@sha256:92dd1bcbd5a2fb466c81b1e4c21fc2495575546a9e6c53b3f7d4ba0b0c29c5be +FROM gitpod/workspace-base@sha256:0f3822450f94084f6a62db4a4282d895591f6a55632dc044fe496f98cb79e75c USER root From e14819c9ecb9850f664e39d64cf8d8ac75f69c74 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 3 Jul 2024 20:15:58 +0000 Subject: [PATCH 086/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa079aaa85..52291d8954 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,7 @@ - Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) +- Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 5acb263f2bb2c8b606fe801db62eda326528d76f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 5 Jul 2024 03:02:30 +0000 Subject: [PATCH 087/574] Update python:3.12-slim Docker digest to d5f1674 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 66ee3ab2f2..7178b65267 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:da2d7af143dab7cd5b0d5a5c9545fe14e67fc24c394fcf1cf15e8ea16cbd8637 +FROM python:3.12-slim@sha256:d5f16749562233aa4bd26538771d76bf0dfd0a0ea7ea8771985e267451397ae4 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From eefec50b0d14065dc95db250e45696f384f3b1dc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 5 Jul 2024 11:20:02 +0200 Subject: [PATCH 088/574] update docstring for deprecated commands --- nf_core/__main__.py | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index f9d6a6aebb..4fa640436d 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1593,7 +1593,7 @@ def command_subworkflows_update( @nf_core_cli.group(deprecated=True, hidden=True) def schema(): """ - DEPRECATED + Use `nf-core pipelines schema ` instead. """ pass @@ -1604,7 +1604,7 @@ def schema(): @click.argument("params", type=click.Path(exists=True), required=True, metavar="") def command_schema_validate(pipeline, params): """ - DEPRECATED + Use `nf-core pipelines schema validate` instead. """ log.warning( "The `[magenta]nf-core schema validate[/]` command is deprecated. Use `[magenta]nf-core pipelines schema validate[/]` instead." @@ -1639,7 +1639,7 @@ def command_schema_validate(pipeline, params): ) def command_schema_build(dir, no_prompts, web_only, url): """ - DEPRECATED + Use `nf-core pipelines schema build` instead. """ log.warning( "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead." @@ -1657,7 +1657,7 @@ def command_schema_build(dir, no_prompts, web_only, url): ) def command_schema_lint(schema_path): """ - DEPRECATED + Use `nf-core pipelines schema lint` instead. """ log.warning( "The `[magenta]nf-core schema lint[/]` command is deprecated. Use `[magenta]nf-core pipelines schema lint[/]` instead." @@ -1699,7 +1699,7 @@ def command_schema_lint(schema_path): ) def command_schema_docs(schema_path, output, format, force, columns): """ - DEPRECATED + Use `nf-core pipelines schema docs` instead. """ log.warning( "The `[magenta]nf-core schema docs[/]` command is deprecated. Use `[magenta]nf-core pipelines schema docs[/]` instead." @@ -1747,7 +1747,7 @@ def command_schema_docs(schema_path, output, format, force, columns): ) def command_create_logo(logo_text, dir, name, theme, width, format, force): """ - DEPRECATED + Use `nf-core pipelines create-logo` instead. """ log.warning( "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead." @@ -1788,7 +1788,7 @@ def command_create_logo(logo_text, dir, name, theme, width, format, force): @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") def command_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ - DEPRECATED + Use `nf-core pipelines sync` instead. """ log.warning( "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead." @@ -1816,7 +1816,7 @@ def command_sync(dir, from_branch, pull_request, github_repository, username, te ) def command_bump_version(ctx, new_version, dir, nextflow): """ - DEPRECATED + Use `nf-core pipelines bump-version` instead. """ log.warning( "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead." @@ -1839,7 +1839,7 @@ def command_bump_version(ctx, new_version, dir, nextflow): @click.pass_context def command_list(ctx, keywords, sort, json, show_archived): """ - DEPRECATED + DEPREUse `nf-core pipelines list` instead.CATED """ log.warning( "The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead." @@ -1907,7 +1907,7 @@ def command_launch( url, ): """ - DEPRECATED + Use `nf-core pipelines launch` instead. """ log.warning( "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead." @@ -1937,7 +1937,7 @@ def command_launch( ) def command_create_params_file(pipeline, revision, output, force, show_hidden): """ - DEPRECATED + Use `nf-core pipelines create-params-file` instead. """ log.warning( "The `[magenta]nf-core create-params-file[/]` command is deprecated. Use `[magenta]nf-core pipelines create-params-file[/]` instead." @@ -2038,7 +2038,7 @@ def command_download( parallel_downloads, ): """ - DEPRECATED + Use `nf-core pipelines download` instead. """ log.warning( "The `[magenta]nf-core download[/]` command is deprecated. Use `[magenta]nf-core pipelines download[/]` instead." @@ -2132,7 +2132,7 @@ def command_lint( sort_by, ): """ - DEPRECATED + Use `nf-core pipelines lint` instead. """ log.warning( "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead." @@ -2164,7 +2164,7 @@ def command_lint( @click.pass_context def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation): """ - DEPRECATED + Use `nf-core pipelines create` instead. """ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." From 17adacadecde4d0fad857fad25ee6e0ef44b4cc2 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 23 Feb 2024 09:42:47 +0100 Subject: [PATCH 089/574] 10 minute hack to try to parse proper input structure from module processes, for meta.yml --- nf_core/components/nfcore_component.py | 30 ++++++++++++++++++-------- nf_core/modules/lint/meta_yml.py | 2 ++ 2 files changed, 23 insertions(+), 9 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 5d0baf63dd..e8f6f0b7a3 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -173,15 +173,27 @@ def get_inputs_from_main_nf(self): log.debug(f"Could not find any inputs in {self.main_nf}") return inputs input_data = data.split("input:")[1].split("output:")[0] - regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" - matches = re.finditer(regex, input_data, re.MULTILINE) - for _, match in enumerate(matches, start=1): - if match.group(3): - input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - inputs.append(input_val) - elif match.group(4): - input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - inputs.append(input_val) + for line in input_data.split("\n"): + theseinputs = [] + regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + matches = re.finditer(regex, line) + for _, match in enumerate(matches, start=1): + input_type = None + input_val = None + if match.group(1): + input_type = match.group(1) + if match.group(3): + input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + elif match.group(4): + input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + if input_type and input_val: + theseinputs.append({ + input_val: { + "type": input_type + } + }) + if len(theseinputs) > 0: + inputs.append(theseinputs) log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") self.inputs = inputs diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 481d50b3ef..6718ed5c21 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -40,6 +40,8 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None """ module.get_inputs_from_main_nf() + print(yaml.dump({"input": module.inputs})) + exit() module.get_outputs_from_main_nf() # Check if we have a patch file, get original file in that case meta_yaml = None From 970b4a0e09249476eaf2153ff57a0aad061d6750 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 4 Jun 2024 11:51:25 +0200 Subject: [PATCH 090/574] get correct format of inputs and outputs --- nf_core/components/nfcore_component.py | 36 +++++++++++++++++--------- 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index e8f6f0b7a3..9a266ab56e 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -174,7 +174,7 @@ def get_inputs_from_main_nf(self): return inputs input_data = data.split("input:")[1].split("output:")[0] for line in input_data.split("\n"): - theseinputs = [] + channel_elements = [] regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" matches = re.finditer(regex, line) for _, match in enumerate(matches, start=1): @@ -187,13 +187,9 @@ def get_inputs_from_main_nf(self): elif match.group(4): input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases if input_type and input_val: - theseinputs.append({ - input_val: { - "type": input_type - } - }) - if len(theseinputs) > 0: - inputs.append(theseinputs) + channel_elements.append({input_val: {"type": input_type}}) + if len(channel_elements) > 0: + inputs.append(channel_elements) log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") self.inputs = inputs @@ -206,9 +202,25 @@ def get_outputs_from_main_nf(self): log.debug(f"Could not find any outputs in {self.main_nf}") return outputs output_data = data.split("output:")[1].split("when:")[0] - regex = r"emit:\s*([^)\s,]+)" - matches = re.finditer(regex, output_data, re.MULTILINE) - for _, match in enumerate(matches, start=1): - outputs.append(match.group(1)) + regex_emit = r"emit:\s*([^)\s,]+)" + regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + for line in output_data.split("\n"): + match_emit = re.search(regex_emit, line) + matches_elements = re.finditer(regex_elements, line) + if not match_emit: + continue + output_channel = {match_emit.group(1): []} + for _, match_element in enumerate(matches_elements, start=1): + output_type = None + output_val = None + if match_element.group(1): + output_type = match_element.group(1) + if match_element.group(3): + output_val = match_element.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + elif match_element.group(4): + output_val = match_element.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + if output_type and output_val: + output_channel[match_emit.group(1)].append({output_val: {"type": output_type}}) + outputs.append(output_channel) log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") self.outputs = outputs From 744b0fd4ae76e684b19affdb8a79f09ce3815daa Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 5 Jun 2024 14:12:23 +0200 Subject: [PATCH 091/574] update module template meta.yml --- nf_core/module-template/meta.yml | 48 +++++++++++++++++--------------- 1 file changed, 25 insertions(+), 23 deletions(-) diff --git a/nf_core/module-template/meta.yml b/nf_core/module-template/meta.yml index 9d3f3c1c12..2dd8e74efa 100644 --- a/nf_core/module-template/meta.yml +++ b/nf_core/module-template/meta.yml @@ -26,42 +26,44 @@ tools: {% endif -%} input: #{% if has_meta %} Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` {% endif %} {% if not_empty_template -%} ## TODO nf-core: Delete / customise this example input {%- endif %} - - {{ 'bam:' if not_empty_template else "input:" }} - type: file - description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} - pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} + - {{ 'bam:' if not_empty_template else "input:" }} + type: file + description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} + pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} {% if not_empty_template -%} ## TODO nf-core: Add a description of all of the variables used as output {% endif -%} output: + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + - {{ 'bam:' if not_empty_template else "output:" }} #{% if has_meta -%} Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` {% endif %} - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" {% if not_empty_template -%} - ## TODO nf-core: Delete / customise this example output + ## TODO nf-core: Delete / customise this example output {%- endif %} - - {{ 'bam:' if not_empty_template else "output:" }} - type: file - description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} - pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} + - {{ '"*.bam":' if not_empty_template else '"*":' }} + type: file + description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} + pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} authors: - "{{ author }}" From c9f6f8fc016a5e0cf8dd4b060876075bb2b655b7 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 5 Jun 2024 15:27:22 +0200 Subject: [PATCH 092/574] add linting for correct inputs and outputs in meta.yml --- nf_core/components/nfcore_component.py | 5 +- nf_core/modules/lint/meta_yml.py | 177 ++++++++++++++----------- 2 files changed, 101 insertions(+), 81 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 9a266ab56e..6ff1f6c171 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -216,10 +216,11 @@ def get_outputs_from_main_nf(self): if match_element.group(1): output_type = match_element.group(1) if match_element.group(3): - output_val = match_element.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + output_val = match_element.group(3) elif match_element.group(4): - output_val = match_element.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + output_val = match_element.group(4) if output_type and output_val: + output_val = output_val.strip("'").strip('"') # remove quotes output_channel[match_emit.group(1)].append({output_val: {"type": output_type}}) outputs.append(output_channel) log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 6718ed5c21..d5615059a5 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -40,8 +40,6 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None """ module.get_inputs_from_main_nf() - print(yaml.dump({"input": module.inputs})) - exit() module.get_outputs_from_main_nf() # Check if we have a patch file, get original file in that case meta_yaml = None @@ -93,93 +91,114 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None ) ) - # Confirm that all input and output channels are specified + # Confirm that all input and output channels are correctly specified if valid_meta_yml: + # Check that inputs are specified in meta.yml + if len(module.inputs) > 0 and "input" not in meta_yaml: + module.failed.append( + ( + "meta_input", + "Inputs not specified in module `meta.yml`", + module.meta_yml, + ) + ) + elif len(module.inputs) > 0: + module.passed.append( + ( + "meta_input", + "Inputs specified in module `meta.yml`", + module.meta_yml, + ) + ) + # Check that all inputs are correctly specified if "input" in meta_yaml: - meta_input = [list(x.keys())[0] for x in meta_yaml["input"]] - for input in module.inputs: - if input in meta_input: - module.passed.append(("meta_input_main_only", f"`{input}` specified", module.meta_yml)) - else: - module.warned.append( - ( - "meta_input_main_only", - f"`{input}` is present as an input in the `main.nf`, but missing in `meta.yml`", - module.meta_yml, - ) + # Obtain list of correct inputs and elements of each input channel + correct_inputs = [] + for input_channel in module.inputs: + channel_elements = [] + for element in input_channel: + channel_elements.append(list(element.keys())[0]) + correct_inputs.append(channel_elements) + # Obtain list of inputs specified in meta.yml + meta_inputs = [] + for input_channel in meta_yaml["input"]: + if isinstance(input_channel, list): # Correct format + channel_elements = [] + for element in input_channel: + channel_elements.append(list(element.keys())[0]) + meta_inputs.append(channel_elements) + elif isinstance(input_channel, dict): # Old format + meta_inputs.append(list(input_channel.keys())[0]) + + if correct_inputs == meta_inputs: + module.passed.append( + ( + "correct_meta_inputs", + "Correct inputs specified in module `meta.yml`", + module.meta_yml, ) - # check if there are any inputs in meta.yml that are not in main.nf - for input in meta_input: - if input in module.inputs: - module.passed.append( - ( - "meta_input_meta_only", - f"`{input}` is present as an input in `meta.yml` and `main.nf`", - module.meta_yml, - ) - ) - else: - module.warned.append( - ( - "meta_input_meta_only", - f"`{input}` is present as an input in `meta.yml` but not in `main.nf`", - module.meta_yml, - ) + ) + else: + module.failed.append( + ( + "correct_meta_inputs", + f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.", + module.meta_yml, ) + ) - if "output" in meta_yaml and meta_yaml["output"] is not None: - meta_output = [list(x.keys())[0] for x in meta_yaml["output"]] - for output in module.outputs: - if output in meta_output: - module.passed.append(("meta_output_main_only", f"`{output}` specified", module.meta_yml)) - else: - module.warned.append( - ( - "meta_output_main_only", - f"`{output}` is present as an output in the `main.nf`, but missing in `meta.yml`", - module.meta_yml, - ) - ) - # check if there are any outputs in meta.yml that are not in main.nf - for output in meta_output: - if output in module.outputs: - module.passed.append( - ( - "meta_output_meta_only", - f"`{output}` is present as an output in `meta.yml` and `main.nf`", - module.meta_yml, - ) - ) - elif output == "meta": - module.passed.append( - ( - "meta_output_meta_only", - f"`{output}` is skipped for `meta.yml` outputs", - module.meta_yml, - ) - ) - else: - module.warned.append( - ( - "meta_output_meta_only", - f"`{output}` is present as an output in `meta.yml` but not in `main.nf`", - module.meta_yml, - ) - ) - # confirm that the name matches the process name in main.nf - if meta_yaml["name"].upper() == module.process_name: - module.passed.append( + # Check that outputs are specified in meta.yml + if len(module.outputs) > 0 and "output" not in meta_yaml: + module.failed.append( ( - "meta_name", - "Correct name specified in `meta.yml`.", + "meta_output", + "Outputs not specified in module `meta.yml`", module.meta_yml, ) ) - else: - module.failed.append( + elif len(module.outputs) > 0: + module.passed.append( ( - "meta_name", - f"Conflicting `process` name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)", + "meta_output", + "Outputs specified in module `meta.yml`", module.meta_yml, ) ) + # Check that all outputs are correctly specified + if "output" in meta_yaml: + # Obtain dictionary of correct outputs and elements of each output channel + correct_outputs = {} + for output_channel in module.outputs: + channel_name = list(output_channel.keys())[0] + channel_elements = [] + for element in output_channel[channel_name]: + channel_elements.append(list(element.keys())[0]) + correct_outputs[channel_name] = channel_elements + # Obtain dictionary of outputs specified in meta.yml + meta_outputs = {} + for output_channel in meta_yaml["output"]: + channel_name = list(output_channel.keys())[0] + if isinstance(output_channel[channel_name], list): # Correct format + channel_elements = [] + for element in output_channel[channel_name]: + channel_elements.append(list(element.keys())[0]) + meta_outputs[channel_name] = channel_elements + elif isinstance(output_channel[channel_name], dict): # Old format + meta_outputs[channel_name] = [] + + if correct_outputs == meta_outputs: + module.passed.append( + ( + "correct_meta_outputs", + "Correct outputs specified in module `meta.yml`", + module.meta_yml, + ) + ) + else: + module.failed.append( + ( + "correct_meta_outputs", + f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.", + module.meta_yml, + ) + ) From d79f487bdaacddedc1781c263574996e1c10760d Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 17 Jun 2024 17:26:37 +0200 Subject: [PATCH 093/574] add update-meta-yml option --- nf_core/__main__.py | 5 +- nf_core/commands_modules.py | 3 +- nf_core/components/lint/__init__.py | 2 + nf_core/components/nfcore_component.py | 4 +- nf_core/modules/lint/__init__.py | 105 +++++++++++++++- nf_core/modules/lint/meta_yml.py | 167 ++++++++++++++++--------- 6 files changed, 225 insertions(+), 61 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 4fa640436d..584947afd0 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1196,7 +1196,10 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): is_flag=True, help="Fix the module version if a newer version is available", ) -def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): +@click.option( + "--update-meta-yml", is_flag=True, help="Update the meta.yml file with the correct format of input and outputs" +) +def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, update_meta_yml): """ Lint one or more modules in a directory. """ diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index 5f7191436c..85471184ca 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -244,7 +244,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile): sys.exit(1) -def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): +def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, update_meta_yml): """ Lint one or more modules in a directory. @@ -277,6 +277,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, show_passed=passed, sort_by=sort_by, fix_version=fix_version, + update_meta_yml=update_meta_yml, ) if len(module_lint.failed) > 0: sys.exit(1) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 499d31e71e..b4194e768e 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -56,6 +56,7 @@ def __init__( component_type, dir, fail_warned=False, + update_meta_yml=False, remote_url=None, branch=None, no_pull=False, @@ -72,6 +73,7 @@ def __init__( ) self.fail_warned = fail_warned + self.update_meta_yml = update_meta_yml self.passed = [] self.warned = [] self.failed = [] diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 6ff1f6c171..dcd76b0e8f 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -187,7 +187,7 @@ def get_inputs_from_main_nf(self): elif match.group(4): input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases if input_type and input_val: - channel_elements.append({input_val: {"type": input_type}}) + channel_elements.append({input_val: {"qualifier": input_type}}) if len(channel_elements) > 0: inputs.append(channel_elements) log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") @@ -221,7 +221,7 @@ def get_outputs_from_main_nf(self): output_val = match_element.group(4) if output_type and output_val: output_val = output_val.strip("'").strip('"') # remove quotes - output_channel[match_emit.group(1)].append({output_val: {"type": output_type}}) + output_channel[match_emit.group(1)].append({output_val: {"qualifier": output_type}}) outputs.append(output_channel) log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") self.outputs = outputs diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index b780144ef7..f6c2069bda 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -11,6 +11,7 @@ import questionary import rich +import yaml import nf_core.modules.modules_utils import nf_core.utils @@ -29,7 +30,12 @@ class ModuleLint(ComponentLint): # Import lint functions from .environment_yml import environment_yml # type: ignore[misc] from .main_nf import main_nf # type: ignore[misc] - from .meta_yml import meta_yml # type: ignore[misc] + from .meta_yml import ( # type: ignore[misc] + meta_yml, + obtain_correct_and_specified_inputs, + obtain_correct_and_specified_outputs, + read_meta_yml, + ) from .module_changes import module_changes # type: ignore[misc] from .module_deprecations import module_deprecations # type: ignore[misc] from .module_patch import module_patch # type: ignore[misc] @@ -41,6 +47,7 @@ def __init__( self, dir, fail_warned=False, + update_meta_yml=False, remote_url=None, branch=None, no_pull=False, @@ -51,6 +58,7 @@ def __init__( component_type="modules", dir=dir, fail_warned=fail_warned, + update_meta_yml=update_meta_yml, remote_url=remote_url, branch=branch, no_pull=no_pull, @@ -213,6 +221,12 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals # Otherwise run all the lint tests else: + mod.get_inputs_from_main_nf() + mod.get_outputs_from_main_nf() + # Update meta.yml file if requested + if self.update_meta_yml: + self.update_meta_yml_file(mod) + if self.repo_type == "pipeline" and self.modules_json: # Set correct sha version = self.modules_json.get_module_version(mod.component_name, mod.repo_url, mod.org) @@ -232,3 +246,92 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals self.failed += warned self.failed += [LintResult(mod, *m) for m in mod.failed] + + def update_meta_yml_file(self, mod): + """ + Update the meta.yml file with the correct inputs and outputs + """ + meta_yml = self.read_meta_yml(mod) + corrected_meta_yml = meta_yml.copy() + + # Obtain inputs and outputs from main.nf and meta.yml + # Used to compare only the structure of channels and elements + # Do not compare features to allow for custom features in meta.yml (i.e. pattern) + if "input" in meta_yml: + correct_inputs, meta_inputs = self.obtain_correct_and_specified_inputs(mod, meta_yml) + if "output" in meta_yml: + correct_outputs, meta_outputs = self.obtain_correct_and_specified_outputs(mod, meta_yml) + + if correct_inputs != meta_inputs: + log.debug( + f"Correct inputs: '{correct_inputs}' differ from current inputs: '{meta_inputs}' in '{mod.meta_yml}'" + ) + corrected_meta_yml["input"] = mod.inputs.copy() # list of lists (channels) of dicts (elements) + for i, channel in enumerate(corrected_meta_yml["input"]): + for j, element in enumerate(channel): + element_name = list(element.keys())[0] + for k, meta_element in enumerate(meta_yml["input"]): + try: + # Handle old format of meta.yml: list of dicts (channels) + if element_name in meta_element.keys(): + # Copy current features of that input element form meta.yml + for feature in meta_element[element_name].keys(): + if feature not in element[element_name].keys(): + corrected_meta_yml["input"][i][j][element_name][feature] = meta_element[ + element_name + ][feature] + break + except AttributeError: + # Handle new format of meta.yml: list of lists (channels) of elements (dicts) + for x, meta_ch_element in enumerate(meta_element): + if element_name in meta_ch_element.keys(): + # Copy current features of that input element form meta.yml + for feature in meta_element[x][element_name].keys(): + if feature not in element[element_name].keys(): + corrected_meta_yml["input"][i][j][element_name][feature] = meta_element[x][ + element_name + ][feature] + break + + if correct_outputs != meta_outputs: + log.debug( + f"Correct outputs: '{correct_outputs}' differ from current outputs: '{meta_outputs}' in '{mod.meta_yml}'" + ) + corrected_meta_yml["output"] = mod.outputs.copy() # list of dicts (channels) with list of dicts (elements) + for i, channel in enumerate(corrected_meta_yml["output"]): + ch_name = list(channel.keys())[0] + for j, element in enumerate(channel[ch_name]): + element_name = list(element.keys())[0] + for k, meta_element in enumerate(meta_yml["output"]): + if element_name in meta_element.keys(): + # Copy current features of that output element form meta.yml + for feature in meta_element[element_name].keys(): + if feature not in element[element_name].keys(): + corrected_meta_yml["output"][i][ch_name][j][element_name][feature] = meta_element[ + element_name + ][feature] + break + elif ch_name in meta_element.keys(): + # When the previous output element was using the name of the channel + # Copy current features of that output element form meta.yml + try: + # Handle old format of meta.yml + for feature in meta_element[ch_name].keys(): + if feature not in element[element_name].keys(): + corrected_meta_yml["output"][i][ch_name][j][element_name][feature] = ( + meta_element[ch_name][feature] + ) + except AttributeError: + # Handle new format of meta.yml + for x, meta_ch_element in enumerate(meta_element[ch_name]): + for meta_ch_element_name in meta_ch_element.keys(): + for feature in meta_ch_element[meta_ch_element_name].keys(): + if feature not in element[element_name].keys(): + corrected_meta_yml["output"][i][ch_name][j][element_name][feature] = ( + meta_ch_element[meta_ch_element_name][feature] + ) + break + + with open(mod.meta_yml, "w") as fh: + log.info(f"Updating {mod.meta_yml}") + yaml.dump(corrected_meta_yml, fh, sort_keys=False, Dumper=nf_core.utils.custom_yaml_dumper()) diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index d5615059a5..9c074ba731 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -1,5 +1,7 @@ import json +import logging from pathlib import Path +from typing import Union import yaml from jsonschema import exceptions, validators @@ -8,6 +10,8 @@ from nf_core.components.nfcore_component import NFCoreComponent from nf_core.modules.modules_differ import ModulesDiffer +log = logging.getLogger(__name__) + def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None: """ @@ -39,28 +43,13 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None """ - module.get_inputs_from_main_nf() - module.get_outputs_from_main_nf() # Check if we have a patch file, get original file in that case - meta_yaml = None - if module.is_patched: - lines = ModulesDiffer.try_apply_patch( - module.component_name, - module_lint_object.modules_repo.repo_path, - module.patch_path, - Path(module.component_dir).relative_to(module.base_dir), - reverse=True, - ).get("meta.yml") - if lines is not None: - meta_yaml = yaml.safe_load("".join(lines)) + meta_yaml = read_meta_yml(module_lint_object, module) if meta_yaml is None: - try: - with open(module.meta_yml) as fh: - meta_yaml = yaml.safe_load(fh) - module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml)) - except FileNotFoundError: - module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml)) - return + module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml)) + return + else: + module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml)) # Confirm that the meta.yml file is valid according to the JSON schema valid_meta_yml = False @@ -110,25 +99,11 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None module.meta_yml, ) ) + else: + log.debug(f"No inputs specified in module `main.nf`: {module.component_name}") # Check that all inputs are correctly specified if "input" in meta_yaml: - # Obtain list of correct inputs and elements of each input channel - correct_inputs = [] - for input_channel in module.inputs: - channel_elements = [] - for element in input_channel: - channel_elements.append(list(element.keys())[0]) - correct_inputs.append(channel_elements) - # Obtain list of inputs specified in meta.yml - meta_inputs = [] - for input_channel in meta_yaml["input"]: - if isinstance(input_channel, list): # Correct format - channel_elements = [] - for element in input_channel: - channel_elements.append(list(element.keys())[0]) - meta_inputs.append(channel_elements) - elif isinstance(input_channel, dict): # Old format - meta_inputs.append(list(input_channel.keys())[0]) + correct_inputs, meta_inputs = obtain_correct_and_specified_inputs(module_lint_object, module, meta_yaml) if correct_inputs == meta_inputs: module.passed.append( @@ -166,25 +141,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None ) # Check that all outputs are correctly specified if "output" in meta_yaml: - # Obtain dictionary of correct outputs and elements of each output channel - correct_outputs = {} - for output_channel in module.outputs: - channel_name = list(output_channel.keys())[0] - channel_elements = [] - for element in output_channel[channel_name]: - channel_elements.append(list(element.keys())[0]) - correct_outputs[channel_name] = channel_elements - # Obtain dictionary of outputs specified in meta.yml - meta_outputs = {} - for output_channel in meta_yaml["output"]: - channel_name = list(output_channel.keys())[0] - if isinstance(output_channel[channel_name], list): # Correct format - channel_elements = [] - for element in output_channel[channel_name]: - channel_elements.append(list(element.keys())[0]) - meta_outputs[channel_name] = channel_elements - elif isinstance(output_channel[channel_name], dict): # Old format - meta_outputs[channel_name] = [] + correct_outputs, meta_outputs = obtain_correct_and_specified_outputs(module_lint_object, module, meta_yaml) if correct_outputs == meta_outputs: module.passed.append( @@ -202,3 +159,101 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None module.meta_yml, ) ) + + +def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> Union[dict, None]: + """ + Read a `meta.yml` file and return it as a dictionary + + Args: + module_lint_object (ComponentLint): The lint object for the module + module (NFCoreComponent): The module to read + + Returns: + dict: The `meta.yml` file as a dictionary + """ + meta_yaml = None + # Check if we have a patch file, get original file in that case + if module.is_patched: + lines = ModulesDiffer.try_apply_patch( + module.component_name, + module_lint_object.modules_repo.repo_path, + module.patch_path, + Path(module.component_dir).relative_to(module.base_dir), + reverse=True, + ).get("meta.yml") + if lines is not None: + meta_yaml = yaml.safe_load("".join(lines)) + if meta_yaml is None: + try: + with open(module.meta_yml) as fh: + meta_yaml = yaml.safe_load(fh) + except FileNotFoundError: + return None + return meta_yaml + + +def obtain_correct_and_specified_inputs(_, module, meta_yaml): + """ + Obtain the list of correct inputs and the elements of each input channel. + + Args: + module (object): The module object. + meta_yaml (dict): The meta.yml dictionary. + + Returns: + tuple: A tuple containing two lists. The first list contains the correct inputs, + and the second list contains the inputs specified in meta.yml. + """ + correct_inputs = [] + for input_channel in module.inputs: + channel_elements = [] + for element in input_channel: + channel_elements.append(list(element.keys())[0]) + correct_inputs.append(channel_elements) + + meta_inputs = [] + for input_channel in meta_yaml["input"]: + if isinstance(input_channel, list): # Correct format + channel_elements = [] + for element in input_channel: + channel_elements.append(list(element.keys())[0]) + meta_inputs.append(channel_elements) + elif isinstance(input_channel, dict): # Old format + meta_inputs.append(list(input_channel.keys())[0]) + + return correct_inputs, meta_inputs + + +def obtain_correct_and_specified_outputs(_, module, meta_yaml): + """ + Obtain the dictionary of correct outputs and elements of each output channel. + + Args: + module (object): The module object. + meta_yaml (dict): The meta.yml dictionary. + + Returns: + correct_outputs (dict): A dictionary containing the correct outputs and their elements. + meta_outputs (dict): A dictionary containing the outputs specified in meta.yml. + """ + correct_outputs = {} + for output_channel in module.outputs: + channel_name = list(output_channel.keys())[0] + channel_elements = [] + for element in output_channel[channel_name]: + channel_elements.append(list(element.keys())[0]) + correct_outputs[channel_name] = channel_elements + + meta_outputs = {} + for output_channel in meta_yaml["output"]: + channel_name = list(output_channel.keys())[0] + if isinstance(output_channel[channel_name], list): # Correct format + channel_elements = [] + for element in output_channel[channel_name]: + channel_elements.append(list(element.keys())[0]) + meta_outputs[channel_name] = channel_elements + elif isinstance(output_channel[channel_name], dict): # Old format + meta_outputs[channel_name] = [] + + return correct_outputs, meta_outputs From 070d792821c2b26e8cc560b0acdc69c21cfe535d Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 21 Jun 2024 11:54:34 +0200 Subject: [PATCH 094/574] add test for nf-core modules lint --update-meta-yml --- tests/__snapshots__/test_create_app.ambr | 264 ++++++++++++----------- tests/modules/lint.py | 9 + tests/test_modules.py | 1 + 3 files changed, 144 insertions(+), 130 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 2ad0772587..ea853c75a3 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -1405,258 +1405,262 @@ font-weight: 700; } - .terminal-3175764146-matrix { + .terminal-1242773313-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3175764146-title { + .terminal-1242773313-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3175764146-r1 { fill: #c5c8c6 } - .terminal-3175764146-r2 { fill: #e3e3e3 } - .terminal-3175764146-r3 { fill: #989898 } - .terminal-3175764146-r4 { fill: #e1e1e1 } - .terminal-3175764146-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3175764146-r6 { fill: #a5a5a5;font-style: italic; } - .terminal-3175764146-r7 { fill: #454a50 } - .terminal-3175764146-r8 { fill: #e2e3e3;font-weight: bold } - .terminal-3175764146-r9 { fill: #1e1e1e } - .terminal-3175764146-r10 { fill: #008139 } - .terminal-3175764146-r11 { fill: #000000 } - .terminal-3175764146-r12 { fill: #e2e2e2 } - .terminal-3175764146-r13 { fill: #18954b } - .terminal-3175764146-r14 { fill: #e2e2e2;font-weight: bold } - .terminal-3175764146-r15 { fill: #969696;font-weight: bold } - .terminal-3175764146-r16 { fill: #808080 } - .terminal-3175764146-r17 { fill: #7ae998 } - .terminal-3175764146-r18 { fill: #507bb3 } - .terminal-3175764146-r19 { fill: #0a180e;font-weight: bold } - .terminal-3175764146-r20 { fill: #dde6ed;font-weight: bold } - .terminal-3175764146-r21 { fill: #001541 } - .terminal-3175764146-r22 { fill: #fea62b;font-weight: bold } - .terminal-3175764146-r23 { fill: #a7a9ab } - .terminal-3175764146-r24 { fill: #e2e3e3 } + .terminal-1242773313-r1 { fill: #c5c8c6 } + .terminal-1242773313-r2 { fill: #e3e3e3 } + .terminal-1242773313-r3 { fill: #989898 } + .terminal-1242773313-r4 { fill: #e1e1e1 } + .terminal-1242773313-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1242773313-r6 { fill: #18954b } + .terminal-1242773313-r7 { fill: #e2e2e2 } + .terminal-1242773313-r8 { fill: #e2e2e2;font-style: italic; } + .terminal-1242773313-r9 { fill: #e2e2e2;font-style: italic;;text-decoration: underline; } + .terminal-1242773313-r10 { fill: #a5a5a5;font-style: italic; } + .terminal-1242773313-r11 { fill: #1e1e1e } + .terminal-1242773313-r12 { fill: #008139 } + .terminal-1242773313-r13 { fill: #454a50 } + .terminal-1242773313-r14 { fill: #787878 } + .terminal-1242773313-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1242773313-r16 { fill: #000000 } + .terminal-1242773313-r17 { fill: #b93c5b } + .terminal-1242773313-r18 { fill: #e2e2e2;font-weight: bold } + .terminal-1242773313-r19 { fill: #969696;font-weight: bold } + .terminal-1242773313-r20 { fill: #808080 } + .terminal-1242773313-r21 { fill: #7ae998 } + .terminal-1242773313-r22 { fill: #507bb3 } + .terminal-1242773313-r23 { fill: #0a180e;font-weight: bold } + .terminal-1242773313-r24 { fill: #dde6ed;font-weight: bold } + .terminal-1242773313-r25 { fill: #001541 } + .terminal-1242773313-r26 { fill: #fea62b;font-weight: bold } + .terminal-1242773313-r27 { fill: #a7a9ab } + .terminal-1242773313-r28 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - -   Now that we have created a new pipeline locally, we can create a new GitHub repository and push    -   the code to it. - - - - - Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - for login. Show  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊GitHub username▎▊••••••••••••                  ▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core                               ▎▊mypipeline                            ▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Create GitHub repo  Finish without creating a repo  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + + Now that we have created a new pipeline locally, we can create a new GitHub repository and push  + the code to it. + + ▌💡 Found GitHub username in local GitHub CLI config + + + + Your GitHub usernameYour GitHub personal access token + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ + ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + BackCreate GitHub repoFinish without creating a repo + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + +  d Toggle dark mode q Quit diff --git a/tests/modules/lint.py b/tests/modules/lint.py index e1a4e27ff8..7798c0a948 100644 --- a/tests/modules/lint.py +++ b/tests/modules/lint.py @@ -59,6 +59,15 @@ def test_modules_lint_new_modules(self): assert len(module_lint.warned) >= 0 +def test_modules_lint_update_meta_yml(self): + """update the meta.yml of a module""" + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules, update_meta_yml=True) + module_lint.lint(print_results=False, all_modules="fastqc") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_no_gitlab(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) diff --git a/tests/test_modules.py b/tests/test_modules.py index 107b245663..69778dcf0b 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -214,6 +214,7 @@ def test_modulesrepo_class(self): test_modules_lint_snapshot_file_missing_fail, test_modules_lint_snapshot_file_not_needed, test_modules_lint_trimgalore, + test_modules_lint_update_meta_yml, test_modules_meta_yml_incorrect_licence_field, test_modules_meta_yml_incorrect_name, test_modules_meta_yml_input_mismatch, From 2b705572a1e8a07a40ac7ea7cb7274d7654a21d1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 4 Jul 2024 11:48:11 +0200 Subject: [PATCH 095/574] remove qualifier --- nf_core/components/nfcore_component.py | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index dcd76b0e8f..3e5a68648d 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -178,16 +178,13 @@ def get_inputs_from_main_nf(self): regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" matches = re.finditer(regex, line) for _, match in enumerate(matches, start=1): - input_type = None input_val = None - if match.group(1): - input_type = match.group(1) if match.group(3): input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases elif match.group(4): input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - if input_type and input_val: - channel_elements.append({input_val: {"qualifier": input_type}}) + if input_val: + channel_elements.append({input_val: {}}) if len(channel_elements) > 0: inputs.append(channel_elements) log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") @@ -211,17 +208,14 @@ def get_outputs_from_main_nf(self): continue output_channel = {match_emit.group(1): []} for _, match_element in enumerate(matches_elements, start=1): - output_type = None output_val = None - if match_element.group(1): - output_type = match_element.group(1) if match_element.group(3): output_val = match_element.group(3) elif match_element.group(4): output_val = match_element.group(4) - if output_type and output_val: + if output_val: output_val = output_val.strip("'").strip('"') # remove quotes - output_channel[match_emit.group(1)].append({output_val: {"qualifier": output_type}}) + output_channel[match_emit.group(1)].append({output_val: {}}) outputs.append(output_channel) log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") self.outputs = outputs From 0f49a88ec2354361c37a7bf3cb43bf6ce980c0ea Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 4 Jul 2024 12:18:12 +0200 Subject: [PATCH 096/574] use param --fix to update the meta.yml --- nf_core/__main__.py | 6 ++---- nf_core/commands_modules.py | 4 ++-- nf_core/components/lint/__init__.py | 4 ++-- nf_core/modules/lint/__init__.py | 6 +++--- nf_core/modules/lint/meta_yml.py | 4 ++-- tests/modules/lint.py | 2 +- 6 files changed, 12 insertions(+), 14 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 584947afd0..9ba23a8b08 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1196,10 +1196,8 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): is_flag=True, help="Fix the module version if a newer version is available", ) -@click.option( - "--update-meta-yml", is_flag=True, help="Update the meta.yml file with the correct format of input and outputs" -) -def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, update_meta_yml): +@click.option("--fix", is_flag=True, help="Fix all linting tests if possible.") +def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, fix): """ Lint one or more modules in a directory. """ diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index 85471184ca..ca80e87bd1 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -244,7 +244,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile): sys.exit(1) -def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, update_meta_yml): +def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, fix): """ Lint one or more modules in a directory. @@ -261,6 +261,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, module_lint = ModuleLint( dir, fail_warned=fail_warned, + fix=fix, registry=ctx.params["registry"], remote_url=ctx.obj["modules_repo_url"], branch=ctx.obj["modules_repo_branch"], @@ -277,7 +278,6 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, show_passed=passed, sort_by=sort_by, fix_version=fix_version, - update_meta_yml=update_meta_yml, ) if len(module_lint.failed) > 0: sys.exit(1) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index b4194e768e..0e3aba23f7 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -56,7 +56,7 @@ def __init__( component_type, dir, fail_warned=False, - update_meta_yml=False, + fix=False, remote_url=None, branch=None, no_pull=False, @@ -73,7 +73,7 @@ def __init__( ) self.fail_warned = fail_warned - self.update_meta_yml = update_meta_yml + self.fix = fix self.passed = [] self.warned = [] self.failed = [] diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index f6c2069bda..58a4c47159 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -47,7 +47,7 @@ def __init__( self, dir, fail_warned=False, - update_meta_yml=False, + fix=False, remote_url=None, branch=None, no_pull=False, @@ -58,7 +58,7 @@ def __init__( component_type="modules", dir=dir, fail_warned=fail_warned, - update_meta_yml=update_meta_yml, + fix=fix, remote_url=remote_url, branch=branch, no_pull=no_pull, @@ -224,7 +224,7 @@ def lint_module(self, mod, progress_bar, registry, local=False, fix_version=Fals mod.get_inputs_from_main_nf() mod.get_outputs_from_main_nf() # Update meta.yml file if requested - if self.update_meta_yml: + if self.fix: self.update_meta_yml_file(mod) if self.repo_type == "pipeline" and self.modules_json: diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 9c074ba731..c3b5f3f283 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -117,7 +117,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None module.failed.append( ( "correct_meta_inputs", - f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.", + f"Incorrect inputs specified in module `meta.yml`. Inputs should contain: {correct_inputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.", module.meta_yml, ) ) @@ -155,7 +155,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None module.failed.append( ( "correct_meta_outputs", - f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --update-meta-yml` to update the `meta.yml` file.", + f"Incorrect outputs specified in module `meta.yml`. Outputs should contain: {correct_outputs}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.", module.meta_yml, ) ) diff --git a/tests/modules/lint.py b/tests/modules/lint.py index 7798c0a948..9b6c6a78c3 100644 --- a/tests/modules/lint.py +++ b/tests/modules/lint.py @@ -61,7 +61,7 @@ def test_modules_lint_new_modules(self): def test_modules_lint_update_meta_yml(self): """update the meta.yml of a module""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules, update_meta_yml=True) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules, fix=True) module_lint.lint(print_results=False, all_modules="fastqc") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 From ef7364dfbc18e8d63271c0be9732d8ac01c45efa Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 4 Jul 2024 12:27:24 +0200 Subject: [PATCH 097/574] create app snapshot from dev branch --- tests/__snapshots__/test_create_app.ambr | 264 +++++++++++------------ 1 file changed, 130 insertions(+), 134 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index ea853c75a3..2ad0772587 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -1405,262 +1405,258 @@ font-weight: 700; } - .terminal-1242773313-matrix { + .terminal-3175764146-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1242773313-title { + .terminal-3175764146-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1242773313-r1 { fill: #c5c8c6 } - .terminal-1242773313-r2 { fill: #e3e3e3 } - .terminal-1242773313-r3 { fill: #989898 } - .terminal-1242773313-r4 { fill: #e1e1e1 } - .terminal-1242773313-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1242773313-r6 { fill: #18954b } - .terminal-1242773313-r7 { fill: #e2e2e2 } - .terminal-1242773313-r8 { fill: #e2e2e2;font-style: italic; } - .terminal-1242773313-r9 { fill: #e2e2e2;font-style: italic;;text-decoration: underline; } - .terminal-1242773313-r10 { fill: #a5a5a5;font-style: italic; } - .terminal-1242773313-r11 { fill: #1e1e1e } - .terminal-1242773313-r12 { fill: #008139 } - .terminal-1242773313-r13 { fill: #454a50 } - .terminal-1242773313-r14 { fill: #787878 } - .terminal-1242773313-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-1242773313-r16 { fill: #000000 } - .terminal-1242773313-r17 { fill: #b93c5b } - .terminal-1242773313-r18 { fill: #e2e2e2;font-weight: bold } - .terminal-1242773313-r19 { fill: #969696;font-weight: bold } - .terminal-1242773313-r20 { fill: #808080 } - .terminal-1242773313-r21 { fill: #7ae998 } - .terminal-1242773313-r22 { fill: #507bb3 } - .terminal-1242773313-r23 { fill: #0a180e;font-weight: bold } - .terminal-1242773313-r24 { fill: #dde6ed;font-weight: bold } - .terminal-1242773313-r25 { fill: #001541 } - .terminal-1242773313-r26 { fill: #fea62b;font-weight: bold } - .terminal-1242773313-r27 { fill: #a7a9ab } - .terminal-1242773313-r28 { fill: #e2e3e3 } + .terminal-3175764146-r1 { fill: #c5c8c6 } + .terminal-3175764146-r2 { fill: #e3e3e3 } + .terminal-3175764146-r3 { fill: #989898 } + .terminal-3175764146-r4 { fill: #e1e1e1 } + .terminal-3175764146-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3175764146-r6 { fill: #a5a5a5;font-style: italic; } + .terminal-3175764146-r7 { fill: #454a50 } + .terminal-3175764146-r8 { fill: #e2e3e3;font-weight: bold } + .terminal-3175764146-r9 { fill: #1e1e1e } + .terminal-3175764146-r10 { fill: #008139 } + .terminal-3175764146-r11 { fill: #000000 } + .terminal-3175764146-r12 { fill: #e2e2e2 } + .terminal-3175764146-r13 { fill: #18954b } + .terminal-3175764146-r14 { fill: #e2e2e2;font-weight: bold } + .terminal-3175764146-r15 { fill: #969696;font-weight: bold } + .terminal-3175764146-r16 { fill: #808080 } + .terminal-3175764146-r17 { fill: #7ae998 } + .terminal-3175764146-r18 { fill: #507bb3 } + .terminal-3175764146-r19 { fill: #0a180e;font-weight: bold } + .terminal-3175764146-r20 { fill: #dde6ed;font-weight: bold } + .terminal-3175764146-r21 { fill: #001541 } + .terminal-3175764146-r22 { fill: #fea62b;font-weight: bold } + .terminal-3175764146-r23 { fill: #a7a9ab } + .terminal-3175764146-r24 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - Now that we have created a new pipeline locally, we can create a new GitHub repository and push  - the code to it. - - ▌💡 Found GitHub username in local GitHub CLI config - - - - Your GitHub usernameYour GitHub personal access token - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎for login.▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊GitHub username▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎Show - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊GitHub token▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊mypipeline▎ - ▊nf-core▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - BackCreate GitHub repoFinish without creating a repo - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - -  d Toggle dark mode q Quit + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Create GitHub repository + +   Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +   the code to it. + + + + + Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + for login. Show  + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + ▊GitHub username▎▊••••••••••••                  ▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + The name of the organisation where the The name of the new GitHub repository + GitHub repo will be cretaed + ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ + ▊nf-core                               ▎▊mypipeline                            ▎ + ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + ▌⚠️ You can't create a repository directly in the nf-core organisation. + ▌Please create the pipeline repo to an organisation where you have access or use your user  + ▌account. A core-team member will be able to transfer the repo to nf-core once the development + ▌has started. + + ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + + ▊▔▔▔▔▔▔▔▔▎Private + ▊▎Select to make the new GitHub repo private. + ▊▁▁▁▁▁▁▁▁▎ + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Create GitHub repo  Finish without creating a repo  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + +  d Toggle dark mode  q Quit  From c7ff082a46f0693ad5e603fc18a9197e7fcc3e90 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 5 Jul 2024 12:20:20 +0200 Subject: [PATCH 098/574] add fix argument --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 9ba23a8b08..1dd92d6b8f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1201,7 +1201,7 @@ def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, """ Lint one or more modules in a directory. """ - modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version) + modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version, fix) # nf-core modules info From 7c4fcc119648ba01977535c07fcfd1044b6e6514 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 21 Jun 2024 11:07:36 +0200 Subject: [PATCH 099/574] add tool identifier from bio.tools and intput and output ontologies --- nf_core/components/components_utils.py | 27 ++++++++++++++++++++++++++ nf_core/components/create.py | 4 ++++ nf_core/module-template/meta.yml | 19 +++++++++++++++++- nf_core/modules/lint/__init__.py | 16 +++++++++++++-- nf_core/modules/lint/meta_yml.py | 8 +++++--- requirements.txt | 1 + 6 files changed, 69 insertions(+), 6 deletions(-) diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 01650a643d..965b28e16a 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -4,6 +4,7 @@ from typing import List, Optional, Tuple import questionary +import requests import rich.prompt import nf_core.utils @@ -152,3 +153,29 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str elif link.startswith("../"): subworkflows.append(name.lower()) return modules, subworkflows + + +def get_biotools_id(tool_name) -> str: + """ + Try to find a bio.tools ID for 'tool' + """ + url = f"https://bio.tools/api/t/?q={tool_name}&format=json" + try: + # Send a GET request to the API + response = requests.get(url) + response.raise_for_status() # Raise an error for bad status codes + # Parse the JSON response + data = response.json() + + # Iterate through the tools in the response to find the tool name + for tool in data["list"]: + if tool["name"].lower() == tool_name: + return tool["biotoolsCURIE"] + + # If the tool name was not found in the response + log.warning(f"Could not find a bio.tools ID for '{tool_name}'") + return "" + + except requests.exceptions.RequestException as e: + log.warning(f"Could not find a bio.tools ID for '{tool_name}': {e}") + return "" diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 5d6c411bdc..426b91c98a 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -20,6 +20,7 @@ import nf_core import nf_core.utils from nf_core.components.components_command import ComponentCommand +from nf_core.components.components_utils import get_biotools_id from nf_core.pipelines.lint_utils import run_prettier_on_file log = logging.getLogger(__name__) @@ -60,6 +61,7 @@ def __init__( self.file_paths: Dict[str, Path] = {} self.not_empty_template = not empty_template self.migrate_pytest = migrate_pytest + self.tool_identifier = "" def create(self): """ @@ -148,6 +150,8 @@ def create(self): if self.component_type == "modules": # Try to find a bioconda package for 'component' self._get_bioconda_tool() + # Try to find a biotools entry for 'component' + self.tool_identifier = get_biotools_id(self.component) # Prompt for GitHub username self._get_username() diff --git a/nf_core/module-template/meta.yml b/nf_core/module-template/meta.yml index 2dd8e74efa..c7c16dcb38 100644 --- a/nf_core/module-template/meta.yml +++ b/nf_core/module-template/meta.yml @@ -20,6 +20,7 @@ tools: tool_dev_url: "{{ tool_dev_url }}" doi: "" licence: {{ tool_licence }} + identifier: {{ tool_identifier }} {% if not_empty_template -%} ## TODO nf-core: Add a description of all of the variables used as input @@ -39,6 +40,14 @@ input: type: file description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} + ontologies: + {% if not_empty_template -%} + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + {% else %} + - edam: "" + {%- endif %} {% if not_empty_template -%} ## TODO nf-core: Add a description of all of the variables used as output @@ -56,7 +65,7 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - {% endif %} + {%- endif %} {% if not_empty_template -%} ## TODO nf-core: Delete / customise this example output {%- endif %} @@ -64,6 +73,14 @@ output: type: file description: {{ 'Sorted BAM/CRAM/SAM file' if not_empty_template else "" }} pattern: {{ '"*.{bam,cram,sam}"' if not_empty_template else "" }} + ontologies: + {% if not_empty_template -%} + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + {% else -%} + - edam: "" + {%- endif %} authors: - "{{ author }}" diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index 58a4c47159..44e00e333a 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -11,10 +11,11 @@ import questionary import rich -import yaml +import ruamel.yaml import nf_core.modules.modules_utils import nf_core.utils +from nf_core.components.components_utils import get_biotools_id from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult from nf_core.pipelines.lint_utils import console @@ -253,6 +254,9 @@ def update_meta_yml_file(self, mod): """ meta_yml = self.read_meta_yml(mod) corrected_meta_yml = meta_yml.copy() + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + yaml.indent(mapping=2, sequence=2, offset=2) # Obtain inputs and outputs from main.nf and meta.yml # Used to compare only the structure of channels and elements @@ -332,6 +336,14 @@ def update_meta_yml_file(self, mod): ) break + # Add bio.tools identifier + for i, tool in enumerate(corrected_meta_yml["tools"]): + tool_name = list(tool.keys())[0] + if "identifier" not in tool[tool_name]: + corrected_meta_yml["tools"][i][tool_name]["identifier"] = get_biotools_id( + mod.component_name if "/" not in mod.component_name else mod.component_name.split("/")[0] + ) + with open(mod.meta_yml, "w") as fh: log.info(f"Updating {mod.meta_yml}") - yaml.dump(corrected_meta_yml, fh, sort_keys=False, Dumper=nf_core.utils.custom_yaml_dumper()) + yaml.dump(corrected_meta_yml, fh) diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index c3b5f3f283..5bba74acfb 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -3,7 +3,7 @@ from pathlib import Path from typing import Union -import yaml +import ruamel.yaml from jsonschema import exceptions, validators from nf_core.components.lint import ComponentLint @@ -173,6 +173,8 @@ def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> dict: The `meta.yml` file as a dictionary """ meta_yaml = None + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True # Check if we have a patch file, get original file in that case if module.is_patched: lines = ModulesDiffer.try_apply_patch( @@ -183,11 +185,11 @@ def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> reverse=True, ).get("meta.yml") if lines is not None: - meta_yaml = yaml.safe_load("".join(lines)) + meta_yaml = yaml.load("".join(lines)) if meta_yaml is None: try: with open(module.meta_yml) as fh: - meta_yaml = yaml.safe_load(fh) + meta_yaml = yaml.load(fh) except FileNotFoundError: return None return meta_yaml diff --git a/requirements.txt b/requirements.txt index ccfc1bc9c1..a85f4e15c5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -24,3 +24,4 @@ tabulate textual==0.71.0 trogon pdiff +ruamel From e757a214ed677daa542853d9f83aee92e76782b0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 25 Jun 2024 11:28:23 +0200 Subject: [PATCH 100/574] fix indentation and run prettier on meta.yml files --- nf_core/modules/lint/__init__.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index 44e00e333a..9314ba07b2 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -17,7 +17,7 @@ import nf_core.utils from nf_core.components.components_utils import get_biotools_id from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult -from nf_core.pipelines.lint_utils import console +from nf_core.pipelines.lint_utils import console, run_prettier_on_file log = logging.getLogger(__name__) @@ -256,7 +256,7 @@ def update_meta_yml_file(self, mod): corrected_meta_yml = meta_yml.copy() yaml = ruamel.yaml.YAML() yaml.preserve_quotes = True - yaml.indent(mapping=2, sequence=2, offset=2) + yaml.indent(mapping=2, sequence=2, offset=0) # Obtain inputs and outputs from main.nf and meta.yml # Used to compare only the structure of channels and elements @@ -347,3 +347,4 @@ def update_meta_yml_file(self, mod): with open(mod.meta_yml, "w") as fh: log.info(f"Updating {mod.meta_yml}") yaml.dump(corrected_meta_yml, fh) + run_prettier_on_file(fh.name) From 7979ced0852c0f66e357bf876b02c2cea8f4e301 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 5 Jul 2024 12:14:56 +0200 Subject: [PATCH 101/574] install correct ruamel library --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a85f4e15c5..61e181cac5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -24,4 +24,4 @@ tabulate textual==0.71.0 trogon pdiff -ruamel +ruamel.yaml From e2c04cc1c5c4ba7bddcc7c17ec7fd67765a56e63 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 5 Jul 2024 13:48:29 +0200 Subject: [PATCH 102/574] update output_dir for api docs to new website structure --- docs/api/generate-api-docs.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/api/generate-api-docs.sh b/docs/api/generate-api-docs.sh index f2b905c0c3..cc65e1bb14 100644 --- a/docs/api/generate-api-docs.sh +++ b/docs/api/generate-api-docs.sh @@ -28,7 +28,7 @@ done # Set the output directory if not set if [[ -z "$output_dir" ]]; then - output_dir="../src/content/api_reference" + output_dir="../sites/docs/src/content/api_reference" fi # if no release is specified, use all releases From ade71b7852947459ab242999306204e85bd10300 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 5 Jul 2024 11:49:37 +0000 Subject: [PATCH 103/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16db104fc6..559a427e90 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,6 +42,7 @@ - Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) +- update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From edcda568d640a3d96fe7b653e8c9d6317a68be45 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 5 Jul 2024 14:19:26 +0000 Subject: [PATCH 104/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6cefa7fc0f..c1dc7978f6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.0 + rev: v0.5.1 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 0ee58ee7f609e44c5150aafda0f2a51435114457 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 5 Jul 2024 14:20:14 +0000 Subject: [PATCH 105/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 559a427e90..6da61b3fe3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,7 @@ - Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From b61d781507b68efab8b8e277806cb3b2290fa8f5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 09:08:22 +0200 Subject: [PATCH 106/574] update awsfulltest linting tests to new structure --- nf_core/pipelines/lint/actions_awsfulltest.py | 4 +++- tests/lint/actions_awsfulltest.py | 16 ++++++++-------- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/nf_core/pipelines/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py index d5a061c935..4cf3bece28 100644 --- a/nf_core/pipelines/lint/actions_awsfulltest.py +++ b/nf_core/pipelines/lint/actions_awsfulltest.py @@ -41,7 +41,9 @@ def actions_awsfulltest(self): # Check that the action is only turned on for published releases try: - if wf[True]["release"]["types"] != ["published"]: + if wf[True]["pull_request"]["branches"] != ["master"]: + raise AssertionError() + if wf[True]["pull_request_review"]["types"] != ["submitted"]: raise AssertionError() if "workflow_dispatch" not in wf[True]: raise AssertionError() diff --git a/tests/lint/actions_awsfulltest.py b/tests/lint/actions_awsfulltest.py index caf7bbf366..d1479bb1e1 100644 --- a/tests/lint/actions_awsfulltest.py +++ b/tests/lint/actions_awsfulltest.py @@ -1,4 +1,4 @@ -import os +from pathlib import Path import yaml @@ -6,7 +6,7 @@ def test_actions_awsfulltest_warn(self): - """Lint test: actions_awsfulltest - WARN""" + """Lint test: actions_awsfulltest - PASS""" self.lint_obj._load() results = self.lint_obj.actions_awsfulltest() assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"] @@ -15,14 +15,14 @@ def test_actions_awsfulltest_warn(self): def test_actions_awsfulltest_pass(self): - """Lint test: actions_awsfulltest - PASS""" + """Lint test: actions_awsfulltest - WARN""" # Edit .github/workflows/awsfulltest.yml to use -profile test_full new_pipeline = self._make_pipeline_copy() - with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: awsfulltest_yml = fh.read() awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ") - with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: fh.write(awsfulltest_yml) # Make lint object @@ -44,10 +44,10 @@ def test_actions_awsfulltest_fail(self): # Edit .github/workflows/awsfulltest.yml to use -profile test_full new_pipeline = self._make_pipeline_copy() - with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: awsfulltest_yml = yaml.safe_load(fh) - del awsfulltest_yml[True]["release"] - with open(os.path.join(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: + del awsfulltest_yml[True]["pull_request_review"] + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: yaml.dump(awsfulltest_yml, fh) # Make lint object From 48981f2dbfd8719a5adb6b5a7c529032ed6fdd7f Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 09:32:10 +0200 Subject: [PATCH 107/574] escape github variables in jinja template --- nf_core/pipeline-template/.github/workflows/awsfulltest.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml index f0d0724424..dc0450be43 100644 --- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml +++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml @@ -20,12 +20,12 @@ jobs: - uses: octokit/request-action@v2.x id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables run: | - JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %} CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform From fd71df4409cb3556f448f9ed04064a53c49375fc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 9 Jul 2024 08:19:17 +0000 Subject: [PATCH 108/574] [automated] Fix code linting --- nf_core/__main__.py | 4 +++- nf_core/commands_subworkflows.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 2be4697ffb..331f536834 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1601,7 +1601,9 @@ def command_subworkflows_update( """ Update DSL2 subworkflow within a pipeline. """ - subworkflows_update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output) + subworkflows_update( + ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output + ) ## DEPRECATED commands since v3.0.0 diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index f220caf93c..a3abce3f85 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -251,7 +251,7 @@ def subworkflows_update( ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], - limit_output + limit_output, ) exit_status = subworkflow_install.update(subworkflow) if not exit_status and install_all: From 0eaa72002e9c11679fcbbd43ea5c39b1679e2424 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 10:54:23 +0200 Subject: [PATCH 109/574] update API docs with new pipeline command structure --- docs/api/_src/api/index.md | 15 ++-- docs/api/_src/api/licences.md | 9 --- docs/api/_src/api/modules.md | 9 --- .../_src/api/{ => pipelines}/bump_version.md | 2 +- docs/api/_src/api/{ => pipelines}/create.md | 2 +- docs/api/_src/api/{ => pipelines}/download.md | 2 +- docs/api/_src/api/pipelines/index.md | 8 ++ docs/api/_src/api/{ => pipelines}/launch.md | 2 +- docs/api/_src/api/{ => pipelines}/lint.md | 4 +- docs/api/_src/api/{ => pipelines}/list.md | 2 +- .../_src/api/{ => pipelines}/params-file.md | 2 +- docs/api/_src/api/{ => pipelines}/schema.md | 2 +- docs/api/_src/api/{ => pipelines}/sync.md | 2 +- docs/api/_src/api/{ => pipelines}/utils.md | 2 +- docs/api/_src/api/subworkflows.md | 9 --- docs/api/_src/index.md | 22 ++---- docs/api/_src/module_lint_tests/index.md | 17 ++-- .../actions_awsfulltest.md | 2 +- .../pipeline_lint_tests/actions_awstest.md | 2 +- .../_src/pipeline_lint_tests/actions_ci.md | 2 +- .../actions_schema_validation.md | 2 +- .../_src/pipeline_lint_tests/base_config.md | 2 +- .../_src/pipeline_lint_tests/files_exist.md | 2 +- .../pipeline_lint_tests/files_unchanged.md | 2 +- docs/api/_src/pipeline_lint_tests/index.md | 31 ++++++-- .../_src/pipeline_lint_tests/merge_markers.md | 2 +- .../pipeline_lint_tests/modules_config.md | 2 +- .../_src/pipeline_lint_tests/modules_json.md | 4 +- .../pipeline_lint_tests/modules_structure.md | 2 +- .../pipeline_lint_tests/multiqc_config.md | 2 +- .../pipeline_lint_tests/nextflow_config.md | 2 +- .../_src/pipeline_lint_tests/nfcore_yml.md | 2 +- .../pipeline_name_conventions.md | 2 +- .../pipeline_lint_tests/pipeline_todos.md | 2 +- docs/api/_src/pipeline_lint_tests/readme.md | 2 +- .../pipeline_lint_tests/schema_description.md | 2 +- .../_src/pipeline_lint_tests/schema_lint.md | 2 +- .../_src/pipeline_lint_tests/schema_params.md | 2 +- .../_src/pipeline_lint_tests/system_exit.md | 2 +- .../pipeline_lint_tests/template_strings.md | 2 +- .../version_consistency.md | 2 +- docs/api/_src/subworkflow_lint_tests/index.md | 14 ++-- docs/api/make_lint_md.py | 77 ++++++++++--------- 43 files changed, 139 insertions(+), 142 deletions(-) delete mode 100644 docs/api/_src/api/licences.md delete mode 100644 docs/api/_src/api/modules.md rename docs/api/_src/api/{ => pipelines}/bump_version.md (72%) rename docs/api/_src/api/{ => pipelines}/create.md (73%) rename docs/api/_src/api/{ => pipelines}/download.md (73%) create mode 100644 docs/api/_src/api/pipelines/index.md rename docs/api/_src/api/{ => pipelines}/launch.md (73%) rename docs/api/_src/api/{ => pipelines}/lint.md (64%) rename docs/api/_src/api/{ => pipelines}/list.md (74%) rename docs/api/_src/api/{ => pipelines}/params-file.md (72%) rename docs/api/_src/api/{ => pipelines}/schema.md (73%) rename docs/api/_src/api/{ => pipelines}/sync.md (74%) rename docs/api/_src/api/{ => pipelines}/utils.md (74%) delete mode 100644 docs/api/_src/api/subworkflows.md diff --git a/docs/api/_src/api/index.md b/docs/api/_src/api/index.md index a1863f7e39..035a896888 100644 --- a/docs/api/_src/api/index.md +++ b/docs/api/_src/api/index.md @@ -1,8 +1,11 @@ -# API Reference +# nf-core/tools documentation -```{toctree} -:glob: true -:maxdepth: 1 +This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package. -* -``` +## Contents + +- [Pipeline commands](./pipeline_lint_tests/) (run by `nf-core pipelines lint`) +- [Module commands](./module_lint_tests/) (run by `nf-core modules lint`) +- [Subworkflow commands](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`) +- [nf-core/tools Python package API reference](./api/) + - [nf-core/tools pipeline commands API referece](./api/pipelines/) diff --git a/docs/api/_src/api/licences.md b/docs/api/_src/api/licences.md deleted file mode 100644 index 95b5f9768b..0000000000 --- a/docs/api/_src/api/licences.md +++ /dev/null @@ -1,9 +0,0 @@ -# nf_core.licences - -```{eval-rst} -.. automodule:: nf_core.licences - :members: - :undoc-members: - :show-inheritance: - :private-members: -``` diff --git a/docs/api/_src/api/modules.md b/docs/api/_src/api/modules.md deleted file mode 100644 index e3f1e39bed..0000000000 --- a/docs/api/_src/api/modules.md +++ /dev/null @@ -1,9 +0,0 @@ -# nf_core.modules - -```{eval-rst} -.. automodule:: nf_core.modules - :members: - :undoc-members: - :show-inheritance: - :private-members: -``` diff --git a/docs/api/_src/api/bump_version.md b/docs/api/_src/api/pipelines/bump_version.md similarity index 72% rename from docs/api/_src/api/bump_version.md rename to docs/api/_src/api/pipelines/bump_version.md index 54c3774408..cd7dc280f6 100644 --- a/docs/api/_src/api/bump_version.md +++ b/docs/api/_src/api/pipelines/bump_version.md @@ -1,7 +1,7 @@ # nf_core.bump_version ```{eval-rst} -.. automodule:: nf_core.bump_version +.. automodule:: nf_core.pipelines.bump_version :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/create.md b/docs/api/_src/api/pipelines/create.md similarity index 73% rename from docs/api/_src/api/create.md rename to docs/api/_src/api/pipelines/create.md index 5d5f6a62d1..576335e951 100644 --- a/docs/api/_src/api/create.md +++ b/docs/api/_src/api/pipelines/create.md @@ -1,7 +1,7 @@ # nf_core.create ```{eval-rst} -.. automodule:: nf_core.create +.. automodule:: nf_core.pipelines.create :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/download.md b/docs/api/_src/api/pipelines/download.md similarity index 73% rename from docs/api/_src/api/download.md rename to docs/api/_src/api/pipelines/download.md index 18ab51376e..540fb92c49 100644 --- a/docs/api/_src/api/download.md +++ b/docs/api/_src/api/pipelines/download.md @@ -1,7 +1,7 @@ # nf_core.download ```{eval-rst} -.. automodule:: nf_core.download +.. automodule:: nf_core.pipelines.download :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/pipelines/index.md b/docs/api/_src/api/pipelines/index.md new file mode 100644 index 0000000000..a1863f7e39 --- /dev/null +++ b/docs/api/_src/api/pipelines/index.md @@ -0,0 +1,8 @@ +# API Reference + +```{toctree} +:glob: true +:maxdepth: 1 + +* +``` diff --git a/docs/api/_src/api/launch.md b/docs/api/_src/api/pipelines/launch.md similarity index 73% rename from docs/api/_src/api/launch.md rename to docs/api/_src/api/pipelines/launch.md index eef777ca87..0f7fc03f64 100644 --- a/docs/api/_src/api/launch.md +++ b/docs/api/_src/api/pipelines/launch.md @@ -1,7 +1,7 @@ # nf_core.launch ```{eval-rst} -.. automodule:: nf_core.launch +.. automodule:: nf_core.pipelines.launch :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/lint.md b/docs/api/_src/api/pipelines/lint.md similarity index 64% rename from docs/api/_src/api/lint.md rename to docs/api/_src/api/pipelines/lint.md index 1380f7ec7b..aa62c404b8 100644 --- a/docs/api/_src/api/lint.md +++ b/docs/api/_src/api/pipelines/lint.md @@ -1,11 +1,11 @@ # nf_core.lint :::{seealso} -See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about specific linting functions. +See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions. ::: ```{eval-rst} -.. automodule:: nf_core.lint +.. automodule:: nf_core.pipelines.lint :members: run_linting :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/list.md b/docs/api/_src/api/pipelines/list.md similarity index 74% rename from docs/api/_src/api/list.md rename to docs/api/_src/api/pipelines/list.md index 35c819bc56..7df7564544 100644 --- a/docs/api/_src/api/list.md +++ b/docs/api/_src/api/pipelines/list.md @@ -1,7 +1,7 @@ # nf_core.list ```{eval-rst} -.. automodule:: nf_core.list +.. automodule:: nf_core.pipelines.list :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/params-file.md b/docs/api/_src/api/pipelines/params-file.md similarity index 72% rename from docs/api/_src/api/params-file.md rename to docs/api/_src/api/pipelines/params-file.md index c5bbfc0f1f..06f27cc592 100644 --- a/docs/api/_src/api/params-file.md +++ b/docs/api/_src/api/pipelines/params-file.md @@ -1,7 +1,7 @@ # nf_core.params_file ```{eval-rst} -.. automodule:: nf_core.params_file +.. automodule:: nf_core.pipelines.params_file :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/schema.md b/docs/api/_src/api/pipelines/schema.md similarity index 73% rename from docs/api/_src/api/schema.md rename to docs/api/_src/api/pipelines/schema.md index a702d28058..c885d9ed23 100644 --- a/docs/api/_src/api/schema.md +++ b/docs/api/_src/api/pipelines/schema.md @@ -1,7 +1,7 @@ # nf_core.schema ```{eval-rst} -.. automodule:: nf_core.schema +.. automodule:: nf_core.pipelines.schema :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/sync.md b/docs/api/_src/api/pipelines/sync.md similarity index 74% rename from docs/api/_src/api/sync.md rename to docs/api/_src/api/pipelines/sync.md index 8cc02209da..da1f468fe5 100644 --- a/docs/api/_src/api/sync.md +++ b/docs/api/_src/api/pipelines/sync.md @@ -1,7 +1,7 @@ # nf_core.sync ```{eval-rst} -.. automodule:: nf_core.sync +.. automodule:: nf_core.pipelines.sync :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/utils.md b/docs/api/_src/api/pipelines/utils.md similarity index 74% rename from docs/api/_src/api/utils.md rename to docs/api/_src/api/pipelines/utils.md index 1353f97ef5..86b8c3f36f 100644 --- a/docs/api/_src/api/utils.md +++ b/docs/api/_src/api/pipelines/utils.md @@ -1,7 +1,7 @@ # nf_core.utils ```{eval-rst} -.. automodule:: nf_core.utils +.. automodule:: nf_core.pipelines.utils :members: :undoc-members: :show-inheritance: diff --git a/docs/api/_src/api/subworkflows.md b/docs/api/_src/api/subworkflows.md deleted file mode 100644 index 438ccd0185..0000000000 --- a/docs/api/_src/api/subworkflows.md +++ /dev/null @@ -1,9 +0,0 @@ -# nf_core.subworkflows - -```{eval-rst} -.. automodule:: nf_core.subworkflows - :members: - :undoc-members: - :show-inheritance: - :private-members: -``` diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md index 037ca95475..d81a0e90d4 100644 --- a/docs/api/_src/index.md +++ b/docs/api/_src/index.md @@ -1,22 +1,10 @@ # nf-core/tools documentation -```{toctree} -:caption: 'Contents:' -:glob: true -:hidden: true -:maxdepth: 2 - -pipeline_lint_tests/index.rst -module_lint_tests/index.rst -subworkflow_lint_tests/index.rst -api/index.rst -``` - -This documentation is for the `nf-core/tools` package. +This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package. ## Contents -- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`) -- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`) -- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`) -- [nf-core/tools Python package API reference](api/index.md) +- [Pipeline code lint tests](./pipeline_lint_tests/) (run by `nf-core pipelines lint`) +- [Module code lint tests](./module_lint_tests/) (run by `nf-core modules lint`) +- [Subworkflow code lint tests](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`) +- [nf-core/tools Python package API reference](./api/) diff --git a/docs/api/_src/module_lint_tests/index.md b/docs/api/_src/module_lint_tests/index.md index dee84d06d8..7039ba2598 100644 --- a/docs/api/_src/module_lint_tests/index.md +++ b/docs/api/_src/module_lint_tests/index.md @@ -1,8 +1,11 @@ -# Module lint tests +# Module Lint Tests -```{toctree} -:glob: true -:maxdepth: 1 - -* -``` + - [environment_yml](./environment_yml/) + - [main_nf](./main_nf/) + - [meta_yml](./meta_yml/) + - [module_changes](./module_changes/) + - [module_deprecations](./module_deprecations/) + - [module_patch](./module_patch/) + - [module_tests](./module_tests/) + - [module_todos](./module_todos/) + - [module_version](./module_version/) diff --git a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md index c0f0aef5a4..4bb47569ac 100644 --- a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md +++ b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md @@ -1,5 +1,5 @@ # actions_awsfulltest ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.actions_awsfulltest +.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awsfulltest ``` diff --git a/docs/api/_src/pipeline_lint_tests/actions_awstest.md b/docs/api/_src/pipeline_lint_tests/actions_awstest.md index 42441c8ac5..b250571a04 100644 --- a/docs/api/_src/pipeline_lint_tests/actions_awstest.md +++ b/docs/api/_src/pipeline_lint_tests/actions_awstest.md @@ -1,5 +1,5 @@ # actions_awstest ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.actions_awstest +.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awstest ``` diff --git a/docs/api/_src/pipeline_lint_tests/actions_ci.md b/docs/api/_src/pipeline_lint_tests/actions_ci.md index 78ea3aea0d..68cbc089ad 100644 --- a/docs/api/_src/pipeline_lint_tests/actions_ci.md +++ b/docs/api/_src/pipeline_lint_tests/actions_ci.md @@ -1,5 +1,5 @@ # actions_ci ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.actions_ci +.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_ci ``` diff --git a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md index f0c98eb213..860acb2d2e 100644 --- a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md +++ b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md @@ -1,5 +1,5 @@ # actions_schema_validation ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.actions_schema_validation +.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_schema_validation ``` diff --git a/docs/api/_src/pipeline_lint_tests/base_config.md b/docs/api/_src/pipeline_lint_tests/base_config.md index 4a56ef9789..803627ced0 100644 --- a/docs/api/_src/pipeline_lint_tests/base_config.md +++ b/docs/api/_src/pipeline_lint_tests/base_config.md @@ -1,5 +1,5 @@ # base_config ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.base_config +.. automethod:: nf_core.pipelines.lint.PipelineLint.base_config ``` diff --git a/docs/api/_src/pipeline_lint_tests/files_exist.md b/docs/api/_src/pipeline_lint_tests/files_exist.md index 309ea62f0b..69890d1690 100644 --- a/docs/api/_src/pipeline_lint_tests/files_exist.md +++ b/docs/api/_src/pipeline_lint_tests/files_exist.md @@ -1,5 +1,5 @@ # files_exist ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.files_exist +.. automethod:: nf_core.pipelines.lint.PipelineLint.files_exist ``` diff --git a/docs/api/_src/pipeline_lint_tests/files_unchanged.md b/docs/api/_src/pipeline_lint_tests/files_unchanged.md index 2f3b04fe1b..3f626e5b8d 100644 --- a/docs/api/_src/pipeline_lint_tests/files_unchanged.md +++ b/docs/api/_src/pipeline_lint_tests/files_unchanged.md @@ -1,5 +1,5 @@ # files_unchanged ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.files_unchanged +.. automethod:: nf_core.pipelines.lint.PipelineLint.files_unchanged ``` diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md index c631610d64..3575c08db4 100644 --- a/docs/api/_src/pipeline_lint_tests/index.md +++ b/docs/api/_src/pipeline_lint_tests/index.md @@ -1,8 +1,25 @@ -# Pipeline lint tests +# Pipeline Lint Tests -```{toctree} -:glob: true -:maxdepth: 1 - -* -``` + - [actions_awsfulltest](./actions_awsfulltest/) + - [actions_awstest](./actions_awstest/) + - [actions_ci](./actions_ci/) + - [actions_schema_validation](./actions_schema_validation/) + - [base_config](./base_config/) + - [files_exist](./files_exist/) + - [files_unchanged](./files_unchanged/) + - [merge_markers](./merge_markers/) + - [modules_config](./modules_config/) + - [modules_json](./modules_json/) + - [modules_structure](./modules_structure/) + - [multiqc_config](./multiqc_config/) + - [nextflow_config](./nextflow_config/) + - [nfcore_yml](./nfcore_yml/) + - [pipeline_name_conventions](./pipeline_name_conventions/) + - [pipeline_todos](./pipeline_todos/) + - [readme](./readme/) + - [schema_description](./schema_description/) + - [schema_lint](./schema_lint/) + - [schema_params](./schema_params/) + - [system_exit](./system_exit/) + - [template_strings](./template_strings/) + - [version_consistency](./version_consistency/) diff --git a/docs/api/_src/pipeline_lint_tests/merge_markers.md b/docs/api/_src/pipeline_lint_tests/merge_markers.md index b52fdba1a8..7b620b4af1 100644 --- a/docs/api/_src/pipeline_lint_tests/merge_markers.md +++ b/docs/api/_src/pipeline_lint_tests/merge_markers.md @@ -1,5 +1,5 @@ # merge_markers ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.merge_markers +.. automethod:: nf_core.pipelines.lint.PipelineLint.merge_markers ``` diff --git a/docs/api/_src/pipeline_lint_tests/modules_config.md b/docs/api/_src/pipeline_lint_tests/modules_config.md index 2a4f51c5a4..c8eac0cf9d 100644 --- a/docs/api/_src/pipeline_lint_tests/modules_config.md +++ b/docs/api/_src/pipeline_lint_tests/modules_config.md @@ -1,5 +1,5 @@ # modules_config ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.modules_config +.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_config ``` diff --git a/docs/api/_src/pipeline_lint_tests/modules_json.md b/docs/api/_src/pipeline_lint_tests/modules_json.md index 0c0ba71a8f..3070f83f57 100644 --- a/docs/api/_src/pipeline_lint_tests/modules_json.md +++ b/docs/api/_src/pipeline_lint_tests/modules_json.md @@ -1,5 +1,5 @@ -# nextflow_config +# modules_json ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.modules_json +.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_json ``` diff --git a/docs/api/_src/pipeline_lint_tests/modules_structure.md b/docs/api/_src/pipeline_lint_tests/modules_structure.md index faa39ca77f..8a83918857 100644 --- a/docs/api/_src/pipeline_lint_tests/modules_structure.md +++ b/docs/api/_src/pipeline_lint_tests/modules_structure.md @@ -1,5 +1,5 @@ # modules_structure ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.modules_structure +.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_structure ``` diff --git a/docs/api/_src/pipeline_lint_tests/multiqc_config.md b/docs/api/_src/pipeline_lint_tests/multiqc_config.md index 311f6b3049..281957749a 100644 --- a/docs/api/_src/pipeline_lint_tests/multiqc_config.md +++ b/docs/api/_src/pipeline_lint_tests/multiqc_config.md @@ -1,5 +1,5 @@ # multiqc_config ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.multiqc_config +.. automethod:: nf_core.pipelines.lint.PipelineLint.multiqc_config ``` diff --git a/docs/api/_src/pipeline_lint_tests/nextflow_config.md b/docs/api/_src/pipeline_lint_tests/nextflow_config.md index e23e966143..98e8df2574 100644 --- a/docs/api/_src/pipeline_lint_tests/nextflow_config.md +++ b/docs/api/_src/pipeline_lint_tests/nextflow_config.md @@ -1,5 +1,5 @@ # nextflow_config ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.nextflow_config +.. automethod:: nf_core.pipelines.lint.PipelineLint.nextflow_config ``` diff --git a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md index f7e797a29c..226eb4c948 100644 --- a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md +++ b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md @@ -1,5 +1,5 @@ # nfcore_yml ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.nfcore_yml +.. automethod:: nf_core.pipelines.lint.PipelineLint.nfcore_yml ``` diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md index 0034319d3d..09396b6afd 100644 --- a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md +++ b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md @@ -1,5 +1,5 @@ # pipeline_name_conventions ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.pipeline_name_conventions +.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_name_conventions ``` diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md index 08e456ea22..8292075b91 100644 --- a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md +++ b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md @@ -1,5 +1,5 @@ # pipeline_todos ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.pipeline_todos +.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_todos ``` diff --git a/docs/api/_src/pipeline_lint_tests/readme.md b/docs/api/_src/pipeline_lint_tests/readme.md index 9583a56e0a..bf947bb61e 100644 --- a/docs/api/_src/pipeline_lint_tests/readme.md +++ b/docs/api/_src/pipeline_lint_tests/readme.md @@ -1,5 +1,5 @@ # readme ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.readme +.. automethod:: nf_core.pipelines.lint.PipelineLint.readme ``` diff --git a/docs/api/_src/pipeline_lint_tests/schema_description.md b/docs/api/_src/pipeline_lint_tests/schema_description.md index 14f756acd2..0429b3cc10 100644 --- a/docs/api/_src/pipeline_lint_tests/schema_description.md +++ b/docs/api/_src/pipeline_lint_tests/schema_description.md @@ -1,5 +1,5 @@ # schema_description ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.schema_description +.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_description ``` diff --git a/docs/api/_src/pipeline_lint_tests/schema_lint.md b/docs/api/_src/pipeline_lint_tests/schema_lint.md index 39be2ea65c..95bd5cc2fc 100644 --- a/docs/api/_src/pipeline_lint_tests/schema_lint.md +++ b/docs/api/_src/pipeline_lint_tests/schema_lint.md @@ -1,5 +1,5 @@ # schema_lint ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.schema_lint +.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_lint ``` diff --git a/docs/api/_src/pipeline_lint_tests/schema_params.md b/docs/api/_src/pipeline_lint_tests/schema_params.md index 80a626e880..8c6594c57b 100644 --- a/docs/api/_src/pipeline_lint_tests/schema_params.md +++ b/docs/api/_src/pipeline_lint_tests/schema_params.md @@ -1,5 +1,5 @@ # schema_params ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.schema_params +.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_params ``` diff --git a/docs/api/_src/pipeline_lint_tests/system_exit.md b/docs/api/_src/pipeline_lint_tests/system_exit.md index 3d0ac20f8d..9ba67d4d2f 100644 --- a/docs/api/_src/pipeline_lint_tests/system_exit.md +++ b/docs/api/_src/pipeline_lint_tests/system_exit.md @@ -1,5 +1,5 @@ # system_exit ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.system_exit +.. automethod:: nf_core.pipelines.lint.PipelineLint.system_exit ``` diff --git a/docs/api/_src/pipeline_lint_tests/template_strings.md b/docs/api/_src/pipeline_lint_tests/template_strings.md index 3d03bfb256..ee334a2a21 100644 --- a/docs/api/_src/pipeline_lint_tests/template_strings.md +++ b/docs/api/_src/pipeline_lint_tests/template_strings.md @@ -1,5 +1,5 @@ # template_strings ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.template_strings +.. automethod:: nf_core.pipelines.lint.PipelineLint.template_strings ``` diff --git a/docs/api/_src/pipeline_lint_tests/version_consistency.md b/docs/api/_src/pipeline_lint_tests/version_consistency.md index e8038f8531..868a348704 100644 --- a/docs/api/_src/pipeline_lint_tests/version_consistency.md +++ b/docs/api/_src/pipeline_lint_tests/version_consistency.md @@ -1,5 +1,5 @@ # version_consistency ```{eval-rst} -.. automethod:: nf_core.lint.PipelineLint.version_consistency +.. automethod:: nf_core.pipelines.lint.PipelineLint.version_consistency ``` diff --git a/docs/api/_src/subworkflow_lint_tests/index.md b/docs/api/_src/subworkflow_lint_tests/index.md index 0ecf590c0d..da8db49a7b 100644 --- a/docs/api/_src/subworkflow_lint_tests/index.md +++ b/docs/api/_src/subworkflow_lint_tests/index.md @@ -1,8 +1,8 @@ -# Subworkflow lint tests +# Subworkflow Lint Tests -```{toctree} -:glob: true -:maxdepth: 1 - -* -``` + - [main_nf](./main_nf/) + - [meta_yml](./meta_yml/) + - [subworkflow_changes](./subworkflow_changes/) + - [subworkflow_tests](./subworkflow_tests/) + - [subworkflow_todos](./subworkflow_todos/) + - [subworkflow_version](./subworkflow_version/) diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py index 48393094b3..7b823a086e 100644 --- a/docs/api/make_lint_md.py +++ b/docs/api/make_lint_md.py @@ -1,53 +1,58 @@ -#!/usr/bin/env python - -import fnmatch -import os +from pathlib import Path +#!/usr/bin/env python +import nf_core.commands_pipelines import nf_core.modules.lint import nf_core.pipelines.lint import nf_core.subworkflows.lint -def make_docs(docs_basedir, lint_tests, md_template): - # Get list of existing .md files - existing_docs = [] - for fn in os.listdir(docs_basedir): - if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"): - existing_docs.append(os.path.join(docs_basedir, fn)) +def create_docs(docs_basedir, lint_tests, md_template): + docs_basedir.mkdir(parents=True, exist_ok=True) + existing_docs = list(docs_basedir.glob("*.md")) + existing_docs.remove(docs_basedir / "index.md") for test_name in lint_tests: - fn = os.path.join(docs_basedir, f"{test_name}.md") - if os.path.exists(fn): + fn = docs_basedir / f"{test_name}.md" + if fn.exists(): existing_docs.remove(fn) else: with open(fn, "w") as fh: fh.write(md_template.format(test_name)) for fn in existing_docs: - os.remove(fn) + fn.unlink() + + +def create_index_file(basedir, title): + index_file = basedir / "index.md" + with open(index_file, "w") as fh: + fh.write(f"# {title}\n\n") + for fn in sorted(basedir.glob("*.md")): + if fn.name != "index.md": + fh.write(f" - [{fn.stem}](./{fn.stem}/)\n") # Create the pipeline docs -pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests") -make_docs( - pipeline_docs_basedir, +pipeline_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "pipeline_lint_tests" +create_docs( + pipeline_lint_docs_basedir, nf_core.pipelines.lint.PipelineLint._get_all_lint_tests(True), """# {0} -```{{eval-rst}} -.. automethod:: nf_core.pipelines.lint.PipelineLint.{0} -``` -""", + ```{{eval-rst}} + .. automethod:: nf_core.pipelines.lint.PipelineLint.{0} + ``` + """, ) +create_index_file(pipeline_lint_docs_basedir, "Pipeline Lint Tests") -# Create the modules lint docs -modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "module_lint_tests") -make_docs( - modules_docs_basedir, - list( - set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union( - nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False) - ) +# Create the modules docs +modules_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "module_lint_tests" +create_docs( + modules_lint_docs_basedir, + set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union( + nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False) ), """# {0} @@ -56,15 +61,14 @@ def make_docs(docs_basedir, lint_tests, md_template): ``` """, ) +create_index_file(modules_lint_docs_basedir, "Module Lint Tests") -# Create the subworkflows lint docs -subworkflows_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "subworkflow_lint_tests") -make_docs( - subworkflows_docs_basedir, - list( - set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union( - nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False) - ) +# Create the subworkflow docs +subworkflow_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "subworkflow_lint_tests" +create_docs( + subworkflow_lint_docs_basedir, + set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union( + nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False) ), """# {0} @@ -73,3 +77,4 @@ def make_docs(docs_basedir, lint_tests, md_template): ``` """, ) +create_index_file(subworkflow_lint_docs_basedir, "Subworkflow Lint Tests") From e8e2e49d5ab69671d9bcbad4dbe3ddf5733fc09b Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 10:55:26 +0200 Subject: [PATCH 110/574] remove unused assets --- docs/api/_src/_static/css/custom.css | 437 ------------------------- docs/api/_src/_static/js/custom.js | 0 docs/api/_src/_static/nf-core-logo.png | Bin 84414 -> 0 bytes docs/api/_src/_templates/layout.html | 4 - 4 files changed, 441 deletions(-) delete mode 100644 docs/api/_src/_static/css/custom.css delete mode 100644 docs/api/_src/_static/js/custom.js delete mode 100644 docs/api/_src/_static/nf-core-logo.png delete mode 100644 docs/api/_src/_templates/layout.html diff --git a/docs/api/_src/_static/css/custom.css b/docs/api/_src/_static/css/custom.css deleted file mode 100644 index e892dd9998..0000000000 --- a/docs/api/_src/_static/css/custom.css +++ /dev/null @@ -1,437 +0,0 @@ -@media (prefers-color-scheme: light) { - a, - a:visited { - color: #246eb9; - } - a:hover, - a:focus, - a:active { - color: #c03221; - } - .wy-nav-side { - background-color: #ededed; - } - .wy-nav-top, - .wy-side-nav-search, - .wy-menu-vertical a:active { - background-color: #32ad65; - } - .wy-menu-vertical a { - color: #343434; - } - .wy-menu-vertical a:hover { - background-color: #abacab85; - } - .wy-menu-vertical header, - .wy-menu-vertical p.caption { - color: #32ad65; - } - - .wy-side-nav-search input[type="text"] { - border: none; - } - - code, - .rst-content code.literal { - background-color: rgba(220, 220, 220, 0.4); - color: #c03221; - border: none; - } - .rst-content .note .admonition-title { - background-color: #72757bfc; - } - - html.writer-html4 .rst-content dl:not(.docutils) > dt, - html.writer-html5 - .rst-content - dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) - > dt { - background-color: #32ad65; - border: none; - } - .rst-content .method > dt > code { - color: #f5f6f7; - } - .rst-content div[class^="highlight"], - .rst-content pre.literal-block { - border: none; - } - .highlight { - background-color: #242424; - color: #e5e6e7; - } - .highlight .hll { - color: #e5e6e7; - background-color: #585b60fc; - } - .highlight .k, - .highlight .nt, - .highlight .no { - color: #246eb9; - } - .highlight .s, - .highlight .s1, - .highlight .s2, - .highlight .na { - color: #32ad65; - } - .highlight .nb, - .highlight .o, - .highlight .cm { - color: #ffbe0b; - } - .highlight .c1 { - color: #88898afc; - } - .highlight .nv, - .py > span { - color: #c03221; - } - .py .sig-param, - .py .sig-paren, - .property .pre { - 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zR=V5QcHrB09IWat#|o1qh=yqV5OsM|f{QB%{iH=L&YIMQ$psMok|u}{hF7>(L^KYi;R{?1si2m&eN!!tmd>Ho z<`0aCn}*$nIDgUKM0KZK2(oU5c}4(U3dm8kG*#7@k#uL1NfEsRUuH_YKRKO^i-tiI zAaERQ^j!VV7SBw{hQC_>h2 - -{% endblock %} From 3f36d108e2da67dd64ac8f25738d17853d9c7622 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 11:14:45 +0200 Subject: [PATCH 111/574] handle mypy warnings --- tests/modules/update.py | 32 +++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/tests/modules/update.py b/tests/modules/update.py index 0fddcc8ba8..b56fc0df1d 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -90,9 +90,9 @@ def test_install_at_hash_and_update_limit_output(self): ) # Copy the module files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") - trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + tmpdir = Path(tempfile.mkdtemp()) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True @@ -112,22 +112,28 @@ def test_install_at_hash_and_update_limit_output(self): # Check for various scenarios for line in log_lines: - if re.match(r"'.+' is unchanged", line): - # Unchanged files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"'.+' was created", line): - # Created files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"'.+' was removed", line): - # Removed files should be reported for both .nf and non-.nf files + if ( + re.match(r"'.+' is unchanged", line) + or re.match(r"'.+' was created", line) + or re.match(r"'.+' was removed", line) + ): + # Unchanged, created, and removed files should be reported for both .nf and non-.nf files assert True elif re.match(r"Changes in '.+' but not shown", line): # Changes not shown should only be for non-.nf files - file_path = re.search(r"'(.+)'", line).group(1) + match = re.search(r"'(.+)'", line) + if match: + file_path = match.group(1) + else: + raise AssertionError("Changes not shown message did not contain a file path") assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" elif re.match(r"Changes in '.+':$", line): # Changes shown should only be for .nf files - file_path = re.search(r"'(.+)'", line).group(1) + match = re.search(r"'(.+)'", line) + if match: + file_path = match.group(1) + else: + raise AssertionError("Changes shown message did not contain a file path") assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" # Clean up From 18eefb7b05e066f787a99bd74d5f845af0fb53d0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 11:27:05 +0200 Subject: [PATCH 112/574] modernize code --- nf_core/modules/modules_json.py | 5 ++- tests/modules/update.py | 67 ++++++++++++++++++--------------- 2 files changed, 40 insertions(+), 32 deletions(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index b0a4fa661f..42c633ed23 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -862,7 +862,7 @@ def module_present(self, module_name, repo_url, install_dir): install_dir, {} ) - def get_modules_json(self): + def get_modules_json(self) -> dict: """ Returns a copy of the loaded modules.json @@ -871,7 +871,8 @@ def get_modules_json(self): """ if self.modules_json is None: self.load() - return copy.deepcopy(self.modules_json) + + return copy.deepcopy(self.modules_json) # type: ignore def get_component_version(self, component_type, component_name, repo_url, install_dir): """ diff --git a/tests/modules/update.py b/tests/modules/update.py index b56fc0df1d..72766779e3 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -1,7 +1,6 @@ import filecmp import io import logging -import os import re import shutil import tempfile @@ -30,15 +29,21 @@ ) +def cmp_module(dir1: Path, dir2: Path) -> bool: + """Compare two versions of the same module""" + files = ["main.nf", "meta.yml"] + return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files) + + def test_install_and_update(self): """Installs a module in the pipeline and updates it (no change)""" self.mods_install.install("trimgalore") update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) # Copy the module files and check that they are unaffected by the update - tmpdir = tempfile.mkdtemp() - trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") - trimgalore_path = os.path.join(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore") + tmpdir = Path(tempfile.mkdtemp()) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True @@ -53,9 +58,9 @@ def test_install_at_hash_and_update(self): ) # Copy the module files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") - trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + tmpdir = Path(tempfile.mkdtemp()) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True @@ -144,7 +149,7 @@ def test_install_at_hash_and_update_limit_output(self): def test_install_at_hash_and_update_and_save_diff_to_file(self): """Installs an old version of a module in the pipeline and updates it""" self.mods_install_old.install("trimgalore") - patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch") + patch_path = Path(self.pipeline_dir, "trimgalore.patch") update_obj = ModuleUpdate( self.pipeline_dir, save_diff_fn=patch_path, @@ -154,9 +159,9 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): ) # Copy the module files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") - trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + tmpdir = Path(tempfile.mkdtemp()) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True @@ -168,7 +173,7 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): """Installs an old version of a module in the pipeline and updates it""" self.mods_install_old.install("trimgalore") - patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch") + patch_path = Path(self.pipeline_dir, "trimgalore.patch") update_obj = ModuleUpdate( self.pipeline_dir, save_diff_fn=patch_path, @@ -179,16 +184,16 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): ) # Copy the module files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - trimgalore_tmpdir = os.path.join(tmpdir, "trimgalore") - trimgalore_path = os.path.join(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + tmpdir = Path(tempfile.mkdtemp()) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True # Check that the patch file was created - assert os.path.exists(patch_path), f"Patch file was not created at {patch_path}" + assert patch_path.exists(), f"Patch file was not created at {patch_path}" # Read the contents of the patch file with open(patch_path) as f: @@ -202,11 +207,19 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): assert True elif re.match(r"Changes in '.+' but not shown", line): # Changes not shown should only be for non-.nf files - file_path = re.search(r"'(.+)'", line).group(1) + match = re.search(r"'(.+)'", line) + if match: + file_path = match.group(1) + else: + raise AssertionError("Changes not shown message did not contain a file path.") assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" elif re.match("diff --git", line): # Diff should only be shown for .nf files - file_path = re.search(r"b/(.+)$", line).group(1) + match = re.search(r"'(.+)'", line) + if match: + file_path = match.group(1) + else: + raise AssertionError("Changes shown message did not contain a file path.") assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}" @@ -235,7 +248,7 @@ def test_update_with_config_fixed_version(self): update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) tools_config["update"] = update_config - with open(os.path.join(self.pipeline_dir, config_fn), "w") as f: + with open(Path(self.pipeline_dir, config_fn), "w") as f: yaml.dump(tools_config, f) # Update all modules in the pipeline @@ -260,7 +273,7 @@ def test_update_with_config_dont_update(self): update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) tools_config["update"] = update_config - with open(os.path.join(self.pipeline_dir, config_fn), "w") as f: + with open(Path(self.pipeline_dir, config_fn), "w") as f: yaml.dump(tools_config, f) # Update all modules in the pipeline @@ -289,7 +302,7 @@ def test_update_with_config_fix_all(self): update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) tools_config["update"] = update_config - with open(os.path.join(self.pipeline_dir, config_fn), "w") as f: + with open(Path(self.pipeline_dir, config_fn), "w") as f: yaml.dump(tools_config, f) # Update all modules in the pipeline @@ -313,7 +326,7 @@ def test_update_with_config_no_updates(self): update_config = {GITLAB_URL: False} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) tools_config["update"] = update_config - with open(os.path.join(self.pipeline_dir, config_fn), "w") as f: + with open(Path(self.pipeline_dir, config_fn), "w") as f: yaml.dump(tools_config, f) # Update all modules in the pipeline @@ -428,7 +441,7 @@ def test_update_only_show_differences(self, mock_prompt): ) update_old.update() - tmpdir = tempfile.mkdtemp() + tmpdir = Path(tempfile.mkdtemp()) shutil.rmtree(tmpdir) shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) @@ -476,7 +489,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt): patch_obj = ModulePatch(self.pipeline_dir) patch_obj.patch("fastqc") # Check that a patch file with the correct name has been created - assert "fastqc.diff" in set(os.listdir(module_path)) + assert "fastqc.diff" in set(Path(module_path).iterdir()) # Update all modules assert update_obj.update() is True @@ -491,12 +504,6 @@ def test_update_only_show_differences_when_patch(self, mock_prompt): assert correct_git_sha != current_git_sha -def cmp_module(dir1, dir2): - """Compare two versions of the same module""" - files = ["main.nf", "meta.yml"] - return all(filecmp.cmp(os.path.join(dir1, f), os.path.join(dir2, f), shallow=False) for f in files) - - def test_update_module_with_extra_config_file(self): """Try updating a module with a config file""" # Install the module From 9f4323a610cee3b968b2efc7fc18f8c332b3afe4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 9 Jul 2024 09:28:42 +0000 Subject: [PATCH 113/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 58e9a36bf3..23fcb83362 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,6 +45,7 @@ - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) +- update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 96b50f4739209a4ccb817b5f087e383533a5b4b0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 11:31:56 +0200 Subject: [PATCH 114/574] template: Use filename in code block for `params.yml` --- nf_core/pipeline-template/docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index 6645e0f6cf..ca64377d24 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -89,9 +89,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run {{ name }} -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' From c22888aea2329abf9a658e8a11a6c3514ad72fd0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 9 Jul 2024 09:33:11 +0000 Subject: [PATCH 115/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 58e9a36bf3..b0b706df1e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Change paths to test data ([#2985](https://github.com/nf-core/tools/pull/2985)) - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042)) - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) +- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) ### Linting From 2525905655a922bdc0cde8af31062c3354c4cad1 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 11:39:30 +0200 Subject: [PATCH 116/574] fix tests --- tests/modules/update.py | 2 +- tests/subworkflows/update.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/modules/update.py b/tests/modules/update.py index 72766779e3..06ae3a294a 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -489,7 +489,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt): patch_obj = ModulePatch(self.pipeline_dir) patch_obj.patch("fastqc") # Check that a patch file with the correct name has been created - assert "fastqc.diff" in set(Path(module_path).iterdir()) + assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")] # Update all modules assert update_obj.update() is True diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 7d1a3808dc..42d09aa66a 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -74,7 +74,7 @@ def test_install_at_hash_and_update_limit_output(self): old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the subworkflow files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() + tmpdir = Path(tempfile.mkdtemp()) sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, tmpdir) From 863a8a1063ad756729bf1b3e979d3ce508002a2b Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 11:45:04 +0200 Subject: [PATCH 117/574] fix shebang and imports --- docs/api/make_lint_md.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py index 7b823a086e..432f0d16b6 100644 --- a/docs/api/make_lint_md.py +++ b/docs/api/make_lint_md.py @@ -1,7 +1,6 @@ +#!/usr/bin/env python from pathlib import Path -#!/usr/bin/env python -import nf_core.commands_pipelines import nf_core.modules.lint import nf_core.pipelines.lint import nf_core.subworkflows.lint From 29075d6bf5895f3af97be456413e350dd56a3b31 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 16:36:37 +0200 Subject: [PATCH 118/574] improve per test clean-up, move component comparison to utils --- nf_core/components/update.py | 14 +++++++++----- tests/modules/update.py | 32 +++++++++++++------------------- tests/subworkflows/update.py | 34 +++++++++++----------------------- tests/utils.py | 21 ++++++++++++++------- 4 files changed, 47 insertions(+), 54 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 37e3f62126..7050b76df8 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -278,11 +278,14 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr ) # Ask the user if they want to install the component - dry_run = not questionary.confirm( - f"Update {self.component_type[:-1]} '{component}'?", - default=False, - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() + if not self.prompt: + dry_run = False + else: + dry_run = not questionary.confirm( + f"Update {self.component_type[:-1]} '{component}'?", + default=False, + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() if not dry_run: # Clear the component directory and move the installed files there @@ -833,6 +836,7 @@ def try_apply_patch( for_git=False, dsp_from_dir=component_relpath, dsp_to_dir=component_relpath, + limit_output=self.limit_output, ) # Move the patched files to the install dir diff --git a/tests/modules/update.py b/tests/modules/update.py index 06ae3a294a..49a261e7b5 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -1,4 +1,3 @@ -import filecmp import io import logging import re @@ -26,28 +25,23 @@ GITLAB_URL, OLD_TRIMGALORE_BRANCH, OLD_TRIMGALORE_SHA, + cmp_component, ) -def cmp_module(dir1: Path, dir2: Path) -> bool: - """Compare two versions of the same module""" - files = ["main.nf", "meta.yml"] - return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files) - - def test_install_and_update(self): """Installs a module in the pipeline and updates it (no change)""" self.mods_install.install("trimgalore") update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) # Copy the module files and check that they are unaffected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) trimgalore_tmpdir = tmpdir / "trimgalore" trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True - assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True def test_install_at_hash_and_update(self): @@ -58,13 +52,13 @@ def test_install_at_hash_and_update(self): ) # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) trimgalore_tmpdir = tmpdir / "trimgalore" trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True - assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False # Check that the modules.json is correctly updated mod_json_obj = ModulesJson(self.pipeline_dir) @@ -95,13 +89,13 @@ def test_install_at_hash_and_update_limit_output(self): ) # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) trimgalore_tmpdir = tmpdir / "trimgalore" trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True - assert cmp_module(trimgalore_tmpdir, trimgalore_path) is False + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False # Check that the modules.json is correctly updated mod_json_obj = ModulesJson(self.pipeline_dir) @@ -159,13 +153,13 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): ) # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) trimgalore_tmpdir = tmpdir / "trimgalore" trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True - assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True # TODO: Apply the patch to the module @@ -184,13 +178,13 @@ def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): ) # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) trimgalore_tmpdir = tmpdir / "trimgalore" trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") shutil.copytree(trimgalore_path, trimgalore_tmpdir) assert update_obj.update("trimgalore") is True - assert cmp_module(trimgalore_tmpdir, trimgalore_path) is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True # Check that the patch file was created assert patch_path.exists(), f"Patch file was not created at {patch_path}" @@ -441,7 +435,7 @@ def test_update_only_show_differences(self, mock_prompt): ) update_old.update() - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) shutil.rmtree(tmpdir) shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) @@ -455,7 +449,7 @@ def test_update_only_show_differences(self, mock_prompt): correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] assert correct_git_sha != current_git_sha - assert cmp_module(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True + assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True # Mock questionary answer: do not update module, only show diffs diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 42d09aa66a..5395d194ae 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -1,4 +1,3 @@ -import filecmp import io import logging import re @@ -14,7 +13,7 @@ from nf_core.modules.update import ModuleUpdate from nf_core.subworkflows.update import SubworkflowUpdate -from ..utils import OLD_SUBWORKFLOWS_SHA +from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component def test_install_and_update(self): @@ -23,8 +22,7 @@ def test_install_and_update(self): update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False) # Copy the sw files and check that they are unaffected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools") shutil.copytree(sw_path, tmpdir) @@ -39,8 +37,8 @@ def test_install_at_hash_and_update(self): old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the sw files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, tmpdir) @@ -69,12 +67,13 @@ def test_install_at_hash_and_update_limit_output(self): ch = logging.StreamHandler(log_capture) logger = logging.getLogger() logger.addHandler(ch) + logger.setLevel(logging.INFO) update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True) old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the subworkflow files and check that they are affected by the update - tmpdir = Path(tempfile.mkdtemp()) + tmpdir = Path(tempfile.TemporaryDirectory().name) sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, tmpdir) @@ -124,7 +123,6 @@ def test_install_at_hash_and_update_limit_output(self): # Clean up logger.removeHandler(ch) log_capture.close() - shutil.rmtree(tmpdir) def test_install_at_hash_and_update_and_save_diff_to_file(self): @@ -134,8 +132,8 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True) # Copy the sw files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, tmpdir) @@ -156,8 +154,7 @@ def test_install_at_hash_and_update_and_save_diff_limit_output(self): update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True) # Copy the sw files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, tmpdir) @@ -196,7 +193,6 @@ def test_install_at_hash_and_update_and_save_diff_limit_output(self): # Clean up patch_path.unlink() - shutil.rmtree(tmpdir) def test_update_all(self): @@ -343,8 +339,7 @@ def test_update_all_linked_components_from_subworkflow(self): old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the sw files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME) modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME) shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows")) @@ -390,8 +385,7 @@ def test_update_all_subworkflows_from_module(self): old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the sw files and check that they are affected by the update - tmpdir = tempfile.mkdtemp() - shutil.rmtree(tmpdir) + tmpdir = Path(tempfile.TemporaryDirectory().name) sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2")) @@ -445,9 +439,3 @@ def test_update_change_of_included_modules(self): assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir() - - -def cmp_component(dir1, dir2): - """Compare two versions of the same component""" - files = ["main.nf", "meta.yml"] - return all(filecmp.cmp(Path(dir1, f), Path(dir2, f), shallow=False) for f in files) diff --git a/tests/utils.py b/tests/utils.py index 9a0fd0896f..151655b8f3 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -2,9 +2,10 @@ Helper functions for tests """ +import filecmp import functools -import os import tempfile +from pathlib import Path from typing import Any, Callable, Tuple import responses @@ -93,18 +94,24 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200) -def create_tmp_pipeline() -> Tuple[str, str, str, str]: +def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: """Create a new Pipeline for testing""" - tmp_dir = tempfile.mkdtemp() - root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) - template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template") + tmp_dir = Path(tempfile.mkdtemp()) + root_repo_dir = Path(__file__).resolve().parent.parent + template_dir = root_repo_dir / "nf_core" / "pipeline-template" pipeline_name = "mypipeline" - pipeline_dir = os.path.join(tmp_dir, pipeline_name) + pipeline_dir = tmp_dir / pipeline_name nf_core.pipelines.create.create.PipelineCreate( - pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir + pipeline_name, "it is mine", "me", no_git=True, outdir=str(pipeline_dir) ).init_pipeline() # return values to instance variables for later use in test methods return tmp_dir, template_dir, pipeline_name, pipeline_dir + + +def cmp_component(dir1: Path, dir2: Path) -> bool: + """Compare two versions of the same component""" + files = ["main.nf", "meta.yml"] + return all(filecmp.cmp(dir1 / f, dir2 / f, shallow=False) for f in files) From c1b955bc12b2becbf92392e673ce3ce619633f88 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 16:44:13 +0200 Subject: [PATCH 119/574] use same output for diff file or print output --- nf_core/modules/modules_differ.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index 34966b2ffd..e79554f2b6 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -180,11 +180,18 @@ def write_diff_file( if diff_status == ModulesDiffer.DiffEnum.UNCHANGED: # The files are identical fh.write(f"'{Path(dsp_from_dir, file)}' is unchanged\n") + elif diff_status == ModulesDiffer.DiffEnum.CREATED: + # The file was created between the commits + fh.write(f"'{Path(dsp_from_dir, file)}' was created\n") + elif diff_status == ModulesDiffer.DiffEnum.REMOVED: + # The file was removed between the commits + fh.write(f"'{Path(dsp_from_dir, file)}' was removed\n") elif limit_output and not file.suffix == ".nf": # Skip printing the diff for files other than main.nf fh.write(f"Changes in '{Path(module, file)}' but not shown\n") else: # The file has changed write the diff lines to the file + fh.write(f"Changes in '{Path(module, file)}':\n") for line in diff: fh.write(line) fh.write("\n") From 71fe3da619910bc74543a0f75f77a3b24f90b9b8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 9 Jul 2024 16:56:24 +0200 Subject: [PATCH 120/574] fix module tests --- tests/modules/update.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/update.py b/tests/modules/update.py index 49a261e7b5..12adbeb829 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -436,7 +436,6 @@ def test_update_only_show_differences(self, mock_prompt): update_old.update() tmpdir = Path(tempfile.TemporaryDirectory().name) - shutil.rmtree(tmpdir) shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) assert update_obj.update() is True From b5833900284b9da51003295b79fb8e3c9b626cbb Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 10 Jul 2024 16:38:16 +0200 Subject: [PATCH 121/574] fix test --- nf_core/components/update.py | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 7050b76df8..81d897fc79 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -278,14 +278,11 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr ) # Ask the user if they want to install the component - if not self.prompt: - dry_run = False - else: - dry_run = not questionary.confirm( - f"Update {self.component_type[:-1]} '{component}'?", - default=False, - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() + dry_run = not questionary.confirm( + f"Update {self.component_type[:-1]} '{component}'?", + default=False, + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() if not dry_run: # Clear the component directory and move the installed files there From 403af3270cc903d57b273fed22699b59090d361a Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 12:15:44 +0200 Subject: [PATCH 122/574] actually test the output --- nf_core/components/update.py | 16 +++++++++------- tests/modules/update.py | 11 ++++++++--- tests/subworkflows/update.py | 22 ++++++++++++---------- 3 files changed, 29 insertions(+), 20 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 81d897fc79..72c6e0254a 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -276,13 +276,15 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr dsp_to_dir=component_dir, limit_output=self.limit_output, ) - - # Ask the user if they want to install the component - dry_run = not questionary.confirm( - f"Update {self.component_type[:-1]} '{component}'?", - default=False, - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() + if self.prompt: + # Ask the user if they want to install the component + dry_run = not questionary.confirm( + f"Update {self.component_type[:-1]} '{component}'?", + default=False, + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() + else: + dry_run = False if not dry_run: # Clear the component directory and move the installed files there diff --git a/tests/modules/update.py b/tests/modules/update.py index 12adbeb829..141a9bed05 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -78,10 +78,11 @@ def test_install_at_hash_and_update_limit_output(self): ch = logging.StreamHandler(log_capture) logger = logging.getLogger() logger.addHandler(ch) + logger.setLevel(logging.INFO) update_obj = ModuleUpdate( self.pipeline_dir, - show_diff=False, + show_diff=True, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH, @@ -98,8 +99,7 @@ def test_install_at_hash_and_update_limit_output(self): assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False # Check that the modules.json is correctly updated - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Get the up-to-date git_sha for the module from the ModuleRepo object correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules") current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] @@ -110,6 +110,7 @@ def test_install_at_hash_and_update_limit_output(self): log_lines = log_output.split("\n") # Check for various scenarios + nf_changes_shown = False for line in log_lines: if ( re.match(r"'.+' is unchanged", line) @@ -134,6 +135,10 @@ def test_install_at_hash_and_update_limit_output(self): else: raise AssertionError("Changes shown message did not contain a file path") assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" + nf_changes_shown = True + + # Ensure that changes in at least one .nf file were shown + assert nf_changes_shown, "No changes in .nf files were shown" # Clean up logger.removeHandler(ch) diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 5395d194ae..e7328813eb 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -69,7 +69,7 @@ def test_install_at_hash_and_update_limit_output(self): logger.addHandler(ch) logger.setLevel(logging.INFO) - update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True, limit_output=True) + update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True) old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Copy the subworkflow files and check that they are affected by the update @@ -98,18 +98,20 @@ def test_install_at_hash_and_update_limit_output(self): # Check for various scenarios nf_changes_shown = False for line in log_lines: - if re.match(r"'.+' is unchanged", line): - # Unchanged files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"'.+' was created", line): - # Created files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"'.+' was removed", line): - # Removed files should be reported for both .nf and non-.nf files + if ( + re.match(r"'.+' is unchanged", line) + or re.match(r"'.+' was created", line) + or re.match(r"'.+' was removed", line) + ): + # Unchanged, created, and removed files should be reported for both .nf and non-.nf files assert True elif re.match(r"Changes in '.+' but not shown", line): # Changes not shown should only be for non-.nf files - file_path = re.search(r"'(.+)'", line).group(1) + match = re.search(r"'(.+)'", line) + if match: + file_path = match.group(1) + else: + raise AssertionError("Changes not shown message did not contain a file path") assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" elif re.match(r"Changes in '.+':$", line): # Changes shown should only be for .nf files From 12c166610bf108954a9661241252198e7aa2e239 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 12:16:08 +0200 Subject: [PATCH 123/574] check that limit_output is set only when it makes sense --- nf_core/components/update.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 72c6e0254a..a896ef0949 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -77,6 +77,8 @@ def _parameter_checks(self): if not self.has_valid_directory(): raise UserWarning("The command was not run in a valid pipeline directory.") + if self.limit_output and not (self.save_diff_fn or self.show_diff): + raise UserWarning("The '--limit-output' flag can only be used with '--preview' or '--save-diff'.") def update(self, component=None, silent=False, updated=None, check_diff_exist=True) -> bool: """Updates a specified module/subworkflow or all modules/subworkflows in a pipeline. From cd827e1f5452c0bb6a8615e1cd4ae6aa065bbd3d Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 12:16:46 +0200 Subject: [PATCH 124/574] remove short option (`l` might be confused with `list` (which we don't have)), fix typo --- nf_core/__main__.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 331f536834..f33c63e87c 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -929,12 +929,11 @@ def command_modules_install(ctx, tool, dir, prompt, force, sha): help="Prompt for the version of the module", ) @click.option( - "-l", "--limit-output", "limit_output", is_flag=True, default=False, - help="Limit ouput to only the difference in main.nf", + help="Limit output to only the difference in main.nf", ) @click.option("-s", "--sha", type=str, metavar="", help="Install module at commit SHA") @click.option( From eb72f09b0923fa325a1935f13fcbc5626c241373 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 14:10:34 +0200 Subject: [PATCH 125/574] update to pytest 8 and move it to dev requirements --- requirements-dev.txt | 3 ++- requirements.txt | 2 -- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index ebfbb530d3..2c7bb0c8cf 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -7,7 +7,6 @@ ruff Sphinx sphinx-rtd-theme textual-dev==1.5.1 -mypy types-PyYAML types-requests types-jsonschema @@ -16,4 +15,6 @@ types-PyYAML types-requests types-setuptools pytest-textual-snapshot==0.4.0 +pytest-workflow>=2.0.0 +pytest>=8.0.0 ruff diff --git a/requirements.txt b/requirements.txt index ccfc1bc9c1..524b739e89 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,8 +11,6 @@ pdiff pre-commit prompt_toolkit>=3.0.3 pydantic>=2.2.1 -pytest-workflow>=2.0.0 -pytest>=7.0.0 pyyaml questionary>=1.8.0 refgenie From 66c8ca5e9d16435e8fc8a8077666af7d61ff9cbb Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 14:10:42 +0200 Subject: [PATCH 126/574] fix deprecation warning --- nf_core/pipelines/download.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 8454f894a2..24de045a68 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -20,7 +20,7 @@ import rich import rich.progress from git.exc import GitCommandError, InvalidGitRepositoryError -from pkg_resources import parse_version as version_parser +from setuptools._distutils.version import LooseVersion as VersionParser import nf_core import nf_core.pipelines.list @@ -1693,7 +1693,7 @@ def tidy_tags_and_branches(self): else: # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns. valid_versions = [ - version_parser(v) + VersionParser(v) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) ] From 66be4a0a52390d2637eafda4e702bc97d3016a73 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 11 Jul 2024 14:10:42 +0200 Subject: [PATCH 127/574] fix deprecation warning --- nf_core/pipelines/download.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 8454f894a2..43b63d8192 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -20,7 +20,7 @@ import rich import rich.progress from git.exc import GitCommandError, InvalidGitRepositoryError -from pkg_resources import parse_version as version_parser +from packaging.version import Version import nf_core import nf_core.pipelines.list @@ -1693,13 +1693,11 @@ def tidy_tags_and_branches(self): else: # desired revisions may contain arbitrary branch names that do not correspond to valid sematic versioning patterns. valid_versions = [ - version_parser(v) - for v in desired_revisions - if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) + Version(v) for v in desired_revisions if re.match(r"\d+\.\d+(?:\.\d+)*(?:[\w\-_])*", v) ] # valid versions sorted in ascending order, last will be aliased as "latest". latest = sorted(valid_versions)[-1] - self.repo.create_head("latest", latest) + self.repo.create_head("latest", str(latest)) self.checkout(latest) if self.repo.head.is_detached: self.repo.head.reset(index=True, working_tree=True) From ed64d5415e22def0d6abc8fc4a9b142d00a3f8b7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 11 Jul 2024 12:31:13 +0000 Subject: [PATCH 128/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7c2f5d99df..706d155d27 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,6 +47,7 @@ - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) +- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From e4cfde9aba2567fdc3903f1039caaa995da7a77f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 15 Jul 2024 09:05:46 +0000 Subject: [PATCH 129/574] chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.2 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c1dc7978f6..872bd61e0a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.1 + rev: v0.5.2 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 5b648fba592bf69d864a5ee88e062bad84906f6d Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 15 Jul 2024 11:15:23 +0200 Subject: [PATCH 130/574] fix tests by mocking questionary confirm --- nf_core/components/update.py | 18 ++++++++---------- tests/modules/update.py | 19 ++++++++++--------- tests/subworkflows/update.py | 6 +++++- 3 files changed, 23 insertions(+), 20 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index a896ef0949..1e31e56271 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -128,7 +128,6 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr components_info = ( self.get_all_components_info() if self.update_all else [self.get_single_component_info(component)] ) - # Save the current state of the modules.json old_modules_json = self.modules_json.get_modules_json() @@ -278,15 +277,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr dsp_to_dir=component_dir, limit_output=self.limit_output, ) - if self.prompt: - # Ask the user if they want to install the component - dry_run = not questionary.confirm( - f"Update {self.component_type[:-1]} '{component}'?", - default=False, - style=nf_core.utils.nfcore_question_style, - ).unsafe_ask() - else: - dry_run = False + # Ask the user if they want to install the component + dry_run = not questionary.confirm( + f"Update {self.component_type[:-1]} '{component}'?", + default=False, + style=nf_core.utils.nfcore_question_style, + ).unsafe_ask() if not dry_run: # Clear the component directory and move the installed files there @@ -397,6 +393,8 @@ def get_single_component_info(self, component): sha = self.sha config_entry = None + if self.update_config is None: + raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory") if any( [ entry.count("/") == 1 diff --git a/tests/modules/update.py b/tests/modules/update.py index 141a9bed05..a19067b344 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -69,7 +69,9 @@ def test_install_at_hash_and_update(self): assert correct_git_sha == current_git_sha -def test_install_at_hash_and_update_limit_output(self): +# Mock questionary answer: do not update module, only show diffs +@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) +def test_install_at_hash_and_update_limit_output(self, mock_prompt): """Installs an old version of a module in the pipeline and updates it with limited output reporting""" assert self.mods_install_old.install("trimgalore") @@ -429,10 +431,8 @@ def test_update_different_branch_mix_modules_branch_test(self): @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False) def test_update_only_show_differences(self, mock_prompt): """Try updating all modules showing differences. - Don't update some of them. + Only show diffs, don't actually save any updated files. Check that the sha in modules.json is not changed.""" - modules_json = ModulesJson(self.pipeline_dir) - update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) # Update modules to a fixed old SHA update_old = ModuleUpdate( @@ -443,16 +443,17 @@ def test_update_only_show_differences(self, mock_prompt): tmpdir = Path(tempfile.TemporaryDirectory().name) shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) - assert update_obj.update() is True + update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) + assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update() - mod_json = modules_json.get_modules_json() + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() # Loop through all modules and check that they are NOT updated (according to the modules.json file) # A module that can be updated but shouldn't is fastqc # Module multiqc is already up to date so don't check mod = "fastqc" - correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] + non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - assert correct_git_sha != current_git_sha + assert non_updated_git_sha != current_git_sha assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True @@ -469,7 +470,7 @@ def test_update_only_show_differences_when_patch(self, mock_prompt): update_old = ModuleUpdate( self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905" ) - update_old.update() + assert update_old.update() # Modify fastqc module, it will have a patch which will be applied during update # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions) diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index e7328813eb..170b2af660 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -4,7 +4,9 @@ import shutil import tempfile from pathlib import Path +from unittest import mock +import questionary import yaml import nf_core.utils @@ -58,7 +60,9 @@ def test_install_at_hash_and_update(self): ) -def test_install_at_hash_and_update_limit_output(self): +# Mock questionary answer: update components +@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) +def test_install_at_hash_and_update_limit_output(self, mock_prompt): """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True""" assert self.subworkflow_install_old.install("fastq_align_bowtie2") From 08a138c8ee6a5f79a1573982927667dc3f0f5782 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 15 Jul 2024 11:15:48 +0200 Subject: [PATCH 131/574] handle new jsonschema error type --- nf_core/modules/lint/environment_yml.py | 2 +- nf_core/modules/lint/meta_yml.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 92281d99c0..e10ef1761d 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -60,7 +60,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) hint = "" if len(e.path) > 0: hint = f"\nCheck the entry for `{e.path[0]}`." - if e.schema.get("message"): + if e.schema and isinstance(e.schema, dict) and "message" in e.schema: e.message = e.schema["message"] module.failed.append( ( diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 481d50b3ef..4c036713c8 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -76,7 +76,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None hint = f"\nCheck the entry for `{e.path[0]}`." if e.message.startswith("None is not of type 'object'") and len(e.path) > 2: hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly." - if e.schema.get("message"): + if e.schema and isinstance(e.schema, dict) and "message" in e.schema: e.message = e.schema["message"] incorrect_value = meta_yaml for key in e.path: From 4d3f793e7a40b4ead7e5134a070523933946316f Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 15 Jul 2024 11:15:48 +0200 Subject: [PATCH 132/574] handle new jsonschema error type --- nf_core/modules/lint/environment_yml.py | 2 +- nf_core/modules/lint/meta_yml.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 92281d99c0..e10ef1761d 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -60,7 +60,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) hint = "" if len(e.path) > 0: hint = f"\nCheck the entry for `{e.path[0]}`." - if e.schema.get("message"): + if e.schema and isinstance(e.schema, dict) and "message" in e.schema: e.message = e.schema["message"] module.failed.append( ( diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 481d50b3ef..4c036713c8 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -76,7 +76,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None hint = f"\nCheck the entry for `{e.path[0]}`." if e.message.startswith("None is not of type 'object'") and len(e.path) > 2: hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly." - if e.schema.get("message"): + if e.schema and isinstance(e.schema, dict) and "message" in e.schema: e.message = e.schema["message"] incorrect_value = meta_yaml for key in e.path: From 716ead4e61a363dd5340fc6b3b0ede15b872c176 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 15 Jul 2024 09:29:34 +0000 Subject: [PATCH 133/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 706d155d27..fe7fdcc28b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -48,6 +48,7 @@ - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) +- handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From e06ebdf422669a405146b57c05c5c59f30395513 Mon Sep 17 00:00:00 2001 From: adamrtalbot <12817534+adamrtalbot@users.noreply.github.com> Date: Mon, 15 Jul 2024 11:52:20 +0100 Subject: [PATCH 134/574] Remove Azure specific documentation which is no longer required --- nf_core/pipeline-template/docs/usage.md | 8 -------- 1 file changed, 8 deletions(-) diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index ca64377d24..bf637219f8 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -207,14 +207,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - {% endif -%} ## Running in the background From e23869120ce320d3d4d4d58856751c358a2d1dd6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 15 Jul 2024 14:55:30 +0200 Subject: [PATCH 135/574] move pipelines tests into `pipelines` subdirectory to mirror command structure --- tests/{ => pipelines}/test_bump_version.py | 0 tests/{ => pipelines}/test_create.py | 2 +- tests/{ => pipelines}/test_create_app.py | 0 tests/{ => pipelines}/test_create_logo.py | 0 tests/{ => pipelines}/test_download.py | 2 +- tests/{ => pipelines}/test_launch.py | 2 +- tests/{ => pipelines}/test_lint.py | 30 +++++++++++----------- tests/{ => pipelines}/test_list.py | 0 tests/{ => pipelines}/test_params_file.py | 0 tests/{ => pipelines}/test_refgenie.py | 0 tests/{ => pipelines}/test_schema.py | 2 +- tests/{ => pipelines}/test_sync.py | 2 +- 12 files changed, 20 insertions(+), 20 deletions(-) rename tests/{ => pipelines}/test_bump_version.py (100%) rename tests/{ => pipelines}/test_create.py (99%) rename tests/{ => pipelines}/test_create_app.py (100%) rename tests/{ => pipelines}/test_create_logo.py (100%) rename tests/{ => pipelines}/test_download.py (99%) rename tests/{ => pipelines}/test_launch.py (99%) rename tests/{ => pipelines}/test_lint.py (90%) rename tests/{ => pipelines}/test_list.py (100%) rename tests/{ => pipelines}/test_params_file.py (100%) rename tests/{ => pipelines}/test_refgenie.py (100%) rename tests/{ => pipelines}/test_schema.py (99%) rename tests/{ => pipelines}/test_sync.py (99%) diff --git a/tests/test_bump_version.py b/tests/pipelines/test_bump_version.py similarity index 100% rename from tests/test_bump_version.py rename to tests/pipelines/test_bump_version.py diff --git a/tests/test_create.py b/tests/pipelines/test_create.py similarity index 99% rename from tests/test_create.py rename to tests/pipelines/test_create.py index 313b6f5354..d93b26bd1a 100644 --- a/tests/test_create.py +++ b/tests/pipelines/test_create.py @@ -9,7 +9,7 @@ import nf_core.pipelines.create.create -from .utils import with_temporary_folder +from ..utils import with_temporary_folder TEST_DATA_DIR = Path(__file__).parent / "data" PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml" diff --git a/tests/test_create_app.py b/tests/pipelines/test_create_app.py similarity index 100% rename from tests/test_create_app.py rename to tests/pipelines/test_create_app.py diff --git a/tests/test_create_logo.py b/tests/pipelines/test_create_logo.py similarity index 100% rename from tests/test_create_logo.py rename to tests/pipelines/test_create_logo.py diff --git a/tests/test_download.py b/tests/pipelines/test_download.py similarity index 99% rename from tests/test_download.py rename to tests/pipelines/test_download.py index c3a8c5546a..ebb76fef72 100644 --- a/tests/test_download.py +++ b/tests/pipelines/test_download.py @@ -18,7 +18,7 @@ from nf_core.synced_repo import SyncedRepo from nf_core.utils import run_cmd -from .utils import with_temporary_folder +from ..utils import with_temporary_folder class DownloadTest(unittest.TestCase): diff --git a/tests/test_launch.py b/tests/pipelines/test_launch.py similarity index 99% rename from tests/test_launch.py rename to tests/pipelines/test_launch.py index 9774853419..b4b285a3c9 100644 --- a/tests/test_launch.py +++ b/tests/pipelines/test_launch.py @@ -11,7 +11,7 @@ import nf_core.pipelines.create.create import nf_core.pipelines.launch -from .utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder +from ..utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder class TestLaunch(TestCase): diff --git a/tests/test_lint.py b/tests/pipelines/test_lint.py similarity index 90% rename from tests/test_lint.py rename to tests/pipelines/test_lint.py index 4e468b7538..460c8f03d8 100644 --- a/tests/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -12,7 +12,7 @@ import nf_core.pipelines.create.create import nf_core.pipelines.lint -from .utils import with_temporary_folder +from ..utils import with_temporary_folder class TestLint(unittest.TestCase): @@ -179,33 +179,33 @@ def test_sphinx_md_files(self): ####################### # SPECIFIC LINT TESTS # ####################### - from .lint.actions_awsfulltest import ( # type: ignore[misc] + from ..lint.actions_awsfulltest import ( # type: ignore[misc] test_actions_awsfulltest_fail, test_actions_awsfulltest_pass, test_actions_awsfulltest_warn, ) - from .lint.actions_awstest import ( # type: ignore[misc] + from ..lint.actions_awstest import ( # type: ignore[misc] test_actions_awstest_fail, test_actions_awstest_pass, ) - from .lint.actions_ci import ( # type: ignore[misc] + from ..lint.actions_ci import ( # type: ignore[misc] test_actions_ci_fail_wrong_nf, test_actions_ci_fail_wrong_trigger, test_actions_ci_pass, ) - from .lint.actions_schema_validation import ( # type: ignore[misc] + from ..lint.actions_schema_validation import ( # type: ignore[misc] test_actions_schema_validation_fails_for_additional_property, test_actions_schema_validation_missing_jobs, test_actions_schema_validation_missing_on, ) - from .lint.configs import ( # type: ignore[misc] + from ..lint.configs import ( # type: ignore[misc] test_ignore_base_config, test_ignore_modules_config, test_superfluous_withname_in_base_config_fails, test_superfluous_withname_in_modules_config_fails, test_withname_in_modules_config, ) - from .lint.files_exist import ( # type: ignore[misc] + from ..lint.files_exist import ( # type: ignore[misc] test_files_exist_depreciated_file, test_files_exist_fail_conditional, test_files_exist_missing_config, @@ -214,13 +214,13 @@ def test_sphinx_md_files(self): test_files_exist_pass_conditional, test_files_exist_pass_conditional_nfschema, ) - from .lint.files_unchanged import ( # type: ignore[misc] + from ..lint.files_unchanged import ( # type: ignore[misc] test_files_unchanged_fail, test_files_unchanged_pass, ) - from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] - from .lint.modules_json import test_modules_json_pass # type: ignore[misc] - from .lint.multiqc_config import ( # type: ignore[misc] + from ..lint.merge_markers import test_merge_markers_found # type: ignore[misc] + from ..lint.modules_json import test_modules_json_pass # type: ignore[misc] + from ..lint.multiqc_config import ( # type: ignore[misc] test_multiqc_config_exists, test_multiqc_config_ignore, test_multiqc_config_missing_report_section_order, @@ -229,7 +229,7 @@ def test_sphinx_md_files(self): test_multiqc_config_report_comment_release_succeed, test_multiqc_incorrect_export_plots, ) - from .lint.nextflow_config import ( # type: ignore[misc] + from ..lint.nextflow_config import ( # type: ignore[misc] test_allow_params_reference_in_main_nf, test_catch_params_assignment_in_main_nf, test_default_values_fail, @@ -242,14 +242,14 @@ def test_sphinx_md_files(self): test_nextflow_config_example_pass, test_nextflow_config_missing_test_profile_failed, ) - from .lint.nfcore_yml import ( # type: ignore[misc] + from ..lint.nfcore_yml import ( # type: ignore[misc] test_nfcore_yml_fail_nfcore_version, test_nfcore_yml_fail_repo_type, test_nfcore_yml_pass, ) - from .lint.template_strings import ( # type: ignore[misc] + from ..lint.template_strings import ( # type: ignore[misc] test_template_strings, test_template_strings_ignore_file, test_template_strings_ignored, ) - from .lint.version_consistency import test_version_consistency # type: ignore[misc] + from ..lint.version_consistency import test_version_consistency # type: ignore[misc] diff --git a/tests/test_list.py b/tests/pipelines/test_list.py similarity index 100% rename from tests/test_list.py rename to tests/pipelines/test_list.py diff --git a/tests/test_params_file.py b/tests/pipelines/test_params_file.py similarity index 100% rename from tests/test_params_file.py rename to tests/pipelines/test_params_file.py diff --git a/tests/test_refgenie.py b/tests/pipelines/test_refgenie.py similarity index 100% rename from tests/test_refgenie.py rename to tests/pipelines/test_refgenie.py diff --git a/tests/test_schema.py b/tests/pipelines/test_schema.py similarity index 99% rename from tests/test_schema.py rename to tests/pipelines/test_schema.py index 4cb157c087..633de3db69 100644 --- a/tests/test_schema.py +++ b/tests/pipelines/test_schema.py @@ -15,7 +15,7 @@ import nf_core.pipelines.create.create import nf_core.pipelines.schema -from .utils import with_temporary_file, with_temporary_folder +from ..utils import with_temporary_file, with_temporary_folder class TestSchema(unittest.TestCase): diff --git a/tests/test_sync.py b/tests/pipelines/test_sync.py similarity index 99% rename from tests/test_sync.py rename to tests/pipelines/test_sync.py index ca90071d95..d7b73c7ffb 100644 --- a/tests/test_sync.py +++ b/tests/pipelines/test_sync.py @@ -14,7 +14,7 @@ import nf_core.pipelines.create.create import nf_core.pipelines.sync -from .utils import with_temporary_folder +from ..utils import with_temporary_folder class TestModules(unittest.TestCase): From 7b3d985ff288b6e4e222a9142bed59707d06935f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 15 Jul 2024 18:02:49 +0200 Subject: [PATCH 136/574] reduce update with limit_output tests --- tests/modules/update.py | 119 ++++++--------------------------- tests/subworkflows/update.py | 123 ++++++++--------------------------- tests/test_modules.py | 5 ++ tests/test_subworkflows.py | 5 ++ 4 files changed, 58 insertions(+), 194 deletions(-) diff --git a/tests/modules/update.py b/tests/modules/update.py index a19067b344..e02b058fbb 100644 --- a/tests/modules/update.py +++ b/tests/modules/update.py @@ -1,6 +1,4 @@ -import io import logging -import re import shutil import tempfile from pathlib import Path @@ -73,15 +71,9 @@ def test_install_at_hash_and_update(self): @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) def test_install_at_hash_and_update_limit_output(self, mock_prompt): """Installs an old version of a module in the pipeline and updates it with limited output reporting""" + self.caplog.set_level(logging.INFO) assert self.mods_install_old.install("trimgalore") - # Capture the logger output - log_capture = io.StringIO() - ch = logging.StreamHandler(log_capture) - logger = logging.getLogger() - logger.addHandler(ch) - logger.setLevel(logging.INFO) - update_obj = ModuleUpdate( self.pipeline_dir, show_diff=True, @@ -90,61 +82,15 @@ def test_install_at_hash_and_update_limit_output(self, mock_prompt): branch=OLD_TRIMGALORE_BRANCH, limit_output=True, ) + assert update_obj.update("trimgalore") - # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - trimgalore_tmpdir = tmpdir / "trimgalore" - trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") - shutil.copytree(trimgalore_path, trimgalore_tmpdir) - - assert update_obj.update("trimgalore") is True - assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False - - # Check that the modules.json is correctly updated - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - # Get the up-to-date git_sha for the module from the ModuleRepo object - correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules") - current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] - assert correct_git_sha == current_git_sha - - # Get the captured log output - log_output = log_capture.getvalue() - log_lines = log_output.split("\n") - - # Check for various scenarios - nf_changes_shown = False - for line in log_lines: - if ( - re.match(r"'.+' is unchanged", line) - or re.match(r"'.+' was created", line) - or re.match(r"'.+' was removed", line) - ): - # Unchanged, created, and removed files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"Changes in '.+' but not shown", line): - # Changes not shown should only be for non-.nf files - match = re.search(r"'(.+)'", line) - if match: - file_path = match.group(1) - else: - raise AssertionError("Changes not shown message did not contain a file path") - assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" - elif re.match(r"Changes in '.+':$", line): - # Changes shown should only be for .nf files - match = re.search(r"'(.+)'", line) - if match: - file_path = match.group(1) - else: - raise AssertionError("Changes shown message did not contain a file path") - assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" - nf_changes_shown = True - - # Ensure that changes in at least one .nf file were shown - assert nf_changes_shown, "No changes in .nf files were shown" - - # Clean up - logger.removeHandler(ch) - log_capture.close() + # Check changes not shown for non-.nf files + assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text + # Check changes shown for .nf files + assert "Changes in 'trimgalore/main.nf'" in self.caplog.text + for line in self.caplog.text.split("\n"): + if line.startswith("---"): + assert line.endswith("main.nf") def test_install_at_hash_and_update_and_save_diff_to_file(self): @@ -173,55 +119,32 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): """Installs an old version of a module in the pipeline and updates it""" + # Install old version of trimgalore self.mods_install_old.install("trimgalore") patch_path = Path(self.pipeline_dir, "trimgalore.patch") + # Update saving the differences to a patch file and with `limit_output` update_obj = ModuleUpdate( self.pipeline_dir, save_diff_fn=patch_path, - sha=OLD_TRIMGALORE_SHA, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH, limit_output=True, ) - - # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - trimgalore_tmpdir = tmpdir / "trimgalore" - trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") - shutil.copytree(trimgalore_path, trimgalore_tmpdir) - - assert update_obj.update("trimgalore") is True - assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True + assert update_obj.update("trimgalore") # Check that the patch file was created assert patch_path.exists(), f"Patch file was not created at {patch_path}" # Read the contents of the patch file - with open(patch_path) as f: - patch_content = f.read() - - # Check the content of the patch file - patch_lines = patch_content.split("\n") - for line in patch_lines: - if re.match(r"'.+' is unchanged", line): - # Unchanged files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"Changes in '.+' but not shown", line): - # Changes not shown should only be for non-.nf files - match = re.search(r"'(.+)'", line) - if match: - file_path = match.group(1) - else: - raise AssertionError("Changes not shown message did not contain a file path.") - assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" - elif re.match("diff --git", line): - # Diff should only be shown for .nf files - match = re.search(r"'(.+)'", line) - if match: - file_path = match.group(1) - else: - raise AssertionError("Changes shown message did not contain a file path.") - assert Path(file_path).suffix == ".nf", f"Diff shown for non-.nf file: {line}" + with open(patch_path) as fh: + patch_content = fh.read() + # Check changes not shown for non-.nf files + assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content + # Check changes only shown for main.nf + assert "Changes in 'trimgalore/main.nf'" in patch_content + for line in patch_content: + if line.startswith("---"): + assert line.endswith("main.nf") def test_update_all(self): diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 170b2af660..0d3a63c7ef 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -64,71 +64,23 @@ def test_install_at_hash_and_update(self): @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) def test_install_at_hash_and_update_limit_output(self, mock_prompt): """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True""" + self.caplog.set_level(logging.INFO) assert self.subworkflow_install_old.install("fastq_align_bowtie2") - # Capture the logger output - log_capture = io.StringIO() - ch = logging.StreamHandler(log_capture) - logger = logging.getLogger() - logger.addHandler(ch) - logger.setLevel(logging.INFO) - update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True) - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Copy the subworkflow files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") - shutil.copytree(sw_path, tmpdir) - - assert update_obj.update("fastq_align_bowtie2") is True - assert cmp_component(tmpdir, sw_path) is False - # Check that the modules.json is correctly updated - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - ) + assert update_obj.update("fastq_align_bowtie2") - # Get the captured log output - log_output = log_capture.getvalue() - log_lines = log_output.split("\n") - - # Check for various scenarios - nf_changes_shown = False - for line in log_lines: - if ( - re.match(r"'.+' is unchanged", line) - or re.match(r"'.+' was created", line) - or re.match(r"'.+' was removed", line) - ): - # Unchanged, created, and removed files should be reported for both .nf and non-.nf files - assert True - elif re.match(r"Changes in '.+' but not shown", line): - # Changes not shown should only be for non-.nf files - match = re.search(r"'(.+)'", line) - if match: - file_path = match.group(1) - else: - raise AssertionError("Changes not shown message did not contain a file path") - assert Path(file_path).suffix != ".nf", f"Changes in .nf file were not shown: {line}" - elif re.match(r"Changes in '.+':$", line): - # Changes shown should only be for .nf files - file_path = re.search(r"'(.+)'", line).group(1) - assert Path(file_path).suffix == ".nf", f"Changes in non-.nf file were shown: {line}" - nf_changes_shown = True - - # Ensure that changes in at least one .nf file were shown - assert nf_changes_shown, "No changes in .nf files were shown" - - # Clean up - logger.removeHandler(ch) - log_capture.close() + # Check changes not shown for non-.nf files + assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text + # Check changes only shown for main.nf files + assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text + for line in self.caplog.text.split("\n"): + if line.startswith("---"): + assert line.endswith("main.nf") def test_install_at_hash_and_update_and_save_diff_to_file(self): @@ -155,50 +107,29 @@ def test_install_at_hash_and_update_and_save_diff_to_file(self): def test_install_at_hash_and_update_and_save_diff_limit_output(self): """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" - assert self.subworkflow_install_old.install("fastq_align_bowtie2") + # Install old version of fastq_align_bowtie2 + self.subworkflow_install_old.install("fastq_align_bowtie2") patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") + # Update saving the differences to a patch file and with `limit_output` update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True) - - # Copy the sw files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") - shutil.copytree(sw_path, tmpdir) - - assert update_obj.update("fastq_align_bowtie2") is True - assert cmp_component(tmpdir, sw_path) is True + assert update_obj.update("fastq_align_bowtie2") # Check that the patch file was created assert patch_path.exists(), f"Patch file was not created at {patch_path}" - nf_changes_shown = False - non_nf_changes_not_shown = False - + # Read the contents of the patch file with open(patch_path) as fh: content = fh.read() - - # Check the first line - assert re.match( - r"Changes in module 'nf-core/fastq_align_bowtie2' between \([a-f0-9]+\) and \([a-f0-9]+\)", - content.split("\n")[0], - ), "Unexpected first line in patch file" - - # Check for .nf file changes shown - nf_changes_shown = bool(re.search(r"Changes in '.*\.nf':\n", content)) - - # Check for non-.nf file changes not shown - non_nf_changes_not_shown = bool(re.search(r"Changes in '.*[^.nf]' but not shown", content)) - - # Check that diff content is only for .nf files - diff_lines = re.findall(r"diff --git.*", content) - for line in diff_lines: - assert re.search(r"\.nf$", line), f"Diff shown for non-.nf file: {line}" - - # Ensure that changes in .nf files were shown and non-.nf files were not shown - assert nf_changes_shown, "No changes in .nf files were shown in the patch file" - assert non_nf_changes_not_shown, "Changes in non-.nf files were not properly limited in the patch file" - - # Clean up - patch_path.unlink() + # Check changes not shown for non-.nf files + assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content + assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content + assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content + assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content + # Check changes only shown for main.nf files + assert "Changes in 'fastq_align_bowtie2/main.nf'" in content + for line in content: + if line.startswith("---"): + assert line.endswith("main.nf") def test_update_all(self): diff --git a/tests/test_modules.py b/tests/test_modules.py index 7dd3132d33..67ba642189 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -5,6 +5,7 @@ import shutil import unittest from pathlib import Path +import pytest import requests_cache import responses @@ -156,6 +157,10 @@ def test_modulesrepo_class(self): assert modrepo.repo_path == "nf-core" assert modrepo.branch == "master" + @pytest.fixture(autouse=True) + def _use_caplog(self, caplog): + self.caplog = caplog + ############################################ # Test of the individual modules commands. # ############################################ diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index b7ebe952db..7b60313110 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -5,6 +5,7 @@ import shutil import unittest from pathlib import Path +import pytest import nf_core.modules import nf_core.pipelines.create.create @@ -113,6 +114,10 @@ def tearDown(self): if os.path.exists(self.tmp_dir): shutil.rmtree(self.tmp_dir) + @pytest.fixture(autouse=True) + def _use_caplog(self, caplog): + self.caplog = caplog + ################################################ # Test of the individual subworkflow commands. # ################################################ From 6325769aaef3b2f53b2bc0321455b90f0aa89528 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 16 Jul 2024 08:21:27 +0000 Subject: [PATCH 137/574] [automated] Fix code linting --- tests/subworkflows/update.py | 2 -- tests/test_modules.py | 2 +- tests/test_subworkflows.py | 1 + 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py index 0d3a63c7ef..42ed716b1c 100644 --- a/tests/subworkflows/update.py +++ b/tests/subworkflows/update.py @@ -1,6 +1,4 @@ -import io import logging -import re import shutil import tempfile from pathlib import Path diff --git a/tests/test_modules.py b/tests/test_modules.py index 67ba642189..6e601ce7ad 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -5,8 +5,8 @@ import shutil import unittest from pathlib import Path -import pytest +import pytest import requests_cache import responses import yaml diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 7b60313110..17bc678cad 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -5,6 +5,7 @@ import shutil import unittest from pathlib import Path + import pytest import nf_core.modules From 891d08ab9472e686686561d8b5426be760782268 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 16:21:43 +0200 Subject: [PATCH 138/574] move lint tests into pipeline folder --- tests/{lint => pipelines}/__init__.py | 0 tests/pipelines/lint/__init__.py | 0 .../lint/actions_awsfulltest.py | 0 tests/{ => pipelines}/lint/actions_awstest.py | 0 tests/{ => pipelines}/lint/actions_ci.py | 0 .../lint/actions_schema_validation.py | 0 tests/{ => pipelines}/lint/configs.py | 0 tests/{ => pipelines}/lint/files_exist.py | 7 +++--- tests/{ => pipelines}/lint/files_unchanged.py | 0 tests/{ => pipelines}/lint/merge_markers.py | 0 tests/{ => pipelines}/lint/modules_json.py | 0 tests/{ => pipelines}/lint/multiqc_config.py | 0 tests/{ => pipelines}/lint/nextflow_config.py | 22 +++++++++---------- tests/{ => pipelines}/lint/nfcore_yml.py | 0 .../{ => pipelines}/lint/template_strings.py | 0 .../lint/version_consistency.py | 2 +- 16 files changed, 15 insertions(+), 16 deletions(-) rename tests/{lint => pipelines}/__init__.py (100%) create mode 100644 tests/pipelines/lint/__init__.py rename tests/{ => pipelines}/lint/actions_awsfulltest.py (100%) rename tests/{ => pipelines}/lint/actions_awstest.py (100%) rename tests/{ => pipelines}/lint/actions_ci.py (100%) rename tests/{ => pipelines}/lint/actions_schema_validation.py (100%) rename tests/{ => pipelines}/lint/configs.py (100%) rename tests/{ => pipelines}/lint/files_exist.py (95%) rename tests/{ => pipelines}/lint/files_unchanged.py (100%) rename tests/{ => pipelines}/lint/merge_markers.py (100%) rename tests/{ => pipelines}/lint/modules_json.py (100%) rename tests/{ => pipelines}/lint/multiqc_config.py (100%) rename tests/{ => pipelines}/lint/nextflow_config.py (95%) rename tests/{ => pipelines}/lint/nfcore_yml.py (100%) rename tests/{ => pipelines}/lint/template_strings.py (100%) rename tests/{ => pipelines}/lint/version_consistency.py (93%) diff --git a/tests/lint/__init__.py b/tests/pipelines/__init__.py similarity index 100% rename from tests/lint/__init__.py rename to tests/pipelines/__init__.py diff --git a/tests/pipelines/lint/__init__.py b/tests/pipelines/lint/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/lint/actions_awsfulltest.py b/tests/pipelines/lint/actions_awsfulltest.py similarity index 100% rename from tests/lint/actions_awsfulltest.py rename to tests/pipelines/lint/actions_awsfulltest.py diff --git a/tests/lint/actions_awstest.py b/tests/pipelines/lint/actions_awstest.py similarity index 100% rename from tests/lint/actions_awstest.py rename to tests/pipelines/lint/actions_awstest.py diff --git a/tests/lint/actions_ci.py b/tests/pipelines/lint/actions_ci.py similarity index 100% rename from tests/lint/actions_ci.py rename to tests/pipelines/lint/actions_ci.py diff --git a/tests/lint/actions_schema_validation.py b/tests/pipelines/lint/actions_schema_validation.py similarity index 100% rename from tests/lint/actions_schema_validation.py rename to tests/pipelines/lint/actions_schema_validation.py diff --git a/tests/lint/configs.py b/tests/pipelines/lint/configs.py similarity index 100% rename from tests/lint/configs.py rename to tests/pipelines/lint/configs.py diff --git a/tests/lint/files_exist.py b/tests/pipelines/lint/files_exist.py similarity index 95% rename from tests/lint/files_exist.py rename to tests/pipelines/lint/files_exist.py index 679d209876..87508e78a8 100644 --- a/tests/lint/files_exist.py +++ b/tests/pipelines/lint/files_exist.py @@ -1,4 +1,3 @@ -import os from pathlib import Path import nf_core.pipelines.lint @@ -31,12 +30,12 @@ def test_files_exist_missing_main(self): assert "File not found: `main.nf`" in results["warned"] -def test_files_exist_depreciated_file(self): - """Check whether depreciated file issues warning""" +def test_files_exist_deprecated_file(self): + """Check whether deprecated file issues warning""" new_pipeline = self._make_pipeline_copy() nf = Path(new_pipeline, "parameters.settings.json") - os.system(f"touch {nf}") + nf.touch() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) lint_obj._load() diff --git a/tests/lint/files_unchanged.py b/tests/pipelines/lint/files_unchanged.py similarity index 100% rename from tests/lint/files_unchanged.py rename to tests/pipelines/lint/files_unchanged.py diff --git a/tests/lint/merge_markers.py b/tests/pipelines/lint/merge_markers.py similarity index 100% rename from tests/lint/merge_markers.py rename to tests/pipelines/lint/merge_markers.py diff --git a/tests/lint/modules_json.py b/tests/pipelines/lint/modules_json.py similarity index 100% rename from tests/lint/modules_json.py rename to tests/pipelines/lint/modules_json.py diff --git a/tests/lint/multiqc_config.py b/tests/pipelines/lint/multiqc_config.py similarity index 100% rename from tests/lint/multiqc_config.py rename to tests/pipelines/lint/multiqc_config.py diff --git a/tests/lint/nextflow_config.py b/tests/pipelines/lint/nextflow_config.py similarity index 95% rename from tests/lint/nextflow_config.py rename to tests/pipelines/lint/nextflow_config.py index b90298f542..d9157c90c6 100644 --- a/tests/lint/nextflow_config.py +++ b/tests/pipelines/lint/nextflow_config.py @@ -8,7 +8,7 @@ def test_nextflow_config_example_pass(self): """Tests that config variable existence test works with good pipeline example""" - self.lint_obj._load_pipeline_config() + self.lint_obj.load_pipeline_config() result = self.lint_obj.nextflow_config() assert len(result["failed"]) == 0 assert len(result["warned"]) == 0 @@ -18,7 +18,7 @@ def test_nextflow_config_bad_name_fail(self): """Tests that config variable existence test fails with bad pipeline name""" new_pipeline = self._make_pipeline_copy() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() lint_obj.nf_config["manifest.name"] = "bad_name" result = lint_obj.nextflow_config() @@ -30,7 +30,7 @@ def test_nextflow_config_dev_in_release_mode_failed(self): """Tests that config variable existence test fails with dev version in release mode""" new_pipeline = self._make_pipeline_copy() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() lint_obj.release_mode = True lint_obj.nf_config["manifest.version"] = "dev_is_bad_name" @@ -50,7 +50,7 @@ def test_nextflow_config_missing_test_profile_failed(self): with open(nf_conf_file, "w") as f: f.write(fail_content) lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) > 0 assert len(result["warned"]) == 0 @@ -60,7 +60,7 @@ def test_default_values_match(self): """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json.""" new_pipeline = self._make_pipeline_copy() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 assert len(result["warned"]) == 0 @@ -86,7 +86,7 @@ def test_default_values_fail(self): with open(nf_schema_file, "w") as f: f.write(fail_content) lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 2 assert ( @@ -107,7 +107,7 @@ def test_catch_params_assignment_in_main_nf(self): with open(main_nf_file, "a") as f: f.write("params.max_time = 42") lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 1 assert ( @@ -124,7 +124,7 @@ def test_allow_params_reference_in_main_nf(self): with open(main_nf_file, "a") as f: f.write("params.max_time == 42") lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 @@ -139,7 +139,7 @@ def test_default_values_ignored(self): "repository_type: pipeline\nlint:\n nextflow_config:\n - config_defaults:\n - params.max_cpus\n" ) lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() lint_obj._load_lint_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 @@ -173,7 +173,7 @@ def test_default_values_float(self): f.write(fail_content) lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 0 assert len(result["warned"]) == 0 @@ -203,7 +203,7 @@ def test_default_values_float_fail(self): f.write(fail_content) lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() result = lint_obj.nextflow_config() assert len(result["failed"]) == 1 diff --git a/tests/lint/nfcore_yml.py b/tests/pipelines/lint/nfcore_yml.py similarity index 100% rename from tests/lint/nfcore_yml.py rename to tests/pipelines/lint/nfcore_yml.py diff --git a/tests/lint/template_strings.py b/tests/pipelines/lint/template_strings.py similarity index 100% rename from tests/lint/template_strings.py rename to tests/pipelines/lint/template_strings.py diff --git a/tests/lint/version_consistency.py b/tests/pipelines/lint/version_consistency.py similarity index 93% rename from tests/lint/version_consistency.py rename to tests/pipelines/lint/version_consistency.py index 1be57969f1..88eadce391 100644 --- a/tests/lint/version_consistency.py +++ b/tests/pipelines/lint/version_consistency.py @@ -6,7 +6,7 @@ def test_version_consistency(self): """Tests that config variable existence test fails with bad pipeline name""" new_pipeline = self._make_pipeline_copy() lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() lint_obj.nextflow_config() result = lint_obj.version_consistency() From 11130e64d513969cfe011e8bdec4ae7da62b488b Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 16:38:59 +0200 Subject: [PATCH 139/574] make pipeline tests a subclass of TestPipeline --- tests/pipelines/test_bump_version.py | 127 ++++++++++----------------- tests/pipelines/test_create_logo.py | 39 +++----- tests/pipelines/test_launch.py | 27 ++---- tests/test_pipelines.py | 37 ++++++++ 4 files changed, 104 insertions(+), 126 deletions(-) create mode 100644 tests/test_pipelines.py diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py index 260637c064..709e82427d 100644 --- a/tests/pipelines/test_bump_version.py +++ b/tests/pipelines/test_bump_version.py @@ -1,86 +1,55 @@ """Some tests covering the bump_version code.""" -import os - import yaml import nf_core.pipelines.bump_version -import nf_core.pipelines.create.create import nf_core.utils - -# pass tmp_path as argument, which is a pytest feature -# see: https://docs.pytest.org/en/latest/how-to/tmp_path.html#the-tmp-path-fixture -def test_bump_pipeline_version(datafiles, tmp_path): - """Test that making a release with the working example files works""" - - # Get a workflow and configs - test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline") - create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir - ) - create_obj.init_pipeline() - pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - pipeline_obj._load() - - # Bump the version number - nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "1.1") - new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - - # Check nextflow.config - new_pipeline_obj._load_pipeline_config() - assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1" - - -def test_dev_bump_pipeline_version(datafiles, tmp_path): - """Test that making a release works with a dev name and a leading v""" - # Get a workflow and configs - test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline") - create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir - ) - create_obj.init_pipeline() - pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - pipeline_obj._load() - - # Bump the version number - nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj, "v1.2dev") - new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - - # Check the pipeline config - new_pipeline_obj._load_pipeline_config() - assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.2dev" - - -def test_bump_nextflow_version(datafiles, tmp_path): - # Get a workflow and configs - test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline") - create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir - ) - create_obj.init_pipeline() - pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - pipeline_obj._load() - - # Bump the version number to a specific version, preferably one - # we're not already on - version = "22.04.3" - nf_core.pipelines.bump_version.bump_nextflow_version(pipeline_obj, version) - new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir) - - # Check nextflow.config - new_pipeline_obj._load_pipeline_config() - assert new_pipeline_obj.nf_config["manifest.nextflowVersion"].strip("'\"") == f"!>={version}" - - # Check .github/workflows/ci.yml - with open(new_pipeline_obj._fp(".github/workflows/ci.yml")) as fh: - ci_yaml = yaml.safe_load(fh) - assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"][0] == version - - # Check README.md - with open(new_pipeline_obj._fp("README.md")) as fh: - readme = fh.read().splitlines() - assert ( - f"[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A5{version}-23aa62.svg)]" - "(https://www.nextflow.io/)" in readme - ) +from ..test_pipelines import TestPipelines + + +class TestBumpVersion(TestPipelines): + def test_bump_pipeline_version(self): + """Test that making a release with the working example files works""" + + # Bump the version number + nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "1.1") + new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) + + # Check nextflow.config + new_pipeline_obj.load_pipeline_config() + assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1" + + def test_dev_bump_pipeline_version(self): + """Test that making a release works with a dev name and a leading v""" + # Bump the version number + nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "v1.2dev") + new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) + + # Check the pipeline config + new_pipeline_obj.load_pipeline_config() + assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.2dev" + + def test_bump_nextflow_version(self): + # Bump the version number to a specific version, preferably one + # we're not already on + version = "22.04.3" + nf_core.pipelines.bump_version.bump_nextflow_version(self.pipeline_obj, version) + new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) + new_pipeline_obj._load() + + # Check nextflow.config + assert new_pipeline_obj.nf_config["manifest.nextflowVersion"].strip("'\"") == f"!>={version}" + + # Check .github/workflows/ci.yml + with open(new_pipeline_obj._fp(".github/workflows/ci.yml")) as fh: + ci_yaml = yaml.safe_load(fh) + assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"][0] == version + + # Check README.md + with open(new_pipeline_obj._fp("README.md")) as fh: + readme = fh.read().splitlines() + assert ( + f"[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A5{version}-23aa62.svg)]" + "(https://www.nextflow.io/)" in readme + ) diff --git a/tests/pipelines/test_create_logo.py b/tests/pipelines/test_create_logo.py index 8942894ce2..9ff9fce562 100644 --- a/tests/pipelines/test_create_logo.py +++ b/tests/pipelines/test_create_logo.py @@ -1,35 +1,24 @@ """Test covering the create-logo command.""" -import tempfile -import unittest from pathlib import Path import nf_core.pipelines.create_logo +from ..test_pipelines import TestPipelines -class TestCreateLogo(unittest.TestCase): - """Class for create-logo tests""" - - # create tempdir in setup step - def setUp(self): - self.tempdir = tempfile.TemporaryDirectory() - self.tempdir_path = Path(self.tempdir.name) - - # delete tempdir in teardown step - def tearDown(self): - self.tempdir.cleanup() +class TestCreateLogo(TestPipelines): def test_create_logo_png(self): """Test that the create-logo command works for PNGs""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG self.assertTrue(logo_fn.suffix == ".png") # Check that the file is the right size - fixture_fn = Path(__file__).parent / "fixtures" / "create_logo.png" + fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo.png" # allow some flexibility in the file size self.assertTrue(int(logo_fn.stat().st_size / 1000) == int(fixture_fn.stat().st_size / 1000)) @@ -37,13 +26,13 @@ def test_create_logo_png_dark(self): """Test that the create-logo command works for dark PNGs""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, theme="dark") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, theme="dark") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG self.assertTrue(logo_fn.suffix == ".png") # Check that the file is the right size - fixture_fn = Path(__file__).parent / "fixtures" / "create_logo_dark.png" + fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo_dark.png" # allow some flexibility in the file size self.assertTrue(int(logo_fn.stat().st_size / 1000) == int(fixture_fn.stat().st_size / 1000)) @@ -51,13 +40,13 @@ def test_create_log_png_width(self): """Test that the create-logo command works for PNGs with a custom width""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, width=100) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, width=100) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a PNG self.assertTrue(logo_fn.suffix == ".png") # Check that the file is the right size - fixture_fn = Path(__file__).parent / "fixtures" / "create_logo_width100.png" + fixture_fn = Path(__file__).parent.parent / "fixtures" / "create_logo_width100.png" # allow some flexibility in the file size self.assertTrue(int(logo_fn.stat().st_size / 100) == int(fixture_fn.stat().st_size / 100)) @@ -65,12 +54,12 @@ def test_create_logo_twice(self): """Test that the create-logo command returns an info message when run twice""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir) # Check that the file exists self.assertTrue(logo_fn.is_file()) # Create the logo again and capture the log output with self.assertLogs(level="INFO") as log: - nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path) + nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir) # Check that the log message is correct self.assertIn("Logo already exists", log.output[0]) @@ -79,14 +68,14 @@ def test_create_logo_without_text_fail(self): # Create a logo with self.assertRaises(UserWarning): - nf_core.pipelines.create_logo.create_logo("", self.tempdir_path) + nf_core.pipelines.create_logo.create_logo("", self.pipeline_dir) def test_create_logo_with_filename(self): """Test that the create-logo command works with a custom filename""" # Create a logo logo_fn = nf_core.pipelines.create_logo.create_logo( - "pipes", Path(self.tempdir_path / "custom_dir"), filename="custom" + "pipes", Path(self.pipeline_dir / "custom_dir"), filename="custom" ) # Check that the file exists self.assertTrue(logo_fn.is_file()) @@ -99,7 +88,7 @@ def test_create_logo_svg(self): """Test that the create-logo command works for SVGs""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, format="svg") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a SVG @@ -115,7 +104,7 @@ def test_create_logo_svg_dark(self): """Test that the create-logo command works for svgs and dark theme""" # Create a logo - logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.tempdir_path, format="svg", theme="dark") + logo_fn = nf_core.pipelines.create_logo.create_logo("pipes", self.pipeline_dir, format="svg", theme="dark") # Check that the file exists self.assertTrue(logo_fn.is_file()) # Check that the file is a SVG diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index b4b285a3c9..c9efa5aa63 100644 --- a/tests/pipelines/test_launch.py +++ b/tests/pipelines/test_launch.py @@ -2,36 +2,18 @@ import json import os -import shutil -from pathlib import Path -from unittest import TestCase, mock +from unittest import mock import pytest import nf_core.pipelines.create.create import nf_core.pipelines.launch -from ..utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder +from ..test_pipelines import TestPipelines +from ..utils import with_temporary_file, with_temporary_folder -class TestLaunch(TestCase): - """Class for launch tests""" - - def setUp(self): - """Create a new PipelineSchema and Launch objects""" - self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline() - self.nf_params_fn = os.path.join(self.tmp_dir, "nf-params.json") - self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) - - def tearDown(self): - """Clean up temporary files and folders""" - - if Path(self.nf_params_fn).exists(): - Path(self.nf_params_fn).unlink() - - if Path(self.tmp_dir).exists(): - shutil.rmtree(self.tmp_dir) - +class TestLaunch(TestPipelines): @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]) @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui") def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui): @@ -43,6 +25,7 @@ def test_launch_file_exists(self, mock_confirm): """Test that we detect an existing params file and return""" # Make an empty params file to be overwritten open(self.nf_params_fn, "a").close() + # Try and to launch, return with error assert self.launcher.launch_pipeline() is False diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py new file mode 100644 index 0000000000..461f046f52 --- /dev/null +++ b/tests/test_pipelines.py @@ -0,0 +1,37 @@ +import shutil +from pathlib import Path +from unittest import TestCase + +from git import Repo + +import nf_core.pipelines.launch +import nf_core.pipelines.lint +from nf_core.utils import Pipeline + +from .utils import create_tmp_pipeline + + +class TestPipelines(TestCase): + def setUp(self) -> None: + """Create a new Pipeline for testing""" + self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline() + self.pipeline_obj = Pipeline(self.pipeline_dir) + Repo.init(self.pipeline_dir) + self.pipeline_obj._load() + + self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json") + self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) + + self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir) + + def tearDown(self) -> None: + """Remove the test pipeline directory""" + shutil.rmtree(self.tmp_dir) + + def _make_pipeline_copy(self): + """Make a copy of the test pipeline that can be edited + + Returns: Path to new temp directory with pipeline""" + new_pipeline = self.tmp_dir / "nf-core-testpipeline-copy" + shutil.copytree(self.pipeline_dir, new_pipeline) + return new_pipeline From 20f0ba6ca7f30acb113e5234e60693eba89a410d Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 16:40:14 +0200 Subject: [PATCH 140/574] move pytest.ini into pyproject.toml --- pyproject.toml | 3 +++ pytest.ini | 7 ------- 2 files changed, 3 insertions(+), 7 deletions(-) delete mode 100644 pytest.ini diff --git a/pyproject.toml b/pyproject.toml index 8168bd7c11..4499324445 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,6 +5,9 @@ requires = ["setuptools>=40.6.0", "wheel"] [tool.pytest.ini_options] markers = ["datafiles: load datafiles"] testpaths = ["tests"] +python_files = ["test_*.py"] +# automatically run coroutine tests with asyncio +asyncio_mode = ["auto"] norecursedirs = [ ".*", "build", diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index fcbd03fa45..0000000000 --- a/pytest.ini +++ /dev/null @@ -1,7 +0,0 @@ -[pytest] -testpaths = - tests -python_files = test_*.py - -# automatically run coroutine tests with asyncio -asyncio_mode = auto From 36050fd44b5dcfb70c6d4fe8b40cb6f45ebc5fd2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 16:54:32 +0200 Subject: [PATCH 141/574] migrate more tests to pathilb, use commonly shared TEST_DATA_DIR var --- nf_core/components/lint/__init__.py | 2 +- nf_core/modules/modules_json.py | 8 ++--- nf_core/pipelines/create/create.py | 6 ++-- nf_core/pipelines/download.py | 7 ++-- nf_core/pipelines/lint/__init__.py | 2 +- nf_core/pipelines/sync.py | 5 +-- nf_core/utils.py | 56 +++++++++++++++++------------ tests/pipelines/test_create.py | 4 +-- tests/pipelines/test_download.py | 12 +++---- tests/test_utils.py | 4 +-- tests/utils.py | 13 +++---- 11 files changed, 66 insertions(+), 53 deletions(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 499d31e71e..6d47f1e7a8 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -117,7 +117,7 @@ def __init__( ) for comp in self.get_local_components() ] - self.config = nf_core.utils.fetch_wf_config(self.dir, cache_config=True) + self.config = nf_core.utils.fetch_wf_config(Path(self.dir), cache_config=True) else: component_dir = Path( self.dir, diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index b0a4fa661f..ca5d9de072 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -38,10 +38,10 @@ def __init__(self, pipeline_dir: str): Args: pipeline_dir (str): The pipeline directory """ - self.dir = pipeline_dir - self.modules_dir = Path(self.dir, "modules") - self.subworkflows_dir = Path(self.dir, "subworkflows") - self.modules_json_path = Path(self.dir, "modules.json") + self.dir = Path(pipeline_dir) + self.modules_dir = self.dir / "modules" + self.subworkflows_dir = self.dir / "subworkflows" + self.modules_json_path = self.dir / "modules.json" self.modules_json = None self.pipeline_modules = None self.pipeline_subworkflows = None diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index bdbbca646f..e9f37306f5 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -50,7 +50,7 @@ def __init__( version: str = "1.0.0dev", no_git: bool = False, force: bool = False, - outdir: Optional[str] = None, + outdir: Optional[Union[Path, str]] = None, template_config: Optional[Union[str, CreateConfig, Path]] = None, organisation: str = "nf-core", from_config_file: bool = False, @@ -61,7 +61,7 @@ def __init__( self.config = template_config elif from_config_file: # Try reading config file - _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".") + _, config_yml = nf_core.utils.load_tools_config(str(outdir) if outdir else ".") # Obtain a CreateConfig object from `.nf-core.yml` config file if "template" in config_yml: self.config = CreateConfig(**config_yml["template"]) @@ -372,6 +372,8 @@ def render_template(self): config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) with open(config_fn, "w") as fh: config_yml.update(template=self.config.model_dump()) + # convert posix path to string for yaml dump + config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"]) yaml.safe_dump(config_yml, fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 43b63d8192..f16430b0a8 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -10,6 +10,7 @@ import tarfile import textwrap from datetime import datetime +from pathlib import Path from typing import List, Optional, Tuple from zipfile import ZipFile @@ -697,7 +698,7 @@ def wf_use_local_configs(self, revision_dirname): with open(nfconfig_fn, "w") as nfconfig_fh: nfconfig_fh.write(nfconfig) - def find_container_images(self, workflow_directory): + def find_container_images(self, workflow_directory: str) -> None: """Find container image names for workflow. Starts by using `nextflow config` to pull out any process.container @@ -716,7 +717,7 @@ def find_container_images(self, workflow_directory): module_findings = [] # Use linting code to parse the pipeline nextflow config - self.nf_config = nf_core.utils.fetch_wf_config(workflow_directory) + self.nf_config = nf_core.utils.fetch_wf_config(Path(workflow_directory)) # Find any config variables that look like a container for k, v in self.nf_config.items(): @@ -1007,7 +1008,7 @@ def gather_registries(self, workflow_directory: str) -> None: # should exist, because find_container_images() is always called before if not self.nf_config: - self.nf_config = nf_core.utils.fetch_wf_config(workflow_directory) + self.nf_config = nf_core.utils.fetch_wf_config(Path(workflow_directory)) # Select registries defined in pipeline config configured_registries = [ diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index cf5ba3913f..b40f0ee292 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -559,7 +559,7 @@ def run_linting( # Load the various pipeline configs lint_obj._load_lint_config() - lint_obj._load_pipeline_config() + lint_obj.load_pipeline_config() lint_obj._list_files() # Create the modules lint object diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index f9a874c7e4..a309fa8c3b 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -5,6 +5,7 @@ import os import re import shutil +from pathlib import Path import git import questionary @@ -69,7 +70,7 @@ def __init__( ): """Initialise syncing object""" - self.pipeline_dir = os.path.abspath(pipeline_dir) + self.pipeline_dir = Path(pipeline_dir).resolve() self.from_branch = from_branch self.original_branch = None self.original_merge_branch = f"nf-core-template-merge-{nf_core.__version__}" @@ -209,7 +210,7 @@ def get_wf_config(self): # Fetch workflow variables log.debug("Fetching workflow config variables") - self.wf_config = nf_core.utils.fetch_wf_config(self.pipeline_dir) + self.wf_config = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir)) # Check that we have the required variables for rvar in self.required_config_vars: diff --git a/nf_core/utils.py b/nf_core/utils.py index 48d1c3ca3d..cf624935b3 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -141,7 +141,7 @@ def __init__(self, wf_path): self.files = [] self.git_sha = None self.minNextflowVersion = None - self.wf_path = wf_path + self.wf_path = Path(wf_path) self.pipeline_name = None self.pipeline_prefix = None self.schema_obj = None @@ -156,13 +156,15 @@ def __init__(self, wf_path): if os.environ.get("GITHUB_PR_COMMIT", "") != "": self.git_sha = os.environ["GITHUB_PR_COMMIT"] - def _load(self): + def __repr__(self) -> str: + return f"" + + def _load(self) -> bool: """Run core load functions""" - self._list_files() - self._load_pipeline_config() - self._load_conda_environment() - def _list_files(self): + return self._list_files() and self.load_pipeline_config() and self._load_conda_environment() + + def _list_files(self) -> bool: """Get a list of all files in the pipeline""" try: # First, try to get the list of files using git @@ -174,18 +176,36 @@ def _list_files(self): self.files.append(full_fn) else: log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!") + return True except subprocess.CalledProcessError as e: # Failed, so probably not initialised as a git repository - just a list of all files log.debug(f"Couldn't call 'git ls-files': {e}") self.files = [] for subdir, _, files in os.walk(self.wf_path): for fn in files: - self.files.append(Path(subdir) / fn) + self.files.append(Path(subdir, str(fn))) + if len(self.files) > 0: + return True + return False + + def _load_conda_environment(self) -> bool: + """Try to load the pipeline environment.yml file, if it exists""" + try: + with open(Path(self.wf_path, "environment.yml")) as fh: + self.conda_config = yaml.safe_load(fh) + return True + except FileNotFoundError: + log.debug("No conda `environment.yml` file found.") + return False - def _load_pipeline_config(self): + def _fp(self, fn): + """Convenience function to get full path to a file in the pipeline""" + return os.path.join(self.wf_path, fn) + + def load_pipeline_config(self) -> bool: """Get the nextflow config for this pipeline - Once loaded, set a few convienence reference class attributes + Once loaded, set a few convenience reference class attributes """ self.nf_config = fetch_wf_config(self.wf_path) @@ -194,18 +214,8 @@ def _load_pipeline_config(self): nextflow_version_match = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", "")) if nextflow_version_match: self.minNextflowVersion = nextflow_version_match.group(0) - - def _load_conda_environment(self): - """Try to load the pipeline environment.yml file, if it exists""" - try: - with open(os.path.join(self.wf_path, "environment.yml")) as fh: - self.conda_config = yaml.safe_load(fh) - except FileNotFoundError: - log.debug("No conda `environment.yml` file found.") - - def _fp(self, fn): - """Convenience function to get full path to a file in the pipeline""" - return os.path.join(self.wf_path, fn) + return True + return False def is_pipeline_directory(wf_path): @@ -229,7 +239,7 @@ def is_pipeline_directory(wf_path): raise UserWarning(warning) -def fetch_wf_config(wf_path: str, cache_config: bool = True) -> dict: +def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict: """Uses Nextflow to retrieve the the configuration variables from a Nextflow workflow. @@ -263,7 +273,7 @@ def fetch_wf_config(wf_path: str, cache_config: bool = True) -> dict: concat_hash = "" for fn in ["nextflow.config", "main.nf"]: try: - with open(Path(wf_path, fn), "rb") as fh: + with open(wf_path / fn, "rb") as fh: concat_hash += hashlib.sha256(fh.read()).hexdigest() except FileNotFoundError: pass diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py index d93b26bd1a..bb27445e70 100644 --- a/tests/pipelines/test_create.py +++ b/tests/pipelines/test_create.py @@ -2,16 +2,14 @@ import os import unittest -from pathlib import Path import git import yaml import nf_core.pipelines.create.create -from ..utils import with_temporary_folder +from ..utils import TEST_DATA_DIR, with_temporary_folder -TEST_DATA_DIR = Path(__file__).parent / "data" PIPELINE_TEMPLATE_YML = TEST_DATA_DIR / "pipeline_create_template.yml" PIPELINE_TEMPLATE_YML_SKIP = TEST_DATA_DIR / "pipeline_create_template_skip.yml" diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py index ebb76fef72..7ed6de3fa7 100644 --- a/tests/pipelines/test_download.py +++ b/tests/pipelines/test_download.py @@ -18,7 +18,7 @@ from nf_core.synced_repo import SyncedRepo from nf_core.utils import run_cmd -from ..utils import with_temporary_folder +from ..utils import TEST_DATA_DIR, with_temporary_folder class DownloadTest(unittest.TestCase): @@ -139,12 +139,12 @@ def test_wf_use_local_configs(self, tmp_path): with tempfile.TemporaryDirectory() as test_outdir: download_obj = DownloadWorkflow(pipeline="dummy", revision="1.2.0", outdir=test_outdir) - shutil.copytree(test_pipeline_dir, os.path.join(test_outdir, "workflow")) + shutil.copytree(test_pipeline_dir, Path(test_outdir, "workflow")) download_obj.download_configs() # Test the function download_obj.wf_use_local_configs("workflow") - wf_config = nf_core.utils.fetch_wf_config(os.path.join(test_outdir, "workflow"), cache_config=False) + wf_config = nf_core.utils.fetch_wf_config(Path(test_outdir, "workflow"), cache_config=False) assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/" # @@ -173,7 +173,7 @@ def test_find_container_images_config_basic(self, tmp_path, mock_fetch_wf_config @mock.patch("nf_core.utils.fetch_wf_config") def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_config): download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path) - result = run_cmd("nextflow", f"config -flat {Path(__file__).resolve().parent / 'data/mock_config_containers'}") + result = run_cmd("nextflow", f"config -flat {TEST_DATA_DIR}'/mock_config_containers'") if result is not None: nfconfig_raw, _ = result config = {} @@ -203,7 +203,7 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co def test_find_container_images_modules(self, tmp_path, mock_fetch_wf_config): download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path) mock_fetch_wf_config.return_value = {} - download_obj.find_container_images(Path(__file__).resolve().parent / "data/mock_module_containers") + download_obj.find_container_images(TEST_DATA_DIR / "mock_module_containers") # mock_docker_single_quay_io.nf assert "quay.io/biocontainers/singlequay:1.9--pyh9f0ad1d_0" in download_obj.containers @@ -546,7 +546,7 @@ def test_remote_container_functionality(self, tmp_dir): outdir=os.path.join(tmp_dir, "new"), revision="3.9", compress_type="none", - container_cache_index=Path(__file__).resolve().parent / "data/testdata_remote_containers.txt", + container_cache_index=TEST_DATA_DIR / "data/testdata_remote_containers.txt", ) download_obj.include_configs = False # suppress prompt, because stderr.is_interactive doesn't. diff --git a/tests/test_utils.py b/tests/test_utils.py index 89ba0444ff..7afe1a532f 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -95,9 +95,9 @@ def test_rich_force_colours_true(self): os.environ.pop("PY_COLORS", None) assert nf_core.utils.rich_force_colors() is True - def test_load_pipeline_config(self): + def testload_pipeline_config(self): """Load the pipeline Nextflow config""" - self.pipeline_obj._load_pipeline_config() + self.pipeline_obj.load_pipeline_config() assert self.pipeline_obj.nf_config["dag.enabled"] == "true" # TODO nf-core: Assess and strip out if no longer required for DSL2 diff --git a/tests/utils.py b/tests/utils.py index 9a0fd0896f..7be0799d6f 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -3,8 +3,8 @@ """ import functools -import os import tempfile +from pathlib import Path from typing import Any, Callable, Tuple import responses @@ -12,6 +12,7 @@ import nf_core.modules import nf_core.pipelines.create.create +TEST_DATA_DIR = Path(__file__).parent / "data" OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386" OLD_TRIMGALORE_BRANCH = "mimic-old-trimgalore" GITLAB_URL = "https://gitlab.com/nf-core/modules-test.git" @@ -93,14 +94,14 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200) -def create_tmp_pipeline() -> Tuple[str, str, str, str]: +def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: """Create a new Pipeline for testing""" - tmp_dir = tempfile.mkdtemp() - root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) - template_dir = os.path.join(root_repo_dir, "nf_core", "pipeline-template") + tmp_dir = Path(tempfile.TemporaryDirectory().name) + root_repo_dir = Path(__file__).resolve().parent.parent + template_dir = Path(root_repo_dir, "nf_core", "pipeline-template") pipeline_name = "mypipeline" - pipeline_dir = os.path.join(tmp_dir, pipeline_name) + pipeline_dir = Path(tmp_dir, pipeline_name) nf_core.pipelines.create.create.PipelineCreate( pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir From fb274107d592b16e7634cc64db149a6b514e88db Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 16:55:00 +0200 Subject: [PATCH 142/574] use testpipeline class in test_lint --- tests/pipelines/test_lint.py | 83 +++++++++++------------------------- 1 file changed, 26 insertions(+), 57 deletions(-) diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index 460c8f03d8..8530fea5ad 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -3,51 +3,20 @@ import fnmatch import json import os -import shutil -import tempfile -import unittest +from pathlib import Path import yaml import nf_core.pipelines.create.create import nf_core.pipelines.lint +from ..test_pipelines import TestPipelines from ..utils import with_temporary_folder -class TestLint(unittest.TestCase): +class TestLint(TestPipelines): """Class for lint tests""" - def setUp(self): - """Function that runs at start of tests for common resources - - Use nf_core.pipelines.create() to make a pipeline that we can use for testing - """ - - self.tmp_dir = tempfile.mkdtemp() - self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline") - self.create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir - ) - self.create_obj.init_pipeline() - - # Base lint object on this directory - self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir) - - def tearDown(self): - """Clean up temporary files and folders""" - - if os.path.exists(self.tmp_dir): - shutil.rmtree(self.tmp_dir) - - def _make_pipeline_copy(self): - """Make a copy of the test pipeline that can be edited - - Returns: Path to new temp directory with pipeline""" - new_pipeline = os.path.join(self.tmp_dir, "nf-core-testpipeline-copy") - shutil.copytree(self.test_pipeline_dir, new_pipeline) - return new_pipeline - ########################## # CORE lint.py FUNCTIONS # ########################## @@ -56,7 +25,7 @@ def test_run_linting_function(self): We don't really check any of this code as it's just a series of function calls and we're testing each of those individually. This is mostly to check for syntax errors.""" - nf_core.pipelines.lint.run_linting(self.test_pipeline_dir, False) + nf_core.pipelines.lint.run_linting(self.pipeline_dir, False) def test_init_pipeline_lint(self): """Simply create a PipelineLint object. @@ -64,11 +33,11 @@ def test_init_pipeline_lint(self): This checks that all of the lint test imports are working properly, we also check that the git sha was found and that the release flag works properly """ - lint_obj = nf_core.pipelines.lint.PipelineLint(self.test_pipeline_dir, True) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True) # Tests that extra test is added for release mode assert "version_consistency" in lint_obj.lint_tests - + assert lint_obj.git_sha # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash assert len(lint_obj.git_sha) > 0 @@ -86,7 +55,7 @@ def test_load_lint_config_ignore_all_tests(self): # Make a config file listing all test names config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} - with open(os.path.join(new_pipeline, ".nf-core.yml"), "w") as fh: + with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: yaml.dump(config_dict, fh) # Load the new lint config file and check @@ -130,7 +99,7 @@ def test_json_output(self, tmp_dir): self.lint_obj.warned.append(("test_three", "This test gave a warning")) # Make a temp dir for the JSON output - json_fn = os.path.join(tmp_dir, "lint_results.json") + json_fn = Path(tmp_dir, "lint_results.json") self.lint_obj._save_json_results(json_fn) # Load created JSON file and check its contents @@ -156,7 +125,7 @@ def test_sphinx_md_files(self): """Check that we have .md files for all lint module code, and that there are no unexpected files (eg. deleted lint tests)""" - docs_basedir = os.path.join( + docs_basedir = Path( os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "docs", "api", "_src", "pipeline_lint_tests" ) @@ -164,12 +133,12 @@ def test_sphinx_md_files(self): existing_docs = [] for fn in os.listdir(docs_basedir): if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"): - existing_docs.append(os.path.join(docs_basedir, fn)) + existing_docs.append(Path(docs_basedir, fn)) # Check .md files against each test name lint_obj = nf_core.pipelines.lint.PipelineLint("", True) for test_name in lint_obj.lint_tests: - fn = os.path.join(docs_basedir, f"{test_name}.md") + fn = Path(docs_basedir, f"{test_name}.md") assert os.path.exists(fn), f"Could not find lint docs .md file: {fn}" existing_docs.remove(fn) @@ -179,34 +148,34 @@ def test_sphinx_md_files(self): ####################### # SPECIFIC LINT TESTS # ####################### - from ..lint.actions_awsfulltest import ( # type: ignore[misc] + from .lint.actions_awsfulltest import ( # type: ignore[misc] test_actions_awsfulltest_fail, test_actions_awsfulltest_pass, test_actions_awsfulltest_warn, ) - from ..lint.actions_awstest import ( # type: ignore[misc] + from .lint.actions_awstest import ( # type: ignore[misc] test_actions_awstest_fail, test_actions_awstest_pass, ) - from ..lint.actions_ci import ( # type: ignore[misc] + from .lint.actions_ci import ( # type: ignore[misc] test_actions_ci_fail_wrong_nf, test_actions_ci_fail_wrong_trigger, test_actions_ci_pass, ) - from ..lint.actions_schema_validation import ( # type: ignore[misc] + from .lint.actions_schema_validation import ( # type: ignore[misc] test_actions_schema_validation_fails_for_additional_property, test_actions_schema_validation_missing_jobs, test_actions_schema_validation_missing_on, ) - from ..lint.configs import ( # type: ignore[misc] + from .lint.configs import ( # type: ignore[misc] test_ignore_base_config, test_ignore_modules_config, test_superfluous_withname_in_base_config_fails, test_superfluous_withname_in_modules_config_fails, test_withname_in_modules_config, ) - from ..lint.files_exist import ( # type: ignore[misc] - test_files_exist_depreciated_file, + from .lint.files_exist import ( # type: ignore[misc] + test_files_exist_deprecated_file, test_files_exist_fail_conditional, test_files_exist_missing_config, test_files_exist_missing_main, @@ -214,13 +183,13 @@ def test_sphinx_md_files(self): test_files_exist_pass_conditional, test_files_exist_pass_conditional_nfschema, ) - from ..lint.files_unchanged import ( # type: ignore[misc] + from .lint.files_unchanged import ( # type: ignore[misc] test_files_unchanged_fail, test_files_unchanged_pass, ) - from ..lint.merge_markers import test_merge_markers_found # type: ignore[misc] - from ..lint.modules_json import test_modules_json_pass # type: ignore[misc] - from ..lint.multiqc_config import ( # type: ignore[misc] + from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] + from .lint.modules_json import test_modules_json_pass # type: ignore[misc] + from .lint.multiqc_config import ( # type: ignore[misc] test_multiqc_config_exists, test_multiqc_config_ignore, test_multiqc_config_missing_report_section_order, @@ -229,7 +198,7 @@ def test_sphinx_md_files(self): test_multiqc_config_report_comment_release_succeed, test_multiqc_incorrect_export_plots, ) - from ..lint.nextflow_config import ( # type: ignore[misc] + from .lint.nextflow_config import ( # type: ignore[misc] test_allow_params_reference_in_main_nf, test_catch_params_assignment_in_main_nf, test_default_values_fail, @@ -242,14 +211,14 @@ def test_sphinx_md_files(self): test_nextflow_config_example_pass, test_nextflow_config_missing_test_profile_failed, ) - from ..lint.nfcore_yml import ( # type: ignore[misc] + from .lint.nfcore_yml import ( # type: ignore[misc] test_nfcore_yml_fail_nfcore_version, test_nfcore_yml_fail_repo_type, test_nfcore_yml_pass, ) - from ..lint.template_strings import ( # type: ignore[misc] + from .lint.template_strings import ( # type: ignore[misc] test_template_strings, test_template_strings_ignore_file, test_template_strings_ignored, ) - from ..lint.version_consistency import test_version_consistency # type: ignore[misc] + from .lint.version_consistency import test_version_consistency # type: ignore[misc] From 1d2076b511665034153d2ed3010508479f1e8e27 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 16 Jul 2024 17:56:42 +0200 Subject: [PATCH 143/574] fix tests --- nf_core/utils.py | 24 ++++++++++++------------ tests/pipelines/test_download.py | 4 ++-- tests/pipelines/test_lint.py | 4 +--- tests/pipelines/test_list.py | 28 ++++++++++++++-------------- tests/test_pipelines.py | 3 --- 5 files changed, 29 insertions(+), 34 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index cf624935b3..9b3775d62d 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -19,7 +19,7 @@ import time from contextlib import contextmanager from pathlib import Path -from typing import Generator, Tuple, Union +from typing import Dict, Generator, List, Optional, Tuple, Union import git import prompt_toolkit @@ -135,22 +135,22 @@ class Pipeline: def __init__(self, wf_path): """Initialise pipeline object""" - self.conda_config = {} - self.conda_package_info = {} - self.nf_config = {} - self.files = [] - self.git_sha = None - self.minNextflowVersion = None + self.conda_config: Dict = {} + self.conda_package_info: Dict = {} + self.nf_config: Dict = {} + self.files: List[Path] = [] + self.git_sha: Optional[str] = None + self.minNextflowVersion: Optional[str] = None self.wf_path = Path(wf_path) - self.pipeline_name = None - self.pipeline_prefix = None - self.schema_obj = None + self.pipeline_name: Optional[str] = None + self.pipeline_prefix: Optional[str] = None + self.schema_obj: Optional[Dict] = None try: repo = git.Repo(self.wf_path) self.git_sha = repo.head.object.hexsha - except Exception: - log.debug(f"Could not find git hash for pipeline: {self.wf_path}") + except Exception as e: + log.debug(f"Could not find git hash for pipeline: {self.wf_path}. {e}") # Overwrite if we have the last commit from the PR - otherwise we get a merge commit hash if os.environ.get("GITHUB_PR_COMMIT", "") != "": diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py index 7ed6de3fa7..d571b82cee 100644 --- a/tests/pipelines/test_download.py +++ b/tests/pipelines/test_download.py @@ -203,7 +203,7 @@ def test__find_container_images_config_nextflow(self, tmp_path, mock_fetch_wf_co def test_find_container_images_modules(self, tmp_path, mock_fetch_wf_config): download_obj = DownloadWorkflow(pipeline="dummy", outdir=tmp_path) mock_fetch_wf_config.return_value = {} - download_obj.find_container_images(TEST_DATA_DIR / "mock_module_containers") + download_obj.find_container_images(str(Path(TEST_DATA_DIR, "mock_module_containers"))) # mock_docker_single_quay_io.nf assert "quay.io/biocontainers/singlequay:1.9--pyh9f0ad1d_0" in download_obj.containers @@ -546,7 +546,7 @@ def test_remote_container_functionality(self, tmp_dir): outdir=os.path.join(tmp_dir, "new"), revision="3.9", compress_type="none", - container_cache_index=TEST_DATA_DIR / "data/testdata_remote_containers.txt", + container_cache_index=str(Path(TEST_DATA_DIR, "testdata_remote_containers.txt")), ) download_obj.include_configs = False # suppress prompt, because stderr.is_interactive doesn't. diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index 8530fea5ad..80d7e1e018 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -125,9 +125,7 @@ def test_sphinx_md_files(self): """Check that we have .md files for all lint module code, and that there are no unexpected files (eg. deleted lint tests)""" - docs_basedir = Path( - os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "docs", "api", "_src", "pipeline_lint_tests" - ) + docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests") # Get list of existing .md files existing_docs = [] diff --git a/tests/pipelines/test_list.py b/tests/pipelines/test_list.py index 21d239287d..32970ae076 100644 --- a/tests/pipelines/test_list.py +++ b/tests/pipelines/test_list.py @@ -14,15 +14,17 @@ import nf_core.pipelines.list -# create a temporary directory that can be used by the tests in this file -tmp = Path(tempfile.mkdtemp()) -tmp_nxf = tmp / "nxf" -tmp_nxf_str = str(tmp_nxf) - class TestList(unittest.TestCase): """Class for list tests""" + def setUp(self) -> None: + # create a temporary directory that can be used by the tests in this file + tmp = Path(tempfile.TemporaryDirectory().name) + self.tmp_nxf = tmp / "nxf" + self.tmp_nxf_str = str(self.tmp_nxf) + os.environ["NXF_ASSETS"] = self.tmp_nxf_str + @mock.patch("subprocess.check_output") def test_working_listcall(self, mock_subprocess): """Test that listing pipelines works""" @@ -105,28 +107,26 @@ def test_local_workflows_compare_and_fail_silently(self): rwf_ex.releases = None - @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str}) @mock.patch("nf_core.pipelines.list.LocalWorkflow") def test_parse_local_workflow_and_succeed(self, mock_local_wf): - test_path = tmp_nxf / "nf-core" + test_path = self.tmp_nxf / "nf-core" if not os.path.isdir(test_path): os.makedirs(test_path) - assert os.environ["NXF_ASSETS"] == tmp_nxf_str - with open(tmp_nxf / "nf-core/dummy-wf", "w") as f: + assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str + with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f: f.write("dummy") workflows_obj = nf_core.pipelines.list.Workflows() workflows_obj.get_local_nf_workflows() assert len(workflows_obj.local_workflows) == 1 - @mock.patch.dict(os.environ, {"NXF_ASSETS": tmp_nxf_str}) @mock.patch("nf_core.pipelines.list.LocalWorkflow") @mock.patch("subprocess.check_output") def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess): - test_path = tmp_nxf / "nf-core" + test_path = self.tmp_nxf / "nf-core" if not os.path.isdir(test_path): os.makedirs(test_path) - assert os.environ["NXF_ASSETS"] == tmp_nxf_str - with open(tmp_nxf / "nf-core/dummy-wf", "w") as f: + assert os.environ["NXF_ASSETS"] == self.tmp_nxf_str + with open(self.tmp_nxf / "nf-core/dummy-wf", "w") as f: f.write("dummy") workflows_obj = nf_core.pipelines.list.Workflows() workflows_obj.get_local_nf_workflows() @@ -135,7 +135,7 @@ def test_parse_local_workflow_home(self, mock_local_wf, mock_subprocess): @mock.patch("git.Repo") def test_local_workflow_investigation(self, mock_repo, mock_stat): local_wf = nf_core.pipelines.list.LocalWorkflow("dummy") - local_wf.local_path = tmp + local_wf.local_path = self.tmp_nxf.parent mock_repo.head.commit.hexsha = "h00r4y" mock_stat.st_mode = 1 local_wf.get_local_nf_workflow_details() diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py index 461f046f52..899c4641ea 100644 --- a/tests/test_pipelines.py +++ b/tests/test_pipelines.py @@ -2,8 +2,6 @@ from pathlib import Path from unittest import TestCase -from git import Repo - import nf_core.pipelines.launch import nf_core.pipelines.lint from nf_core.utils import Pipeline @@ -16,7 +14,6 @@ def setUp(self) -> None: """Create a new Pipeline for testing""" self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline() self.pipeline_obj = Pipeline(self.pipeline_dir) - Repo.init(self.pipeline_dir) self.pipeline_obj._load() self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json") From 65084dd6143d3be44121689b84ec3a00fa857356 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 16 Jul 2024 18:48:35 +0000 Subject: [PATCH 144/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe7fdcc28b..6bc07e2a7d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) +- Rrestructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) ### Download From 45fdfb9ddd06e0b75fef592475ce166ee89894da Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 09:57:57 +0200 Subject: [PATCH 145/574] more fine-grained setup steps --- nf_core/pipelines/create/create.py | 2 +- nf_core/utils.py | 2 +- tests/pipelines/test_launch.py | 13 +++++++++---- tests/pipelines/test_lint.py | 4 ++++ tests/pipelines/test_list.py | 5 ++--- tests/test_pipelines.py | 8 -------- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index e9f37306f5..8cfa09491f 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -61,7 +61,7 @@ def __init__( self.config = template_config elif from_config_file: # Try reading config file - _, config_yml = nf_core.utils.load_tools_config(str(outdir) if outdir else ".") + _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".") # Obtain a CreateConfig object from `.nf-core.yml` config file if "template" in config_yml: self.config = CreateConfig(**config_yml["template"]) diff --git a/nf_core/utils.py b/nf_core/utils.py index 9b3775d62d..ead871aed1 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -133,7 +133,7 @@ class Pipeline: schema_obj (obj): A :class:`PipelineSchema` object """ - def __init__(self, wf_path): + def __init__(self, wf_path: Path) -> None: """Initialise pipeline object""" self.conda_config: Dict = {} self.conda_package_info: Dict = {} diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index c9efa5aa63..03bc0e98be 100644 --- a/tests/pipelines/test_launch.py +++ b/tests/pipelines/test_launch.py @@ -1,7 +1,7 @@ """Tests covering the pipeline launch code.""" import json -import os +from pathlib import Path from unittest import mock import pytest @@ -14,6 +14,11 @@ class TestLaunch(TestPipelines): + def setUp(self) -> None: + super().setUp() + self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json") + self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) + @mock.patch.object(nf_core.pipelines.launch.Launch, "prompt_web_gui", side_effect=[True]) @mock.patch.object(nf_core.pipelines.launch.Launch, "launch_web_gui") def test_launch_pipeline(self, mock_webbrowser, mock_lauch_web_gui): @@ -47,12 +52,12 @@ def test_get_pipeline_schema(self): @with_temporary_folder def test_make_pipeline_schema(self, tmp_path): """Create a workflow, but delete the schema file, then try to load it""" - test_pipeline_dir = os.path.join(tmp_path, "wf") + test_pipeline_dir = Path(tmp_path, "wf") create_obj = nf_core.pipelines.create.create.PipelineCreate( "testpipeline", "a description", "Me", outdir=test_pipeline_dir, no_git=True ) create_obj.init_pipeline() - os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json")) + Path(test_pipeline_dir, "nextflow_schema.json").unlink() self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn) self.launcher.get_pipeline_schema() assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2 @@ -300,7 +305,7 @@ def test_build_command_params(self): # Check command assert ( self.launcher.nextflow_cmd - == f'nextflow run {self.pipeline_dir} -params-file "{os.path.relpath(self.nf_params_fn)}"' + == f'nextflow run {self.pipeline_dir} -params-file "{Path(self.nf_params_fn).relative_to(Path.cwd())}"' ) # Check saved parameters file with open(self.nf_params_fn) as fh: diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index 80d7e1e018..800ffa16b3 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -17,6 +17,10 @@ class TestLint(TestPipelines): """Class for lint tests""" + def setUp(self) -> None: + super().setUp() + self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir) + ########################## # CORE lint.py FUNCTIONS # ########################## diff --git a/tests/pipelines/test_list.py b/tests/pipelines/test_list.py index 32970ae076..aacc3805e8 100644 --- a/tests/pipelines/test_list.py +++ b/tests/pipelines/test_list.py @@ -4,10 +4,9 @@ import os import tempfile import time -import unittest from datetime import datetime from pathlib import Path -from unittest import mock +from unittest import TestCase, mock import pytest from rich.console import Console @@ -15,7 +14,7 @@ import nf_core.pipelines.list -class TestList(unittest.TestCase): +class TestList(TestCase): """Class for list tests""" def setUp(self) -> None: diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py index 899c4641ea..656ccbef55 100644 --- a/tests/test_pipelines.py +++ b/tests/test_pipelines.py @@ -1,9 +1,6 @@ import shutil -from pathlib import Path from unittest import TestCase -import nf_core.pipelines.launch -import nf_core.pipelines.lint from nf_core.utils import Pipeline from .utils import create_tmp_pipeline @@ -16,11 +13,6 @@ def setUp(self) -> None: self.pipeline_obj = Pipeline(self.pipeline_dir) self.pipeline_obj._load() - self.nf_params_fn = Path(self.pipeline_dir, "nf-params.json") - self.launcher = nf_core.pipelines.launch.Launch(self.pipeline_dir, params_out=self.nf_params_fn) - - self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir) - def tearDown(self) -> None: """Remove the test pipeline directory""" shutil.rmtree(self.tmp_dir) From 189015f1b12809bce71744801823c6fa4a956c58 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 10:00:53 +0200 Subject: [PATCH 146/574] don't run list_files on every init, only needed for one linting step --- nf_core/pipelines/lint/__init__.py | 1 - nf_core/pipelines/lint/template_strings.py | 3 +- nf_core/utils.py | 53 +++++++++++----------- tests/test_utils.py | 4 +- 4 files changed, 31 insertions(+), 30 deletions(-) diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index b40f0ee292..d731cb018d 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -560,7 +560,6 @@ def run_linting( # Load the various pipeline configs lint_obj._load_lint_config() lint_obj.load_pipeline_config() - lint_obj._list_files() # Create the modules lint object module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress) diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py index 9b015bc209..90c47203f6 100644 --- a/nf_core/pipelines/lint/template_strings.py +++ b/nf_core/pipelines/lint/template_strings.py @@ -39,10 +39,11 @@ def template_strings(self): ignored = [] # Files that should be ignored according to the linting config ignore_files = self.lint_config.get("template_strings", []) + files = self.list_files() # Loop through files, searching for string num_matches = 0 - for fn in self.files: + for fn in files: if str(fn.relative_to(self.wf_path)) in ignore_files: ignored.append(f"Ignoring Jinja template strings in file `{fn}`") continue diff --git a/nf_core/utils.py b/nf_core/utils.py index ead871aed1..b5719a2b15 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -162,31 +162,7 @@ def __repr__(self) -> str: def _load(self) -> bool: """Run core load functions""" - return self._list_files() and self.load_pipeline_config() and self._load_conda_environment() - - def _list_files(self) -> bool: - """Get a list of all files in the pipeline""" - try: - # First, try to get the list of files using git - git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines() - self.files = [] - for fn in git_ls_files: - full_fn = Path(self.wf_path) / fn.decode("utf-8") - if full_fn.is_file(): - self.files.append(full_fn) - else: - log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!") - return True - except subprocess.CalledProcessError as e: - # Failed, so probably not initialised as a git repository - just a list of all files - log.debug(f"Couldn't call 'git ls-files': {e}") - self.files = [] - for subdir, _, files in os.walk(self.wf_path): - for fn in files: - self.files.append(Path(subdir, str(fn))) - if len(self.files) > 0: - return True - return False + return self.load_pipeline_config() and self._load_conda_environment() def _load_conda_environment(self) -> bool: """Try to load the pipeline environment.yml file, if it exists""" @@ -202,6 +178,31 @@ def _fp(self, fn): """Convenience function to get full path to a file in the pipeline""" return os.path.join(self.wf_path, fn) + def list_files(self) -> List[Path]: + """Get a list of all files in the pipeline""" + files = [] + try: + # First, try to get the list of files using git + git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines() + for fn in git_ls_files: + full_fn = Path(self.wf_path) / fn.decode("utf-8") + if full_fn.is_file(): + files.append(full_fn) + else: + log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!") + except subprocess.CalledProcessError as e: + # Failed, so probably not initialised as a git repository - just a list of all files + log.debug(f"Couldn't call 'git ls-files': {e}") + files = [] + for file_path in self.wf_path.rglob("*"): + if file_path.is_file(): + # Append the file path to the list + files.append(file_path.relative_to(self.wf_path)) + if len(files) == 0: + log.debug(f"No files found in pipeline: {self.wf_path}") + + return files + def load_pipeline_config(self) -> bool: """Get the nextflow config for this pipeline @@ -1082,7 +1083,7 @@ def determine_base_dir(directory="."): return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir -def get_first_available_path(directory, paths): +def get_first_available_path(directory: Union[Path, str], paths: List[str]) -> Union[Path, None]: for p in paths: if Path(directory, p).is_file(): return Path(directory, p) diff --git a/tests/test_utils.py b/tests/test_utils.py index 7afe1a532f..f61f3584e2 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -109,7 +109,7 @@ def testload_pipeline_config(self): def test_list_files_git(self): """Test listing pipeline files using `git ls`""" - self.pipeline_obj._list_files() + self.pipeline_obj.list_files() assert Path(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files @with_temporary_folder @@ -119,7 +119,7 @@ def test_list_files_no_git(self, tmpdir): tmp_fn = Path(tmpdir, "testfile") tmp_fn.touch() pipeline_obj = nf_core.utils.Pipeline(tmpdir) - pipeline_obj._list_files() + pipeline_obj.list_files() assert tmp_fn in pipeline_obj.files @mock.patch("os.path.exists") From 2ddc860183729642bd69169b3d948fa3ec273d46 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 10:01:29 +0200 Subject: [PATCH 147/574] create git repo with testpipeline --- tests/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/utils.py b/tests/utils.py index 38a10fa810..ef8f334669 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -105,7 +105,7 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: pipeline_dir = tmp_dir / pipeline_name nf_core.pipelines.create.create.PipelineCreate( - pipeline_name, "it is mine", "me", no_git=True, outdir=str(pipeline_dir) + pipeline_name, "it is mine", "me", no_git=False, outdir=str(pipeline_dir) ).init_pipeline() # return values to instance variables for later use in test methods From c313fed6a08c0e157a93a19a14d4d77946ad6d50 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 10:25:45 +0200 Subject: [PATCH 148/574] update textual snapshots to new location --- .editorconfig | 2 +- .../__snapshots__/test_create_app.ambr | 0 tests/pipelines/test_create_app.py | 26 ++++++++++--------- 3 files changed, 15 insertions(+), 13 deletions(-) rename tests/{ => pipelines}/__snapshots__/test_create_app.ambr (100%) diff --git a/.editorconfig b/.editorconfig index 5aa8697d30..f266805d6e 100644 --- a/.editorconfig +++ b/.editorconfig @@ -21,7 +21,7 @@ indent_style = unset [**/Makefile] indent_style = unset -[tests/__snapshots__/*] +[tests/pipelines/__snapshots__/*] charset = unset end_of_line = unset insert_final_newline = unset diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr similarity index 100% rename from tests/__snapshots__/test_create_app.ambr rename to tests/pipelines/__snapshots__/test_create_app.ambr diff --git a/tests/pipelines/test_create_app.py b/tests/pipelines/test_create_app.py index 8c89b92cba..9a02f04f00 100644 --- a/tests/pipelines/test_create_app.py +++ b/tests/pipelines/test_create_app.py @@ -4,6 +4,8 @@ from nf_core.pipelines.create import PipelineCreateApp +INIT_FILE = "../../nf_core/pipelines/create/__init__.py" + async def test_app_bindings(): """Test that the app bindings work.""" @@ -23,7 +25,7 @@ async def test_app_bindings(): def test_welcome(snap_compare): """Test snapshot for the first screen in the app. The welcome screen.""" - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50)) + assert snap_compare(INIT_FILE, terminal_size=(100, 50)) def test_choose_type(snap_compare): @@ -36,7 +38,7 @@ def test_choose_type(snap_compare): async def run_before(pilot) -> None: await pilot.click("#start") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_basic_details_nfcore(snap_compare): @@ -51,7 +53,7 @@ async def run_before(pilot) -> None: await pilot.click("#start") await pilot.click("#type_nfcore") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_basic_details_custom(snap_compare): @@ -66,7 +68,7 @@ async def run_before(pilot) -> None: await pilot.click("#start") await pilot.click("#type_custom") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_type_nfcore(snap_compare): @@ -89,7 +91,7 @@ async def run_before(pilot) -> None: await pilot.press("M", "e") await pilot.click("#next") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_type_nfcore_validation(snap_compare): @@ -108,7 +110,7 @@ async def run_before(pilot) -> None: await pilot.click("#next") await pilot.pause() - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_type_custom(snap_compare): @@ -132,7 +134,7 @@ async def run_before(pilot) -> None: await pilot.press("M", "e") await pilot.click("#next") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_final_details(snap_compare): @@ -157,7 +159,7 @@ async def run_before(pilot) -> None: await pilot.click("#next") await pilot.click("#continue") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_customisation_help(snap_compare): @@ -184,7 +186,7 @@ async def run_before(pilot) -> None: await pilot.press("tab") await pilot.press("enter") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_github_question(tmpdir, snap_compare): @@ -216,7 +218,7 @@ async def run_before(pilot) -> None: await pilot.app.workers.wait_for_complete() await pilot.click("#close_screen") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) @mock.patch("nf_core.pipelines.create.githubrepo.GithubRepo._get_github_credentials") @@ -255,7 +257,7 @@ async def run_before(pilot) -> None: await pilot.click("#close_screen") await pilot.click("#github_repo") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) def test_github_exit_message(tmpdir, snap_compare): @@ -291,4 +293,4 @@ async def run_before(pilot) -> None: await pilot.click("#github_repo") await pilot.click("#exit") - assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before) + assert snap_compare(INIT_FILE, terminal_size=(100, 50), run_before=run_before) From d6560656873b8bc448cde44975c78fb0abc39e02 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 11:19:49 +0200 Subject: [PATCH 149/574] fix tests --- nf_core/pipelines/launch.py | 5 +++-- nf_core/utils.py | 2 +- tests/pipelines/test_launch.py | 5 +---- tests/test_utils.py | 8 ++++---- tests/utils.py | 2 +- 5 files changed, 10 insertions(+), 12 deletions(-) diff --git a/nf_core/pipelines/launch.py b/nf_core/pipelines/launch.py index 3a5f97e78f..e03982a25a 100644 --- a/nf_core/pipelines/launch.py +++ b/nf_core/pipelines/launch.py @@ -7,6 +7,7 @@ import re import subprocess import webbrowser +from pathlib import Path import questionary from rich.console import Console @@ -46,7 +47,7 @@ def __init__( self.schema_obj = None self.use_params_file = False if command_only else True self.params_in = params_in - self.params_out = params_out if params_out else os.path.join(os.getcwd(), "nf-params.json") + self.params_out = params_out if params_out else Path.cwd() / "nf-params.json" self.save_all = save_all self.show_hidden = show_hidden self.web_schema_launch_url = url if url else "https://nf-co.re/launch" @@ -697,7 +698,7 @@ def build_command(self): # Write the user selection to a file and run nextflow with that if self.use_params_file: dump_json_with_prettier(self.params_out, self.schema_obj.input_params) - self.nextflow_cmd += f' -params-file "{os.path.relpath(self.params_out)}"' + self.nextflow_cmd += f' -params-file "{Path(self.params_out)}"' # Call nextflow with a list of command line flags else: diff --git a/nf_core/utils.py b/nf_core/utils.py index b5719a2b15..0cd812cb04 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -197,7 +197,7 @@ def list_files(self) -> List[Path]: for file_path in self.wf_path.rglob("*"): if file_path.is_file(): # Append the file path to the list - files.append(file_path.relative_to(self.wf_path)) + files.append(file_path) if len(files) == 0: log.debug(f"No files found in pipeline: {self.wf_path}") diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index 03bc0e98be..da7618d486 100644 --- a/tests/pipelines/test_launch.py +++ b/tests/pipelines/test_launch.py @@ -303,10 +303,7 @@ def test_build_command_params(self): self.launcher.schema_obj.input_params.update({"input": "custom_input"}) self.launcher.build_command() # Check command - assert ( - self.launcher.nextflow_cmd - == f'nextflow run {self.pipeline_dir} -params-file "{Path(self.nf_params_fn).relative_to(Path.cwd())}"' - ) + assert self.launcher.nextflow_cmd == f'nextflow run {self.pipeline_dir} -params-file "{self.nf_params_fn}"' # Check saved parameters file with open(self.nf_params_fn) as fh: try: diff --git a/tests/test_utils.py b/tests/test_utils.py index f61f3584e2..860cba5ba6 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -109,8 +109,8 @@ def testload_pipeline_config(self): def test_list_files_git(self): """Test listing pipeline files using `git ls`""" - self.pipeline_obj.list_files() - assert Path(self.test_pipeline_dir, "main.nf") in self.pipeline_obj.files + files = self.pipeline_obj.list_files() + assert Path(self.test_pipeline_dir, "main.nf") in files @with_temporary_folder def test_list_files_no_git(self, tmpdir): @@ -119,8 +119,8 @@ def test_list_files_no_git(self, tmpdir): tmp_fn = Path(tmpdir, "testfile") tmp_fn.touch() pipeline_obj = nf_core.utils.Pipeline(tmpdir) - pipeline_obj.list_files() - assert tmp_fn in pipeline_obj.files + files = pipeline_obj.list_files() + assert tmp_fn in files @mock.patch("os.path.exists") @mock.patch("os.makedirs") diff --git a/tests/utils.py b/tests/utils.py index ef8f334669..90c4ae0418 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -105,7 +105,7 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: pipeline_dir = tmp_dir / pipeline_name nf_core.pipelines.create.create.PipelineCreate( - pipeline_name, "it is mine", "me", no_git=False, outdir=str(pipeline_dir) + pipeline_name, "it is mine", "me", no_git=False, outdir=pipeline_dir ).init_pipeline() # return values to instance variables for later use in test methods From 21cdbbdd2871fe74d337ee755e83680c2ad820f6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 12:07:12 +0200 Subject: [PATCH 150/574] remove asyncio mode (and see what happens) --- pyproject.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4499324445..775f04c9a1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,8 +6,6 @@ requires = ["setuptools>=40.6.0", "wheel"] markers = ["datafiles: load datafiles"] testpaths = ["tests"] python_files = ["test_*.py"] -# automatically run coroutine tests with asyncio -asyncio_mode = ["auto"] norecursedirs = [ ".*", "build", From e0a82d51bf231dfc04629bf32105cacc10c8556c Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 12:08:14 +0200 Subject: [PATCH 151/574] fix refgenie tests --- nf_core/pipelines/create/create.py | 9 ++++++--- nf_core/pipelines/create_logo.py | 1 - nf_core/pipelines/lint/files_exist.py | 2 +- nf_core/pipelines/refgenie.py | 2 +- requirements.txt | 4 ++-- tests/pipelines/lint/files_exist.py | 2 +- tests/pipelines/test_refgenie.py | 20 ++++++++++---------- 7 files changed, 21 insertions(+), 19 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 8cfa09491f..c5af956690 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -355,7 +355,6 @@ def render_template(self): # Remove all unused parameters in the nextflow schema if not self.jinja_params["igenomes"] or not self.jinja_params["nf_core_configs"]: self.update_nextflow_schema() - if self.config.is_nfcore: # Make a logo and save it, if it is a nf-core pipeline self.make_pipeline_logo() @@ -513,11 +512,15 @@ def fix_linting(self): def make_pipeline_logo(self): """Fetch a logo for the new pipeline from the nf-core website""" email_logo_path = Path(self.outdir) / "assets" - create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=self.force) + create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=bool(self.force)) for theme in ["dark", "light"]: readme_logo_path = Path(self.outdir) / "docs" / "images" create_logo( - text=self.jinja_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force + text=self.jinja_params["short_name"], + dir=readme_logo_path, + width=600, + theme=theme, + force=bool(self.force), ) def git_init_pipeline(self): diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py index 1e96b7032c..780bafd7f5 100644 --- a/nf_core/pipelines/create_logo.py +++ b/nf_core/pipelines/create_logo.py @@ -20,7 +20,6 @@ def create_logo( force: bool = False, ) -> Path: """Create a logo for a pipeline.""" - if not text: raise UserWarning("Please provide the name of the text to put on the logo.") dir = Path(dir) diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py index c6f622b3e0..edad62aab8 100644 --- a/nf_core/pipelines/lint/files_exist.py +++ b/nf_core/pipelines/lint/files_exist.py @@ -5,7 +5,7 @@ log = logging.getLogger(__name__) -def files_exist(self) -> Dict[str, Union[List[str], bool]]: +def files_exist(self) -> Dict[str, List[str]]: """Checks a given pipeline directory for required files. Iterates through the pipeline's directory content and checks that specified diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py index de9201bcd6..19ef4b5121 100644 --- a/nf_core/pipelines/refgenie.py +++ b/nf_core/pipelines/refgenie.py @@ -183,7 +183,7 @@ def update_config(rgc): # Save the updated genome config try: - with open(refgenie_genomes_config_file, "w+") as fh: + with open(str(refgenie_genomes_config_file), "w+") as fh: fh.write(refgenie_genomes) log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}") except FileNotFoundError: diff --git a/requirements.txt b/requirements.txt index 524b739e89..fb658be2fb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,10 +9,10 @@ packaging pillow pdiff pre-commit -prompt_toolkit>=3.0.3 +prompt_toolkit<=3.0.36 pydantic>=2.2.1 pyyaml -questionary>=1.8.0 +questionary>=2.0.1 refgenie requests requests_cache diff --git a/tests/pipelines/lint/files_exist.py b/tests/pipelines/lint/files_exist.py index 87508e78a8..4ae167b1d0 100644 --- a/tests/pipelines/lint/files_exist.py +++ b/tests/pipelines/lint/files_exist.py @@ -14,7 +14,7 @@ def test_files_exist_missing_config(self): lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline" results = lint_obj.files_exist() - assert results["failed"] == ["File not found: `CHANGELOG.md`"] + assert "File not found: `CHANGELOG.md`" in results["failed"] def test_files_exist_missing_main(self): diff --git a/tests/pipelines/test_refgenie.py b/tests/pipelines/test_refgenie.py index 23cc0dd14a..734a2368bd 100644 --- a/tests/pipelines/test_refgenie.py +++ b/tests/pipelines/test_refgenie.py @@ -5,6 +5,7 @@ import subprocess import tempfile import unittest +from pathlib import Path class TestRefgenie(unittest.TestCase): @@ -14,36 +15,35 @@ def setUp(self): """ Prepare a refgenie config file """ - self.tmp_dir = tempfile.mkdtemp() - self.NXF_HOME = os.path.join(self.tmp_dir, ".nextflow") - self.NXF_REFGENIE_PATH = os.path.join(self.NXF_HOME, "nf-core", "refgenie_genomes.config") - self.REFGENIE = os.path.join(self.tmp_dir, "genomes_config.yaml") - self.translation_file = os.path.join(self.tmp_dir, "alias_translations.yaml") + self.tmp_dir = Path(tempfile.TemporaryDirectory().name) + self.NXF_HOME = self.tmp_dir / ".nextflow" + self.NXF_REFGENIE_PATH = self.NXF_HOME / "nf-core" / "refgenie_genomes.config" + self.REFGENIE = self.tmp_dir / "genomes_config.yaml" + self.translation_file = self.tmp_dir / "alias_translations.yaml" # Set NXF_HOME environment variable # avoids adding includeConfig statement to config file outside the current tmpdir try: self.NXF_HOME_ORIGINAL = os.environ["NXF_HOME"] except Exception: self.NXF_HOME_ORIGINAL = None - os.environ["NXF_HOME"] = self.NXF_HOME + os.environ["NXF_HOME"] = str(self.NXF_HOME) # create NXF_HOME and nf-core directories - os.makedirs(os.path.join(self.NXF_HOME, "nf-core"), exist_ok=True) + nf_core_dir = self.NXF_HOME / "nf-core" + nf_core_dir.mkdir(parents=True, exist_ok=True) # Initialize a refgenie config os.system(f"refgenie init -c {self.REFGENIE}") # Add NXF_REFGENIE_PATH to refgenie config with open(self.REFGENIE, "a") as fh: - fh.write(f"nextflow_config: {os.path.join(self.NXF_REFGENIE_PATH)}\n") + fh.write(f"nextflow_config: {self.NXF_REFGENIE_PATH}\n") # Add an alias translation to YAML file with open(self.translation_file, "a") as fh: fh.write("ensembl_gtf: gtf\n") def tearDown(self) -> None: - # Remove the tempdir again - os.system(f"rm -rf {self.tmp_dir}") # Reset NXF_HOME environment variable if self.NXF_HOME_ORIGINAL is None: del os.environ["NXF_HOME"] From 1fde6ca6e70866d0a8b7a7a79ade75afefcf36bb Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 13:12:43 +0200 Subject: [PATCH 152/574] add cleanup step to some download tests --- nf_core/pipelines/download.py | 2 +- tests/pipelines/test_download.py | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index f16430b0a8..797909636c 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -231,7 +231,7 @@ def download_workflow(self): summary_log.append(f"Enabled for Seqera Platform: '{self.platform}'") # Check that the outdir doesn't already exist - if os.path.exists(self.outdir): + if self.outdir is not None and os.path.exists(self.outdir): if not self.force: raise DownloadError( f"Output directory '{self.outdir}' already exists (use [red]--force[/] to overwrite)" diff --git a/tests/pipelines/test_download.py b/tests/pipelines/test_download.py index d571b82cee..a898d37b70 100644 --- a/tests/pipelines/test_download.py +++ b/tests/pipelines/test_download.py @@ -13,6 +13,7 @@ import pytest import nf_core.pipelines.create.create +import nf_core.pipelines.list import nf_core.utils from nf_core.pipelines.download import ContainerError, DownloadWorkflow, WorkflowRepo from nf_core.synced_repo import SyncedRepo @@ -643,6 +644,11 @@ def test_download_workflow_for_platform(self, tmp_dir, _): in download_obj.containers ) # indirect definition via $container variable. + # clean-up + # remove "nf-core-rnaseq*" directories + for path in Path().cwd().glob("nf-core-rnaseq*"): + shutil.rmtree(path) + # # Brief test adding a single custom tag to Seqera Platform download # @@ -659,6 +665,11 @@ def test_download_workflow_for_platform_with_one_custom_tag(self, _, tmp_dir): ) assert isinstance(download_obj.additional_tags, list) and len(download_obj.additional_tags) == 1 + # clean-up + # remove "nf-core-rnaseq*" directories + for path in Path().cwd().glob("nf-core-rnaseq*"): + shutil.rmtree(path) + # # Test adding custom tags to Seqera Platform download (full test) # @@ -727,3 +738,8 @@ def test_download_workflow_for_platform_with_custom_tags(self, _, tmp_dir): "[red]Could not apply invalid `--tag` specification[/]: 'What is this?'", } ) + + # clean-up + # remove "nf-core-rnaseq*" directories + for path in Path().cwd().glob("nf-core-rnaseq*"): + shutil.rmtree(path) From a0f788dc1d7a8059e8077ca3413397f9f38cc3be Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 13:40:39 +0200 Subject: [PATCH 153/574] start converting linting tests to new subclass structure --- nf_core/pipelines/create_logo.py | 13 ++-- tests/pipelines/lint/actions_awsfulltest.py | 60 ------------------ .../lint/test_actions_awsfulltest.py | 61 +++++++++++++++++++ tests/pipelines/test_lint.py | 20 +++--- 4 files changed, 77 insertions(+), 77 deletions(-) delete mode 100644 tests/pipelines/lint/actions_awsfulltest.py create mode 100644 tests/pipelines/lint/test_actions_awsfulltest.py diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py index 780bafd7f5..0643d2e295 100644 --- a/nf_core/pipelines/create_logo.py +++ b/nf_core/pipelines/create_logo.py @@ -90,11 +90,14 @@ def create_logo( color = theme == "dark" and (250, 250, 250) or (5, 5, 5) draw.text((110, 465), text, color, font=font) - # Crop to max width - img = img.crop((0, 0, max_width, height)) - - # Resize - img = img.resize((width, int((width / max_width) * height))) + if img is not None: + # Crop to max width + img = img.crop((0, 0, max_width, height)) + + # Resize + img = img.resize((width, int((width / max_width) * height))) + else: + log.error("Failed to create logo, no image object created.") # Save to cache Path(cache_path.parent).mkdir(parents=True, exist_ok=True) diff --git a/tests/pipelines/lint/actions_awsfulltest.py b/tests/pipelines/lint/actions_awsfulltest.py deleted file mode 100644 index d1479bb1e1..0000000000 --- a/tests/pipelines/lint/actions_awsfulltest.py +++ /dev/null @@ -1,60 +0,0 @@ -from pathlib import Path - -import yaml - -import nf_core.pipelines.lint - - -def test_actions_awsfulltest_warn(self): - """Lint test: actions_awsfulltest - PASS""" - self.lint_obj._load() - results = self.lint_obj.actions_awsfulltest() - assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"] - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - - -def test_actions_awsfulltest_pass(self): - """Lint test: actions_awsfulltest - WARN""" - - # Edit .github/workflows/awsfulltest.yml to use -profile test_full - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: - awsfulltest_yml = fh.read() - awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ") - with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: - fh.write(awsfulltest_yml) - - # Make lint object - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_awsfulltest() - assert results["passed"] == [ - "`.github/workflows/awsfulltest.yml` is triggered correctly", - "`.github/workflows/awsfulltest.yml` does not use `-profile test`", - ] - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - - -def test_actions_awsfulltest_fail(self): - """Lint test: actions_awsfulltest - FAIL""" - - # Edit .github/workflows/awsfulltest.yml to use -profile test_full - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: - awsfulltest_yml = yaml.safe_load(fh) - del awsfulltest_yml[True]["pull_request_review"] - with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: - yaml.dump(awsfulltest_yml, fh) - - # Make lint object - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_awsfulltest() - assert results["failed"] == ["`.github/workflows/awsfulltest.yml` is not triggered correctly"] - assert "`.github/workflows/awsfulltest.yml` does not use `-profile test`" in results["passed"] - assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/lint/test_actions_awsfulltest.py b/tests/pipelines/lint/test_actions_awsfulltest.py new file mode 100644 index 0000000000..5c070fd5cf --- /dev/null +++ b/tests/pipelines/lint/test_actions_awsfulltest.py @@ -0,0 +1,61 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintActionsAwsfulltest(TestLint): + def test_actions_awsfulltest_warn(self): + """Lint test: actions_awsfulltest - PASS""" + self.lint_obj._load() + results = self.lint_obj.actions_awsfulltest() + assert "`.github/workflows/awsfulltest.yml` is triggered correctly" in results["passed"] + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + + def test_actions_awsfulltest_pass(self): + """Lint test: actions_awsfulltest - WARN""" + + # Edit .github/workflows/awsfulltest.yml to use -profile test_full + new_pipeline = self._make_pipeline_copy() + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: + awsfulltest_yml = fh.read() + awsfulltest_yml = awsfulltest_yml.replace("-profile test ", "-profile test_full ") + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: + fh.write(awsfulltest_yml) + + # Make lint object + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + + results = lint_obj.actions_awsfulltest() + assert results["passed"] == [ + "`.github/workflows/awsfulltest.yml` is triggered correctly", + "`.github/workflows/awsfulltest.yml` does not use `-profile test`", + ] + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + + def test_actions_awsfulltest_fail(self): + """Lint test: actions_awsfulltest - FAIL""" + + # Edit .github/workflows/awsfulltest.yml to use -profile test_full + new_pipeline = self._make_pipeline_copy() + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml")) as fh: + awsfulltest_yml = yaml.safe_load(fh) + del awsfulltest_yml[True]["pull_request_review"] + with open(Path(new_pipeline, ".github", "workflows", "awsfulltest.yml"), "w") as fh: + yaml.dump(awsfulltest_yml, fh) + + # Make lint object + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + + results = lint_obj.actions_awsfulltest() + assert results["failed"] == ["`.github/workflows/awsfulltest.yml` is not triggered correctly"] + assert "`.github/workflows/awsfulltest.yml` does not use `-profile test`" in results["passed"] + assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index 800ffa16b3..54279cd064 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -1,8 +1,6 @@ """Some tests covering the linting code.""" -import fnmatch import json -import os from pathlib import Path import yaml @@ -133,16 +131,18 @@ def test_sphinx_md_files(self): # Get list of existing .md files existing_docs = [] - for fn in os.listdir(docs_basedir): - if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"): - existing_docs.append(Path(docs_basedir, fn)) + existing_docs = [ + str(Path(docs_basedir, fn)) + for fn in Path(docs_basedir).iterdir() + if fn.match("*.md") and not fn.match("index.md") + ] # Check .md files against each test name lint_obj = nf_core.pipelines.lint.PipelineLint("", True) for test_name in lint_obj.lint_tests: fn = Path(docs_basedir, f"{test_name}.md") - assert os.path.exists(fn), f"Could not find lint docs .md file: {fn}" - existing_docs.remove(fn) + assert fn.exists(), f"Could not find lint docs .md file: {fn}" + existing_docs.remove(str(fn)) # Check that we have no remaining .md files that we didn't expect assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}" @@ -150,11 +150,7 @@ def test_sphinx_md_files(self): ####################### # SPECIFIC LINT TESTS # ####################### - from .lint.actions_awsfulltest import ( # type: ignore[misc] - test_actions_awsfulltest_fail, - test_actions_awsfulltest_pass, - test_actions_awsfulltest_warn, - ) + from .lint.actions_awstest import ( # type: ignore[misc] test_actions_awstest_fail, test_actions_awstest_pass, From 13be56f73d50e753d941301ed9a84424d3fa3022 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 13:41:25 +0200 Subject: [PATCH 154/574] update prettier version --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c1dc7978f6..bcf7ff65ce 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.2.5 + - prettier@3.3.3 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python rev: "2.7.3" From da155abe4945be13eaa5beb3654dd342dc9d5b19 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 13:54:53 +0200 Subject: [PATCH 155/574] import linting tests correctly to avoid "module is not callable" warnings --- nf_core/pipelines/lint/__init__.py | 73 +++++++++++++++++++----------- 1 file changed, 47 insertions(+), 26 deletions(-) diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index d731cb018d..93f6523709 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -30,6 +30,29 @@ from nf_core.utils import plural_s as _s from nf_core.utils import strip_ansi_codes +from .actions_awsfulltest import actions_awsfulltest +from .actions_awstest import actions_awstest +from .actions_ci import actions_ci +from .actions_schema_validation import actions_schema_validation +from .configs import base_config, modules_config +from .files_exist import files_exist +from .files_unchanged import files_unchanged +from .merge_markers import merge_markers +from .modules_json import modules_json +from .modules_structure import modules_structure +from .multiqc_config import multiqc_config +from .nextflow_config import nextflow_config +from .nfcore_yml import nfcore_yml +from .pipeline_name_conventions import pipeline_name_conventions +from .pipeline_todos import pipeline_todos +from .readme import readme +from .schema_description import schema_description +from .schema_lint import schema_lint +from .schema_params import schema_params +from .system_exit import system_exit +from .template_strings import template_strings +from .version_consistency import version_consistency + log = logging.getLogger(__name__) @@ -52,32 +75,30 @@ class PipelineLint(nf_core.utils.Pipeline): warned (list): A list of tuples of the form: ``(, )`` """ - from .actions_awsfulltest import actions_awsfulltest # type: ignore[misc] - from .actions_awstest import actions_awstest # type: ignore[misc] - from .actions_ci import actions_ci # type: ignore[misc] - from .actions_schema_validation import ( # type: ignore[misc] - actions_schema_validation, - ) - from .configs import base_config, modules_config # type: ignore[misc] - from .files_exist import files_exist # type: ignore[misc] - from .files_unchanged import files_unchanged # type: ignore[misc] - from .merge_markers import merge_markers # type: ignore[misc] - from .modules_json import modules_json # type: ignore[misc] - from .modules_structure import modules_structure # type: ignore[misc] - from .multiqc_config import multiqc_config # type: ignore[misc] - from .nextflow_config import nextflow_config # type: ignore[misc] - from .nfcore_yml import nfcore_yml # type: ignore[misc] - from .pipeline_name_conventions import ( # type: ignore[misc] - pipeline_name_conventions, - ) - from .pipeline_todos import pipeline_todos # type: ignore[misc] - from .readme import readme # type: ignore[misc] - from .schema_description import schema_description # type: ignore[misc] - from .schema_lint import schema_lint # type: ignore[misc] - from .schema_params import schema_params # type: ignore[misc] - from .system_exit import system_exit # type: ignore[misc] - from .template_strings import template_strings # type: ignore[misc] - from .version_consistency import version_consistency # type: ignore[misc] + # Import all linting tests as methods for this class + actions_awsfulltest = actions_awsfulltest + actions_awstest = actions_awstest + actions_ci = actions_ci + actions_schema_validation = actions_schema_validation + base_config = base_config + modules_config = modules_config + files_exist = files_exist + files_unchanged = files_unchanged + merge_markers = merge_markers + modules_json = modules_json + modules_structure = modules_structure + multiqc_config = multiqc_config + nextflow_config = nextflow_config + nfcore_yml = nfcore_yml + pipeline_name_conventions = pipeline_name_conventions + pipeline_todos = pipeline_todos + readme = readme + schema_description = schema_description + schema_lint = schema_lint + schema_params = schema_params + system_exit = system_exit + template_strings = template_strings + version_consistency = version_consistency def __init__( self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False From 4c77621e8816a0ec5da9d9096efc89e77e5951f6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 14:31:33 +0200 Subject: [PATCH 156/574] convert rest of the lint test to new subclass structure --- tests/pipelines/lint/actions_awstest.py | 37 -- tests/pipelines/lint/actions_ci.py | 49 --- .../lint/actions_schema_validation.py | 66 ---- tests/pipelines/lint/configs.py | 89 ----- tests/pipelines/lint/files_exist.py | 97 ----- tests/pipelines/lint/files_unchanged.py | 26 -- tests/pipelines/lint/merge_markers.py | 22 -- tests/pipelines/lint/modules_json.py | 6 - tests/pipelines/lint/multiqc_config.py | 129 ------- tests/pipelines/lint/nextflow_config.py | 211 ----------- tests/pipelines/lint/nfcore_yml.py | 53 --- tests/pipelines/lint/template_strings.py | 53 --- tests/pipelines/lint/test_actions_awstest.py | 39 ++ tests/pipelines/lint/test_actions_ci.py | 50 +++ .../lint/test_actions_schema_validation.py | 62 +++ tests/pipelines/lint/test_configs.py | 91 +++++ tests/pipelines/lint/test_files_exist.py | 91 +++++ tests/pipelines/lint/test_files_unchanged.py | 28 ++ tests/pipelines/lint/test_merge_markers.py | 25 ++ tests/pipelines/lint/test_modules_json.py | 10 + tests/pipelines/lint/test_multiqc_config.py | 127 +++++++ tests/pipelines/lint/test_nextflow_config.py | 200 ++++++++++ tests/pipelines/lint/test_nfcore_yml.py | 57 +++ tests/pipelines/lint/test_template_strings.py | 55 +++ .../lint/test_version_consistency.py | 19 + tests/pipelines/lint/version_consistency.py | 14 - tests/pipelines/test_lint.py | 354 ++++++++---------- 27 files changed, 1012 insertions(+), 1048 deletions(-) delete mode 100644 tests/pipelines/lint/actions_awstest.py delete mode 100644 tests/pipelines/lint/actions_ci.py delete mode 100644 tests/pipelines/lint/actions_schema_validation.py delete mode 100644 tests/pipelines/lint/configs.py delete mode 100644 tests/pipelines/lint/files_exist.py delete mode 100644 tests/pipelines/lint/files_unchanged.py delete mode 100644 tests/pipelines/lint/merge_markers.py delete mode 100644 tests/pipelines/lint/modules_json.py delete mode 100644 tests/pipelines/lint/multiqc_config.py delete mode 100644 tests/pipelines/lint/nextflow_config.py delete mode 100644 tests/pipelines/lint/nfcore_yml.py delete mode 100644 tests/pipelines/lint/template_strings.py create mode 100644 tests/pipelines/lint/test_actions_awstest.py create mode 100644 tests/pipelines/lint/test_actions_ci.py create mode 100644 tests/pipelines/lint/test_actions_schema_validation.py create mode 100644 tests/pipelines/lint/test_configs.py create mode 100644 tests/pipelines/lint/test_files_exist.py create mode 100644 tests/pipelines/lint/test_files_unchanged.py create mode 100644 tests/pipelines/lint/test_merge_markers.py create mode 100644 tests/pipelines/lint/test_modules_json.py create mode 100644 tests/pipelines/lint/test_multiqc_config.py create mode 100644 tests/pipelines/lint/test_nextflow_config.py create mode 100644 tests/pipelines/lint/test_nfcore_yml.py create mode 100644 tests/pipelines/lint/test_template_strings.py create mode 100644 tests/pipelines/lint/test_version_consistency.py delete mode 100644 tests/pipelines/lint/version_consistency.py diff --git a/tests/pipelines/lint/actions_awstest.py b/tests/pipelines/lint/actions_awstest.py deleted file mode 100644 index 259bf866bf..0000000000 --- a/tests/pipelines/lint/actions_awstest.py +++ /dev/null @@ -1,37 +0,0 @@ -import os - -import yaml - -import nf_core.pipelines.lint - - -def test_actions_awstest_pass(self): - """Lint test: actions_awstest - PASS""" - self.lint_obj._load() - results = self.lint_obj.actions_awstest() - assert results["passed"] == ["'.github/workflows/awstest.yml' is triggered correctly"] - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - - -def test_actions_awstest_fail(self): - """Lint test: actions_awsfulltest - FAIL""" - - # Edit .github/workflows/awsfulltest.yml to use -profile test_full - new_pipeline = self._make_pipeline_copy() - with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml")) as fh: - awstest_yml = yaml.safe_load(fh) - awstest_yml[True]["push"] = ["master"] - with open(os.path.join(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh: - yaml.dump(awstest_yml, fh) - - # Make lint object - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_awstest() - assert results["failed"] == ["'.github/workflows/awstest.yml' is not triggered correctly"] - assert len(results.get("warned", [])) == 0 - assert len(results.get("passed", [])) == 0 - assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/lint/actions_ci.py b/tests/pipelines/lint/actions_ci.py deleted file mode 100644 index eb438b881d..0000000000 --- a/tests/pipelines/lint/actions_ci.py +++ /dev/null @@ -1,49 +0,0 @@ -import os - -import yaml - -import nf_core.pipelines.lint - - -def test_actions_ci_pass(self): - """Lint test: actions_ci - PASS""" - self.lint_obj._load() - results = self.lint_obj.actions_ci() - assert results["passed"] == [ - "'.github/workflows/ci.yml' is triggered on expected events", - "'.github/workflows/ci.yml' checks minimum NF version", - ] - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - - -def test_actions_ci_fail_wrong_nf(self): - """Lint test: actions_ci - FAIL - wrong minimum version of Nextflow tested""" - self.lint_obj._load() - self.lint_obj.minNextflowVersion = "1.2.3" - results = self.lint_obj.actions_ci() - assert results["failed"] == ["Minimum pipeline NF version '1.2.3' is not tested in '.github/workflows/ci.yml'"] - - -def test_actions_ci_fail_wrong_trigger(self): - """Lint test: actions_actions_ci - FAIL - workflow triggered incorrectly, NF ver not checked at all""" - - # Edit .github/workflows/actions_ci.yml to mess stuff up! - new_pipeline = self._make_pipeline_copy() - with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml")) as fh: - ci_yml = yaml.safe_load(fh) - ci_yml[True]["push"] = ["dev", "patch"] - ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]} - with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml"), "w") as fh: - yaml.dump(ci_yml, fh) - - # Make lint object - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_ci() - assert results["failed"] == [ - "'.github/workflows/ci.yml' is not triggered on expected events", - "'.github/workflows/ci.yml' does not check minimum NF version", - ] diff --git a/tests/pipelines/lint/actions_schema_validation.py b/tests/pipelines/lint/actions_schema_validation.py deleted file mode 100644 index 4b00e7bf40..0000000000 --- a/tests/pipelines/lint/actions_schema_validation.py +++ /dev/null @@ -1,66 +0,0 @@ -from pathlib import Path - -import yaml - -import nf_core.pipelines.lint - - -def test_actions_schema_validation_missing_jobs(self): - """Missing 'jobs' field should result in failure""" - new_pipeline = self._make_pipeline_copy() - - awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml" - with open(awstest_yml_path) as fh: - awstest_yml = yaml.safe_load(fh) - awstest_yml.pop("jobs") - with open(awstest_yml_path, "w") as fh: - yaml.dump(awstest_yml, fh) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_schema_validation() - - assert "Workflow validation failed for awstest.yml: 'jobs' is a required property" in results["failed"][0] - - -def test_actions_schema_validation_missing_on(self): - """Missing 'on' field should result in failure""" - new_pipeline = self._make_pipeline_copy() - - awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml" - with open(awstest_yml_path) as fh: - awstest_yml = yaml.safe_load(fh) - awstest_yml.pop(True) - with open(awstest_yml_path, "w") as fh: - yaml.dump(awstest_yml, fh) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_schema_validation() - - assert results["failed"][0] == "Missing 'on' keyword in awstest.yml" - assert "Workflow validation failed for awstest.yml: 'on' is a required property" in results["failed"][1] - - -def test_actions_schema_validation_fails_for_additional_property(self): - """Missing 'jobs' field should result in failure""" - new_pipeline = self._make_pipeline_copy() - - awstest_yml_path = Path(new_pipeline) / ".github" / "workflows" / "awstest.yml" - with open(awstest_yml_path) as fh: - awstest_yml = yaml.safe_load(fh) - awstest_yml["not_jobs"] = awstest_yml["jobs"] - with open(awstest_yml_path, "w") as fh: - yaml.dump(awstest_yml, fh) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.actions_schema_validation() - - assert ( - "Workflow validation failed for awstest.yml: Additional properties are not allowed ('not_jobs' was unexpected)" - in results["failed"][0] - ) diff --git a/tests/pipelines/lint/configs.py b/tests/pipelines/lint/configs.py deleted file mode 100644 index 3ca35cab8c..0000000000 --- a/tests/pipelines/lint/configs.py +++ /dev/null @@ -1,89 +0,0 @@ -from pathlib import Path - -import yaml - -import nf_core.pipelines.create -import nf_core.pipelines.lint - - -def test_withname_in_modules_config(self): - """Tests finding withName in modules.config passes linting.""" - - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.modules_config() - assert len(result["failed"]) == 0 - assert any( - ["`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]] - ) - - -def test_superfluous_withname_in_modules_config_fails(self): - """Tests finding withName in modules.config fails linting.""" - new_pipeline = self._make_pipeline_copy() - # Add withName to modules.config - modules_config = Path(new_pipeline) / "conf" / "modules.config" - with open(modules_config, "a") as f: - f.write("\nwithName: 'BPIPE' {\n cache = false \n}") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline, hide_progress=False) - lint_obj._load() - result = lint_obj.modules_config() - assert len(result["failed"]) == 1 - assert result["failed"][0].startswith("`conf/modules.config` contains `withName:BPIPE`") - - -def test_ignore_modules_config(self): - """Tests ignoring the modules.config passes linting.""" - new_pipeline = self._make_pipeline_copy() - # ignore modules.config in linting - with open(Path(new_pipeline) / ".nf-core.yml") as f: - content = yaml.safe_load(f) - old_content = content.copy() - content["lint"] = {"modules_config": False} - with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: - yaml.dump(content, f) - Path(new_pipeline, "conf", "modules.config").unlink() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.modules_config() - assert len(result["ignored"]) == 1 - assert result["ignored"][0].startswith("`conf/modules.config` not found, but it is ignored.") - # cleanup - with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: - yaml.dump(old_content, f) - - -def test_superfluous_withname_in_base_config_fails(self): - """Tests finding withName in base.config fails linting.""" - new_pipeline = self._make_pipeline_copy() - # Add withName to base.config - base_config = Path(new_pipeline) / "conf" / "base.config" - with open(base_config, "a") as f: - f.write("\nwithName:CUSTOM_DUMPSOFTWAREVERSIONS {\n cache = false \n}") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.base_config() - assert len(result["failed"]) == 1 - assert result["failed"][0].startswith("`conf/base.config` contains `withName:CUSTOM_DUMPSOFTWAREVERSIONS`") - - -def test_ignore_base_config(self): - """Tests ignoring the base.config passes linting.""" - new_pipeline = self._make_pipeline_copy() - # ignore base.config in linting - with open(Path(new_pipeline) / ".nf-core.yml") as f: - content = yaml.safe_load(f) - old_content = content.copy() - content["lint"] = {"base_config": False} - with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: - yaml.dump(content, f) - Path(new_pipeline, "conf", "base.config").unlink() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.base_config() - assert len(result["ignored"]) == 1 - assert result["ignored"][0].startswith("`conf/base.config` not found, but it is ignored.") - # cleanup - with open(Path(new_pipeline) / ".nf-core.yml", "w") as f: - yaml.dump(old_content, f) diff --git a/tests/pipelines/lint/files_exist.py b/tests/pipelines/lint/files_exist.py deleted file mode 100644 index 4ae167b1d0..0000000000 --- a/tests/pipelines/lint/files_exist.py +++ /dev/null @@ -1,97 +0,0 @@ -from pathlib import Path - -import nf_core.pipelines.lint - - -def test_files_exist_missing_config(self): - """Lint test: critical files missing FAIL""" - new_pipeline = self._make_pipeline_copy() - - Path(new_pipeline, "CHANGELOG.md").unlink() - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline" - - results = lint_obj.files_exist() - assert "File not found: `CHANGELOG.md`" in results["failed"] - - -def test_files_exist_missing_main(self): - """Check if missing main issues warning""" - new_pipeline = self._make_pipeline_copy() - - Path(new_pipeline, "main.nf").unlink() - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.files_exist() - assert "File not found: `main.nf`" in results["warned"] - - -def test_files_exist_deprecated_file(self): - """Check whether deprecated file issues warning""" - new_pipeline = self._make_pipeline_copy() - - nf = Path(new_pipeline, "parameters.settings.json") - nf.touch() - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.files_exist() - assert results["failed"] == ["File must be removed: `parameters.settings.json`"] - - -def test_files_exist_pass(self): - """Lint check should pass if all files are there""" - - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.files_exist() - assert results["failed"] == [] - - -def test_files_exist_pass_conditional(self): - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - lint_obj.nf_config["plugins"] = [] - lib_dir = Path(new_pipeline, "lib") - lib_dir.mkdir() - (lib_dir / "nfcore_external_java_deps.jar").touch() - results = lint_obj.files_exist() - assert results["failed"] == [] - assert results["ignored"] == [] - - -def test_files_exist_fail_conditional(self): - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - lib_dir = Path(new_pipeline, "lib") - lib_dir.mkdir() - (lib_dir / "nfcore_external_java_deps.jar").touch() - results = lint_obj.files_exist() - assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"] - assert results["ignored"] == [] - - -def test_files_exist_pass_conditional_nfschema(self): - new_pipeline = self._make_pipeline_copy() - # replace nf-validation with nf-schema in nextflow.config - with open(Path(new_pipeline, "nextflow.config")) as f: - config = f.read() - config = config.replace("nf-validation", "nf-schema") - with open(Path(new_pipeline, "nextflow.config"), "w") as f: - f.write(config) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - lint_obj.nf_config["manifest.schema"] = "nf-core" - results = lint_obj.files_exist() - assert results["failed"] == [] - assert results["ignored"] == [] diff --git a/tests/pipelines/lint/files_unchanged.py b/tests/pipelines/lint/files_unchanged.py deleted file mode 100644 index 07a7229191..0000000000 --- a/tests/pipelines/lint/files_unchanged.py +++ /dev/null @@ -1,26 +0,0 @@ -from pathlib import Path - -import nf_core.pipelines.lint - - -def test_files_unchanged_pass(self): - self.lint_obj._load() - results = self.lint_obj.files_unchanged() - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - assert not results.get("could_fix", True) - - -def test_files_unchanged_fail(self): - failing_file = Path(".github", "CONTRIBUTING.md") - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, failing_file), "a") as fh: - fh.write("THIS SHOULD NOT BE HERE") - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - results = lint_obj.files_unchanged() - assert len(results["failed"]) > 0 - assert str(failing_file) in results["failed"][0] - assert results["could_fix"] diff --git a/tests/pipelines/lint/merge_markers.py b/tests/pipelines/lint/merge_markers.py deleted file mode 100644 index 0e3699e190..0000000000 --- a/tests/pipelines/lint/merge_markers.py +++ /dev/null @@ -1,22 +0,0 @@ -import os - -import nf_core.pipelines.lint - - -def test_merge_markers_found(self): - """Missing 'jobs' field should result in failure""" - new_pipeline = self._make_pipeline_copy() - - with open(os.path.join(new_pipeline, "main.nf")) as fh: - main_nf_content = fh.read() - main_nf_content = ">>>>>>>\n" + main_nf_content - with open(os.path.join(new_pipeline, "main.nf"), "w") as fh: - fh.write(main_nf_content) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - - results = lint_obj.merge_markers() - assert len(results["failed"]) > 0 - assert len(results["passed"]) == 0 - assert "Merge marker '>>>>>>>' in " in results["failed"][0] diff --git a/tests/pipelines/lint/modules_json.py b/tests/pipelines/lint/modules_json.py deleted file mode 100644 index f025daa7f1..0000000000 --- a/tests/pipelines/lint/modules_json.py +++ /dev/null @@ -1,6 +0,0 @@ -def test_modules_json_pass(self): - self.lint_obj._load() - results = self.lint_obj.modules_json() - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("passed", [])) > 0 diff --git a/tests/pipelines/lint/multiqc_config.py b/tests/pipelines/lint/multiqc_config.py deleted file mode 100644 index 7f1fdbd67c..0000000000 --- a/tests/pipelines/lint/multiqc_config.py +++ /dev/null @@ -1,129 +0,0 @@ -from pathlib import Path - -import yaml - -import nf_core.pipelines.lint - - -def test_multiqc_config_exists(self): - """Test that linting fails if the multiqc_config.yml file is missing""" - # Delete the file - new_pipeline = self._make_pipeline_copy() - Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.multiqc_config() - assert result["failed"] == ["`assets/multiqc_config.yml` not found."] - - -def test_multiqc_config_ignore(self): - """Test that linting succeeds if the multiqc_config.yml file is missing but ignored""" - # Delete the file - new_pipeline = self._make_pipeline_copy() - Path(Path(new_pipeline, "assets", "multiqc_config.yml")).unlink() - with open(Path(new_pipeline, ".nf-core.yml")) as f: - content = yaml.safe_load(f) - old_content = content.copy() - content["lint"] = {"multiqc_config": False} - with open(Path(new_pipeline, ".nf-core.yml"), "w") as f: - yaml.dump(content, f) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.multiqc_config() - assert result["ignored"] == ["`assets/multiqc_config.yml` not found, but it is ignored."] - - # cleanup - with open(Path(new_pipeline, ".nf-core.yml"), "w") as f: - yaml.dump(old_content, f) - - -def test_multiqc_config_missing_report_section_order(self): - """Test that linting fails if the multiqc_config.yml file is missing the report_section_order""" - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh: - mqc_yml = yaml.safe_load(fh) - mqc_yml_tmp = mqc_yml.copy() - mqc_yml.pop("report_section_order") - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.multiqc_config() - # Reset the file - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml_tmp, fh) - assert result["failed"] == ["`assets/multiqc_config.yml` does not contain `report_section_order`"] - - -def test_multiqc_incorrect_export_plots(self): - """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots""" - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh: - mqc_yml = yaml.safe_load(fh) - mqc_yml_tmp = mqc_yml.copy() - mqc_yml["export_plots"] = False - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.multiqc_config() - # Reset the file - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml_tmp, fh) - assert result["failed"] == ["`assets/multiqc_config.yml` does not contain 'export_plots: true'."] - - -def test_multiqc_config_report_comment_fail(self): - """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment""" - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh: - mqc_yml = yaml.safe_load(fh) - mqc_yml_tmp = mqc_yml.copy() - mqc_yml["report_comment"] = "This is a test" - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.multiqc_config() - # Reset the file - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml_tmp, fh) - assert len(result["failed"]) == 1 - assert result["failed"][0].startswith("`assets/multiqc_config.yml` does not contain a matching 'report_comment'.") - - -def test_multiqc_config_report_comment_release_fail(self): - """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version""" - new_pipeline = self._make_pipeline_copy() - with open(Path(new_pipeline, "assets", "multiqc_config.yml")) as fh: - mqc_yml = yaml.safe_load(fh) - mqc_yml_tmp = mqc_yml.copy() - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml, fh) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - # bump version - lint_obj.nf_config["manifest.version"] = "1.0" - result = lint_obj.multiqc_config() - # Reset the file - with open(Path(new_pipeline, "assets", "multiqc_config.yml"), "w") as fh: - yaml.safe_dump(mqc_yml_tmp, fh) - assert len(result["failed"]) == 1 - assert result["failed"][0].startswith("`assets/multiqc_config.yml` does not contain a matching 'report_comment'.") - - -def test_multiqc_config_report_comment_release_succeed(self): - """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version""" - - import nf_core.pipelines.bump_version - - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - # bump version using the bump_version function - nf_core.pipelines.bump_version.bump_pipeline_version(lint_obj, "1.0") - # lint again - lint_obj._load() - result = lint_obj.multiqc_config() - assert "`assets/multiqc_config.yml` contains a matching 'report_comment'." in result["passed"] diff --git a/tests/pipelines/lint/nextflow_config.py b/tests/pipelines/lint/nextflow_config.py deleted file mode 100644 index d9157c90c6..0000000000 --- a/tests/pipelines/lint/nextflow_config.py +++ /dev/null @@ -1,211 +0,0 @@ -import os -import re -from pathlib import Path - -import nf_core.pipelines.create.create -import nf_core.pipelines.lint - - -def test_nextflow_config_example_pass(self): - """Tests that config variable existence test works with good pipeline example""" - self.lint_obj.load_pipeline_config() - result = self.lint_obj.nextflow_config() - assert len(result["failed"]) == 0 - assert len(result["warned"]) == 0 - - -def test_nextflow_config_bad_name_fail(self): - """Tests that config variable existence test fails with bad pipeline name""" - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - - lint_obj.nf_config["manifest.name"] = "bad_name" - result = lint_obj.nextflow_config() - assert len(result["failed"]) > 0 - assert len(result["warned"]) == 0 - - -def test_nextflow_config_dev_in_release_mode_failed(self): - """Tests that config variable existence test fails with dev version in release mode""" - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - - lint_obj.release_mode = True - lint_obj.nf_config["manifest.version"] = "dev_is_bad_name" - result = lint_obj.nextflow_config() - assert len(result["failed"]) > 0 - assert len(result["warned"]) == 0 - - -def test_nextflow_config_missing_test_profile_failed(self): - """Test failure if config file does not contain `test` profile.""" - new_pipeline = self._make_pipeline_copy() - # Change the name of the test profile so there is no such profile - nf_conf_file = os.path.join(new_pipeline, "nextflow.config") - with open(nf_conf_file) as f: - content = f.read() - fail_content = re.sub(r"\btest\b", "testfail", content) - with open(nf_conf_file, "w") as f: - f.write(fail_content) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) > 0 - assert len(result["warned"]) == 0 - - -def test_default_values_match(self): - """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json.""" - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 0 - assert len(result["warned"]) == 0 - assert "Config default value correct: params.max_cpus" in str(result["passed"]) - assert "Config default value correct: params.validate_params" in str(result["passed"]) - - -def test_default_values_fail(self): - """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json.""" - new_pipeline = self._make_pipeline_copy() - # Change the default value of max_cpus in nextflow.config - nf_conf_file = Path(new_pipeline) / "nextflow.config" - with open(nf_conf_file) as f: - content = f.read() - fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content) - with open(nf_conf_file, "w") as f: - f.write(fail_content) - # Change the default value of max_memory in nextflow_schema.json - nf_schema_file = Path(new_pipeline) / "nextflow_schema.json" - with open(nf_schema_file) as f: - content = f.read() - fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content) - with open(nf_schema_file, "w") as f: - f.write(fail_content) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 2 - assert ( - "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`." - in result["failed"] - ) - assert ( - "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`." - in result["failed"] - ) - - -def test_catch_params_assignment_in_main_nf(self): - """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json.""" - new_pipeline = self._make_pipeline_copy() - # Add parameter assignment in main.nf - main_nf_file = Path(new_pipeline) / "main.nf" - with open(main_nf_file, "a") as f: - f.write("params.max_time = 42") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 1 - assert ( - result["failed"][0] - == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`." - ) - - -def test_allow_params_reference_in_main_nf(self): - """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges.""" - new_pipeline = self._make_pipeline_copy() - # Add parameter reference in main.nf - main_nf_file = Path(new_pipeline) / "main.nf" - with open(main_nf_file, "a") as f: - f.write("params.max_time == 42") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 0 - - -def test_default_values_ignored(self): - """Test ignoring linting of default values.""" - new_pipeline = self._make_pipeline_copy() - # Add max_cpus to the ignore list - nf_core_yml = Path(new_pipeline) / ".nf-core.yml" - with open(nf_core_yml, "w") as f: - f.write( - "repository_type: pipeline\nlint:\n nextflow_config:\n - config_defaults:\n - params.max_cpus\n" - ) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - lint_obj._load_lint_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 0 - assert len(result["ignored"]) == 1 - assert "Config default value correct: params.max_cpu" not in str(result["passed"]) - assert "Config default ignored: params.max_cpus" in str(result["ignored"]) - - -def test_default_values_float(self): - """Test comparing two float values.""" - new_pipeline = self._make_pipeline_copy() - # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` - nf_conf_file = Path(new_pipeline) / "nextflow.config" - with open(nf_conf_file) as f: - content = f.read() - fail_content = re.sub( - r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content - ) - with open(nf_conf_file, "w") as f: - f.write(fail_content) - # Add a float value `dummy` to the nextflow_schema.json - nf_schema_file = Path(new_pipeline) / "nextflow_schema.json" - with open(nf_schema_file) as f: - content = f.read() - fail_content = re.sub( - r'"validate_params": {', - ' "dummy": {"type": "number","default":0.000000001},\n"validate_params": {', - content, - ) - with open(nf_schema_file, "w") as f: - f.write(fail_content) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - assert len(result["failed"]) == 0 - assert len(result["warned"]) == 0 - assert "Config default value correct: params.dummy" in str(result["passed"]) - - -def test_default_values_float_fail(self): - """Test comparing two float values.""" - new_pipeline = self._make_pipeline_copy() - # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` - nf_conf_file = Path(new_pipeline) / "nextflow.config" - with open(nf_conf_file) as f: - content = f.read() - fail_content = re.sub( - r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content - ) - with open(nf_conf_file, "w") as f: - f.write(fail_content) - # Add a float value `dummy` to the nextflow_schema.json - nf_schema_file = Path(new_pipeline) / "nextflow_schema.json" - with open(nf_schema_file) as f: - content = f.read() - fail_content = re.sub( - r'"validate_params": {', ' "dummy": {"type": "float","default":0.000001},\n"validate_params": {', content - ) - with open(nf_schema_file, "w") as f: - f.write(fail_content) - - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - result = lint_obj.nextflow_config() - - assert len(result["failed"]) == 1 - assert len(result["warned"]) == 0 - assert "Config default value incorrect: `params.dummy" in str(result["failed"]) diff --git a/tests/pipelines/lint/nfcore_yml.py b/tests/pipelines/lint/nfcore_yml.py deleted file mode 100644 index 94d2870e11..0000000000 --- a/tests/pipelines/lint/nfcore_yml.py +++ /dev/null @@ -1,53 +0,0 @@ -import re -from pathlib import Path - -import nf_core.pipelines.create -import nf_core.pipelines.lint - - -def test_nfcore_yml_pass(self): - """Lint test: nfcore_yml - PASS""" - self.lint_obj._load() - results = self.lint_obj.nfcore_yml() - - assert "Repository type in `.nf-core.yml` is valid" in str(results["passed"]) - assert "nf-core version in `.nf-core.yml` is set to the latest version" in str(results["passed"]) - assert len(results.get("warned", [])) == 0 - assert len(results.get("failed", [])) == 0 - assert len(results.get("ignored", [])) == 0 - - -def test_nfcore_yml_fail_repo_type(self): - """Lint test: nfcore_yml - FAIL - repository type not set""" - new_pipeline = self._make_pipeline_copy() - nf_core_yml = Path(new_pipeline) / ".nf-core.yml" - with open(nf_core_yml) as fh: - content = fh.read() - new_content = content.replace("repository_type: pipeline", "repository_type: foo") - with open(nf_core_yml, "w") as fh: - fh.write(new_content) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - results = lint_obj.nfcore_yml() - assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"]) - assert len(results.get("warned", [])) == 0 - assert len(results.get("passed", [])) >= 0 - assert len(results.get("ignored", [])) == 0 - - -def test_nfcore_yml_fail_nfcore_version(self): - """Lint test: nfcore_yml - FAIL - nf-core version not set""" - new_pipeline = self._make_pipeline_copy() - nf_core_yml = Path(new_pipeline) / ".nf-core.yml" - with open(nf_core_yml) as fh: - content = fh.read() - new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content) - with open(nf_core_yml, "w") as fh: - fh.write(new_content) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - results = lint_obj.nfcore_yml() - assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"]) - assert len(results.get("failed", [])) == 0 - assert len(results.get("passed", [])) >= 0 - assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/lint/template_strings.py b/tests/pipelines/lint/template_strings.py deleted file mode 100644 index 2db9e20a3f..0000000000 --- a/tests/pipelines/lint/template_strings.py +++ /dev/null @@ -1,53 +0,0 @@ -import subprocess -from pathlib import Path - -import nf_core.pipelines.create -import nf_core.pipelines.lint - - -def test_template_strings(self): - """Tests finding a template string in a file fails linting.""" - new_pipeline = self._make_pipeline_copy() - # Add template string to a file - txt_file = Path(new_pipeline) / "docs" / "test.txt" - with open(txt_file, "w") as f: - f.write("my {{ template_string }}") - subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline) - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.template_strings() - assert len(result["failed"]) == 1 - assert len(result["ignored"]) == 0 - - -def test_template_strings_ignored(self): - """Tests ignoring template_strings""" - new_pipeline = self._make_pipeline_copy() - # Ignore template_strings test - nf_core_yml = Path(new_pipeline) / ".nf-core.yml" - with open(nf_core_yml, "w") as f: - f.write("repository_type: pipeline\nlint:\n template_strings: False") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - lint_obj._lint_pipeline() - assert len(lint_obj.failed) == 0 - assert len(lint_obj.ignored) == 1 - - -def test_template_strings_ignore_file(self): - """Tests ignoring template_strings file""" - new_pipeline = self._make_pipeline_copy() - # Add template string to a file - txt_file = Path(new_pipeline) / "docs" / "test.txt" - with open(txt_file, "w") as f: - f.write("my {{ template_string }}") - subprocess.check_output(["git", "add", "docs"], cwd=new_pipeline) - # Ignore template_strings test - nf_core_yml = Path(new_pipeline) / ".nf-core.yml" - with open(nf_core_yml, "w") as f: - f.write("repository_type: pipeline\nlint:\n template_strings:\n - docs/test.txt") - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj._load() - result = lint_obj.template_strings() - assert len(result["failed"]) == 0 - assert len(result["ignored"]) == 1 diff --git a/tests/pipelines/lint/test_actions_awstest.py b/tests/pipelines/lint/test_actions_awstest.py new file mode 100644 index 0000000000..51b55cb867 --- /dev/null +++ b/tests/pipelines/lint/test_actions_awstest.py @@ -0,0 +1,39 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintActionsAws(TestLint): + def test_actions_awstest_pass(self): + """Lint test: actions_awstest - PASS""" + self.lint_obj._load() + results = self.lint_obj.actions_awstest() + assert results["passed"] == ["'.github/workflows/awstest.yml' is triggered correctly"] + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + + def test_actions_awstest_fail(self): + """Lint test: actions_awsfulltest - FAIL""" + + # Edit .github/workflows/awsfulltest.yml to use -profile test_full + new_pipeline = self._make_pipeline_copy() + with open(Path(new_pipeline, ".github", "workflows", "awstest.yml")) as fh: + awstest_yml = yaml.safe_load(fh) + awstest_yml[True]["push"] = ["master"] + with open(Path(new_pipeline, ".github", "workflows", "awstest.yml"), "w") as fh: + yaml.dump(awstest_yml, fh) + + # Make lint object + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + + results = lint_obj.actions_awstest() + assert results["failed"] == ["'.github/workflows/awstest.yml' is not triggered correctly"] + assert len(results.get("warned", [])) == 0 + assert len(results.get("passed", [])) == 0 + assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/lint/test_actions_ci.py b/tests/pipelines/lint/test_actions_ci.py new file mode 100644 index 0000000000..7319ce4b0c --- /dev/null +++ b/tests/pipelines/lint/test_actions_ci.py @@ -0,0 +1,50 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintActionsCi(TestLint): + def test_actions_ci_pass(self): + """Lint test: actions_ci - PASS""" + self.lint_obj._load() + results = self.lint_obj.actions_ci() + assert results["passed"] == [ + "'.github/workflows/ci.yml' is triggered on expected events", + "'.github/workflows/ci.yml' checks minimum NF version", + ] + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + + def test_actions_ci_fail_wrong_nf(self): + """Lint test: actions_ci - FAIL - wrong minimum version of Nextflow tested""" + self.lint_obj._load() + self.lint_obj.minNextflowVersion = "1.2.3" + results = self.lint_obj.actions_ci() + assert results["failed"] == ["Minimum pipeline NF version '1.2.3' is not tested in '.github/workflows/ci.yml'"] + + def test_actions_ci_fail_wrong_trigger(self): + """Lint test: actions_actions_ci - FAIL - workflow triggered incorrectly, NF ver not checked at all""" + + # Edit .github/workflows/actions_ci.yml to mess stuff up! + new_pipeline = self._make_pipeline_copy() + with open(Path(new_pipeline, ".github", "workflows", "ci.yml")) as fh: + ci_yml = yaml.safe_load(fh) + ci_yml[True]["push"] = ["dev", "patch"] + ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]} + with open(Path(new_pipeline, ".github", "workflows", "ci.yml"), "w") as fh: + yaml.dump(ci_yml, fh) + + # Make lint object + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + + results = lint_obj.actions_ci() + assert results["failed"] == [ + "'.github/workflows/ci.yml' is not triggered on expected events", + "'.github/workflows/ci.yml' does not check minimum NF version", + ] diff --git a/tests/pipelines/lint/test_actions_schema_validation.py b/tests/pipelines/lint/test_actions_schema_validation.py new file mode 100644 index 0000000000..34f6b5fcb8 --- /dev/null +++ b/tests/pipelines/lint/test_actions_schema_validation.py @@ -0,0 +1,62 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintActionsSchemaValidation(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + self.awstest_yml_path = Path(self.new_pipeline) / ".github" / "workflows" / "awstest.yml" + with open(self.awstest_yml_path) as fh: + self.awstest_yml = yaml.safe_load(fh) + + def test_actions_schema_validation_missing_jobs(self): + """Missing 'jobs' field should result in failure""" + + self.awstest_yml.pop("jobs") + with open(self.awstest_yml_path, "w") as fh: + yaml.dump(self.awstest_yml, fh) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.actions_schema_validation() + + assert "Workflow validation failed for awstest.yml: 'jobs' is a required property" in results["failed"][0] + + def test_actions_schema_validation_missing_on(self): + """Missing 'on' field should result in failure""" + + self.awstest_yml.pop(True) + with open(self.awstest_yml_path, "w") as fh: + yaml.dump(self.awstest_yml, fh) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.actions_schema_validation() + + assert results["failed"][0] == "Missing 'on' keyword in awstest.yml" + assert "Workflow validation failed for awstest.yml: 'on' is a required property" in results["failed"][1] + + def test_actions_schema_validation_fails_for_additional_property(self): + """Missing 'jobs' field should result in failure""" + + self.awstest_yml["not_jobs"] = self.awstest_yml["jobs"] + with open(self.awstest_yml_path, "w") as fh: + yaml.dump(self.awstest_yml, fh) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.actions_schema_validation() + + assert ( + "Workflow validation failed for awstest.yml: Additional properties are not allowed ('not_jobs' was unexpected)" + in results["failed"][0] + ) diff --git a/tests/pipelines/lint/test_configs.py b/tests/pipelines/lint/test_configs.py new file mode 100644 index 0000000000..7bb6329b5b --- /dev/null +++ b/tests/pipelines/lint/test_configs.py @@ -0,0 +1,91 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.create +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintConfigs(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + def test_withname_in_modules_config(self): + """Tests finding withName in modules.config passes linting.""" + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.modules_config() + assert len(result["failed"]) == 0 + assert any( + ["`FASTQC` found in `conf/modules.config` and Nextflow scripts." in passed for passed in result["passed"]] + ) + + def test_superfluous_withname_in_modules_config_fails(self): + """Tests finding withName in modules.config fails linting.""" + + # Add withName to modules.config + modules_config = Path(self.new_pipeline) / "conf" / "modules.config" + with open(modules_config, "a") as f: + f.write("\nwithName: 'BPIPE' {\n cache = false \n}") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline, hide_progress=False) + lint_obj._load() + result = lint_obj.modules_config() + assert len(result["failed"]) == 1 + assert result["failed"][0].startswith("`conf/modules.config` contains `withName:BPIPE`") + + def test_ignore_modules_config(self): + """Tests ignoring the modules.config passes linting.""" + + # ignore modules.config in linting + with open(Path(self.new_pipeline) / ".nf-core.yml") as f: + content = yaml.safe_load(f) + old_content = content.copy() + content["lint"] = {"modules_config": False} + with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f: + yaml.dump(content, f) + Path(self.new_pipeline, "conf", "modules.config").unlink() + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.modules_config() + assert len(result["ignored"]) == 1 + assert result["ignored"][0].startswith("`conf/modules.config` not found, but it is ignored.") + # cleanup + with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f: + yaml.dump(old_content, f) + + def test_superfluous_withname_in_base_config_fails(self): + """Tests finding withName in base.config fails linting.""" + + # Add withName to base.config + base_config = Path(self.new_pipeline) / "conf" / "base.config" + with open(base_config, "a") as f: + f.write("\nwithName:CUSTOM_DUMPSOFTWAREVERSIONS {\n cache = false \n}") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.base_config() + assert len(result["failed"]) == 1 + assert result["failed"][0].startswith("`conf/base.config` contains `withName:CUSTOM_DUMPSOFTWAREVERSIONS`") + + def test_ignore_base_config(self): + """Tests ignoring the base.config passes linting.""" + + # ignore base.config in linting + with open(Path(self.new_pipeline) / ".nf-core.yml") as f: + content = yaml.safe_load(f) + old_content = content.copy() + content["lint"] = {"base_config": False} + with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f: + yaml.dump(content, f) + Path(self.new_pipeline, "conf", "base.config").unlink() + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.base_config() + assert len(result["ignored"]) == 1 + assert result["ignored"][0].startswith("`conf/base.config` not found, but it is ignored.") + # cleanup + with open(Path(self.new_pipeline) / ".nf-core.yml", "w") as f: + yaml.dump(old_content, f) diff --git a/tests/pipelines/lint/test_files_exist.py b/tests/pipelines/lint/test_files_exist.py new file mode 100644 index 0000000000..85ba817536 --- /dev/null +++ b/tests/pipelines/lint/test_files_exist.py @@ -0,0 +1,91 @@ +from pathlib import Path + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintFilesExist(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + def test_files_exist_missing_config(self): + """Lint test: critical files missing FAIL""" + + Path(self.new_pipeline, "CHANGELOG.md").unlink() + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + lint_obj.nf_config["manifest.name"] = "nf-core/testpipeline" + + results = lint_obj.files_exist() + assert "File not found: `CHANGELOG.md`" in results["failed"] + + def test_files_exist_missing_main(self): + """Check if missing main issues warning""" + + Path(self.new_pipeline, "main.nf").unlink() + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.files_exist() + assert "File not found: `main.nf`" in results["warned"] + + def test_files_exist_deprecated_file(self): + """Check whether deprecated file issues warning""" + + nf = Path(self.new_pipeline, "parameters.settings.json") + nf.touch() + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.files_exist() + assert results["failed"] == ["File must be removed: `parameters.settings.json`"] + + def test_files_exist_pass(self): + """Lint check should pass if all files are there""" + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + + results = lint_obj.files_exist() + assert results["failed"] == [] + + def test_files_exist_pass_conditional(self): + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + lint_obj.nf_config["plugins"] = [] + lib_dir = Path(self.new_pipeline, "lib") + lib_dir.mkdir() + (lib_dir / "nfcore_external_java_deps.jar").touch() + results = lint_obj.files_exist() + assert results["failed"] == [] + assert results["ignored"] == [] + + def test_files_exist_fail_conditional(self): + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + lib_dir = Path(self.new_pipeline, "lib") + lib_dir.mkdir() + (lib_dir / "nfcore_external_java_deps.jar").touch() + results = lint_obj.files_exist() + assert results["failed"] == ["File must be removed: `lib/nfcore_external_java_deps.jar`"] + assert results["ignored"] == [] + + def test_files_exist_pass_conditional_nfschema(self): + # replace nf-validation with nf-schema in nextflow.config + with open(Path(self.new_pipeline, "nextflow.config")) as f: + config = f.read() + config = config.replace("nf-validation", "nf-schema") + with open(Path(self.new_pipeline, "nextflow.config"), "w") as f: + f.write(config) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + lint_obj.nf_config["manifest.schema"] = "nf-core" + results = lint_obj.files_exist() + assert results["failed"] == [] + assert results["ignored"] == [] diff --git a/tests/pipelines/lint/test_files_unchanged.py b/tests/pipelines/lint/test_files_unchanged.py new file mode 100644 index 0000000000..4282b49958 --- /dev/null +++ b/tests/pipelines/lint/test_files_unchanged.py @@ -0,0 +1,28 @@ +from pathlib import Path + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintFilesUnchanged(TestLint): + def test_files_unchanged_pass(self): + self.lint_obj._load() + results = self.lint_obj.files_unchanged() + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + assert not results.get("could_fix", True) + + def test_files_unchanged_fail(self): + failing_file = Path(".github", "CONTRIBUTING.md") + new_pipeline = self._make_pipeline_copy() + with open(Path(new_pipeline, failing_file), "a") as fh: + fh.write("THIS SHOULD NOT BE HERE") + + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + results = lint_obj.files_unchanged() + assert len(results["failed"]) > 0 + assert str(failing_file) in results["failed"][0] + assert results["could_fix"] diff --git a/tests/pipelines/lint/test_merge_markers.py b/tests/pipelines/lint/test_merge_markers.py new file mode 100644 index 0000000000..3094d8f8d1 --- /dev/null +++ b/tests/pipelines/lint/test_merge_markers.py @@ -0,0 +1,25 @@ +import os + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintMergeMarkers(TestLint): + def test_merge_markers_found(self): + """Missing 'jobs' field should result in failure""" + new_pipeline = self._make_pipeline_copy() + + with open(os.path.join(new_pipeline, "main.nf")) as fh: + main_nf_content = fh.read() + main_nf_content = ">>>>>>>\n" + main_nf_content + with open(os.path.join(new_pipeline, "main.nf"), "w") as fh: + fh.write(main_nf_content) + + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj._load() + + results = lint_obj.merge_markers() + assert len(results["failed"]) > 0 + assert len(results["passed"]) == 0 + assert "Merge marker '>>>>>>>' in " in results["failed"][0] diff --git a/tests/pipelines/lint/test_modules_json.py b/tests/pipelines/lint/test_modules_json.py new file mode 100644 index 0000000000..0d8333d9a2 --- /dev/null +++ b/tests/pipelines/lint/test_modules_json.py @@ -0,0 +1,10 @@ +from ..test_lint import TestLint + + +class TestLintModulesJson(TestLint): + def test_modules_json_pass(self): + self.lint_obj._load() + results = self.lint_obj.modules_json() + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("passed", [])) > 0 diff --git a/tests/pipelines/lint/test_multiqc_config.py b/tests/pipelines/lint/test_multiqc_config.py new file mode 100644 index 0000000000..5da6e567ec --- /dev/null +++ b/tests/pipelines/lint/test_multiqc_config.py @@ -0,0 +1,127 @@ +from pathlib import Path + +import yaml + +import nf_core.pipelines.bump_version +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintMultiqcConfig(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + self.multiqc_config_yml = Path(self.new_pipeline, "assets", "multiqc_config.yml") + + def test_multiqc_config_exists(self): + """Test that linting fails if the multiqc_config.yml file is missing""" + # Delete the file + self.multiqc_config_yml.unlink() + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.multiqc_config() + assert result["failed"] == ["`assets/multiqc_config.yml` not found."] + + def test_multiqc_config_ignore(self): + """Test that linting succeeds if the multiqc_config.yml file is missing but ignored""" + # Delete the file + self.multiqc_config_yml.unlink() + with open(Path(self.new_pipeline, ".nf-core.yml")) as f: + content = yaml.safe_load(f) + old_content = content.copy() + content["lint"] = {"multiqc_config": False} + with open(Path(self.new_pipeline, ".nf-core.yml"), "w") as f: + yaml.dump(content, f) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.multiqc_config() + assert result["ignored"] == ["`assets/multiqc_config.yml` not found, but it is ignored."] + + # cleanup + with open(Path(self.new_pipeline, ".nf-core.yml"), "w") as f: + yaml.dump(old_content, f) + + def test_multiqc_config_missing_report_section_order(self): + """Test that linting fails if the multiqc_config.yml file is missing the report_section_order""" + with open(self.multiqc_config_yml) as fh: + mqc_yml = yaml.safe_load(fh) + mqc_yml_tmp = mqc_yml.copy() + mqc_yml.pop("report_section_order") + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml, fh) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.multiqc_config() + # Reset the file + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml_tmp, fh) + assert result["failed"] == ["`assets/multiqc_config.yml` does not contain `report_section_order`"] + + def test_multiqc_incorrect_export_plots(self): + """Test that linting fails if the multiqc_config.yml file has an incorrect value for export_plots""" + with open(self.multiqc_config_yml) as fh: + mqc_yml = yaml.safe_load(fh) + mqc_yml_tmp = mqc_yml.copy() + mqc_yml["export_plots"] = False + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml, fh) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.multiqc_config() + # Reset the file + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml_tmp, fh) + assert result["failed"] == ["`assets/multiqc_config.yml` does not contain 'export_plots: true'."] + + def test_multiqc_config_report_comment_fail(self): + """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment""" + with open(self.multiqc_config_yml) as fh: + mqc_yml = yaml.safe_load(fh) + mqc_yml_tmp = mqc_yml.copy() + mqc_yml["report_comment"] = "This is a test" + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml, fh) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.multiqc_config() + # Reset the file + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml_tmp, fh) + assert len(result["failed"]) == 1 + assert result["failed"][0].startswith( + "`assets/multiqc_config.yml` does not contain a matching 'report_comment'." + ) + + def test_multiqc_config_report_comment_release_fail(self): + """Test that linting fails if the multiqc_config.yml file has an incorrect report_comment for a release version""" + with open(self.multiqc_config_yml) as fh: + mqc_yml = yaml.safe_load(fh) + mqc_yml_tmp = mqc_yml.copy() + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml, fh) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + # bump version + lint_obj.nf_config["manifest.version"] = "1.0" + result = lint_obj.multiqc_config() + # Reset the file + with open(self.multiqc_config_yml, "w") as fh: + yaml.safe_dump(mqc_yml_tmp, fh) + assert len(result["failed"]) == 1 + assert result["failed"][0].startswith( + "`assets/multiqc_config.yml` does not contain a matching 'report_comment'." + ) + + def test_multiqc_config_report_comment_release_succeed(self): + """Test that linting fails if the multiqc_config.yml file has a correct report_comment for a release version""" + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + # bump version using the bump_version function + nf_core.pipelines.bump_version.bump_pipeline_version(lint_obj, "1.0") + # lint again + lint_obj._load() + result = lint_obj.multiqc_config() + assert "`assets/multiqc_config.yml` contains a matching 'report_comment'." in result["passed"] diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py new file mode 100644 index 0000000000..01173aec34 --- /dev/null +++ b/tests/pipelines/lint/test_nextflow_config.py @@ -0,0 +1,200 @@ +import os +import re +from pathlib import Path + +import nf_core.pipelines.create.create +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintNextflowConfig(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + def test_nextflow_config_example_pass(self): + """Tests that config variable existence test works with good pipeline example""" + self.lint_obj.load_pipeline_config() + result = self.lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + assert len(result["warned"]) == 0 + + def test_default_values_match(self): + """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json.""" + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + assert len(result["warned"]) == 0 + assert "Config default value correct: params.max_cpus" in str(result["passed"]) + assert "Config default value correct: params.validate_params" in str(result["passed"]) + + def test_nextflow_config_bad_name_fail(self): + """Tests that config variable existence test fails with bad pipeline name""" + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + + lint_obj.nf_config["manifest.name"] = "bad_name" + result = lint_obj.nextflow_config() + assert len(result["failed"]) > 0 + assert len(result["warned"]) == 0 + + def test_nextflow_config_dev_in_release_mode_failed(self): + """Tests that config variable existence test fails with dev version in release mode""" + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + + lint_obj.release_mode = True + lint_obj.nf_config["manifest.version"] = "dev_is_bad_name" + result = lint_obj.nextflow_config() + assert len(result["failed"]) > 0 + assert len(result["warned"]) == 0 + + def test_nextflow_config_missing_test_profile_failed(self): + """Test failure if config file does not contain `test` profile.""" + # Change the name of the test profile so there is no such profile + nf_conf_file = os.path.join(self.new_pipeline, "nextflow.config") + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub(r"\btest\b", "testfail", content) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) > 0 + assert len(result["warned"]) == 0 + + def test_default_values_fail(self): + """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json.""" + # Change the default value of max_cpus in nextflow.config + nf_conf_file = Path(self.new_pipeline) / "nextflow.config" + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + # Change the default value of max_memory in nextflow_schema.json + nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json" + with open(nf_schema_file) as f: + content = f.read() + fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content) + with open(nf_schema_file, "w") as f: + f.write(fail_content) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 2 + assert ( + "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`." + in result["failed"] + ) + assert ( + "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`." + in result["failed"] + ) + + def test_catch_params_assignment_in_main_nf(self): + """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json.""" + # Add parameter assignment in main.nf + main_nf_file = Path(self.new_pipeline) / "main.nf" + with open(main_nf_file, "a") as f: + f.write("params.max_time = 42") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 1 + assert ( + result["failed"][0] + == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`." + ) + + def test_allow_params_reference_in_main_nf(self): + """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges.""" + # Add parameter reference in main.nf + main_nf_file = Path(self.new_pipeline) / "main.nf" + with open(main_nf_file, "a") as f: + f.write("params.max_time == 42") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + + def test_default_values_ignored(self): + """Test ignoring linting of default values.""" + # Add max_cpus to the ignore list + nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml" + with open(nf_core_yml, "w") as f: + f.write( + "repository_type: pipeline\nlint:\n nextflow_config:\n - config_defaults:\n - params.max_cpus\n" + ) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + lint_obj._load_lint_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + assert len(result["ignored"]) == 1 + assert "Config default value correct: params.max_cpu" not in str(result["passed"]) + assert "Config default ignored: params.max_cpus" in str(result["ignored"]) + + def test_default_values_float(self): + """Test comparing two float values.""" + # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` + nf_conf_file = Path(self.new_pipeline) / "nextflow.config" + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub( + r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content + ) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + # Add a float value `dummy` to the nextflow_schema.json + nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json" + with open(nf_schema_file) as f: + content = f.read() + fail_content = re.sub( + r'"validate_params": {', + ' "dummy": {"type": "number","default":0.000000001},\n"validate_params": {', + content, + ) + with open(nf_schema_file, "w") as f: + f.write(fail_content) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + assert len(result["failed"]) == 0 + assert len(result["warned"]) == 0 + assert "Config default value correct: params.dummy" in str(result["passed"]) + + def test_default_values_float_fail(self): + """Test comparing two float values.""" + # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params` + nf_conf_file = Path(self.new_pipeline) / "nextflow.config" + with open(nf_conf_file) as f: + content = f.read() + fail_content = re.sub( + r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content + ) + with open(nf_conf_file, "w") as f: + f.write(fail_content) + # Add a float value `dummy` to the nextflow_schema.json + nf_schema_file = Path(self.new_pipeline) / "nextflow_schema.json" + with open(nf_schema_file) as f: + content = f.read() + fail_content = re.sub( + r'"validate_params": {', + ' "dummy": {"type": "float","default":0.000001},\n"validate_params": {', + content, + ) + with open(nf_schema_file, "w") as f: + f.write(fail_content) + + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj.load_pipeline_config() + result = lint_obj.nextflow_config() + + assert len(result["failed"]) == 1 + assert len(result["warned"]) == 0 + assert "Config default value incorrect: `params.dummy" in str(result["failed"]) diff --git a/tests/pipelines/lint/test_nfcore_yml.py b/tests/pipelines/lint/test_nfcore_yml.py new file mode 100644 index 0000000000..955c00da81 --- /dev/null +++ b/tests/pipelines/lint/test_nfcore_yml.py @@ -0,0 +1,57 @@ +import re +from pathlib import Path + +import nf_core.pipelines.create +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintNfCoreYml(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + self.nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml" + + def test_nfcore_yml_pass(self): + """Lint test: nfcore_yml - PASS""" + self.lint_obj._load() + results = self.lint_obj.nfcore_yml() + + assert "Repository type in `.nf-core.yml` is valid" in str(results["passed"]) + assert "nf-core version in `.nf-core.yml` is set to the latest version" in str(results["passed"]) + assert len(results.get("warned", [])) == 0 + assert len(results.get("failed", [])) == 0 + assert len(results.get("ignored", [])) == 0 + + def test_nfcore_yml_fail_repo_type(self): + """Lint test: nfcore_yml - FAIL - repository type not set""" + + with open(self.nf_core_yml) as fh: + content = fh.read() + new_content = content.replace("repository_type: pipeline", "repository_type: foo") + with open(self.nf_core_yml, "w") as fh: + fh.write(new_content) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + results = lint_obj.nfcore_yml() + assert "Repository type in `.nf-core.yml` is not valid." in str(results["failed"]) + assert len(results.get("warned", [])) == 0 + assert len(results.get("passed", [])) >= 0 + assert len(results.get("ignored", [])) == 0 + + def test_nfcore_yml_fail_nfcore_version(self): + """Lint test: nfcore_yml - FAIL - nf-core version not set""" + + with open(self.nf_core_yml) as fh: + content = fh.read() + new_content = re.sub(r"nf_core_version:.+", "nf_core_version: foo", content) + with open(self.nf_core_yml, "w") as fh: + fh.write(new_content) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + results = lint_obj.nfcore_yml() + assert "nf-core version in `.nf-core.yml` is not set to the latest version." in str(results["warned"]) + assert len(results.get("failed", [])) == 0 + assert len(results.get("passed", [])) >= 0 + assert len(results.get("ignored", [])) == 0 diff --git a/tests/pipelines/lint/test_template_strings.py b/tests/pipelines/lint/test_template_strings.py new file mode 100644 index 0000000000..406ba63e0c --- /dev/null +++ b/tests/pipelines/lint/test_template_strings.py @@ -0,0 +1,55 @@ +import subprocess +from pathlib import Path + +import nf_core.pipelines.create +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintTemplateStrings(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + def test_template_strings(self): + """Tests finding a template string in a file fails linting.""" + # Add template string to a file + txt_file = Path(self.new_pipeline) / "docs" / "test.txt" + with open(txt_file, "w") as f: + f.write("my {{ template_string }}") + subprocess.check_output(["git", "add", "docs"], cwd=self.new_pipeline) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.template_strings() + assert len(result["failed"]) == 1 + assert len(result["ignored"]) == 0 + + def test_template_strings_ignored(self): + """Tests ignoring template_strings""" + # Ignore template_strings test + nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml" + with open(nf_core_yml, "w") as f: + f.write("repository_type: pipeline\nlint:\n template_strings: False") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + lint_obj._lint_pipeline() + assert len(lint_obj.failed) == 0 + assert len(lint_obj.ignored) == 1 + + def test_template_strings_ignore_file(self): + """Tests ignoring template_strings file""" + # Add template string to a file + txt_file = Path(self.new_pipeline) / "docs" / "test.txt" + with open(txt_file, "w") as f: + f.write("my {{ template_string }}") + subprocess.check_output(["git", "add", "docs"], cwd=self.new_pipeline) + # Ignore template_strings test + nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml" + with open(nf_core_yml, "w") as f: + f.write("repository_type: pipeline\nlint:\n template_strings:\n - docs/test.txt") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + result = lint_obj.template_strings() + assert len(result["failed"]) == 0 + assert len(result["ignored"]) == 1 diff --git a/tests/pipelines/lint/test_version_consistency.py b/tests/pipelines/lint/test_version_consistency.py new file mode 100644 index 0000000000..c5a2cc74f1 --- /dev/null +++ b/tests/pipelines/lint/test_version_consistency.py @@ -0,0 +1,19 @@ +import nf_core.pipelines.create.create +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintVersionConsistency(TestLint): + def test_version_consistency(self): + """Tests that config variable existence test fails with bad pipeline name""" + new_pipeline = self._make_pipeline_copy() + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + lint_obj.load_pipeline_config() + lint_obj.nextflow_config() + + result = lint_obj.version_consistency() + assert result["passed"] == [ + "Version tags are numeric and consistent between container, release tag and config." + ] + assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"] diff --git a/tests/pipelines/lint/version_consistency.py b/tests/pipelines/lint/version_consistency.py deleted file mode 100644 index 88eadce391..0000000000 --- a/tests/pipelines/lint/version_consistency.py +++ /dev/null @@ -1,14 +0,0 @@ -import nf_core.pipelines.create.create -import nf_core.pipelines.lint - - -def test_version_consistency(self): - """Tests that config variable existence test fails with bad pipeline name""" - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - lint_obj.load_pipeline_config() - lint_obj.nextflow_config() - - result = lint_obj.version_consistency() - assert result["passed"] == ["Version tags are numeric and consistent between container, release tag and config."] - assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"] diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index 54279cd064..b3eac17cb8 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -19,204 +19,166 @@ def setUp(self) -> None: super().setUp() self.lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir) - ########################## - # CORE lint.py FUNCTIONS # - ########################## - def test_run_linting_function(self): - """Run the master run_linting() function in lint.py - - We don't really check any of this code as it's just a series of function calls - and we're testing each of those individually. This is mostly to check for syntax errors.""" - nf_core.pipelines.lint.run_linting(self.pipeline_dir, False) - - def test_init_pipeline_lint(self): - """Simply create a PipelineLint object. - - This checks that all of the lint test imports are working properly, - we also check that the git sha was found and that the release flag works properly - """ - lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True) - - # Tests that extra test is added for release mode - assert "version_consistency" in lint_obj.lint_tests - assert lint_obj.git_sha - # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash - assert len(lint_obj.git_sha) > 0 - - def test_load_lint_config_not_found(self): - """Try to load a linting config file that doesn't exist""" - self.lint_obj._load_lint_config() - assert self.lint_obj.lint_config == {} - - def test_load_lint_config_ignore_all_tests(self): - """Try to load a linting config file that ignores all tests""" - - # Make a copy of the test pipeline and create a lint object - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - - # Make a config file listing all test names - config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} - with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: - yaml.dump(config_dict, fh) - - # Load the new lint config file and check - lint_obj._load_lint_config() - assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests) - - # Try running linting and make sure that all tests are ignored - lint_obj._lint_pipeline() - assert len(lint_obj.passed) == 0 - assert len(lint_obj.warned) == 0 - assert len(lint_obj.failed) == 0 - assert len(lint_obj.ignored) == len(lint_obj.lint_tests) - - @with_temporary_folder - def test_json_output(self, tmp_dir): - """ - Test creation of a JSON file with lint results - - Expected JSON output: - { - "nf_core_tools_version": "1.10.dev0", - "date_run": "2020-06-05 10:56:42", - "tests_pass": [ - [ 1, "This test passed"], - [ 2, "This test also passed"] - ], - "tests_warned": [ - [ 2, "This test gave a warning"] - ], - "tests_failed": [], - "num_tests_pass": 2, - "num_tests_warned": 1, - "num_tests_failed": 0, - "has_tests_pass": true, - "has_tests_warned": true, - "has_tests_failed": false - } - """ - self.lint_obj.passed.append(("test_one", "This test passed")) - self.lint_obj.passed.append(("test_two", "This test also passed")) - self.lint_obj.warned.append(("test_three", "This test gave a warning")) - - # Make a temp dir for the JSON output - json_fn = Path(tmp_dir, "lint_results.json") - self.lint_obj._save_json_results(json_fn) - - # Load created JSON file and check its contents - with open(json_fn) as fh: - try: - saved_json = json.load(fh) - except json.JSONDecodeError as e: - raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}") - assert saved_json["num_tests_pass"] > 0 - assert saved_json["num_tests_warned"] > 0 - assert saved_json["num_tests_ignored"] == 0 - assert saved_json["num_tests_failed"] == 0 - assert saved_json["has_tests_pass"] - assert saved_json["has_tests_warned"] - assert not saved_json["has_tests_ignored"] - assert not saved_json["has_tests_failed"] - - def test_wrap_quotes(self): - md = self.lint_obj._wrap_quotes(["one", "two", "three"]) - assert md == "`one` or `two` or `three`" - - def test_sphinx_md_files(self): - """Check that we have .md files for all lint module code, - and that there are no unexpected files (eg. deleted lint tests)""" - - docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests") - - # Get list of existing .md files - existing_docs = [] - existing_docs = [ - str(Path(docs_basedir, fn)) - for fn in Path(docs_basedir).iterdir() - if fn.match("*.md") and not fn.match("index.md") - ] - - # Check .md files against each test name - lint_obj = nf_core.pipelines.lint.PipelineLint("", True) - for test_name in lint_obj.lint_tests: - fn = Path(docs_basedir, f"{test_name}.md") - assert fn.exists(), f"Could not find lint docs .md file: {fn}" - existing_docs.remove(str(fn)) - - # Check that we have no remaining .md files that we didn't expect - assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}" + +########################## +# CORE lint.py FUNCTIONS # +########################## +def test_run_linting_function(self): + """Run the master run_linting() function in lint.py + + We don't really check any of this code as it's just a series of function calls + and we're testing each of those individually. This is mostly to check for syntax errors.""" + nf_core.pipelines.lint.run_linting(self.pipeline_dir, False) + + +def test_init_pipeline_lint(self): + """Simply create a PipelineLint object. + + This checks that all of the lint test imports are working properly, + we also check that the git sha was found and that the release flag works properly + """ + lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True) + + # Tests that extra test is added for release mode + assert "version_consistency" in lint_obj.lint_tests + assert lint_obj.git_sha + # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash + assert len(lint_obj.git_sha) > 0 + + +def test_load_lint_config_not_found(self): + """Try to load a linting config file that doesn't exist""" + self.lint_obj._load_lint_config() + assert self.lint_obj.lint_config == {} + + +def test_load_lint_config_ignore_all_tests(self): + """Try to load a linting config file that ignores all tests""" + + # Make a copy of the test pipeline and create a lint object + new_pipeline = self._make_pipeline_copy() + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + + # Make a config file listing all test names + config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} + with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: + yaml.dump(config_dict, fh) + + # Load the new lint config file and check + lint_obj._load_lint_config() + assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests) + + # Try running linting and make sure that all tests are ignored + lint_obj._lint_pipeline() + assert len(lint_obj.passed) == 0 + assert len(lint_obj.warned) == 0 + assert len(lint_obj.failed) == 0 + assert len(lint_obj.ignored) == len(lint_obj.lint_tests) + + +@with_temporary_folder +def test_json_output(self, tmp_dir): + """ + Test creation of a JSON file with lint results + + Expected JSON output: + { + "nf_core_tools_version": "1.10.dev0", + "date_run": "2020-06-05 10:56:42", + "tests_pass": [ + [ 1, "This test passed"], + [ 2, "This test also passed"] + ], + "tests_warned": [ + [ 2, "This test gave a warning"] + ], + "tests_failed": [], + "num_tests_pass": 2, + "num_tests_warned": 1, + "num_tests_failed": 0, + "has_tests_pass": true, + "has_tests_warned": true, + "has_tests_failed": false + } + """ + self.lint_obj.passed.append(("test_one", "This test passed")) + self.lint_obj.passed.append(("test_two", "This test also passed")) + self.lint_obj.warned.append(("test_three", "This test gave a warning")) + + # Make a temp dir for the JSON output + json_fn = Path(tmp_dir, "lint_results.json") + self.lint_obj._save_json_results(json_fn) + + # Load created JSON file and check its contents + with open(json_fn) as fh: + try: + saved_json = json.load(fh) + except json.JSONDecodeError as e: + raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}") + assert saved_json["num_tests_pass"] > 0 + assert saved_json["num_tests_warned"] > 0 + assert saved_json["num_tests_ignored"] == 0 + assert saved_json["num_tests_failed"] == 0 + assert saved_json["has_tests_pass"] + assert saved_json["has_tests_warned"] + assert not saved_json["has_tests_ignored"] + assert not saved_json["has_tests_failed"] + + +def test_wrap_quotes(self): + md = self.lint_obj._wrap_quotes(["one", "two", "three"]) + assert md == "`one` or `two` or `three`" + + +def test_sphinx_md_files(self): + """Check that we have .md files for all lint module code, + and that there are no unexpected files (eg. deleted lint tests)""" + + docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests") + + # Get list of existing .md files + existing_docs = [] + existing_docs = [ + str(Path(docs_basedir, fn)) + for fn in Path(docs_basedir).iterdir() + if fn.match("*.md") and not fn.match("index.md") + ] + + # Check .md files against each test name + lint_obj = nf_core.pipelines.lint.PipelineLint("", True) + for test_name in lint_obj.lint_tests: + fn = Path(docs_basedir, f"{test_name}.md") + assert fn.exists(), f"Could not find lint docs .md file: {fn}" + existing_docs.remove(str(fn)) + + # Check that we have no remaining .md files that we didn't expect + assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}" ####################### # SPECIFIC LINT TESTS # ####################### - from .lint.actions_awstest import ( # type: ignore[misc] - test_actions_awstest_fail, - test_actions_awstest_pass, - ) - from .lint.actions_ci import ( # type: ignore[misc] - test_actions_ci_fail_wrong_nf, - test_actions_ci_fail_wrong_trigger, - test_actions_ci_pass, - ) - from .lint.actions_schema_validation import ( # type: ignore[misc] - test_actions_schema_validation_fails_for_additional_property, - test_actions_schema_validation_missing_jobs, - test_actions_schema_validation_missing_on, - ) - from .lint.configs import ( # type: ignore[misc] - test_ignore_base_config, - test_ignore_modules_config, - test_superfluous_withname_in_base_config_fails, - test_superfluous_withname_in_modules_config_fails, - test_withname_in_modules_config, - ) - from .lint.files_exist import ( # type: ignore[misc] - test_files_exist_deprecated_file, - test_files_exist_fail_conditional, - test_files_exist_missing_config, - test_files_exist_missing_main, - test_files_exist_pass, - test_files_exist_pass_conditional, - test_files_exist_pass_conditional_nfschema, - ) - from .lint.files_unchanged import ( # type: ignore[misc] - test_files_unchanged_fail, - test_files_unchanged_pass, - ) - from .lint.merge_markers import test_merge_markers_found # type: ignore[misc] - from .lint.modules_json import test_modules_json_pass # type: ignore[misc] - from .lint.multiqc_config import ( # type: ignore[misc] - test_multiqc_config_exists, - test_multiqc_config_ignore, - test_multiqc_config_missing_report_section_order, - test_multiqc_config_report_comment_fail, - test_multiqc_config_report_comment_release_fail, - test_multiqc_config_report_comment_release_succeed, - test_multiqc_incorrect_export_plots, - ) - from .lint.nextflow_config import ( # type: ignore[misc] - test_allow_params_reference_in_main_nf, - test_catch_params_assignment_in_main_nf, - test_default_values_fail, - test_default_values_float, - test_default_values_float_fail, - test_default_values_ignored, - test_default_values_match, - test_nextflow_config_bad_name_fail, - test_nextflow_config_dev_in_release_mode_failed, - test_nextflow_config_example_pass, - test_nextflow_config_missing_test_profile_failed, - ) - from .lint.nfcore_yml import ( # type: ignore[misc] - test_nfcore_yml_fail_nfcore_version, - test_nfcore_yml_fail_repo_type, - test_nfcore_yml_pass, - ) - from .lint.template_strings import ( # type: ignore[misc] - test_template_strings, - test_template_strings_ignore_file, - test_template_strings_ignored, - ) - from .lint.version_consistency import test_version_consistency # type: ignore[misc] + # from .lint.nextflow_config import ( # type: ignore[misc] + # test_allow_params_reference_in_main_nf, + # test_catch_params_assignment_in_main_nf, + # test_default_values_fail, + # test_default_values_float, + # test_default_values_float_fail, + # test_default_values_ignored, + # test_default_values_match, + # test_nextflow_config_bad_name_fail, + # test_nextflow_config_dev_in_release_mode_failed, + # test_nextflow_config_example_pass, + # test_nextflow_config_missing_test_profile_failed, + # ) + # from .lint.nfcore_yml import ( # type: ignore[misc] + # test_nfcore_yml_fail_nfcore_version, + # test_nfcore_yml_fail_repo_type, + # test_nfcore_yml_pass, + # ) + # from .lint.template_strings import ( # type: ignore[misc] + # test_template_strings, + # test_template_strings_ignore_file, + # test_template_strings_ignored, + # ) + # from .lint.version_consistency import test_version_consistency # type: ignore[misc] From fcc43fd0c337ead404fba843eab51820d0f014a9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 14:51:51 +0200 Subject: [PATCH 157/574] add more tests to CI --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 4e873385e8..fea96b4526 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -67,7 +67,7 @@ jobs: - name: List tests id: list_tests run: | - echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT + echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT outputs: tests: ${{ steps.list_tests.outputs.tests }} From a779d12b7fff23ce9e93b905f49f37221276af43 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 15:15:40 +0200 Subject: [PATCH 158/574] simplify sed command --- .github/workflows/pytest.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index fea96b4526..18f9b28098 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -67,7 +67,7 @@ jobs: - name: List tests id: list_tests run: | - echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT + echo "tests=$(find tests/**/test_* | tac | sed 's/.*\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT outputs: tests: ${{ steps.list_tests.outputs.tests }} @@ -132,7 +132,7 @@ jobs: - name: Test with pytest run: | - python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$? + python3 -m pytest tests/**/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$? # don't fail if no tests were collected, e.g. for test_licence.py if [ "${exit_code}" -eq 5 ]; then echo "No tests were collected" From ca0769bd76b207881a8e77d3a18f3902b2307474 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 15:31:01 +0200 Subject: [PATCH 159/574] fix ci tests --- .github/workflows/pytest.yml | 11 +- tests/pipelines/test_lint.py | 284 +++++++++++++++-------------------- 2 files changed, 133 insertions(+), 162 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 18f9b28098..72bacaeab9 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -67,7 +67,7 @@ jobs: - name: List tests id: list_tests run: | - echo "tests=$(find tests/**/test_* | tac | sed 's/.*\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT + echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT outputs: tests: ${{ steps.list_tests.outputs.tests }} @@ -132,7 +132,7 @@ jobs: - name: Test with pytest run: | - python3 -m pytest tests/**/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$? + python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$? # don't fail if no tests were collected, e.g. for test_licence.py if [ "${exit_code}" -eq 5 ]; then echo "No tests were collected" @@ -149,10 +149,15 @@ jobs: name: Snapshot Report ${{ matrix.test }} path: ./snapshot_report.html + - name: remove slashes from test name + run: | + test=$(echo ${{ matrix.test }} | sed 's/\//__/g') + echo "test=${test}" >> $GITHUB_ENV + - name: Upload coverage uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: - name: coverage_${{ matrix.test }} + name: coverage_${{ env.test }} path: .coverage coverage: diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index b3eac17cb8..ab8bcf6b24 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -23,162 +23,128 @@ def setUp(self) -> None: ########################## # CORE lint.py FUNCTIONS # ########################## -def test_run_linting_function(self): - """Run the master run_linting() function in lint.py - - We don't really check any of this code as it's just a series of function calls - and we're testing each of those individually. This is mostly to check for syntax errors.""" - nf_core.pipelines.lint.run_linting(self.pipeline_dir, False) - - -def test_init_pipeline_lint(self): - """Simply create a PipelineLint object. - - This checks that all of the lint test imports are working properly, - we also check that the git sha was found and that the release flag works properly - """ - lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True) - - # Tests that extra test is added for release mode - assert "version_consistency" in lint_obj.lint_tests - assert lint_obj.git_sha - # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash - assert len(lint_obj.git_sha) > 0 - - -def test_load_lint_config_not_found(self): - """Try to load a linting config file that doesn't exist""" - self.lint_obj._load_lint_config() - assert self.lint_obj.lint_config == {} - - -def test_load_lint_config_ignore_all_tests(self): - """Try to load a linting config file that ignores all tests""" - - # Make a copy of the test pipeline and create a lint object - new_pipeline = self._make_pipeline_copy() - lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) - - # Make a config file listing all test names - config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} - with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: - yaml.dump(config_dict, fh) - - # Load the new lint config file and check - lint_obj._load_lint_config() - assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests) - - # Try running linting and make sure that all tests are ignored - lint_obj._lint_pipeline() - assert len(lint_obj.passed) == 0 - assert len(lint_obj.warned) == 0 - assert len(lint_obj.failed) == 0 - assert len(lint_obj.ignored) == len(lint_obj.lint_tests) - - -@with_temporary_folder -def test_json_output(self, tmp_dir): - """ - Test creation of a JSON file with lint results - - Expected JSON output: - { - "nf_core_tools_version": "1.10.dev0", - "date_run": "2020-06-05 10:56:42", - "tests_pass": [ - [ 1, "This test passed"], - [ 2, "This test also passed"] - ], - "tests_warned": [ - [ 2, "This test gave a warning"] - ], - "tests_failed": [], - "num_tests_pass": 2, - "num_tests_warned": 1, - "num_tests_failed": 0, - "has_tests_pass": true, - "has_tests_warned": true, - "has_tests_failed": false - } - """ - self.lint_obj.passed.append(("test_one", "This test passed")) - self.lint_obj.passed.append(("test_two", "This test also passed")) - self.lint_obj.warned.append(("test_three", "This test gave a warning")) - - # Make a temp dir for the JSON output - json_fn = Path(tmp_dir, "lint_results.json") - self.lint_obj._save_json_results(json_fn) - - # Load created JSON file and check its contents - with open(json_fn) as fh: - try: - saved_json = json.load(fh) - except json.JSONDecodeError as e: - raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}") - assert saved_json["num_tests_pass"] > 0 - assert saved_json["num_tests_warned"] > 0 - assert saved_json["num_tests_ignored"] == 0 - assert saved_json["num_tests_failed"] == 0 - assert saved_json["has_tests_pass"] - assert saved_json["has_tests_warned"] - assert not saved_json["has_tests_ignored"] - assert not saved_json["has_tests_failed"] - - -def test_wrap_quotes(self): - md = self.lint_obj._wrap_quotes(["one", "two", "three"]) - assert md == "`one` or `two` or `three`" - - -def test_sphinx_md_files(self): - """Check that we have .md files for all lint module code, - and that there are no unexpected files (eg. deleted lint tests)""" - - docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests") - - # Get list of existing .md files - existing_docs = [] - existing_docs = [ - str(Path(docs_basedir, fn)) - for fn in Path(docs_basedir).iterdir() - if fn.match("*.md") and not fn.match("index.md") - ] - - # Check .md files against each test name - lint_obj = nf_core.pipelines.lint.PipelineLint("", True) - for test_name in lint_obj.lint_tests: - fn = Path(docs_basedir, f"{test_name}.md") - assert fn.exists(), f"Could not find lint docs .md file: {fn}" - existing_docs.remove(str(fn)) - - # Check that we have no remaining .md files that we didn't expect - assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}" - - ####################### - # SPECIFIC LINT TESTS # - ####################### - - # from .lint.nextflow_config import ( # type: ignore[misc] - # test_allow_params_reference_in_main_nf, - # test_catch_params_assignment_in_main_nf, - # test_default_values_fail, - # test_default_values_float, - # test_default_values_float_fail, - # test_default_values_ignored, - # test_default_values_match, - # test_nextflow_config_bad_name_fail, - # test_nextflow_config_dev_in_release_mode_failed, - # test_nextflow_config_example_pass, - # test_nextflow_config_missing_test_profile_failed, - # ) - # from .lint.nfcore_yml import ( # type: ignore[misc] - # test_nfcore_yml_fail_nfcore_version, - # test_nfcore_yml_fail_repo_type, - # test_nfcore_yml_pass, - # ) - # from .lint.template_strings import ( # type: ignore[misc] - # test_template_strings, - # test_template_strings_ignore_file, - # test_template_strings_ignored, - # ) - # from .lint.version_consistency import test_version_consistency # type: ignore[misc] +class TestPipelinesLint(TestLint): + def test_run_linting_function(self): + """Run the master run_linting() function in lint.py + + We don't really check any of this code as it's just a series of function calls + and we're testing each of those individually. This is mostly to check for syntax errors.""" + nf_core.pipelines.lint.run_linting(self.pipeline_dir, False) + + def test_init_pipeline_lint(self): + """Simply create a PipelineLint object. + + This checks that all of the lint test imports are working properly, + we also check that the git sha was found and that the release flag works properly + """ + lint_obj = nf_core.pipelines.lint.PipelineLint(self.pipeline_dir, True) + + # Tests that extra test is added for release mode + assert "version_consistency" in lint_obj.lint_tests + assert lint_obj.git_sha + # Tests that parent nf_core.utils.Pipeline class __init__() is working to find git hash + assert len(lint_obj.git_sha) > 0 + + def test_load_lint_config_not_found(self): + """Try to load a linting config file that doesn't exist""" + self.lint_obj._load_lint_config() + assert self.lint_obj.lint_config == {} + + def test_load_lint_config_ignore_all_tests(self): + """Try to load a linting config file that ignores all tests""" + + # Make a copy of the test pipeline and create a lint object + new_pipeline = self._make_pipeline_copy() + lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) + + # Make a config file listing all test names + config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} + with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: + yaml.dump(config_dict, fh) + + # Load the new lint config file and check + lint_obj._load_lint_config() + assert sorted(list(lint_obj.lint_config.keys())) == sorted(lint_obj.lint_tests) + + # Try running linting and make sure that all tests are ignored + lint_obj._lint_pipeline() + assert len(lint_obj.passed) == 0 + assert len(lint_obj.warned) == 0 + assert len(lint_obj.failed) == 0 + assert len(lint_obj.ignored) == len(lint_obj.lint_tests) + + @with_temporary_folder + def test_json_output(self, tmp_dir): + """ + Test creation of a JSON file with lint results + + Expected JSON output: + { + "nf_core_tools_version": "1.10.dev0", + "date_run": "2020-06-05 10:56:42", + "tests_pass": [ + [ 1, "This test passed"], + [ 2, "This test also passed"] + ], + "tests_warned": [ + [ 2, "This test gave a warning"] + ], + "tests_failed": [], + "num_tests_pass": 2, + "num_tests_warned": 1, + "num_tests_failed": 0, + "has_tests_pass": true, + "has_tests_warned": true, + "has_tests_failed": false + } + """ + self.lint_obj.passed.append(("test_one", "This test passed")) + self.lint_obj.passed.append(("test_two", "This test also passed")) + self.lint_obj.warned.append(("test_three", "This test gave a warning")) + + # Make a temp dir for the JSON output + json_fn = Path(tmp_dir, "lint_results.json") + self.lint_obj._save_json_results(json_fn) + + # Load created JSON file and check its contents + with open(json_fn) as fh: + try: + saved_json = json.load(fh) + except json.JSONDecodeError as e: + raise UserWarning(f"Unable to load JSON file '{json_fn}' due to error {e}") + assert saved_json["num_tests_pass"] > 0 + assert saved_json["num_tests_warned"] > 0 + assert saved_json["num_tests_ignored"] == 0 + assert saved_json["num_tests_failed"] == 0 + assert saved_json["has_tests_pass"] + assert saved_json["has_tests_warned"] + assert not saved_json["has_tests_ignored"] + assert not saved_json["has_tests_failed"] + + def test_wrap_quotes(self): + md = self.lint_obj._wrap_quotes(["one", "two", "three"]) + assert md == "`one` or `two` or `three`" + + def test_sphinx_md_files(self): + """Check that we have .md files for all lint module code, + and that there are no unexpected files (eg. deleted lint tests)""" + + docs_basedir = Path(Path(__file__).parent.parent.parent, "docs", "api", "_src", "pipeline_lint_tests") + + # Get list of existing .md files + existing_docs = [] + existing_docs = [ + str(Path(docs_basedir, fn)) + for fn in Path(docs_basedir).iterdir() + if fn.match("*.md") and not fn.match("index.md") + ] + + # Check .md files against each test name + lint_obj = nf_core.pipelines.lint.PipelineLint("", True) + for test_name in lint_obj.lint_tests: + fn = Path(docs_basedir, f"{test_name}.md") + assert fn.exists(), f"Could not find lint docs .md file: {fn}" + existing_docs.remove(str(fn)) + + # Check that we have no remaining .md files that we didn't expect + assert len(existing_docs) == 0, f"Unexpected lint docs .md files found: {', '.join(existing_docs)}" From 768cfc31fff05bf4136d987f7dc811599766b7f9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 15:36:13 +0200 Subject: [PATCH 160/574] find ALL test files in CI --- .github/workflows/pytest.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 72bacaeab9..dc88031886 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -67,7 +67,7 @@ jobs: - name: List tests id: list_tests run: | - echo "tests=$(find tests/**/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT + echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT outputs: tests: ${{ steps.list_tests.outputs.tests }} From 3aee9cbfd0950a7f78cfcd273ce7a61bbc3d4ed9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 15:49:21 +0200 Subject: [PATCH 161/574] add pytest-asyncio --- requirements-dev.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-dev.txt b/requirements-dev.txt index 2c7bb0c8cf..82087edcba 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -14,6 +14,7 @@ types-Markdown types-PyYAML types-requests types-setuptools +pytest-asyncio pytest-textual-snapshot==0.4.0 pytest-workflow>=2.0.0 pytest>=8.0.0 From 09b0623a9682b58b1be9b5fe12bba117805681b4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 17 Jul 2024 16:10:41 +0200 Subject: [PATCH 162/574] convert subworkflow tests to new structure --- nf_core/modules/bump_versions.py | 7 +- nf_core/modules/modules_json.py | 3 +- tests/subworkflows/create.py | 110 -------- tests/subworkflows/info.py | 64 ----- tests/subworkflows/install.py | 154 ----------- tests/subworkflows/lint.py | 403 ----------------------------- tests/subworkflows/list.py | 49 ---- tests/subworkflows/remove.py | 100 ------- tests/subworkflows/test_create.py | 109 ++++++++ tests/subworkflows/test_info.py | 63 +++++ tests/subworkflows/test_install.py | 157 +++++++++++ tests/subworkflows/test_lint.py | 391 ++++++++++++++++++++++++++++ tests/subworkflows/test_list.py | 48 ++++ tests/subworkflows/test_remove.py | 101 ++++++++ tests/subworkflows/test_update.py | 370 ++++++++++++++++++++++++++ tests/subworkflows/update.py | 376 --------------------------- tests/test_subworkflows.py | 105 +++----- 17 files changed, 1278 insertions(+), 1332 deletions(-) delete mode 100644 tests/subworkflows/create.py delete mode 100644 tests/subworkflows/info.py delete mode 100644 tests/subworkflows/install.py delete mode 100644 tests/subworkflows/lint.py delete mode 100644 tests/subworkflows/list.py delete mode 100644 tests/subworkflows/remove.py create mode 100644 tests/subworkflows/test_create.py create mode 100644 tests/subworkflows/test_info.py create mode 100644 tests/subworkflows/test_install.py create mode 100644 tests/subworkflows/test_lint.py create mode 100644 tests/subworkflows/test_list.py create mode 100644 tests/subworkflows/test_remove.py create mode 100644 tests/subworkflows/test_update.py delete mode 100644 tests/subworkflows/update.py diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 6556dcf0f4..fae3793079 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -176,7 +176,12 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: try: response = nf_core.utils.anaconda_package(bp) except (LookupError, ValueError): - self.failed.append((f"Conda version not specified correctly: {module.main_nf}", module.component_name)) + self.failed.append( + ( + f"Conda version not specified correctly: {module.main_nf.relative_to(self.dir)}", + module.component_name, + ) + ) return False # Check that required version is available at all diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 0d6779a8d4..2c2f1a32c9 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -6,6 +6,7 @@ import shutil import tempfile from pathlib import Path +from typing import Union import git import questionary @@ -31,7 +32,7 @@ class ModulesJson: An object for handling a 'modules.json' file in a pipeline """ - def __init__(self, pipeline_dir: str): + def __init__(self, pipeline_dir: Union[str, Path]): """ Initialise the object. diff --git a/tests/subworkflows/create.py b/tests/subworkflows/create.py deleted file mode 100644 index 002b889671..0000000000 --- a/tests/subworkflows/create.py +++ /dev/null @@ -1,110 +0,0 @@ -import os -import shutil -from pathlib import Path -from unittest import mock - -import pytest -import yaml -from git.repo import Repo - -import nf_core.subworkflows -from tests.utils import GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL - - -def test_subworkflows_create_succeed(self): - """Succeed at creating a subworkflow from the template inside a pipeline""" - subworkflow_create = nf_core.subworkflows.SubworkflowCreate( - self.pipeline_dir, "test_subworkflow_local", "@author", True - ) - subworkflow_create.create() - assert os.path.exists(os.path.join(self.pipeline_dir, "subworkflows", "local", "test_subworkflow_local.nf")) - - -def test_subworkflows_create_fail_exists(self): - """Fail at creating the same subworkflow twice""" - subworkflow_create = nf_core.subworkflows.SubworkflowCreate( - self.pipeline_dir, "test_subworkflow2", "@author", False - ) - subworkflow_create.create() - with pytest.raises(UserWarning) as excinfo: - subworkflow_create.create() - assert "Subworkflow file exists already" in str(excinfo.value) - - -def test_subworkflows_create_nfcore_modules(self): - """Create a subworkflow in nf-core/modules clone""" - subworkflow_create = nf_core.subworkflows.SubworkflowCreate( - self.nfcore_modules, "test_subworkflow", "@author", force=True - ) - subworkflow_create.create() - assert os.path.exists(os.path.join(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf")) - assert os.path.exists( - os.path.join(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test") - ) - - -@mock.patch("rich.prompt.Confirm.ask") -def test_subworkflows_migrate(self, mock_rich_ask): - """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test""" - pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools") - subworkflow_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "bam_stats_samtools") - - # Clone modules repo with pytests - shutil.rmtree(self.nfcore_modules) - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) - with open(subworkflow_dir / "main.nf") as fh: - old_main_nf = fh.read() - with open(subworkflow_dir / "meta.yml") as fh: - old_meta_yml = fh.read() - - # Create a subworkflow with --migrate-pytest - mock_rich_ask.return_value = True - subworkflow_create = nf_core.subworkflows.SubworkflowCreate( - self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True - ) - subworkflow_create.create() - - with open(subworkflow_dir / "main.nf") as fh: - new_main_nf = fh.read() - with open(subworkflow_dir / "meta.yml") as fh: - new_meta_yml = fh.read() - nextflow_config = subworkflow_dir / "tests" / "nextflow.config" - - # Check that old files have been copied to the new module - assert old_main_nf == new_main_nf - assert old_meta_yml == new_meta_yml - assert nextflow_config.is_file() - - # Check that pytest folder is deleted - assert not pytest_dir.is_dir() - - # Check that pytest_modules.yml is updated - with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: - modules_yml = yaml.safe_load(fh) - assert "subworkflows/bam_stats_samtools" not in modules_yml.keys() - - -@mock.patch("rich.prompt.Confirm.ask") -def test_subworkflows_migrate_no_delete(self, mock_rich_ask): - """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test. - Test that pytest directory is not deleted.""" - pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools") - - # Clone modules repo with pytests - shutil.rmtree(self.nfcore_modules) - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) - - # Create a module with --migrate-pytest - mock_rich_ask.return_value = False - module_create = nf_core.subworkflows.SubworkflowCreate( - self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True - ) - module_create.create() - - # Check that pytest folder is not deleted - assert pytest_dir.is_dir() - - # Check that pytest_modules.yml is updated - with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: - modules_yml = yaml.safe_load(fh) - assert "subworkflows/bam_stats_samtools" not in modules_yml.keys() diff --git a/tests/subworkflows/info.py b/tests/subworkflows/info.py deleted file mode 100644 index 688120ac02..0000000000 --- a/tests/subworkflows/info.py +++ /dev/null @@ -1,64 +0,0 @@ -from rich.console import Console - -import nf_core.subworkflows - -from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL - - -def test_subworkflows_info_remote(self): - """Test getting info about a remote subworkflow""" - mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools") - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Subworkflow: bam_sort_stats_samtools" in output - assert "Inputs" in output - assert "Outputs" in output - - -def test_subworkflows_info_remote_gitlab(self): - """Test getting info about a subworkflow in the remote gitlab repo""" - mods_info = nf_core.subworkflows.SubworkflowInfo( - self.pipeline_dir, "bam_sort_stats_samtools", remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH - ) - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Subworkflow: bam_sort_stats_samtools" in output - assert "Inputs" in output - assert "Outputs" in output - assert "--git-remote" in output - - -def test_subworkflows_info_local(self): - """Test getting info about a locally installed subworkflow""" - self.subworkflow_install.install("bam_sort_stats_samtools") - mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools") - mods_info.local = True - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Subworkflow: bam_sort_stats_samtools" in output - assert "Inputs" in output - assert "Outputs" in output - - -def test_subworkflows_info_in_modules_repo(self): - """Test getting info about a locally subworkflow in the modules repo""" - self.subworkflow_install.install("bam_sort_stats_samtools") - mods_info = nf_core.subworkflows.SubworkflowInfo(self.nfcore_modules, "bam_sort_stats_samtools") - mods_info.local = True - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Subworkflow: bam_sort_stats_samtools" in output - assert "Inputs" in output - assert "Outputs" in output diff --git a/tests/subworkflows/install.py b/tests/subworkflows/install.py deleted file mode 100644 index dfe71686fb..0000000000 --- a/tests/subworkflows/install.py +++ /dev/null @@ -1,154 +0,0 @@ -import os - -import pytest - -from nf_core.modules.modules_json import ModulesJson -from nf_core.subworkflows.install import SubworkflowInstall - -from ..utils import ( - GITLAB_BRANCH_TEST_BRANCH, - GITLAB_REPO, - GITLAB_SUBWORKFLOWS_BRANCH, - GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, - GITLAB_URL, - with_temporary_folder, -) - - -def test_subworkflow_install_nopipeline(self): - """Test installing a subworkflow - no pipeline given""" - self.subworkflow_install.dir = None - assert self.subworkflow_install.install("foo") is False - - -@with_temporary_folder -def test_subworkflows_install_emptypipeline(self, tmpdir): - """Test installing a subworkflow - empty dir given""" - os.mkdir(os.path.join(tmpdir, "nf-core-pipe")) - self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe") - with pytest.raises(UserWarning) as excinfo: - self.subworkflow_install.install("foo") - assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) - - -def test_subworkflows_install_nosubworkflow(self): - """Test installing a subworkflow - unrecognised subworkflow given""" - assert self.subworkflow_install.install("foo") is False - - -def test_subworkflows_install_bam_sort_stats_samtools(self): - """Test installing a subworkflow - bam_sort_stats_samtools""" - assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False - subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools") - sub_subworkflow_path = os.path.join(self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools") - samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort") - samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") - samtools_idxstats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats") - samtools_flagstat_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat") - assert os.path.exists(subworkflow_path) - assert os.path.exists(sub_subworkflow_path) - assert os.path.exists(samtools_index_path) - assert os.path.exists(samtools_sort_path) - assert os.path.exists(samtools_stats_path) - assert os.path.exists(samtools_idxstats_path) - assert os.path.exists(samtools_flagstat_path) - - -def test_subworkflows_install_bam_sort_stats_samtools_twice(self): - """Test installing a subworkflow - bam_sort_stats_samtools already there""" - self.subworkflow_install.install("bam_sort_stats_samtools") - assert self.subworkflow_install.install("bam_sort_stats_samtools") is False - - -def test_subworkflows_install_from_gitlab(self): - """Test installing a subworkflow from GitLab""" - assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is True - # Verify that the branch entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - assert ( - modules_json.get_component_branch(self.component_type, "bam_stats_samtools", GITLAB_URL, GITLAB_REPO) - == GITLAB_SUBWORKFLOWS_BRANCH - ) - - -def test_subworkflows_install_different_branch_fail(self): - """Test installing a subworkflow from a different branch""" - install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) - # The bam_stats_samtools subworkflow does not exists in the branch-test branch - assert install_obj.install("bam_stats_samtools") is False - - -def test_subworkflows_install_tracking(self): - """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" - self.subworkflow_install.install("bam_sort_stats_samtools") - - # Verify that the installed_by entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - mod_json = modules_json.get_modules_json() - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ - "bam_sort_stats_samtools" - ]["installed_by"] == ["subworkflows"] - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][ - "installed_by" - ] == ["bam_sort_stats_samtools"] - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/stats"][ - "installed_by" - ] == ["bam_stats_samtools"] - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/sort"][ - "installed_by" - ] == ["bam_sort_stats_samtools"] - - # Clean directory - self.subworkflow_remove.remove("bam_sort_stats_samtools") - - -def test_subworkflows_install_tracking_added_already_installed(self): - """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" - self.subworkflow_install.install("bam_sort_stats_samtools") - self.subworkflow_install.install("bam_stats_samtools") - - # Verify that the installed_by entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - mod_json = modules_json.get_modules_json() - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ - "bam_sort_stats_samtools" - ]["installed_by"] == ["subworkflows"] - assert sorted( - mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][ - "installed_by" - ] - ) == sorted(["bam_sort_stats_samtools", "subworkflows"]) - - # Clean directory - self.subworkflow_remove.remove("bam_sort_stats_samtools") - self.subworkflow_remove.remove("bam_stats_samtools") - - -def test_subworkflows_install_tracking_added_super_subworkflow(self): - """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" - self.subworkflow_install.install("bam_stats_samtools") - self.subworkflow_install.install("bam_sort_stats_samtools") - - # Verify that the installed_by entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - mod_json = modules_json.get_modules_json() - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ - "bam_sort_stats_samtools" - ]["installed_by"] == ["subworkflows"] - assert sorted( - mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"]["bam_stats_samtools"][ - "installed_by" - ] - ) == sorted(["subworkflows", "bam_sort_stats_samtools"]) - - -def test_subworkflows_install_alternate_remote(self): - """Test installing a module from a different remote with the same organization path""" - install_obj = SubworkflowInstall( - self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH - ) - # Install a subworkflow from GitLab which is also installed from GitHub with the same org_path - with pytest.raises(Exception) as excinfo: - install_obj.install("fastqc") - assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py deleted file mode 100644 index 540f421ad2..0000000000 --- a/tests/subworkflows/lint.py +++ /dev/null @@ -1,403 +0,0 @@ -import json -import shutil -from pathlib import Path - -import pytest - -import nf_core.subworkflows - -from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL - - -def test_subworkflows_lint(self): - """Test linting the fastq_align_bowtie2 subworkflow""" - self.subworkflow_install.install("fastq_align_bowtie2") - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) - subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2") - assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_empty(self): - """Test linting a pipeline with no subworkflows installed""" - self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True) - self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True) - self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True) - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) - - -def test_subworkflows_lint_new_subworkflow(self): - """lint a new subworkflow""" - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=True, all_subworkflows=True) - assert len(subworkflow_lint.failed) == 0 - - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_no_gitlab(self): - """Test linting a pipeline with no subworkflows installed""" - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) - - -def test_subworkflows_lint_gitlab_subworkflows(self): - """Lint subworkflows from a different remote""" - self.subworkflow_install_gitlab.install("bam_stats_samtools") - subworkflow_lint = nf_core.subworkflows.SubworkflowLint( - dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH - ) - subworkflow_lint.lint(print_results=False, all_subworkflows=True) - assert len(subworkflow_lint.failed) == 0 - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_multiple_remotes(self): - """Lint subworkflows from a different remote""" - self.subworkflow_install_gitlab.install("bam_stats_samtools") - self.subworkflow_install.install("fastq_align_bowtie2") - subworkflow_lint = nf_core.subworkflows.SubworkflowLint( - dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH - ) - subworkflow_lint.lint(print_results=False, all_subworkflows=True) - assert len(subworkflow_lint.failed) == 0 - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_snapshot_file(self): - """Test linting a subworkflow with a snapshot file""" - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_snapshot_file_missing_fail(self): - """Test linting a subworkflow with a snapshot file missing, which should fail""" - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ).unlink() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ).touch() - assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_snapshot_file_not_needed(self): - """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" - with open( - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test", - ) - ) as fh: - content = fh.read() - new_content = content.replace("snapshot(", "snap (") - with open( - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test", - ), - "w", - ) as fh: - fh.write(new_content) - - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ).unlink() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ).touch() - assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - - -def test_subworkflows_lint_less_than_two_modules_warning(self): - """Test linting a subworkflow with less than two modules""" - self.subworkflow_install.install("bam_stats_samtools") - # Remove two modules - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ) - ) as fh: - content = fh.read() - new_content = content.replace( - "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'", - "", - ) - new_content = new_content.replace( - "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'", - "", - ) - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ), - "w", - ) as fh: - fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) - subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") - assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) > 0 - assert subworkflow_lint.warned[0].lint_test == "main_nf_include" - # cleanup - self.subworkflow_remove.remove("bam_stats_samtools", force=True) - - -def test_subworkflows_lint_include_multiple_alias(self): - """Test linting a subworkflow with multiple include methods""" - self.subworkflow_install.install("bam_stats_samtools") - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ) - ) as fh: - content = fh.read() - new_content = content.replace("SAMTOOLS_STATS", "SAMTOOLS_STATS_1") - new_content = new_content.replace( - "include { SAMTOOLS_STATS_1 ", - "include { SAMTOOLS_STATS as SAMTOOLS_STATS_1; SAMTOOLS_STATS as SAMTOOLS_STATS_2 ", - ) - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ), - "w", - ) as fh: - fh.write(new_content) - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) - subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") - assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) == 2 - assert any( - [ - x.message == "Included component 'SAMTOOLS_STATS_1' versions are added in main.nf" - for x in subworkflow_lint.passed - ] - ) - assert any([x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed]) - assert any( - [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned] - ) - - # cleanup - self.subworkflow_remove.remove("bam_stats_samtools", force=True) - - -def test_subworkflows_lint_capitalization_fail(self): - """Test linting a subworkflow with a capitalization fail""" - self.subworkflow_install.install("bam_stats_samtools") - # change workflow name to lowercase - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ) - ) as fh: - content = fh.read() - new_content = content.replace("workflow BAM_STATS_SAMTOOLS {", "workflow bam_stats_samtools {") - with open( - Path( - self.pipeline_dir, - "subworkflows", - "nf-core", - "bam_stats_samtools", - "main.nf", - ), - "w", - ) as fh: - fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) - subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") - assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - assert any([x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed]) - - # cleanup - self.subworkflow_remove.remove("bam_stats_samtools", force=True) - - -def test_subworkflows_absent_version(self): - """Test linting a nf-test module if the versions is absent in the snapshot file `""" - snap_file = Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ) - with open(snap_file) as fh: - content = fh.read() - new_content = content.replace("versions", "foo") - with open(snap_file, "w") as fh: - fh.write(new_content) - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 0 - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}" - assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned]) - - # cleanup - with open(snap_file, "w") as fh: - fh.write(content) - - -def test_subworkflows_missing_test_dir(self): - """Test linting a nf-test subworkflow if the tests directory is missing""" - test_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests") - test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy") - shutil.rmtree(test_dir) - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 0 - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}" - assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned]) - - # cleanup - shutil.copytree(test_dir_copy, test_dir) - - -def test_subworkflows_missing_main_nf(self): - """Test linting a nf-test subworkflow if the main.nf file is missing""" - main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf") - main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy") - main_nf.unlink() - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - assert subworkflow_lint.failed[0].lint_test == "main_nf_exists" - - # cleanup - shutil.copy(main_nf_copy, main_nf) - - -def test_subworkflows_empty_file_in_snapshot(self): - """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" - snap_file = Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ) - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - assert subworkflow_lint.failed[0].lint_test == "test_snap_md5sum" - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - - -def test_subworkflows_empty_file_in_stub_snapshot(self): - """Test linting a nf-test subworkflow with an empty file sha sum in the stub test snapshot, which should make it not fail""" - snap_file = Path( - self.nfcore_modules, - "subworkflows", - "nf-core", - "test_subworkflow", - "tests", - "main.nf.test.snap", - ) - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - assert any(x.lint_test == "test_snap_md5sum" for x in subworkflow_lint.passed) - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) diff --git a/tests/subworkflows/list.py b/tests/subworkflows/list.py deleted file mode 100644 index c65999d42c..0000000000 --- a/tests/subworkflows/list.py +++ /dev/null @@ -1,49 +0,0 @@ -from rich.console import Console - -import nf_core.subworkflows - -from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL - - -def test_subworkflows_list_remote(self): - """Test listing available subworkflows""" - subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True) - listed_subworkflows = subworkflows_list.list_components() - console = Console(record=True) - console.print(listed_subworkflows) - output = console.export_text() - assert "bam_stats" in output - - -def test_subworkflows_list_remote_gitlab(self): - """Test listing the subworkflows in the remote gitlab repo""" - subworkflows_list = nf_core.subworkflows.SubworkflowList( - None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH - ) - listed_subworkflows = subworkflows_list.list_components() - console = Console(record=True) - console.print(listed_subworkflows) - output = console.export_text() - assert "bam_stats" in output - - -def test_subworkflows_install_and_list_subworkflows(self): - """Test listing locally installed subworkflows""" - self.subworkflow_install.install("bam_sort_stats_samtools") - subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False) - listed_subworkflows = subworkflows_list.list_components() - console = Console(record=True) - console.print(listed_subworkflows) - output = console.export_text() - assert "bam_stats" in output - - -def test_subworkflows_install_gitlab_and_list_subworkflows(self): - """Test listing locally installed subworkflows""" - self.subworkflow_install_gitlab.install("bam_sort_stats_samtools") - subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False) - listed_subworkflows = subworkflows_list.list_components() - console = Console(record=True) - console.print(listed_subworkflows) - output = console.export_text() - assert "bam_stats" in output diff --git a/tests/subworkflows/remove.py b/tests/subworkflows/remove.py deleted file mode 100644 index c6a3b98454..0000000000 --- a/tests/subworkflows/remove.py +++ /dev/null @@ -1,100 +0,0 @@ -from pathlib import Path - -from nf_core.modules.modules_json import ModulesJson - - -def test_subworkflows_remove_uninstalled_subworkflow(self): - """Test removing subworkflow without installing it""" - assert self.subworkflow_remove.remove("bam_sort_stats_samtools") is False - - -def test_subworkflows_remove_subworkflow(self): - """Test removing subworkflow and all it's dependencies after installing it""" - self.subworkflow_install.install("bam_sort_stats_samtools") - - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") - bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") - bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - ModulesJson(self.pipeline_dir) - mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() - assert self.subworkflow_remove.remove("bam_sort_stats_samtools") - mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json() - assert Path.exists(bam_sort_stats_samtools_path) is False - assert Path.exists(bam_stats_samtools_path) is False - assert Path.exists(samtools_index_path) is False - assert mod_json_before != mod_json_after - # assert subworkflows key is removed from modules.json - assert ( - "bam_sort_stats_samtools" - not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys() - ) - assert "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys() - - -def test_subworkflows_remove_subworkflow_keep_installed_module(self): - """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module""" - self.subworkflow_install.install("bam_sort_stats_samtools") - self.mods_install.install("samtools/index") - - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") - bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") - bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - - mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() - assert self.subworkflow_remove.remove("bam_sort_stats_samtools") - mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json() - - assert Path.exists(bam_sort_stats_samtools_path) is False - assert Path.exists(bam_stats_samtools_path) is False - assert Path.exists(samtools_index_path) is True - assert mod_json_before != mod_json_after - # assert subworkflows key is removed from modules.json - assert ( - "bam_sort_stats_samtools" - not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys() - ) - assert ( - "samtools/index" - in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys() - ) - - -def test_subworkflows_remove_one_of_two_subworkflow(self): - """Test removing subworkflow and all it's dependencies after installing it""" - self.subworkflow_install.install("bam_sort_stats_samtools") - self.subworkflow_install.install("bam_stats_samtools") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") - bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") - bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") - - assert self.subworkflow_remove.remove("bam_sort_stats_samtools") - - assert Path.exists(subworkflow_path) is True - assert Path.exists(bam_sort_stats_samtools_path) is False - assert Path.exists(bam_stats_samtools_path) is True - assert Path.exists(samtools_index_path) is False - assert Path.exists(samtools_stats_path) is True - self.subworkflow_remove.remove("bam_stats_samtools") - - -def test_subworkflows_remove_included_subworkflow(self): - """Test removing subworkflow which is installed by another subworkflow and all it's dependencies.""" - self.subworkflow_install.install("bam_sort_stats_samtools") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") - bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") - bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") - - assert self.subworkflow_remove.remove("bam_stats_samtools") is False - - assert Path.exists(subworkflow_path) is True - assert Path.exists(bam_sort_stats_samtools_path) is True - assert Path.exists(bam_stats_samtools_path) is True - assert Path.exists(samtools_index_path) is True - assert Path.exists(samtools_stats_path) is True - self.subworkflow_remove.remove("bam_sort_stats_samtools") diff --git a/tests/subworkflows/test_create.py b/tests/subworkflows/test_create.py new file mode 100644 index 0000000000..48cb482260 --- /dev/null +++ b/tests/subworkflows/test_create.py @@ -0,0 +1,109 @@ +import shutil +from pathlib import Path +from unittest import mock + +import pytest +import yaml +from git.repo import Repo + +import nf_core.subworkflows +from tests.utils import GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL + +from ..test_subworkflows import TestSubworkflows + + +class TestSubworkflowsCreate(TestSubworkflows): + def test_subworkflows_create_succeed(self): + """Succeed at creating a subworkflow from the template inside a pipeline""" + subworkflow_create = nf_core.subworkflows.SubworkflowCreate( + self.pipeline_dir, "test_subworkflow_local", "@author", True + ) + subworkflow_create.create() + assert Path(self.pipeline_dir, "subworkflows", "local", "test_subworkflow_local.nf").exists() + + def test_subworkflows_create_fail_exists(self): + """Fail at creating the same subworkflow twice""" + subworkflow_create = nf_core.subworkflows.SubworkflowCreate( + self.pipeline_dir, "test_subworkflow2", "@author", False + ) + subworkflow_create.create() + with pytest.raises(UserWarning) as excinfo: + subworkflow_create.create() + assert "Subworkflow file exists already" in str(excinfo.value) + + def test_subworkflows_create_nfcore_modules(self): + """Create a subworkflow in nf-core/modules clone""" + subworkflow_create = nf_core.subworkflows.SubworkflowCreate( + self.nfcore_modules, "test_subworkflow", "@author", force=True + ) + subworkflow_create.create() + assert Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf").exists() + + assert Path( + self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test" + ).exists() + + @mock.patch("rich.prompt.Confirm.ask") + def test_subworkflows_migrate(self, mock_rich_ask): + """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test""" + pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools") + subworkflow_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "bam_stats_samtools") + + # Clone modules repo with pytests + shutil.rmtree(self.nfcore_modules) + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) + with open(subworkflow_dir / "main.nf") as fh: + old_main_nf = fh.read() + with open(subworkflow_dir / "meta.yml") as fh: + old_meta_yml = fh.read() + + # Create a subworkflow with --migrate-pytest + mock_rich_ask.return_value = True + subworkflow_create = nf_core.subworkflows.SubworkflowCreate( + self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True + ) + subworkflow_create.create() + + with open(subworkflow_dir / "main.nf") as fh: + new_main_nf = fh.read() + with open(subworkflow_dir / "meta.yml") as fh: + new_meta_yml = fh.read() + nextflow_config = subworkflow_dir / "tests" / "nextflow.config" + + # Check that old files have been copied to the new module + assert old_main_nf == new_main_nf + assert old_meta_yml == new_meta_yml + assert nextflow_config.is_file() + + # Check that pytest folder is deleted + assert not pytest_dir.is_dir() + + # Check that pytest_modules.yml is updated + with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: + modules_yml = yaml.safe_load(fh) + assert "subworkflows/bam_stats_samtools" not in modules_yml.keys() + + @mock.patch("rich.prompt.Confirm.ask") + def test_subworkflows_migrate_no_delete(self, mock_rich_ask): + """Create a subworkflow with the --migrate-pytest option to convert pytest to nf-test. + Test that pytest directory is not deleted.""" + pytest_dir = Path(self.nfcore_modules, "tests", "subworkflows", "nf-core", "bam_stats_samtools") + + # Clone modules repo with pytests + shutil.rmtree(self.nfcore_modules) + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) + + # Create a module with --migrate-pytest + mock_rich_ask.return_value = False + module_create = nf_core.subworkflows.SubworkflowCreate( + self.nfcore_modules, "bam_stats_samtools", migrate_pytest=True + ) + module_create.create() + + # Check that pytest folder is not deleted + assert pytest_dir.is_dir() + + # Check that pytest_modules.yml is updated + with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: + modules_yml = yaml.safe_load(fh) + assert "subworkflows/bam_stats_samtools" not in modules_yml.keys() diff --git a/tests/subworkflows/test_info.py b/tests/subworkflows/test_info.py new file mode 100644 index 0000000000..cf0f492710 --- /dev/null +++ b/tests/subworkflows/test_info.py @@ -0,0 +1,63 @@ +from rich.console import Console + +import nf_core.subworkflows + +from ..test_subworkflows import TestSubworkflows +from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL + + +class TestSubworkflowsInfo(TestSubworkflows): + def test_subworkflows_info_remote(self): + """Test getting info about a remote subworkflow""" + mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools") + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Subworkflow: bam_sort_stats_samtools" in output + assert "Inputs" in output + assert "Outputs" in output + + def test_subworkflows_info_remote_gitlab(self): + """Test getting info about a subworkflow in the remote gitlab repo""" + mods_info = nf_core.subworkflows.SubworkflowInfo( + self.pipeline_dir, "bam_sort_stats_samtools", remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + ) + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Subworkflow: bam_sort_stats_samtools" in output + assert "Inputs" in output + assert "Outputs" in output + assert "--git-remote" in output + + def test_subworkflows_info_local(self): + """Test getting info about a locally installed subworkflow""" + self.subworkflow_install.install("bam_sort_stats_samtools") + mods_info = nf_core.subworkflows.SubworkflowInfo(self.pipeline_dir, "bam_sort_stats_samtools") + mods_info.local = True + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Subworkflow: bam_sort_stats_samtools" in output + assert "Inputs" in output + assert "Outputs" in output + + def test_subworkflows_info_in_modules_repo(self): + """Test getting info about a locally subworkflow in the modules repo""" + self.subworkflow_install.install("bam_sort_stats_samtools") + mods_info = nf_core.subworkflows.SubworkflowInfo(self.nfcore_modules, "bam_sort_stats_samtools") + mods_info.local = True + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Subworkflow: bam_sort_stats_samtools" in output + assert "Inputs" in output + assert "Outputs" in output diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py new file mode 100644 index 0000000000..e0b2fc1ab6 --- /dev/null +++ b/tests/subworkflows/test_install.py @@ -0,0 +1,157 @@ +import os +from pathlib import Path + +import pytest + +from nf_core.modules.modules_json import ModulesJson +from nf_core.subworkflows.install import SubworkflowInstall + +from ..test_subworkflows import TestSubworkflows +from ..utils import ( + GITLAB_BRANCH_TEST_BRANCH, + GITLAB_REPO, + GITLAB_SUBWORKFLOWS_BRANCH, + GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, + GITLAB_URL, + with_temporary_folder, +) + + +class TestSubworkflowsInstall(TestSubworkflows): + def test_subworkflow_install_nopipeline(self): + """Test installing a subworkflow - no pipeline given""" + assert self.subworkflow_install.dir is not None + self.subworkflow_install.dir = "" + assert self.subworkflow_install.install("foo") is False + + @with_temporary_folder + def test_subworkflows_install_emptypipeline(self, tmpdir): + """Test installing a subworkflow - empty dir given""" + + Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True) + self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe") + with pytest.raises(UserWarning) as excinfo: + self.subworkflow_install.install("foo") + assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) + + def test_subworkflows_install_nosubworkflow(self): + """Test installing a subworkflow - unrecognised subworkflow given""" + assert self.subworkflow_install.install("foo") is False + + def test_subworkflows_install_bam_sort_stats_samtools(self): + """Test installing a subworkflow - bam_sort_stats_samtools""" + assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False + subworkflow_path = os.path.join( + self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools" + ) + sub_subworkflow_path = os.path.join( + self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools" + ) + samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort") + samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") + samtools_idxstats_path = os.path.join( + self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats" + ) + samtools_flagstat_path = os.path.join( + self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat" + ) + assert os.path.exists(subworkflow_path) + assert os.path.exists(sub_subworkflow_path) + assert os.path.exists(samtools_index_path) + assert os.path.exists(samtools_sort_path) + assert os.path.exists(samtools_stats_path) + assert os.path.exists(samtools_idxstats_path) + assert os.path.exists(samtools_flagstat_path) + + def test_subworkflows_install_bam_sort_stats_samtools_twice(self): + """Test installing a subworkflow - bam_sort_stats_samtools already there""" + self.subworkflow_install.install("bam_sort_stats_samtools") + assert self.subworkflow_install.install("bam_sort_stats_samtools") is False + + def test_subworkflows_install_from_gitlab(self): + """Test installing a subworkflow from GitLab""" + assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is True + # Verify that the branch entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + assert ( + modules_json.get_component_branch(self.component_type, "bam_stats_samtools", GITLAB_URL, GITLAB_REPO) + == GITLAB_SUBWORKFLOWS_BRANCH + ) + + def test_subworkflows_install_different_branch_fail(self): + """Test installing a subworkflow from a different branch""" + install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) + # The bam_stats_samtools subworkflow does not exists in the branch-test branch + assert install_obj.install("bam_stats_samtools") is False + + def test_subworkflows_install_tracking(self): + """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" + self.subworkflow_install.install("bam_sort_stats_samtools") + + # Verify that the installed_by entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + mod_json = modules_json.get_modules_json() + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_sort_stats_samtools" + ]["installed_by"] == ["subworkflows"] + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_stats_samtools" + ]["installed_by"] == ["bam_sort_stats_samtools"] + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/stats"][ + "installed_by" + ] == ["bam_stats_samtools"] + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["samtools/sort"][ + "installed_by" + ] == ["bam_sort_stats_samtools"] + + # Clean directory + self.subworkflow_remove.remove("bam_sort_stats_samtools") + + def test_subworkflows_install_tracking_added_already_installed(self): + """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" + self.subworkflow_install.install("bam_sort_stats_samtools") + self.subworkflow_install.install("bam_stats_samtools") + + # Verify that the installed_by entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + mod_json = modules_json.get_modules_json() + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_sort_stats_samtools" + ]["installed_by"] == ["subworkflows"] + assert sorted( + mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_stats_samtools" + ]["installed_by"] + ) == sorted(["bam_sort_stats_samtools", "subworkflows"]) + + # Clean directory + self.subworkflow_remove.remove("bam_sort_stats_samtools") + self.subworkflow_remove.remove("bam_stats_samtools") + + def test_subworkflows_install_tracking_added_super_subworkflow(self): + """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" + self.subworkflow_install.install("bam_stats_samtools") + self.subworkflow_install.install("bam_sort_stats_samtools") + + # Verify that the installed_by entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + mod_json = modules_json.get_modules_json() + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_sort_stats_samtools" + ]["installed_by"] == ["subworkflows"] + assert sorted( + mod_json["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"]["nf-core"][ + "bam_stats_samtools" + ]["installed_by"] + ) == sorted(["subworkflows", "bam_sort_stats_samtools"]) + + def test_subworkflows_install_alternate_remote(self): + """Test installing a module from a different remote with the same organization path""" + install_obj = SubworkflowInstall( + self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH + ) + # Install a subworkflow from GitLab which is also installed from GitHub with the same org_path + with pytest.raises(Exception) as excinfo: + install_obj.install("fastqc") + assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py new file mode 100644 index 0000000000..f8c9bedbf3 --- /dev/null +++ b/tests/subworkflows/test_lint.py @@ -0,0 +1,391 @@ +import json +import shutil +from pathlib import Path + +import pytest + +import nf_core.subworkflows + +from ..test_subworkflows import TestSubworkflows +from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL + + +class TestSubworkflowsLint(TestSubworkflows): + def test_subworkflows_lint(self): + """Test linting the fastq_align_bowtie2 subworkflow""" + self.subworkflow_install.install("fastq_align_bowtie2") + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2") + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_empty(self): + """Test linting a pipeline with no subworkflows installed""" + self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True) + self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True) + self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True) + with pytest.raises(LookupError): + nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + + def test_subworkflows_lint_new_subworkflow(self): + """lint a new subworkflow""" + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=True, all_subworkflows=True) + assert len(subworkflow_lint.failed) == 0 + + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_no_gitlab(self): + """Test linting a pipeline with no subworkflows installed""" + with pytest.raises(LookupError): + nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + + def test_subworkflows_lint_gitlab_subworkflows(self): + """Lint subworkflows from a different remote""" + self.subworkflow_install_gitlab.install("bam_stats_samtools") + subworkflow_lint = nf_core.subworkflows.SubworkflowLint( + dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + ) + subworkflow_lint.lint(print_results=False, all_subworkflows=True) + assert len(subworkflow_lint.failed) == 0 + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_multiple_remotes(self): + """Lint subworkflows from a different remote""" + self.subworkflow_install_gitlab.install("bam_stats_samtools") + self.subworkflow_install.install("fastq_align_bowtie2") + subworkflow_lint = nf_core.subworkflows.SubworkflowLint( + dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + ) + subworkflow_lint.lint(print_results=False, all_subworkflows=True) + assert len(subworkflow_lint.failed) == 0 + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_snapshot_file(self): + """Test linting a subworkflow with a snapshot file""" + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_snapshot_file_missing_fail(self): + """Test linting a subworkflow with a snapshot file missing, which should fail""" + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).unlink() + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).touch() + assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_snapshot_file_not_needed(self): + """Test linting a subworkflow which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" + with open( + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test", + ) + ) as fh: + content = fh.read() + new_content = content.replace("snapshot(", "snap (") + with open( + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test", + ), + "w", + ) as fh: + fh.write(new_content) + + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).unlink() + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ).touch() + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_less_than_two_modules_warning(self): + """Test linting a subworkflow with less than two modules""" + self.subworkflow_install.install("bam_stats_samtools") + # Remove two modules + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: + content = fh.read() + new_content = content.replace( + "include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main'", + "", + ) + new_content = new_content.replace( + "include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main'", + "", + ) + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: + fh.write(new_content) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") + assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) > 0 + assert subworkflow_lint.warned[0].lint_test == "main_nf_include" + # cleanup + self.subworkflow_remove.remove("bam_stats_samtools", force=True) + + def test_subworkflows_lint_include_multiple_alias(self): + """Test linting a subworkflow with multiple include methods""" + self.subworkflow_install.install("bam_stats_samtools") + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: + content = fh.read() + new_content = content.replace("SAMTOOLS_STATS", "SAMTOOLS_STATS_1") + new_content = new_content.replace( + "include { SAMTOOLS_STATS_1 ", + "include { SAMTOOLS_STATS as SAMTOOLS_STATS_1; SAMTOOLS_STATS as SAMTOOLS_STATS_2 ", + ) + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: + fh.write(new_content) + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") + assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) == 2 + assert any( + [ + x.message == "Included component 'SAMTOOLS_STATS_1' versions are added in main.nf" + for x in subworkflow_lint.passed + ] + ) + assert any( + [x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed] + ) + assert any( + [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned] + ) + + # cleanup + self.subworkflow_remove.remove("bam_stats_samtools", force=True) + + def test_subworkflows_lint_capitalization_fail(self): + """Test linting a subworkflow with a capitalization fail""" + self.subworkflow_install.install("bam_stats_samtools") + # change workflow name to lowercase + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ) + ) as fh: + content = fh.read() + new_content = content.replace("workflow BAM_STATS_SAMTOOLS {", "workflow bam_stats_samtools {") + with open( + Path( + self.pipeline_dir, + "subworkflows", + "nf-core", + "bam_stats_samtools", + "main.nf", + ), + "w", + ) as fh: + fh.write(new_content) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") + assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + assert any([x.lint_test == "workflow_capitals" for x in subworkflow_lint.failed]) + + # cleanup + self.subworkflow_remove.remove("bam_stats_samtools", force=True) + + def test_subworkflows_absent_version(self): + """Test linting a nf-test module if the versions is absent in the snapshot file `""" + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) + with open(snap_file) as fh: + content = fh.read() + new_content = content.replace("versions", "foo") + with open(snap_file, "w") as fh: + fh.write(new_content) + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0 + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}" + assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned]) + + # cleanup + with open(snap_file, "w") as fh: + fh.write(content) + + def test_subworkflows_missing_test_dir(self): + """Test linting a nf-test subworkflow if the tests directory is missing""" + test_dir = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests") + test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy") + shutil.rmtree(test_dir) + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0 + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}" + assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned]) + + # cleanup + shutil.copytree(test_dir_copy, test_dir) + + def test_subworkflows_missing_main_nf(self): + """Test linting a nf-test subworkflow if the main.nf file is missing""" + main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf") + main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy") + main_nf.unlink() + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + assert subworkflow_lint.failed[0].lint_test == "main_nf_exists" + + # cleanup + shutil.copy(main_nf_copy, main_nf) + + def test_subworkflows_empty_file_in_snapshot(self): + """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + assert subworkflow_lint.failed[0].lint_test == "test_snap_md5sum" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + def test_subworkflows_empty_file_in_stub_snapshot(self): + """Test linting a nf-test subworkflow with an empty file sha sum in the stub test snapshot, which should make it not fail""" + snap_file = Path( + self.nfcore_modules, + "subworkflows", + "nf-core", + "test_subworkflow", + "tests", + "main.nf.test.snap", + ) + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + assert any(x.lint_test == "test_snap_md5sum" for x in subworkflow_lint.passed) + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py new file mode 100644 index 0000000000..5e4e6feb0a --- /dev/null +++ b/tests/subworkflows/test_list.py @@ -0,0 +1,48 @@ +from rich.console import Console + +import nf_core.subworkflows + +from ..test_subworkflows import TestSubworkflows +from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL + + +class TestSubworkflowsList(TestSubworkflows): + def test_subworkflows_list_remote(self): + """Test listing available subworkflows""" + subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True) + listed_subworkflows = subworkflows_list.list_components() + console = Console(record=True) + console.print(listed_subworkflows) + output = console.export_text() + assert "bam_stats" in output + + def test_subworkflows_list_remote_gitlab(self): + """Test listing the subworkflows in the remote gitlab repo""" + subworkflows_list = nf_core.subworkflows.SubworkflowList( + None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + ) + listed_subworkflows = subworkflows_list.list_components() + console = Console(record=True) + console.print(listed_subworkflows) + output = console.export_text() + assert "bam_stats" in output + + def test_subworkflows_install_and_list_subworkflows(self): + """Test listing locally installed subworkflows""" + self.subworkflow_install.install("bam_sort_stats_samtools") + subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False) + listed_subworkflows = subworkflows_list.list_components() + console = Console(record=True) + console.print(listed_subworkflows) + output = console.export_text() + assert "bam_stats" in output + + def test_subworkflows_install_gitlab_and_list_subworkflows(self): + """Test listing locally installed subworkflows""" + self.subworkflow_install_gitlab.install("bam_sort_stats_samtools") + subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False) + listed_subworkflows = subworkflows_list.list_components() + console = Console(record=True) + console.print(listed_subworkflows) + output = console.export_text() + assert "bam_stats" in output diff --git a/tests/subworkflows/test_remove.py b/tests/subworkflows/test_remove.py new file mode 100644 index 0000000000..61c016b232 --- /dev/null +++ b/tests/subworkflows/test_remove.py @@ -0,0 +1,101 @@ +from pathlib import Path + +from nf_core.modules.modules_json import ModulesJson + +from ..test_subworkflows import TestSubworkflows + + +class TestSubworkflowsRemove(TestSubworkflows): + def test_subworkflows_remove_uninstalled_subworkflow(self): + """Test removing subworkflow without installing it""" + assert self.subworkflow_remove.remove("bam_sort_stats_samtools") is False + + def test_subworkflows_remove_subworkflow(self): + """Test removing subworkflow and all it's dependencies after installing it""" + self.subworkflow_install.install("bam_sort_stats_samtools") + + subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") + bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") + samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + ModulesJson(self.pipeline_dir) + mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() + assert self.subworkflow_remove.remove("bam_sort_stats_samtools") + mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json() + assert Path.exists(bam_sort_stats_samtools_path) is False + assert Path.exists(bam_stats_samtools_path) is False + assert Path.exists(samtools_index_path) is False + assert mod_json_before != mod_json_after + # assert subworkflows key is removed from modules.json + assert ( + "bam_sort_stats_samtools" + not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys() + ) + assert ( + "samtools/index" not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"].keys() + ) + + def test_subworkflows_remove_subworkflow_keep_installed_module(self): + """Test removing subworkflow and all it's dependencies after installing it, except for a separately installed module""" + self.subworkflow_install.install("bam_sort_stats_samtools") + self.mods_install.install("samtools/index") + + subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") + bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") + samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + + mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() + assert self.subworkflow_remove.remove("bam_sort_stats_samtools") + mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json() + + assert Path.exists(bam_sort_stats_samtools_path) is False + assert Path.exists(bam_stats_samtools_path) is False + assert Path.exists(samtools_index_path) is True + assert mod_json_before != mod_json_after + # assert subworkflows key is removed from modules.json + assert ( + "bam_sort_stats_samtools" + not in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["subworkflows"].keys() + ) + assert ( + "samtools/index" + in mod_json_after["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"].keys() + ) + + def test_subworkflows_remove_one_of_two_subworkflow(self): + """Test removing subworkflow and all it's dependencies after installing it""" + self.subworkflow_install.install("bam_sort_stats_samtools") + self.subworkflow_install.install("bam_stats_samtools") + subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") + bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") + samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") + + assert self.subworkflow_remove.remove("bam_sort_stats_samtools") + + assert Path.exists(subworkflow_path) is True + assert Path.exists(bam_sort_stats_samtools_path) is False + assert Path.exists(bam_stats_samtools_path) is True + assert Path.exists(samtools_index_path) is False + assert Path.exists(samtools_stats_path) is True + self.subworkflow_remove.remove("bam_stats_samtools") + + def test_subworkflows_remove_included_subworkflow(self): + """Test removing subworkflow which is installed by another subworkflow and all it's dependencies.""" + self.subworkflow_install.install("bam_sort_stats_samtools") + subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") + bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") + samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") + + assert self.subworkflow_remove.remove("bam_stats_samtools") is False + + assert Path.exists(subworkflow_path) is True + assert Path.exists(bam_sort_stats_samtools_path) is True + assert Path.exists(bam_stats_samtools_path) is True + assert Path.exists(samtools_index_path) is True + assert Path.exists(samtools_stats_path) is True + self.subworkflow_remove.remove("bam_sort_stats_samtools") diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py new file mode 100644 index 0000000000..d3b2433572 --- /dev/null +++ b/tests/subworkflows/test_update.py @@ -0,0 +1,370 @@ +import logging +import shutil +import tempfile +from pathlib import Path +from unittest import mock + +import questionary +import yaml + +import nf_core.utils +from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE +from nf_core.modules.update import ModuleUpdate +from nf_core.subworkflows.update import SubworkflowUpdate + +from ..test_subworkflows import TestSubworkflows +from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component + + +class TestSubworkflowsUpdate(TestSubworkflows): + def test_install_and_update(self): + """Installs a subworkflow in the pipeline and updates it (no change)""" + self.subworkflow_install.install("bam_stats_samtools") + update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False) + + # Copy the sw files and check that they are unaffected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools") + shutil.copytree(sw_path, tmpdir) + + assert update_obj.update("bam_stats_samtools") is True + assert cmp_component(tmpdir, sw_path) is True + + def test_install_at_hash_and_update(self): + """Installs an old version of a subworkflow in the pipeline and updates it""" + assert self.subworkflow_install_old.install("fastq_align_bowtie2") + update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True) + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Copy the sw files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") + shutil.copytree(sw_path, tmpdir) + + assert update_obj.update("fastq_align_bowtie2") is True + assert cmp_component(tmpdir, sw_path) is False + + # Check that the modules.json is correctly updated + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + # Get the up-to-date git_sha for the sw from the ModulesRepo object + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + ) + + # Mock questionary answer: update components + @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) + def test_install_at_hash_and_update_limit_output(self, mock_prompt): + """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True""" + self.caplog.set_level(logging.INFO) + assert self.subworkflow_install_old.install("fastq_align_bowtie2") + + update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True) + + assert update_obj.update("fastq_align_bowtie2") + + # Check changes not shown for non-.nf files + assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text + assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text + # Check changes only shown for main.nf files + assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text + for line in self.caplog.text.split("\n"): + if line.startswith("---"): + assert line.endswith("main.nf") + + def test_install_at_hash_and_update_and_save_diff_to_file(self): + """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" + assert self.subworkflow_install_old.install("fastq_align_bowtie2") + patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") + update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True) + + # Copy the sw files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") + shutil.copytree(sw_path, tmpdir) + + assert update_obj.update("fastq_align_bowtie2") is True + assert cmp_component(tmpdir, sw_path) is True + + with open(patch_path) as fh: + line = fh.readline() + assert line.startswith( + "Changes in module 'nf-core/fastq_align_bowtie2' between (f3c078809a2513f1c95de14f6633fe1f03572fdb) and" + ) + + def test_install_at_hash_and_update_and_save_diff_limit_output(self): + """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" + # Install old version of fastq_align_bowtie2 + self.subworkflow_install_old.install("fastq_align_bowtie2") + patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") + # Update saving the differences to a patch file and with `limit_output` + update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True) + assert update_obj.update("fastq_align_bowtie2") + + # Check that the patch file was created + assert patch_path.exists(), f"Patch file was not created at {patch_path}" + + # Read the contents of the patch file + with open(patch_path) as fh: + content = fh.read() + # Check changes not shown for non-.nf files + assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content + assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content + assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content + assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content + # Check changes only shown for main.nf files + assert "Changes in 'fastq_align_bowtie2/main.nf'" in content + for line in content: + if line.startswith("---"): + assert line.endswith("main.nf") + + def test_update_all(self): + """Updates all subworkflows present in the pipeline""" + # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools + self.subworkflow_install.install("fastq_align_bowtie2") + # Update all subworkflows + update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) + assert update_obj.update() is True + + # We must reload the modules.json to get the updated version + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + # Loop through all subworkflows and check that they are updated (according to the modules.json file) + for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]: + correct_git_sha = list(update_obj.modules_repo.get_component_git_log(sw, "subworkflows", depth=1))[0][ + "git_sha" + ] + current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw][ + "git_sha" + ] + assert correct_git_sha == current_git_sha + + def test_update_with_config_fixed_version(self): + """Try updating when there are entries in the .nf-core.yml""" + # Install subworkflow at the latest version + assert self.subworkflow_install.install("fastq_align_bowtie2") + + # Fix the subworkflow version in the .nf-core.yml to an old version + update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all subworkflows in the pipeline + update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) + assert update_obj.update() is True + + # Check that the git sha for fastq_align_bowtie2 is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME] + assert ( + "git_sha" + in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] + ) + assert ( + mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + == OLD_SUBWORKFLOWS_SHA + ) + + def test_update_with_config_dont_update(self): + """Try updating when sw is to be ignored""" + # Install an old version of fastq_align_bowtie2 + self.subworkflow_install_old.install("fastq_align_bowtie2") + + # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml + update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all modules in the pipeline + update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) + assert update_obj.update() is True + + # Check that the git sha for fastq_align_bowtie2 is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME] + assert ( + "git_sha" + in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] + ) + assert ( + mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + == OLD_SUBWORKFLOWS_SHA + ) + + def test_update_with_config_fix_all(self): + """Fix the version of all nf-core subworkflows""" + # Install subworkflow at the latest version + assert self.subworkflow_install.install("fastq_align_bowtie2") + + # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version + update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update fastq_align_bowtie2 + update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False) + assert update_obj.update("fastq_align_bowtie2") is True + + # Check that the git sha for fastq_align_bowtie2 is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert ( + "git_sha" + in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] + ) + assert ( + mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + == OLD_SUBWORKFLOWS_SHA + ) + + def test_update_with_config_no_updates(self): + """Don't update any nf-core subworkflows""" + # Install an old version of fastq_align_bowtie2 + self.subworkflow_install_old.install("fastq_align_bowtie2") + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Set all repository updates to False + update_config = {NF_CORE_MODULES_REMOTE: False} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all subworkflows in the pipeline + update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) + assert update_obj.update() is True + + # Check that the git sha for fastq_align_bowtie2 is correctly downgraded and none of the subworkflows has changed + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]: + assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw] + assert ( + mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] + == old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] + ) + + def test_update_all_linked_components_from_subworkflow(self): + """Update a subworkflow and all modules and subworkflows used on it""" + # Install an old version of fastq_align_bowtie2 + self.subworkflow_install_old.install("fastq_align_bowtie2") + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Copy the sw files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME) + modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME) + shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows")) + shutil.copytree(modules_path, Path(tmpdir, "modules")) + + # Update fastq_align_bowtie2 and all modules and subworkflows used by that + update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False) + assert update_obj.update("fastq_align_bowtie2") is True + + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + # Loop through all modules and subworkflows used in fastq_align_bowtie2 + # check that they are updated (according to the modules.json file) + for sw in ["fastq_align_bowtie2", "bam_sort_stats_samtools", "bam_stats_samtools"]: + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] + ) + for mod in [ + "bowtie2/align", + "samtools/index", + "samtools/sort", + "samtools/flagstat", + "samtools/idxstats", + "samtools/stats", + ]: + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] + ) + # Check that the subworkflow files are updated + assert ( + cmp_component( + Path(tmpdir, "subworkflows", "fastq_align_bowtie2"), Path(subworkflows_path, "fastq_align_bowtie2") + ) + is False + ) + + def test_update_all_subworkflows_from_module(self): + """Update a module and all subworkflows that use this module""" + # Install an old version of fastq_align_bowtie2 and thus all modules used by it (bowtie2/align) + self.subworkflow_install_old.install("fastq_align_bowtie2") + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Copy the sw files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") + shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2")) + + # Update bowtie2/align and all subworkflows using it + update_obj = ModuleUpdate(self.pipeline_dir, update_deps=True, show_diff=False) + assert update_obj.update("bowtie2/align") is True + + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + # Check that bowtie2/align and fastq_align_bowtie2 are updated + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ + "git_sha" + ] + ) + assert cmp_component(Path(tmpdir, "fastq_align_bowtie2"), sw_path) is False + assert ( + old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"] + != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"] + ) + + def test_update_change_of_included_modules(self): + """Update a subworkflow which has a module change in the new version.""" + # Install an old version of vcf_annotate_ensemblvep with tabix/bgziptabix and without tabix/tabix + self.subworkflow_install_module_change.install("vcf_annotate_ensemblvep") + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Check that tabix/bgziptabix is there + assert "tabix/bgziptabix" in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir() + # Check that tabix/tabix is not there + assert "tabix/tabix" not in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir() + + # Update vcf_annotate_ensemblvep without tabix/bgziptabix and with tabix/tabix + update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False) + assert update_obj.update("vcf_annotate_ensemblvep") is True + + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Check that tabix/bgziptabix is not there + assert "tabix/bgziptabix" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir() + # Check that tabix/tabix is there + assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir() + # Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming) + assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] + assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir() diff --git a/tests/subworkflows/update.py b/tests/subworkflows/update.py deleted file mode 100644 index 42ed716b1c..0000000000 --- a/tests/subworkflows/update.py +++ /dev/null @@ -1,376 +0,0 @@ -import logging -import shutil -import tempfile -from pathlib import Path -from unittest import mock - -import questionary -import yaml - -import nf_core.utils -from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE -from nf_core.modules.update import ModuleUpdate -from nf_core.subworkflows.update import SubworkflowUpdate - -from ..utils import OLD_SUBWORKFLOWS_SHA, cmp_component - - -def test_install_and_update(self): - """Installs a subworkflow in the pipeline and updates it (no change)""" - self.subworkflow_install.install("bam_stats_samtools") - update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False) - - # Copy the sw files and check that they are unaffected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "bam_stats_samtools") - shutil.copytree(sw_path, tmpdir) - - assert update_obj.update("bam_stats_samtools") is True - assert cmp_component(tmpdir, sw_path) is True - - -def test_install_at_hash_and_update(self): - """Installs an old version of a subworkflow in the pipeline and updates it""" - assert self.subworkflow_install_old.install("fastq_align_bowtie2") - update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=False, update_deps=True) - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Copy the sw files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") - shutil.copytree(sw_path, tmpdir) - - assert update_obj.update("fastq_align_bowtie2") is True - assert cmp_component(tmpdir, sw_path) is False - - # Check that the modules.json is correctly updated - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - # Get the up-to-date git_sha for the sw from the ModulesRepo object - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - ) - - -# Mock questionary answer: update components -@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) -def test_install_at_hash_and_update_limit_output(self, mock_prompt): - """Installs an old version of a subworkflow in the pipeline and updates it with limit_output=True""" - self.caplog.set_level(logging.INFO) - assert self.subworkflow_install_old.install("fastq_align_bowtie2") - - update_obj = SubworkflowUpdate(self.pipeline_dir, show_diff=True, update_deps=True, limit_output=True) - - assert update_obj.update("fastq_align_bowtie2") - - # Check changes not shown for non-.nf files - assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in self.caplog.text - assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in self.caplog.text - assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in self.caplog.text - assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in self.caplog.text - # Check changes only shown for main.nf files - assert "Changes in 'fastq_align_bowtie2/main.nf'" in self.caplog.text - for line in self.caplog.text.split("\n"): - if line.startswith("---"): - assert line.endswith("main.nf") - - -def test_install_at_hash_and_update_and_save_diff_to_file(self): - """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" - assert self.subworkflow_install_old.install("fastq_align_bowtie2") - patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") - update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True) - - # Copy the sw files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") - shutil.copytree(sw_path, tmpdir) - - assert update_obj.update("fastq_align_bowtie2") is True - assert cmp_component(tmpdir, sw_path) is True - - with open(patch_path) as fh: - line = fh.readline() - assert line.startswith( - "Changes in module 'nf-core/fastq_align_bowtie2' between (f3c078809a2513f1c95de14f6633fe1f03572fdb) and" - ) - - -def test_install_at_hash_and_update_and_save_diff_limit_output(self): - """Installs an old version of a sw in the pipeline and updates it. Save differences to a file.""" - # Install old version of fastq_align_bowtie2 - self.subworkflow_install_old.install("fastq_align_bowtie2") - patch_path = Path(self.pipeline_dir, "fastq_align_bowtie2.patch") - # Update saving the differences to a patch file and with `limit_output` - update_obj = SubworkflowUpdate(self.pipeline_dir, save_diff_fn=patch_path, update_deps=True, limit_output=True) - assert update_obj.update("fastq_align_bowtie2") - - # Check that the patch file was created - assert patch_path.exists(), f"Patch file was not created at {patch_path}" - - # Read the contents of the patch file - with open(patch_path) as fh: - content = fh.read() - # Check changes not shown for non-.nf files - assert "Changes in 'fastq_align_bowtie2/meta.yml' but not shown" in content - assert "Changes in 'bam_sort_stats_samtools/meta.yml' but not shown" in content - assert "Changes in 'bam_stats_samtools/meta.yml' but not shown" in content - assert "Changes in 'samtools/flagstat/meta.yml' but not shown" in content - # Check changes only shown for main.nf files - assert "Changes in 'fastq_align_bowtie2/main.nf'" in content - for line in content: - if line.startswith("---"): - assert line.endswith("main.nf") - - -def test_update_all(self): - """Updates all subworkflows present in the pipeline""" - # Install subworkflows fastq_align_bowtie2, bam_sort_stats_samtools, bam_stats_samtools - self.subworkflow_install.install("fastq_align_bowtie2") - # Update all subworkflows - update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) - assert update_obj.update() is True - - # We must reload the modules.json to get the updated version - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - # Loop through all subworkflows and check that they are updated (according to the modules.json file) - for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]: - correct_git_sha = list(update_obj.modules_repo.get_component_git_log(sw, "subworkflows", depth=1))[0]["git_sha"] - current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] - assert correct_git_sha == current_git_sha - - -def test_update_with_config_fixed_version(self): - """Try updating when there are entries in the .nf-core.yml""" - # Install subworkflow at the latest version - assert self.subworkflow_install.install("fastq_align_bowtie2") - - # Fix the subworkflow version in the .nf-core.yml to an old version - update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all subworkflows in the pipeline - update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) - assert update_obj.update() is True - - # Check that the git sha for fastq_align_bowtie2 is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME] - assert ( - "git_sha" - in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] - ) - assert ( - mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - == OLD_SUBWORKFLOWS_SHA - ) - - -def test_update_with_config_dont_update(self): - """Try updating when sw is to be ignored""" - # Install an old version of fastq_align_bowtie2 - self.subworkflow_install_old.install("fastq_align_bowtie2") - - # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml - update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all modules in the pipeline - update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) - assert update_obj.update() is True - - # Check that the git sha for fastq_align_bowtie2 is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert "fastq_align_bowtie2" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME] - assert ( - "git_sha" - in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] - ) - assert ( - mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - == OLD_SUBWORKFLOWS_SHA - ) - - -def test_update_with_config_fix_all(self): - """Fix the version of all nf-core subworkflows""" - # Install subworkflow at the latest version - assert self.subworkflow_install.install("fastq_align_bowtie2") - - # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version - update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update fastq_align_bowtie2 - update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False) - assert update_obj.update("fastq_align_bowtie2") is True - - # Check that the git sha for fastq_align_bowtie2 is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert ( - "git_sha" - in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"] - ) - assert ( - mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - == OLD_SUBWORKFLOWS_SHA - ) - - -def test_update_with_config_no_updates(self): - """Don't update any nf-core subworkflows""" - # Install an old version of fastq_align_bowtie2 - self.subworkflow_install_old.install("fastq_align_bowtie2") - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Set all repository updates to False - update_config = {NF_CORE_MODULES_REMOTE: False} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all subworkflows in the pipeline - update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) - assert update_obj.update() is True - - # Check that the git sha for fastq_align_bowtie2 is correctly downgraded and none of the subworkflows has changed - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - for sw in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]: - assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw] - assert ( - mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] - == old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] - ) - - -def test_update_all_linked_components_from_subworkflow(self): - """Update a subworkflow and all modules and subworkflows used on it""" - # Install an old version of fastq_align_bowtie2 - self.subworkflow_install_old.install("fastq_align_bowtie2") - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Copy the sw files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - subworkflows_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME) - modules_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME) - shutil.copytree(subworkflows_path, Path(tmpdir, "subworkflows")) - shutil.copytree(modules_path, Path(tmpdir, "modules")) - - # Update fastq_align_bowtie2 and all modules and subworkflows used by that - update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False) - assert update_obj.update("fastq_align_bowtie2") is True - - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - # Loop through all modules and subworkflows used in fastq_align_bowtie2 - # check that they are updated (according to the modules.json file) - for sw in ["fastq_align_bowtie2", "bam_sort_stats_samtools", "bam_stats_samtools"]: - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME][sw]["git_sha"] - ) - for mod in [ - "bowtie2/align", - "samtools/index", - "samtools/sort", - "samtools/flagstat", - "samtools/idxstats", - "samtools/stats", - ]: - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - ) - # Check that the subworkflow files are updated - assert ( - cmp_component( - Path(tmpdir, "subworkflows", "fastq_align_bowtie2"), Path(subworkflows_path, "fastq_align_bowtie2") - ) - is False - ) - - -def test_update_all_subworkflows_from_module(self): - """Update a module and all subworkflows that use this module""" - # Install an old version of fastq_align_bowtie2 and thus all modules used by it (bowtie2/align) - self.subworkflow_install_old.install("fastq_align_bowtie2") - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Copy the sw files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - sw_path = Path(self.pipeline_dir, "subworkflows", NF_CORE_MODULES_NAME, "fastq_align_bowtie2") - shutil.copytree(sw_path, Path(tmpdir, "fastq_align_bowtie2")) - - # Update bowtie2/align and all subworkflows using it - update_obj = ModuleUpdate(self.pipeline_dir, update_deps=True, show_diff=False) - assert update_obj.update("bowtie2/align") is True - - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - # Check that bowtie2/align and fastq_align_bowtie2 are updated - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["subworkflows"][NF_CORE_MODULES_NAME]["fastq_align_bowtie2"][ - "git_sha" - ] - ) - assert cmp_component(Path(tmpdir, "fastq_align_bowtie2"), sw_path) is False - assert ( - old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"] - != mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]["bowtie2/align"]["git_sha"] - ) - - -def test_update_change_of_included_modules(self): - """Update a subworkflow which has a module change in the new version.""" - # Install an old version of vcf_annotate_ensemblvep with tabix/bgziptabix and without tabix/tabix - self.subworkflow_install_module_change.install("vcf_annotate_ensemblvep") - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Check that tabix/bgziptabix is there - assert "tabix/bgziptabix" in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir() - # Check that tabix/tabix is not there - assert "tabix/tabix" not in old_mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir() - - # Update vcf_annotate_ensemblvep without tabix/bgziptabix and with tabix/tabix - update_obj = SubworkflowUpdate(self.pipeline_dir, update_deps=True, show_diff=False) - assert update_obj.update("vcf_annotate_ensemblvep") is True - - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Check that tabix/bgziptabix is not there - assert "tabix/bgziptabix" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert not Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/bgziptabix").is_dir() - # Check that tabix/tabix is there - assert "tabix/tabix" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "tabix/tabix").is_dir() - # Check that ensemblevep is not there but instead we have ensemblevep/vep (due to a file re-naming) - assert "ensemblvep" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert "ensemblvep/vep" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME] - assert Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "ensemblvep/vep").is_dir() diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 17bc678cad..af581fc9ab 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -119,77 +119,34 @@ def tearDown(self): def _use_caplog(self, caplog): self.caplog = caplog - ################################################ - # Test of the individual subworkflow commands. # - ################################################ - - from .subworkflows.create import ( # type: ignore[misc] - test_subworkflows_create_fail_exists, - test_subworkflows_create_nfcore_modules, - test_subworkflows_create_succeed, - test_subworkflows_migrate, - test_subworkflows_migrate_no_delete, - ) - from .subworkflows.info import ( # type: ignore[misc] - test_subworkflows_info_in_modules_repo, - test_subworkflows_info_local, - test_subworkflows_info_remote, - test_subworkflows_info_remote_gitlab, - ) - from .subworkflows.install import ( # type: ignore[misc] - test_subworkflow_install_nopipeline, - test_subworkflows_install_alternate_remote, - test_subworkflows_install_bam_sort_stats_samtools, - test_subworkflows_install_bam_sort_stats_samtools_twice, - test_subworkflows_install_different_branch_fail, - test_subworkflows_install_emptypipeline, - test_subworkflows_install_from_gitlab, - test_subworkflows_install_nosubworkflow, - test_subworkflows_install_tracking, - test_subworkflows_install_tracking_added_already_installed, - test_subworkflows_install_tracking_added_super_subworkflow, - ) - from .subworkflows.lint import ( # type: ignore[misc] - test_subworkflows_absent_version, - test_subworkflows_empty_file_in_snapshot, - test_subworkflows_empty_file_in_stub_snapshot, - test_subworkflows_lint, - test_subworkflows_lint_capitalization_fail, - test_subworkflows_lint_empty, - test_subworkflows_lint_gitlab_subworkflows, - test_subworkflows_lint_include_multiple_alias, - test_subworkflows_lint_less_than_two_modules_warning, - test_subworkflows_lint_multiple_remotes, - test_subworkflows_lint_new_subworkflow, - test_subworkflows_lint_no_gitlab, - test_subworkflows_lint_snapshot_file, - test_subworkflows_lint_snapshot_file_missing_fail, - test_subworkflows_lint_snapshot_file_not_needed, - ) - from .subworkflows.list import ( # type: ignore[misc] - test_subworkflows_install_and_list_subworkflows, - test_subworkflows_install_gitlab_and_list_subworkflows, - test_subworkflows_list_remote, - test_subworkflows_list_remote_gitlab, - ) - from .subworkflows.remove import ( # type: ignore[misc] - test_subworkflows_remove_included_subworkflow, - test_subworkflows_remove_one_of_two_subworkflow, - test_subworkflows_remove_subworkflow, - test_subworkflows_remove_subworkflow_keep_installed_module, - ) - from .subworkflows.update import ( # type: ignore[misc] - test_install_and_update, - test_install_at_hash_and_update, - test_install_at_hash_and_update_and_save_diff_limit_output, - test_install_at_hash_and_update_and_save_diff_to_file, - test_install_at_hash_and_update_limit_output, - test_update_all, - test_update_all_linked_components_from_subworkflow, - test_update_all_subworkflows_from_module, - test_update_change_of_included_modules, - test_update_with_config_dont_update, - test_update_with_config_fix_all, - test_update_with_config_fixed_version, - test_update_with_config_no_updates, - ) + # ################################################ + # # Test of the individual subworkflow commands. # + # ################################################ + + # from .subworkflows.list import ( # type: ignore[misc] + # test_subworkflows_install_and_list_subworkflows, + # test_subworkflows_install_gitlab_and_list_subworkflows, + # test_subworkflows_list_remote, + # test_subworkflows_list_remote_gitlab, + # ) + # from .subworkflows.remove import ( # type: ignore[misc] + # test_subworkflows_remove_included_subworkflow, + # test_subworkflows_remove_one_of_two_subworkflow, + # test_subworkflows_remove_subworkflow, + # test_subworkflows_remove_subworkflow_keep_installed_module, + # ) + # from .subworkflows.update import ( # type: ignore[misc] + # test_install_and_update, + # test_install_at_hash_and_update, + # test_install_at_hash_and_update_and_save_diff_limit_output, + # test_install_at_hash_and_update_and_save_diff_to_file, + # test_install_at_hash_and_update_limit_output, + # test_update_all, + # test_update_all_linked_components_from_subworkflow, + # test_update_all_subworkflows_from_module, + # test_update_change_of_included_modules, + # test_update_with_config_dont_update, + # test_update_with_config_fix_all, + # test_update_with_config_fixed_version, + # test_update_with_config_no_updates, + # ) From c00623dda555b708dca2fc7e90d62a5aaa65d6c4 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Wed, 17 Jul 2024 16:20:43 +0200 Subject: [PATCH 163/574] Remove release announcement for non nf-core pipelines --- nf_core/pipelines/create/create.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index bdbbca646f..f9ba2ff7f6 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -92,6 +92,7 @@ def __init__( "CODE_OF_CONDUCT.md", ".github/workflows/awsfulltest.yml", ".github/workflows/awstest.yml", + ".github/workflows/release-announcements.yml" ], } # Get list of files we're skipping with the supplied skip keys From c71dac8e6e2217324a417b9b58c60716102b1ae5 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 16 Jul 2024 09:54:59 +0000 Subject: [PATCH 164/574] Update python:3.12-slim Docker digest to f11725a --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7178b65267..8943b70627 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:d5f16749562233aa4bd26538771d76bf0dfd0a0ea7ea8771985e267451397ae4 +FROM python:3.12-slim@sha256:f11725aba18c19664a408902103365eaf8013823ffc56270f921d1dc78a198cb LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 33a4b67479000a458774b68c107a6c5794bcfec5 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 17 Jul 2024 13:50:05 +0000 Subject: [PATCH 165/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 823e000beb..fba54a9539 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -50,6 +50,7 @@ - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) +- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 4e7be452d4fb16f8949a6bde0de70271bb5977a8 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Wed, 17 Jul 2024 16:28:01 +0200 Subject: [PATCH 166/574] Ran pre commit --- nf_core/pipelines/create/create.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index f9ba2ff7f6..27ca8ac847 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -92,7 +92,7 @@ def __init__( "CODE_OF_CONDUCT.md", ".github/workflows/awsfulltest.yml", ".github/workflows/awstest.yml", - ".github/workflows/release-announcements.yml" + ".github/workflows/release-announcements.yml", ], } # Get list of files we're skipping with the supplied skip keys From 77f9dd73d1e4a755406e70af4ad5bdc462eaa1ba Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Wed, 17 Jul 2024 16:32:30 +0200 Subject: [PATCH 167/574] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fba54a9539..8cda88788b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042)) - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) +- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) +- Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) ### Linting From 789a7841af08b9f621043e8701a79c39a8c9877e Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Wed, 17 Jul 2024 17:01:15 +0200 Subject: [PATCH 168/574] Fix number of arguments for pipelines_create --- nf_core/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index f33c63e87c..192c7cd139 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2181,14 +2181,14 @@ def command_lint( help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", ) @click.pass_context -def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation): +def command_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): """ Use `nf-core pipelines create` instead. """ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation) + pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation) # Main script is being run - launch the CLI From 2f66b482c0945099d8bdca78dbffb96810482525 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 17 Jul 2024 15:05:41 +0000 Subject: [PATCH 169/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fba54a9539..b3f1688e72 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -51,6 +51,7 @@ - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) +- Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From f7be79d6d599918af49513fb41bd5943df9b7e60 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 18 Jul 2024 10:12:10 +0200 Subject: [PATCH 170/574] migrate modules tests to new structure --- nf_core/components/components_command.py | 4 +- nf_core/modules/bump_versions.py | 3 +- tests/modules/bump_versions.py | 50 -- tests/modules/create.py | 165 ----- tests/modules/info.py | 63 -- tests/modules/install.py | 95 --- tests/modules/lint.py | 892 ----------------------- tests/modules/list.py | 134 ---- tests/modules/modules_json.py | 253 ------- tests/modules/patch.py | 360 --------- tests/modules/remove.py | 22 - tests/modules/test_bump_versions.py | 50 ++ tests/modules/test_create.py | 164 +++++ tests/modules/test_info.py | 62 ++ tests/modules/test_install.py | 90 +++ tests/modules/test_lint.py | 865 ++++++++++++++++++++++ tests/modules/test_list.py | 126 ++++ tests/modules/test_modules_json.py | 245 +++++++ tests/modules/test_patch.py | 365 ++++++++++ tests/modules/test_remove.py | 26 + tests/modules/test_update.py | 435 +++++++++++ tests/modules/update.py | 444 ----------- tests/test_modules.py | 128 ---- 23 files changed, 2432 insertions(+), 2609 deletions(-) delete mode 100644 tests/modules/bump_versions.py delete mode 100644 tests/modules/create.py delete mode 100644 tests/modules/info.py delete mode 100644 tests/modules/install.py delete mode 100644 tests/modules/lint.py delete mode 100644 tests/modules/list.py delete mode 100644 tests/modules/modules_json.py delete mode 100644 tests/modules/patch.py delete mode 100644 tests/modules/remove.py create mode 100644 tests/modules/test_bump_versions.py create mode 100644 tests/modules/test_create.py create mode 100644 tests/modules/test_info.py create mode 100644 tests/modules/test_install.py create mode 100644 tests/modules/test_lint.py create mode 100644 tests/modules/test_list.py create mode 100644 tests/modules/test_modules_json.py create mode 100644 tests/modules/test_patch.py create mode 100644 tests/modules/test_remove.py create mode 100644 tests/modules/test_update.py delete mode 100644 tests/modules/update.py diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 4df67639e2..aa1dccc0d4 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -22,7 +22,7 @@ class ComponentCommand: def __init__( self, component_type: str, - dir: str, + dir: Union[str, Path], remote_url: Optional[str] = None, branch: Optional[str] = None, no_pull: bool = False, @@ -33,7 +33,7 @@ def __init__( Initialise the ComponentClass object """ self.component_type = component_type - self.dir = dir + self.dir = Path(dir) if dir else None self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.hide_progress = hide_progress self.no_prompts = no_prompts diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index fae3793079..1b94d5910c 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -6,6 +6,7 @@ import logging import os import re +from pathlib import Path from typing import Any, Dict, List, Optional, Tuple, Union import questionary @@ -30,7 +31,7 @@ class ModuleVersionBumper(ComponentCommand): # type: ignore[misc] def __init__( self, - pipeline_dir: str, + pipeline_dir: Union[str, Path], remote_url: Optional[str] = None, branch: Optional[str] = None, no_pull: bool = False, diff --git a/tests/modules/bump_versions.py b/tests/modules/bump_versions.py deleted file mode 100644 index ce8c6dbe11..0000000000 --- a/tests/modules/bump_versions.py +++ /dev/null @@ -1,50 +0,0 @@ -import os -import re - -import pytest - -import nf_core.modules -from nf_core.modules.modules_utils import ModuleExceptionError - - -def test_modules_bump_versions_single_module(self): - """Test updating a single module""" - # Change the bpipe/test version to an older version - env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml") - with open(env_yml_path) as fh: - content = fh.read() - new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content) - with open(env_yml_path, "w") as fh: - fh.write(new_content) - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(module="bpipe/test") - assert len(version_bumper.failed) == 0 - - -def test_modules_bump_versions_all_modules(self): - """Test updating all modules""" - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(all_modules=True) - assert len(version_bumper.failed) == 0 - - -def test_modules_bump_versions_fail(self): - """Fail updating a module with wrong name""" - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - with pytest.raises(ModuleExceptionError) as excinfo: - version_bumper.bump_versions(module="no/module") - assert "Could not find the specified module:" in str(excinfo.value) - - -def test_modules_bump_versions_fail_unknown_version(self): - """Fail because of an unknown version""" - # Change the bpipe/test version to an older version - env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml") - with open(env_yml_path) as fh: - content = fh.read() - new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content) - with open(env_yml_path, "w") as fh: - fh.write(new_content) - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(module="bpipe/test") - assert "Conda package had unknown version" in version_bumper.failed[0][0] diff --git a/tests/modules/create.py b/tests/modules/create.py deleted file mode 100644 index cf39621f07..0000000000 --- a/tests/modules/create.py +++ /dev/null @@ -1,165 +0,0 @@ -import os -import shutil -from pathlib import Path -from unittest import mock - -import pytest -import requests_cache -import responses -import yaml -from git.repo import Repo - -import nf_core.modules -from tests.utils import ( - GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, - GITLAB_URL, - mock_anaconda_api_calls, - mock_biocontainers_api_calls, -) - - -def test_modules_create_succeed(self): - """Succeed at creating the TrimGalore! module""" - with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") - mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") - module_create = nf_core.modules.ModuleCreate( - self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore" - ) - with requests_cache.disabled(): - module_create.create() - assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf")) - - -def test_modules_create_fail_exists(self): - """Fail at creating the same module twice""" - with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") - mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") - module_create = nf_core.modules.ModuleCreate( - self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore" - ) - with requests_cache.disabled(): - module_create.create() - with pytest.raises(UserWarning) as excinfo: - with requests_cache.disabled(): - module_create.create() - assert "Module file exists already" in str(excinfo.value) - - -def test_modules_create_nfcore_modules(self): - """Create a module in nf-core/modules clone""" - with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "fastqc", "0.11.9") - mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9") - module_create = nf_core.modules.ModuleCreate( - self.nfcore_modules, "fastqc", "@author", "process_low", False, False - ) - with requests_cache.disabled(): - module_create.create() - assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf")) - assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test")) - - -def test_modules_create_nfcore_modules_subtool(self): - """Create a tool/subtool module in a nf-core/modules clone""" - with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "star", "2.8.10a") - mock_biocontainers_api_calls(rsps, "star", "2.8.10a") - module_create = nf_core.modules.ModuleCreate( - self.nfcore_modules, "star/index", "@author", "process_medium", False, False - ) - with requests_cache.disabled(): - module_create.create() - assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf")) - assert os.path.exists( - os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test") - ) - - -@mock.patch("rich.prompt.Confirm.ask") -def test_modules_migrate(self, mock_rich_ask): - """Create a module with the --migrate-pytest option to convert pytest to nf-test""" - pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") - module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort") - - # Clone modules repo with pytests - shutil.rmtree(self.nfcore_modules) - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) - with open(module_dir / "main.nf") as fh: - old_main_nf = fh.read() - with open(module_dir / "meta.yml") as fh: - old_meta_yml = fh.read() - - # Create a module with --migrate-pytest - mock_rich_ask.return_value = True - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) - module_create.create() - - with open(module_dir / "main.nf") as fh: - new_main_nf = fh.read() - with open(module_dir / "meta.yml") as fh: - new_meta_yml = fh.read() - nextflow_config = module_dir / "tests" / "nextflow.config" - - # Check that old files have been copied to the new module - assert old_main_nf == new_main_nf - assert old_meta_yml == new_meta_yml - assert nextflow_config.is_file() - - # Check that pytest folder is deleted - assert not pytest_dir.is_dir() - - # Check that pytest_modules.yml is updated - with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: - modules_yml = yaml.safe_load(fh) - assert "samtools/sort" not in modules_yml.keys() - - -@mock.patch("rich.prompt.Confirm.ask") -def test_modules_migrate_no_delete(self, mock_rich_ask): - """Create a module with the --migrate-pytest option to convert pytest to nf-test. - Test that pytest directory is not deleted.""" - pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") - - # Clone modules repo with pytests - shutil.rmtree(self.nfcore_modules) - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) - - # Create a module with --migrate-pytest - mock_rich_ask.return_value = False - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) - module_create.create() - - # Check that pytest folder is not deleted - assert pytest_dir.is_dir() - - # Check that pytest_modules.yml is updated - with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: - modules_yml = yaml.safe_load(fh) - assert "samtools/sort" not in modules_yml.keys() - - -@mock.patch("rich.prompt.Confirm.ask") -def test_modules_migrate_symlink(self, mock_rich_ask): - """Create a module with the --migrate-pytest option to convert pytest with symlinks to nf-test. - Test that the symlink is deleted and the file is copied.""" - - pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") - module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort") - - # Clone modules repo with pytests - shutil.rmtree(self.nfcore_modules) - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) - - # Create a symlinked file in the pytest directory - symlink_file = pytest_dir / "symlink_file.txt" - symlink_file.symlink_to(module_dir / "main.nf") - - # Create a module with --migrate-pytest - mock_rich_ask.return_value = True - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) - module_create.create() - - # Check that symlink is deleted - assert not symlink_file.is_symlink() diff --git a/tests/modules/info.py b/tests/modules/info.py deleted file mode 100644 index 2dbd48b240..0000000000 --- a/tests/modules/info.py +++ /dev/null @@ -1,63 +0,0 @@ -from rich.console import Console - -import nf_core.modules - -from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL - - -def test_modules_info_remote(self): - """Test getting info about a remote module""" - mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc") - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Module: fastqc" in output - assert "Inputs" in output - assert "Outputs" in output - - -def test_modules_info_remote_gitlab(self): - """Test getting info about a module in the remote gitlab repo""" - mods_info = nf_core.modules.ModuleInfo( - self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH - ) - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Module: fastqc" in output - assert "Inputs" in output - assert "Outputs" in output - assert "--git-remote" in output - - -def test_modules_info_local(self): - """Test getting info about a locally installed module""" - self.mods_install.install("trimgalore") - mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore") - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Module: trimgalore" in output - assert "Inputs" in output - assert "Outputs" in output - assert "Location" in output - - -def test_modules_info_in_modules_repo(self): - """Test getting info about a module in the modules repo""" - mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc") - mods_info.local = True - mods_info_output = mods_info.get_component_info() - console = Console(record=True) - console.print(mods_info_output) - output = console.export_text() - - assert "Module: fastqc" in output - assert "Inputs" in output - assert "Outputs" in output diff --git a/tests/modules/install.py b/tests/modules/install.py deleted file mode 100644 index deca31204e..0000000000 --- a/tests/modules/install.py +++ /dev/null @@ -1,95 +0,0 @@ -import os - -import pytest - -from nf_core.modules.install import ModuleInstall -from nf_core.modules.modules_json import ModulesJson - -from ..utils import ( - GITLAB_BRANCH_ORG_PATH_BRANCH, - GITLAB_BRANCH_TEST_BRANCH, - GITLAB_REPO, - GITLAB_URL, - with_temporary_folder, -) - - -def test_modules_install_nopipeline(self): - """Test installing a module - no pipeline given""" - self.mods_install.dir = None - assert self.mods_install.install("foo") is False - - -@with_temporary_folder -def test_modules_install_emptypipeline(self, tmpdir): - """Test installing a module - empty dir given""" - os.mkdir(os.path.join(tmpdir, "nf-core-pipe")) - self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe") - with pytest.raises(UserWarning) as excinfo: - self.mods_install.install("foo") - assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) - - -def test_modules_install_nomodule(self): - """Test installing a module - unrecognised module given""" - assert self.mods_install.install("foo") is False - - -def test_modules_install_trimgalore(self): - """Test installing a module - TrimGalore!""" - assert self.mods_install.install("trimgalore") is not False - module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "trimgalore") - assert os.path.exists(module_path) - - -def test_modules_install_trimgalore_twice(self): - """Test installing a module - TrimGalore! already there""" - self.mods_install.install("trimgalore") - assert self.mods_install.install("trimgalore") is True - - -def test_modules_install_from_gitlab(self): - """Test installing a module from GitLab""" - assert self.mods_install_gitlab.install("fastqc") is True - - -def test_modules_install_different_branch_fail(self): - """Test installing a module from a different branch""" - install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) - # The FastQC module does not exists in the branch-test branch - assert install_obj.install("fastqc") is False - - -def test_modules_install_different_branch_succeed(self): - """Test installing a module from a different branch""" - install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) - # The fastp module does exists in the branch-test branch - assert install_obj.install("fastp") is True - - # Verify that the branch entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - assert ( - modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) - == GITLAB_BRANCH_TEST_BRANCH - ) - - -def test_modules_install_tracking(self): - """Test installing a module and finding 'modules' in the installed_by section of modules.json""" - self.mods_install.install("trimgalore") - - # Verify that the installed_by entry was added correctly - modules_json = ModulesJson(self.pipeline_dir) - mod_json = modules_json.get_modules_json() - assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][ - "installed_by" - ] == ["modules"] - - -def test_modules_install_alternate_remote(self): - """Test installing a module from a different remote with the same organization path""" - install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_ORG_PATH_BRANCH) - # Install fastqc from GitLab which is also installed from GitHub with the same org_path - with pytest.raises(Exception) as excinfo: - install_obj.install("fastqc") - assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) diff --git a/tests/modules/lint.py b/tests/modules/lint.py deleted file mode 100644 index e1a4e27ff8..0000000000 --- a/tests/modules/lint.py +++ /dev/null @@ -1,892 +0,0 @@ -import json -from pathlib import Path - -import pytest -import yaml -from git.repo import Repo - -import nf_core.modules -from nf_core.modules.lint import main_nf -from nf_core.utils import set_wd - -from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL -from .patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf - - -def setup_patch(pipeline_dir: str, modify_module: bool): - install_obj = nf_core.modules.ModuleInstall( - pipeline_dir, - prompt=False, - force=False, - remote_url=GITLAB_URL, - branch=PATCH_BRANCH, - sha=CORRECT_SHA, - ) - - # Install the module - install_obj.install(BISMARK_ALIGN) - - if modify_module: - # Modify the module - module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - modify_main_nf(module_path / "main.nf") - - -def test_modules_lint_trimgalore(self): - """Test linting the TrimGalore! module""" - self.mods_install.install("trimgalore") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) - module_lint.lint(print_results=False, module="trimgalore") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_empty(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.ModuleLint(dir=self.pipeline_dir) - - -def test_modules_lint_new_modules(self): - """lint a new module""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_no_gitlab(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) - - -def test_modules_lint_gitlab_modules(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("fastqc") - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 2 - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_multiple_remotes(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 1 - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_registry(self): - """Test linting the samtools module and alternative registry""" - self.mods_install.install("samtools") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws") - module_lint.lint(print_results=False, module="samtools") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) - module_lint.lint(print_results=False, module="samtools") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_patched_modules(self): - """ - Test creating a patch file and applying it to a new version of the the files - """ - setup_patch(self.pipeline_dir, True) - - # Create a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - # change temporarily working directory to the pipeline directory - # to avoid error from try_apply_patch() during linting - with set_wd(self.pipeline_dir): - module_lint = nf_core.modules.ModuleLint( - dir=self.pipeline_dir, - remote_url=GITLAB_URL, - branch=PATCH_BRANCH, - hide_progress=True, - ) - module_lint.lint( - print_results=False, - all_modules=True, - ) - - assert len(module_lint.failed) == 1 - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - - self.main_nf = "main_nf" - - -PROCESS_LABEL_GOOD = ( - """ - label 'process_high' - cpus 12 - """, - 1, - 0, - 0, -) -PROCESS_LABEL_NON_ALPHANUMERIC = ( - """ - label 'a:label:with:colons' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_CONFLICTING = ( - """ - label 'process_high' - label 'process_low' - cpus 12 - """, - 0, - 1, - 0, -) -PROCESS_LABEL_GOOD_DUPLICATES = ( - """ - label 'process_high' - label 'process_high' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( - """ - label 'process_high' - label 'process_extra_label' - cpus 12 - """, - 1, - 1, - 0, -) -PROCESS_LABEL_NONSTANDARD = ( - """ - label 'process_extra_label' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_NONSTANDARD_DUPLICATES = ( - """ - label process_extra_label - label process_extra_label - cpus 12 - """, - 0, - 3, - 0, -) -PROCESS_LABEL_NONE_FOUND = ( - """ - cpus 12 - """, - 0, - 1, - 0, -) - -PROCESS_LABEL_TEST_CASES = [ - PROCESS_LABEL_GOOD, - PROCESS_LABEL_NON_ALPHANUMERIC, - PROCESS_LABEL_GOOD_CONFLICTING, - PROCESS_LABEL_GOOD_DUPLICATES, - PROCESS_LABEL_GOOD_AND_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD_DUPLICATES, - PROCESS_LABEL_NONE_FOUND, -] - - -def test_modules_lint_check_process_labels(self): - for test_case in PROCESS_LABEL_TEST_CASES: - process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - main_nf.check_process_labels(mocked_ModuleLint, process.splitlines()) - assert len(mocked_ModuleLint.passed) == passed - assert len(mocked_ModuleLint.warned) == warned - assert len(mocked_ModuleLint.failed) == failed - - -# Test cases for linting the container definitions - -CONTAINER_SINGLE_GOOD = ( - "Single-line container definition should pass", - """ - container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package - """, - 2, # passed - 0, # warned - 0, # failed -) - -CONTAINER_TWO_LINKS_GOOD = ( - "Multi-line container definition should pass", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 6, - 0, - 0, -) - -CONTAINER_WITH_SPACE_BAD = ( - "Space in container URL should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 5, - 0, - 1, -) - -CONTAINER_MULTIPLE_DBLQUOTES_BAD = ( - "Incorrect quoting of container string should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" - """, - 4, - 0, - 1, -) - -CONTAINER_TEST_CASES = [ - CONTAINER_SINGLE_GOOD, - CONTAINER_TWO_LINKS_GOOD, - CONTAINER_WITH_SPACE_BAD, - CONTAINER_MULTIPLE_DBLQUOTES_BAD, -] - - -def test_modules_lint_check_url(self): - for test_case in CONTAINER_TEST_CASES: - test, process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - for line in process.splitlines(): - if line.strip(): - main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io") - - assert ( - len(mocked_ModuleLint.passed) == passed - ), f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}." - assert ( - len(mocked_ModuleLint.warned) == warned - ), f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}." - assert ( - len(mocked_ModuleLint.failed) == failed - ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." - - -def test_modules_lint_snapshot_file(self): - """Test linting a module with a snapshot file""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_lint_snapshot_file_missing_fail(self): - """Test linting a module with a snapshot file missing, which should fail""" - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ).unlink() - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ).touch() - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snapshot_exists" - - -def test_modules_lint_snapshot_file_not_needed(self): - """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ) - ) as fh: - content = fh.read() - new_content = content.replace("snapshot(", "snap (") - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ), - "w", - ) as fh: - fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_environment_yml_file_doesnt_exists(self): - """Test linting a module with an environment.yml file""" - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml").rename( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml.bak", - ) - ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml.bak", - ).rename( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ) - ) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_exists" - - -def test_modules_environment_yml_file_sorted_correctly(self): - """Test linting a module with a correctly sorted environment.yml file""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_environment_yml_file_sorted_incorrectly(self): - """Test linting a module with an incorrectly sorted environment.yml file""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ) - ) as fh: - yaml_content = yaml.safe_load(fh) - # Add a new dependency to the environment.yml file and reverse the order - yaml_content["dependencies"].append("z") - yaml_content["dependencies"].reverse() - yaml_content = yaml.dump(yaml_content) - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - # we fix the sorting on the fly, so this should pass - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -def test_modules_environment_yml_file_not_array(self): - """Test linting a module with an incorrectly formatted environment.yml file""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ) - ) as fh: - yaml_content = yaml.safe_load(fh) - yaml_content["dependencies"] = "z" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_valid" - - -def test_modules_environment_yml_file_name_mismatch(self): - """Test linting a module with a different name in the environment.yml file""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ) - ) as fh: - yaml_content = yaml.safe_load(fh) - yaml_content["name"] = "bpipe-test" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - # reset changes - yaml_content["name"] = "bpipe_test" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml.dump(yaml_content)) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_name" - - -def test_modules_meta_yml_incorrect_licence_field(self): - """Test linting a module with an incorrect Licence field in meta.yml""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: - meta_yml = yaml.safe_load(fh) - meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - # reset changes - meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_yml_valid" - - -def test_modules_meta_yml_input_mismatch(self): - """Test linting a module with an extra entry in input fields in meta.yml compared to module.input""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: - main_nf = fh.read() - main_nf_new = main_nf.replace("path bam", "path bai") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2 - lint_tests = [x.lint_test for x in module_lint.warned] - # check that it is there twice: - assert lint_tests.count("meta_input_meta_only") == 1 - assert lint_tests.count("meta_input_main_only") == 1 - - -def test_modules_meta_yml_output_mismatch(self): - """Test linting a module with an extra entry in output fields in meta.yml compared to module.output""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: - main_nf = fh.read() - main_nf_new = main_nf.replace("emit: bam", "emit: bai") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2 - lint_tests = [x.lint_test for x in module_lint.warned] - # check that it is there twice: - assert lint_tests.count("meta_output_meta_only") == 1 - assert lint_tests.count("meta_output_main_only") == 1 - - -def test_modules_meta_yml_incorrect_name(self): - """Test linting a module with an incorrect name in meta.yml""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: - meta_yml = yaml.safe_load(fh) - meta_yml["name"] = "bpipe/test" - # need to make the same change to the environment.yml file - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ) - ) as fh: - environment_yml = yaml.safe_load(fh) - environment_yml["name"] = "bpipe/test" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml.dump(environment_yml)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - # reset changes - meta_yml["name"] = "bpipe_test" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - environment_yml["name"] = "bpipe_test" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "environment.yml", - ), - "w", - ) as fh: - fh.write(yaml.dump(environment_yml)) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_name" - - -def test_modules_missing_test_dir(self): - """Test linting a module with a missing test directory""" - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") - ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") - ) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_dir_exists" - - -def test_modules_missing_test_main_nf(self): - """Test linting a module with a missing test/main.nf file""" - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ).rename( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.bak", - ) - ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.bak", - ).rename( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ) - ) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_main_nf_exists" - - -def test_modules_unused_pytest_files(self): - """Test linting a nf-test module with files still present in `tests/modules/`""" - Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_old_test_dir" - - -def test_nftest_failing_linting(self): - """Test linting a module which includes other modules in nf-test tests. - Linting tests""" - # Clone modules repo with testing modules - tmp_dir = self.nfcore_modules.parent - self.nfcore_modules = Path(tmp_dir, "modules-test") - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) - - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="kallisto/quant") - - assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_valid" - assert module_lint.failed[1].lint_test == "meta_yml_valid" - assert module_lint.failed[2].lint_test == "test_main_tags" - assert "kallisto/index" in module_lint.failed[2].message - - -def test_modules_absent_version(self): - """Test linting a nf-test module if the versions is absent in the snapshot file `""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ) - ) as fh: - content = fh.read() - new_content = content.replace("versions", "foo") - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ), - "w", - ) as fh: - fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ), - "w", - ) as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snap_versions" - - -def test_modules_empty_file_in_snapshot(self): - """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" - snap_file = Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ) - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snap_md5sum" - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - - -def test_modules_empty_file_in_stub_snapshot(self): - """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" - snap_file = Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ) - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed) - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) diff --git a/tests/modules/list.py b/tests/modules/list.py deleted file mode 100644 index 3cb00a84d6..0000000000 --- a/tests/modules/list.py +++ /dev/null @@ -1,134 +0,0 @@ -import json -from pathlib import Path - -import yaml -from rich.console import Console - -import nf_core.modules - -from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL - - -def test_modules_list_remote(self): - """Test listing available modules""" - mods_list = nf_core.modules.ModuleList(None, remote=True) - listed_mods = mods_list.list_components() - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "fastqc" in output - - -def test_modules_list_remote_gitlab(self): - """Test listing the modules in the remote gitlab repo""" - mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) - listed_mods = mods_list.list_components() - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "fastqc" in output - - -def test_modules_list_pipeline(self): - """Test listing locally installed modules""" - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components() - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "fastqc" in output - assert "multiqc" in output - - -def test_modules_install_and_list_pipeline(self): - """Test listing locally installed modules""" - self.mods_install.install("trimgalore") - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components() - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "trimgalore" in output - - -def test_modules_install_gitlab_and_list_pipeline(self): - """Test listing locally installed modules""" - self.mods_install_gitlab.install("fastqc") - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components() - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "fastqc" in output - - -def test_modules_list_local_json(self): - """Test listing locally installed modules as JSON""" - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components(print_json=True) - listed_mods = json.loads(listed_mods) - assert "fastqc" in listed_mods - assert "multiqc" in listed_mods - - -def test_modules_list_remote_json(self): - """Test listing available modules as JSON""" - mods_list = nf_core.modules.ModuleList(None, remote=True) - listed_mods = mods_list.list_components(print_json=True) - listed_mods = json.loads(listed_mods) - assert "fastqc" in listed_mods - assert "multiqc" in listed_mods - - -def test_modules_list_with_one_keyword(self): - """Test listing available modules with one keyword""" - mods_list = nf_core.modules.ModuleList(None, remote=True) - listed_mods = mods_list.list_components(keywords=["qc"]) - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "multiqc" in output - - -def test_modules_list_with_keywords(self): - """Test listing available modules with multiple keywords""" - mods_list = nf_core.modules.ModuleList(None, remote=True) - listed_mods = mods_list.list_components(keywords=["fastq", "qc"]) - console = Console(record=True) - console.print(listed_mods) - output = console.export_text() - assert "fastqc" in output - - -def test_modules_list_with_unused_keyword(self): - """Test listing available modules with an unused keyword""" - mods_list = nf_core.modules.ModuleList(None, remote=True) - with self.assertLogs(level="INFO") as log: - listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"]) - self.assertIn("No available", log.output[0]) - # expect empty list - assert listed_mods == "" - - -def test_modules_list_in_wrong_repo_fail(self): - """Test listing available modules in a non-pipeline repo""" - # modify repotype in .nf-core.yml - with open(Path(self.pipeline_dir, ".nf-core.yml")) as fh: - nf_core_yml = yaml.safe_load(fh) - nf_core_yml_orig = nf_core_yml.copy() - nf_core_yml["repository_type"] = "modules" - nf_core_yml["org_path"] = "nf-core" - - print(nf_core_yml) - with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh: - yaml.safe_dump(nf_core_yml, fh) - # expect error logged - with self.assertLogs(level="ERROR") as log: - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components() - self.assertIn("must be run from a pipeline directory", log.output[0]) - # expect empty list - assert listed_mods == "" - # restore .nf-core.yml - with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh: - yaml.safe_dump(nf_core_yml_orig, fh) diff --git a/tests/modules/modules_json.py b/tests/modules/modules_json.py deleted file mode 100644 index e0100adfb7..0000000000 --- a/tests/modules/modules_json.py +++ /dev/null @@ -1,253 +0,0 @@ -import copy -import json -import shutil -from pathlib import Path - -from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import ( - NF_CORE_MODULES_DEFAULT_BRANCH, - NF_CORE_MODULES_NAME, - NF_CORE_MODULES_REMOTE, - ModulesRepo, -) -from nf_core.modules.patch import ModulePatch - - -def test_get_modules_json(self): - """Checks that the get_modules_json function returns the correct result""" - mod_json_path = Path(self.pipeline_dir, "modules.json") - with open(mod_json_path) as fh: - try: - mod_json_sb = json.load(fh) - except json.JSONDecodeError as e: - raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") - - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - - # Check that the modules.json hasn't changed - assert mod_json == mod_json_sb - - -def test_mod_json_update(self): - """Checks whether the update function works properly""" - mod_json_obj = ModulesJson(self.pipeline_dir) - # Update the modules.json file - mod_repo_obj = ModulesRepo() - mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False) - mod_json = mod_json_obj.get_modules_json() - assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] - assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"] - assert "GIT_SHA" == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"] - assert ( - NF_CORE_MODULES_DEFAULT_BRANCH - == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"] - ) - assert "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"] - - -def test_mod_json_create(self): - """Test creating a modules.json file from scratch""" - mod_json_path = Path(self.pipeline_dir, "modules.json") - # Remove the existing modules.json file - mod_json_path.unlink() - - # Create the new modules.json file - # (There are no prompts as long as there are only nf-core modules) - ModulesJson(self.pipeline_dir).create() - - # Check that the file exists - assert (mod_json_path).exists() - - # Get the contents of the file - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - - mods = ["fastqc", "multiqc"] - for mod in mods: - assert mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] - assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod] - assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod] - - -def modify_main_nf(path): - """Modify a file to test patch creation""" - with open(path) as fh: - lines = fh.readlines() - # Modify $meta.id to $meta.single_end - lines[1] = ' tag "$meta.single_end"\n' - with open(path, "w") as fh: - fh.writelines(lines) - - -def test_mod_json_create_with_patch(self): - """Test creating a modules.json file from scratch when there are patched modules""" - mod_json_path = Path(self.pipeline_dir, "modules.json") - - # Modify the module - module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc") - modify_main_nf(module_path / "main.nf") - - # Try creating a patch file - patch_obj = ModulePatch(self.pipeline_dir, NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_DEFAULT_BRANCH) - patch_obj.patch("fastqc") - - # Remove the existing modules.json file - mod_json_path.unlink() - - # Create the new modules.json file - ModulesJson(self.pipeline_dir).create() - - # Check that the file exists - assert mod_json_path.is_file() - - # Get the contents of the file - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - - # Check that fastqc is in the file - assert "fastqc" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] - assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"] - assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"] - - # Check that fastqc/main.nf maintains the changes - with open(module_path / "main.nf") as fh: - lines = fh.readlines() - assert lines[1] == ' tag "$meta.single_end"\n' - - -def test_mod_json_up_to_date(self): - """ - Checks if the modules.json file is up to date - when no changes have been made to the pipeline - """ - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json_before = mod_json_obj.get_modules_json() - mod_json_obj.check_up_to_date() - mod_json_after = mod_json_obj.get_modules_json() - - # Check that the modules.json hasn't changed - assert mod_json_before == mod_json_after - - -def test_mod_json_up_to_date_module_removed(self): - """ - Reinstall a module that has an entry in the modules.json - but is missing in the pipeline - """ - # Remove the fastqc module - fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc") - shutil.rmtree(fastqc_path) - - # Check that the modules.json file is up to date, and reinstall the module - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json_obj.check_up_to_date() - - # Check that the module has been reinstalled - files = ["main.nf", "meta.yml"] - assert fastqc_path.exists() - for f in files: - assert Path(fastqc_path, f).exists() - - -def test_mod_json_up_to_date_reinstall_fails(self): - """ - Try reinstalling a module where the git_sha is invalid - """ - mod_json_obj = ModulesJson(self.pipeline_dir) - - # Update the fastqc module entry to an invalid git_sha - mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True) - - # Remove the fastqc module - fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc") - shutil.rmtree(fastqc_path) - - # Check that the modules.json file is up to date, and remove the fastqc module entry - mod_json_obj.check_up_to_date() - mod_json = mod_json_obj.get_modules_json() - - # Check that the module has been removed from the modules.json - assert "fastqc" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] - - -def test_mod_json_repo_present(self): - """Tests the repo_present function""" - mod_json_obj = ModulesJson(self.pipeline_dir) - - assert mod_json_obj.repo_present(NF_CORE_MODULES_REMOTE) is True - assert mod_json_obj.repo_present("INVALID_REPO") is False - - -def test_mod_json_module_present(self): - """Tests the module_present function""" - mod_json_obj = ModulesJson(self.pipeline_dir) - - assert mod_json_obj.module_present("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is True - assert mod_json_obj.module_present("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is False - assert mod_json_obj.module_present("fastqc", "INVALID_REPO", "INVALID_DIR") is False - assert mod_json_obj.module_present("INVALID_MODULE", "INVALID_REPO", "INVALID_DIR") is False - - -def test_mod_json_get_module_version(self): - """Test the get_module_version function""" - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - assert ( - mod_json_obj.get_module_version("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) - == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]["git_sha"] - ) - assert mod_json_obj.get_module_version("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is None - - -def test_mod_json_dump(self): - """Tests the dump function""" - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - # Remove the modules.json file - mod_json_path = Path(self.pipeline_dir, "modules.json") - mod_json_path.unlink() - - # Check that the dump function creates the file - mod_json_obj.dump() - assert mod_json_path.exists() - - # Check that the dump function writes the correct content - with open(mod_json_path) as f: - try: - mod_json_new = json.load(f) - except json.JSONDecodeError as e: - raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") - assert mod_json == mod_json_new - - -def test_mod_json_with_empty_modules_value(self): - # Load module.json and remove the modules entry - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json_obj.create() # Create modules.json explicitly to get correct module sha - mod_json_orig = mod_json_obj.get_modules_json() - mod_json = copy.deepcopy(mod_json_orig) - mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = "" - # save the altered module.json and load it again to check if it will fix itself - mod_json_obj.modules_json = mod_json - mod_json_obj.dump() - mod_json_obj_new = ModulesJson(self.pipeline_dir) - mod_json_obj_new.check_up_to_date() - mod_json_new = mod_json_obj_new.get_modules_json() - assert mod_json_orig == mod_json_new - - -def test_mod_json_with_missing_modules_entry(self): - # Load module.json and remove the modules entry - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json_obj.create() # Create modules.json explicitly to get correct module sha - mod_json_orig = mod_json_obj.get_modules_json() - mod_json = copy.deepcopy(mod_json_orig) - mod_json["repos"][NF_CORE_MODULES_REMOTE].pop("modules") - # save the altered module.json and load it again to check if it will fix itself - mod_json_obj.modules_json = mod_json - mod_json_obj.dump() - mod_json_obj_new = ModulesJson(self.pipeline_dir) - mod_json_obj_new.check_up_to_date() - mod_json_new = mod_json_obj_new.get_modules_json() - assert mod_json_orig == mod_json_new diff --git a/tests/modules/patch.py b/tests/modules/patch.py deleted file mode 100644 index 513ea8a433..0000000000 --- a/tests/modules/patch.py +++ /dev/null @@ -1,360 +0,0 @@ -import os -import tempfile -from pathlib import Path -from unittest import mock - -import pytest - -import nf_core.components.components_command -import nf_core.modules - -from ..utils import GITLAB_URL - -""" -Test the 'nf-core modules patch' command - -Uses a branch (patch-tester) in the GitLab nf-core/modules-test repo when -testing if the update commands works correctly with patch files -""" - -ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2" -CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f" -SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e" -FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73" -BISMARK_ALIGN = "bismark/align" -REPO_NAME = "nf-core-test" -PATCH_BRANCH = "patch-tester" -REPO_URL = "https://gitlab.com/nf-core/modules-test.git" - - -def setup_patch(pipeline_dir, modify_module): - install_obj = nf_core.modules.ModuleInstall( - pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA - ) - - # Install the module - install_obj.install(BISMARK_ALIGN) - - if modify_module: - # Modify the module - module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - modify_main_nf(module_path / "main.nf") - - -def modify_main_nf(path): - """Modify a file to test patch creation""" - with open(path) as fh: - lines = fh.readlines() - # We want a patch file that looks something like: - # - tuple val(meta), path(reads) - # - path index - # + tuple val(meta), path(reads), path(index) - for line_index in range(len(lines)): - if lines[line_index] == " tuple val(meta), path(reads)\n": - lines[line_index] = " tuple val(meta), path(reads), path(index)\n" - elif lines[line_index] == " path index\n": - to_pop = line_index - lines.pop(to_pop) - with open(path, "w") as fh: - fh.writelines(lines) - - -def test_create_patch_no_change(self): - """Test creating a patch when there is no change to the module""" - setup_patch(self.pipeline_dir, False) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - with pytest.raises(UserWarning): - patch_obj.patch(BISMARK_ALIGN) - - module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - - # Check that no patch file has been added to the directory - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} - - # Check the 'modules.json' contains no patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None - - -def test_create_patch_change(self): - """Test creating a patch when there is a change to the module""" - setup_patch(self.pipeline_dir, True) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - # Check that the correct lines are in the patch file - with open(module_path / patch_fn) as fh: - patch_lines = fh.readlines() - module_relpath = module_path.relative_to(self.pipeline_dir) - assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf" - assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines - assert "- tuple val(meta), path(reads)\n" in patch_lines - assert "- path index\n" in patch_lines - assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines - - -def test_create_patch_try_apply_successful(self): - """ - Test creating a patch file and applying it to a new version of the the files - """ - - setup_patch(self.pipeline_dir, True) - module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN) - module_path = Path(self.pipeline_dir, module_relpath) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - update_obj = nf_core.modules.ModuleUpdate( - self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH - ) - # Install the new files - install_dir = Path(tempfile.mkdtemp()) - update_obj.install_component_files(BISMARK_ALIGN, SUCCEED_SHA, update_obj.modules_repo, install_dir) - - # Try applying the patch - module_install_dir = install_dir / BISMARK_ALIGN - patch_relpath = module_relpath / patch_fn - assert update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_relpath, module_path, module_install_dir) is True - - # Move the files from the temporary directory - update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA) - - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - # Check that the correct lines are in the patch file - with open(module_path / patch_fn) as fh: - patch_lines = fh.readlines() - module_relpath = module_path.relative_to(self.pipeline_dir) - assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines - assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines - assert "- tuple val(meta), path(reads)\n" in patch_lines - assert "- path index\n" in patch_lines - assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines - - # Check that 'main.nf' is updated correctly - with open(module_path / "main.nf") as fh: - main_nf_lines = fh.readlines() - # These lines should have been removed by the patch - assert " tuple val(meta), path(reads)\n" not in main_nf_lines - assert " path index\n" not in main_nf_lines - # This line should have been added - assert " tuple val(meta), path(reads), path(index)\n" in main_nf_lines - - -def test_create_patch_try_apply_failed(self): - """ - Test creating a patch file and applying it to a new version of the the files - """ - - setup_patch(self.pipeline_dir, True) - module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN) - module_path = Path(self.pipeline_dir, module_relpath) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - update_obj = nf_core.modules.ModuleUpdate( - self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH - ) - # Install the new files - install_dir = Path(tempfile.mkdtemp()) - update_obj.install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, install_dir) - - # Try applying the patch - module_install_dir = install_dir / BISMARK_ALIGN - patch_path = module_relpath / patch_fn - assert update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_path, module_path, module_install_dir) is False - - -def test_create_patch_update_success(self): - """ - Test creating a patch file and the updating the module - - Should have the same effect as 'test_create_patch_try_apply_successful' - but uses higher level api - """ - - setup_patch(self.pipeline_dir, True) - module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - # Update the module - update_obj = nf_core.modules.ModuleUpdate( - self.pipeline_dir, - sha=SUCCEED_SHA, - show_diff=False, - update_deps=True, - remote_url=GITLAB_URL, - branch=PATCH_BRANCH, - ) - assert update_obj.update(BISMARK_ALIGN) - - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ), modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) - - # Check that the correct lines are in the patch file - with open(module_path / patch_fn) as fh: - patch_lines = fh.readlines() - module_relpath = module_path.relative_to(self.pipeline_dir) - assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines - assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines - assert "- tuple val(meta), path(reads)\n" in patch_lines - assert "- path index\n" in patch_lines - assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines - - # Check that 'main.nf' is updated correctly - with open(module_path / "main.nf") as fh: - main_nf_lines = fh.readlines() - # These lines should have been removed by the patch - assert " tuple val(meta), path(reads)\n" not in main_nf_lines - assert " path index\n" not in main_nf_lines - # This line should have been added - assert " tuple val(meta), path(reads), path(index)\n" in main_nf_lines - - -def test_create_patch_update_fail(self): - """ - Test creating a patch file and updating a module when there is a diff conflict - """ - - setup_patch(self.pipeline_dir, True) - module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - # Save the file contents for downstream comparison - with open(module_path / patch_fn) as fh: - patch_contents = fh.read() - - update_obj = nf_core.modules.ModuleUpdate( - self.pipeline_dir, sha=FAIL_SHA, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=PATCH_BRANCH - ) - update_obj.update(BISMARK_ALIGN) - - # Check that the installed files have not been affected by the attempted patch - temp_dir = Path(tempfile.mkdtemp()) - nf_core.components.components_command.ComponentCommand( - "modules", self.pipeline_dir, GITLAB_URL, PATCH_BRANCH - ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir) - - temp_module_dir = temp_dir / BISMARK_ALIGN - for file in os.listdir(temp_module_dir): - assert file in os.listdir(module_path) - with open(module_path / file) as fh: - installed = fh.read() - with open(temp_module_dir / file) as fh: - shouldbe = fh.read() - assert installed == shouldbe - - # Check that the patch file is unaffected - with open(module_path / patch_fn) as fh: - new_patch_contents = fh.read() - assert patch_contents == new_patch_contents - - -def test_remove_patch(self): - """Test creating a patch when there is no change to the module""" - setup_patch(self.pipeline_dir, True) - - # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - - # Check that a patch file with the correct name has been created - patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} - - # Check the 'modules.json' contains a patch file for the module - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( - "modules", REPO_NAME, BISMARK_ALIGN, patch_fn - ) - - with mock.patch.object(nf_core.components.patch.questionary, "confirm") as mock_questionary: - mock_questionary.unsafe_ask.return_value = True - patch_obj.remove(BISMARK_ALIGN) - # Check that the diff file has been removed - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} - - # Check that the 'modules.json' entry has been removed - modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) - assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None diff --git a/tests/modules/remove.py b/tests/modules/remove.py deleted file mode 100644 index e412fd35a8..0000000000 --- a/tests/modules/remove.py +++ /dev/null @@ -1,22 +0,0 @@ -import os - - -def test_modules_remove_trimgalore(self): - """Test removing TrimGalore! module after installing it""" - self.mods_install.install("trimgalore") - module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore") - assert self.mods_remove.remove("trimgalore") - assert os.path.exists(module_path) is False - - -def test_modules_remove_trimgalore_uninstalled(self): - """Test removing TrimGalore! module without installing it""" - assert self.mods_remove.remove("trimgalore") is False - - -def test_modules_remove_multiqc_from_gitlab(self): - """Test removing multiqc module after installing it from an alternative source""" - self.mods_install_gitlab.install("multiqc") - module_path = os.path.join(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc") - assert self.mods_remove_gitlab.remove("multiqc", force=True) - assert os.path.exists(module_path) is False diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py new file mode 100644 index 0000000000..29e030668d --- /dev/null +++ b/tests/modules/test_bump_versions.py @@ -0,0 +1,50 @@ +import os +import re + +import pytest + +import nf_core.modules +from nf_core.modules.modules_utils import ModuleExceptionError + +from ..test_modules import TestModules + + +class TestModulesBumpVersions(TestModules): + def test_modules_bump_versions_single_module(self): + """Test updating a single module""" + # Change the bpipe/test version to an older version + env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml") + with open(env_yml_path) as fh: + content = fh.read() + new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content) + with open(env_yml_path, "w") as fh: + fh.write(new_content) + version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper.bump_versions(module="bpipe/test") + assert len(version_bumper.failed) == 0 + + def test_modules_bump_versions_all_modules(self): + """Test updating all modules""" + version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper.bump_versions(all_modules=True) + assert len(version_bumper.failed) == 0 + + def test_modules_bump_versions_fail(self): + """Fail updating a module with wrong name""" + version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + with pytest.raises(ModuleExceptionError) as excinfo: + version_bumper.bump_versions(module="no/module") + assert "Could not find the specified module:" in str(excinfo.value) + + def test_modules_bump_versions_fail_unknown_version(self): + """Fail because of an unknown version""" + # Change the bpipe/test version to an older version + env_yml_path = os.path.join(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml") + with open(env_yml_path) as fh: + content = fh.read() + new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content) + with open(env_yml_path, "w") as fh: + fh.write(new_content) + version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper.bump_versions(module="bpipe/test") + assert "Conda package had unknown version" in version_bumper.failed[0][0] diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py new file mode 100644 index 0000000000..c847501830 --- /dev/null +++ b/tests/modules/test_create.py @@ -0,0 +1,164 @@ +import os +import shutil +from pathlib import Path +from unittest import mock + +import pytest +import requests_cache +import responses +import yaml +from git.repo import Repo + +import nf_core.modules +from tests.utils import ( + GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, + GITLAB_URL, + mock_anaconda_api_calls, + mock_biocontainers_api_calls, +) + +from ..test_modules import TestModules + + +class TestModulesCreate(TestModules): + def test_modules_create_succeed(self): + """Succeed at creating the TrimGalore! module""" + with responses.RequestsMock() as rsps: + mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") + mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") + module_create = nf_core.modules.ModuleCreate( + self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore" + ) + with requests_cache.disabled(): + module_create.create() + assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf")) + + def test_modules_create_fail_exists(self): + """Fail at creating the same module twice""" + with responses.RequestsMock() as rsps: + mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") + mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") + module_create = nf_core.modules.ModuleCreate( + self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore" + ) + with requests_cache.disabled(): + module_create.create() + with pytest.raises(UserWarning) as excinfo: + with requests_cache.disabled(): + module_create.create() + assert "Module file exists already" in str(excinfo.value) + + def test_modules_create_nfcore_modules(self): + """Create a module in nf-core/modules clone""" + with responses.RequestsMock() as rsps: + mock_anaconda_api_calls(rsps, "fastqc", "0.11.9") + mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9") + module_create = nf_core.modules.ModuleCreate( + self.nfcore_modules, "fastqc", "@author", "process_low", False, False + ) + with requests_cache.disabled(): + module_create.create() + assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "main.nf")) + assert os.path.exists( + os.path.join(self.nfcore_modules, "modules", "nf-core", "fastqc", "tests", "main.nf.test") + ) + + def test_modules_create_nfcore_modules_subtool(self): + """Create a tool/subtool module in a nf-core/modules clone""" + with responses.RequestsMock() as rsps: + mock_anaconda_api_calls(rsps, "star", "2.8.10a") + mock_biocontainers_api_calls(rsps, "star", "2.8.10a") + module_create = nf_core.modules.ModuleCreate( + self.nfcore_modules, "star/index", "@author", "process_medium", False, False + ) + with requests_cache.disabled(): + module_create.create() + assert os.path.exists(os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "main.nf")) + assert os.path.exists( + os.path.join(self.nfcore_modules, "modules", "nf-core", "star", "index", "tests", "main.nf.test") + ) + + @mock.patch("rich.prompt.Confirm.ask") + def test_modules_migrate(self, mock_rich_ask): + """Create a module with the --migrate-pytest option to convert pytest to nf-test""" + pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") + module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort") + + # Clone modules repo with pytests + shutil.rmtree(self.nfcore_modules) + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) + with open(module_dir / "main.nf") as fh: + old_main_nf = fh.read() + with open(module_dir / "meta.yml") as fh: + old_meta_yml = fh.read() + + # Create a module with --migrate-pytest + mock_rich_ask.return_value = True + module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create.create() + + with open(module_dir / "main.nf") as fh: + new_main_nf = fh.read() + with open(module_dir / "meta.yml") as fh: + new_meta_yml = fh.read() + nextflow_config = module_dir / "tests" / "nextflow.config" + + # Check that old files have been copied to the new module + assert old_main_nf == new_main_nf + assert old_meta_yml == new_meta_yml + assert nextflow_config.is_file() + + # Check that pytest folder is deleted + assert not pytest_dir.is_dir() + + # Check that pytest_modules.yml is updated + with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: + modules_yml = yaml.safe_load(fh) + assert "samtools/sort" not in modules_yml.keys() + + @mock.patch("rich.prompt.Confirm.ask") + def test_modules_migrate_no_delete(self, mock_rich_ask): + """Create a module with the --migrate-pytest option to convert pytest to nf-test. + Test that pytest directory is not deleted.""" + pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") + + # Clone modules repo with pytests + shutil.rmtree(self.nfcore_modules) + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) + + # Create a module with --migrate-pytest + mock_rich_ask.return_value = False + module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create.create() + + # Check that pytest folder is not deleted + assert pytest_dir.is_dir() + + # Check that pytest_modules.yml is updated + with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh: + modules_yml = yaml.safe_load(fh) + assert "samtools/sort" not in modules_yml.keys() + + @mock.patch("rich.prompt.Confirm.ask") + def test_modules_migrate_symlink(self, mock_rich_ask): + """Create a module with the --migrate-pytest option to convert pytest with symlinks to nf-test. + Test that the symlink is deleted and the file is copied.""" + + pytest_dir = Path(self.nfcore_modules, "tests", "modules", "nf-core", "samtools", "sort") + module_dir = Path(self.nfcore_modules, "modules", "nf-core", "samtools", "sort") + + # Clone modules repo with pytests + shutil.rmtree(self.nfcore_modules) + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH) + + # Create a symlinked file in the pytest directory + symlink_file = pytest_dir / "symlink_file.txt" + symlink_file.symlink_to(module_dir / "main.nf") + + # Create a module with --migrate-pytest + mock_rich_ask.return_value = True + module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create.create() + + # Check that symlink is deleted + assert not symlink_file.is_symlink() diff --git a/tests/modules/test_info.py b/tests/modules/test_info.py new file mode 100644 index 0000000000..8906854044 --- /dev/null +++ b/tests/modules/test_info.py @@ -0,0 +1,62 @@ +from rich.console import Console + +import nf_core.modules + +from ..test_modules import TestModules +from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL + + +class TestModulesCreate(TestModules): + def test_modules_info_remote(self): + """Test getting info about a remote module""" + mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc") + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Module: fastqc" in output + assert "Inputs" in output + assert "Outputs" in output + + def test_modules_info_remote_gitlab(self): + """Test getting info about a module in the remote gitlab repo""" + mods_info = nf_core.modules.ModuleInfo( + self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH + ) + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Module: fastqc" in output + assert "Inputs" in output + assert "Outputs" in output + assert "--git-remote" in output + + def test_modules_info_local(self): + """Test getting info about a locally installed module""" + self.mods_install.install("trimgalore") + mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore") + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Module: trimgalore" in output + assert "Inputs" in output + assert "Outputs" in output + assert "Location" in output + + def test_modules_info_in_modules_repo(self): + """Test getting info about a module in the modules repo""" + mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc") + mods_info.local = True + mods_info_output = mods_info.get_component_info() + console = Console(record=True) + console.print(mods_info_output) + output = console.export_text() + + assert "Module: fastqc" in output + assert "Inputs" in output + assert "Outputs" in output diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py new file mode 100644 index 0000000000..b90f01ee61 --- /dev/null +++ b/tests/modules/test_install.py @@ -0,0 +1,90 @@ +import os +from pathlib import Path + +import pytest + +from nf_core.modules.install import ModuleInstall +from nf_core.modules.modules_json import ModulesJson + +from ..test_modules import TestModules +from ..utils import ( + GITLAB_BRANCH_ORG_PATH_BRANCH, + GITLAB_BRANCH_TEST_BRANCH, + GITLAB_REPO, + GITLAB_URL, + with_temporary_folder, +) + + +class TestModulesCreate(TestModules): + def test_modules_install_nopipeline(self): + """Test installing a module - no pipeline given""" + self.mods_install.dir = None + assert self.mods_install.install("foo") is False + + @with_temporary_folder + def test_modules_install_emptypipeline(self, tmpdir): + """Test installing a module - empty dir given""" + os.mkdir(os.path.join(tmpdir, "nf-core-pipe")) + self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe") + with pytest.raises(UserWarning) as excinfo: + self.mods_install.install("foo") + assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) + + def test_modules_install_nomodule(self): + """Test installing a module - unrecognised module given""" + assert self.mods_install.install("foo") is False + + def test_modules_install_trimgalore(self): + """Test installing a module - TrimGalore!""" + assert self.mods_install.install("trimgalore") is not False + assert self.mods_install.dir is not None + module_path = Path(self.mods_install.dir, "modules", "nf-core", "trimgalore") + assert os.path.exists(module_path) + + def test_modules_install_trimgalore_twice(self): + """Test installing a module - TrimGalore! already there""" + self.mods_install.install("trimgalore") + assert self.mods_install.install("trimgalore") is True + + def test_modules_install_from_gitlab(self): + """Test installing a module from GitLab""" + assert self.mods_install_gitlab.install("fastqc") is True + + def test_modules_install_different_branch_fail(self): + """Test installing a module from a different branch""" + install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) + # The FastQC module does not exists in the branch-test branch + assert install_obj.install("fastqc") is False + + def test_modules_install_different_branch_succeed(self): + """Test installing a module from a different branch""" + install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) + # The fastp module does exists in the branch-test branch + assert install_obj.install("fastp") is True + + # Verify that the branch entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + assert ( + modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) + == GITLAB_BRANCH_TEST_BRANCH + ) + + def test_modules_install_tracking(self): + """Test installing a module and finding 'modules' in the installed_by section of modules.json""" + self.mods_install.install("trimgalore") + + # Verify that the installed_by entry was added correctly + modules_json = ModulesJson(self.pipeline_dir) + mod_json = modules_json.get_modules_json() + assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][ + "installed_by" + ] == ["modules"] + + def test_modules_install_alternate_remote(self): + """Test installing a module from a different remote with the same organization path""" + install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_ORG_PATH_BRANCH) + # Install fastqc from GitLab which is also installed from GitHub with the same org_path + with pytest.raises(Exception) as excinfo: + install_obj.install("fastqc") + assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py new file mode 100644 index 0000000000..6448916acf --- /dev/null +++ b/tests/modules/test_lint.py @@ -0,0 +1,865 @@ +import json +from pathlib import Path +from typing import Union + +import pytest +import yaml +from git.repo import Repo + +import nf_core.modules +from nf_core.modules.lint import main_nf +from nf_core.utils import set_wd + +from ..test_modules import TestModules +from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL +from .test_patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf + +PROCESS_LABEL_GOOD = ( + """ + label 'process_high' + cpus 12 + """, + 1, + 0, + 0, +) +PROCESS_LABEL_NON_ALPHANUMERIC = ( + """ + label 'a:label:with:colons' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_GOOD_CONFLICTING = ( + """ + label 'process_high' + label 'process_low' + cpus 12 + """, + 0, + 1, + 0, +) +PROCESS_LABEL_GOOD_DUPLICATES = ( + """ + label 'process_high' + label 'process_high' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( + """ + label 'process_high' + label 'process_extra_label' + cpus 12 + """, + 1, + 1, + 0, +) +PROCESS_LABEL_NONSTANDARD = ( + """ + label 'process_extra_label' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_NONSTANDARD_DUPLICATES = ( + """ + label process_extra_label + label process_extra_label + cpus 12 + """, + 0, + 3, + 0, +) +PROCESS_LABEL_NONE_FOUND = ( + """ + cpus 12 + """, + 0, + 1, + 0, +) + +PROCESS_LABEL_TEST_CASES = [ + PROCESS_LABEL_GOOD, + PROCESS_LABEL_NON_ALPHANUMERIC, + PROCESS_LABEL_GOOD_CONFLICTING, + PROCESS_LABEL_GOOD_DUPLICATES, + PROCESS_LABEL_GOOD_AND_NONSTANDARD, + PROCESS_LABEL_NONSTANDARD, + PROCESS_LABEL_NONSTANDARD_DUPLICATES, + PROCESS_LABEL_NONE_FOUND, +] + + +# Test cases for linting the container definitions + +CONTAINER_SINGLE_GOOD = ( + "Single-line container definition should pass", + """ + container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package + """, + 2, # passed + 0, # warned + 0, # failed +) + +CONTAINER_TWO_LINKS_GOOD = ( + "Multi-line container definition should pass", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 6, + 0, + 0, +) + +CONTAINER_WITH_SPACE_BAD = ( + "Space in container URL should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 5, + 0, + 1, +) + +CONTAINER_MULTIPLE_DBLQUOTES_BAD = ( + "Incorrect quoting of container string should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" + """, + 4, + 0, + 1, +) + +CONTAINER_TEST_CASES = [ + CONTAINER_SINGLE_GOOD, + CONTAINER_TWO_LINKS_GOOD, + CONTAINER_WITH_SPACE_BAD, + CONTAINER_MULTIPLE_DBLQUOTES_BAD, +] + + +class TestModulesCreate(TestModules): + def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): + install_obj = nf_core.modules.ModuleInstall( + pipeline_dir, + prompt=False, + force=False, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + sha=CORRECT_SHA, + ) + + # Install the module + install_obj.install(BISMARK_ALIGN) + + if modify_module: + # Modify the module + module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + modify_main_nf(module_path / "main.nf") + + def test_modules_lint_trimgalore(self): + """Test linting the TrimGalore! module""" + self.mods_install.install("trimgalore") + module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) + module_lint.lint(print_results=False, module="trimgalore") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_empty(self): + """Test linting a pipeline with no modules installed""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + with pytest.raises(LookupError): + nf_core.modules.ModuleLint(dir=self.pipeline_dir) + + def test_modules_lint_new_modules(self): + """lint a new module""" + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_no_gitlab(self): + """Test linting a pipeline with no modules installed""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + with pytest.raises(LookupError): + nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + + def test_modules_lint_gitlab_modules(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("fastqc") + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 2 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_multiple_remotes(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 1 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_registry(self): + """Test linting the samtools module and alternative registry""" + self.mods_install.install("samtools") + module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws") + module_lint.lint(print_results=False, module="samtools") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_patched_modules(self): + """ + Test creating a patch file and applying it to a new version of the the files + """ + self._setup_patch(str(self.pipeline_dir), True) + + # Create a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + # change temporarily working directory to the pipeline directory + # to avoid error from try_apply_patch() during linting + with set_wd(self.pipeline_dir): + module_lint = nf_core.modules.ModuleLint( + dir=self.pipeline_dir, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + hide_progress=True, + ) + module_lint.lint( + print_results=False, + all_modules=True, + ) + + assert len(module_lint.failed) == 1 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_check_process_labels(self): + for test_case in PROCESS_LABEL_TEST_CASES: + process, passed, warned, failed = test_case + mocked_ModuleLint = MockModuleLint() + main_nf.check_process_labels(mocked_ModuleLint, process.splitlines()) + assert len(mocked_ModuleLint.passed) == passed + assert len(mocked_ModuleLint.warned) == warned + assert len(mocked_ModuleLint.failed) == failed + + def test_modules_lint_check_url(self): + for test_case in CONTAINER_TEST_CASES: + test, process, passed, warned, failed = test_case + mocked_ModuleLint = MockModuleLint() + for line in process.splitlines(): + if line.strip(): + main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io") + + assert ( + len(mocked_ModuleLint.passed) == passed + ), f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}." + assert ( + len(mocked_ModuleLint.warned) == warned + ), f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}." + assert ( + len(mocked_ModuleLint.failed) == failed + ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." + + def test_modules_lint_snapshot_file(self): + """Test linting a module with a snapshot file""" + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_snapshot_file_missing_fail(self): + """Test linting a module with a snapshot file missing, which should fail""" + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).unlink() + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).touch() + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snapshot_exists" + + def test_modules_lint_snapshot_file_not_needed(self): + """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ) + ) as fh: + content = fh.read() + new_content = content.replace("snapshot(", "snap (") + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ), + "w", + ) as fh: + fh.write(new_content) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_doesnt_exists(self): + """Test linting a module with an environment.yml file""" + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "environment.yml").rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml.bak", + ) + ) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml.bak", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_exists" + + def test_modules_environment_yml_file_sorted_correctly(self): + """Test linting a module with a correctly sorted environment.yml file""" + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_sorted_incorrectly(self): + """Test linting a module with an incorrectly sorted environment.yml file""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: + yaml_content = yaml.safe_load(fh) + # Add a new dependency to the environment.yml file and reverse the order + yaml_content["dependencies"].append("z") + yaml_content["dependencies"].reverse() + yaml_content = yaml.dump(yaml_content) + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml_content) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + # we fix the sorting on the fly, so this should pass + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_not_array(self): + """Test linting a module with an incorrectly formatted environment.yml file""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: + yaml_content = yaml.safe_load(fh) + yaml_content["dependencies"] = "z" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml.dump(yaml_content)) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_valid" + + def test_modules_environment_yml_file_name_mismatch(self): + """Test linting a module with a different name in the environment.yml file""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: + yaml_content = yaml.safe_load(fh) + yaml_content["name"] = "bpipe-test" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml.dump(yaml_content)) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + # reset changes + yaml_content["name"] = "bpipe_test" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml.dump(yaml_content)) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_name" + + def test_modules_meta_yml_incorrect_licence_field(self): + """Test linting a module with an incorrect Licence field in meta.yml""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: + meta_yml = yaml.safe_load(fh) + meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]" + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # reset changes + meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "meta_yml_valid" + + def test_modules_meta_yml_input_mismatch(self): + """Test linting a module with an extra entry in input fields in meta.yml compared to module.input""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: + main_nf = fh.read() + main_nf_new = main_nf.replace("path bam", "path bai") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf_new) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) == 2 + lint_tests = [x.lint_test for x in module_lint.warned] + # check that it is there twice: + assert lint_tests.count("meta_input_meta_only") == 1 + assert lint_tests.count("meta_input_main_only") == 1 + + def test_modules_meta_yml_output_mismatch(self): + """Test linting a module with an extra entry in output fields in meta.yml compared to module.output""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: + main_nf = fh.read() + main_nf_new = main_nf.replace("emit: bam", "emit: bai") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf_new) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) == 2 + lint_tests = [x.lint_test for x in module_lint.warned] + # check that it is there twice: + assert lint_tests.count("meta_output_meta_only") == 1 + assert lint_tests.count("meta_output_main_only") == 1 + + def test_modules_meta_yml_incorrect_name(self): + """Test linting a module with an incorrect name in meta.yml""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: + meta_yml = yaml.safe_load(fh) + meta_yml["name"] = "bpipe/test" + # need to make the same change to the environment.yml file + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ) + ) as fh: + environment_yml = yaml.safe_load(fh) + environment_yml["name"] = "bpipe/test" + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml.dump(environment_yml)) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # reset changes + meta_yml["name"] = "bpipe_test" + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + environment_yml["name"] = "bpipe_test" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "environment.yml", + ), + "w", + ) as fh: + fh.write(yaml.dump(environment_yml)) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "meta_name" + + def test_modules_missing_test_dir(self): + """Test linting a module with a missing test directory""" + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") + ) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") + ) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_dir_exists" + + def test_modules_missing_test_main_nf(self): + """Test linting a module with a missing test/main.nf file""" + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.bak", + ) + ) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.bak", + ).rename( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ) + ) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_main_nf_exists" + + def test_modules_unused_pytest_files(self): + """Test linting a nf-test module with files still present in `tests/modules/`""" + Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_old_test_dir" + + def test_nftest_failing_linting(self): + """Test linting a module which includes other modules in nf-test tests. + Linting tests""" + # Clone modules repo with testing modules + tmp_dir = self.nfcore_modules.parent + self.nfcore_modules = Path(tmp_dir, "modules-test") + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) + + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="kallisto/quant") + + assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_valid" + assert module_lint.failed[1].lint_test == "meta_yml_valid" + assert module_lint.failed[2].lint_test == "test_main_tags" + assert "kallisto/index" in module_lint.failed[2].message + + def test_modules_absent_version(self): + """Test linting a nf-test module if the versions is absent in the snapshot file `""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) + ) as fh: + content = fh.read() + new_content = content.replace("versions", "foo") + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ), + "w", + ) as fh: + fh.write(new_content) + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ), + "w", + ) as fh: + fh.write(content) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snap_versions" + + def test_modules_empty_file_in_snapshot(self): + """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" + snap_file = Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snap_md5sum" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + def test_modules_empty_file_in_stub_snapshot(self): + """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" + snap_file = Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ) + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed) + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + + self.main_nf = "main_nf" diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py new file mode 100644 index 0000000000..81484cc8f0 --- /dev/null +++ b/tests/modules/test_list.py @@ -0,0 +1,126 @@ +import json +from pathlib import Path + +import yaml +from rich.console import Console + +import nf_core.modules + +from ..test_modules import TestModules +from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL + + +class TestModulesCreate(TestModules): + def test_modules_list_remote(self): + """Test listing available modules""" + mods_list = nf_core.modules.ModuleList(None, remote=True) + listed_mods = mods_list.list_components() + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "fastqc" in output + + def test_modules_list_remote_gitlab(self): + """Test listing the modules in the remote gitlab repo""" + mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) + listed_mods = mods_list.list_components() + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "fastqc" in output + + def test_modules_list_pipeline(self): + """Test listing locally installed modules""" + mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + listed_mods = mods_list.list_components() + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "fastqc" in output + assert "multiqc" in output + + def test_modules_install_and_list_pipeline(self): + """Test listing locally installed modules""" + self.mods_install.install("trimgalore") + mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + listed_mods = mods_list.list_components() + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "trimgalore" in output + + def test_modules_install_gitlab_and_list_pipeline(self): + """Test listing locally installed modules""" + self.mods_install_gitlab.install("fastqc") + mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + listed_mods = mods_list.list_components() + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "fastqc" in output + + def test_modules_list_local_json(self): + """Test listing locally installed modules as JSON""" + mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + listed_mods = mods_list.list_components(print_json=True) + listed_mods = json.loads(listed_mods) + assert "fastqc" in listed_mods + assert "multiqc" in listed_mods + + def test_modules_list_remote_json(self): + """Test listing available modules as JSON""" + mods_list = nf_core.modules.ModuleList(None, remote=True) + listed_mods = mods_list.list_components(print_json=True) + listed_mods = json.loads(listed_mods) + assert "fastqc" in listed_mods + assert "multiqc" in listed_mods + + def test_modules_list_with_one_keyword(self): + """Test listing available modules with one keyword""" + mods_list = nf_core.modules.ModuleList(None, remote=True) + listed_mods = mods_list.list_components(keywords=["qc"]) + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "multiqc" in output + + def test_modules_list_with_keywords(self): + """Test listing available modules with multiple keywords""" + mods_list = nf_core.modules.ModuleList(None, remote=True) + listed_mods = mods_list.list_components(keywords=["fastq", "qc"]) + console = Console(record=True) + console.print(listed_mods) + output = console.export_text() + assert "fastqc" in output + + def test_modules_list_with_unused_keyword(self): + """Test listing available modules with an unused keyword""" + mods_list = nf_core.modules.ModuleList(None, remote=True) + with self.assertLogs(level="INFO") as log: + listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"]) + self.assertIn("No available", log.output[0]) + # expect empty list + assert listed_mods == "" + + def test_modules_list_in_wrong_repo_fail(self): + """Test listing available modules in a non-pipeline repo""" + # modify repotype in .nf-core.yml + with open(Path(self.pipeline_dir, ".nf-core.yml")) as fh: + nf_core_yml = yaml.safe_load(fh) + nf_core_yml_orig = nf_core_yml.copy() + nf_core_yml["repository_type"] = "modules" + nf_core_yml["org_path"] = "nf-core" + + print(nf_core_yml) + with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh: + yaml.safe_dump(nf_core_yml, fh) + # expect error logged + with self.assertLogs(level="ERROR") as log: + mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + listed_mods = mods_list.list_components() + self.assertIn("must be run from a pipeline directory", log.output[0]) + # expect empty list + assert listed_mods == "" + # restore .nf-core.yml + with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh: + yaml.safe_dump(nf_core_yml_orig, fh) diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py new file mode 100644 index 0000000000..319b5ad657 --- /dev/null +++ b/tests/modules/test_modules_json.py @@ -0,0 +1,245 @@ +import copy +import json +import shutil +from pathlib import Path + +from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_repo import ( + NF_CORE_MODULES_DEFAULT_BRANCH, + NF_CORE_MODULES_NAME, + NF_CORE_MODULES_REMOTE, + ModulesRepo, +) +from nf_core.modules.patch import ModulePatch + +from ..test_modules import TestModules + + +class TestModulesCreate(TestModules): + def test_get_modules_json(self): + """Checks that the get_modules_json function returns the correct result""" + mod_json_path = Path(self.pipeline_dir, "modules.json") + with open(mod_json_path) as fh: + try: + mod_json_sb = json.load(fh) + except json.JSONDecodeError as e: + raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") + + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + + # Check that the modules.json hasn't changed + assert mod_json == mod_json_sb + + def test_mod_json_update(self): + """Checks whether the update function works properly""" + mod_json_obj = ModulesJson(self.pipeline_dir) + # Update the modules.json file + mod_repo_obj = ModulesRepo() + mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False) + mod_json = mod_json_obj.get_modules_json() + assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] + assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"] + assert "GIT_SHA" == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["git_sha"] + assert ( + NF_CORE_MODULES_DEFAULT_BRANCH + == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["branch"] + ) + assert ( + "modules" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"]["installed_by"] + ) + + def test_mod_json_create(self): + """Test creating a modules.json file from scratch""" + mod_json_path = Path(self.pipeline_dir, "modules.json") + # Remove the existing modules.json file + mod_json_path.unlink() + + # Create the new modules.json file + # (There are no prompts as long as there are only nf-core modules) + ModulesJson(self.pipeline_dir).create() + + # Check that the file exists + assert (mod_json_path).exists() + + # Get the contents of the file + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + + mods = ["fastqc", "multiqc"] + for mod in mods: + assert mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] + assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod] + assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"][mod] + + def _modify_main_nf(self, path): + """Modify a file to test patch creation""" + with open(path) as fh: + lines = fh.readlines() + # Modify $meta.id to $meta.single_end + lines[1] = ' tag "$meta.single_end"\n' + with open(path, "w") as fh: + fh.writelines(lines) + + def test_mod_json_create_with_patch(self): + """Test creating a modules.json file from scratch when there are patched modules""" + mod_json_path = Path(self.pipeline_dir, "modules.json") + + # Modify the module + module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc") + self._modify_main_nf(module_path / "main.nf") + + # Try creating a patch file + patch_obj = ModulePatch(self.pipeline_dir, NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_DEFAULT_BRANCH) + patch_obj.patch("fastqc") + + # Remove the existing modules.json file + mod_json_path.unlink() + + # Create the new modules.json file + ModulesJson(self.pipeline_dir).create() + + # Check that the file exists + assert mod_json_path.is_file() + + # Get the contents of the file + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + + # Check that fastqc is in the file + assert "fastqc" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] + assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"] + assert "branch" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"] + + # Check that fastqc/main.nf maintains the changes + with open(module_path / "main.nf") as fh: + lines = fh.readlines() + assert lines[1] == ' tag "$meta.single_end"\n' + + def test_mod_json_up_to_date(self): + """ + Checks if the modules.json file is up to date + when no changes have been made to the pipeline + """ + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json_before = mod_json_obj.get_modules_json() + mod_json_obj.check_up_to_date() + mod_json_after = mod_json_obj.get_modules_json() + + # Check that the modules.json hasn't changed + assert mod_json_before == mod_json_after + + def test_mod_json_up_to_date_module_removed(self): + """ + Reinstall a module that has an entry in the modules.json + but is missing in the pipeline + """ + # Remove the fastqc module + fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc") + shutil.rmtree(fastqc_path) + + # Check that the modules.json file is up to date, and reinstall the module + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json_obj.check_up_to_date() + + # Check that the module has been reinstalled + files = ["main.nf", "meta.yml"] + assert fastqc_path.exists() + for f in files: + assert Path(fastqc_path, f).exists() + + def test_mod_json_up_to_date_reinstall_fails(self): + """ + Try reinstalling a module where the git_sha is invalid + """ + mod_json_obj = ModulesJson(self.pipeline_dir) + + # Update the fastqc module entry to an invalid git_sha + mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True) + + # Remove the fastqc module + fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc") + shutil.rmtree(fastqc_path) + + # Check that the modules.json file is up to date, and remove the fastqc module entry + mod_json_obj.check_up_to_date() + mod_json = mod_json_obj.get_modules_json() + + # Check that the module has been removed from the modules.json + assert "fastqc" not in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] + + def test_mod_json_repo_present(self): + """Tests the repo_present function""" + mod_json_obj = ModulesJson(self.pipeline_dir) + + assert mod_json_obj.repo_present(NF_CORE_MODULES_REMOTE) is True + assert mod_json_obj.repo_present("INVALID_REPO") is False + + def test_mod_json_module_present(self): + """Tests the module_present function""" + mod_json_obj = ModulesJson(self.pipeline_dir) + + assert mod_json_obj.module_present("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is True + assert mod_json_obj.module_present("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is False + assert mod_json_obj.module_present("fastqc", "INVALID_REPO", "INVALID_DIR") is False + assert mod_json_obj.module_present("INVALID_MODULE", "INVALID_REPO", "INVALID_DIR") is False + + def test_mod_json_get_module_version(self): + """Test the get_module_version function""" + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + assert ( + mod_json_obj.get_module_version("fastqc", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) + == mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["fastqc"]["git_sha"] + ) + assert mod_json_obj.get_module_version("INVALID_MODULE", NF_CORE_MODULES_REMOTE, NF_CORE_MODULES_NAME) is None + + def test_mod_json_dump(self): + """Tests the dump function""" + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + # Remove the modules.json file + mod_json_path = Path(self.pipeline_dir, "modules.json") + mod_json_path.unlink() + + # Check that the dump function creates the file + mod_json_obj.dump() + assert mod_json_path.exists() + + # Check that the dump function writes the correct content + with open(mod_json_path) as f: + try: + mod_json_new = json.load(f) + except json.JSONDecodeError as e: + raise UserWarning(f"Unable to load JSON file '{mod_json_path}' due to error {e}") + assert mod_json == mod_json_new + + def test_mod_json_with_empty_modules_value(self): + # Load module.json and remove the modules entry + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json_obj.create() # Create modules.json explicitly to get correct module sha + mod_json_orig = mod_json_obj.get_modules_json() + mod_json = copy.deepcopy(mod_json_orig) + mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = "" + # save the altered module.json and load it again to check if it will fix itself + mod_json_obj.modules_json = mod_json + mod_json_obj.dump() + mod_json_obj_new = ModulesJson(self.pipeline_dir) + mod_json_obj_new.check_up_to_date() + mod_json_new = mod_json_obj_new.get_modules_json() + assert mod_json_orig == mod_json_new + + def test_mod_json_with_missing_modules_entry(self): + # Load module.json and remove the modules entry + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json_obj.create() # Create modules.json explicitly to get correct module sha + mod_json_orig = mod_json_obj.get_modules_json() + mod_json = copy.deepcopy(mod_json_orig) + mod_json["repos"][NF_CORE_MODULES_REMOTE].pop("modules") + # save the altered module.json and load it again to check if it will fix itself + mod_json_obj.modules_json = mod_json + mod_json_obj.dump() + mod_json_obj_new = ModulesJson(self.pipeline_dir) + mod_json_obj_new.check_up_to_date() + mod_json_new = mod_json_obj_new.get_modules_json() + assert mod_json_orig == mod_json_new diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py new file mode 100644 index 0000000000..230bb1ce8f --- /dev/null +++ b/tests/modules/test_patch.py @@ -0,0 +1,365 @@ +import os +import tempfile +from pathlib import Path +from unittest import mock + +import pytest + +import nf_core.components.components_command +import nf_core.modules + +from ..test_modules import TestModules +from ..utils import GITLAB_URL + +""" +Test the 'nf-core modules patch' command + +Uses a branch (patch-tester) in the GitLab nf-core/modules-test repo when +testing if the update commands works correctly with patch files +""" + +ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2" +CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f" +SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e" +FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73" +BISMARK_ALIGN = "bismark/align" +REPO_NAME = "nf-core-test" +PATCH_BRANCH = "patch-tester" +REPO_URL = "https://gitlab.com/nf-core/modules-test.git" + + +def setup_patch(pipeline_dir, modify_module): + install_obj = nf_core.modules.ModuleInstall( + pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA + ) + + # Install the module + install_obj.install(BISMARK_ALIGN) + + if modify_module: + # Modify the module + module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + modify_main_nf(module_path / "main.nf") + + +def modify_main_nf(path): + """Modify a file to test patch creation""" + with open(path) as fh: + lines = fh.readlines() + # We want a patch file that looks something like: + # - tuple val(meta), path(reads) + # - path index + # + tuple val(meta), path(reads), path(index) + for line_index in range(len(lines)): + if lines[line_index] == " tuple val(meta), path(reads)\n": + lines[line_index] = " tuple val(meta), path(reads), path(index)\n" + elif lines[line_index] == " path index\n": + to_pop = line_index + lines.pop(to_pop) + with open(path, "w") as fh: + fh.writelines(lines) + + +class TestModulesCreate(TestModules): + def test_create_patch_no_change(self): + """Test creating a patch when there is no change to the module""" + setup_patch(self.pipeline_dir, False) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + with pytest.raises(UserWarning): + patch_obj.patch(BISMARK_ALIGN) + + module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + + # Check that no patch file has been added to the directory + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} + + # Check the 'modules.json' contains no patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None + + def test_create_patch_change(self): + """Test creating a patch when there is a change to the module""" + setup_patch(self.pipeline_dir, True) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + # Check that the correct lines are in the patch file + with open(module_path / patch_fn) as fh: + patch_lines = fh.readlines() + module_relpath = module_path.relative_to(self.pipeline_dir) + assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines, module_relpath / "main.nf" + assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines + assert "- tuple val(meta), path(reads)\n" in patch_lines + assert "- path index\n" in patch_lines + assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines + + def test_create_patch_try_apply_successful(self): + """ + Test creating a patch file and applying it to a new version of the the files + """ + + setup_patch(self.pipeline_dir, True) + module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN) + module_path = Path(self.pipeline_dir, module_relpath) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + update_obj = nf_core.modules.ModuleUpdate( + self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH + ) + # Install the new files + install_dir = Path(tempfile.mkdtemp()) + update_obj.install_component_files(BISMARK_ALIGN, SUCCEED_SHA, update_obj.modules_repo, install_dir) + + # Try applying the patch + module_install_dir = install_dir / BISMARK_ALIGN + patch_relpath = module_relpath / patch_fn + assert ( + update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_relpath, module_path, module_install_dir) is True + ) + + # Move the files from the temporary directory + update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA) + + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + # Check that the correct lines are in the patch file + with open(module_path / patch_fn) as fh: + patch_lines = fh.readlines() + module_relpath = module_path.relative_to(self.pipeline_dir) + assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines + assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines + assert "- tuple val(meta), path(reads)\n" in patch_lines + assert "- path index\n" in patch_lines + assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines + + # Check that 'main.nf' is updated correctly + with open(module_path / "main.nf") as fh: + main_nf_lines = fh.readlines() + # These lines should have been removed by the patch + assert " tuple val(meta), path(reads)\n" not in main_nf_lines + assert " path index\n" not in main_nf_lines + # This line should have been added + assert " tuple val(meta), path(reads), path(index)\n" in main_nf_lines + + def test_create_patch_try_apply_failed(self): + """ + Test creating a patch file and applying it to a new version of the the files + """ + + setup_patch(self.pipeline_dir, True) + module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN) + module_path = Path(self.pipeline_dir, module_relpath) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + update_obj = nf_core.modules.ModuleUpdate( + self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH + ) + # Install the new files + install_dir = Path(tempfile.mkdtemp()) + update_obj.install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, install_dir) + + # Try applying the patch + module_install_dir = install_dir / BISMARK_ALIGN + patch_path = module_relpath / patch_fn + assert ( + update_obj.try_apply_patch(BISMARK_ALIGN, REPO_NAME, patch_path, module_path, module_install_dir) is False + ) + + def test_create_patch_update_success(self): + """ + Test creating a patch file and the updating the module + + Should have the same effect as 'test_create_patch_try_apply_successful' + but uses higher level api + """ + + setup_patch(self.pipeline_dir, True) + module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + # Update the module + update_obj = nf_core.modules.ModuleUpdate( + self.pipeline_dir, + sha=SUCCEED_SHA, + show_diff=False, + update_deps=True, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + ) + assert update_obj.update(BISMARK_ALIGN) + + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ), modules_json_obj.get_patch_fn(BISMARK_ALIGN, GITLAB_URL, REPO_NAME) + + # Check that the correct lines are in the patch file + with open(module_path / patch_fn) as fh: + patch_lines = fh.readlines() + module_relpath = module_path.relative_to(self.pipeline_dir) + assert f"--- {module_relpath / 'main.nf'}\n" in patch_lines + assert f"+++ {module_relpath / 'main.nf'}\n" in patch_lines + assert "- tuple val(meta), path(reads)\n" in patch_lines + assert "- path index\n" in patch_lines + assert "+ tuple val(meta), path(reads), path(index)\n" in patch_lines + + # Check that 'main.nf' is updated correctly + with open(module_path / "main.nf") as fh: + main_nf_lines = fh.readlines() + # These lines should have been removed by the patch + assert " tuple val(meta), path(reads)\n" not in main_nf_lines + assert " path index\n" not in main_nf_lines + # This line should have been added + assert " tuple val(meta), path(reads), path(index)\n" in main_nf_lines + + def test_create_patch_update_fail(self): + """ + Test creating a patch file and updating a module when there is a diff conflict + """ + + setup_patch(self.pipeline_dir, True) + module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + # Check that a patch file with the correct name has been created + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + # Save the file contents for downstream comparison + with open(module_path / patch_fn) as fh: + patch_contents = fh.read() + + update_obj = nf_core.modules.ModuleUpdate( + self.pipeline_dir, + sha=FAIL_SHA, + show_diff=False, + update_deps=True, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + ) + update_obj.update(BISMARK_ALIGN) + + # Check that the installed files have not been affected by the attempted patch + temp_dir = Path(tempfile.mkdtemp()) + nf_core.components.components_command.ComponentCommand( + "modules", self.pipeline_dir, GITLAB_URL, PATCH_BRANCH + ).install_component_files(BISMARK_ALIGN, FAIL_SHA, update_obj.modules_repo, temp_dir) + + temp_module_dir = temp_dir / BISMARK_ALIGN + for file in os.listdir(temp_module_dir): + assert file in os.listdir(module_path) + with open(module_path / file) as fh: + installed = fh.read() + with open(temp_module_dir / file) as fh: + shouldbe = fh.read() + assert installed == shouldbe + + # Check that the patch file is unaffected + with open(module_path / patch_fn) as fh: + new_patch_contents = fh.read() + assert patch_contents == new_patch_contents + + def test_remove_patch(self): + """Test creating a patch when there is no change to the module""" + setup_patch(self.pipeline_dir, True) + + # Try creating a patch file + patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + + # Check that a patch file with the correct name has been created + patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + + # Check the 'modules.json' contains a patch file for the module + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) == Path( + "modules", REPO_NAME, BISMARK_ALIGN, patch_fn + ) + + with mock.patch.object(nf_core.components.patch.questionary, "confirm") as mock_questionary: + mock_questionary.unsafe_ask.return_value = True + patch_obj.remove(BISMARK_ALIGN) + # Check that the diff file has been removed + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} + + # Check that the 'modules.json' entry has been removed + modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) + assert modules_json_obj.get_patch_fn(BISMARK_ALIGN, REPO_URL, REPO_NAME) is None diff --git a/tests/modules/test_remove.py b/tests/modules/test_remove.py new file mode 100644 index 0000000000..a80c8b0986 --- /dev/null +++ b/tests/modules/test_remove.py @@ -0,0 +1,26 @@ +import os +from pathlib import Path + +from ..test_modules import TestModules + + +class TestModulesRemove(TestModules): + def test_modules_remove_trimgalore(self): + """Test removing TrimGalore! module after installing it""" + self.mods_install.install("trimgalore") + assert self.mods_install.dir is not None + module_path = Path(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore") + assert self.mods_remove.remove("trimgalore") + assert os.path.exists(module_path) is False + + def test_modules_remove_trimgalore_uninstalled(self): + """Test removing TrimGalore! module without installing it""" + assert self.mods_remove.remove("trimgalore") is False + + def test_modules_remove_multiqc_from_gitlab(self): + """Test removing multiqc module after installing it from an alternative source""" + self.mods_install_gitlab.install("multiqc") + assert self.mods_install.dir is not None + module_path = Path(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc") + assert self.mods_remove_gitlab.remove("multiqc", force=True) + assert os.path.exists(module_path) is False diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py new file mode 100644 index 0000000000..a33aac3775 --- /dev/null +++ b/tests/modules/test_update.py @@ -0,0 +1,435 @@ +import logging +import shutil +import tempfile +from pathlib import Path +from unittest import mock + +import questionary +import yaml + +import nf_core.utils +from nf_core.modules.install import ModuleInstall +from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE +from nf_core.modules.patch import ModulePatch +from nf_core.modules.update import ModuleUpdate + +from ..test_modules import TestModules +from ..utils import ( + GITLAB_BRANCH_TEST_BRANCH, + GITLAB_BRANCH_TEST_NEW_SHA, + GITLAB_BRANCH_TEST_OLD_SHA, + GITLAB_DEFAULT_BRANCH, + GITLAB_REPO, + GITLAB_URL, + OLD_TRIMGALORE_BRANCH, + OLD_TRIMGALORE_SHA, + cmp_component, +) + + +class TestModulesInstall(TestModules): + def test_install_and_update(self): + """Installs a module in the pipeline and updates it (no change)""" + self.mods_install.install("trimgalore") + update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) + + # Copy the module files and check that they are unaffected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore") + shutil.copytree(trimgalore_path, trimgalore_tmpdir) + + assert update_obj.update("trimgalore") is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True + + def test_install_at_hash_and_update(self): + """Installs an old version of a module in the pipeline and updates it""" + assert self.mods_install_old.install("trimgalore") + update_obj = ModuleUpdate( + self.pipeline_dir, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH + ) + + # Copy the module files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + shutil.copytree(trimgalore_path, trimgalore_tmpdir) + + assert update_obj.update("trimgalore") is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False + + # Check that the modules.json is correctly updated + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + # Get the up-to-date git_sha for the module from the ModulesRepo object + correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules") + current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] + assert correct_git_sha == current_git_sha + + # Mock questionary answer: do not update module, only show diffs + @mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) + def test_install_at_hash_and_update_limit_output(self, mock_prompt): + """Installs an old version of a module in the pipeline and updates it with limited output reporting""" + self.caplog.set_level(logging.INFO) + assert self.mods_install_old.install("trimgalore") + + update_obj = ModuleUpdate( + self.pipeline_dir, + show_diff=True, + update_deps=True, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + limit_output=True, + ) + assert update_obj.update("trimgalore") + + # Check changes not shown for non-.nf files + assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text + # Check changes shown for .nf files + assert "Changes in 'trimgalore/main.nf'" in self.caplog.text + for line in self.caplog.text.split("\n"): + if line.startswith("---"): + assert line.endswith("main.nf") + + def test_install_at_hash_and_update_and_save_diff_to_file(self): + """Installs an old version of a module in the pipeline and updates it""" + self.mods_install_old.install("trimgalore") + patch_path = Path(self.pipeline_dir, "trimgalore.patch") + update_obj = ModuleUpdate( + self.pipeline_dir, + save_diff_fn=patch_path, + sha=OLD_TRIMGALORE_SHA, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + ) + + # Copy the module files and check that they are affected by the update + tmpdir = Path(tempfile.TemporaryDirectory().name) + trimgalore_tmpdir = tmpdir / "trimgalore" + trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") + shutil.copytree(trimgalore_path, trimgalore_tmpdir) + + assert update_obj.update("trimgalore") is True + assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True + + # TODO: Apply the patch to the module + + def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): + """Installs an old version of a module in the pipeline and updates it""" + # Install old version of trimgalore + self.mods_install_old.install("trimgalore") + patch_path = Path(self.pipeline_dir, "trimgalore.patch") + # Update saving the differences to a patch file and with `limit_output` + update_obj = ModuleUpdate( + self.pipeline_dir, + save_diff_fn=patch_path, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + limit_output=True, + ) + assert update_obj.update("trimgalore") + + # Check that the patch file was created + assert patch_path.exists(), f"Patch file was not created at {patch_path}" + + # Read the contents of the patch file + with open(patch_path) as fh: + patch_content = fh.read() + # Check changes not shown for non-.nf files + assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content + # Check changes only shown for main.nf + assert "Changes in 'trimgalore/main.nf'" in patch_content + for line in patch_content: + if line.startswith("---"): + assert line.endswith("main.nf") + + def test_update_all(self): + """Updates all modules present in the pipeline""" + update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False) + # Get the current modules.json + assert update_obj.update() is True + + # We must reload the modules.json to get the updated version + mod_json_obj = ModulesJson(self.pipeline_dir) + mod_json = mod_json_obj.get_modules_json() + # Loop through all modules and check that they are updated (according to the modules.json file) + for mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]: + correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] + current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] + assert correct_git_sha == current_git_sha + + def test_update_with_config_fixed_version(self): + """Try updating when there are entries in the .nf-core.yml""" + # Install trimgalore at the latest version + assert self.mods_install_trimgalore.install("trimgalore") + + # Fix the trimgalore version in the .nf-core.yml to an old version + update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all modules in the pipeline + update_obj = ModuleUpdate( + self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH + ) + assert update_obj.update() is True + + # Check that the git sha for trimgalore is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO] + assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] + assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA + + def test_update_with_config_dont_update(self): + """Try updating when module is to be ignored""" + # Install an old version of trimgalore + self.mods_install_old.install("trimgalore") + + # Set the trimgalore field to no update in the .nf-core.yml + update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all modules in the pipeline + update_obj = ModuleUpdate( + self.pipeline_dir, + update_all=True, + show_diff=False, + sha=OLD_TRIMGALORE_SHA, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + ) + assert update_obj.update() is True + + # Check that the git sha for trimgalore is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO] + assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] + assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA + + def test_update_with_config_fix_all(self): + """Fix the version of all nf-core modules""" + self.mods_install_trimgalore.install("trimgalore") + + # Fix the version of all nf-core modules in the .nf-core.yml to an old version + update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all modules in the pipeline + update_obj = ModuleUpdate( + self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH + ) + assert update_obj.update() is True + + # Check that the git sha for trimgalore is correctly downgraded + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] + assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA + + def test_update_with_config_no_updates(self): + """Don't update any nf-core modules""" + assert self.mods_install_old.install("trimgalore") + old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + + # Fix the version of all nf-core modules in the .nf-core.yml to an old version + update_config = {GITLAB_URL: False} + config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) + tools_config["update"] = update_config + with open(Path(self.pipeline_dir, config_fn), "w") as f: + yaml.dump(tools_config, f) + + # Update all modules in the pipeline + update_obj = ModuleUpdate( + self.pipeline_dir, + update_all=True, + show_diff=False, + sha=OLD_TRIMGALORE_SHA, + remote_url=GITLAB_URL, + branch=OLD_TRIMGALORE_BRANCH, + ) + assert update_obj.update() is True + + # Check that the git sha for trimgalore is correctly downgraded and none of the modules has changed + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + for module in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]: + assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module] + assert ( + mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"] + == old_mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"] + ) + + def test_update_different_branch_single_module(self): + """Try updating a module in a specific branch""" + install_obj = ModuleInstall( + self.pipeline_dir, + prompt=False, + force=False, + remote_url=GITLAB_URL, + branch=GITLAB_BRANCH_TEST_BRANCH, + sha=GITLAB_BRANCH_TEST_OLD_SHA, + ) + assert install_obj.install("fastp") + + update_obj = ModuleUpdate( + self.pipeline_dir, + update_deps=True, + remote_url=GITLAB_URL, + branch=GITLAB_BRANCH_TEST_BRANCH, + show_diff=False, + ) + update_obj.update("fastp") + + # Verify that the branch entry was updated correctly + modules_json = ModulesJson(self.pipeline_dir) + assert ( + modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) + == GITLAB_BRANCH_TEST_BRANCH + ) + assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA + + def test_update_different_branch_mixed_modules_main(self): + """Try updating all modules where MultiQC is installed from main branch""" + # Install fastp + assert self.mods_install_gitlab_old.install("fastp") + + # Install MultiQC from gitlab default branch + assert self.mods_install_gitlab.install("multiqc") + + # Try updating + update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False) + assert update_obj.update() is True + + modules_json = ModulesJson(self.pipeline_dir) + # Verify that the branch entry was updated correctly + assert ( + modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) + == GITLAB_BRANCH_TEST_BRANCH + ) + assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA + # MultiQC is present in both branches but should've been updated using the 'main' branch + assert ( + modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO) + == GITLAB_DEFAULT_BRANCH + ) + + def test_update_different_branch_mix_modules_branch_test(self): + """Try updating all modules where MultiQC is installed from branch-test branch""" + # Install multiqc from the branch-test branch + assert self.mods_install_gitlab_old.install( + "multiqc" + ) # Force as the same module is installed from github nf-core modules repo + modules_json = ModulesJson(self.pipeline_dir) + update_obj = ModuleUpdate( + self.pipeline_dir, + update_all=True, + show_diff=False, + remote_url=GITLAB_URL, + branch=GITLAB_BRANCH_TEST_BRANCH, + sha=GITLAB_BRANCH_TEST_NEW_SHA, + ) + assert update_obj.update() + + assert ( + modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO) + == GITLAB_BRANCH_TEST_BRANCH + ) + assert modules_json.get_module_version("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA + + # Mock questionary answer: do not update module, only show diffs + @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False) + def test_update_only_show_differences(self, mock_prompt): + """Try updating all modules showing differences. + Only show diffs, don't actually save any updated files. + Check that the sha in modules.json is not changed.""" + + # Update modules to a fixed old SHA + update_old = ModuleUpdate( + self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905" + ) + update_old.update() + + tmpdir = Path(tempfile.TemporaryDirectory().name) + shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) + + update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) + assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update() + + mod_json = ModulesJson(self.pipeline_dir).get_modules_json() + # Loop through all modules and check that they are NOT updated (according to the modules.json file) + # A module that can be updated but shouldn't is fastqc + # Module multiqc is already up to date so don't check + mod = "fastqc" + non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] + current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] + assert non_updated_git_sha != current_git_sha + assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True + + # Mock questionary answer: do not update module, only show diffs + @mock.patch.object(questionary.Question, "unsafe_ask", return_value=False) + def test_update_only_show_differences_when_patch(self, mock_prompt): + """Try updating all modules showing differences when there's a patched module. + Don't update some of them. + Check that the sha in modules.json is not changed.""" + modules_json = ModulesJson(self.pipeline_dir) + update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) + + # Update modules to a fixed old SHA + update_old = ModuleUpdate( + self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905" + ) + assert update_old.update() + + # Modify fastqc module, it will have a patch which will be applied during update + # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions) + module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc") + main_path = Path(module_path, "main.nf") + with open(main_path) as fh: + lines = fh.readlines() + for line_index in range(len(lines)): + if lines[line_index] == " label 'process_medium'\n": + lines[line_index] = " label 'process_low'\n" + break + with open(main_path, "w") as fh: + fh.writelines(lines) + # Create a patch file + patch_obj = ModulePatch(self.pipeline_dir) + patch_obj.patch("fastqc") + # Check that a patch file with the correct name has been created + assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")] + + # Update all modules + assert update_obj.update() is True + + mod_json = modules_json.get_modules_json() + # Loop through all modules and check that they are NOT updated (according to the modules.json file) + # A module that can be updated but shouldn't is fastqc + # Module multiqc is already up to date so don't check + mod = "fastqc" + correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] + current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] + assert correct_git_sha != current_git_sha + + def test_update_module_with_extra_config_file(self): + """Try updating a module with a config file""" + # Install the module + assert self.mods_install.install("trimgalore") + # Add a nextflow_test.config file to the module + trimgalore_path = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") + Path(trimgalore_path, "nextflow_test.config").touch() + with open(Path(trimgalore_path, "nextflow_test.config"), "w") as fh: + fh.write("params.my_param = 'my_value'\n") + # Update the module + update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) + assert update_obj.update("trimgalore") + # Check that the nextflow_test.config file is still there + assert Path(trimgalore_path, "nextflow_test.config").exists() + with open(Path(trimgalore_path, "nextflow_test.config")) as fh: + assert "params.my_param = 'my_value'" in fh.read() diff --git a/tests/modules/update.py b/tests/modules/update.py deleted file mode 100644 index e02b058fbb..0000000000 --- a/tests/modules/update.py +++ /dev/null @@ -1,444 +0,0 @@ -import logging -import shutil -import tempfile -from pathlib import Path -from unittest import mock - -import questionary -import yaml - -import nf_core.utils -from nf_core.modules.install import ModuleInstall -from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE -from nf_core.modules.patch import ModulePatch -from nf_core.modules.update import ModuleUpdate - -from ..utils import ( - GITLAB_BRANCH_TEST_BRANCH, - GITLAB_BRANCH_TEST_NEW_SHA, - GITLAB_BRANCH_TEST_OLD_SHA, - GITLAB_DEFAULT_BRANCH, - GITLAB_REPO, - GITLAB_URL, - OLD_TRIMGALORE_BRANCH, - OLD_TRIMGALORE_SHA, - cmp_component, -) - - -def test_install_and_update(self): - """Installs a module in the pipeline and updates it (no change)""" - self.mods_install.install("trimgalore") - update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) - - # Copy the module files and check that they are unaffected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - trimgalore_tmpdir = tmpdir / "trimgalore" - trimgalore_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "trimgalore") - shutil.copytree(trimgalore_path, trimgalore_tmpdir) - - assert update_obj.update("trimgalore") is True - assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True - - -def test_install_at_hash_and_update(self): - """Installs an old version of a module in the pipeline and updates it""" - assert self.mods_install_old.install("trimgalore") - update_obj = ModuleUpdate( - self.pipeline_dir, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH - ) - - # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - trimgalore_tmpdir = tmpdir / "trimgalore" - trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") - shutil.copytree(trimgalore_path, trimgalore_tmpdir) - - assert update_obj.update("trimgalore") is True - assert cmp_component(trimgalore_tmpdir, trimgalore_path) is False - - # Check that the modules.json is correctly updated - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - # Get the up-to-date git_sha for the module from the ModulesRepo object - correct_git_sha = update_obj.modules_repo.get_latest_component_version("trimgalore", "modules") - current_git_sha = mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] - assert correct_git_sha == current_git_sha - - -# Mock questionary answer: do not update module, only show diffs -@mock.patch.object(questionary.Question, "unsafe_ask", return_value=True) -def test_install_at_hash_and_update_limit_output(self, mock_prompt): - """Installs an old version of a module in the pipeline and updates it with limited output reporting""" - self.caplog.set_level(logging.INFO) - assert self.mods_install_old.install("trimgalore") - - update_obj = ModuleUpdate( - self.pipeline_dir, - show_diff=True, - update_deps=True, - remote_url=GITLAB_URL, - branch=OLD_TRIMGALORE_BRANCH, - limit_output=True, - ) - assert update_obj.update("trimgalore") - - # Check changes not shown for non-.nf files - assert "Changes in 'trimgalore/meta.yml' but not shown" in self.caplog.text - # Check changes shown for .nf files - assert "Changes in 'trimgalore/main.nf'" in self.caplog.text - for line in self.caplog.text.split("\n"): - if line.startswith("---"): - assert line.endswith("main.nf") - - -def test_install_at_hash_and_update_and_save_diff_to_file(self): - """Installs an old version of a module in the pipeline and updates it""" - self.mods_install_old.install("trimgalore") - patch_path = Path(self.pipeline_dir, "trimgalore.patch") - update_obj = ModuleUpdate( - self.pipeline_dir, - save_diff_fn=patch_path, - sha=OLD_TRIMGALORE_SHA, - remote_url=GITLAB_URL, - branch=OLD_TRIMGALORE_BRANCH, - ) - - # Copy the module files and check that they are affected by the update - tmpdir = Path(tempfile.TemporaryDirectory().name) - trimgalore_tmpdir = tmpdir / "trimgalore" - trimgalore_path = Path(self.pipeline_dir, "modules", GITLAB_REPO, "trimgalore") - shutil.copytree(trimgalore_path, trimgalore_tmpdir) - - assert update_obj.update("trimgalore") is True - assert cmp_component(trimgalore_tmpdir, trimgalore_path) is True - - # TODO: Apply the patch to the module - - -def test_install_at_hash_and_update_and_save_diff_to_file_limit_output(self): - """Installs an old version of a module in the pipeline and updates it""" - # Install old version of trimgalore - self.mods_install_old.install("trimgalore") - patch_path = Path(self.pipeline_dir, "trimgalore.patch") - # Update saving the differences to a patch file and with `limit_output` - update_obj = ModuleUpdate( - self.pipeline_dir, - save_diff_fn=patch_path, - remote_url=GITLAB_URL, - branch=OLD_TRIMGALORE_BRANCH, - limit_output=True, - ) - assert update_obj.update("trimgalore") - - # Check that the patch file was created - assert patch_path.exists(), f"Patch file was not created at {patch_path}" - - # Read the contents of the patch file - with open(patch_path) as fh: - patch_content = fh.read() - # Check changes not shown for non-.nf files - assert "Changes in 'trimgalore/meta.yml' but not shown" in patch_content - # Check changes only shown for main.nf - assert "Changes in 'trimgalore/main.nf'" in patch_content - for line in patch_content: - if line.startswith("---"): - assert line.endswith("main.nf") - - -def test_update_all(self): - """Updates all modules present in the pipeline""" - update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False) - # Get the current modules.json - assert update_obj.update() is True - - # We must reload the modules.json to get the updated version - mod_json_obj = ModulesJson(self.pipeline_dir) - mod_json = mod_json_obj.get_modules_json() - # Loop through all modules and check that they are updated (according to the modules.json file) - for mod in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME]: - correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] - current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - assert correct_git_sha == current_git_sha - - -def test_update_with_config_fixed_version(self): - """Try updating when there are entries in the .nf-core.yml""" - # Install trimgalore at the latest version - assert self.mods_install_trimgalore.install("trimgalore") - - # Fix the trimgalore version in the .nf-core.yml to an old version - update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all modules in the pipeline - update_obj = ModuleUpdate( - self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH - ) - assert update_obj.update() is True - - # Check that the git sha for trimgalore is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO] - assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] - assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA - - -def test_update_with_config_dont_update(self): - """Try updating when module is to be ignored""" - # Install an old version of trimgalore - self.mods_install_old.install("trimgalore") - - # Set the trimgalore field to no update in the .nf-core.yml - update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all modules in the pipeline - update_obj = ModuleUpdate( - self.pipeline_dir, - update_all=True, - show_diff=False, - sha=OLD_TRIMGALORE_SHA, - remote_url=GITLAB_URL, - branch=OLD_TRIMGALORE_BRANCH, - ) - assert update_obj.update() is True - - # Check that the git sha for trimgalore is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert "trimgalore" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO] - assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] - assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA - - -def test_update_with_config_fix_all(self): - """Fix the version of all nf-core modules""" - self.mods_install_trimgalore.install("trimgalore") - - # Fix the version of all nf-core modules in the .nf-core.yml to an old version - update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all modules in the pipeline - update_obj = ModuleUpdate( - self.pipeline_dir, update_all=True, show_diff=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH - ) - assert update_obj.update() is True - - # Check that the git sha for trimgalore is correctly downgraded - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"] - assert mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]["trimgalore"]["git_sha"] == OLD_TRIMGALORE_SHA - - -def test_update_with_config_no_updates(self): - """Don't update any nf-core modules""" - assert self.mods_install_old.install("trimgalore") - old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - - # Fix the version of all nf-core modules in the .nf-core.yml to an old version - update_config = {GITLAB_URL: False} - config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config - with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) - - # Update all modules in the pipeline - update_obj = ModuleUpdate( - self.pipeline_dir, - update_all=True, - show_diff=False, - sha=OLD_TRIMGALORE_SHA, - remote_url=GITLAB_URL, - branch=OLD_TRIMGALORE_BRANCH, - ) - assert update_obj.update() is True - - # Check that the git sha for trimgalore is correctly downgraded and none of the modules has changed - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - for module in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO]: - assert "git_sha" in mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module] - assert ( - mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"] - == old_mod_json["repos"][GITLAB_URL]["modules"][GITLAB_REPO][module]["git_sha"] - ) - - -def test_update_different_branch_single_module(self): - """Try updating a module in a specific branch""" - install_obj = ModuleInstall( - self.pipeline_dir, - prompt=False, - force=False, - remote_url=GITLAB_URL, - branch=GITLAB_BRANCH_TEST_BRANCH, - sha=GITLAB_BRANCH_TEST_OLD_SHA, - ) - assert install_obj.install("fastp") - - update_obj = ModuleUpdate( - self.pipeline_dir, update_deps=True, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH, show_diff=False - ) - update_obj.update("fastp") - - # Verify that the branch entry was updated correctly - modules_json = ModulesJson(self.pipeline_dir) - assert ( - modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) - == GITLAB_BRANCH_TEST_BRANCH - ) - assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA - - -def test_update_different_branch_mixed_modules_main(self): - """Try updating all modules where MultiQC is installed from main branch""" - # Install fastp - assert self.mods_install_gitlab_old.install("fastp") - - # Install MultiQC from gitlab default branch - assert self.mods_install_gitlab.install("multiqc") - - # Try updating - update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=False) - assert update_obj.update() is True - - modules_json = ModulesJson(self.pipeline_dir) - # Verify that the branch entry was updated correctly - assert ( - modules_json.get_component_branch(self.component_type, "fastp", GITLAB_URL, GITLAB_REPO) - == GITLAB_BRANCH_TEST_BRANCH - ) - assert modules_json.get_module_version("fastp", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA - # MultiQC is present in both branches but should've been updated using the 'main' branch - assert ( - modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO) - == GITLAB_DEFAULT_BRANCH - ) - - -def test_update_different_branch_mix_modules_branch_test(self): - """Try updating all modules where MultiQC is installed from branch-test branch""" - # Install multiqc from the branch-test branch - assert self.mods_install_gitlab_old.install( - "multiqc" - ) # Force as the same module is installed from github nf-core modules repo - modules_json = ModulesJson(self.pipeline_dir) - update_obj = ModuleUpdate( - self.pipeline_dir, - update_all=True, - show_diff=False, - remote_url=GITLAB_URL, - branch=GITLAB_BRANCH_TEST_BRANCH, - sha=GITLAB_BRANCH_TEST_NEW_SHA, - ) - assert update_obj.update() - - assert ( - modules_json.get_component_branch(self.component_type, "multiqc", GITLAB_URL, GITLAB_REPO) - == GITLAB_BRANCH_TEST_BRANCH - ) - assert modules_json.get_module_version("multiqc", GITLAB_URL, GITLAB_REPO) == GITLAB_BRANCH_TEST_NEW_SHA - - -# Mock questionary answer: do not update module, only show diffs -@mock.patch.object(questionary.Question, "unsafe_ask", return_value=False) -def test_update_only_show_differences(self, mock_prompt): - """Try updating all modules showing differences. - Only show diffs, don't actually save any updated files. - Check that the sha in modules.json is not changed.""" - - # Update modules to a fixed old SHA - update_old = ModuleUpdate( - self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905" - ) - update_old.update() - - tmpdir = Path(tempfile.TemporaryDirectory().name) - shutil.copytree(Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME), tmpdir) - - update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) - assert ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True).update() - - mod_json = ModulesJson(self.pipeline_dir).get_modules_json() - # Loop through all modules and check that they are NOT updated (according to the modules.json file) - # A module that can be updated but shouldn't is fastqc - # Module multiqc is already up to date so don't check - mod = "fastqc" - non_updated_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] - current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - assert non_updated_git_sha != current_git_sha - assert cmp_component(Path(tmpdir, mod), Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, mod)) is True - - -# Mock questionary answer: do not update module, only show diffs -@mock.patch.object(questionary.Question, "unsafe_ask", return_value=False) -def test_update_only_show_differences_when_patch(self, mock_prompt): - """Try updating all modules showing differences when there's a patched module. - Don't update some of them. - Check that the sha in modules.json is not changed.""" - modules_json = ModulesJson(self.pipeline_dir) - update_obj = ModuleUpdate(self.pipeline_dir, update_all=True, show_diff=True) - - # Update modules to a fixed old SHA - update_old = ModuleUpdate( - self.pipeline_dir, update_all=True, show_diff=False, sha="5e34754d42cd2d5d248ca8673c0a53cdf5624905" - ) - assert update_old.update() - - # Modify fastqc module, it will have a patch which will be applied during update - # We modify fastqc because it's one of the modules that can be updated and there's another one before it (custom/dumpsoftwareversions) - module_path = Path(self.pipeline_dir, "modules", "nf-core", "fastqc") - main_path = Path(module_path, "main.nf") - with open(main_path) as fh: - lines = fh.readlines() - for line_index in range(len(lines)): - if lines[line_index] == " label 'process_medium'\n": - lines[line_index] = " label 'process_low'\n" - break - with open(main_path, "w") as fh: - fh.writelines(lines) - # Create a patch file - patch_obj = ModulePatch(self.pipeline_dir) - patch_obj.patch("fastqc") - # Check that a patch file with the correct name has been created - assert "fastqc.diff" in [f.name for f in module_path.glob("*.diff")] - - # Update all modules - assert update_obj.update() is True - - mod_json = modules_json.get_modules_json() - # Loop through all modules and check that they are NOT updated (according to the modules.json file) - # A module that can be updated but shouldn't is fastqc - # Module multiqc is already up to date so don't check - mod = "fastqc" - correct_git_sha = list(update_obj.modules_repo.get_component_git_log(mod, "modules", depth=1))[0]["git_sha"] - current_git_sha = mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"][NF_CORE_MODULES_NAME][mod]["git_sha"] - assert correct_git_sha != current_git_sha - - -def test_update_module_with_extra_config_file(self): - """Try updating a module with a config file""" - # Install the module - assert self.mods_install.install("trimgalore") - # Add a nextflow_test.config file to the module - trimgalore_path = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") - Path(trimgalore_path, "nextflow_test.config").touch() - with open(Path(trimgalore_path, "nextflow_test.config"), "w") as fh: - fh.write("params.my_param = 'my_value'\n") - # Update the module - update_obj = ModuleUpdate(self.pipeline_dir, show_diff=False) - assert update_obj.update("trimgalore") - # Check that the nextflow_test.config file is still there - assert Path(trimgalore_path, "nextflow_test.config").exists() - with open(Path(trimgalore_path, "nextflow_test.config")) as fh: - assert "params.my_param = 'my_value'" in fh.read() diff --git a/tests/test_modules.py b/tests/test_modules.py index 6e601ce7ad..13bf32f971 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -160,131 +160,3 @@ def test_modulesrepo_class(self): @pytest.fixture(autouse=True) def _use_caplog(self, caplog): self.caplog = caplog - - ############################################ - # Test of the individual modules commands. # - ############################################ - - from .modules.bump_versions import ( # type: ignore[misc] - test_modules_bump_versions_all_modules, - test_modules_bump_versions_fail, - test_modules_bump_versions_fail_unknown_version, - test_modules_bump_versions_single_module, - ) - from .modules.create import ( # type: ignore[misc] - test_modules_create_fail_exists, - test_modules_create_nfcore_modules, - test_modules_create_nfcore_modules_subtool, - test_modules_create_succeed, - test_modules_migrate, - test_modules_migrate_no_delete, - test_modules_migrate_symlink, - ) - from .modules.info import ( # type: ignore[misc] - test_modules_info_in_modules_repo, - test_modules_info_local, - test_modules_info_remote, - test_modules_info_remote_gitlab, - ) - from .modules.install import ( # type: ignore[misc] - test_modules_install_alternate_remote, - test_modules_install_different_branch_fail, - test_modules_install_different_branch_succeed, - test_modules_install_emptypipeline, - test_modules_install_from_gitlab, - test_modules_install_nomodule, - test_modules_install_nopipeline, - test_modules_install_tracking, - test_modules_install_trimgalore, - test_modules_install_trimgalore_twice, - ) - from .modules.lint import ( # type: ignore[misc] - test_modules_absent_version, - test_modules_empty_file_in_snapshot, - test_modules_empty_file_in_stub_snapshot, - test_modules_environment_yml_file_doesnt_exists, - test_modules_environment_yml_file_name_mismatch, - test_modules_environment_yml_file_not_array, - test_modules_environment_yml_file_sorted_correctly, - test_modules_environment_yml_file_sorted_incorrectly, - test_modules_lint_check_process_labels, - test_modules_lint_check_url, - test_modules_lint_empty, - test_modules_lint_gitlab_modules, - test_modules_lint_multiple_remotes, - test_modules_lint_new_modules, - test_modules_lint_no_gitlab, - test_modules_lint_patched_modules, - test_modules_lint_snapshot_file, - test_modules_lint_snapshot_file_missing_fail, - test_modules_lint_snapshot_file_not_needed, - test_modules_lint_trimgalore, - test_modules_meta_yml_incorrect_licence_field, - test_modules_meta_yml_incorrect_name, - test_modules_meta_yml_input_mismatch, - test_modules_meta_yml_output_mismatch, - test_modules_missing_test_dir, - test_modules_missing_test_main_nf, - test_modules_unused_pytest_files, - test_nftest_failing_linting, - ) - from .modules.list import ( # type: ignore[misc] - test_modules_install_and_list_pipeline, - test_modules_install_gitlab_and_list_pipeline, - test_modules_list_in_wrong_repo_fail, - test_modules_list_local_json, - test_modules_list_pipeline, - test_modules_list_remote, - test_modules_list_remote_gitlab, - test_modules_list_remote_json, - test_modules_list_with_keywords, - test_modules_list_with_one_keyword, - test_modules_list_with_unused_keyword, - ) - from .modules.modules_json import ( # type: ignore[misc] - test_get_modules_json, - test_mod_json_create, - test_mod_json_create_with_patch, - test_mod_json_dump, - test_mod_json_get_module_version, - test_mod_json_module_present, - test_mod_json_repo_present, - test_mod_json_up_to_date, - test_mod_json_up_to_date_module_removed, - test_mod_json_up_to_date_reinstall_fails, - test_mod_json_update, - test_mod_json_with_empty_modules_value, - test_mod_json_with_missing_modules_entry, - ) - from .modules.patch import ( # type: ignore[misc] - test_create_patch_change, - test_create_patch_no_change, - test_create_patch_try_apply_failed, - test_create_patch_try_apply_successful, - test_create_patch_update_fail, - test_create_patch_update_success, - test_remove_patch, - ) - from .modules.remove import ( # type: ignore[misc] - test_modules_remove_multiqc_from_gitlab, - test_modules_remove_trimgalore, - test_modules_remove_trimgalore_uninstalled, - ) - from .modules.update import ( # type: ignore[misc] - test_install_and_update, - test_install_at_hash_and_update, - test_install_at_hash_and_update_and_save_diff_to_file, - test_install_at_hash_and_update_and_save_diff_to_file_limit_output, - test_install_at_hash_and_update_limit_output, - test_update_all, - test_update_different_branch_mix_modules_branch_test, - test_update_different_branch_mixed_modules_main, - test_update_different_branch_single_module, - test_update_module_with_extra_config_file, - test_update_only_show_differences, - test_update_only_show_differences_when_patch, - test_update_with_config_dont_update, - test_update_with_config_fix_all, - test_update_with_config_fixed_version, - test_update_with_config_no_updates, - ) From 772ff5244af03351e35584a28154a94818f2cd5f Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Thu, 18 Jul 2024 11:25:23 +0200 Subject: [PATCH 171/574] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8cda88788b..b80a63c6a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,6 @@ - Run awsfulltest on PRs to `master` with two PR approvals ([#3042](https://github.com/nf-core/tools/pull/3042)) - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) -- Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) ### Linting From d95f7f8631f0605319f8a80d4ab2199b08e6fea4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 18 Jul 2024 10:14:54 +0200 Subject: [PATCH 172/574] avoid naming collision with variable name `dir` --- nf_core/commands_pipelines.py | 8 ++-- nf_core/components/components_command.py | 52 +++++++++++------------ nf_core/components/components_test.py | 4 +- nf_core/components/install.py | 16 +++---- nf_core/components/lint/__init__.py | 54 +++++++++++++----------- nf_core/components/update.py | 49 ++++++++++++--------- nf_core/modules/lint/__init__.py | 9 ++-- nf_core/modules/modules_json.py | 18 ++++---- nf_core/pipelines/create_logo.py | 14 +++--- 9 files changed, 121 insertions(+), 103 deletions(-) diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py index 3f569bfe35..deb1f691a5 100644 --- a/nf_core/commands_pipelines.py +++ b/nf_core/commands_pipelines.py @@ -308,7 +308,7 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern # nf-core pipelines create-logo -def pipelines_create_logo(logo_text, dir, name, theme, width, format, force): +def pipelines_create_logo(logo_text, directory, name, theme, width, format, force): """ Generate a logo with the nf-core logo template. @@ -317,9 +317,9 @@ def pipelines_create_logo(logo_text, dir, name, theme, width, format, force): from nf_core.pipelines.create_logo import create_logo try: - if dir == ".": - dir = Path.cwd() - logo_path = create_logo(logo_text, dir, name, theme, width, format, force) + if directory == ".": + directory = Path.cwd() + logo_path = create_logo(logo_text, directory, name, theme, width, format, force) # Print path to logo relative to current working directory try: logo_path = Path(logo_path).relative_to(Path.cwd()) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index aa1dccc0d4..bf80b46113 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -22,7 +22,7 @@ class ComponentCommand: def __init__( self, component_type: str, - dir: Union[str, Path], + directory: Union[str, Path], remote_url: Optional[str] = None, branch: Optional[str] = None, no_pull: bool = False, @@ -33,7 +33,7 @@ def __init__( Initialise the ComponentClass object """ self.component_type = component_type - self.dir = Path(dir) if dir else None + self.directory = Path(directory) if directory else None self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.hide_progress = hide_progress self.no_prompts = no_prompts @@ -49,8 +49,8 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ try: - if self.dir: - self.dir, self.repo_type, self.org = get_repo_info(self.dir, use_prompt=not self.no_prompts) + if self.directory: + self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts) else: self.repo_type = None self.org = "" @@ -68,7 +68,7 @@ def get_local_components(self) -> List[str]: """ Get the local modules/subworkflows in a pipeline """ - local_component_dir = Path(self.dir, self.component_type, "local") + local_component_dir = Path(self.directory, self.component_type, "local") return [ str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf" ] @@ -78,9 +78,9 @@ def get_components_clone_modules(self) -> List[str]: Get the modules/subworkflows repository available in a clone of nf-core/modules """ if self.component_type == "modules": - component_base_path = Path(self.dir, self.default_modules_path) + component_base_path = Path(self.directory, self.default_modules_path) elif self.component_type == "subworkflows": - component_base_path = Path(self.dir, self.default_subworkflows_path) + component_base_path = Path(self.directory, self.default_subworkflows_path) return [ str(Path(dir).relative_to(component_base_path)) for dir, _, files in os.walk(component_base_path) @@ -91,23 +91,23 @@ def has_valid_directory(self) -> bool: """Check that we were given a pipeline or clone of nf-core/modules""" if self.repo_type == "modules": return True - if self.dir is None or not os.path.exists(self.dir): - log.error(f"Could not find directory: {self.dir}") + if self.directory is None or not os.path.exists(self.directory): + log.error(f"Could not find directory: {self.directory}") return False - main_nf = os.path.join(self.dir, "main.nf") - nf_config = os.path.join(self.dir, "nextflow.config") + main_nf = os.path.join(self.directory, "main.nf") + nf_config = os.path.join(self.directory, "nextflow.config") if not os.path.exists(main_nf) and not os.path.exists(nf_config): - if Path(self.dir).resolve().parts[-1].startswith("nf-core"): - raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'") - log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.dir}'") + if Path(self.directory).resolve().parts[-1].startswith("nf-core"): + raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") + log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") return True def has_modules_file(self) -> None: """Checks whether a module.json file has been created and creates one if it is missing""" - modules_json_path = os.path.join(self.dir, "modules.json") + modules_json_path = os.path.join(self.directory, "modules.json") if not os.path.exists(modules_json_path): log.info("Creating missing 'module.json' file.") - ModulesJson(self.dir).create() + ModulesJson(self.directory).create() def clear_component_dir(self, component_name: str, component_dir: str) -> bool: """ @@ -122,7 +122,7 @@ def clear_component_dir(self, component_name: str, component_dir: str) -> bool: try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in os.walk(self.dir, topdown=False): + for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False): if not dir_names and not filenames: try: os.rmdir(dir_path) @@ -147,7 +147,7 @@ def components_from_repo(self, install_dir: str) -> List[str]: Returns: [str]: The names of the modules/subworkflows """ - repo_dir = Path(self.dir, self.component_type, install_dir) + repo_dir = Path(self.directory, self.component_type, install_dir) if not repo_dir.exists(): raise LookupError(f"Nothing installed from {install_dir} in pipeline") @@ -180,7 +180,7 @@ def load_lint_config(self) -> None: Add parsed config to the `self.lint_config` class attribute. """ - _, tools_config = nf_core.utils.load_tools_config(self.dir) + _, tools_config = nf_core.utils.load_tools_config(self.directory) self.lint_config = tools_config.get("lint", {}) def check_modules_structure(self) -> None: @@ -193,9 +193,9 @@ def check_modules_structure(self) -> None: """ if self.repo_type == "pipeline": wrong_location_modules: List[Path] = [] - for directory, _, files in os.walk(Path(self.dir, "modules")): + for directory, _, files in os.walk(Path(self.directory, "modules")): if "main.nf" in files: - module_path = Path(directory).relative_to(Path(self.dir, "modules")) + module_path = Path(directory).relative_to(Path(self.directory, "modules")) parts = module_path.parts # Check that there are modules installed directly under the 'modules' directory if parts[1] == "modules": @@ -215,9 +215,9 @@ def check_modules_structure(self) -> None: wrong_dir = Path(modules_dir, module) shutil.move(str(wrong_dir), str(correct_dir)) log.info(f"Moved {wrong_dir} to {correct_dir}.") - shutil.rmtree(Path(self.dir, "modules", self.modules_repo.repo_path, "modules")) + shutil.rmtree(Path(self.directory, "modules", self.modules_repo.repo_path, "modules")) # Regenerate modules.json file - modules_json = ModulesJson(self.dir) + modules_json = ModulesJson(self.directory) modules_json.check_up_to_date() def check_patch_paths(self, patch_path: Path, module_name: str) -> None: @@ -243,12 +243,12 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None: for line in lines: fh.write(line) # Update path in modules.json if the file is in the correct format - modules_json = ModulesJson(self.dir) + modules_json = ModulesJson(self.directory) modules_json.load() if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None: modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][ self.modules_repo.repo_path - ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve())) + ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve())) modules_json.dump() def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]: @@ -262,7 +262,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[ """ include_stmts: Dict[str, List[Dict[str, Union[int, str]]]] = {} if self.repo_type == "pipeline": - workflow_files = Path(self.dir, "workflows").glob("*.nf") + workflow_files = Path(self.directory, "workflows").glob("*.nf") for workflow_file in workflow_files: with open(workflow_file) as fh: # Check if component path is in the file using mmap diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py index 9b81f54f06..f9b891004a 100644 --- a/nf_core/components/components_test.py +++ b/nf_core/components/components_test.py @@ -93,7 +93,7 @@ def run(self) -> None: os.environ["NFT_DIFF_ARGS"] = ( "--line-numbers --expand-tabs=2" # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences ) - with nf_core.utils.set_wd(Path(self.dir)): + with nf_core.utils.set_wd(Path(self.directory)): self.check_snapshot_stability() if len(self.errors) > 0: errors = "\n - ".join(self.errors) @@ -126,7 +126,7 @@ def check_inputs(self) -> None: self.component_dir = Path(self.component_type, self.modules_repo.repo_path, *self.component_name.split("/")) # First, sanity check that the module directory exists - if not Path(self.dir, self.component_dir).is_dir(): + if not Path(self.directory, self.component_dir).is_dir(): raise UserWarning( f"Cannot find directory '{self.component_dir}'.{' Should be TOOL/SUBTOOL or TOOL' if self.component_type == 'modules' else ''}" ) diff --git a/nf_core/components/install.py b/nf_core/components/install.py index 6385ee4092..dddc3f93ec 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -54,7 +54,7 @@ def install(self, component, silent=False): self.check_modules_structure() # Verify that 'modules.json' is consistent with the installed modules and subworkflows - modules_json = ModulesJson(self.dir) + modules_json = ModulesJson(self.directory) if not silent: modules_json.check_up_to_date() @@ -79,7 +79,7 @@ def install(self, component, silent=False): ) # Set the install folder based on the repository name - install_folder = Path(self.dir, self.component_type, self.modules_repo.repo_path) + install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path) # Compute the component directory component_dir = Path(install_folder, component) @@ -134,14 +134,14 @@ def install(self, component, silent=False): log.info(f"Use the following statement to include this {self.component_type[:-1]}:") Console().print( Syntax( - f"include {{ {component_name} }} from '../{Path(install_folder, component).relative_to(self.dir)}/main'", + f"include {{ {component_name} }} from '../{Path(install_folder, component).relative_to(self.directory)}/main'", "groovy", theme="ansi_dark", padding=1, ) ) if self.component_type == "subworkflows": - subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.dir) + subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.directory) if os.path.isfile(subworkflow_config): log.info("Add the following config statement to use this subworkflow:") Console().print( @@ -261,9 +261,9 @@ def clean_modules_json(self, component, modules_repo, modules_json): Remove installed version of module/subworkflow from modules.json """ for repo_url, repo_content in modules_json.modules_json["repos"].items(): - for dir, dir_components in repo_content[self.component_type].items(): + for directory, dir_components in repo_content[self.component_type].items(): for name, component_values in dir_components.items(): - if name == component and dir == modules_repo.repo_path: + if name == component and directory == modules_repo.repo_path: repo_to_remove = repo_url log.debug( f"Removing {self.component_type[:-1]} '{modules_repo.repo_path}/{component}' from repo '{repo_to_remove}' from modules.json." @@ -285,7 +285,7 @@ def check_alternate_remotes(self, modules_json): modules_json.load() for repo_url, repo_content in modules_json.modules_json.get("repos", dict()).items(): for component_type in repo_content: - for dir in repo_content.get(component_type, dict()).keys(): - if dir == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url: + for directory in repo_content.get(component_type, dict()).keys(): + if directory == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url: return True return False diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 6d47f1e7a8..7dd39bd904 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -7,6 +7,7 @@ import operator import os from pathlib import Path +from typing import List, Optional, Union import rich.box import rich.console @@ -53,18 +54,18 @@ class ComponentLint(ComponentCommand): def __init__( self, - component_type, - dir, - fail_warned=False, - remote_url=None, - branch=None, - no_pull=False, - registry=None, - hide_progress=False, + component_type: str, + directory: Union[str, Path], + fail_warned: bool = False, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + registry: Optional[str] = None, + hide_progress: bool = False, ): super().__init__( component_type, - dir=dir, + directory=directory, remote_url=remote_url, branch=branch, no_pull=no_pull, @@ -72,18 +73,18 @@ def __init__( ) self.fail_warned = fail_warned - self.passed = [] - self.warned = [] - self.failed = [] + self.passed: List[str] = [] + self.warned: List[str] = [] + self.failed: List[str] = [] if self.component_type == "modules": self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline") else: self.lint_tests = self.get_all_subworkflow_lint_tests(self.repo_type == "pipeline") if self.repo_type == "pipeline": - modules_json = ModulesJson(self.dir) + modules_json = ModulesJson(self.directory) modules_json.check_up_to_date() - self.all_remote_components = [] + self.all_remote_components: List[NFCoreComponent] = [] for repo_url, components in modules_json.get_all_components(self.component_type).items(): if remote_url is not None and remote_url != repo_url: continue @@ -92,9 +93,9 @@ def __init__( NFCoreComponent( comp, repo_url, - Path(self.dir, self.component_type, org, comp), + Path(self.directory, self.component_type, org, comp), self.repo_type, - Path(self.dir), + Path(self.directory), self.component_type, ) ) @@ -102,7 +103,7 @@ def __init__( raise LookupError( f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." ) - local_component_dir = Path(self.dir, self.component_type, "local") + local_component_dir = Path(self.directory, self.component_type, "local") self.all_local_components = [] if local_component_dir.exists(): self.all_local_components = [ @@ -111,20 +112,20 @@ def __init__( None, Path(local_component_dir, comp), self.repo_type, - Path(self.dir), + Path(self.directory), self.component_type, remote_component=False, ) for comp in self.get_local_components() ] - self.config = nf_core.utils.fetch_wf_config(Path(self.dir), cache_config=True) + self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True) else: component_dir = Path( - self.dir, + self.directory, self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path, ) self.all_remote_components = [ - NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.dir), self.component_type) + NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.directory), self.component_type) for m in self.get_components_clone_modules() ] self.all_local_components = [] @@ -132,7 +133,9 @@ def __init__( raise LookupError(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? - self.config = nf_core.utils.fetch_wf_config(Path(self.dir).joinpath("tests", "config"), cache_config=True) + self.config = nf_core.utils.fetch_wf_config( + Path(self.directory).joinpath("tests", "config"), cache_config=True + ) if registry is None: self.registry = self.config.get("docker.registry", "quay.io") @@ -143,6 +146,9 @@ def __init__( self.lint_config = None self.modules_json = None + def __repr__(self) -> str: + return f"ComponentLint({self.component_type}, {self.directory})" + @staticmethod def get_all_module_lint_tests(is_pipeline): if is_pipeline: @@ -168,7 +174,7 @@ def get_all_subworkflow_lint_tests(is_pipeline): def set_up_pipeline_files(self): self.load_lint_config() - self.modules_json = ModulesJson(self.dir) + self.modules_json = ModulesJson(self.directory) self.modules_json.load() # Only continue if a lint config has been loaded @@ -243,7 +249,7 @@ def format_result(test_results, table): module_name = lint_result.component_name # Make the filename clickable to open in VSCode - file_path = os.path.relpath(lint_result.file_path, self.dir) + file_path = os.path.relpath(lint_result.file_path, self.directory) file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]" table.add_row( diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 1e31e56271..9b24b6c0c9 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -51,7 +51,7 @@ def __init__( self.update_deps = update_deps self.component = None self.update_config = None - self.modules_json = ModulesJson(self.dir) + self.modules_json = ModulesJson(self.directory) self.branch = branch def _parameter_checks(self): @@ -96,9 +96,12 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr if updated is None: updated = [] - _, tool_config = nf_core.utils.load_tools_config(self.dir) + _, tool_config = nf_core.utils.load_tools_config(self.directory) self.update_config = tool_config.get("update", {}) + if self.update_config is None: + raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory") + self._parameter_checks() # Check modules directory structure @@ -171,7 +174,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr component_install_dir = install_tmp_dir / component # Compute the component directory - component_dir = os.path.join(self.dir, self.component_type, modules_repo.repo_path, component) + component_dir = Path(self.directory, self.component_type, modules_repo.repo_path, component) if sha is not None: version = sha @@ -318,7 +321,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr self.save_diff_fn, old_modules_json, self.modules_json.get_modules_json(), - Path(self.dir, "modules.json"), + Path(self.directory, "modules.json"), ) if exit_value and not silent: log.info( @@ -479,7 +482,9 @@ def get_all_components_info(self, branch=None): # Loop through all the modules/subworkflows in the pipeline # and check if they have an entry in the '.nf-core.yml' file for repo_name, components in self.modules_json.get_all_components(self.component_type).items(): - if repo_name not in self.update_config or self.update_config[repo_name] is True: + if isinstance(self.update_config, dict) and ( + repo_name not in self.update_config or self.update_config[repo_name] is True + ): # There aren't restrictions for the repository in .nf-core.yml file components_info[repo_name] = {} for component_dir, component in components: @@ -503,7 +508,7 @@ def get_all_components_info(self, branch=None): ), ) ] - elif isinstance(self.update_config[repo_name], dict): + elif isinstance(self.update_config, dict) and isinstance(self.update_config[repo_name], dict): # If it is a dict, then there are entries for individual components or component directories for component_dir in set([dir for dir, _ in components]): if isinstance(self.update_config[repo_name][component_dir], str): @@ -535,8 +540,8 @@ def get_all_components_info(self, branch=None): if self.sha is not None: overridden_repos.append(repo_name) elif self.update_config[repo_name][component_dir] is False: - for dir, component in components: - if dir == component_dir: + for directory, component in components: + if directory == component_dir: skipped_components.append(f"{component_dir}/{components}") elif isinstance(self.update_config[repo_name][component_dir], dict): # If it's a dict, there are entries for individual components @@ -596,7 +601,7 @@ def get_all_components_info(self, branch=None): raise UserWarning( f"{self.component_type[:-1].title()} '{component}' in '{component_dir}' has an invalid entry in '.nf-core.yml'" ) - elif isinstance(self.update_config[repo_name], str): + elif isinstance(self.update_config, dict) and isinstance(self.update_config[repo_name], str): # If a string is given it is the commit SHA to which we should update to custom_sha = self.update_config[repo_name] components_info[repo_name] = {} @@ -623,8 +628,10 @@ def get_all_components_info(self, branch=None): ] if self.sha is not None: overridden_repos.append(repo_name) - elif self.update_config[repo_name] is False: + elif isinstance(self.update_config, dict) and self.update_config[repo_name] is False: skipped_repos.append(repo_name) + elif not isinstance(self.update_config, dict): + raise UserWarning("`.nf-core.yml` is not correctly formatted.") else: raise UserWarning(f"Repo '{repo_name}' has an invalid entry in '.nf-core.yml'") @@ -712,8 +719,10 @@ def setup_diff_file(self, check_diff_exist=True): self.save_diff_fn = questionary.path( "Enter the filename: ", style=nf_core.utils.nfcore_question_style ).unsafe_ask() - - self.save_diff_fn = Path(self.save_diff_fn) + if self.save_diff_fn is not None: + self.save_diff_fn = Path(self.save_diff_fn) + else: + raise UserWarning("No filename provided for saving the diff file") if not check_diff_exist: # This guarantees that the file exists after calling the function @@ -744,7 +753,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path """ temp_component_dir = Path(install_folder, component) files = [file_path for file_path in temp_component_dir.rglob("*") if file_path.is_file()] - pipeline_path = Path(self.dir, self.component_type, repo_path, component) + pipeline_path = Path(self.directory, self.component_type, repo_path, component) if pipeline_path.exists(): pipeline_files = [f.name for f in pipeline_path.iterdir() if f.is_file()] @@ -795,7 +804,7 @@ def try_apply_patch( component_fullname = str(Path(repo_path, component)) log.info(f"Found patch for {self.component_type[:-1]} '{component_fullname}'. Trying to apply it to new files") - patch_path = Path(self.dir / patch_relpath) + patch_path = Path(self.directory / patch_relpath) component_relpath = Path(self.component_type, repo_path, component) # Check that paths in patch file are updated @@ -928,29 +937,31 @@ def update_linked_components( def manage_changes_in_linked_components(self, component, modules_to_update, subworkflows_to_update): """Check for linked components added or removed in the new subworkflow version""" if self.component_type == "subworkflows": - subworkflow_directory = Path(self.dir, self.component_type, self.modules_repo.repo_path, component) + subworkflow_directory = Path(self.directory, self.component_type, self.modules_repo.repo_path, component) included_modules, included_subworkflows = get_components_to_install(subworkflow_directory) # If a module/subworkflow has been removed from the subworkflow for module in modules_to_update: if module not in included_modules: log.info(f"Removing module '{module}' which is not included in '{component}' anymore.") - remove_module_object = ComponentRemove("modules", self.dir) + remove_module_object = ComponentRemove("modules", self.directory) remove_module_object.remove(module, removed_by=component) for subworkflow in subworkflows_to_update: if subworkflow not in included_subworkflows: log.info(f"Removing subworkflow '{subworkflow}' which is not included in '{component}' anymore.") - remove_subworkflow_object = ComponentRemove("subworkflows", self.dir) + remove_subworkflow_object = ComponentRemove("subworkflows", self.directory) remove_subworkflow_object.remove(subworkflow, removed_by=component) # If a new module/subworkflow is included in the subworklfow and wasn't included before for module in included_modules: if module not in modules_to_update: log.info(f"Installing newly included module '{module}' for '{component}'") - install_module_object = ComponentInstall(self.dir, "modules", installed_by=component) + install_module_object = ComponentInstall(self.directory, "modules", installed_by=component) install_module_object.install(module, silent=True) for subworkflow in included_subworkflows: if subworkflow not in subworkflows_to_update: log.info(f"Installing newly included subworkflow '{subworkflow}' for '{component}'") - install_subworkflow_object = ComponentInstall(self.dir, "subworkflows", installed_by=component) + install_subworkflow_object = ComponentInstall( + self.directory, "subworkflows", installed_by=component + ) install_subworkflow_object.install(subworkflow, silent=True) def _change_component_type(self, new_component_type): diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index b780144ef7..90d39104d2 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -11,6 +11,7 @@ import questionary import rich +import rich.progress import nf_core.modules.modules_utils import nf_core.utils @@ -39,7 +40,7 @@ class ModuleLint(ComponentLint): def __init__( self, - dir, + directory, fail_warned=False, remote_url=None, branch=None, @@ -49,7 +50,7 @@ def __init__( ): super().__init__( component_type="modules", - dir=dir, + directory=directory, fail_warned=fail_warned, remote_url=remote_url, branch=branch, @@ -127,9 +128,9 @@ def lint( remote_modules = self.all_remote_components if self.repo_type == "modules": - log.info(f"Linting modules repo: [magenta]'{self.dir}'") + log.info(f"Linting modules repo: [magenta]'{self.directory}'") else: - log.info(f"Linting pipeline: [magenta]'{self.dir}'") + log.info(f"Linting pipeline: [magenta]'{self.directory}'") if module: log.info(f"Linting module: [magenta]'{module}'") diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 2c2f1a32c9..63c356a79a 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -39,10 +39,10 @@ def __init__(self, pipeline_dir: Union[str, Path]): Args: pipeline_dir (str): The pipeline directory """ - self.dir = Path(pipeline_dir) - self.modules_dir = self.dir / "modules" - self.subworkflows_dir = self.dir / "subworkflows" - self.modules_json_path = self.dir / "modules.json" + self.directory = Path(pipeline_dir) + self.modules_dir = self.directory / "modules" + self.subworkflows_dir = self.directory / "subworkflows" + self.modules_json_path = self.directory / "modules.json" self.modules_json = None self.pipeline_modules = None self.pipeline_subworkflows = None @@ -63,7 +63,7 @@ def create(self): Raises: UserWarning: If the creation fails """ - pipeline_config = nf_core.utils.fetch_wf_config(self.dir) + pipeline_config = nf_core.utils.fetch_wf_config(self.directory) pipeline_name = pipeline_config.get("manifest.name", "") pipeline_url = pipeline_config.get("manifest.homePage", "") new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}} @@ -72,7 +72,7 @@ def create(self): if rich.prompt.Confirm.ask( "[bold][blue]?[/] Can't find a ./modules directory. Would you like me to create one?", default=True ): - log.info(f"Creating ./modules directory in '{self.dir}'") + log.info(f"Creating ./modules directory in '{self.directory}'") self.modules_dir.mkdir() else: raise UserWarning("Cannot proceed without a ./modules directory.") @@ -153,7 +153,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None # The function might rename some directories, keep track of them renamed_dirs = {} # Check if there are any untracked repositories - dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos]) + dirs_not_covered = self.directory_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos]) if len(dirs_not_covered) > 0: log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'") # Loop until all directories in the base directory are covered by a remote @@ -203,7 +203,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None if component_type not in repos[nrepo_remote]: repos[nrepo_remote][component_type] = {} repos[nrepo_remote][component_type][nrepo_name] = {} - dirs_not_covered = self.dir_tree_uncovered( + dirs_not_covered = self.directory_tree_uncovered( directory, [Path(name) for url in repos for name in repos[url][component_type]] ) @@ -816,7 +816,7 @@ def try_apply_patch_reverse(self, module, repo_name, patch_relpath, module_dir): LookupError: If patch was not applied """ module_fullname = str(Path(repo_name, module)) - patch_path = Path(self.dir / patch_relpath) + patch_path = Path(self.directory / patch_relpath) try: new_files = ModulesDiffer.try_apply_patch(module, repo_name, patch_path, module_dir, reverse=True) diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py index 0643d2e295..f49e98e93c 100644 --- a/nf_core/pipelines/create_logo.py +++ b/nf_core/pipelines/create_logo.py @@ -12,7 +12,7 @@ def create_logo( text: str, - dir: Union[Path, str], + directory: Union[Path, str], filename: str = "", theme: str = "light", width: int = 2300, @@ -22,10 +22,10 @@ def create_logo( """Create a logo for a pipeline.""" if not text: raise UserWarning("Please provide the name of the text to put on the logo.") - dir = Path(dir) - if not dir.is_dir(): - log.debug(f"Creating directory {dir}") - dir.mkdir(parents=True, exist_ok=True) + directory = Path(directory) + if not directory.is_dir(): + log.debug(f"Creating directory {directory}") + directory.mkdir(parents=True, exist_ok=True) assets = Path(nf_core.__file__).parent / "assets/logo" if format == "svg": @@ -43,7 +43,7 @@ def create_logo( # save the svg logo_filename = f"nf-core-{text}_logo_{theme}.svg" if not filename else filename logo_filename = f"{logo_filename}.svg" if not logo_filename.lower().endswith(".svg") else logo_filename - logo_path = Path(dir, logo_filename) + logo_path = Path(directory, logo_filename) with open(logo_path, "w") as fh: fh.write(svg) @@ -51,7 +51,7 @@ def create_logo( logo_filename = f"nf-core-{text}_logo_{theme}.png" if not filename else filename logo_filename = f"{logo_filename}.png" if not logo_filename.lower().endswith(".png") else logo_filename cache_name = f"nf-core-{text}_logo_{theme}_{width}.png" - logo_path = Path(dir, logo_filename) + logo_path = Path(directory, logo_filename) # Check if we haven't already created this logo if logo_path.is_file() and not force: From 089bb672b13265d40b5cd5cc7e96146943288402 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 18 Jul 2024 16:31:08 +0200 Subject: [PATCH 173/574] Fix the command_create by putting the plain param again --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 192c7cd139..1892189964 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2181,7 +2181,7 @@ def command_lint( help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)", ) @click.pass_context -def command_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation): +def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation): """ Use `nf-core pipelines create` instead. """ From dcb1dc0b6802d39494389bfb401d75647b201e83 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 18 Jul 2024 16:41:38 +0200 Subject: [PATCH 174/574] Automatically add a default version in pipelines_create --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 1892189964..152814c9cc 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation) + pipelines_create(ctx, name, description, author, version="1.0.0dev", force, outdir, template_yaml, organisation) # Main script is being run - launch the CLI From 9dc96b8768e4a289cb6784924c7f29e07ed4a39c Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 18 Jul 2024 17:03:45 +0200 Subject: [PATCH 175/574] Add default version --- nf_core/__main__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 152814c9cc..cb99bdedcc 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2169,7 +2169,7 @@ def command_lint( ) @click.option("-d", "--description", type=str, help="A short description of your pipeline") @click.option("-a", "--author", type=str, help="Name of the main author(s)") -@click.option("--version", type=str, help="The initial version number to use") +@click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use") @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists") @click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") @@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - pipelines_create(ctx, name, description, author, version="1.0.0dev", force, outdir, template_yaml, organisation) + pipelines_create(ctx, name, description, author, force, outdir, template_yaml, organisation) # Main script is being run - launch the CLI From 60973a19a2381f89b11ff6c408c9f150ff6a1d55 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 19 Jul 2024 06:45:58 +0200 Subject: [PATCH 176/574] fix ALL the mypy errors --- nf_core/commands_pipelines.py | 2 +- nf_core/components/components_command.py | 10 +- nf_core/components/components_utils.py | 8 +- nf_core/components/create.py | 2 +- nf_core/components/info.py | 66 +++++---- nf_core/components/install.py | 42 +++--- nf_core/components/lint/__init__.py | 38 +++--- nf_core/components/list.py | 10 +- nf_core/components/nfcore_component.py | 51 ++++--- nf_core/components/patch.py | 4 + nf_core/components/remove.py | 19 ++- nf_core/modules/bump_versions.py | 12 +- nf_core/modules/lint/__init__.py | 60 ++++++--- nf_core/modules/lint/environment_yml.py | 6 +- nf_core/modules/lint/main_nf.py | 21 ++- nf_core/modules/lint/meta_yml.py | 6 +- nf_core/modules/modules_differ.py | 16 ++- nf_core/modules/modules_json.py | 126 ++++++++++++------ nf_core/modules/modules_repo.py | 9 +- nf_core/modules/modules_utils.py | 12 +- .../subworkflows/lint/subworkflow_tests.py | 7 +- nf_core/synced_repo.py | 58 +++++--- nf_core/utils.py | 16 ++- 23 files changed, 381 insertions(+), 220 deletions(-) diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py index deb1f691a5..432a36aaee 100644 --- a/nf_core/commands_pipelines.py +++ b/nf_core/commands_pipelines.py @@ -284,7 +284,7 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. To keep nf-core pipelines up to date with improvements in the main - template, we use a method of synchronisation that uses a special + template, we use a method of w that uses a special git branch called [cyan i]TEMPLATE[/]. This command updates the [cyan i]TEMPLATE[/] branch with the latest version of diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index bf80b46113..13a6fed338 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -33,7 +33,7 @@ def __init__( Initialise the ComponentClass object """ self.component_type = component_type - self.directory = Path(directory) if directory else None + self.directory = Path(directory) self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.hide_progress = hide_progress self.no_prompts = no_prompts @@ -109,13 +109,13 @@ def has_modules_file(self) -> None: log.info("Creating missing 'module.json' file.") ModulesJson(self.directory).create() - def clear_component_dir(self, component_name: str, component_dir: str) -> bool: + def clear_component_dir(self, component_name: str, component_dir: Union[str, Path]) -> bool: """ Removes all files in the module/subworkflow directory Args: component_name (str): The name of the module/subworkflow - component_dir (str): The path to the module/subworkflow in the module repository + component_dir (str, Path): The path to the module/subworkflow """ @@ -156,7 +156,7 @@ def components_from_repo(self, install_dir: str) -> List[str]: ] def install_component_files( - self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: str + self, component_name: str, component_version: str, modules_repo: ModulesRepo, install_dir: Union[str, Path] ) -> bool: """ Installs a module/subworkflow into the given directory @@ -165,7 +165,7 @@ def install_component_files( component_name (str): The name of the module/subworkflow component_version (str): Git SHA for the version of the module/subworkflow to be installed modules_repo (ModulesRepo): A correctly configured ModulesRepo object - install_dir (str): The path to where the module/subworkflow should be installed (should be the 'modules/' or 'subworkflows/' dir of the pipeline) + install_dir (str, Path): The path to where the module/subworkflow should be installed (should be the 'modules/' or 'subworkflows/' dir of the pipeline) Returns: (bool): Whether the operation was successful of not diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 01650a643d..32f6c0fc11 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -1,7 +1,7 @@ import logging import re from pathlib import Path -from typing import List, Optional, Tuple +from typing import List, Optional, Tuple, Union import questionary import rich.prompt @@ -12,7 +12,7 @@ log = logging.getLogger(__name__) -def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[str, Optional[str], str]: +def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]: """ Determine whether this is a pipeline repository or a clone of nf-core/modules @@ -23,7 +23,7 @@ def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[st raise UserWarning(f"Could not find directory: {directory}") # Try to find the root directory - base_dir: str = nf_core.utils.determine_base_dir(directory) + base_dir: Path = nf_core.utils.determine_base_dir(directory) # Figure out the repository type from the .nf-core.yml config file if we can config_fn, tools_config = nf_core.utils.load_tools_config(base_dir) @@ -132,7 +132,7 @@ def prompt_component_version_sha( return git_sha -def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str]]: +def get_components_to_install(subworkflow_dir: Union[str, Path]) -> Tuple[List[str], List[str]]: """ Parse the subworkflow main.nf file to retrieve all imported modules and subworkflows. """ diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 5d6c411bdc..532c2a46d6 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -29,7 +29,7 @@ class ComponentCreate(ComponentCommand): def __init__( self, component_type: str, - directory: str = ".", + directory: Path = Path("."), component: str = "", author: Optional[str] = None, process_label: Optional[str] = None, diff --git a/nf_core/components/info.py b/nf_core/components/info.py index 54fc0004dc..8597875af4 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -1,6 +1,7 @@ import logging import os from pathlib import Path +from typing import Dict, Optional, Union import questionary import yaml @@ -57,25 +58,26 @@ class ComponentInfo(ComponentCommand): def __init__( self, - component_type, - pipeline_dir, - component_name, - remote_url=None, - branch=None, - no_pull=False, + component_type: str, + pipeline_dir: Union[str, Path], + component_name: str, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, ): super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) - self.meta = None - self.local_path = None - self.remote_location = None - self.local = None + self.meta: Optional[Dict] = None + self.local_path: Optional[Path] = None + self.remote_location: Optional[str] = None + self.local: bool = False + self.modules_json: Optional[ModulesJson] = None if self.repo_type == "pipeline": # Check modules directory structure if self.component_type == "modules": self.check_modules_structure() # Check modules.json up to date - self.modules_json = ModulesJson(self.dir) + self.modules_json = ModulesJson(self.directory) self.modules_json.check_up_to_date() else: self.modules_json = None @@ -95,6 +97,7 @@ def init_mod_name(self, component): Args: module: str: Module name to check """ + assert self.modules_json is not None # mypy if component is None: self.local = questionary.confirm( f"Is the {self.component_type[:-1]} locally installed?", style=nf_core.utils.nfcore_question_style @@ -103,12 +106,12 @@ def init_mod_name(self, component): if self.repo_type == "modules": components = self.get_components_clone_modules() else: - components = self.modules_json.get_all_components(self.component_type).get( - self.modules_repo.remote_url, {} + all_components = self.modules_json.get_all_components(self.component_type).get( + self.modules_repo.remote_url, [] ) components = [ component if directory == self.modules_repo.repo_path else f"{directory}/{component}" - for directory, component in components + for directory, component in all_components ] if not components: raise UserWarning( @@ -133,11 +136,13 @@ def init_mod_name(self, component): if self.repo_type == "pipeline": # check if the module is locally installed local_paths = self.modules_json.get_all_components(self.component_type).get( - self.modules_repo.remote_url, {} - ) + self.modules_repo.remote_url + ) # type: ignore + if local_paths is None: + raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}") for directory, comp in local_paths: if comp == component: - component_base_path = Path(self.dir, self.component_type) + component_base_path = Path(self.directory, self.component_type) self.local_path = Path(component_base_path, directory, component) break if self.local_path: @@ -166,20 +171,22 @@ def get_local_yaml(self): """Attempt to get the meta.yml file from a locally installed module/subworkflow. Returns: - dict or bool: Parsed meta.yml found, False otherwise + Optional[dict]: Parsed meta.yml if found, None otherwise """ + assert self.modules_json is not None # mypy if self.repo_type == "pipeline": # Try to find and load the meta.yml file - component_base_path = Path(self.dir, self.component_type) + component_base_path = Path(self.directory, self.component_type) # Check that we have any modules/subworkflows installed from this repo components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url) - component_names = [component for _, component in components] if components is None: raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}") + component_names = [component for _, component in components] + if self.component in component_names: - install_dir = [dir for dir, module in components if module == self.component][0] + install_dir = [directory for directory, module in components if module == self.component][0] comp_dir = Path(component_base_path, install_dir, self.component) meta_fn = Path(comp_dir, "meta.yml") if meta_fn.exists(): @@ -190,7 +197,7 @@ def get_local_yaml(self): log.debug(f"{self.component_type[:-1].title()} '{self.component}' meta.yml not found locally") else: - component_base_path = Path(self.dir, self.component_type, self.org) + component_base_path = Path(self.directory, self.component_type, self.org) if self.component in os.listdir(component_base_path): comp_dir = Path(component_base_path, self.component) meta_fn = Path(comp_dir, "meta.yml") @@ -203,7 +210,7 @@ def get_local_yaml(self): return None - def get_remote_yaml(self): + def get_remote_yaml(self) -> Optional[dict]: """Attempt to get the meta.yml file from a remote repo. Returns: @@ -211,11 +218,11 @@ def get_remote_yaml(self): """ # Check if our requested module/subworkflow is there if self.component not in self.modules_repo.get_avail_components(self.component_type): - return False + return None file_contents = self.modules_repo.get_meta_yml(self.component_type, self.component) if file_contents is None: - return False + return None self.remote_location = self.modules_repo.remote_url return yaml.safe_load(file_contents) @@ -242,7 +249,8 @@ def generate_component_info_help(self): "\n" ) ) - + if self.meta is None: + raise UserWarning("No meta.yml file found") if self.meta.get("tools"): tools_strings = [] for tool in self.meta["tools"]: @@ -307,21 +315,21 @@ def generate_component_info_help(self): # Print include statement if self.local_path: - install_folder = Path(self.dir, self.component_type, self.modules_repo.repo_path) + install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path) component_name = "_".join(self.component.upper().split("/")) renderables.append( Text.from_markup(f"\n [blue]Use the following statement to include this {self.component_type[:-1]}:") ) renderables.append( Syntax( - f"include {{ {component_name} }} from '../{Path(install_folder, self.component).relative_to(self.dir)}/main'", + f"include {{ {component_name} }} from '../{Path(install_folder, self.component).relative_to(self.directory)}/main'", "groovy", theme="ansi_dark", padding=1, ) ) if self.component_type == "subworkflows": - subworkflow_config = Path(install_folder, self.component, "nextflow.config").relative_to(self.dir) + subworkflow_config = Path(install_folder, self.component, "nextflow.config").relative_to(self.directory) if os.path.isfile(subworkflow_config): renderables.append( Text.from_markup("\n [blue]Add the following config statement to use this subworkflow:") diff --git a/nf_core/components/install.py b/nf_core/components/install.py index dddc3f93ec..e6c31b3cbb 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -1,11 +1,13 @@ import logging import os from pathlib import Path +from typing import List, Optional, Union import questionary from rich.console import Console from rich.syntax import Syntax +import nf_core.components import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.components_command import ComponentCommand @@ -22,26 +24,26 @@ class ComponentInstall(ComponentCommand): def __init__( self, - pipeline_dir, - component_type, - force=False, - prompt=False, - sha=None, - remote_url=None, - branch=None, - no_pull=False, - installed_by=False, + pipeline_dir: Union[str, Path], + component_type: str, + force: bool = False, + prompt: bool = False, + sha: Optional[str] = None, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + installed_by: Optional[List[str]] = None, ): super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.force = force self.prompt = prompt self.sha = sha - if installed_by: + if installed_by is not None: self.installed_by = installed_by else: - self.installed_by = self.component_type + self.installed_by = [self.component_type] - def install(self, component, silent=False): + def install(self, component: str, silent: bool = False) -> bool: if self.repo_type == "modules": log.error(f"You cannot install a {component} in a clone of nf-core/modules") return False @@ -67,8 +69,11 @@ def install(self, component, silent=False): # Verify SHA if not self.modules_repo.verify_sha(self.prompt, self.sha): return False + if self.modules_repo is None: + return False # Check and verify component name + component = self.collect_and_verify_name(component, self.modules_repo) if not component: return False @@ -156,19 +161,21 @@ def install_included_components(self, subworkflow_dir): modules_to_install, subworkflows_to_install = get_components_to_install(subworkflow_dir) for s_install in subworkflows_to_install: original_installed = self.installed_by - self.installed_by = Path(subworkflow_dir).parts[-1] + self.installed_by = [Path(subworkflow_dir).parts[-1]] self.install(s_install, silent=True) self.installed_by = original_installed for m_install in modules_to_install: original_component_type = self.component_type self.component_type = "modules" original_installed = self.installed_by - self.installed_by = Path(subworkflow_dir).parts[-1] + self.installed_by = [Path(subworkflow_dir).parts[-1]] self.install(m_install, silent=True) self.component_type = original_component_type self.installed_by = original_installed - def collect_and_verify_name(self, component, modules_repo): + def collect_and_verify_name( + self, component: Optional[str], modules_repo: nf_core.modules.modules_repo.ModulesRepo + ) -> str: """ Collect component name. Check that the supplied name is an available module/subworkflow. @@ -180,18 +187,19 @@ def collect_and_verify_name(self, component, modules_repo): style=nf_core.utils.nfcore_question_style, ).unsafe_ask() + if component is None: + return "" + # Check that the supplied name is an available module/subworkflow if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha): log.error( f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}." ) log.info(f"Use the command 'nf-core {self.component_type} list' to view available software") - return False if not modules_repo.component_exists(component, self.component_type, commit=self.sha): warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})" log.warning(warn_msg) - return False return component diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 7dd39bd904..2cd59dc489 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -7,7 +7,7 @@ import operator import os from pathlib import Path -from typing import List, Optional, Union +from typing import List, Optional, Tuple, Union import rich.box import rich.console @@ -37,12 +37,12 @@ class LintExceptionError(Exception): class LintResult: """An object to hold the results of a lint test""" - def __init__(self, component, lint_test, message, file_path): + def __init__(self, component: NFCoreComponent, lint_test: str, message: str, file_path: Path): self.component = component self.lint_test = lint_test self.message = message self.file_path = file_path - self.component_name = component.component_name + self.component_name: str = component.component_name @rich.repr.auto @@ -73,9 +73,9 @@ def __init__( ) self.fail_warned = fail_warned - self.passed: List[str] = [] - self.warned: List[str] = [] - self.failed: List[str] = [] + self.passed: List[LintResult] = [] + self.warned: List[LintResult] = [] + self.failed: List[LintResult] = [] if self.component_type == "modules": self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline") else: @@ -88,17 +88,21 @@ def __init__( for repo_url, components in modules_json.get_all_components(self.component_type).items(): if remote_url is not None and remote_url != repo_url: continue - for org, comp in components: - self.all_remote_components.append( - NFCoreComponent( - comp, - repo_url, - Path(self.directory, self.component_type, org, comp), - self.repo_type, - Path(self.directory), - self.component_type, - ) + if isinstance(components, str): + raise LookupError( + f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again." ) + org, comp = components + self.all_remote_components.append( + NFCoreComponent( + comp, + repo_url, + Path(self.directory, self.component_type, org, comp), + self.repo_type, + Path(self.directory), + self.component_type, + ) + ) if not self.all_remote_components: raise LookupError( f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." @@ -119,7 +123,7 @@ def __init__( for comp in self.get_local_components() ] self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True) - else: + elif self.repo_type == "modules": component_dir = Path( self.directory, self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path, diff --git a/nf_core/components/list.py b/nf_core/components/list.py index f5f2744e17..b24732e5c3 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -1,6 +1,6 @@ import json import logging -from typing import Dict, List, Optional, Tuple, Union, cast +from typing import Dict, List, Optional, Union, cast import rich.table @@ -87,18 +87,18 @@ def pattern_msg(keywords: List[str]) -> str: return "" # Verify that 'modules.json' is consistent with the installed modules - modules_json: ModulesJson = ModulesJson(self.dir) + modules_json: ModulesJson = ModulesJson(self.directory) modules_json.check_up_to_date() # Filter by keywords - repos_with_comps: Dict[str, List[Tuple[str, str]]] = { + repos_with_comps = { repo_url: [comp for comp in components if all(k in comp[1] for k in keywords)] for repo_url, components in modules_json.get_all_components(self.component_type).items() } # Nothing found if sum(map(len, repos_with_comps)) == 0: - log.info(f"No nf-core {self.component_type} found in '{self.dir}'{pattern_msg(keywords)}") + log.info(f"No nf-core {self.component_type} found in '{self.directory}'{pattern_msg(keywords)}") return "" table.add_column("Repository") @@ -160,5 +160,5 @@ def pattern_msg(keywords: List[str]) -> str: f"{pattern_msg(keywords)}:\n" ) else: - log.info(f"{self.component_type.capitalize()} installed in '{self.dir}'{pattern_msg(keywords)}:\n") + log.info(f"{self.component_type.capitalize()} installed in '{self.directory}'{pattern_msg(keywords)}:\n") return table diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 5d0baf63dd..1433122225 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -5,7 +5,7 @@ import logging import re from pathlib import Path -from typing import Union +from typing import List, Optional, Tuple, Union log = logging.getLogger(__name__) @@ -18,13 +18,13 @@ class NFCoreComponent: def __init__( self, - component_name, - repo_url, - component_dir, - repo_type, - base_dir, - component_type, - remote_component=True, + component_name: str, + repo_url: Optional[str], + component_dir: Path, + repo_type: str, + base_dir: Path, + component_type: str, + remote_component: bool = True, ): """ Initialize the object @@ -46,21 +46,21 @@ def __init__( self.component_dir = component_dir self.repo_type = repo_type self.base_dir = base_dir - self.passed = [] - self.warned = [] - self.failed = [] - self.inputs = [] - self.outputs = [] - self.has_meta = False - self.git_sha = None - self.is_patched = False + self.passed: List[Tuple[str, str, Path]] = [] + self.warned: List[Tuple[str, str, Path]] = [] + self.failed: List[Tuple[str, str, Path]] = [] + self.inputs: List[str] = [] + self.outputs: List[str] = [] + self.has_meta: bool = False + self.git_sha: Optional[str] = None + self.is_patched: bool = False if remote_component: # Initialize the important files - self.main_nf = Path(self.component_dir, "main.nf") - self.meta_yml = Path(self.component_dir, "meta.yml") + self.main_nf: Path = Path(self.component_dir, "main.nf") + self.meta_yml: Optional[Path] = Path(self.component_dir, "meta.yml") self.process_name = "" - self.environment_yml = Path(self.component_dir, "environment.yml") + self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml") repo_dir = self.component_dir.parts[: self.component_dir.parts.index(self.component_name.split("/")[0])][-1] self.org = repo_dir @@ -79,8 +79,8 @@ def __init__( self.component_name = self.component_dir.stem # These attributes are only used by nf-core modules # so just initialize them to None - self.meta_yml = "" - self.environment_yml = "" + self.meta_yml = None + self.environment_yml = None self.test_dir = None self.test_yml = None self.test_main_nf = None @@ -155,10 +155,10 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st included_components.append(component) return included_components - def get_inputs_from_main_nf(self): + def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" - inputs = [] - with open(self.main_nf) as f: + inputs: List[str] = [] + with open(str(self.main_nf)) as f: data = f.read() # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo # regex matches: @@ -171,7 +171,6 @@ def get_inputs_from_main_nf(self): # don't match anything inside comments or after "output:" if "input:" not in data: log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs input_data = data.split("input:")[1].split("output:")[0] regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" matches = re.finditer(regex, input_data, re.MULTILINE) @@ -187,7 +186,7 @@ def get_inputs_from_main_nf(self): def get_outputs_from_main_nf(self): outputs = [] - with open(self.main_nf) as f: + with open(str(self.main_nf)) as f: data = f.read() # get output values from main.nf after "output:". the names are always after "emit:" if "output:" not in data: diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py index 55d5747451..5b29c152d8 100644 --- a/nf_core/components/patch.py +++ b/nf_core/components/patch.py @@ -30,6 +30,10 @@ def _parameter_checks(self, component): raise UserWarning("The command was not run in a valid pipeline directory.") components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url) + if components is None: + raise UserWarning( + f"No {self.component_type[:-1]}s found in the 'modules.json' file for the remote '{self.modules_repo.remote_url}'" + ) component_names = [component for _, component in components] if component is not None and component not in component_names: diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py index 8d884db6c4..c2c5843918 100644 --- a/nf_core/components/remove.py +++ b/nf_core/components/remove.py @@ -58,10 +58,10 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals removed_components = [] # Get the module/subworkflow directory - component_dir = Path(self.dir, self.component_type, repo_path, component) + component_dir = Path(self.directory, self.component_type, repo_path, component) # Load the modules.json file - modules_json = ModulesJson(self.dir) + modules_json = ModulesJson(self.directory) modules_json.load() # Verify that the module/subworkflow is actually installed @@ -98,9 +98,16 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals for file, stmts in include_stmts.items(): renderables = [] for stmt in stmts: + # check that the line number is integer + if not isinstance(stmt["line_number"], int): + log.error( + f"Could not parse line number '{stmt['line_number']}' in '{file}'. Please report this issue." + ) + continue + renderables.append( Syntax( - stmt["line"], + str(stmt["line"]), "groovy", theme="ansi_dark", line_numbers=True, @@ -123,7 +130,7 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals style=nf_core.utils.nfcore_question_style, ).unsafe_ask(): # add the component back to modules.json - if not ComponentInstall(self.dir, self.component_type, force=True).install( + if not ComponentInstall(self.directory, self.component_type, force=True).install( component, silent=True ): log.warning( @@ -133,7 +140,9 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals return removed # Remove the component files of all entries removed from modules.json removed = ( - True if self.clear_component_dir(component, Path(self.dir, removed_component_dir)) or removed else False + True + if self.clear_component_dir(component, Path(self.directory, removed_component_dir)) or removed + else False ) removed_components.append(component) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 1b94d5910c..fb0dc7d50d 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -76,10 +76,10 @@ def bump_versions( ) # Get list of all modules - _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.dir) + _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory) # Load the .nf-core.yml config - _, self.tools_config = nf_core.utils.load_tools_config(self.dir) + _, self.tools_config = nf_core.utils.load_tools_config(self.directory) # Prompt for module or all if module is None and not all_modules: @@ -179,7 +179,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: except (LookupError, ValueError): self.failed.append( ( - f"Conda version not specified correctly: {module.main_nf.relative_to(self.dir)}", + f"Conda version not specified correctly: {Path(module.main_nf).relative_to(self.directory)}", module.component_name, ) ) @@ -245,12 +245,12 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: fh.write(content) # change version in environment.yml - with open(module.environment_yml) as fh: + with open(str(module.environment_yml)) as fh: env_yml = yaml.safe_load(fh) env_yml["dependencies"][0] = re.sub( bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0] ) - with open(module.environment_yml, "w") as fh: + with open(str(module.environment_yml), "w") as fh: yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper()) self.updated.append( @@ -272,7 +272,7 @@ def get_bioconda_version(self, module: NFCoreComponent) -> List[str]: # Check whether file exists and load it bioconda_packages = [] try: - with open(module.environment_yml) as fh: + with open(str(module.environment_yml)) as fh: env_yml = yaml.safe_load(fh) bioconda_packages = env_yml.get("dependencies", []) except FileNotFoundError: diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index 90d39104d2..2b10b4df5a 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -8,18 +8,33 @@ import logging import os +from pathlib import Path +from typing import List, Optional, Union import questionary import rich import rich.progress +import nf_core.components +import nf_core.components.nfcore_component import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult +from nf_core.components.nfcore_component import NFCoreComponent from nf_core.pipelines.lint_utils import console log = logging.getLogger(__name__) +from .environment_yml import environment_yml +from .main_nf import main_nf +from .meta_yml import meta_yml +from .module_changes import module_changes +from .module_deprecations import module_deprecations +from .module_patch import module_patch +from .module_tests import module_tests +from .module_todos import module_todos +from .module_version import module_version + class ModuleLint(ComponentLint): """ @@ -28,25 +43,25 @@ class ModuleLint(ComponentLint): """ # Import lint functions - from .environment_yml import environment_yml # type: ignore[misc] - from .main_nf import main_nf # type: ignore[misc] - from .meta_yml import meta_yml # type: ignore[misc] - from .module_changes import module_changes # type: ignore[misc] - from .module_deprecations import module_deprecations # type: ignore[misc] - from .module_patch import module_patch # type: ignore[misc] - from .module_tests import module_tests # type: ignore[misc] - from .module_todos import module_todos # type: ignore[misc] - from .module_version import module_version # type: ignore[misc] + environment_yml = environment_yml + main_nf = main_nf + meta_yml = meta_yml + module_changes = module_changes + module_deprecations = module_deprecations + module_patch = module_patch + module_tests = module_tests + module_todos = module_todos + module_version = module_version def __init__( self, - directory, - fail_warned=False, - remote_url=None, - branch=None, - no_pull=False, - registry=None, - hide_progress=False, + directory: Union[str, Path], + fail_warned: bool = False, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + registry: Optional[str] = None, + hide_progress: bool = False, ): super().__init__( component_type="modules", @@ -155,7 +170,9 @@ def lint( self._print_results(show_passed=show_passed, sort_by=sort_by) self.print_summary() - def lint_modules(self, modules, registry="quay.io", local=False, fix_version=False): + def lint_modules( + self, modules: List[NFCoreComponent], registry: str = "quay.io", local: bool = False, fix_version: bool = False + ) -> None: """ Lint a list of modules @@ -185,7 +202,14 @@ def lint_modules(self, modules, registry="quay.io", local=False, fix_version=Fal progress_bar.update(lint_progress, advance=1, test_name=mod.component_name) self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version) - def lint_module(self, mod, progress_bar, registry, local=False, fix_version=False): + def lint_module( + self, + mod: NFCoreComponent, + progress_bar: rich.progress.Progress, + registry: str, + local: bool = False, + fix_version: bool = False, + ): """ Perform linting on one module diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index e10ef1761d..e34b9d5856 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -5,7 +5,7 @@ import yaml from jsonschema import exceptions, validators -from nf_core.components.lint import ComponentLint +from nf_core.components.lint import ComponentLint, LintExceptionError from nf_core.components.nfcore_component import NFCoreComponent from nf_core.utils import custom_yaml_dumper @@ -22,8 +22,10 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) """ env_yml = None # load the environment.yml file + if module.environment_yml is None: + raise LintExceptionError("Module does not have an `environment.yml` file") try: - with open(Path(module.component_dir, "environment.yml")) as fh: + with open(str(module.environment_yml)) as fh: env_yml = yaml.safe_load(fh) module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml)) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 81308ba5c5..985a92fa1f 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -6,19 +6,24 @@ import re import sqlite3 from pathlib import Path +from typing import List, Tuple from urllib.parse import urlparse, urlunparse import requests import yaml +from rich.progress import Progress import nf_core import nf_core.modules.modules_utils +from nf_core.components.nfcore_component import NFCoreComponent from nf_core.modules.modules_differ import ModulesDiffer log = logging.getLogger(__name__) -def main_nf(module_lint_object, module, fix_version, registry, progress_bar): +def main_nf( + module_lint_object, module: NFCoreComponent, fix_version: bool, registry: str, progress_bar: Progress +) -> Tuple[List[str], List[str]]: """ Lint a ``main.nf`` module file @@ -43,7 +48,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar): # Check if we have a patch file affecting the 'main.nf' file # otherwise read the lines directly from the module - lines = None + lines: List[str] = [] if module.is_patched: lines = ModulesDiffer.try_apply_patch( module.component_name, @@ -51,8 +56,9 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar): module.patch_path, Path(module.component_dir).relative_to(module.base_dir), reverse=True, - ).get("main.nf") - if lines is None: + ).get("main.nf", [""]) + + if not lines: try: # Check whether file exists and load it with open(module.main_nf) as fh: @@ -60,10 +66,13 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar): module.passed.append(("main_nf_exists", "Module file exists", module.main_nf)) except FileNotFoundError: module.failed.append(("main_nf_exists", "Module file does not exist", module.main_nf)) - return deprecated_i = ["initOptions", "saveFiles", "getSoftwareName", "getProcessName", "publishDir"] - lines_j = "\n".join(lines) + if lines is not None: + lines_j = "\n".join(lines) + else: + lines_j = "" + for i in deprecated_i: if i in lines_j: module.failed.append( diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 4c036713c8..32110b7131 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -4,7 +4,7 @@ import yaml from jsonschema import exceptions, validators -from nf_core.components.lint import ComponentLint +from nf_core.components.lint import ComponentLint, LintExceptionError from nf_core.components.nfcore_component import NFCoreComponent from nf_core.modules.modules_differ import ModulesDiffer @@ -53,9 +53,11 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None ).get("meta.yml") if lines is not None: meta_yaml = yaml.safe_load("".join(lines)) + if module.meta_yml is None: + raise LintExceptionError("Module does not have a `meta.yml` file") if meta_yaml is None: try: - with open(module.meta_yml) as fh: + with open(str(module.meta_yml)) as fh: meta_yaml = yaml.safe_load(fh) module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml)) except FileNotFoundError: diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index e79554f2b6..36d927f084 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -4,6 +4,7 @@ import logging import os from pathlib import Path +from typing import List, Union from rich.console import Console from rich.syntax import Syntax @@ -295,7 +296,7 @@ def print_diff( console.print(Syntax("".join(diff), "diff", theme="ansi_dark", padding=1)) @staticmethod - def per_file_patch(patch_fn): + def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, List[str]]: """ Splits a patch file for several files into one patch per file. @@ -306,12 +307,12 @@ def per_file_patch(patch_fn): dict[str, str]: A dictionary indexed by the filenames with the file patches as values """ - with open(patch_fn) as fh: + with open(str(patch_fn)) as fh: lines = fh.readlines() patches = {} i = 0 - patch_lines = [] + patch_lines: list[str] = [] key = "preamble" while i < len(lines): line = lines[i] @@ -391,12 +392,12 @@ def try_apply_single_patch(file_lines, patch, reverse=False): """ Tries to apply a patch to a modified file. Since the line numbers in the patch does not agree if the file is modified, the old and new - lines in the patch are reconstructed and then we look for the old lines + lines inpatch are reconstructed and then we look for the old lines in the modified file. If all hunk in the patch are found in the new file it is updated with the new lines from the patch file. Args: - new_fn (str | Path): Path to the modified file + file_lines ([str]): The lines of the file to be patched patch (str | Path): (Outdated) patch for the file reverse (bool): Apply the patch in reverse @@ -450,7 +451,9 @@ def try_apply_single_patch(file_lines, patch, reverse=False): return patched_new_lines @staticmethod - def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False): + def try_apply_patch( + module: str, repo_path: Union[str, Path], patch_path: Union[str, Path], module_dir: Path, reverse: bool = False + ) -> dict[str, List[str]]: """ Try applying a full patch file to a module @@ -459,6 +462,7 @@ def try_apply_patch(module, repo_path, patch_path, module_dir, reverse=False): repo_path (str): Name of the repository where the module resides patch_path (str): The absolute path to the patch file to be applied module_dir (Path): The directory containing the module + reverse (bool): Apply the patch in reverse Returns: dict[str, str]: A dictionary with file paths (relative to the pipeline dir) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 63c356a79a..faeb84fc35 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -6,7 +6,7 @@ import shutil import tempfile from pathlib import Path -from typing import Union +from typing import Any, List, Optional, Tuple, Union import git import questionary @@ -153,7 +153,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None # The function might rename some directories, keep track of them renamed_dirs = {} # Check if there are any untracked repositories - dirs_not_covered = self.directory_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos]) + dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos]) if len(dirs_not_covered) > 0: log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'") # Loop until all directories in the base directory are covered by a remote @@ -203,7 +203,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None if component_type not in repos[nrepo_remote]: repos[nrepo_remote][component_type] = {} repos[nrepo_remote][component_type][nrepo_name] = {} - dirs_not_covered = self.directory_tree_uncovered( + dirs_not_covered = self.dir_tree_uncovered( directory, [Path(name) for url in repos for name in repos[url][component_type]] ) @@ -244,7 +244,9 @@ def dir_tree_uncovered(self, components_directory, repos): depth += 1 return dirs_not_covered - def determine_branches_and_shas(self, component_type, install_dir, remote_url, components): + def determine_branches_and_shas( + self, component_type: str, install_dir: Union[str, Path], remote_url: str, components: List[Path] + ) -> dict[Path, dict[str, Any]]: """ Determines what branch and commit sha each module/subworkflow in the pipeline belongs to @@ -265,6 +267,8 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c repo_path = self.modules_dir / install_dir elif component_type == "subworkflows": repo_path = self.subworkflows_dir / install_dir + else: + raise ValueError(f"Unknown component type '{component_type}'") # Get the branches present in the repository, as well as the default branch available_branches = ModulesRepo.get_remote_branches(remote_url) sb_local = [] @@ -282,16 +286,16 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c if patch_file.is_file(): temp_module_dir = self.try_apply_patch_reverse(component, install_dir, patch_file, component_path) correct_commit_sha = self.find_correct_commit_sha( - component_type, component, temp_module_dir, modules_repo + component_type, str(component), temp_module_dir, modules_repo ) else: correct_commit_sha = self.find_correct_commit_sha( - component_type, component, component_path, modules_repo + component_type, str(component), component_path, modules_repo ) if correct_commit_sha is None: # Check in the old path correct_commit_sha = self.find_correct_commit_sha( - component_type, component, repo_path / component_type / component, modules_repo + component_type, str(component), repo_path / component_type / component, modules_repo ) if correct_commit_sha is None: log.info( @@ -334,7 +338,7 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c # Clean up the modules/subworkflows we were unable to find the sha for for component in sb_local: log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory") - self.move_component_to_local(component_type, component, install_dir) + self.move_component_to_local(component_type, component, str(install_dir)) for component in dead_components: log.debug(f"Removing {component_type[:-1]} {Path(install_dir, component)}'") @@ -342,7 +346,13 @@ def determine_branches_and_shas(self, component_type, install_dir, remote_url, c return repo_entry - def find_correct_commit_sha(self, component_type, component_name, component_path, modules_repo): + def find_correct_commit_sha( + self, + component_type: str, + component_name: Union[str, Path], + component_path: Union[str, Path], + modules_repo: ModulesRepo, + ) -> Optional[str]: """ Returns the SHA for the latest commit where the local files are identical to the remote files Args: @@ -370,24 +380,27 @@ def find_correct_commit_sha(self, component_type, component_name, component_path return commit_sha return None - def move_component_to_local(self, component_type, component, repo_name): + def move_component_to_local(self, component_type: str, component: Union[str, Path], repo_name: str): """ Move a module/subworkflow to the 'local' directory Args: - component (str): The name of the module/subworkflow + component_type (str): The type of component, either 'modules' or 'subworkflows' + component (Union[str,Path]): The name of the module/subworkflow repo_name (str): The name of the repository the module resides in """ if component_type == "modules": directory = self.modules_dir elif component_type == "subworkflows": directory = self.subworkflows_dir + else: + raise ValueError(f"Unknown component type '{component_type}'") current_path = directory / repo_name / component local_dir = directory / "local" if not local_dir.exists(): local_dir.mkdir() - to_name = component + to_name = str(component) # Check if there is already a subdirectory with the name while (local_dir / to_name).exists(): # Add a time suffix to the path to make it unique @@ -395,7 +408,7 @@ def move_component_to_local(self, component_type, component, repo_name): to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}" shutil.move(current_path, local_dir / to_name) - def unsynced_components(self): + def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]: """ Compute the difference between the modules/subworkflows in the directory and the modules/subworkflows in the 'modules.json' file. This is done by looking at all @@ -406,6 +419,7 @@ def unsynced_components(self): by the modules.json file, and modules/subworkflows in the modules.json where the installation directory is missing """ + assert self.modules_json is not None # mypy # Add all modules from modules.json to missing_installation missing_installation = copy.deepcopy(self.modules_json["repos"]) # Obtain the path of all installed modules @@ -429,14 +443,27 @@ def unsynced_components(self): return untracked_dirs_modules, untracked_dirs_subworkflows, missing_installation - def parse_dirs(self, dirs, missing_installation, component_type): + def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_type: str) -> Tuple[List[Path], dict]: + """ + Parse directories and check if they are tracked in the modules.json file + + Args: + dirs ([ Path ]): List of directories to check + missing_installation (dict): Dictionary with the modules.json entries + component_type (str): The type of component, either 'modules' or 'subworkflows' + + Returns: + (untracked_dirs ([ Path ]), missing_installation (dict)): List of directories that are not tracked + by the modules.json file, and the updated missing_installation dictionary + """ + untracked_dirs = [] for dir_ in dirs: # Check if the module/subworkflows directory exists in modules.json install_dir = dir_.parts[0] - component = str(Path(*dir_.parts[1:])) + component = Path(*dir_.parts[1:]) component_in_file = False - git_url = None + git_url = "" for repo in missing_installation: if component_type in missing_installation[repo]: if install_dir in missing_installation[repo][component_type]: @@ -453,9 +480,7 @@ def parse_dirs(self, dirs, missing_installation, component_type): # Check if the entry has a git sha and branch before removing components_dict = module_repo[component_type][install_dir] if "git_sha" not in components_dict[component] or "branch" not in components_dict[component]: - self.determine_branches_and_shas( - component_type, component, git_url, module_repo["base_path"], [component] - ) + self.determine_branches_and_shas(component_type, component, git_url, [component]) # Remove the module/subworkflow from modules/subworkflows without installation module_repo[component_type][install_dir].pop(component) if len(module_repo[component_type][install_dir]) == 0: @@ -470,13 +495,14 @@ def parse_dirs(self, dirs, missing_installation, component_type): return untracked_dirs, missing_installation - def has_git_url_and_modules(self): + def has_git_url_and_modules(self) -> bool: """ Check that all repo entries in the modules.json has a git url and a modules dict entry Returns: (bool): True if they are found for all repos, False otherwise """ + assert self.modules_json is not None # mypy for repo_url, repo_entry in self.modules_json.get("repos", {}).items(): if "modules" not in repo_entry: if "subworkflows" in repo_entry: @@ -538,7 +564,7 @@ def reinstall_repo(self, install_dir, remote_url, module_entries): failed_to_install.append(module) return failed_to_install - def check_up_to_date(self): + def check_up_to_date(self) -> bool: """ Checks whether the modules and subworkflows installed in the directory are consistent with the entries in the 'modules.json' file and vice versa. @@ -558,6 +584,8 @@ def check_up_to_date(self): self.load() if not self.has_git_url_and_modules(): raise UserWarning + + assert self.modules_json is not None # mypy # check that all "installed_by" entries are lists and not strings # [these strings come from an older dev version, so this check can probably be removed in a future release] for _, repo_entry in self.modules_json.get("repos", {}).items(): @@ -601,7 +629,7 @@ def check_up_to_date(self): if len(subworkflows_missing_from_modules_json) > 0: dump_modules_json = True self.resolve_missing_from_modules_json(subworkflows_missing_from_modules_json, "subworkflows") - + assert self.modules_json is not None # mypy # If the "installed_by" value is not present for modules/subworkflows, add it. for repo, repo_content in self.modules_json["repos"].items(): for component_type, dir_content in repo_content.items(): @@ -626,8 +654,9 @@ def check_up_to_date(self): if dump_modules_json: self.dump(run_prettier=True) + return True - def load(self): + def load(self) -> None: """ Loads the modules.json file into the variable 'modules_json' @@ -648,14 +677,14 @@ def load(self): def update( self, - component_type, - modules_repo, - component_name, - component_version, - installed_by, - installed_by_log=None, - write_file=True, - ): + component_type: str, + modules_repo: ModulesRepo, + component_name: str, + component_version: str, + installed_by: Optional[List[str]], + installed_by_log: Optional[List[str]] = None, + write_file: bool = True, + ) -> bool: """ Updates the 'module.json' file with new module/subworkflow info @@ -675,9 +704,11 @@ def update( if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy repo_name = modules_repo.repo_path remote_url = modules_repo.remote_url branch = modules_repo.branch + if remote_url not in self.modules_json["repos"]: self.modules_json["repos"][remote_url] = {component_type: {repo_name: {}}} if component_type not in self.modules_json["repos"][remote_url]: @@ -757,6 +788,8 @@ def add_patch_entry(self, module_name, repo_url, install_dir, patch_filename, wr """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy + if repo_url not in self.modules_json["repos"]: raise LookupError(f"Repo '{repo_url}' not present in 'modules.json'") if module_name not in self.modules_json["repos"][repo_url]["modules"][install_dir]: @@ -768,6 +801,8 @@ def add_patch_entry(self, module_name, repo_url, install_dir, patch_filename, wr def remove_patch_entry(self, module_name, repo_url, install_dir, write_file=True): if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy + try: del self.modules_json["repos"][repo_url]["modules"][install_dir][module_name]["patch"] except KeyError: @@ -789,6 +824,7 @@ def get_patch_fn(self, module_name, repo_url, install_dir): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy path = ( self.modules_json["repos"] .get(repo_url, {}) @@ -845,6 +881,8 @@ def repo_present(self, repo_name): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy + return repo_name in self.modules_json.get("repos", {}) def module_present(self, module_name, repo_url, install_dir): @@ -859,6 +897,7 @@ def module_present(self, module_name, repo_url, install_dir): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy return module_name in self.modules_json.get("repos", {}).get(repo_url, {}).get("modules", {}).get( install_dir, {} ) @@ -872,8 +911,8 @@ def get_modules_json(self) -> dict: """ if self.modules_json is None: self.load() - - return copy.deepcopy(self.modules_json) # type: ignore + assert self.modules_json is not None # mypy + return copy.deepcopy(self.modules_json) def get_component_version(self, component_type, component_name, repo_url, install_dir): """ @@ -889,6 +928,7 @@ def get_component_version(self, component_type, component_name, repo_url, instal """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy return ( self.modules_json.get("repos", {}) .get(repo_url, {}) @@ -912,6 +952,7 @@ def get_module_version(self, module_name, repo_url, install_dir): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy return ( self.modules_json.get("repos", {}) .get(repo_url, {}) @@ -935,6 +976,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy return ( self.modules_json.get("repos", {}) .get(repo_url, {}) @@ -944,7 +986,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir): .get("git_sha", None) ) - def get_all_components(self, component_type): + def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)]]: """ Retrieves all pipeline modules/subworkflows that are reported in the modules.json @@ -954,6 +996,8 @@ def get_all_components(self, component_type): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy + if self.pipeline_components is None: self.pipeline_components = {} for repo, repo_entry in self.modules_json.get("repos", {}).items(): @@ -987,6 +1031,7 @@ def get_dependent_components( if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy component_types = ["modules"] if component_type == "modules" else ["modules", "subworkflows"] # Find all components that have an entry of install by of a given component, recursively call this function for subworkflows for type in component_types: @@ -1016,10 +1061,11 @@ def get_installed_by_entries(self, component_type, name): """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy installed_by_entries = {} - for repo_url, repo_entry in self.modules_json.get("repos", {}).items(): + for _, repo_entry in self.modules_json.get("repos", {}).items(): if component_type in repo_entry: - for install_dir, components in repo_entry[component_type].items(): + for _, components in repo_entry[component_type].items(): if name in components: installed_by_entries = components[name]["installed_by"] break @@ -1037,6 +1083,7 @@ def get_component_branch(self, component_type, component, repo_url, install_dir) """ if self.modules_json is None: self.load() + assert self.modules_json is not None # mypy branch = ( self.modules_json["repos"] .get(repo_url, {}) @@ -1096,7 +1143,8 @@ def resolve_missing_installation(self, missing_installation, component_type): log.info( f"Was unable to reinstall some {component_type}. Removing 'modules.json' entries: {', '.join(uninstallable_components)}" ) - + if self.modules_json is None: + raise UserWarning("No modules.json file found") for (repo_url, install_dir), component_entries in remove_from_mod_json.items(): for component in component_entries: self.modules_json["repos"][repo_url][component_type][install_dir].pop(component) @@ -1113,7 +1161,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component log.info( f"Recomputing commit SHAs for {component_type} which were missing from 'modules.json': {', '.join(format_missing)}" ) - + assert self.modules_json is not None # mypy # Get the remotes we are missing tracked_repos = {repo_url: (repo_entry) for repo_url, repo_entry in self.modules_json["repos"].items()} repos, _ = self.get_pipeline_module_repositories(component_type, self.modules_dir, tracked_repos) @@ -1186,7 +1234,7 @@ def recreate_dependencies(self, repo, org, subworkflow): sw_path = Path(self.subworkflows_dir, org, subworkflow) dep_mods, dep_subwfs = get_components_to_install(sw_path) - + assert self.modules_json is not None # mypy for dep_mod in dep_mods: installed_by = self.modules_json["repos"][repo]["modules"][org][dep_mod]["installed_by"] if installed_by == ["modules"]: diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index 9694920274..b345dfe8b4 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -1,6 +1,7 @@ import logging import os import shutil +from typing import Optional import git import rich @@ -35,7 +36,13 @@ class ModulesRepo(SyncedRepo): local_repo_statuses = {} no_pull_global = False - def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=False): + def __init__( + self, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + hide_progress: bool = False, + ): """ Initializes the object and clones the git repository if it is not already present """ diff --git a/nf_core/modules/modules_utils.py b/nf_core/modules/modules_utils.py index 6796de41ec..ecfe5f24ee 100644 --- a/nf_core/modules/modules_utils.py +++ b/nf_core/modules/modules_utils.py @@ -36,7 +36,7 @@ def repo_full_name_from_remote(remote_url: str) -> str: return path -def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], List[NFCoreComponent]]: +def get_installed_modules(directory: Path, repo_type="modules") -> Tuple[List[str], List[NFCoreComponent]]: """ Make a list of all modules installed in this repository @@ -52,15 +52,15 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis # initialize lists local_modules: List[str] = [] nfcore_modules_names: List[str] = [] - local_modules_dir: Optional[str] = None - nfcore_modules_dir = os.path.join(dir, "modules", "nf-core") + local_modules_dir: Optional[Path] = None + nfcore_modules_dir = Path(directory, "modules", "nf-core") # Get local modules if repo_type == "pipeline": - local_modules_dir = os.path.join(dir, "modules", "local") + local_modules_dir = Path(directory, "modules", "local") # Filter local modules - if os.path.exists(local_modules_dir): + if local_modules_dir.exists(): local_modules = os.listdir(local_modules_dir) local_modules = sorted([x for x in local_modules if x.endswith(".nf")]) @@ -89,7 +89,7 @@ def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], Lis "nf-core/modules", Path(nfcore_modules_dir, m), repo_type=repo_type, - base_dir=Path(dir), + base_dir=directory, component_type="modules", ) for m in nfcore_modules_names diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index 601f351fda..af39334744 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -202,9 +202,12 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): f"subworkflows_{org_alphabet}", ] included_components = [] - if subworkflow.main_nf.is_file(): + if subworkflow.main_nf is not None and Path(subworkflow.main_nf).is_file(): included_components = subworkflow._get_included_components(subworkflow.main_nf) - chained_components_tags = subworkflow._get_included_components_in_chained_tests(subworkflow.nftest_main_nf) + if subworkflow.nftest_main_nf is not None and subworkflow.nftest_main_nf.is_file(): + chained_components_tags = subworkflow._get_included_components_in_chained_tests( + subworkflow.nftest_main_nf + ) log.debug(f"Included components: {included_components}") log.debug(f"Required tags: {required_tags}") log.debug(f"Included components for chained nf-tests: {chained_components_tags}") diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 4d6a3f6a4e..4b69d4af87 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -4,7 +4,7 @@ import shutil from configparser import NoOptionError, NoSectionError from pathlib import Path -from typing import Dict +from typing import Dict, Optional, Union import git from git.exc import GitCommandError @@ -51,9 +51,14 @@ def update(self, op_code, cur_count, max_count=None, message=""): """ if not self.progress_bar.tasks[self.tid].started: self.progress_bar.start_task(self.tid) - self.progress_bar.update( - self.tid, total=max_count, completed=cur_count, state=f"{cur_count / max_count * 100:.1f}%" - ) + if cur_count is not None and max_count is not None: + cur_count = float(cur_count) + max_count = float(max_count) + state = f"{cur_count / max_count * 100:.1f}%" + else: + state = "Unknown" + + self.progress_bar.update(self.tid, total=max_count, completed=cur_count, state=state) class SyncedRepo: @@ -139,6 +144,9 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa self.avail_module_names = None + def setup_local_repo(self, remote_url, branch, hide_progress): + pass + def verify_sha(self, prompt, sha): """ Verify that 'sha' and 'prompt' arguments are not provided together. @@ -258,7 +266,7 @@ def component_exists(self, component_name, component_type, checkout=True, commit """ return component_name in self.get_avail_components(component_type, checkout=checkout, commit=commit) - def get_component_dir(self, component_name, component_type): + def get_component_dir(self, component_name: str, component_type: str) -> Path: """ Returns the file path of a module/subworkflow directory in the repo. Does not verify that the path exists. @@ -269,11 +277,15 @@ def get_component_dir(self, component_name, component_type): component_path (str): The path of the module/subworkflow in the local copy of the repository """ if component_type == "modules": - return os.path.join(self.modules_dir, component_name) + return Path(self.modules_dir, component_name) elif component_type == "subworkflows": - return os.path.join(self.subworkflows_dir, component_name) + return Path(self.subworkflows_dir, component_name) + else: + raise ValueError(f"Invalid component type: {component_type}") - def install_component(self, component_name, install_dir, commit, component_type): + def install_component( + self, component_name: str, install_dir: Union[str, Path], commit: str, component_type: str + ) -> bool: """ Install the module/subworkflow files into a pipeline at the given commit @@ -281,6 +293,7 @@ def install_component(self, component_name, install_dir, commit, component_type) component_name (str): The name of the module/subworkflow install_dir (str): The path where the module/subworkflow should be installed commit (str): The git SHA for the version of the module/subworkflow to be installed + component_type (str): Either 'modules' or 'subworkflows' Returns: (bool): Whether the operation was successful or not @@ -332,6 +345,8 @@ def component_files_identical(self, component_name, base_path, commit, component return files_identical def ensure_git_user_config(self, default_name: str, default_email: str) -> None: + if self.repo is None: + raise ValueError("Repository not initialized") try: with self.repo.config_reader() as git_config: user_name = git_config.get_value("user", "name", default=None) @@ -346,7 +361,7 @@ def ensure_git_user_config(self, default_name: str, default_email: str) -> None: if not user_email: git_config.set_value("user", "email", default_email) - def get_component_git_log(self, component_name, component_type, depth=None): + def get_component_git_log(self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None): """ Fetches the commit history the of requested module/subworkflow since a given date. The default value is not arbitrary - it is the last time the structure of the nf-core/modules repository was had an @@ -358,19 +373,26 @@ def get_component_git_log(self, component_name, component_type, depth=None): Returns: ( dict ): Iterator of commit SHAs and associated (truncated) message """ + + if self.repo is None: + raise ValueError("Repository not initialized") self.checkout_branch() - component_path = os.path.join(component_type, self.repo_path, component_name) + component_path = Path(component_type, self.repo_path, component_name) + commits_new = self.repo.iter_commits(max_count=depth, paths=component_path) - commits_new = [ - {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_new - ] + if not commits_new: + raise ValueError(f"Could not find any commits for '{component_name}' in '{self.remote_url}'") + else: + commits_new = [ + {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_new + ] commits_old = [] if component_type == "modules": # Grab commits also from previous modules structure - component_path = os.path.join("modules", component_name) + component_path = Path("modules", component_name) commits_old = self.repo.iter_commits(max_count=depth, paths=component_path) commits_old = [ - {"git_sha": commit.hexsha, "trunc_message": commit.message.partition("\n")[0]} for commit in commits_old + {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_old ] commits = iter(commits_new + commits_old) return commits @@ -385,6 +407,8 @@ def sha_exists_on_branch(self, sha): """ Verifies that a given commit sha exists on the branch """ + if self.repo is None: + raise ValueError("Repository not initialized") self.checkout_branch() return sha in (commit.hexsha for commit in self.repo.iter_commits()) @@ -399,10 +423,12 @@ def get_commit_info(self, sha): Raises: LookupError: If the search for the commit fails """ + if self.repo is None: + raise ValueError("Repository not initialized") self.checkout_branch() for commit in self.repo.iter_commits(): if commit.hexsha == sha: - message = commit.message.partition("\n")[0] + message = commit.message.splitlines()[0] date_obj = commit.committed_datetime date = str(date_obj.date()) return message, date diff --git a/nf_core/utils.py b/nf_core/utils.py index 0cd812cb04..d1e9ccfe95 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -22,11 +22,12 @@ from typing import Dict, Generator, List, Optional, Tuple, Union import git -import prompt_toolkit +import prompt_toolkit.styles import questionary -import requests +import requests.auth import requests_cache import rich +import rich.markup import yaml from packaging.version import Version from rich.live import Live @@ -524,8 +525,9 @@ def __call__(self, r): self.auth_mode = f"gh CLI config: {gh_cli_config['github.com']['user']}" except Exception: ex_type, ex_value, _ = sys.exc_info() - output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}") - log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}") + if ex_type is not None: + output = rich.markup.escape(f"{ex_type.__name__}: {ex_value}") + log.debug(f"Couldn't auto-auth with GitHub CLI auth from '{gh_cli_config_fn}': [red]{output}") # Default auth if we have a GitHub Token (eg. GitHub Actions CI) if os.environ.get("GITHUB_TOKEN") is not None and self.auth is None: @@ -804,6 +806,8 @@ def get_tag_date(tag_date): singularity_image = all_singularity[k]["image"] current_date = date docker_image_name = docker_image["image_name"].lstrip("quay.io/") + if singularity_image is None: + raise LookupError(f"Could not find singularity container for {package}") return docker_image_name, singularity_image["image_name"] except TypeError: raise LookupError(f"Could not find docker or singularity container for {package}") @@ -1072,7 +1076,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]: return config_fn, tools_config -def determine_base_dir(directory="."): +def determine_base_dir(directory: Union[Path, str] = ".") -> Path: base_dir = start_dir = Path(directory).absolute() # Only iterate up the tree if the start dir doesn't have a config while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent: @@ -1080,7 +1084,7 @@ def determine_base_dir(directory="."): config_fn = get_first_available_path(base_dir, CONFIG_PATHS) if config_fn: break - return directory if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir + return Path(directory) if (base_dir == start_dir or str(base_dir) == base_dir.root) else base_dir def get_first_available_path(directory: Union[Path, str], paths: List[str]) -> Union[Path, None]: From 69d59a81c3b23a583857c1f2d03db04cdd3f0da9 Mon Sep 17 00:00:00 2001 From: LaurenceKuhl Date: Fri, 19 Jul 2024 08:44:03 +0200 Subject: [PATCH 177/574] Update nf_core/__main__.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index cb99bdedcc..3da153ee1f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2188,7 +2188,7 @@ def command_create(ctx, name, description, author, version, force, outdir, templ log.warning( "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead." ) - pipelines_create(ctx, name, description, author, force, outdir, template_yaml, organisation) + pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation) # Main script is being run - launch the CLI From 6a4ff6133f7efbe74f321c20436635d778166d14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 22 Jul 2024 09:40:06 +0200 Subject: [PATCH 178/574] Update .pre-commit-config.yaml --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 872bd61e0a..fc2011cb99 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.2 + rev: v0.5.4 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 61898dc14663fa3e81f78fdd5a62756217de7dc5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 22 Jul 2024 11:11:55 +0200 Subject: [PATCH 179/574] fix rich imports, remove boolean type for `installed_by`, fix more occurences of `dir` --- nf_core/components/create.py | 1 + nf_core/components/patch.py | 10 +-- nf_core/modules/install.py | 2 +- nf_core/modules/modules_repo.py | 1 + nf_core/modules/patch.py | 2 +- nf_core/pipelines/create/create.py | 6 +- nf_core/subworkflows/install.py | 2 +- nf_core/subworkflows/lint/__init__.py | 8 +-- .../subworkflows/lint/subworkflow_version.py | 2 +- tests/modules/test_install.py | 8 +-- tests/modules/test_lint.py | 62 +++++++++---------- tests/modules/test_remove.py | 8 +-- tests/subworkflows/test_install.py | 45 ++++++-------- tests/subworkflows/test_lint.py | 40 ++++++------ tests/subworkflows/test_remove.py | 20 +++--- 15 files changed, 109 insertions(+), 108 deletions(-) diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 532c2a46d6..413790099d 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -14,6 +14,7 @@ import jinja2 import questionary import rich +import rich.prompt import yaml from packaging.version import parse as parse_version diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py index 5b29c152d8..0332a1fe42 100644 --- a/nf_core/components/patch.py +++ b/nf_core/components/patch.py @@ -15,7 +15,7 @@ class ComponentPatch(ComponentCommand): - def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=False): + def __init__(self, pipeline_dir, component_type, remote_url=None, branch=None, no_pull=False, installed_by=None): super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.modules_json = ModulesJson(pipeline_dir) @@ -88,8 +88,8 @@ def patch(self, component=None): patch_filename = f"{component.replace('/', '-')}.diff" component_relpath = Path(self.component_type, component_dir, component) patch_relpath = Path(component_relpath, patch_filename) - component_current_dir = Path(self.dir, component_relpath) - patch_path = Path(self.dir, patch_relpath) + component_current_dir = Path(self.directory, component_relpath) + patch_path = Path(self.directory, patch_relpath) if patch_path.exists(): remove = questionary.confirm( @@ -189,8 +189,8 @@ def remove(self, component): patch_filename = f"{component.replace('/', '-')}.diff" component_relpath = Path(self.component_type, component_dir, component) patch_relpath = Path(component_relpath, patch_filename) - patch_path = Path(self.dir, patch_relpath) - component_path = Path(self.dir, component_relpath) + patch_path = Path(self.directory, patch_relpath) + component_path = Path(self.directory, component_relpath) if patch_path.exists(): remove = questionary.confirm( diff --git a/nf_core/modules/install.py b/nf_core/modules/install.py index e1755cee98..7055abe49a 100644 --- a/nf_core/modules/install.py +++ b/nf_core/modules/install.py @@ -11,7 +11,7 @@ def __init__( remote_url=None, branch=None, no_pull=False, - installed_by=False, + installed_by=None, ): super().__init__( pipeline_dir, diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index b345dfe8b4..a979ae45b8 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -6,6 +6,7 @@ import git import rich import rich.progress +import rich.prompt from git.exc import GitCommandError, InvalidGitRepositoryError import nf_core.modules.modules_json diff --git a/nf_core/modules/patch.py b/nf_core/modules/patch.py index b4e86f2d19..bbad0d428e 100644 --- a/nf_core/modules/patch.py +++ b/nf_core/modules/patch.py @@ -6,5 +6,5 @@ class ModulePatch(ComponentPatch): - def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=False): + def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=None): super().__init__(pipeline_dir, "modules", remote_url, branch, no_pull, installed_by) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index c5af956690..aecba94236 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -512,12 +512,14 @@ def fix_linting(self): def make_pipeline_logo(self): """Fetch a logo for the new pipeline from the nf-core website""" email_logo_path = Path(self.outdir) / "assets" - create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=bool(self.force)) + create_logo( + text=self.jinja_params["short_name"], directory=email_logo_path, theme="light", force=bool(self.force) + ) for theme in ["dark", "light"]: readme_logo_path = Path(self.outdir) / "docs" / "images" create_logo( text=self.jinja_params["short_name"], - dir=readme_logo_path, + directory=readme_logo_path, width=600, theme=theme, force=bool(self.force), diff --git a/nf_core/subworkflows/install.py b/nf_core/subworkflows/install.py index 6c5cfb12b2..70a6b0afa5 100644 --- a/nf_core/subworkflows/install.py +++ b/nf_core/subworkflows/install.py @@ -11,7 +11,7 @@ def __init__( remote_url=None, branch=None, no_pull=False, - installed_by=False, + installed_by=None, ): super().__init__( pipeline_dir, diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index a3cacf2952..a073710884 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -36,7 +36,7 @@ class SubworkflowLint(ComponentLint): def __init__( self, - dir, + directory, fail_warned=False, remote_url=None, branch=None, @@ -46,7 +46,7 @@ def __init__( ): super().__init__( component_type="subworkflows", - dir=dir, + directory=directory, fail_warned=fail_warned, remote_url=remote_url, branch=branch, @@ -122,9 +122,9 @@ def lint( remote_subworkflows = self.all_remote_components if self.repo_type == "modules": - log.info(f"Linting modules repo: [magenta]'{self.dir}'") + log.info(f"Linting modules repo: [magenta]'{self.directory}'") else: - log.info(f"Linting pipeline: [magenta]'{self.dir}'") + log.info(f"Linting pipeline: [magenta]'{self.directory}'") if subworkflow: log.info(f"Linting subworkflow: [magenta]'{subworkflow}'") diff --git a/nf_core/subworkflows/lint/subworkflow_version.py b/nf_core/subworkflows/lint/subworkflow_version.py index 5801abd885..1acb95e779 100644 --- a/nf_core/subworkflows/lint/subworkflow_version.py +++ b/nf_core/subworkflows/lint/subworkflow_version.py @@ -21,7 +21,7 @@ def subworkflow_version(subworkflow_lint_object, subworkflow): newer version of the subworkflow available. """ - modules_json_path = Path(subworkflow_lint_object.dir, "modules.json") + modules_json_path = Path(subworkflow_lint_object.directory, "modules.json") # Verify that a git_sha exists in the `modules.json` file for this module version = subworkflow_lint_object.modules_json.get_subworkflow_version( subworkflow.component_name, subworkflow.repo_url, subworkflow.org diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py index b90f01ee61..cfdaac47ed 100644 --- a/tests/modules/test_install.py +++ b/tests/modules/test_install.py @@ -19,14 +19,14 @@ class TestModulesCreate(TestModules): def test_modules_install_nopipeline(self): """Test installing a module - no pipeline given""" - self.mods_install.dir = None + self.mods_install.directory = None assert self.mods_install.install("foo") is False @with_temporary_folder def test_modules_install_emptypipeline(self, tmpdir): """Test installing a module - empty dir given""" os.mkdir(os.path.join(tmpdir, "nf-core-pipe")) - self.mods_install.dir = os.path.join(tmpdir, "nf-core-pipe") + self.mods_install.directory = os.path.join(tmpdir, "nf-core-pipe") with pytest.raises(UserWarning) as excinfo: self.mods_install.install("foo") assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) @@ -38,8 +38,8 @@ def test_modules_install_nomodule(self): def test_modules_install_trimgalore(self): """Test installing a module - TrimGalore!""" assert self.mods_install.install("trimgalore") is not False - assert self.mods_install.dir is not None - module_path = Path(self.mods_install.dir, "modules", "nf-core", "trimgalore") + assert self.mods_install.directory is not None + module_path = Path(self.mods_install.directory, "modules", "nf-core", "trimgalore") assert os.path.exists(module_path) def test_modules_install_trimgalore_twice(self): diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index 6448916acf..fc9871db2e 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -180,7 +180,7 @@ def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): def test_modules_lint_trimgalore(self): """Test linting the TrimGalore! module""" self.mods_install.install("trimgalore") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) + module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="trimgalore") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -191,11 +191,11 @@ def test_modules_lint_empty(self): self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) with pytest.raises(LookupError): - nf_core.modules.ModuleLint(dir=self.pipeline_dir) + nf_core.modules.ModuleLint(directory=self.pipeline_dir) def test_modules_lint_new_modules(self): """lint a new module""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -206,13 +206,13 @@ def test_modules_lint_no_gitlab(self): self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) with pytest.raises(LookupError): - nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) def test_modules_lint_gitlab_modules(self): """Lint modules from a different remote""" self.mods_install_gitlab.install("fastqc") self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 2 assert len(module_lint.passed) > 0 @@ -221,7 +221,7 @@ def test_modules_lint_gitlab_modules(self): def test_modules_lint_multiple_remotes(self): """Lint modules from a different remote""" self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 1 assert len(module_lint.passed) > 0 @@ -229,14 +229,14 @@ def test_modules_lint_multiple_remotes(self): def test_modules_lint_registry(self): """Test linting the samtools module and alternative registry""" - self.mods_install.install("samtools") - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws") - module_lint.lint(print_results=False, module="samtools") + assert self.mods_install.install("samtools/sort") + module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") + module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir) - module_lint.lint(print_results=False, module="samtools") + module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -255,7 +255,7 @@ def test_modules_lint_patched_modules(self): # to avoid error from try_apply_patch() during linting with set_wd(self.pipeline_dir): module_lint = nf_core.modules.ModuleLint( - dir=self.pipeline_dir, + directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=PATCH_BRANCH, hide_progress=True, @@ -298,7 +298,7 @@ def test_modules_lint_check_url(self): def test_modules_lint_snapshot_file(self): """Test linting a module with a snapshot file""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -315,7 +315,7 @@ def test_modules_lint_snapshot_file_missing_fail(self): "tests", "main.nf.test.snap", ).unlink() - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -359,7 +359,7 @@ def test_modules_lint_snapshot_file_not_needed(self): "w", ) as fh: fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -377,7 +377,7 @@ def test_modules_environment_yml_file_doesnt_exists(self): "environment.yml.bak", ) ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -403,7 +403,7 @@ def test_modules_environment_yml_file_doesnt_exists(self): def test_modules_environment_yml_file_sorted_correctly(self): """Test linting a module with a correctly sorted environment.yml file""" - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -438,7 +438,7 @@ def test_modules_environment_yml_file_sorted_incorrectly(self): "w", ) as fh: fh.write(yaml_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # we fix the sorting on the fly, so this should pass assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -471,7 +471,7 @@ def test_modules_environment_yml_file_not_array(self): "w", ) as fh: fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -504,7 +504,7 @@ def test_modules_environment_yml_file_name_mismatch(self): "w", ) as fh: fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes yaml_content["name"] = "bpipe_test" @@ -536,7 +536,7 @@ def test_modules_meta_yml_incorrect_licence_field(self): "w", ) as fh: fh.write(yaml.dump(meta_yml)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes @@ -559,7 +559,7 @@ def test_modules_meta_yml_input_mismatch(self): main_nf_new = main_nf.replace("path bam", "path bai") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf) @@ -578,7 +578,7 @@ def test_modules_meta_yml_output_mismatch(self): main_nf_new = main_nf.replace("emit: bam", "emit: bai") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf) @@ -625,7 +625,7 @@ def test_modules_meta_yml_incorrect_name(self): "w", ) as fh: fh.write(yaml.dump(environment_yml)) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes @@ -659,7 +659,7 @@ def test_modules_missing_test_dir(self): Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") @@ -690,7 +690,7 @@ def test_modules_missing_test_main_nf(self): "main.nf.test.bak", ) ) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -719,7 +719,7 @@ def test_modules_missing_test_main_nf(self): def test_modules_unused_pytest_files(self): """Test linting a nf-test module with files still present in `tests/modules/`""" Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -735,7 +735,7 @@ def test_nftest_failing_linting(self): self.nfcore_modules = Path(tmp_dir, "modules-test") Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="kallisto/quant") assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -774,7 +774,7 @@ def test_modules_absent_version(self): "w", ) as fh: fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open( Path( @@ -812,7 +812,7 @@ def test_modules_empty_file_in_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -841,7 +841,7 @@ def test_modules_empty_file_in_stub_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules) + module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 diff --git a/tests/modules/test_remove.py b/tests/modules/test_remove.py index a80c8b0986..2caece7ce5 100644 --- a/tests/modules/test_remove.py +++ b/tests/modules/test_remove.py @@ -8,8 +8,8 @@ class TestModulesRemove(TestModules): def test_modules_remove_trimgalore(self): """Test removing TrimGalore! module after installing it""" self.mods_install.install("trimgalore") - assert self.mods_install.dir is not None - module_path = Path(self.mods_install.dir, "modules", "nf-core", "modules", "trimgalore") + assert self.mods_install.directory is not None + module_path = Path(self.mods_install.directory, "modules", "nf-core", "modules", "trimgalore") assert self.mods_remove.remove("trimgalore") assert os.path.exists(module_path) is False @@ -20,7 +20,7 @@ def test_modules_remove_trimgalore_uninstalled(self): def test_modules_remove_multiqc_from_gitlab(self): """Test removing multiqc module after installing it from an alternative source""" self.mods_install_gitlab.install("multiqc") - assert self.mods_install.dir is not None - module_path = Path(self.mods_install_gitlab.dir, "modules", "nf-core-test", "multiqc") + assert self.mods_install.directory is not None + module_path = Path(self.mods_install_gitlab.directory, "modules", "nf-core-test", "multiqc") assert self.mods_remove_gitlab.remove("multiqc", force=True) assert os.path.exists(module_path) is False diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py index e0b2fc1ab6..af1ad92415 100644 --- a/tests/subworkflows/test_install.py +++ b/tests/subworkflows/test_install.py @@ -1,4 +1,3 @@ -import os from pathlib import Path import pytest @@ -20,8 +19,8 @@ class TestSubworkflowsInstall(TestSubworkflows): def test_subworkflow_install_nopipeline(self): """Test installing a subworkflow - no pipeline given""" - assert self.subworkflow_install.dir is not None - self.subworkflow_install.dir = "" + assert self.subworkflow_install.directory is not None + self.subworkflow_install.directory = Path("non_existent_dir") assert self.subworkflow_install.install("foo") is False @with_temporary_folder @@ -29,7 +28,7 @@ def test_subworkflows_install_emptypipeline(self, tmpdir): """Test installing a subworkflow - empty dir given""" Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True) - self.subworkflow_install.dir = os.path.join(tmpdir, "nf-core-pipe") + self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe") with pytest.raises(UserWarning) as excinfo: self.subworkflow_install.install("foo") assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) @@ -41,28 +40,22 @@ def test_subworkflows_install_nosubworkflow(self): def test_subworkflows_install_bam_sort_stats_samtools(self): """Test installing a subworkflow - bam_sort_stats_samtools""" assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False - subworkflow_path = os.path.join( - self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_sort_stats_samtools" + subworkflow_path = Path( + self.subworkflow_install.directory, "subworkflows", "nf-core", "bam_sort_stats_samtools" ) - sub_subworkflow_path = os.path.join( - self.subworkflow_install.dir, "subworkflows", "nf-core", "bam_stats_samtools" - ) - samtools_index_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_sort_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "sort") - samtools_stats_path = os.path.join(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") - samtools_idxstats_path = os.path.join( - self.subworkflow_install.dir, "modules", "nf-core", "samtools", "idxstats" - ) - samtools_flagstat_path = os.path.join( - self.subworkflow_install.dir, "modules", "nf-core", "samtools", "flagstat" - ) - assert os.path.exists(subworkflow_path) - assert os.path.exists(sub_subworkflow_path) - assert os.path.exists(samtools_index_path) - assert os.path.exists(samtools_sort_path) - assert os.path.exists(samtools_stats_path) - assert os.path.exists(samtools_idxstats_path) - assert os.path.exists(samtools_flagstat_path) + sub_subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core", "bam_stats_samtools") + samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index") + samtools_sort_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "sort") + samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats") + samtools_idxstats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "idxstats") + samtools_flagstat_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "flagstat") + assert subworkflow_path.exists() + assert sub_subworkflow_path.exists() + assert samtools_index_path.exists() + assert samtools_sort_path.exists() + assert samtools_stats_path.exists() + assert samtools_idxstats_path.exists() + assert samtools_flagstat_path.exists() def test_subworkflows_install_bam_sort_stats_samtools_twice(self): """Test installing a subworkflow - bam_sort_stats_samtools already there""" @@ -87,7 +80,7 @@ def test_subworkflows_install_different_branch_fail(self): def test_subworkflows_install_tracking(self): """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" - self.subworkflow_install.install("bam_sort_stats_samtools") + assert self.subworkflow_install.install("bam_sort_stats_samtools") # Verify that the installed_by entry was added correctly modules_json = ModulesJson(self.pipeline_dir) diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py index f8c9bedbf3..38bcc2b2c0 100644 --- a/tests/subworkflows/test_lint.py +++ b/tests/subworkflows/test_lint.py @@ -14,7 +14,7 @@ class TestSubworkflowsLint(TestSubworkflows): def test_subworkflows_lint(self): """Test linting the fastq_align_bowtie2 subworkflow""" self.subworkflow_install.install("fastq_align_bowtie2") - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_bowtie2") assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -26,11 +26,11 @@ def test_subworkflows_lint_empty(self): self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True) self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True) with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) def test_subworkflows_lint_new_subworkflow(self): """lint a new subworkflow""" - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=True, all_subworkflows=True) assert len(subworkflow_lint.failed) == 0 @@ -40,13 +40,13 @@ def test_subworkflows_lint_new_subworkflow(self): def test_subworkflows_lint_no_gitlab(self): """Test linting a pipeline with no subworkflows installed""" with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) def test_subworkflows_lint_gitlab_subworkflows(self): """Lint subworkflows from a different remote""" self.subworkflow_install_gitlab.install("bam_stats_samtools") subworkflow_lint = nf_core.subworkflows.SubworkflowLint( - dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH ) subworkflow_lint.lint(print_results=False, all_subworkflows=True) assert len(subworkflow_lint.failed) == 0 @@ -58,7 +58,7 @@ def test_subworkflows_lint_multiple_remotes(self): self.subworkflow_install_gitlab.install("bam_stats_samtools") self.subworkflow_install.install("fastq_align_bowtie2") subworkflow_lint = nf_core.subworkflows.SubworkflowLint( - dir=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH ) subworkflow_lint.lint(print_results=False, all_subworkflows=True) assert len(subworkflow_lint.failed) == 0 @@ -67,7 +67,7 @@ def test_subworkflows_lint_multiple_remotes(self): def test_subworkflows_lint_snapshot_file(self): """Test linting a subworkflow with a snapshot file""" - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -83,7 +83,7 @@ def test_subworkflows_lint_snapshot_file_missing_fail(self): "tests", "main.nf.test.snap", ).unlink() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") Path( self.nfcore_modules, @@ -132,7 +132,7 @@ def test_subworkflows_lint_snapshot_file_not_needed(self): "tests", "main.nf.test.snap", ).unlink() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") Path( self.nfcore_modules, @@ -179,7 +179,7 @@ def test_subworkflows_lint_less_than_two_modules_warning(self): "w", ) as fh: fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -218,7 +218,7 @@ def test_subworkflows_lint_include_multiple_alias(self): ) as fh: fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -265,7 +265,7 @@ def test_subworkflows_lint_capitalization_fail(self): "w", ) as fh: fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools") assert len(subworkflow_lint.failed) >= 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -276,7 +276,7 @@ def test_subworkflows_lint_capitalization_fail(self): self.subworkflow_remove.remove("bam_stats_samtools", force=True) def test_subworkflows_absent_version(self): - """Test linting a nf-test module if the versions is absent in the snapshot file `""" + """Test linting a nf-test subworkflow if the versions is absent in the snapshot file `""" snap_file = Path( self.nfcore_modules, "subworkflows", @@ -291,7 +291,11 @@ def test_subworkflows_absent_version(self): with open(snap_file, "w") as fh: fh.write(new_content) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + import ipdb + + ipdb.set_trace() + + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0 assert len(subworkflow_lint.passed) > 0 @@ -308,7 +312,7 @@ def test_subworkflows_missing_test_dir(self): test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy") shutil.rmtree(test_dir) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0 assert len(subworkflow_lint.passed) > 0 @@ -324,7 +328,7 @@ def test_subworkflows_missing_main_nf(self): main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy") main_nf.unlink() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -351,7 +355,7 @@ def test_subworkflows_empty_file_in_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 @@ -379,7 +383,7 @@ def test_subworkflows_empty_file_in_stub_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 diff --git a/tests/subworkflows/test_remove.py b/tests/subworkflows/test_remove.py index 61c016b232..bad5a2ddbb 100644 --- a/tests/subworkflows/test_remove.py +++ b/tests/subworkflows/test_remove.py @@ -14,10 +14,10 @@ def test_subworkflows_remove_subworkflow(self): """Test removing subworkflow and all it's dependencies after installing it""" self.subworkflow_install.install("bam_sort_stats_samtools") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core") bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index") ModulesJson(self.pipeline_dir) mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() assert self.subworkflow_remove.remove("bam_sort_stats_samtools") @@ -40,10 +40,10 @@ def test_subworkflows_remove_subworkflow_keep_installed_module(self): self.subworkflow_install.install("bam_sort_stats_samtools") self.mods_install.install("samtools/index") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core") bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") + samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index") mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json() assert self.subworkflow_remove.remove("bam_sort_stats_samtools") @@ -67,11 +67,11 @@ def test_subworkflows_remove_one_of_two_subworkflow(self): """Test removing subworkflow and all it's dependencies after installing it""" self.subworkflow_install.install("bam_sort_stats_samtools") self.subworkflow_install.install("bam_stats_samtools") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core") bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") + samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index") + samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats") assert self.subworkflow_remove.remove("bam_sort_stats_samtools") @@ -85,11 +85,11 @@ def test_subworkflows_remove_one_of_two_subworkflow(self): def test_subworkflows_remove_included_subworkflow(self): """Test removing subworkflow which is installed by another subworkflow and all it's dependencies.""" self.subworkflow_install.install("bam_sort_stats_samtools") - subworkflow_path = Path(self.subworkflow_install.dir, "subworkflows", "nf-core") + subworkflow_path = Path(self.subworkflow_install.directory, "subworkflows", "nf-core") bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools") bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools") - samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index") - samtools_stats_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "stats") + samtools_index_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "index") + samtools_stats_path = Path(self.subworkflow_install.directory, "modules", "nf-core", "samtools", "stats") assert self.subworkflow_remove.remove("bam_stats_samtools") is False From 47229ff0bc9a30f8b5ee95e7b308d5445ad7339a Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 22 Jul 2024 12:15:33 +0200 Subject: [PATCH 180/574] fix types and tests --- nf_core/components/components_command.py | 1 + nf_core/components/components_utils.py | 4 +- nf_core/components/info.py | 8 +- nf_core/components/install.py | 9 +- nf_core/components/lint/__init__.py | 32 +++--- nf_core/components/list.py | 4 +- nf_core/components/nfcore_component.py | 6 +- nf_core/modules/lint/module_version.py | 8 +- nf_core/modules/modules_json.py | 123 +++++++++++++---------- nf_core/modules/modules_repo.py | 5 +- nf_core/synced_repo.py | 63 ++++++------ nf_core/utils.py | 52 +++++++--- 12 files changed, 185 insertions(+), 130 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 13a6fed338..8d200021c2 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -38,6 +38,7 @@ def __init__( self.hide_progress = hide_progress self.no_prompts = no_prompts self._configure_repo_and_paths() + self.repo_type: Optional[str] = None def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 32f6c0fc11..743efd386d 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -27,7 +27,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P # Figure out the repository type from the .nf-core.yml config file if we can config_fn, tools_config = nf_core.utils.load_tools_config(base_dir) - repo_type: Optional[str] = tools_config.get("repository_type", None) + repo_type = tools_config.get("repository_type", None) # If not set, prompt the user if not repo_type and use_prompt: @@ -101,7 +101,7 @@ def prompt_component_version_sha( git_sha = "" page_nbr = 1 - all_commits = modules_repo.get_component_git_log(component_name, component_type) + all_commits = iter(modules_repo.get_component_git_log(component_name, component_type)) next_page_commits = [next(all_commits, None) for _ in range(10)] next_page_commits = [commit for commit in next_page_commits if commit is not None] diff --git a/nf_core/components/info.py b/nf_core/components/info.py index 8597875af4..d07486f638 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -97,7 +97,6 @@ def init_mod_name(self, component): Args: module: str: Module name to check """ - assert self.modules_json is not None # mypy if component is None: self.local = questionary.confirm( f"Is the {self.component_type[:-1]} locally installed?", style=nf_core.utils.nfcore_question_style @@ -105,7 +104,8 @@ def init_mod_name(self, component): if self.local: if self.repo_type == "modules": components = self.get_components_clone_modules() - else: + elif self.repo_type == "pipeline": + assert self.modules_json is not None # mypy all_components = self.modules_json.get_all_components(self.component_type).get( self.modules_repo.remote_url, [] ) @@ -117,6 +117,8 @@ def init_mod_name(self, component): raise UserWarning( f"No {self.component_type[:-1]} installed from '{self.modules_repo.remote_url}'" ) + else: + raise UserWarning("Unknown repository type") else: components = self.modules_repo.get_avail_components(self.component_type) components.sort() @@ -174,8 +176,8 @@ def get_local_yaml(self): Optional[dict]: Parsed meta.yml if found, None otherwise """ - assert self.modules_json is not None # mypy if self.repo_type == "pipeline": + assert self.modules_json is not None # mypy # Try to find and load the meta.yml file component_base_path = Path(self.directory, self.component_type) # Check that we have any modules/subworkflows installed from this repo diff --git a/nf_core/components/install.py b/nf_core/components/install.py index e6c31b3cbb..aa8aac81e6 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -100,8 +100,11 @@ def install(self, component: str, silent: bool = False) -> bool: modules_json.load() modules_json.update(self.component_type, self.modules_repo, component, current_version, self.installed_by) return False - - version = self.get_version(component, self.sha, self.prompt, current_version, self.modules_repo) + try: + version = self.get_version(component, self.sha, self.prompt, current_version, self.modules_repo) + except UserWarning as e: + log.error(e) + return False if not version: return False @@ -174,7 +177,7 @@ def install_included_components(self, subworkflow_dir): self.installed_by = original_installed def collect_and_verify_name( - self, component: Optional[str], modules_repo: nf_core.modules.modules_repo.ModulesRepo + self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo" ) -> str: """ Collect component name. diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 2cd59dc489..ada3ee30c2 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -92,17 +92,17 @@ def __init__( raise LookupError( f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again." ) - org, comp = components - self.all_remote_components.append( - NFCoreComponent( - comp, - repo_url, - Path(self.directory, self.component_type, org, comp), - self.repo_type, - Path(self.directory), - self.component_type, + for org, comp in components: + self.all_remote_components.append( + NFCoreComponent( + comp, + repo_url, + Path(self.directory, self.component_type, org, comp), + self.repo_type, + Path(self.directory), + self.component_type, + ) ) - ) if not self.all_remote_components: raise LookupError( f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." @@ -123,7 +123,7 @@ def __init__( for comp in self.get_local_components() ] self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True) - elif self.repo_type == "modules": + else: component_dir = Path( self.directory, self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path, @@ -141,11 +141,11 @@ def __init__( Path(self.directory).joinpath("tests", "config"), cache_config=True ) - if registry is None: - self.registry = self.config.get("docker.registry", "quay.io") - else: - self.registry = registry - log.debug(f"Registry set to {self.registry}") + if registry is None: + self.registry = self.config.get("docker.registry", "quay.io") + else: + self.registry = registry + log.debug(f"Registry set to {self.registry}") self.lint_config = None self.modules_json = None diff --git a/nf_core/components/list.py b/nf_core/components/list.py index b24732e5c3..67468b4a5a 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -5,7 +5,7 @@ import rich.table from nf_core.components.components_command import ComponentCommand -from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_json import ModulesJson, ModulesJsonModuleEntry from nf_core.modules.modules_repo import ModulesRepo log = logging.getLogger(__name__) @@ -110,7 +110,7 @@ def pattern_msg(keywords: List[str]) -> str: modules_json_file = modules_json.modules_json for repo_url, component_with_dir in sorted(repos_with_comps.items()): - repo_entry: Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]] + repo_entry: Dict[str, Dict[str, Dict[str, ModulesJsonModuleEntry]]] if modules_json_file is None: log.warning(f"Modules JSON file '{modules_json.modules_json_path}' is missing. ") continue diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 1433122225..0c63141c73 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -21,7 +21,7 @@ def __init__( component_name: str, repo_url: Optional[str], component_dir: Path, - repo_type: str, + repo_type: Optional[str], base_dir: Path, component_type: str, remote_component: bool = True, @@ -54,6 +54,7 @@ def __init__( self.has_meta: bool = False self.git_sha: Optional[str] = None self.is_patched: bool = False + self.branch: Optional[str] = None if remote_component: # Initialize the important files @@ -85,6 +86,9 @@ def __init__( self.test_yml = None self.test_main_nf = None + def __repr__(self) -> str: + return f"" + def _get_main_nf_tags(self, test_main_nf: Union[Path, str]): """Collect all tags from the main.nf.test file.""" tags = [] diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py index d08658f5da..d0ef17a44d 100644 --- a/nf_core/modules/lint/module_version.py +++ b/nf_core/modules/lint/module_version.py @@ -8,11 +8,12 @@ import nf_core import nf_core.modules.modules_repo import nf_core.modules.modules_utils +from nf_core.modules.modules_utils import NFCoreComponent log = logging.getLogger(__name__) -def module_version(module_lint_object, module): +def module_version(module_lint_object: "nf_core.modules.lint.ModuleLint", module: "NFCoreComponent"): """ Verifies that the module has a version specified in the ``modules.json`` file @@ -20,8 +21,9 @@ def module_version(module_lint_object, module): containing a commit SHA. If that is true, it verifies that there are no newer version of the module available. """ - - modules_json_path = Path(module_lint_object.dir, "modules.json") + assert module_lint_object.modules_json is not None # mypy + assert module.repo_url is not None # mypy + modules_json_path = Path(module_lint_object.directory, "modules.json") # Verify that a git_sha exists in the `modules.json` file for this module version = module_lint_object.modules_json.get_module_version(module.component_name, module.repo_url, module.org) if version is None: diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index faeb84fc35..c0e41d1b42 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -6,7 +6,7 @@ import shutil import tempfile from pathlib import Path -from typing import Any, List, Optional, Tuple, Union +from typing import Dict, List, NotRequired, Optional, Tuple, TypedDict, Union import git import questionary @@ -27,6 +27,19 @@ log = logging.getLogger(__name__) +class ModulesJsonModuleEntry(TypedDict): + branch: str + git_sha: str + installed_by: List[str] + patch: NotRequired[str] + + +class ModulesJsonType(TypedDict): + name: str + homePage: str + repos: Dict[str, Dict[str, Dict[str, Dict[str, ModulesJsonModuleEntry]]]] + + class ModulesJson: """ An object for handling a 'modules.json' file in a pipeline @@ -43,10 +56,10 @@ def __init__(self, pipeline_dir: Union[str, Path]): self.modules_dir = self.directory / "modules" self.subworkflows_dir = self.directory / "subworkflows" self.modules_json_path = self.directory / "modules.json" - self.modules_json = None + self.modules_json: Optional[ModulesJsonType] = None self.pipeline_modules = None self.pipeline_subworkflows = None - self.pipeline_components = None + self.pipeline_components: Optional[Dict[str, List[Tuple[str, str]]]] = None def __str__(self): if self.modules_json is None: @@ -56,7 +69,7 @@ def __str__(self): def __repr__(self): return self.__str__() - def create(self): + def create(self) -> None: """ Creates the modules.json file from the modules and subworkflows installed in the pipeline directory @@ -66,7 +79,7 @@ def create(self): pipeline_config = nf_core.utils.fetch_wf_config(self.directory) pipeline_name = pipeline_config.get("manifest.name", "") pipeline_url = pipeline_config.get("manifest.homePage", "") - new_modules_json = {"name": pipeline_name.strip("'"), "homePage": pipeline_url.strip("'"), "repos": {}} + new_modules_json = ModulesJsonType(name=pipeline_name, homePage=pipeline_url, repos={}) if not self.modules_dir.exists(): if rich.prompt.Confirm.ask( @@ -79,7 +92,6 @@ def create(self): # Get repositories repos, _ = self.get_pipeline_module_repositories("modules", self.modules_dir) - # Get all module/subworkflow names in the repos repo_module_names = self.get_component_names_from_repo(repos, self.modules_dir) repo_subworkflow_names = self.get_component_names_from_repo(repos, self.subworkflows_dir) @@ -105,7 +117,9 @@ def create(self): self.modules_json = new_modules_json self.dump() - def get_component_names_from_repo(self, repos, directory): + def get_component_names_from_repo( + self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, str | List[str]]]]]], directory: Path + ) -> List[Tuple[str, List[str], str]]: """ Get component names from repositories in a pipeline. @@ -122,8 +136,8 @@ def get_component_names_from_repo(self, repos, directory): components = ( repo_url, [ - str(Path(component_name).relative_to(directory / modules_repo.repo_path)) - for component_name, _, file_names in os.walk(directory / modules_repo.repo_path) + str(component_name.relative_to(directory / modules_repo.repo_path)) + for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path) if "main.nf" in file_names ], modules_repo.repo_path, @@ -131,7 +145,9 @@ def get_component_names_from_repo(self, repos, directory): names.append(components) return names - def get_pipeline_module_repositories(self, component_type, directory, repos=None): + def get_pipeline_module_repositories( + self, component_type: str, directory: Path, repos: Optional[Dict] = None + ) -> Tuple[Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]], Dict[Path, Path]]: """ Finds all module repositories in the modules and subworkflows directory. Ignores the local modules/subworkflows. @@ -153,6 +169,7 @@ def get_pipeline_module_repositories(self, component_type, directory, repos=None # The function might rename some directories, keep track of them renamed_dirs = {} # Check if there are any untracked repositories + dirs_not_covered = self.dir_tree_uncovered(directory, [Path(ModulesRepo(url).repo_path) for url in repos]) if len(dirs_not_covered) > 0: log.info(f"Found custom {component_type[:-1]} repositories when creating 'modules.json'") @@ -245,8 +262,12 @@ def dir_tree_uncovered(self, components_directory, repos): return dirs_not_covered def determine_branches_and_shas( - self, component_type: str, install_dir: Union[str, Path], remote_url: str, components: List[Path] - ) -> dict[Path, dict[str, Any]]: + self, + component_type: str, + install_dir: Union[str, Path], + remote_url: str, + components: List[str], + ) -> Dict[str, ModulesJsonModuleEntry]: """ Determines what branch and commit sha each module/subworkflow in the pipeline belongs to @@ -273,10 +294,10 @@ def determine_branches_and_shas( available_branches = ModulesRepo.get_remote_branches(remote_url) sb_local = [] dead_components = [] - repo_entry = {} + repo_entry: Dict[str, ModulesJsonModuleEntry] = {} for component in sorted(components): modules_repo = default_modules_repo - component_path = repo_path / component + component_path = Path(repo_path, component) correct_commit_sha = None tried_branches = {default_modules_repo.branch} found_sha = False @@ -286,16 +307,16 @@ def determine_branches_and_shas( if patch_file.is_file(): temp_module_dir = self.try_apply_patch_reverse(component, install_dir, patch_file, component_path) correct_commit_sha = self.find_correct_commit_sha( - component_type, str(component), temp_module_dir, modules_repo + component_type, component, temp_module_dir, modules_repo ) else: correct_commit_sha = self.find_correct_commit_sha( - component_type, str(component), component_path, modules_repo + component_type, component, component_path, modules_repo ) if correct_commit_sha is None: # Check in the old path correct_commit_sha = self.find_correct_commit_sha( - component_type, str(component), repo_path / component_type / component, modules_repo + component_type, component, repo_path / component_type / component, modules_repo ) if correct_commit_sha is None: log.info( @@ -328,7 +349,7 @@ def determine_branches_and_shas( else: found_sha = True break - if found_sha: + if found_sha and correct_commit_sha is not None: repo_entry[component] = { "branch": modules_repo.branch, "git_sha": correct_commit_sha, @@ -337,7 +358,7 @@ def determine_branches_and_shas( # Clean up the modules/subworkflows we were unable to find the sha for for component in sb_local: - log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory") + log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, str(component))}' to 'local' directory") self.move_component_to_local(component_type, component, str(install_dir)) for component in dead_components: @@ -408,14 +429,14 @@ def move_component_to_local(self, component_type: str, component: Union[str, Pat to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}" shutil.move(current_path, local_dir / to_name) - def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]: + def unsynced_components(self) -> Tuple[List[str], List[str], dict]: """ Compute the difference between the modules/subworkflows in the directory and the modules/subworkflows in the 'modules.json' file. This is done by looking at all directories containing a 'main.nf' file Returns: - (untrack_dirs ([ Path ]), missing_installation (dict)): Directories that are not tracked + (untrack_dirs ([ str ]), missing_installation (dict)): Directories that are not tracked by the modules.json file, and modules/subworkflows in the modules.json where the installation directory is missing """ @@ -443,7 +464,7 @@ def unsynced_components(self) -> Tuple[List[Path], List[Path], dict]: return untracked_dirs_modules, untracked_dirs_subworkflows, missing_installation - def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_type: str) -> Tuple[List[Path], dict]: + def parse_dirs(self, dirs: List[Path], missing_installation: Dict, component_type: str) -> Tuple[List[str], Dict]: """ Parse directories and check if they are tracked in the modules.json file @@ -461,9 +482,10 @@ def parse_dirs(self, dirs: List[Path], missing_installation: dict, component_typ for dir_ in dirs: # Check if the module/subworkflows directory exists in modules.json install_dir = dir_.parts[0] - component = Path(*dir_.parts[1:]) + component = "/".join(dir_.parts[1:]) component_in_file = False git_url = "" + for repo in missing_installation: if component_type in missing_installation[repo]: if install_dir in missing_installation[repo][component_type]: @@ -564,7 +586,7 @@ def reinstall_repo(self, install_dir, remote_url, module_entries): failed_to_install.append(module) return failed_to_install - def check_up_to_date(self) -> bool: + def check_up_to_date(self): """ Checks whether the modules and subworkflows installed in the directory are consistent with the entries in the 'modules.json' file and vice versa. @@ -715,14 +737,12 @@ def update( self.modules_json["repos"][remote_url][component_type] = {repo_name: {}} repo_component_entry = self.modules_json["repos"][remote_url][component_type][repo_name] if component_name not in repo_component_entry: - repo_component_entry[component_name] = {} + repo_component_entry[component_name] = {"branch": "", "git_sha": "", "installed_by": []} repo_component_entry[component_name]["git_sha"] = component_version repo_component_entry[component_name]["branch"] = branch try: if installed_by not in repo_component_entry[component_name]["installed_by"] and installed_by is not None: - repo_component_entry[component_name]["installed_by"].append(installed_by) - except KeyError: - repo_component_entry[component_name]["installed_by"] = [installed_by] + repo_component_entry[component_name]["installed_by"] += installed_by finally: new_installed_by = repo_component_entry[component_name]["installed_by"] + list(installed_by_log) repo_component_entry[component_name]["installed_by"] = sorted([*set(new_installed_by)]) @@ -912,7 +932,7 @@ def get_modules_json(self) -> dict: if self.modules_json is None: self.load() assert self.modules_json is not None # mypy - return copy.deepcopy(self.modules_json) + return copy.deepcopy(self.modules_json) # type: ignore def get_component_version(self, component_type, component_name, repo_url, install_dir): """ @@ -938,7 +958,7 @@ def get_component_version(self, component_type, component_name, repo_url, instal .get("git_sha", None) ) - def get_module_version(self, module_name, repo_url, install_dir): + def get_module_version(self, module_name: str, repo_url: str, install_dir: str) -> Optional[str]: """ Returns the version of a module @@ -953,14 +973,11 @@ def get_module_version(self, module_name, repo_url, install_dir): if self.modules_json is None: self.load() assert self.modules_json is not None # mypy - return ( - self.modules_json.get("repos", {}) - .get(repo_url, {}) - .get("modules", {}) - .get(install_dir, {}) - .get(module_name, {}) - .get("git_sha", None) - ) + try: + sha = self.modules_json["repos"][repo_url]["modules"][install_dir][module_name]["git_sha"] + except KeyError: + sha = None + return sha def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir): """ @@ -986,7 +1003,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir): .get("git_sha", None) ) - def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)]]: + def get_all_components(self, component_type: str) -> dict[str, List[Tuple[(str, str)]]]: """ Retrieves all pipeline modules/subworkflows that are reported in the modules.json @@ -1002,8 +1019,8 @@ def get_all_components(self, component_type: str) -> dict[str, Tuple[(str, str)] self.pipeline_components = {} for repo, repo_entry in self.modules_json.get("repos", {}).items(): if component_type in repo_entry: - for dir, components in repo_entry[component_type].items(): - self.pipeline_components[repo] = [(dir, m) for m in components] + for directory, components in repo_entry[component_type].items(): + self.pipeline_components[repo] = [(directory, m) for m in components] return self.pipeline_components @@ -1072,7 +1089,9 @@ def get_installed_by_entries(self, component_type, name): return installed_by_entries - def get_component_branch(self, component_type, component, repo_url, install_dir): + def get_component_branch( + self, component_type: str, component: Union[str, Path], repo_url: str, install_dir: str + ) -> str: """ Gets the branch from which the module/subworkflow was installed @@ -1084,14 +1103,10 @@ def get_component_branch(self, component_type, component, repo_url, install_dir) if self.modules_json is None: self.load() assert self.modules_json is not None # mypy - branch = ( - self.modules_json["repos"] - .get(repo_url, {}) - .get(component_type, {}) - .get(install_dir, {}) - .get(component, {}) - .get("branch") - ) + try: + branch = self.modules_json["repos"][repo_url][component_type][install_dir][str(component)]["branch"] + except (KeyError, TypeError): + branch = None if branch is None: raise LookupError( f"Could not find branch information for component '{Path(install_dir, component)}'." @@ -1112,7 +1127,7 @@ def dump(self, run_prettier: bool = False) -> None: with open(self.modules_json_path, "w") as fh: json.dump(self.modules_json, fh, indent=4) - def resolve_missing_installation(self, missing_installation, component_type): + def resolve_missing_installation(self, missing_installation: Dict, component_type: str) -> None: missing_but_in_mod_json = [ f"'{component_type}/{install_dir}/{component}'" for repo_url, contents in missing_installation.items() @@ -1168,7 +1183,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component # Get tuples of components that miss installation and their install directory def components_with_repos(): - for dir in missing_from_modules_json: + for directory in missing_from_modules_json: for repo_url in repos: modules_repo = ModulesRepo(repo_url) paths_in_directory = [] @@ -1178,12 +1193,12 @@ def components_with_repos(): ) for dir_name, _, _ in os.walk(repo_url_path): if component_type == "modules": - if len(Path(dir).parts) > 1: # The module name is TOOL/SUBTOOL + if len(Path(directory).parts) > 1: # The module name is TOOL/SUBTOOL paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) pass paths_in_directory.append(Path(dir_name).parts[-1]) if dir in paths_in_directory: - yield (modules_repo.repo_path, dir) + yield (modules_repo.repo_path, directory) # Add all components into a dictionary with install directories repos_with_components = {} diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index a979ae45b8..daa7b59811 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -1,6 +1,7 @@ import logging import os import shutil +from pathlib import Path from typing import Optional import git @@ -72,8 +73,8 @@ def __init__( self.verify_branch() # Convenience variable - self.modules_dir = os.path.join(self.local_repo_dir, "modules", self.repo_path) - self.subworkflows_dir = os.path.join(self.local_repo_dir, "subworkflows", self.repo_path) + self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path) + self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path) self.avail_module_names = None diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 4b69d4af87..33e7f0a54a 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -4,7 +4,7 @@ import shutil from configparser import NoOptionError, NoSectionError from pathlib import Path -from typing import Dict, Optional, Union +from typing import Dict, Iterable, Optional, Union import git from git.exc import GitCommandError @@ -121,28 +121,32 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa remote_url = NF_CORE_MODULES_REMOTE self.remote_url = remote_url + self.fullname = None + self.local_repo_dir = None self.repo = None # TODO: SyncedRepo doesn't have this method and both the ModulesRepo and # the WorkflowRepo define their own including custom init methods. This needs # fixing. self.setup_local_repo(remote_url, branch, hide_progress) + if self.local_repo_dir is None: + raise ValueError("Repository not initialized") + else: + config_fn, repo_config = load_tools_config(self.local_repo_dir) + try: + self.repo_path = repo_config["org_path"] + except KeyError: + raise UserWarning(f"'org_path' key not present in {config_fn.name}") - config_fn, repo_config = load_tools_config(self.local_repo_dir) - try: - self.repo_path = repo_config["org_path"] - except KeyError: - raise UserWarning(f"'org_path' key not present in {config_fn.name}") - - # Verify that the repo seems to be correctly configured - if self.repo_path != NF_CORE_MODULES_NAME or self.branch: - self.verify_branch() + # Verify that the repo seems to be correctly configured + if self.repo_path != NF_CORE_MODULES_NAME or self.branch: + self.verify_branch() - # Convenience variable - self.modules_dir = os.path.join(self.local_repo_dir, "modules", self.repo_path) - self.subworkflows_dir = os.path.join(self.local_repo_dir, "subworkflows", self.repo_path) + # Convenience variable + self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path) + self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path) - self.avail_module_names = None + self.avail_module_names = None def setup_local_repo(self, remote_url, branch, hide_progress): pass @@ -361,7 +365,9 @@ def ensure_git_user_config(self, default_name: str, default_email: str) -> None: if not user_email: git_config.set_value("user", "email", default_email) - def get_component_git_log(self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None): + def get_component_git_log( + self, component_name: Union[str, Path], component_type: str, depth: Optional[int] = None + ) -> Iterable[Dict[str, str]]: """ Fetches the commit history the of requested module/subworkflow since a given date. The default value is not arbitrary - it is the last time the structure of the nf-core/modules repository was had an @@ -373,35 +379,32 @@ def get_component_git_log(self, component_name: Union[str, Path], component_type Returns: ( dict ): Iterator of commit SHAs and associated (truncated) message """ - if self.repo is None: raise ValueError("Repository not initialized") self.checkout_branch() component_path = Path(component_type, self.repo_path, component_name) - commits_new = self.repo.iter_commits(max_count=depth, paths=component_path) - if not commits_new: - raise ValueError(f"Could not find any commits for '{component_name}' in '{self.remote_url}'") - else: - commits_new = [ - {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_new - ] - commits_old = [] + commits_new_iter = self.repo.iter_commits(max_count=depth, paths=component_path) + commits_old_iter = [] if component_type == "modules": # Grab commits also from previous modules structure - component_path = Path("modules", component_name) - commits_old = self.repo.iter_commits(max_count=depth, paths=component_path) - commits_old = [ - {"git_sha": commit.hexsha, "trunc_message": commit.message.splitlines()[0]} for commit in commits_old - ] + old_component_path = Path("modules", component_name) + commits_old_iter = self.repo.iter_commits(max_count=depth, paths=old_component_path) + + commits_old = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_old_iter] + commits_new = [{"git_sha": commit.hexsha, "trunc_message": commit.message} for commit in commits_new_iter] commits = iter(commits_new + commits_old) + return commits def get_latest_component_version(self, component_name, component_type): """ Returns the latest commit in the repository """ - return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"] + try: + return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"] + except UserWarning: + return None def sha_exists_on_branch(self, sha): """ diff --git a/nf_core/utils.py b/nf_core/utils.py index d1e9ccfe95..4d0566b1af 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -30,6 +30,7 @@ import rich.markup import yaml from packaging.version import Version +from pydantic import BaseModel, ValidationError from rich.live import Live from rich.spinner import Spinner @@ -175,9 +176,9 @@ def _load_conda_environment(self) -> bool: log.debug("No conda `environment.yml` file found.") return False - def _fp(self, fn): + def _fp(self, fn: Union[str, Path]) -> Path: """Convenience function to get full path to a file in the pipeline""" - return os.path.join(self.wf_path, fn) + return Path(self.wf_path, fn) def list_files(self) -> List[Path]: """Get a list of all files in the pipeline""" @@ -191,9 +192,8 @@ def list_files(self) -> List[Path]: files.append(full_fn) else: log.debug(f"`git ls-files` returned '{full_fn}' but could not open it!") - except subprocess.CalledProcessError as e: + except subprocess.CalledProcessError: # Failed, so probably not initialised as a git repository - just a list of all files - log.debug(f"Couldn't call 'git ls-files': {e}") files = [] for file_path in self.wf_path.rglob("*"): if file_path.is_file(): @@ -1041,7 +1041,26 @@ def get_repo_releases_branches(pipeline, wfs): DEPRECATED_CONFIG_PATHS = [".nf-core-lint.yml", ".nf-core-lint.yaml"] -def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]: +class NFCoreTemplateConfig(BaseModel): + org: str + name: str + description: str + author: str + version: Optional[str] + force: Optional[bool] + outdir: Optional[str] + skip_features: Optional[list] + is_nfcore: Optional[bool] + + +class NFCoreYamlConfig(BaseModel): + nf_core_version: str + repository_type: str + org_path: str + template: NFCoreTemplateConfig + + +def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYamlConfig]: """ Parse the nf-core.yml configuration file @@ -1059,21 +1078,26 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, dict]: if config_fn is None: depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS) if depr_path: - log.error( - f"Deprecated `{depr_path.name}` file found! The file will not be loaded. " - f"Please rename the file to `{CONFIG_PATHS[0]}`." + raise AssertionError( + f"Deprecated `{depr_path.name}` file found! Please rename the file to `{CONFIG_PATHS[0]}`." ) else: - log.debug(f"No tools config file found: {CONFIG_PATHS[0]}") - return Path(directory, CONFIG_PATHS[0]), {} - - with open(config_fn) as fh: + raise AssertionError(f"Could not find a config file in the directory '{directory}'") + with open(str(config_fn)) as fh: tools_config = yaml.safe_load(fh) + # If the file is empty - tools_config = tools_config or {} + if tools_config is None: + raise AssertionError(f"Config file '{config_fn}' is empty") + + # Check for required fields + try: + nf_core_yaml_config = NFCoreYamlConfig(**tools_config) + except ValidationError as e: + raise AssertionError(f"Config file '{config_fn}' is invalid: {e}") log.debug("Using config file: %s", config_fn) - return config_fn, tools_config + return config_fn, nf_core_yaml_config def determine_base_dir(directory: Union[Path, str] = ".") -> Path: From b2336adaf288e3c64d02c28fb7e3e58cd22bd4cc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 23 Jul 2024 14:24:21 +0200 Subject: [PATCH 181/574] remove remaining mention to 'defaults' --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 48d1c3ca3d..d5bf328b59 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -635,7 +635,7 @@ def anaconda_package(dep, dep_channels=None): """ if dep_channels is None: - dep_channels = ["conda-forge", "bioconda", "defaults"] + dep_channels = ["conda-forge", "bioconda"] # Check if each dependency is the latest available version if "=" in dep: From 297735e06df52450a6a133dade10ad45a3f1799e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 10:46:34 +0200 Subject: [PATCH 182/574] add --fix option to fix the meta.yml of subworkflows --- nf_core/__main__.py | 5 +- nf_core/commands_subworkflows.py | 3 +- nf_core/components/nfcore_component.py | 142 +++++++++++++++---------- nf_core/subworkflows/lint/__init__.py | 55 +++++++++- nf_core/subworkflows/lint/meta_yml.py | 6 ++ tests/subworkflows/lint.py | 9 ++ tests/test_subworkflows.py | 1 + 7 files changed, 162 insertions(+), 59 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 1dd92d6b8f..dd800ad810 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1431,11 +1431,12 @@ def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disabl help="Sort lint output by subworkflow or test name.", show_default=True, ) -def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +@click.option("--fix", is_flag=True, help="Fix all linting tests if possible.") +def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix): """ Lint one or more subworkflows in a directory. """ - subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by) + subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix) # nf-core subworkflows info diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index cc1a544eca..70a0c94edc 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -102,7 +102,7 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi sys.exit(1) -def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix): """ Lint one or more subworkflows in a directory. @@ -119,6 +119,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo subworkflow_lint = SubworkflowLint( dir, fail_warned=fail_warned, + fix=fix, registry=ctx.params["registry"], remote_url=ctx.obj["modules_repo_url"], branch=ctx.obj["modules_repo_branch"], diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 3e5a68648d..db817db905 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -41,6 +41,7 @@ def __init__( remote_component (bool): Whether the module is to be treated as a nf-core or local component """ + self.component_type = component_type self.component_name = component_name self.repo_url = repo_url self.component_dir = component_dir @@ -155,67 +156,98 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st included_components.append(component) return included_components - def get_inputs_from_main_nf(self): + def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" inputs = [] with open(self.main_nf) as f: data = f.read() - # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo - # regex matches: - # val(foo) - # path(bar) - # val foo - # val bar - # path bar - # path foo - # don't match anything inside comments or after "output:" - if "input:" not in data: - log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs - input_data = data.split("input:")[1].split("output:")[0] - for line in input_data.split("\n"): - channel_elements = [] - regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" - matches = re.finditer(regex, line) - for _, match in enumerate(matches, start=1): - input_val = None - if match.group(3): - input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - elif match.group(4): - input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - if input_val: - channel_elements.append({input_val: {}}) - if len(channel_elements) > 0: - inputs.append(channel_elements) - log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") - self.inputs = inputs + if self.component_type == "modules": + # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo + # regex matches: + # val(foo) + # path(bar) + # val foo + # val bar + # path bar + # path foo + # don't match anything inside comments or after "output:" + if "input:" not in data: + log.debug(f"Could not find any inputs in {self.main_nf}") + return inputs + input_data = data.split("input:")[1].split("output:")[0] + for line in input_data.split("\n"): + channel_elements = [] + regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + matches = re.finditer(regex, line) + for _, match in enumerate(matches, start=1): + input_val = None + if match.group(3): + input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + elif match.group(4): + input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + if input_val: + channel_elements.append({input_val: {}}) + if len(channel_elements) > 0: + inputs.append(channel_elements) + log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") + self.inputs = inputs + elif self.component_type == "subworkflows": + # get input values from main.nf after "take:" + if "take:" not in data: + log.debug(f"Could not find any inputs in {self.main_nf}") + return inputs + # get all lines between "take" and "main" or "emit" + input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0] + for line in input_data.split("\n"): + try: + inputs.append(line.split()[0]) + except IndexError: + # Empty lines + pass + log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") + self.inputs = inputs def get_outputs_from_main_nf(self): outputs = [] with open(self.main_nf) as f: data = f.read() - # get output values from main.nf after "output:". the names are always after "emit:" - if "output:" not in data: - log.debug(f"Could not find any outputs in {self.main_nf}") - return outputs - output_data = data.split("output:")[1].split("when:")[0] - regex_emit = r"emit:\s*([^)\s,]+)" - regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))" - for line in output_data.split("\n"): - match_emit = re.search(regex_emit, line) - matches_elements = re.finditer(regex_elements, line) - if not match_emit: - continue - output_channel = {match_emit.group(1): []} - for _, match_element in enumerate(matches_elements, start=1): - output_val = None - if match_element.group(3): - output_val = match_element.group(3) - elif match_element.group(4): - output_val = match_element.group(4) - if output_val: - output_val = output_val.strip("'").strip('"') # remove quotes - output_channel[match_emit.group(1)].append({output_val: {}}) - outputs.append(output_channel) - log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") - self.outputs = outputs + if self.component_type == "modules": + # get output values from main.nf after "output:". the names are always after "emit:" + if "output:" not in data: + log.debug(f"Could not find any outputs in {self.main_nf}") + return outputs + output_data = data.split("output:")[1].split("when:")[0] + regex_emit = r"emit:\s*([^)\s,]+)" + regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + for line in output_data.split("\n"): + match_emit = re.search(regex_emit, line) + matches_elements = re.finditer(regex_elements, line) + if not match_emit: + continue + output_channel = {match_emit.group(1): []} + for _, match_element in enumerate(matches_elements, start=1): + output_val = None + if match_element.group(3): + output_val = match_element.group(3) + elif match_element.group(4): + output_val = match_element.group(4) + if output_val: + output_val = output_val.strip("'").strip('"') # remove quotes + output_channel[match_emit.group(1)].append({output_val: {}}) + outputs.append(output_channel) + log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") + self.outputs = outputs + elif self.component_type == "subworkflows": + # get output values from main.nf after "emit:". Can be named outputs or not. + if "emit:" not in data: + log.debug(f"Could not find any outputs in {self.main_nf}") + return outputs + output_data = data.split("emit:")[1].split("}")[0] + for line in output_data.split("\n"): + try: + outputs.append(line.split("=")[0].split()[0]) + except IndexError: + # Empty lines + pass + log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") + self.outputs = outputs diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index a3cacf2952..e0911e5bd9 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -11,11 +11,12 @@ import questionary import rich +import ruamel.yaml import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult -from nf_core.pipelines.lint_utils import console +from nf_core.pipelines.lint_utils import console, run_prettier_on_file log = logging.getLogger(__name__) @@ -38,6 +39,7 @@ def __init__( self, dir, fail_warned=False, + fix=False, remote_url=None, branch=None, no_pull=False, @@ -48,6 +50,7 @@ def __init__( component_type="subworkflows", dir=dir, fail_warned=fail_warned, + fix=fix, remote_url=remote_url, branch=branch, no_pull=no_pull, @@ -207,6 +210,10 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): # Otherwise run all the lint tests else: + # Update meta.yml file if requested + if self.fix: + self.update_meta_yml_file(swf) + if self.repo_type == "pipeline" and self.modules_json: # Set correct sha version = self.modules_json.get_subworkflow_version(swf.component_name, swf.repo_url, swf.org) @@ -223,3 +230,49 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): self.failed += warned self.failed += [LintResult(swf, *s) for s in swf.failed] + + + def update_meta_yml_file(self, swf): + """ + Update the meta.yml file with the correct inputs and outputs + """ + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + yaml.indent(mapping=2, sequence=2, offset=0) + + # Read meta.yml + with open(swf.meta_yml) as fh: + meta_yaml = yaml.load(fh) + meta_yaml_corrected = meta_yaml.copy() + # Obtain inputs and outputs from main.nf + swf.get_inputs_from_main_nf() + swf.get_outputs_from_main_nf() + + # Compare inputs and add them if missing + if "input" in meta_yaml: + # Delete inputs from meta.yml which are not present in main.nf + meta_yaml_corrected["input"] = [input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs] + # Obtain inputs from main.nf missing in meta.yml + inputs_correct = [list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs] + inputs_missing = [input for input in swf.inputs if input not in inputs_correct] + # Add missing inputs to meta.yml + for missing_input in inputs_missing: + meta_yaml_corrected["input"].append({missing_input: {"description": ""}}) + + if "output" in meta_yaml: + # Delete outputs from meta.yml which are not present in main.nf + meta_yaml_corrected["output"] = [output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs] + # Obtain output from main.nf missing in meta.yml + outputs_correct = [list(output.keys())[0] for output in meta_yaml_corrected["output"] if list(output.keys())[0] in swf.outputs] + outputs_missing = [output for output in swf.outputs if output not in outputs_correct] + # Add missing inputs to meta.yml + for missing_output in outputs_missing: + meta_yaml_corrected["output"].append({missing_output: {"description": ""}}) + + # Write corrected meta.yml to file + with open(swf.meta_yml, "w") as fh: + log.info(f"Updating {swf.meta_yml}") + yaml.dump(meta_yaml_corrected, fh) + run_prettier_on_file(fh.name) + + diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py index 24e75eddbf..633061e247 100644 --- a/nf_core/subworkflows/lint/meta_yml.py +++ b/nf_core/subworkflows/lint/meta_yml.py @@ -1,4 +1,5 @@ import json +import logging from pathlib import Path import jsonschema.validators @@ -6,6 +7,7 @@ import nf_core.components.components_utils +log = logging.getLogger(__name__) def meta_yml(subworkflow_lint_object, subworkflow): """ @@ -65,6 +67,8 @@ def meta_yml(subworkflow_lint_object, subworkflow): subworkflow.passed.append(("meta_input", f"`{input}` specified", subworkflow.meta_yml)) else: subworkflow.failed.append(("meta_input", f"`{input}` missing in `meta.yml`", subworkflow.meta_yml)) + else: + log.debug(f"No inputs specified in subworkflow `main.nf`: {subworkflow.component_name}") if "output" in meta_yaml: meta_output = [list(x.keys())[0] for x in meta_yaml["output"]] @@ -75,6 +79,8 @@ def meta_yml(subworkflow_lint_object, subworkflow): subworkflow.failed.append( ("meta_output", f"`{output}` missing in `meta.yml`", subworkflow.meta_yml) ) + else: + log.debug(f"No outputs specified in subworkflow `main.nf`: {subworkflow.component_name}") # confirm that the name matches the process name in main.nf if meta_yaml["name"].upper() == subworkflow.workflow_name: diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py index 540f421ad2..35e2c6b519 100644 --- a/tests/subworkflows/lint.py +++ b/tests/subworkflows/lint.py @@ -38,6 +38,15 @@ def test_subworkflows_lint_new_subworkflow(self): assert len(subworkflow_lint.warned) >= 0 +def test_subworkflows_lint_update_meta_yml(self): + """update the meta.yml of a subworkflow""" + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules, fix=True) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_no_gitlab(self): """Test linting a pipeline with no subworkflows installed""" with pytest.raises(LookupError): diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 786ba53836..cb8bcf7a56 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -159,6 +159,7 @@ def tearDown(self): test_subworkflows_lint_snapshot_file, test_subworkflows_lint_snapshot_file_missing_fail, test_subworkflows_lint_snapshot_file_not_needed, + test_subworkflows_lint_update_meta_yml, ) from .subworkflows.list import ( # type: ignore[misc] test_subworkflows_install_and_list_subworkflows, From a79a4f0e0c4ad3546c39d22ef46ce74e9bc25de8 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 12:12:17 +0200 Subject: [PATCH 183/574] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16db104fc6..e25e8f8948 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ ### Components - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) +- Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077)) ### General From 2d2be3877fe04dbc4ddb80cf525be0db13083740 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 16:03:33 +0200 Subject: [PATCH 184/574] fix typing and linting --- nf_core/components/nfcore_component.py | 11 +++++------ nf_core/subworkflows/lint/__init__.py | 21 ++++++++++++++------- nf_core/subworkflows/lint/meta_yml.py | 1 + 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index db817db905..39a4ba51f4 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -158,7 +158,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" - inputs = [] + inputs: list[list | str] = [] with open(self.main_nf) as f: data = f.read() if self.component_type == "modules": @@ -173,10 +173,10 @@ def get_inputs_from_main_nf(self) -> None: # don't match anything inside comments or after "output:" if "input:" not in data: log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs + return input_data = data.split("input:")[1].split("output:")[0] for line in input_data.split("\n"): - channel_elements = [] + channel_elements: list[dict] = [] regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" matches = re.finditer(regex, line) for _, match in enumerate(matches, start=1): @@ -195,15 +195,14 @@ def get_inputs_from_main_nf(self) -> None: # get input values from main.nf after "take:" if "take:" not in data: log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs + return # get all lines between "take" and "main" or "emit" input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0] for line in input_data.split("\n"): try: inputs.append(line.split()[0]) except IndexError: - # Empty lines - pass + pass # Empty lines log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") self.inputs = inputs diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index e0911e5bd9..22025d2a07 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -231,7 +231,6 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): self.failed += [LintResult(swf, *s) for s in swf.failed] - def update_meta_yml_file(self, swf): """ Update the meta.yml file with the correct inputs and outputs @@ -251,9 +250,13 @@ def update_meta_yml_file(self, swf): # Compare inputs and add them if missing if "input" in meta_yaml: # Delete inputs from meta.yml which are not present in main.nf - meta_yaml_corrected["input"] = [input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs] + meta_yaml_corrected["input"] = [ + input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs + ] # Obtain inputs from main.nf missing in meta.yml - inputs_correct = [list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs] + inputs_correct = [ + list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs + ] inputs_missing = [input for input in swf.inputs if input not in inputs_correct] # Add missing inputs to meta.yml for missing_input in inputs_missing: @@ -261,9 +264,15 @@ def update_meta_yml_file(self, swf): if "output" in meta_yaml: # Delete outputs from meta.yml which are not present in main.nf - meta_yaml_corrected["output"] = [output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs] + meta_yaml_corrected["output"] = [ + output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs + ] # Obtain output from main.nf missing in meta.yml - outputs_correct = [list(output.keys())[0] for output in meta_yaml_corrected["output"] if list(output.keys())[0] in swf.outputs] + outputs_correct = [ + list(output.keys())[0] + for output in meta_yaml_corrected["output"] + if list(output.keys())[0] in swf.outputs + ] outputs_missing = [output for output in swf.outputs if output not in outputs_correct] # Add missing inputs to meta.yml for missing_output in outputs_missing: @@ -274,5 +283,3 @@ def update_meta_yml_file(self, swf): log.info(f"Updating {swf.meta_yml}") yaml.dump(meta_yaml_corrected, fh) run_prettier_on_file(fh.name) - - diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py index 633061e247..be282bc453 100644 --- a/nf_core/subworkflows/lint/meta_yml.py +++ b/nf_core/subworkflows/lint/meta_yml.py @@ -9,6 +9,7 @@ log = logging.getLogger(__name__) + def meta_yml(subworkflow_lint_object, subworkflow): """ Lint a ``meta.yml`` file From ff1a49520f69d228acead56fc232760ded321fe3 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 24 Jul 2024 14:21:12 +0200 Subject: [PATCH 185/574] avoid circular import due to modules_json being importetd --- nf_core/modules/__init__.py | 12 ----- nf_core/modules/lint/module_version.py | 5 +- tests/modules/test_bump_versions.py | 10 ++-- tests/modules/test_create.py | 16 +++--- tests/modules/test_info.py | 10 ++-- tests/modules/test_install.py | 6 +-- tests/modules/test_lint.py | 69 +++++++++++++------------- tests/modules/test_list.py | 26 +++++----- tests/modules/test_modules_json.py | 4 +- tests/modules/test_patch.py | 29 ++++++----- tests/modules/test_update.py | 20 +++++--- tests/test_subworkflows.py | 43 +--------------- 12 files changed, 105 insertions(+), 145 deletions(-) diff --git a/nf_core/modules/__init__.py b/nf_core/modules/__init__.py index 6be871ece8..e69de29bb2 100644 --- a/nf_core/modules/__init__.py +++ b/nf_core/modules/__init__.py @@ -1,12 +0,0 @@ -from .bump_versions import ModuleVersionBumper -from .create import ModuleCreate -from .info import ModuleInfo -from .install import ModuleInstall -from .lint import ModuleLint -from .list import ModuleList -from .modules_json import ModulesJson -from .modules_repo import ModulesRepo -from .modules_utils import ModuleExceptionError -from .patch import ModulePatch -from .remove import ModuleRemove -from .update import ModuleUpdate diff --git a/nf_core/modules/lint/module_version.py b/nf_core/modules/lint/module_version.py index d0ef17a44d..207d5e9418 100644 --- a/nf_core/modules/lint/module_version.py +++ b/nf_core/modules/lint/module_version.py @@ -6,6 +6,7 @@ from pathlib import Path import nf_core +import nf_core.modules.lint import nf_core.modules.modules_repo import nf_core.modules.modules_utils from nf_core.modules.modules_utils import NFCoreComponent @@ -40,8 +41,8 @@ def module_version(module_lint_object: "nf_core.modules.lint.ModuleLint", module ) modules_repo = nf_core.modules.modules_repo.ModulesRepo(remote_url=module.repo_url, branch=module.branch) - module_git_log = modules_repo.get_component_git_log(module.component_name, "modules") - if version == next(module_git_log)["git_sha"]: + module_git_log = list(modules_repo.get_component_git_log(module.component_name, "modules")) + if version == module_git_log[0]["git_sha"]: module.passed.append(("module_version", "Module is the latest version", module.component_dir)) else: module.warned.append(("module_version", "New version available", module.component_dir)) diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index 29e030668d..d46b8747c8 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -3,7 +3,7 @@ import pytest -import nf_core.modules +import nf_core.modules.bump_versions from nf_core.modules.modules_utils import ModuleExceptionError from ..test_modules import TestModules @@ -19,19 +19,19 @@ def test_modules_bump_versions_single_module(self): new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content) with open(env_yml_path, "w") as fh: fh.write(new_content) - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) version_bumper.bump_versions(module="bpipe/test") assert len(version_bumper.failed) == 0 def test_modules_bump_versions_all_modules(self): """Test updating all modules""" - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) version_bumper.bump_versions(all_modules=True) assert len(version_bumper.failed) == 0 def test_modules_bump_versions_fail(self): """Fail updating a module with wrong name""" - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) with pytest.raises(ModuleExceptionError) as excinfo: version_bumper.bump_versions(module="no/module") assert "Could not find the specified module:" in str(excinfo.value) @@ -45,6 +45,6 @@ def test_modules_bump_versions_fail_unknown_version(self): new_content = re.sub(r"bioconda::bpipe=\d.\d.\d\D?", r"bioconda::bpipe=xxx", content) with open(env_yml_path, "w") as fh: fh.write(new_content) - version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) version_bumper.bump_versions(module="bpipe/test") assert "Conda package had unknown version" in version_bumper.failed[0][0] diff --git a/tests/modules/test_create.py b/tests/modules/test_create.py index c847501830..219f869997 100644 --- a/tests/modules/test_create.py +++ b/tests/modules/test_create.py @@ -9,7 +9,7 @@ import yaml from git.repo import Repo -import nf_core.modules +import nf_core.modules.create from tests.utils import ( GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH, GITLAB_URL, @@ -26,7 +26,7 @@ def test_modules_create_succeed(self): with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") - module_create = nf_core.modules.ModuleCreate( + module_create = nf_core.modules.create.ModuleCreate( self.pipeline_dir, "trimgalore", "@author", "process_single", True, True, conda_name="trim-galore" ) with requests_cache.disabled(): @@ -38,7 +38,7 @@ def test_modules_create_fail_exists(self): with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "trim-galore", "0.6.7") mock_biocontainers_api_calls(rsps, "trim-galore", "0.6.7") - module_create = nf_core.modules.ModuleCreate( + module_create = nf_core.modules.create.ModuleCreate( self.pipeline_dir, "trimgalore", "@author", "process_single", False, False, conda_name="trim-galore" ) with requests_cache.disabled(): @@ -53,7 +53,7 @@ def test_modules_create_nfcore_modules(self): with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "fastqc", "0.11.9") mock_biocontainers_api_calls(rsps, "fastqc", "0.11.9") - module_create = nf_core.modules.ModuleCreate( + module_create = nf_core.modules.create.ModuleCreate( self.nfcore_modules, "fastqc", "@author", "process_low", False, False ) with requests_cache.disabled(): @@ -68,7 +68,7 @@ def test_modules_create_nfcore_modules_subtool(self): with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "star", "2.8.10a") mock_biocontainers_api_calls(rsps, "star", "2.8.10a") - module_create = nf_core.modules.ModuleCreate( + module_create = nf_core.modules.create.ModuleCreate( self.nfcore_modules, "star/index", "@author", "process_medium", False, False ) with requests_cache.disabled(): @@ -94,7 +94,7 @@ def test_modules_migrate(self, mock_rich_ask): # Create a module with --migrate-pytest mock_rich_ask.return_value = True - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) module_create.create() with open(module_dir / "main.nf") as fh: @@ -128,7 +128,7 @@ def test_modules_migrate_no_delete(self, mock_rich_ask): # Create a module with --migrate-pytest mock_rich_ask.return_value = False - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) module_create.create() # Check that pytest folder is not deleted @@ -157,7 +157,7 @@ def test_modules_migrate_symlink(self, mock_rich_ask): # Create a module with --migrate-pytest mock_rich_ask.return_value = True - module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) + module_create = nf_core.modules.create.ModuleCreate(self.nfcore_modules, "samtools/sort", migrate_pytest=True) module_create.create() # Check that symlink is deleted diff --git a/tests/modules/test_info.py b/tests/modules/test_info.py index 8906854044..8e60bed316 100644 --- a/tests/modules/test_info.py +++ b/tests/modules/test_info.py @@ -1,6 +1,6 @@ from rich.console import Console -import nf_core.modules +import nf_core.modules.info from ..test_modules import TestModules from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL @@ -9,7 +9,7 @@ class TestModulesCreate(TestModules): def test_modules_info_remote(self): """Test getting info about a remote module""" - mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "fastqc") + mods_info = nf_core.modules.info.ModuleInfo(self.pipeline_dir, "fastqc") mods_info_output = mods_info.get_component_info() console = Console(record=True) console.print(mods_info_output) @@ -21,7 +21,7 @@ def test_modules_info_remote(self): def test_modules_info_remote_gitlab(self): """Test getting info about a module in the remote gitlab repo""" - mods_info = nf_core.modules.ModuleInfo( + mods_info = nf_core.modules.info.ModuleInfo( self.pipeline_dir, "fastqc", remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH ) mods_info_output = mods_info.get_component_info() @@ -37,7 +37,7 @@ def test_modules_info_remote_gitlab(self): def test_modules_info_local(self): """Test getting info about a locally installed module""" self.mods_install.install("trimgalore") - mods_info = nf_core.modules.ModuleInfo(self.pipeline_dir, "trimgalore") + mods_info = nf_core.modules.info.ModuleInfo(self.pipeline_dir, "trimgalore") mods_info_output = mods_info.get_component_info() console = Console(record=True) console.print(mods_info_output) @@ -50,7 +50,7 @@ def test_modules_info_local(self): def test_modules_info_in_modules_repo(self): """Test getting info about a module in the modules repo""" - mods_info = nf_core.modules.ModuleInfo(self.nfcore_modules, "fastqc") + mods_info = nf_core.modules.info.ModuleInfo(self.nfcore_modules, "fastqc") mods_info.local = True mods_info_output = mods_info.get_component_info() console = Console(record=True) diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py index cfdaac47ed..8f7ac0a1dc 100644 --- a/tests/modules/test_install.py +++ b/tests/modules/test_install.py @@ -19,14 +19,14 @@ class TestModulesCreate(TestModules): def test_modules_install_nopipeline(self): """Test installing a module - no pipeline given""" - self.mods_install.directory = None + self.pipeline_dir = None assert self.mods_install.install("foo") is False @with_temporary_folder def test_modules_install_emptypipeline(self, tmpdir): """Test installing a module - empty dir given""" - os.mkdir(os.path.join(tmpdir, "nf-core-pipe")) - self.mods_install.directory = os.path.join(tmpdir, "nf-core-pipe") + Path(tmpdir, "nf-core-pipe").mkdir() + self.mods_install.directory = Path(tmpdir, "nf-core-pipe") with pytest.raises(UserWarning) as excinfo: self.mods_install.install("foo") assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index fc9871db2e..dfe288a6ee 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -6,8 +6,9 @@ import yaml from git.repo import Repo -import nf_core.modules -from nf_core.modules.lint import main_nf +import nf_core.modules.lint +import nf_core.modules.patch +from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels from nf_core.utils import set_wd from ..test_modules import TestModules @@ -160,7 +161,7 @@ class TestModulesCreate(TestModules): def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): - install_obj = nf_core.modules.ModuleInstall( + install_obj = nf_core.modules.install.ModuleInstall( pipeline_dir, prompt=False, force=False, @@ -180,7 +181,7 @@ def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): def test_modules_lint_trimgalore(self): """Test linting the TrimGalore! module""" self.mods_install.install("trimgalore") - module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="trimgalore") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -191,11 +192,11 @@ def test_modules_lint_empty(self): self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) with pytest.raises(LookupError): - nf_core.modules.ModuleLint(directory=self.pipeline_dir) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) def test_modules_lint_new_modules(self): """lint a new module""" - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -206,13 +207,13 @@ def test_modules_lint_no_gitlab(self): self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) with pytest.raises(LookupError): - nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) def test_modules_lint_gitlab_modules(self): """Lint modules from a different remote""" self.mods_install_gitlab.install("fastqc") self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 2 assert len(module_lint.passed) > 0 @@ -221,7 +222,7 @@ def test_modules_lint_gitlab_modules(self): def test_modules_lint_multiple_remotes(self): """Lint modules from a different remote""" self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 1 assert len(module_lint.passed) > 0 @@ -230,12 +231,12 @@ def test_modules_lint_multiple_remotes(self): def test_modules_lint_registry(self): """Test linting the samtools module and alternative registry""" assert self.mods_install.install("samtools/sort") - module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - module_lint = nf_core.modules.ModuleLint(directory=self.pipeline_dir) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -248,13 +249,13 @@ def test_modules_lint_patched_modules(self): self._setup_patch(str(self.pipeline_dir), True) # Create a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) # change temporarily working directory to the pipeline directory # to avoid error from try_apply_patch() during linting with set_wd(self.pipeline_dir): - module_lint = nf_core.modules.ModuleLint( + module_lint = nf_core.modules.lint.ModuleLint( directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=PATCH_BRANCH, @@ -273,7 +274,7 @@ def test_modules_lint_check_process_labels(self): for test_case in PROCESS_LABEL_TEST_CASES: process, passed, warned, failed = test_case mocked_ModuleLint = MockModuleLint() - main_nf.check_process_labels(mocked_ModuleLint, process.splitlines()) + check_process_labels(mocked_ModuleLint, process.splitlines()) assert len(mocked_ModuleLint.passed) == passed assert len(mocked_ModuleLint.warned) == warned assert len(mocked_ModuleLint.failed) == failed @@ -284,7 +285,7 @@ def test_modules_lint_check_url(self): mocked_ModuleLint = MockModuleLint() for line in process.splitlines(): if line.strip(): - main_nf.check_container_link_line(mocked_ModuleLint, line, registry="quay.io") + check_container_link_line(mocked_ModuleLint, line, registry="quay.io") assert ( len(mocked_ModuleLint.passed) == passed @@ -298,7 +299,7 @@ def test_modules_lint_check_url(self): def test_modules_lint_snapshot_file(self): """Test linting a module with a snapshot file""" - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -315,7 +316,7 @@ def test_modules_lint_snapshot_file_missing_fail(self): "tests", "main.nf.test.snap", ).unlink() - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -359,7 +360,7 @@ def test_modules_lint_snapshot_file_not_needed(self): "w", ) as fh: fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -377,7 +378,7 @@ def test_modules_environment_yml_file_doesnt_exists(self): "environment.yml.bak", ) ) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -403,7 +404,7 @@ def test_modules_environment_yml_file_doesnt_exists(self): def test_modules_environment_yml_file_sorted_correctly(self): """Test linting a module with a correctly sorted environment.yml file""" - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -438,7 +439,7 @@ def test_modules_environment_yml_file_sorted_incorrectly(self): "w", ) as fh: fh.write(yaml_content) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # we fix the sorting on the fly, so this should pass assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -471,7 +472,7 @@ def test_modules_environment_yml_file_not_array(self): "w", ) as fh: fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -504,7 +505,7 @@ def test_modules_environment_yml_file_name_mismatch(self): "w", ) as fh: fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes yaml_content["name"] = "bpipe_test" @@ -536,7 +537,7 @@ def test_modules_meta_yml_incorrect_licence_field(self): "w", ) as fh: fh.write(yaml.dump(meta_yml)) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes @@ -559,7 +560,7 @@ def test_modules_meta_yml_input_mismatch(self): main_nf_new = main_nf.replace("path bam", "path bai") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf) @@ -578,7 +579,7 @@ def test_modules_meta_yml_output_mismatch(self): main_nf_new = main_nf.replace("emit: bam", "emit: bai") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf_new) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf) @@ -625,7 +626,7 @@ def test_modules_meta_yml_incorrect_name(self): "w", ) as fh: fh.write(yaml.dump(environment_yml)) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # reset changes @@ -659,7 +660,7 @@ def test_modules_missing_test_dir(self): Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") ) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") @@ -690,7 +691,7 @@ def test_modules_missing_test_main_nf(self): "main.nf.test.bak", ) ) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path( self.nfcore_modules, @@ -719,7 +720,7 @@ def test_modules_missing_test_main_nf(self): def test_modules_unused_pytest_files(self): """Test linting a nf-test module with files still present in `tests/modules/`""" Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -735,7 +736,7 @@ def test_nftest_failing_linting(self): self.nfcore_modules = Path(tmp_dir, "modules-test") Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="kallisto/quant") assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -774,7 +775,7 @@ def test_modules_absent_version(self): "w", ) as fh: fh.write(new_content) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") with open( Path( @@ -812,7 +813,7 @@ def test_modules_empty_file_in_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -841,7 +842,7 @@ def test_modules_empty_file_in_stub_snapshot(self): with open(snap_file, "w") as fh: json.dump(snap, fh) - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py index 81484cc8f0..fdbb61f69e 100644 --- a/tests/modules/test_list.py +++ b/tests/modules/test_list.py @@ -4,7 +4,7 @@ import yaml from rich.console import Console -import nf_core.modules +import nf_core.modules.list from ..test_modules import TestModules from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL @@ -13,7 +13,7 @@ class TestModulesCreate(TestModules): def test_modules_list_remote(self): """Test listing available modules""" - mods_list = nf_core.modules.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(None, remote=True) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -22,7 +22,9 @@ def test_modules_list_remote(self): def test_modules_list_remote_gitlab(self): """Test listing the modules in the remote gitlab repo""" - mods_list = nf_core.modules.ModuleList(None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) + mods_list = nf_core.modules.list.ModuleList( + None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH + ) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -31,7 +33,7 @@ def test_modules_list_remote_gitlab(self): def test_modules_list_pipeline(self): """Test listing locally installed modules""" - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -42,7 +44,7 @@ def test_modules_list_pipeline(self): def test_modules_install_and_list_pipeline(self): """Test listing locally installed modules""" self.mods_install.install("trimgalore") - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -52,7 +54,7 @@ def test_modules_install_and_list_pipeline(self): def test_modules_install_gitlab_and_list_pipeline(self): """Test listing locally installed modules""" self.mods_install_gitlab.install("fastqc") - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -61,7 +63,7 @@ def test_modules_install_gitlab_and_list_pipeline(self): def test_modules_list_local_json(self): """Test listing locally installed modules as JSON""" - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) listed_mods = mods_list.list_components(print_json=True) listed_mods = json.loads(listed_mods) assert "fastqc" in listed_mods @@ -69,7 +71,7 @@ def test_modules_list_local_json(self): def test_modules_list_remote_json(self): """Test listing available modules as JSON""" - mods_list = nf_core.modules.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(None, remote=True) listed_mods = mods_list.list_components(print_json=True) listed_mods = json.loads(listed_mods) assert "fastqc" in listed_mods @@ -77,7 +79,7 @@ def test_modules_list_remote_json(self): def test_modules_list_with_one_keyword(self): """Test listing available modules with one keyword""" - mods_list = nf_core.modules.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(None, remote=True) listed_mods = mods_list.list_components(keywords=["qc"]) console = Console(record=True) console.print(listed_mods) @@ -86,7 +88,7 @@ def test_modules_list_with_one_keyword(self): def test_modules_list_with_keywords(self): """Test listing available modules with multiple keywords""" - mods_list = nf_core.modules.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(None, remote=True) listed_mods = mods_list.list_components(keywords=["fastq", "qc"]) console = Console(record=True) console.print(listed_mods) @@ -95,7 +97,7 @@ def test_modules_list_with_keywords(self): def test_modules_list_with_unused_keyword(self): """Test listing available modules with an unused keyword""" - mods_list = nf_core.modules.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(None, remote=True) with self.assertLogs(level="INFO") as log: listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"]) self.assertIn("No available", log.output[0]) @@ -116,7 +118,7 @@ def test_modules_list_in_wrong_repo_fail(self): yaml.safe_dump(nf_core_yml, fh) # expect error logged with self.assertLogs(level="ERROR") as log: - mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False) + mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) listed_mods = mods_list.list_components() self.assertIn("must be run from a pipeline directory", log.output[0]) # expect empty list diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py index 319b5ad657..2ab058fa70 100644 --- a/tests/modules/test_modules_json.py +++ b/tests/modules/test_modules_json.py @@ -36,7 +36,7 @@ def test_mod_json_update(self): mod_json_obj = ModulesJson(self.pipeline_dir) # Update the modules.json file mod_repo_obj = ModulesRepo() - mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", "modules", write_file=False) + mod_json_obj.update("modules", mod_repo_obj, "MODULE_NAME", "GIT_SHA", ["modules"], write_file=False) mod_json = mod_json_obj.get_modules_json() assert "MODULE_NAME" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"] assert "git_sha" in mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"]["nf-core"]["MODULE_NAME"] @@ -155,7 +155,7 @@ def test_mod_json_up_to_date_reinstall_fails(self): mod_json_obj = ModulesJson(self.pipeline_dir) # Update the fastqc module entry to an invalid git_sha - mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", "modules", write_file=True) + mod_json_obj.update("modules", ModulesRepo(), "fastqc", "INVALID_GIT_SHA", ["modules"], write_file=True) # Remove the fastqc module fastqc_path = Path(self.pipeline_dir, "modules", NF_CORE_MODULES_NAME, "fastqc") diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py index 230bb1ce8f..c3eb94d374 100644 --- a/tests/modules/test_patch.py +++ b/tests/modules/test_patch.py @@ -6,7 +6,10 @@ import pytest import nf_core.components.components_command -import nf_core.modules +import nf_core.components.patch +import nf_core.modules.modules_json +import nf_core.modules.patch +import nf_core.modules.update from ..test_modules import TestModules from ..utils import GITLAB_URL @@ -29,7 +32,7 @@ def setup_patch(pipeline_dir, modify_module): - install_obj = nf_core.modules.ModuleInstall( + install_obj = nf_core.modules.install.ModuleInstall( pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA ) @@ -66,7 +69,7 @@ def test_create_patch_no_change(self): setup_patch(self.pipeline_dir, False) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) with pytest.raises(UserWarning): patch_obj.patch(BISMARK_ALIGN) @@ -84,7 +87,7 @@ def test_create_patch_change(self): setup_patch(self.pipeline_dir, True) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) @@ -119,7 +122,7 @@ def test_create_patch_try_apply_successful(self): module_path = Path(self.pipeline_dir, module_relpath) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" @@ -132,7 +135,7 @@ def test_create_patch_try_apply_successful(self): "modules", REPO_NAME, BISMARK_ALIGN, patch_fn ) - update_obj = nf_core.modules.ModuleUpdate( + update_obj = nf_core.modules.update.ModuleUpdate( self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH ) # Install the new files @@ -187,7 +190,7 @@ def test_create_patch_try_apply_failed(self): module_path = Path(self.pipeline_dir, module_relpath) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" @@ -200,7 +203,7 @@ def test_create_patch_try_apply_failed(self): "modules", REPO_NAME, BISMARK_ALIGN, patch_fn ) - update_obj = nf_core.modules.ModuleUpdate( + update_obj = nf_core.modules.update.ModuleUpdate( self.pipeline_dir, sha=FAIL_SHA, remote_url=GITLAB_URL, branch=PATCH_BRANCH ) # Install the new files @@ -226,7 +229,7 @@ def test_create_patch_update_success(self): module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" @@ -240,7 +243,7 @@ def test_create_patch_update_success(self): ) # Update the module - update_obj = nf_core.modules.ModuleUpdate( + update_obj = nf_core.modules.update.ModuleUpdate( self.pipeline_dir, sha=SUCCEED_SHA, show_diff=False, @@ -287,7 +290,7 @@ def test_create_patch_update_fail(self): module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" @@ -304,7 +307,7 @@ def test_create_patch_update_fail(self): with open(module_path / patch_fn) as fh: patch_contents = fh.read() - update_obj = nf_core.modules.ModuleUpdate( + update_obj = nf_core.modules.update.ModuleUpdate( self.pipeline_dir, sha=FAIL_SHA, show_diff=False, @@ -339,7 +342,7 @@ def test_remove_patch(self): setup_patch(self.pipeline_dir, True) # Try creating a patch file - patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) patch_obj.patch(BISMARK_ALIGN) module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py index a33aac3775..1f81eab487 100644 --- a/tests/modules/test_update.py +++ b/tests/modules/test_update.py @@ -167,9 +167,10 @@ def test_update_with_config_fixed_version(self): # Fix the trimgalore version in the .nf-core.yml to an old version update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": OLD_TRIMGALORE_SHA}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all modules in the pipeline update_obj = ModuleUpdate( @@ -191,9 +192,10 @@ def test_update_with_config_dont_update(self): # Set the trimgalore field to no update in the .nf-core.yml update_config = {GITLAB_URL: {GITLAB_REPO: {"trimgalore": False}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all modules in the pipeline update_obj = ModuleUpdate( @@ -219,9 +221,10 @@ def test_update_with_config_fix_all(self): # Fix the version of all nf-core modules in the .nf-core.yml to an old version update_config = {GITLAB_URL: OLD_TRIMGALORE_SHA} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all modules in the pipeline update_obj = ModuleUpdate( @@ -242,9 +245,10 @@ def test_update_with_config_no_updates(self): # Fix the version of all nf-core modules in the .nf-core.yml to an old version update_config = {GITLAB_URL: False} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all modules in the pipeline update_obj = ModuleUpdate( diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index af581fc9ab..7c18ab0a2d 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -1,14 +1,13 @@ """Tests covering the subworkflows commands""" import json -import os -import shutil import unittest from pathlib import Path import pytest import nf_core.modules +import nf_core.modules.install import nf_core.pipelines.create.create import nf_core.subworkflows @@ -104,49 +103,11 @@ def setUp(self): force=False, sha="8c343b3c8a0925949783dc547666007c245c235b", ) - self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True) + self.mods_install = nf_core.modules.install.ModuleInstall(self.pipeline_dir, prompt=False, force=True) # Set up remove objects self.subworkflow_remove = nf_core.subworkflows.SubworkflowRemove(self.pipeline_dir) - def tearDown(self): - """Clean up temporary files and folders""" - - if os.path.exists(self.tmp_dir): - shutil.rmtree(self.tmp_dir) - @pytest.fixture(autouse=True) def _use_caplog(self, caplog): self.caplog = caplog - - # ################################################ - # # Test of the individual subworkflow commands. # - # ################################################ - - # from .subworkflows.list import ( # type: ignore[misc] - # test_subworkflows_install_and_list_subworkflows, - # test_subworkflows_install_gitlab_and_list_subworkflows, - # test_subworkflows_list_remote, - # test_subworkflows_list_remote_gitlab, - # ) - # from .subworkflows.remove import ( # type: ignore[misc] - # test_subworkflows_remove_included_subworkflow, - # test_subworkflows_remove_one_of_two_subworkflow, - # test_subworkflows_remove_subworkflow, - # test_subworkflows_remove_subworkflow_keep_installed_module, - # ) - # from .subworkflows.update import ( # type: ignore[misc] - # test_install_and_update, - # test_install_at_hash_and_update, - # test_install_at_hash_and_update_and_save_diff_limit_output, - # test_install_at_hash_and_update_and_save_diff_to_file, - # test_install_at_hash_and_update_limit_output, - # test_update_all, - # test_update_all_linked_components_from_subworkflow, - # test_update_all_subworkflows_from_module, - # test_update_change_of_included_modules, - # test_update_with_config_dont_update, - # test_update_with_config_fix_all, - # test_update_with_config_fixed_version, - # test_update_with_config_no_updates, - # ) From 0cf5f8b2f6f36d7904d95368c2ae2964bcbc09af Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 09:08:04 +0200 Subject: [PATCH 186/574] remove broken _repr_ (breaks because not all parameters are intilaized) --- nf_core/components/lint/__init__.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index ada3ee30c2..f5ce3ddb7f 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -45,7 +45,6 @@ def __init__(self, component: NFCoreComponent, lint_test: str, message: str, fil self.component_name: str = component.component_name -@rich.repr.auto class ComponentLint(ComponentCommand): """ An object for linting modules and subworkflows either in a clone of the 'nf-core/modules' From 879e808b37f5bf7ed4e15aaef111ba025779a08f Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:27:14 +0200 Subject: [PATCH 187/574] add types --- nf_core/components/components_command.py | 1 - nf_core/components/components_utils.py | 16 +- nf_core/components/create.py | 21 +-- nf_core/components/info.py | 14 +- nf_core/components/install.py | 4 + nf_core/components/lint/__init__.py | 12 +- nf_core/components/nfcore_component.py | 1 + nf_core/modules/bump_versions.py | 10 +- nf_core/modules/modules_json.py | 7 +- nf_core/pipelines/create/create.py | 50 +++--- nf_core/pipelines/create/utils.py | 20 +-- nf_core/pipelines/lint/__init__.py | 24 +-- nf_core/pipelines/lint/modules_json.py | 9 +- nf_core/subworkflows/lint/main_nf.py | 14 +- nf_core/synced_repo.py | 33 ++-- tests/pipelines/test_sync.py | 186 ++++++++++------------- tests/subworkflows/test_lint.py | 42 +++-- 17 files changed, 232 insertions(+), 232 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 8d200021c2..13a6fed338 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -38,7 +38,6 @@ def __init__( self.hide_progress = hide_progress self.no_prompts = no_prompts self._configure_repo_and_paths() - self.repo_type: Optional[str] = None def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 743efd386d..e4e2ff092b 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -27,7 +27,9 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P # Figure out the repository type from the .nf-core.yml config file if we can config_fn, tools_config = nf_core.utils.load_tools_config(base_dir) - repo_type = tools_config.get("repository_type", None) + if config_fn is None: + raise UserWarning(f"Could not find a config file in directory: {base_dir}") + repo_type = getattr(tools_config, "repository_type", None) or None # If not set, prompt the user if not repo_type and use_prompt: @@ -55,13 +57,11 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P # Check if it's a valid answer if repo_type not in ["pipeline", "modules"]: raise UserWarning(f"Invalid repository type: '{repo_type}'") - + org: str = "" # Check for org if modules repo - if repo_type == "pipeline": - org = "" - elif repo_type == "modules": - org = tools_config.get("org_path", None) - if org is None: + if repo_type == "modules": + org = getattr(tools_config, "org_path", "") or "" + if org == "": log.warning("Organisation path not defined in %s [key: org_path]", config_fn.name) org = questionary.text( "What is the organisation path under which modules and subworkflows are stored?", @@ -70,7 +70,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P ).unsafe_ask() log.info("To avoid this prompt in the future, add the 'org_path' key to a root '%s' file.", config_fn.name) if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this config now?", default=True): - with open(config_fn, "a+") as fh: + with open(str(config_fn), "a+") as fh: fh.write(f"org_path: {org}\n") log.info(f"Config added to '{config_fn.name}'") diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 413790099d..fdcf402b47 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -62,7 +62,7 @@ def __init__( self.not_empty_template = not empty_template self.migrate_pytest = migrate_pytest - def create(self): + def create(self) -> bool: """ Create a new DSL2 module or subworkflow from the nf-core template. @@ -106,12 +106,12 @@ def create(self): ``` """ - if self.component_type == "modules": # Check modules directory structure self.check_modules_structure() # Check whether the given directory is a nf-core pipeline or a clone of nf-core/modules + log.info(f"Repository type: [blue]{self.repo_type}") if self.directory != ".": log.info(f"Base directory: '{self.directory}'") @@ -161,7 +161,7 @@ def create(self): self.org_alphabet = not_alphabet.sub("", self.org) # Create component template with jinja2 - self._render_template() + assert self._render_template() log.info(f"Created component template: '{self.component_name}'") if self.migrate_pytest: @@ -171,7 +171,9 @@ def create(self): self._print_and_delete_pytest_files() new_files = [str(path) for path in self.file_paths.values()] + log.info("Created following files:\n " + "\n ".join(new_files)) + return True def _get_bioconda_tool(self): """ @@ -265,7 +267,7 @@ def _get_module_structure_components(self): default=True, ) - def _render_template(self): + def _render_template(self) -> Optional[bool]: """ Create new module/subworkflow files with Jinja2. """ @@ -288,7 +290,7 @@ def _render_template(self): # Write output to the target file log.debug(f"Writing output to: '{dest_fn}'") dest_fn.parent.mkdir(exist_ok=True, parents=True) - with open(dest_fn, "w") as fh: + with open(str(dest_fn), "w") as fh: log.debug(f"Writing output to: '{dest_fn}'") fh.write(rendered_output) @@ -297,6 +299,7 @@ def _render_template(self): Path(nf_core.__file__).parent / f"{self.component_type[:-1]}-template" / template_fn ).stat() dest_fn.chmod(template_stat.st_mode) + return True def _collect_name_prompt(self): """ @@ -340,7 +343,7 @@ def _collect_name_prompt(self): elif self.component_type == "subworkflows": self.component = rich.prompt.Prompt.ask("[violet]Name of subworkflow").strip() - def _get_component_dirs(self): + def _get_component_dirs(self) -> Dict[str, Path]: """Given a directory and a tool/subtool or subworkflow, set the file paths and check if they already exist Returns dict: keys are relative paths to template files, vals are target paths. @@ -372,9 +375,8 @@ def _get_component_dirs(self): # Set file paths file_paths["main.nf"] = component_file - if self.repo_type == "modules": + elif self.repo_type == "modules": component_dir = Path(self.directory, self.component_type, self.org, self.component_dir) - # Check if module/subworkflow directories exist already if component_dir.exists() and not self.force_overwrite and not self.migrate_pytest: raise UserWarning( @@ -403,7 +405,6 @@ def _get_component_dirs(self): raise UserWarning( f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'" ) - # Set file paths # For modules - can be tool/ or tool/subtool/ so can't do in template directory structure file_paths["main.nf"] = component_dir / "main.nf" @@ -411,6 +412,8 @@ def _get_component_dirs(self): if self.component_type == "modules": file_paths["environment.yml"] = component_dir / "environment.yml" file_paths["tests/main.nf.test.j2"] = component_dir / "tests" / "main.nf.test" + else: + raise ValueError("`repo_type` not set correctly") return file_paths diff --git a/nf_core/components/info.py b/nf_core/components/info.py index d07486f638..a296fcaccf 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -136,17 +136,17 @@ def init_mod_name(self, component): ).unsafe_ask() else: if self.repo_type == "pipeline": + assert self.modules_json is not None # mypy # check if the module is locally installed local_paths = self.modules_json.get_all_components(self.component_type).get( self.modules_repo.remote_url ) # type: ignore - if local_paths is None: - raise LookupError(f"No {self.component_type[:-1]} installed from {self.modules_repo.remote_url}") - for directory, comp in local_paths: - if comp == component: - component_base_path = Path(self.directory, self.component_type) - self.local_path = Path(component_base_path, directory, component) - break + if local_paths is not None: + for directory, comp in local_paths: + if comp == component: + component_base_path = Path(self.directory, self.component_type) + self.local_path = Path(component_base_path, directory, component) + break if self.local_path: self.local = True diff --git a/nf_core/components/install.py b/nf_core/components/install.py index aa8aac81e6..8f47913283 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -69,8 +69,12 @@ def install(self, component: str, silent: bool = False) -> bool: # Verify SHA if not self.modules_repo.verify_sha(self.prompt, self.sha): return False + + # verify self.modules_repo entries: if self.modules_repo is None: return False + if self.modules_repo.repo_path is None: + return False # Check and verify component name diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index f5ce3ddb7f..e2475ef62c 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -75,6 +75,11 @@ def __init__( self.passed: List[LintResult] = [] self.warned: List[LintResult] = [] self.failed: List[LintResult] = [] + self.all_local_components: List[NFCoreComponent] = [] + + self.lint_config = None + self.modules_json = None + if self.component_type == "modules": self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline") else: @@ -107,7 +112,7 @@ def __init__( f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." ) local_component_dir = Path(self.directory, self.component_type, "local") - self.all_local_components = [] + if local_component_dir.exists(): self.all_local_components = [ NFCoreComponent( @@ -122,7 +127,7 @@ def __init__( for comp in self.get_local_components() ] self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True) - else: + elif self.repo_type == "modules": component_dir = Path( self.directory, self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path, @@ -146,9 +151,6 @@ def __init__( self.registry = registry log.debug(f"Registry set to {self.registry}") - self.lint_config = None - self.modules_json = None - def __repr__(self) -> str: return f"ComponentLint({self.component_type}, {self.directory})" diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 0c63141c73..129871d68c 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -55,6 +55,7 @@ def __init__( self.git_sha: Optional[str] = None self.is_patched: bool = False self.branch: Optional[str] = None + self.workflow_name: Optional[str] = None if remote_component: # Initialize the important files diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index fb0dc7d50d..2d8854e3c0 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -7,7 +7,7 @@ import os import re from pathlib import Path -from typing import Any, Dict, List, Optional, Tuple, Union +from typing import List, Optional, Tuple, Union import questionary import yaml @@ -22,13 +22,13 @@ import nf_core.utils from nf_core.components.components_command import ComponentCommand from nf_core.components.nfcore_component import NFCoreComponent -from nf_core.utils import custom_yaml_dumper, rich_force_colors +from nf_core.utils import NFCoreYamlConfig, custom_yaml_dumper, rich_force_colors from nf_core.utils import plural_s as _s log = logging.getLogger(__name__) -class ModuleVersionBumper(ComponentCommand): # type: ignore[misc] +class ModuleVersionBumper(ComponentCommand): def __init__( self, pipeline_dir: Union[str, Path], @@ -43,7 +43,7 @@ def __init__( self.failed: List[Tuple[str, str]] = [] self.ignored: List[Tuple[str, str]] = [] self.show_up_to_date: Optional[bool] = None - self.tools_config: Dict[str, Any] = {} + self.tools_config: Optional[NFCoreYamlConfig] def bump_versions( self, module: Union[str, None] = None, all_modules: bool = False, show_uptodate: bool = False @@ -160,7 +160,7 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: return False # Don't update if blocked in blacklist - self.bump_versions_config = self.tools_config.get("bump-versions", {}) + self.bump_versions_config = getattr(self.tools_config, "bump-versions", {}) or {} if module.component_name in self.bump_versions_config: config_version = self.bump_versions_config[module.component_name] if not config_version: diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index c0e41d1b42..02ce6fa5a2 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -922,7 +922,7 @@ def module_present(self, module_name, repo_url, install_dir): install_dir, {} ) - def get_modules_json(self) -> dict: + def get_modules_json(self) -> ModulesJsonType: """ Returns a copy of the loaded modules.json @@ -932,7 +932,7 @@ def get_modules_json(self) -> dict: if self.modules_json is None: self.load() assert self.modules_json is not None # mypy - return copy.deepcopy(self.modules_json) # type: ignore + return copy.deepcopy(self.modules_json) def get_component_version(self, component_type, component_name, repo_url, install_dir): """ @@ -1182,6 +1182,7 @@ def resolve_missing_from_modules_json(self, missing_from_modules_json, component repos, _ = self.get_pipeline_module_repositories(component_type, self.modules_dir, tracked_repos) # Get tuples of components that miss installation and their install directory + def components_with_repos(): for directory in missing_from_modules_json: for repo_url in repos: @@ -1197,7 +1198,7 @@ def components_with_repos(): paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) pass paths_in_directory.append(Path(dir_name).parts[-1]) - if dir in paths_in_directory: + if directory in paths_in_directory: yield (modules_repo.repo_path, directory) # Add all components into a dictionary with install directories diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index aecba94236..b7d86c5bd7 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -8,9 +8,10 @@ import re import shutil from pathlib import Path -from typing import Optional, Union +from typing import Dict, List, Optional, Union import git +import git.config import jinja2 import yaml @@ -61,12 +62,15 @@ def __init__( self.config = template_config elif from_config_file: # Try reading config file - _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".") - # Obtain a CreateConfig object from `.nf-core.yml` config file - if "template" in config_yml: - self.config = CreateConfig(**config_yml["template"]) - else: - raise UserWarning("The template configuration was not provided in '.nf-core.yml'.") + try: + _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd()) + # Obtain a CreateConfig object from `.nf-core.yml` config file + if config_yml is not None and getattr(config_yml, "template", None) is not None: + self.config = CreateConfig(**config_yml["template"]) + else: + raise UserWarning("The template configuration was not provided in '.nf-core.yml'.") + except (FileNotFoundError, UserWarning): + log.debug("The '.nf-core.yml' configuration file was not found.") elif (name and description and author) or ( template_config and (isinstance(template_config, str) or isinstance(template_config, Path)) ): @@ -191,7 +195,10 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): skip_paths (list): List of template areas which contain paths to skip. """ # Try reading config file - _, config_yml = nf_core.utils.load_tools_config(pipeline_dir) + try: + _, config_yml = nf_core.utils.load_tools_config(pipeline_dir) + except UserWarning: + config_yml = None # Define the different template areas, and what actions to take for each # if they are skipped @@ -230,13 +237,13 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): jinja_params["name_docker"] = jinja_params["name"].replace(jinja_params["org"], jinja_params["prefix_nodash"]) jinja_params["logo_light"] = f"{jinja_params['name_noslash']}_logo_light.png" jinja_params["logo_dark"] = f"{jinja_params['name_noslash']}_logo_dark.png" - - if ( - "lint" in config_yml - and "nextflow_config" in config_yml["lint"] - and "manifest.name" in config_yml["lint"]["nextflow_config"] - ): - return jinja_params, skip_paths + if config_yml is not None: + if ( + hasattr(config_yml, "lint") + and hasattr(config_yml["lint"], "nextflow_config") + and hasattr(config_yml["lint"]["nextflow_config"], "manifest.name") + ): + return jinja_params, skip_paths # Check that the pipeline name matches the requirements if not re.match(r"^[a-z]+$", jinja_params["short_name"]): @@ -417,7 +424,7 @@ def fix_linting(self): """ # Create a lint config short_name = self.jinja_params["short_name"] - lint_config = { + lint_config: Dict[str, List[str]] = { "files_exist": [ "CODE_OF_CONDUCT.md", f"assets/nf-core-{short_name}_logo_light.png", @@ -503,9 +510,10 @@ def fix_linting(self): # Add the lint content to the preexisting nf-core config config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir) - nf_core_yml["lint"] = lint_config - with open(self.outdir / config_fn, "w") as fh: - yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False) + if config_fn is not None and nf_core_yml is not None: + nf_core_yml.lint = lint_config + with open(self.outdir / config_fn, "w") as fh: + yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False) run_prettier_on_file(os.path.join(self.outdir, config_fn)) @@ -531,9 +539,9 @@ def git_init_pipeline(self): Raises: UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'. """ - default_branch = self.default_branch + default_branch: Optional[str] = self.default_branch try: - default_branch = default_branch or git.config.GitConfigParser().get_value("init", "defaultBranch") + default_branch = default_branch or str(git.config.GitConfigParser().get_value("init", "defaultBranch")) except configparser.Error: log.debug("Could not read init.defaultBranch") if default_branch in ["dev", "TEMPLATE"]: diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index c15d61e266..88994c9361 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -3,9 +3,9 @@ from contextvars import ContextVar from logging import LogRecord from pathlib import Path -from typing import Any, Dict, Iterator, Optional, Union +from typing import Any, Dict, Iterator, Union -from pydantic import BaseModel, ConfigDict, ValidationError, ValidationInfo, field_validator +from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator from rich.logging import RichHandler from textual import on from textual._context import active_app @@ -16,6 +16,8 @@ from textual.widget import Widget from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch +from nf_core.utils import NFCoreTemplateConfig + # Use ContextVar to define a context on the model initialization _init_context_var: ContextVar = ContextVar("_init_context_var", default={}) @@ -33,19 +35,9 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]: NFCORE_PIPELINE_GLOBAL: bool = True -class CreateConfig(BaseModel): +class CreateConfig(NFCoreTemplateConfig): """Pydantic model for the nf-core create config.""" - org: Optional[str] = None - name: Optional[str] = None - description: Optional[str] = None - author: Optional[str] = None - version: Optional[str] = None - force: Optional[bool] = True - outdir: Optional[str] = None - skip_features: Optional[list] = None - is_nfcore: Optional[bool] = None - model_config = ConfigDict(extra="allow") def __init__(self, /, **data: Any) -> None: @@ -103,7 +95,7 @@ class TextInput(Static): and validation messages. """ - def __init__(self, field_id, placeholder, description, default=None, password=None, **kwargs) -> None: + def __init__(self, field_id, placeholder, description, default="", password=False, **kwargs) -> None: """Initialise the widget with our values. Pass on kwargs upstream for standard usage.""" diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index 93f6523709..ed833d3219 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -151,15 +151,15 @@ def _get_all_lint_tests(release_mode): "nfcore_yml", ] + (["version_consistency"] if release_mode else []) - def _load(self): + def _load(self) -> bool: """Load information about the pipeline into the PipelineLint object""" # Load everything using the parent object super()._load() # Load lint object specific stuff - self._load_lint_config() + return self._load_lint_config() - def _load_lint_config(self): + def _load_lint_config(self) -> bool: """Parse a pipeline lint config file. Load the '.nf-core.yml' config file and extract @@ -168,14 +168,19 @@ def _load_lint_config(self): Add parsed config to the `self.lint_config` class attribute. """ _, tools_config = nf_core.utils.load_tools_config(self.wf_path) - self.lint_config = tools_config.get("lint", {}) + self.lint_config = getattr(tools_config, "lint", {}) or {} + is_correct = True # Check if we have any keys that don't match lint test names - for k in self.lint_config: - if k not in self.lint_tests: - log.warning(f"Found unrecognised test name '{k}' in pipeline lint config") + if self.lint_config is not None: + for k in self.lint_config: + if k not in self.lint_tests: + log.warning(f"Found unrecognised test name '{k}' in pipeline lint config") + is_correct = False - def _lint_pipeline(self): + return is_correct + + def _lint_pipeline(self) -> None: """Main linting function. Takes the pipeline directory as the primary input and iterates through @@ -240,7 +245,8 @@ def _lint_pipeline(self): "Running lint checks", total=len(self.lint_tests), test_name=self.lint_tests[0] ) for test_name in self.lint_tests: - if self.lint_config.get(test_name, {}) is False: + lint_test = self.lint_config.get(test_name, {}) if self.lint_config is not None else {} + if lint_test is False: log.debug(f"Skipping lint test '{test_name}'") self.ignored.append((test_name, test_name)) continue diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py index dd0a59d558..5ce2054036 100644 --- a/nf_core/pipelines/lint/modules_json.py +++ b/nf_core/pipelines/lint/modules_json.py @@ -1,9 +1,10 @@ from pathlib import Path +from typing import Dict, List -from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_json import ModulesJson, ModulesJsonType -def modules_json(self): +def modules_json(self) -> Dict[str, List[str]]: """Make sure all modules described in the ``modules.json`` file are actually installed Every module installed from ``nf-core/modules`` must have an entry in the ``modules.json`` file @@ -18,10 +19,10 @@ def modules_json(self): # Load pipeline modules and modules.json _modules_json = ModulesJson(self.wf_path) _modules_json.load() - modules_json_dict = _modules_json.modules_json + modules_json_dict: ModulesJsonType | None = _modules_json.modules_json modules_dir = Path(self.wf_path, "modules") - if _modules_json: + if _modules_json and modules_json_dict is not None: all_modules_passed = True for repo in modules_json_dict["repos"].keys(): diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py index c73559502c..edca32bf30 100644 --- a/nf_core/subworkflows/lint/main_nf.py +++ b/nf_core/subworkflows/lint/main_nf.py @@ -4,12 +4,14 @@ import logging import re -from typing import List +from typing import List, Tuple + +from nf_core.components.nfcore_component import NFCoreComponent log = logging.getLogger(__name__) -def main_nf(_, subworkflow): +def main_nf(_, subworkflow: NFCoreComponent) -> Tuple[List[str], List[str]]: """ Lint a ``main.nf`` subworkflow file @@ -25,8 +27,8 @@ def main_nf(_, subworkflow): * The subworkflow emits a software version """ - inputs = [] - outputs = [] + inputs: List[str] = [] + outputs: List[str] = [] # Read the lines directly from the subworkflow lines = None @@ -38,7 +40,7 @@ def main_nf(_, subworkflow): subworkflow.passed.append(("main_nf_exists", "Subworkflow file exists", subworkflow.main_nf)) except FileNotFoundError: subworkflow.failed.append(("main_nf_exists", "Subworkflow file does not exist", subworkflow.main_nf)) - return + return inputs, outputs # Go through subworkflow main.nf file and switch state according to current section # Perform section-specific linting @@ -199,7 +201,7 @@ def check_subworkflow_section(self, lines: List[str]) -> List[str]: return includes -def check_workflow_section(self, lines): +def check_workflow_section(self, lines: List[str]) -> None: """Lint the workflow definition of a subworkflow before Specifically checks that the name is all capital letters diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 33e7f0a54a..8af0ee9a08 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -4,7 +4,7 @@ import shutil from configparser import NoOptionError, NoSectionError from pathlib import Path -from typing import Dict, Iterable, Optional, Union +from typing import Dict, Iterable, List, Optional, Union import git from git.exc import GitCommandError @@ -129,14 +129,16 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa # the WorkflowRepo define their own including custom init methods. This needs # fixing. self.setup_local_repo(remote_url, branch, hide_progress) + if self.local_repo_dir is None: raise ValueError("Repository not initialized") else: config_fn, repo_config = load_tools_config(self.local_repo_dir) - try: - self.repo_path = repo_config["org_path"] - except KeyError: - raise UserWarning(f"'org_path' key not present in {config_fn.name}") + if config_fn is not None and repo_config is not None: + try: + self.repo_path = repo_config.org_path + except KeyError: + raise UserWarning(f"'org_path' key not present in {config_fn.name}") # Verify that the repo seems to be correctly configured if self.repo_path != NF_CORE_MODULES_NAME or self.branch: @@ -148,6 +150,9 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa self.avail_module_names = None + def __repr__(self) -> str: + return f"SyncedRepo({self.remote_url}, {self.branch})" + def setup_local_repo(self, remote_url, branch, hide_progress): pass @@ -402,8 +407,12 @@ def get_latest_component_version(self, component_name, component_type): Returns the latest commit in the repository """ try: - return list(self.get_component_git_log(component_name, component_type, depth=1))[0]["git_sha"] - except UserWarning: + git_logs = list(self.get_component_git_log(component_name, component_type, depth=1)) + if not git_logs: + return None + return git_logs[0]["git_sha"] + except Exception as e: + log.debug(f"Could not get latest version of {component_name}: {e}") return None def sha_exists_on_branch(self, sha): @@ -437,7 +446,9 @@ def get_commit_info(self, sha): return message, date raise LookupError(f"Commit '{sha}' not found in the '{self.remote_url}'") - def get_avail_components(self, component_type, checkout=True, commit=None): + def get_avail_components( + self, component_type: str, checkout: bool = True, commit: Optional[str] = None + ) -> List[str]: """ Gets the names of the modules/subworkflows in the repository. They are detected by checking which directories have a 'main.nf' file @@ -456,9 +467,9 @@ def get_avail_components(self, component_type, checkout=True, commit=None): directory = self.subworkflows_dir # Module/Subworkflow directories are characterized by having a 'main.nf' file avail_component_names = [ - os.path.relpath(dirpath, start=directory) - for dirpath, _, file_names in os.walk(directory) - if "main.nf" in file_names + str(Path(dirpath).relative_to(directory)) + for dirpath, _, files in Path.walk(directory) + if "main.nf" in files ] return avail_component_names diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py index d7b73c7ffb..b6955e6714 100644 --- a/tests/pipelines/test_sync.py +++ b/tests/pipelines/test_sync.py @@ -2,50 +2,104 @@ import json import os -import shutil -import tempfile -import unittest from pathlib import Path +from typing import Dict, List, Union from unittest import mock import git import pytest +import yaml import nf_core.pipelines.create.create import nf_core.pipelines.sync +from nf_core.utils import NFCoreYamlConfig +from ..test_pipelines import TestPipelines from ..utils import with_temporary_folder -class TestModules(unittest.TestCase): +class MockResponse: + def __init__(self, data: Union[Dict, List[Dict]], status_code: int, url: str): + self.url: str = url + self.status_code: int = status_code + self.from_cache: bool = False + self.reason: str = "Mocked response" + self.data: Union[Dict, List[Dict]] = data + self.content: str = json.dumps(data) + self.headers: Dict[str, str] = {"content-encoding": "test", "connection": "fake"} + + def json(self): + return self.data + + +def mocked_requests_get(url) -> MockResponse: + """Helper function to emulate POST requests responses from the web""" + + url_template = "https://api.github.com/repos/{}/response/" + if url == Path(url_template.format("no_existing_pr"), "pulls?head=TEMPLATE&base=None"): + return MockResponse([], 200, url) + if url == Path(url_template.format("list_prs"), "pulls"): + response_data = [ + { + "state": "closed", + "head": {"ref": "nf-core-template-merge-2"}, + "base": {"ref": "master"}, + "html_url": "pr_url", + } + ] + [ + { + "state": "open", + "head": {"ref": f"nf-core-template-merge-{branch_no}"}, + "base": {"ref": "master"}, + "html_url": "pr_url", + } + for branch_no in range(3, 7) + ] + return MockResponse(response_data, 200, url) + + return MockResponse([{"html_url": url}], 404, url) + + +def mocked_requests_patch(url: str, data: str, **kwargs) -> MockResponse: + """Helper function to emulate POST requests responses from the web""" + + if url == "url_to_update_pr": + return MockResponse({"html_url": "great_success"}, 200, url) + # convert data to dict + response = json.loads(data) + response["patch_url"] = url + return MockResponse(response, 404, url) + + +def mocked_requests_post(url, **kwargs): + """Helper function to emulate POST requests responses from the web""" + + if url == "https://api.github.com/repos/no_existing_pr/response/pulls": + return MockResponse({"html_url": "great_success"}, 201, url) + + return MockResponse({}, 404, url) + + +class TestModules(TestPipelines): """Class for modules tests""" def setUp(self): - """Create a new pipeline to test""" - self.tmp_dir = tempfile.mkdtemp() - self.pipeline_dir = os.path.join(self.tmp_dir, "testpipeline") - default_branch = "master" - self.create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testing", - "test pipeline", - "tester", - outdir=self.pipeline_dir, - default_branch=default_branch, - ) - self.create_obj.init_pipeline() - self.remote_path = os.path.join(self.tmp_dir, "remote_repo") + super().setUp() + self.remote_path = Path(self.tmp_dir, "remote_repo") self.remote_repo = git.Repo.init(self.remote_path, bare=True) if self.remote_repo.active_branch.name != "master": - self.remote_repo.active_branch.rename(default_branch) - - def tearDown(self): - if os.path.exists(self.tmp_dir): - shutil.rmtree(self.tmp_dir) + self.remote_repo.active_branch.rename("master") @with_temporary_folder - def test_inspect_sync_dir_notgit(self, tmp_dir): + def test_inspect_sync_dir_notgit(self, tmp_dir: str): """Try syncing an empty directory""" + nf_core_yml_path = Path(tmp_dir, ".nf-core.yml") + nf_core_yml = NFCoreYamlConfig(repository_type="pipeline") + + with open(nf_core_yml_path, "w") as fh: + yaml.dump(nf_core_yml.model_dump(), fh) + psync = nf_core.pipelines.sync.PipelineSync(tmp_dir) with pytest.raises(nf_core.pipelines.sync.SyncExceptionError) as exc_info: psync.inspect_sync_dir() @@ -227,88 +281,6 @@ def test_push_merge_branch_without_create_branch(self): psync.push_merge_branch() assert exc_info.value.args[0].startswith(f"Could not push branch '{psync.merge_branch}'") - def mocked_requests_get(url, **kwargs): - """Helper function to emulate POST requests responses from the web""" - - class MockResponse: - def __init__(self, data, status_code): - self.url = kwargs.get("url") - self.status_code = status_code - self.from_cache = False - self.reason = "Mocked response" - self.data = data - self.content = json.dumps(data) - self.headers = {"content-encoding": "test", "connection": "fake"} - - def json(self): - return self.data - - url_template = "https://api.github.com/repos/{}/response/" - if url == os.path.join(url_template.format("no_existing_pr"), "pulls?head=TEMPLATE&base=None"): - response_data = [] - return MockResponse(response_data, 200) - if url == os.path.join(url_template.format("list_prs"), "pulls"): - response_data = [ - { - "state": "closed", - "head": {"ref": "nf-core-template-merge-2"}, - "base": {"ref": "master"}, - "html_url": "pr_url", - } - ] + [ - { - "state": "open", - "head": {"ref": f"nf-core-template-merge-{branch_no}"}, - "base": {"ref": "master"}, - "html_url": "pr_url", - } - for branch_no in range(3, 7) - ] - return MockResponse(response_data, 200) - - return MockResponse({"html_url": url}, 404) - - def mocked_requests_patch(url, **kwargs): - """Helper function to emulate POST requests responses from the web""" - - class MockResponse: - def __init__(self, data, status_code): - self.url = kwargs.get("url") - self.status_code = status_code - self.from_cache = False - self.reason = "Mocked" - self.content = json.dumps(data) - self.headers = {"content-encoding": "test", "connection": "fake"} - - if url == "url_to_update_pr": - response_data = {"html_url": "great_success"} - return MockResponse(response_data, 200) - - return MockResponse({"patch_url": url}, 404) - - def mocked_requests_post(url, **kwargs): - """Helper function to emulate POST requests responses from the web""" - - class MockResponse: - def __init__(self, data, status_code): - self.url = kwargs.get("url") - self.status_code = status_code - self.from_cache = False - self.reason = "Mocked" - self.data = data - self.content = json.dumps(data) - self.headers = {"content-encoding": "test", "connection": "fake"} - - def json(self): - return self.data - - if url == "https://api.github.com/repos/no_existing_pr/response/pulls": - response_data = {"html_url": "great_success"} - return MockResponse(response_data, 201) - - response_data = {} - return MockResponse(response_data, 404) - @mock.patch("nf_core.utils.gh_api.get", side_effect=mocked_requests_get) @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) def test_make_pull_request_success(self, mock_post, mock_get): @@ -354,7 +326,7 @@ def test_close_open_template_merge_prs(self, mock_get): prs = mock_get(f"https://api.github.com/repos/{psync.gh_repo}/pulls").data for pr in prs: - if pr["state"] == "open": + if pr.get("state", None) == "open": mock_close_open_pr.assert_any_call(pr) @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @@ -368,7 +340,7 @@ def test_close_open_pr(self, mock_patch, mock_post): psync.gh_username = "bad_url" psync.gh_repo = "bad_url/response" os.environ["GITHUB_AUTH_TOKEN"] = "test" - pr = { + pr: Dict[str, Union[str, Dict[str, str]]] = { "state": "open", "head": {"ref": "nf-core-template-merge-3"}, "base": {"ref": "master"}, diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py index 38bcc2b2c0..2693008707 100644 --- a/tests/subworkflows/test_lint.py +++ b/tests/subworkflows/test_lint.py @@ -291,10 +291,6 @@ def test_subworkflows_absent_version(self): with open(snap_file, "w") as fh: fh.write(new_content) - import ipdb - - ipdb.set_trace() - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0 @@ -312,31 +308,33 @@ def test_subworkflows_missing_test_dir(self): test_dir_copy = shutil.copytree(test_dir, test_dir.parent / "tests_copy") shutil.rmtree(test_dir) - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(self.nfcore_modules) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 0 + assert len(subworkflow_lint.failed) == 1 assert len(subworkflow_lint.passed) > 0 assert len(subworkflow_lint.warned) >= 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}" - assert any([x.lint_test == "test_dir_versions" for x in subworkflow_lint.warned]) + assert any([x.lint_test == "test_dir_exists" for x in subworkflow_lint.failed]) # cleanup shutil.copytree(test_dir_copy, test_dir) - def test_subworkflows_missing_main_nf(self): - """Test linting a nf-test subworkflow if the main.nf file is missing""" - main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf") - main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy") - main_nf.unlink() - - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) - subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") - assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" - assert len(subworkflow_lint.passed) > 0 - assert len(subworkflow_lint.warned) >= 0 - assert subworkflow_lint.failed[0].lint_test == "main_nf_exists" - - # cleanup - shutil.copy(main_nf_copy, main_nf) + # There are many steps before the actual main_nf linting where we rely on the main_nf file to exist, so this test is not possible for now + # def test_subworkflows_missing_main_nf(self): + # """Test linting a nf-test subworkflow if the main.nf file is missing""" + + # subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules) + # main_nf = Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "main.nf") + # main_nf_copy = shutil.copy(main_nf, main_nf.parent / "main_nf_copy") + # main_nf.unlink() + # subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + # assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + # assert len(subworkflow_lint.passed) > 0 + # assert len(subworkflow_lint.warned) >= 0 + # assert subworkflow_lint.failed[0].lint_test == "main_nf_exists" + + # # cleanup + # shutil.copy(main_nf_copy, main_nf) + # shutil.rmtree(Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow_backup")) def test_subworkflows_empty_file_in_snapshot(self): """Test linting a nf-test subworkflow with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" From 178146f75baf6322e36a752c234c628dde9953c5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:34:26 +0200 Subject: [PATCH 188/574] fix export of pydantic models --- nf_core/components/components_command.py | 5 +- nf_core/components/update.py | 52 +++++----- nf_core/modules/modules_repo.py | 1 + nf_core/pipelines/create/create.py | 15 +-- nf_core/pipelines/lint_utils.py | 10 +- nf_core/utils.py | 50 ++++++---- tests/pipelines/lint/test_nextflow_config.py | 15 ++- tests/subworkflows/test_update.py | 20 ++-- tests/test_modules.py | 44 ++++----- tests/test_utils.py | 99 +++++++------------- tests/utils.py | 29 +++++- 11 files changed, 182 insertions(+), 158 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 13a6fed338..a6b46d1b61 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -181,7 +181,10 @@ def load_lint_config(self) -> None: Add parsed config to the `self.lint_config` class attribute. """ _, tools_config = nf_core.utils.load_tools_config(self.directory) - self.lint_config = tools_config.get("lint", {}) + if tools_config is None: + raise UserWarning("Could not load `.nf-core.yml` file.") + else: + self.lint_config = tools_config.get("lint", {}) def check_modules_structure(self) -> None: """ diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 9b24b6c0c9..eb15f976bf 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -97,11 +97,7 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr updated = [] _, tool_config = nf_core.utils.load_tools_config(self.directory) - self.update_config = tool_config.get("update", {}) - - if self.update_config is None: - raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory") - + self.update_config = getattr(tool_config, "update", {}) or {} self._parameter_checks() # Check modules directory structure @@ -396,27 +392,26 @@ def get_single_component_info(self, component): sha = self.sha config_entry = None - if self.update_config is None: - raise UserWarning("Could not find '.nf-core.yml' file in pipeline directory") - if any( - [ - entry.count("/") == 1 - and (entry.endswith("modules") or entry.endswith("subworkflows")) - and not (entry.endswith(".git") or entry.endswith(".git/")) - for entry in self.update_config.keys() - ] - ): - raise UserWarning( - "Your '.nf-core.yml' file format is outdated. " - "The format should be of the form:\n" - "update:\n :\n :\n :" - ) - if isinstance(self.update_config.get(self.modules_repo.remote_url, {}), str): - # If the repo entry is a string, it's the sha to update to - config_entry = self.update_config.get(self.modules_repo.remote_url, {}) - elif component in self.update_config.get(self.modules_repo.remote_url, {}).get(install_dir, {}): - # If the component to update is in .nf-core.yml config file - config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component) + if self.update_config is not None: + if any( + [ + entry.count("/") == 1 + and (entry.endswith("modules") or entry.endswith("subworkflows")) + and not (entry.endswith(".git") or entry.endswith(".git/")) + for entry in self.update_config.keys() + ] + ): + raise UserWarning( + "Your '.nf-core.yml' file format is outdated. " + "The format should be of the form:\n" + "update:\n :\n :\n :" + ) + if isinstance(self.update_config.get(self.modules_repo.remote_url, {}), str): + # If the repo entry is a string, it's the sha to update to + config_entry = self.update_config.get(self.modules_repo.remote_url, {}) + elif component in self.update_config.get(self.modules_repo.remote_url, {}).get(install_dir, {}): + # If the component to update is in .nf-core.yml config file + config_entry = self.update_config[self.modules_repo.remote_url][install_dir].get(component) if config_entry is not None and config_entry is not True: if config_entry is False: log.warn( @@ -481,6 +476,7 @@ def get_all_components_info(self, branch=None): components_info = {} # Loop through all the modules/subworkflows in the pipeline # and check if they have an entry in the '.nf-core.yml' file + for repo_name, components in self.modules_json.get_all_components(self.component_type).items(): if isinstance(self.update_config, dict) and ( repo_name not in self.update_config or self.update_config[repo_name] is True @@ -630,10 +626,8 @@ def get_all_components_info(self, branch=None): overridden_repos.append(repo_name) elif isinstance(self.update_config, dict) and self.update_config[repo_name] is False: skipped_repos.append(repo_name) - elif not isinstance(self.update_config, dict): - raise UserWarning("`.nf-core.yml` is not correctly formatted.") else: - raise UserWarning(f"Repo '{repo_name}' has an invalid entry in '.nf-core.yml'") + log.debug(f"no update config for {repo_name} in `.nf-core.yml`") if skipped_repos: skipped_str = "', '".join(skipped_repos) diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index daa7b59811..7d576d4aef 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -63,6 +63,7 @@ def __init__( self.setup_local_repo(remote_url, branch, hide_progress) config_fn, repo_config = load_tools_config(self.local_repo_dir) + assert config_fn is not None and repo_config is not None # mypy try: self.repo_path = repo_config["org_path"] except KeyError: diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index b7d86c5bd7..deeb5554af 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -376,13 +376,14 @@ def render_template(self): if self.config: config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) - with open(config_fn, "w") as fh: - config_yml.update(template=self.config.model_dump()) - # convert posix path to string for yaml dump - config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"]) - yaml.safe_dump(config_yml, fh) - log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") - run_prettier_on_file(self.outdir / config_fn) + if config_fn is not None and config_yml is not None: + with open(str(config_fn), "w") as fh: + config_yml.template = self.config.model_dump() + # convert posix path to string for yaml dump + config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"]) + yaml.safe_dump(config_yml.model_dump(), fh) + log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") + run_prettier_on_file(self.outdir / config_fn) def update_nextflow_schema(self): """ diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py index 4ccf790076..ccab76295f 100644 --- a/nf_core/pipelines/lint_utils.py +++ b/nf_core/pipelines/lint_utils.py @@ -110,9 +110,13 @@ def ignore_file(lint_name: str, file_path: Path, dir_path: Path) -> List[List[st passed: List[str] = [] failed: List[str] = [] ignored: List[str] = [] - _, lint_conf = nf_core.utils.load_tools_config(dir_path) - lint_conf = lint_conf.get("lint", {}) - ignore_entry: List[str] | bool = lint_conf.get(lint_name, []) + _, pipeline_conf = nf_core.utils.load_tools_config(dir_path) + lint_conf = getattr(pipeline_conf, "lint", None) or None + + if lint_conf is None: + ignore_entry: List[str] = [] + else: + ignore_entry = lint_conf.get(lint_name, []) full_path = dir_path / file_path # Return a failed status if we can't find the file if not full_path.is_file(): diff --git a/nf_core/utils.py b/nf_core/utils.py index 4d0566b1af..6794cf04fe 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -19,7 +19,7 @@ import time from contextlib import contextmanager from pathlib import Path -from typing import Dict, Generator, List, Optional, Tuple, Union +from typing import Any, Dict, Generator, List, Optional, Tuple, Union import git import prompt_toolkit.styles @@ -1042,25 +1042,37 @@ def get_repo_releases_branches(pipeline, wfs): class NFCoreTemplateConfig(BaseModel): - org: str - name: str - description: str - author: str - version: Optional[str] - force: Optional[bool] - outdir: Optional[str] - skip_features: Optional[list] - is_nfcore: Optional[bool] + org: Optional[str] = None + name: Optional[str] = None + description: Optional[str] = None + author: Optional[str] = None + version: Optional[str] = None + force: Optional[bool] = None + outdir: Optional[str] = None + skip_features: Optional[list] = None + is_nfcore: Optional[bool] = None + + +LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]] class NFCoreYamlConfig(BaseModel): - nf_core_version: str repository_type: str - org_path: str - template: NFCoreTemplateConfig + nf_core_version: Optional[str] = None + org_path: Optional[str] = None + lint: LintConfigType = None + template: Optional[NFCoreTemplateConfig] = None + bump_version: Optional[Dict[str, bool]] = None + update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None + + def __getitem__(self, item: str) -> Any: + return getattr(self, item) + + def get(self, item: str, default: Any = None) -> Any: + return getattr(self, item, default) -def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYamlConfig]: +def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path], Optional[NFCoreYamlConfig]]: """ Parse the nf-core.yml configuration file @@ -1078,11 +1090,12 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYa if config_fn is None: depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS) if depr_path: - raise AssertionError( + raise UserWarning( f"Deprecated `{depr_path.name}` file found! Please rename the file to `{CONFIG_PATHS[0]}`." ) else: - raise AssertionError(f"Could not find a config file in the directory '{directory}'") + log.debug(f"Could not find a config file in the directory '{directory}'") + return Path(directory, CONFIG_PATHS[0]), None with open(str(config_fn)) as fh: tools_config = yaml.safe_load(fh) @@ -1094,7 +1107,10 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Path, NFCoreYa try: nf_core_yaml_config = NFCoreYamlConfig(**tools_config) except ValidationError as e: - raise AssertionError(f"Config file '{config_fn}' is invalid: {e}") + error_message = f"Config file '{config_fn}' is invalid" + for error in e.errors(): + error_message += f"\n{error['loc'][0]}: {error['msg']}" + raise AssertionError(error_message) log.debug("Using config file: %s", config_fn) return config_fn, nf_core_yaml_config diff --git a/tests/pipelines/lint/test_nextflow_config.py b/tests/pipelines/lint/test_nextflow_config.py index 01173aec34..3cc9355452 100644 --- a/tests/pipelines/lint/test_nextflow_config.py +++ b/tests/pipelines/lint/test_nextflow_config.py @@ -2,8 +2,11 @@ import re from pathlib import Path +import yaml + import nf_core.pipelines.create.create import nf_core.pipelines.lint +from nf_core.utils import NFCoreYamlConfig from ..test_lint import TestLint @@ -124,11 +127,13 @@ def test_allow_params_reference_in_main_nf(self): def test_default_values_ignored(self): """Test ignoring linting of default values.""" # Add max_cpus to the ignore list - nf_core_yml = Path(self.new_pipeline) / ".nf-core.yml" - with open(nf_core_yml, "w") as f: - f.write( - "repository_type: pipeline\nlint:\n nextflow_config:\n - config_defaults:\n - params.max_cpus\n" - ) + nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml" + nf_core_yml = NFCoreYamlConfig( + repository_type="pipeline", lint={"nextflow_config": [{"config_defaults": ["params.max_cpus"]}]} + ) + with open(nf_core_yml_path, "w") as f: + yaml.dump(nf_core_yml.model_dump(), f) + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) lint_obj.load_pipeline_config() lint_obj._load_lint_config() diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py index d3b2433572..7b17a621bc 100644 --- a/tests/subworkflows/test_update.py +++ b/tests/subworkflows/test_update.py @@ -156,9 +156,10 @@ def test_update_with_config_fixed_version(self): # Fix the subworkflow version in the .nf-core.yml to an old version update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": OLD_SUBWORKFLOWS_SHA}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all subworkflows in the pipeline update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) @@ -186,9 +187,10 @@ def test_update_with_config_dont_update(self): # Set the fastq_align_bowtie2 field to no update in the .nf-core.yml update_config = {NF_CORE_MODULES_REMOTE: {NF_CORE_MODULES_NAME: {"fastq_align_bowtie2": False}}} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all modules in the pipeline update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) @@ -216,9 +218,10 @@ def test_update_with_config_fix_all(self): # Fix the version of all nf-core subworkflows in the .nf-core.yml to an old version update_config = {NF_CORE_MODULES_REMOTE: OLD_SUBWORKFLOWS_SHA} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update fastq_align_bowtie2 update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=False, update_deps=True, show_diff=False) @@ -246,9 +249,10 @@ def test_update_with_config_no_updates(self): # Set all repository updates to False update_config = {NF_CORE_MODULES_REMOTE: False} config_fn, tools_config = nf_core.utils.load_tools_config(self.pipeline_dir) - tools_config["update"] = update_config + setattr(tools_config, "update", update_config) + assert config_fn is not None and tools_config is not None # mypy with open(Path(self.pipeline_dir, config_fn), "w") as f: - yaml.dump(tools_config, f) + yaml.dump(tools_config.model_dump(), f) # Update all subworkflows in the pipeline update_obj = SubworkflowUpdate(self.pipeline_dir, update_all=True, show_diff=False) diff --git a/tests/test_modules.py b/tests/test_modules.py index 13bf32f971..9ce74fd4e1 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -1,8 +1,6 @@ """Tests covering the modules commands""" import json -import os -import shutil import unittest from pathlib import Path @@ -12,7 +10,13 @@ import yaml import nf_core.modules +import nf_core.modules.create +import nf_core.modules.install +import nf_core.modules.modules_repo +import nf_core.modules.remove import nf_core.pipelines.create.create +from nf_core import __version__ +from nf_core.utils import NFCoreYamlConfig from .utils import ( GITLAB_BRANCH_TEST_BRANCH, @@ -34,24 +38,28 @@ def create_modules_repo_dummy(tmp_dir): Path(root_dir, "modules", "nf-core").mkdir(parents=True) Path(root_dir, "tests", "modules", "nf-core").mkdir(parents=True) Path(root_dir, "tests", "config").mkdir(parents=True) + + nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core") with open(Path(root_dir, ".nf-core.yml"), "w") as fh: - fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"]) + yaml.dump(nf_core_yml.model_dump(), fh) # mock biocontainers and anaconda response with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules - module_create = nf_core.modules.ModuleCreate(root_dir, "bpipe/test", "@author", "process_single", False, False) + module_create = nf_core.modules.create.ModuleCreate( + root_dir, "bpipe/test", "@author", "process_single", False, False + ) with requests_cache.disabled(): - module_create.create() + assert module_create.create() # Remove doi from meta.yml which makes lint fail meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml") - with open(meta_yml_path) as fh: + with open(str(meta_yml_path)) as fh: meta_yml = yaml.safe_load(fh) del meta_yml["tools"][0]["bpipe"]["doi"] - with open(meta_yml_path, "w") as fh: + with open(str(meta_yml_path), "w") as fh: yaml.dump(meta_yml, fh) # Add dummy content to main.nf.test.snap test_snap_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap") @@ -102,8 +110,8 @@ def setUp(self): self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline() # Set up install objects - self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True) - self.mods_install_old = nf_core.modules.ModuleInstall( + self.mods_install = nf_core.modules.install.ModuleInstall(self.pipeline_dir, prompt=False, force=True) + self.mods_install_old = nf_core.modules.install.ModuleInstall( self.pipeline_dir, prompt=False, force=False, @@ -111,21 +119,21 @@ def setUp(self): remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH, ) - self.mods_install_trimgalore = nf_core.modules.ModuleInstall( + self.mods_install_trimgalore = nf_core.modules.install.ModuleInstall( self.pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH, ) - self.mods_install_gitlab = nf_core.modules.ModuleInstall( + self.mods_install_gitlab = nf_core.modules.install.ModuleInstall( self.pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH, ) - self.mods_install_gitlab_old = nf_core.modules.ModuleInstall( + self.mods_install_gitlab_old = nf_core.modules.install.ModuleInstall( self.pipeline_dir, prompt=False, force=False, @@ -135,8 +143,8 @@ def setUp(self): ) # Set up remove objects - self.mods_remove = nf_core.modules.ModuleRemove(self.pipeline_dir) - self.mods_remove_gitlab = nf_core.modules.ModuleRemove( + self.mods_remove = nf_core.modules.remove.ModuleRemove(self.pipeline_dir) + self.mods_remove_gitlab = nf_core.modules.remove.ModuleRemove( self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH, @@ -145,15 +153,9 @@ def setUp(self): # Set up the nf-core/modules repo dummy self.nfcore_modules = create_modules_repo_dummy(self.tmp_dir) - def tearDown(self): - """Clean up temporary files and folders""" - - if os.path.exists(self.tmp_dir): - shutil.rmtree(self.tmp_dir) - def test_modulesrepo_class(self): """Initialise a modules repo object""" - modrepo = nf_core.modules.ModulesRepo() + modrepo = nf_core.modules.modules_repo.ModulesRepo() assert modrepo.repo_path == "nf-core" assert modrepo.branch == "master" diff --git a/tests/test_utils.py b/tests/test_utils.py index 860cba5ba6..0d012716a9 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,9 +1,6 @@ """Tests covering for utility functions.""" import os -import shutil -import tempfile -import unittest from pathlib import Path from unittest import mock @@ -14,6 +11,7 @@ import nf_core.pipelines.list import nf_core.utils +from .test_pipelines import TestPipelines from .utils import with_temporary_folder TEST_DATA_DIR = Path(__file__).parent / "data" @@ -28,31 +26,9 @@ def test_strip_ansi_codes(): assert stripped == "ls examplefile.zip" -class TestUtils(unittest.TestCase): +class TestUtils(TestPipelines): """Class for utils tests""" - def setUp(self): - """Function that runs at start of tests for common resources - - Use nf_core.pipelines.create() to make a pipeline that we can use for testing - """ - self.tmp_dir = tempfile.mkdtemp() - self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline") - self.create_obj = nf_core.pipelines.create.create.PipelineCreate( - "testpipeline", - "This is a test pipeline", - "Test McTestFace", - no_git=True, - outdir=self.test_pipeline_dir, - ) - self.create_obj.init_pipeline() - # Base Pipeline object on this directory - self.pipeline_obj = nf_core.utils.Pipeline(self.test_pipeline_dir) - - def tearDown(self): - if os.path.exists(self.tmp_dir): - shutil.rmtree(self.tmp_dir) - def test_check_if_outdated_1(self): current_version = "1.0" remote_version = "2.0" @@ -110,7 +86,7 @@ def testload_pipeline_config(self): def test_list_files_git(self): """Test listing pipeline files using `git ls`""" files = self.pipeline_obj.list_files() - assert Path(self.test_pipeline_dir, "main.nf") in files + assert Path(self.pipeline_dir, "main.nf") in files @with_temporary_folder def test_list_files_no_git(self, tmpdir): @@ -193,46 +169,39 @@ def test_get_repo_releases_branches_not_exists_slash(self): with pytest.raises(AssertionError): nf_core.utils.get_repo_releases_branches("made-up/pipeline", wfs) - -def test_validate_file_md5(): - # MD5(test) = d8e8fca2dc0f896fd7cb4cb0031ba249 - test_file = TEST_DATA_DIR / "test.txt" - test_file_md5 = "d8e8fca2dc0f896fd7cb4cb0031ba249" - different_md5 = "9e7b964750cf0bb08ee960fce356b6d6" - non_hex_string = "s" - assert nf_core.utils.validate_file_md5(test_file, test_file_md5) - with pytest.raises(IOError): - nf_core.utils.validate_file_md5(test_file, different_md5) - with pytest.raises(ValueError): - nf_core.utils.validate_file_md5(test_file, non_hex_string) - - -def test_nested_setitem(): - d = {"a": {"b": {"c": "value"}}} - nf_core.utils.nested_setitem(d, ["a", "b", "c"], "value new") - assert d["a"]["b"]["c"] == "value new" - assert d == {"a": {"b": {"c": "value new"}}} - - -def test_nested_delitem(): - d = {"a": {"b": {"c": "value"}}} - nf_core.utils.nested_delitem(d, ["a", "b", "c"]) - assert "c" not in d["a"]["b"] - assert d == {"a": {"b": {}}} - - -def test_set_wd(): - with tempfile.TemporaryDirectory() as tmpdirname: - with nf_core.utils.set_wd(tmpdirname): + def test_validate_file_md5(self): + # MD5(test) = d8e8fca2dc0f896fd7cb4cb0031ba249 + test_file = TEST_DATA_DIR / "test.txt" + test_file_md5 = "d8e8fca2dc0f896fd7cb4cb0031ba249" + different_md5 = "9e7b964750cf0bb08ee960fce356b6d6" + non_hex_string = "s" + assert nf_core.utils.validate_file_md5(test_file, test_file_md5) + with pytest.raises(IOError): + nf_core.utils.validate_file_md5(test_file, different_md5) + with pytest.raises(ValueError): + nf_core.utils.validate_file_md5(test_file, non_hex_string) + + def test_nested_setitem(self): + d = {"a": {"b": {"c": "value"}}} + nf_core.utils.nested_setitem(d, ["a", "b", "c"], "value new") + assert d["a"]["b"]["c"] == "value new" + assert d == {"a": {"b": {"c": "value new"}}} + + def test_nested_delitem(self): + d = {"a": {"b": {"c": "value"}}} + nf_core.utils.nested_delitem(d, ["a", "b", "c"]) + assert "c" not in d["a"]["b"] + assert d == {"a": {"b": {}}} + + def test_set_wd(self): + with nf_core.utils.set_wd(self.tmp_dir): context_wd = Path().resolve() - assert context_wd == Path(tmpdirname).resolve() + assert context_wd == Path(self.tmp_dir).resolve() assert context_wd != Path().resolve() - -def test_set_wd_revert_on_raise(): - wd_before_context = Path().resolve() - with tempfile.TemporaryDirectory() as tmpdirname: + def test_set_wd_revert_on_raise(self): + wd_before_context = Path().resolve() with pytest.raises(Exception): - with nf_core.utils.set_wd(tmpdirname): + with nf_core.utils.set_wd(self.tmp_dir): raise Exception - assert wd_before_context == Path().resolve() + assert wd_before_context == Path().resolve() diff --git a/tests/utils.py b/tests/utils.py index 90c4ae0418..1d5a8a115d 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -9,9 +9,12 @@ from typing import Any, Callable, Tuple import responses +import yaml import nf_core.modules import nf_core.pipelines.create.create +from nf_core import __version__ +from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlConfig TEST_DATA_DIR = Path(__file__).parent / "data" OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386" @@ -95,7 +98,7 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200) -def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: +def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: """Create a new Pipeline for testing""" tmp_dir = Path(tempfile.TemporaryDirectory().name) @@ -103,9 +106,31 @@ def create_tmp_pipeline() -> Tuple[Path, Path, str, Path]: template_dir = root_repo_dir / "nf_core" / "pipeline-template" pipeline_name = "mypipeline" pipeline_dir = tmp_dir / pipeline_name + pipeline_dir.mkdir(parents=True) + + nf_core_yml = NFCoreYamlConfig( + nf_core_version=__version__, + repository_type="modules", + org_path="nf-core", + lint=None, + template=NFCoreTemplateConfig( + name="mypipeline", + author="me", + description="it is mine", + org="nf-core", + version=None, + force=True, + is_nfcore=None, + skip_features=None, + outdir=None, + ), + bump_version=None, + ) + with open(str(Path(pipeline_dir, ".nf-core.yml")), "w") as fh: + yaml.dump(nf_core_yml.model_dump(), fh) nf_core.pipelines.create.create.PipelineCreate( - pipeline_name, "it is mine", "me", no_git=False, outdir=pipeline_dir + pipeline_name, "it is mine", "me", no_git=no_git, outdir=pipeline_dir, force=True ).init_pipeline() # return values to instance variables for later use in test methods From d0a968ceb3ffe85e87303cc0d63838dbbc6a71b9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:35:06 +0200 Subject: [PATCH 189/574] fix tests --- nf_core/modules/lint/__init__.py | 4 +- nf_core/pipelines/lint/files_exist.py | 2 +- nf_core/pipelines/lint/nfcore_yml.py | 3 +- nf_core/pipelines/lint/schema_description.py | 2 +- nf_core/pipelines/lint/template_strings.py | 2 +- nf_core/pipelines/sync.py | 45 ++++++++++--------- .../subworkflows/lint/subworkflow_tests.py | 11 +++-- tests/modules/test_modules_json.py | 2 +- tests/pipelines/test_lint.py | 4 +- 9 files changed, 39 insertions(+), 36 deletions(-) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index 2b10b4df5a..cea75d8f2e 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -228,7 +228,7 @@ def lint_module( # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class # Only check the main script in case of a local module if local: - self.main_nf(mod, fix_version, self.registry, progress_bar) + self.main_nf(mod, fix_version, registry, progress_bar) self.passed += [LintResult(mod, *m) for m in mod.passed] warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)] if not self.fail_warned: @@ -245,7 +245,7 @@ def lint_module( for test_name in self.lint_tests: if test_name == "main_nf": - getattr(self, test_name)(mod, fix_version, self.registry, progress_bar) + getattr(self, test_name)(mod, fix_version, registry, progress_bar) else: getattr(self, test_name)(mod) diff --git a/nf_core/pipelines/lint/files_exist.py b/nf_core/pipelines/lint/files_exist.py index edad62aab8..ad0605dcf7 100644 --- a/nf_core/pipelines/lint/files_exist.py +++ b/nf_core/pipelines/lint/files_exist.py @@ -205,7 +205,7 @@ def files_exist(self) -> Dict[str, List[str]]: ] # Remove files that should be ignored according to the linting config - ignore_files = self.lint_config.get("files_exist", []) + ignore_files = self.lint_config.get("files_exist", []) if self.lint_config is not None else [] def pf(file_path: Union[str, Path]) -> Path: return Path(self.wf_path, file_path) diff --git a/nf_core/pipelines/lint/nfcore_yml.py b/nf_core/pipelines/lint/nfcore_yml.py index f23b2f1a84..e0d5fb2005 100644 --- a/nf_core/pipelines/lint/nfcore_yml.py +++ b/nf_core/pipelines/lint/nfcore_yml.py @@ -27,8 +27,7 @@ def nfcore_yml(self) -> Dict[str, List[str]]: ignored: List[str] = [] # Remove field that should be ignored according to the linting config - ignore_configs = self.lint_config.get(".nf-core", []) - + ignore_configs = self.lint_config.get(".nf-core", []) if self.lint_config is not None else [] try: with open(Path(self.wf_path, ".nf-core.yml")) as fh: content = fh.read() diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py index 82165b6e7d..d617e40949 100644 --- a/nf_core/pipelines/lint/schema_description.py +++ b/nf_core/pipelines/lint/schema_description.py @@ -24,7 +24,7 @@ def schema_description(self): self.schema_obj.load_lint_schema() # Get parameters that should be ignored according to the linting config - ignore_params = self.lint_config.get("schema_description", []) + ignore_params = self.lint_config.get("schema_description", []) if self.lint_config is not None else [] # Get ungrouped params if "properties" in self.schema_obj.schema.keys(): diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py index 90c47203f6..37a1f64daf 100644 --- a/nf_core/pipelines/lint/template_strings.py +++ b/nf_core/pipelines/lint/template_strings.py @@ -38,7 +38,7 @@ def template_strings(self): failed = [] ignored = [] # Files that should be ignored according to the linting config - ignore_files = self.lint_config.get("template_strings", []) + ignore_files = self.lint_config.get("template_strings", []) if self.lint_config is not None else [] files = self.list_files() # Loop through files, searching for string diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index a309fa8c3b..b1da99a626 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -10,6 +10,7 @@ import git import questionary import requests +import requests.auth import requests_cache import rich import yaml @@ -86,23 +87,23 @@ def __init__( self.pr_url = "" self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config(self.pipeline_dir) - + assert self.config_yml_path is not None # mypy # Throw deprecation warning if template_yaml_path is set if template_yaml_path is not None: log.warning( f"The `template_yaml_path` argument is deprecated. Saving pipeline creation settings in .nf-core.yml instead. Please remove {template_yaml_path} file." ) - if "template" in self.config_yml: + if getattr(self.config_yml, "template", None) is not None: overwrite_template = questionary.confirm( f"A template section already exists in '{self.config_yml_path}'. Do you want to overwrite?", style=nf_core.utils.nfcore_question_style, default=False, ).unsafe_ask() - if overwrite_template or "template" not in self.config_yml: + if overwrite_template or getattr(self.config_yml, "template", None) is None: with open(template_yaml_path) as f: - self.config_yml["template"] = yaml.safe_load(f) + self.config_yml.template = yaml.safe_load(f) with open(self.config_yml_path, "w") as fh: - yaml.safe_dump(self.config_yml, fh) + yaml.safe_dump(self.config_yml.model_dump(), fh) log.info(f"Saved pipeline creation settings to '{self.config_yml_path}'") raise SystemExit( f"Please commit your changes and delete the {template_yaml_path} file. Then run the sync command again." @@ -259,11 +260,12 @@ def make_template_pipeline(self): # Only show error messages from pipeline creation logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR) - + assert self.config_yml_path is not None + assert self.config_yml is not None # Re-write the template yaml info from .nf-core.yml config - if "template" in self.config_yml: + if getattr(self.config_yml, "template", None) is not None: with open(self.config_yml_path, "w") as config_path: - yaml.safe_dump(self.config_yml, config_path) + yaml.safe_dump(self.config_yml.model_dump(), config_path) try: nf_core.pipelines.create.create.PipelineCreate( @@ -411,21 +413,24 @@ def close_open_template_merge_prs(self): return False for pr in list_prs_json: - log.debug(f"Looking at PR from '{pr['head']['ref']}': {pr['html_url']}") - # Ignore closed PRs - if pr["state"] != "open": - log.debug(f"Ignoring PR as state not open ({pr['state']}): {pr['html_url']}") - continue + if isinstance(pr, int): + log.debug(f"Incorrect PR format: {pr}") + else: + log.debug(f"Looking at PR from '{pr['head']['ref']}': {pr['html_url']}") + # Ignore closed PRs + if pr["state"] != "open": + log.debug(f"Ignoring PR as state not open ({pr['state']}): {pr['html_url']}") + continue - # Don't close the new PR that we just opened - if pr["head"]["ref"] == self.merge_branch: - continue + # Don't close the new PR that we just opened + if pr["head"]["ref"] == self.merge_branch: + continue - # PR is from an automated branch and goes to our target base - if pr["head"]["ref"].startswith("nf-core-template-merge-") and pr["base"]["ref"] == self.from_branch: - self.close_open_pr(pr) + # PR is from an automated branch and goes to our target base + if pr["head"]["ref"].startswith("nf-core-template-merge-") and pr["base"]["ref"] == self.from_branch: + self.close_open_pr(pr) - def close_open_pr(self, pr): + def close_open_pr(self, pr) -> bool: """Given a PR API response, add a comment and close.""" log.debug(f"Attempting to close PR: '{pr['html_url']}'") diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py index af39334744..7ca825f04f 100644 --- a/nf_core/subworkflows/lint/subworkflow_tests.py +++ b/nf_core/subworkflows/lint/subworkflow_tests.py @@ -27,14 +27,14 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): repo_dir = subworkflow.component_dir.parts[ : subworkflow.component_dir.parts.index(subworkflow.component_name.split("/")[0]) ][-1] - test_dir = Path( + pytest_dir = Path( subworkflow.base_dir, "tests", "subworkflows", repo_dir, subworkflow.component_name, ) - pytest_main_nf = Path(test_dir, "main.nf") + pytest_main_nf = Path(pytest_dir, "main.nf") is_pytest = pytest_main_nf.is_file() log.debug(f"{pytest_main_nf} is pytest: {is_pytest}") if subworkflow.nftest_testdir.is_dir(): @@ -265,8 +265,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent): # Check that the old test directory does not exist if not is_pytest: - old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name) - if old_test_dir.is_dir(): - subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir)) + if pytest_dir.is_dir(): + subworkflow.failed.append(("test_old_test_dir", "old test directory exists", pytest_dir)) else: - subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir)) + subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", pytest_dir)) diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py index 2ab058fa70..845f9c3e34 100644 --- a/tests/modules/test_modules_json.py +++ b/tests/modules/test_modules_json.py @@ -220,7 +220,7 @@ def test_mod_json_with_empty_modules_value(self): mod_json_obj.create() # Create modules.json explicitly to get correct module sha mod_json_orig = mod_json_obj.get_modules_json() mod_json = copy.deepcopy(mod_json_orig) - mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = "" + mod_json["repos"][NF_CORE_MODULES_REMOTE]["modules"] = {} # save the altered module.json and load it again to check if it will fix itself mod_json_obj.modules_json = mod_json mod_json_obj.dump() diff --git a/tests/pipelines/test_lint.py b/tests/pipelines/test_lint.py index ab8bcf6b24..9ca29d249f 100644 --- a/tests/pipelines/test_lint.py +++ b/tests/pipelines/test_lint.py @@ -47,7 +47,7 @@ def test_init_pipeline_lint(self): def test_load_lint_config_not_found(self): """Try to load a linting config file that doesn't exist""" - self.lint_obj._load_lint_config() + assert self.lint_obj._load_lint_config() assert self.lint_obj.lint_config == {} def test_load_lint_config_ignore_all_tests(self): @@ -58,7 +58,7 @@ def test_load_lint_config_ignore_all_tests(self): lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline) # Make a config file listing all test names - config_dict = {"lint": {test_name: False for test_name in lint_obj.lint_tests}} + config_dict = {"repository_type": "pipeline", "lint": {test_name: False for test_name in lint_obj.lint_tests}} with open(Path(new_pipeline, ".nf-core.yml"), "w") as fh: yaml.dump(config_dict, fh) From 33f461aa5a3a888dd0914796c99b3201b2a06f3e Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:35:26 +0200 Subject: [PATCH 190/574] migrate to pathlib --- nf_core/modules/modules_json.py | 2 +- nf_core/pipelines/create/create.py | 2 +- tests/pipelines/test_create.py | 11 +++++++---- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 02ce6fa5a2..01785c6d65 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -1192,7 +1192,7 @@ def components_with_repos(): self.modules_dir, modules_repo.repo_path, ) - for dir_name, _, _ in os.walk(repo_url_path): + for dir_name, _, _ in Path.walk(repo_url_path): if component_type == "modules": if len(Path(directory).parts) > 1: # The module name is TOOL/SUBTOOL paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index deeb5554af..f032db7f69 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -516,7 +516,7 @@ def fix_linting(self): with open(self.outdir / config_fn, "w") as fh: yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False) - run_prettier_on_file(os.path.join(self.outdir, config_fn)) + run_prettier_on_file(Path(self.outdir, config_fn)) def make_pipeline_logo(self): """Fetch a logo for the new pipeline from the nf-core website""" diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py index bb27445e70..35cff5cab6 100644 --- a/tests/pipelines/test_create.py +++ b/tests/pipelines/test_create.py @@ -2,6 +2,7 @@ import os import unittest +from pathlib import Path import git import yaml @@ -22,7 +23,8 @@ def setUp(self): self.pipeline_version = "1.0.0" self.default_branch = "default" - def test_pipeline_creation(self): + @with_temporary_folder + def test_pipeline_creation(self, tmp_path): pipeline = nf_core.pipelines.create.create.PipelineCreate( name=self.pipeline_name, description=self.pipeline_description, @@ -30,6 +32,7 @@ def test_pipeline_creation(self): version=self.pipeline_version, no_git=False, force=True, + outdir=tmp_path, default_branch=self.default_branch, ) @@ -51,10 +54,10 @@ def test_pipeline_creation_initiation(self, tmp_path): default_branch=self.default_branch, ) pipeline.init_pipeline() - assert os.path.isdir(os.path.join(pipeline.outdir, ".git")) + assert Path(pipeline.outdir, ".git").is_dir() assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch() - assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml")) - with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh: + assert not Path(pipeline.outdir, "pipeline_template.yml").exists() + with open(Path(pipeline.outdir, ".nf-core.yml")) as fh: assert "template" in fh.read() @with_temporary_folder From 1473611b9025ec4221e91fdbe0709723c59962b8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:35:44 +0200 Subject: [PATCH 191/574] change import strategy for lint tests --- nf_core/subworkflows/lint/__init__.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index a073710884..b366ddfb51 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -19,6 +19,14 @@ log = logging.getLogger(__name__) +# Import lint functions +from .main_nf import main_nf # type: ignore[misc] +from .meta_yml import meta_yml # type: ignore[misc] +from .subworkflow_changes import subworkflow_changes # type: ignore[misc] +from .subworkflow_tests import subworkflow_tests # type: ignore[misc] +from .subworkflow_todos import subworkflow_todos # type: ignore[misc] +from .subworkflow_version import subworkflow_version # type: ignore[misc] + class SubworkflowLint(ComponentLint): """ @@ -26,13 +34,12 @@ class SubworkflowLint(ComponentLint): repository or in any nf-core pipeline directory """ - # Import lint functions - from .main_nf import main_nf # type: ignore[misc] - from .meta_yml import meta_yml # type: ignore[misc] - from .subworkflow_changes import subworkflow_changes # type: ignore[misc] - from .subworkflow_tests import subworkflow_tests # type: ignore[misc] - from .subworkflow_todos import subworkflow_todos # type: ignore[misc] - from .subworkflow_version import subworkflow_version # type: ignore[misc] + main_nf = main_nf + meta_yml = meta_yml + subworkflow_changes = subworkflow_changes + subworkflow_tests = subworkflow_tests + subworkflow_todos = subworkflow_todos + subworkflow_version = subworkflow_version def __init__( self, From 9dc61d61059bb2cb2b2bed4c7001251b01e863df Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 13:37:36 +0200 Subject: [PATCH 192/574] migrate to pathlib --- nf_core/components/components_command.py | 40 +++++++++++-------- nf_core/components/list.py | 3 +- nf_core/modules/modules_repo.py | 10 +++-- nf_core/pipelines/lint/actions_awsfulltest.py | 9 +++-- nf_core/pipelines/lint/actions_awstest.py | 6 +-- nf_core/pipelines/lint/actions_ci.py | 6 +-- .../lint/actions_schema_validation.py | 7 ++-- nf_core/pipelines/lint/files_unchanged.py | 8 ++-- nf_core/pipelines/lint/merge_markers.py | 32 +++++++-------- nf_core/pipelines/lint/modules_structure.py | 3 +- nf_core/pipelines/lint/nextflow_config.py | 19 ++++----- nf_core/pipelines/lint/pipeline_todos.py | 20 +++++----- nf_core/pipelines/lint/readme.py | 6 +-- 13 files changed, 90 insertions(+), 79 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index a6b46d1b61..4440dc32a4 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -1,6 +1,5 @@ import logging import mmap -import os import shutil from pathlib import Path from typing import Dict, List, Optional, Union @@ -22,7 +21,9 @@ class ComponentCommand: def __init__( self, component_type: str, - directory: Union[str, Path], + directory: Union[ + str, Path + ], # TODO: This is actually None sometimes (e.g. in test_modules_list_remote), need to rewrite the logic here to handle these cases elegantly, for example setting a default path remote_url: Optional[str] = None, branch: Optional[str] = None, no_pull: bool = False, @@ -33,7 +34,7 @@ def __init__( Initialise the ComponentClass object """ self.component_type = component_type - self.directory = Path(directory) + self.directory = directory self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.hide_progress = hide_progress self.no_prompts = no_prompts @@ -47,18 +48,21 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: Args: nf_dir_req (bool, optional): Whether this command requires being run in the nf-core modules repo or a nf-core pipeline repository. Defaults to True. """ - try: if self.directory: - self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts) + self.directory, self.repo_type, self.org = get_repo_info( + Path(self.directory), use_prompt=not self.no_prompts + ) else: self.repo_type = None self.org = "" + except UserWarning: if nf_dir_req: raise self.repo_type = None self.org = "" + self.default_modules_path = Path("modules", self.org) self.default_tests_path = Path("tests", "modules", self.org) self.default_subworkflows_path = Path("subworkflows", self.org) @@ -82,8 +86,8 @@ def get_components_clone_modules(self) -> List[str]: elif self.component_type == "subworkflows": component_base_path = Path(self.directory, self.default_subworkflows_path) return [ - str(Path(dir).relative_to(component_base_path)) - for dir, _, files in os.walk(component_base_path) + str(Path(directory).relative_to(component_base_path)) + for directory, _, files in Path.walk(component_base_path) if "main.nf" in files ] @@ -91,12 +95,12 @@ def has_valid_directory(self) -> bool: """Check that we were given a pipeline or clone of nf-core/modules""" if self.repo_type == "modules": return True - if self.directory is None or not os.path.exists(self.directory): + if self.directory is None or not Path(self.directory).exists(): log.error(f"Could not find directory: {self.directory}") return False - main_nf = os.path.join(self.directory, "main.nf") - nf_config = os.path.join(self.directory, "nextflow.config") - if not os.path.exists(main_nf) and not os.path.exists(nf_config): + main_nf = Path(self.directory, "main.nf") + nf_config = Path(self.directory, "nextflow.config") + if not main_nf.exists() and not nf_config.exists(): if Path(self.directory).resolve().parts[-1].startswith("nf-core"): raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") @@ -104,8 +108,8 @@ def has_valid_directory(self) -> bool: def has_modules_file(self) -> None: """Checks whether a module.json file has been created and creates one if it is missing""" - modules_json_path = os.path.join(self.directory, "modules.json") - if not os.path.exists(modules_json_path): + modules_json_path = Path(self.directory, "modules.json") + if not modules_json_path.exists(): log.info("Creating missing 'module.json' file.") ModulesJson(self.directory).create() @@ -122,10 +126,10 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False): + for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False): if not dir_names and not filenames: try: - os.rmdir(dir_path) + dir_path.rmdir() except OSError: pass else: @@ -152,7 +156,9 @@ def components_from_repo(self, install_dir: str) -> List[str]: raise LookupError(f"Nothing installed from {install_dir} in pipeline") return [ - str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files + str(Path(dir_path).relative_to(repo_dir)) + for dir_path, _, files in Path.walk(repo_dir) + if "main.nf" in files ] def install_component_files( @@ -196,7 +202,7 @@ def check_modules_structure(self) -> None: """ if self.repo_type == "pipeline": wrong_location_modules: List[Path] = [] - for directory, _, files in os.walk(Path(self.directory, "modules")): + for directory, _, files in Path.walk(Path(self.directory, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.directory, "modules")) parts = module_path.parts diff --git a/nf_core/components/list.py b/nf_core/components/list.py index 67468b4a5a..0a6b654467 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -1,5 +1,6 @@ import json import logging +from pathlib import Path from typing import Dict, List, Optional, Union, cast import rich.table @@ -15,7 +16,7 @@ class ComponentList(ComponentCommand): def __init__( self, component_type: str, - pipeline_dir: str, + pipeline_dir: Union[str, Path], remote: bool = True, remote_url: Optional[str] = None, branch: Optional[str] = None, diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index 7d576d4aef..bc92072e3b 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -63,16 +63,18 @@ def __init__( self.setup_local_repo(remote_url, branch, hide_progress) config_fn, repo_config = load_tools_config(self.local_repo_dir) - assert config_fn is not None and repo_config is not None # mypy + if config_fn is None or repo_config is None: + raise UserWarning(f"Could not find a configuration file in {self.local_repo_dir}") try: - self.repo_path = repo_config["org_path"] + self.repo_path = repo_config.org_path except KeyError: raise UserWarning(f"'org_path' key not present in {config_fn.name}") # Verify that the repo seems to be correctly configured if self.repo_path != NF_CORE_MODULES_NAME or self.branch: self.verify_branch() - + if self.repo_path is None: + raise UserWarning(f"Could not find the org_path in the configuration file: {config_fn.name}") # Convenience variable self.modules_dir = Path(self.local_repo_dir, "modules", self.repo_path) self.subworkflows_dir = Path(self.local_repo_dir, "subworkflows", self.repo_path) @@ -96,7 +98,7 @@ def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False): branch (str): name of branch to use Sets self.repo """ - self.local_repo_dir = os.path.join(NFCORE_DIR if not in_cache else NFCORE_CACHE_DIR, self.fullname) + self.local_repo_dir = Path(NFCORE_DIR if not in_cache else NFCORE_CACHE_DIR, self.fullname) try: if not os.path.exists(self.local_repo_dir): try: diff --git a/nf_core/pipelines/lint/actions_awsfulltest.py b/nf_core/pipelines/lint/actions_awsfulltest.py index 4cf3bece28..7ea167f6c9 100644 --- a/nf_core/pipelines/lint/actions_awsfulltest.py +++ b/nf_core/pipelines/lint/actions_awsfulltest.py @@ -1,9 +1,10 @@ -import os +from pathlib import Path +from typing import Dict, List import yaml -def actions_awsfulltest(self): +def actions_awsfulltest(self) -> Dict[str, List[str]]: """Checks the GitHub Actions awsfulltest is valid. In addition to small test datasets run on GitHub Actions, we provide the possibility of testing the pipeline on full size datasets on AWS. @@ -29,8 +30,8 @@ def actions_awsfulltest(self): warned = [] failed = [] - fn = os.path.join(self.wf_path, ".github", "workflows", "awsfulltest.yml") - if os.path.isfile(fn): + fn = Path(self.wf_path, ".github", "workflows", "awsfulltest.yml") + if fn.is_file(): try: with open(fn) as fh: wf = yaml.safe_load(fh) diff --git a/nf_core/pipelines/lint/actions_awstest.py b/nf_core/pipelines/lint/actions_awstest.py index 7c55998944..7e4c0fc497 100644 --- a/nf_core/pipelines/lint/actions_awstest.py +++ b/nf_core/pipelines/lint/actions_awstest.py @@ -1,4 +1,4 @@ -import os +from pathlib import Path import yaml @@ -22,8 +22,8 @@ def actions_awstest(self): * Must be turned on for ``workflow_dispatch``. """ - fn = os.path.join(self.wf_path, ".github", "workflows", "awstest.yml") - if not os.path.isfile(fn): + fn = Path(self.wf_path, ".github", "workflows", "awstest.yml") + if not fn.is_file(): return {"ignored": [f"'awstest.yml' workflow not found: `{fn}`"]} try: diff --git a/nf_core/pipelines/lint/actions_ci.py b/nf_core/pipelines/lint/actions_ci.py index a3e7d54b66..74f433ef80 100644 --- a/nf_core/pipelines/lint/actions_ci.py +++ b/nf_core/pipelines/lint/actions_ci.py @@ -1,4 +1,4 @@ -import os +from pathlib import Path import yaml @@ -40,10 +40,10 @@ def actions_ci(self): """ passed = [] failed = [] - fn = os.path.join(self.wf_path, ".github", "workflows", "ci.yml") + fn = Path(self.wf_path, ".github", "workflows", "ci.yml") # Return an ignored status if we can't find the file - if not os.path.isfile(fn): + if not fn.is_file(): return {"ignored": ["'.github/workflows/ci.yml' not found"]} try: diff --git a/nf_core/pipelines/lint/actions_schema_validation.py b/nf_core/pipelines/lint/actions_schema_validation.py index b4be42b54c..a057d80589 100644 --- a/nf_core/pipelines/lint/actions_schema_validation.py +++ b/nf_core/pipelines/lint/actions_schema_validation.py @@ -1,6 +1,5 @@ -import glob import logging -import os +from pathlib import Path from typing import Any, Dict, List import jsonschema @@ -26,7 +25,7 @@ def actions_schema_validation(self) -> Dict[str, List[str]]: logging.getLogger("nf_core.pipelines.schema").setLevel(logging.ERROR) # Get all workflow files - action_workflows = glob.glob(os.path.join(self.wf_path, ".github/workflows/*.y*ml")) + action_workflows = list(Path(self.wf_path).glob(".github/workflows/*.y*ml")) # Load the GitHub workflow schema r = requests.get("https://json.schemastore.org/github-workflow", allow_redirects=True) @@ -40,7 +39,7 @@ def actions_schema_validation(self) -> Dict[str, List[str]]: # Validate all workflows against the schema for wf_path in action_workflows: - wf = os.path.basename(wf_path) + wf = wf_path.name # load workflow try: diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py index bafd8aec78..300b3674b2 100644 --- a/nf_core/pipelines/lint/files_unchanged.py +++ b/nf_core/pipelines/lint/files_unchanged.py @@ -112,7 +112,8 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]: logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR) # Generate a new pipeline with nf-core create that we can compare to - tmp_dir = tempfile.mkdtemp() + tmp_dir = Path(tempfile.TemporaryDirectory().name) + tmp_dir.mkdir(parents=True) # Create a template.yaml file for the pipeline creation template_yaml = { @@ -123,10 +124,11 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]: } template_yaml_path = Path(tmp_dir, "template.yaml") + with open(template_yaml_path, "w") as fh: yaml.dump(template_yaml, fh, default_flow_style=False) - test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}") + test_pipeline_dir = Path(tmp_dir, f"{prefix}-{short_name}") create_obj = nf_core.pipelines.create.create.PipelineCreate( None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=template_yaml_path ) @@ -141,7 +143,7 @@ def _tf(file_path: Union[str, Path]) -> Path: """Helper function - get file path for template file""" return Path(test_pipeline_dir, file_path) - ignore_files = self.lint_config.get("files_unchanged", []) + ignore_files = self.lint_config.get("files_unchanged", []) if self.lint_config is not None else [] # Files that must be completely unchanged from template for files in files_exact: diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py index d57b63fd19..208c9f4bcc 100644 --- a/nf_core/pipelines/lint/merge_markers.py +++ b/nf_core/pipelines/lint/merge_markers.py @@ -1,6 +1,6 @@ import fnmatch import logging -import os +from pathlib import Path import nf_core.utils @@ -35,36 +35,36 @@ def merge_markers(self): failed = [] ignored = [] - ignored_config = self.lint_config.get("merge_markers", []) + ignored_config = self.lint_config.get("merge_markers", []) if self.lint_config is not None else [] ignore = [".git"] - if os.path.isfile(os.path.join(self.wf_path, ".gitignore")): - with open(os.path.join(self.wf_path, ".gitignore"), encoding="latin1") as fh: + if Path(self.wf_path, ".gitignore").is_file(): + with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh: for line in fh: - ignore.append(os.path.basename(line.strip().rstrip("/"))) - for root, dirs, files in os.walk(self.wf_path, topdown=True): + ignore.append(Path(line.strip().rstrip("/")).name) + for root, dirs, files in Path.walk(self.wf_path, top_down=True): # Ignore files for i_base in ignore: - i = os.path.join(root, i_base) - dirs[:] = [d for d in dirs if not fnmatch.fnmatch(os.path.join(root, d), i)] - files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)] + i = str(Path(root, i_base)) + dirs[:] = [d for d in dirs if not fnmatch.fnmatch(str(Path(root, d)), i)] + files[:] = [f for f in files if not fnmatch.fnmatch(str(Path(root, f)), i)] for fname in files: # File ignored in config - if os.path.relpath(os.path.join(root, fname), self.wf_path) in ignored_config: - ignored.append(f"Ignoring file `{os.path.join(root, fname)}`") + if str(Path(root, fname).relative_to(self.wf_path)) in ignored_config: + ignored.append(f"Ignoring file `{Path(root, fname)}`") continue # Skip binary files - if nf_core.utils.is_file_binary(os.path.join(root, fname)): + if nf_core.utils.is_file_binary(Path(root, fname)): continue try: - with open(os.path.join(root, fname), encoding="latin1") as fh: + with open(Path(root, fname), encoding="latin1") as fh: for line in fh: if ">>>>>>>" in line: - failed.append(f"Merge marker '>>>>>>>' in `{os.path.join(root, fname)}`: {line[:30]}") + failed.append(f"Merge marker '>>>>>>>' in `{Path(root, fname)}`: {line[:30]}") if "<<<<<<<" in line: - failed.append(f"Merge marker '<<<<<<<' in `{os.path.join(root, fname)}`: {line[:30]}") + failed.append(f"Merge marker '<<<<<<<' in `{Path(root, fname)}`: {line[:30]}") except FileNotFoundError: - log.debug(f"Could not open file {os.path.join(root, fname)} in merge_markers lint test") + log.debug(f"Could not open file {Path(root, fname)} in merge_markers lint test") if len(failed) == 0: passed.append("No merge markers found in pipeline files") return {"passed": passed, "failed": failed, "ignored": ignored} diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py index 9d9b4c9fc0..fd29942ed6 100644 --- a/nf_core/pipelines/lint/modules_structure.py +++ b/nf_core/pipelines/lint/modules_structure.py @@ -1,5 +1,4 @@ import logging -import os from pathlib import Path log = logging.getLogger(__name__) @@ -20,7 +19,7 @@ def modules_structure(self): modules/nf-core/modules/TOOL/SUBTOOL """ wrong_location_modules = [] - for directory, _, files in os.walk(Path(self.wf_path, "modules")): + for directory, _, files in Path.walk(Path(self.wf_path, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.wf_path, "modules")) parts = module_path.parts diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index f62100a70a..96323af94d 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -1,14 +1,14 @@ import logging -import os import re from pathlib import Path +from typing import Dict, List, Optional, Union from nf_core.pipelines.schema import PipelineSchema log = logging.getLogger(__name__) -def nextflow_config(self): +def nextflow_config(self) -> Dict[str, List[str]]: """Checks the pipeline configuration for required variables. All nf-core pipelines are required to be configured with a minimal set of variable @@ -173,7 +173,7 @@ def nextflow_config(self): ] # Remove field that should be ignored according to the linting config - ignore_configs = self.lint_config.get("nextflow_config", []) + ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else [] for cfs in config_fail: for cf in cfs: @@ -205,12 +205,13 @@ def nextflow_config(self): failed.append(f"Config variable (incorrectly) found: {self._wrap_quotes(cf)}") # Check and warn if the process configuration is done with deprecated syntax + process_with_deprecated_syntax = list( set( [ - re.search(r"^(process\.\$.*?)\.+.*$", ck).group(1) + match.group(1) for ck in self.nf_config.keys() - if re.match(r"^(process\.\$.*?)\.+.*$", ck) + if (match := re.match(r"^(process\.\$.*?)\.+.*$", ck)) is not None ] ) ) @@ -313,7 +314,7 @@ def nextflow_config(self): r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")', r"}", ] - path = os.path.join(self.wf_path, "nextflow.config") + path = Path(self.wf_path, "nextflow.config") i = 0 with open(path) as f: for line in f: @@ -335,7 +336,7 @@ def nextflow_config(self): ) # Check for the availability of the "test" configuration profile by parsing nextflow.config - with open(os.path.join(self.wf_path, "nextflow.config")) as f: + with open(Path(self.wf_path, "nextflow.config")) as f: content = f.read() # Remove comments @@ -379,8 +380,8 @@ def nextflow_config(self): if param in ignore_defaults: ignored.append(f"Config default ignored: {param}") elif param in self.nf_config.keys(): - config_default = None - schema_default = None + config_default: Optional[Union[str, float, int]] = None + schema_default: Optional[Union[str, float, int]] = None if schema.schema_types[param_name] == "boolean": schema_default = str(schema.schema_defaults[param_name]).lower() config_default = str(self.nf_config[param]).lower() diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py index ba6ec79150..530d853764 100644 --- a/nf_core/pipelines/lint/pipeline_todos.py +++ b/nf_core/pipelines/lint/pipeline_todos.py @@ -1,6 +1,6 @@ import fnmatch import logging -import os +from pathlib import Path log = logging.getLogger(__name__) @@ -39,19 +39,19 @@ def pipeline_todos(self, root_dir=None): root_dir = self.wf_path ignore = [".git"] - if os.path.isfile(os.path.join(root_dir, ".gitignore")): - with open(os.path.join(root_dir, ".gitignore"), encoding="latin1") as fh: + if Path(root_dir, ".gitignore").is_file(): + with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh: for line in fh: - ignore.append(os.path.basename(line.strip().rstrip("/"))) - for root, dirs, files in os.walk(root_dir, topdown=True): + ignore.append(Path(line.strip().rstrip("/")).name) + for root, dirs, files in Path.walk(root_dir, top_down=True): # Ignore files for i_base in ignore: - i = os.path.join(root, i_base) - dirs[:] = [d for d in dirs if not fnmatch.fnmatch(os.path.join(root, d), i)] - files[:] = [f for f in files if not fnmatch.fnmatch(os.path.join(root, f), i)] + i = str(Path(root, i_base)) + dirs[:] = [d for d in dirs if not fnmatch.fnmatch(str(Path(root, d)), i)] + files[:] = [f for f in files if not fnmatch.fnmatch(str(Path(root, f)), i)] for fname in files: try: - with open(os.path.join(root, fname), encoding="latin1") as fh: + with open(Path(root, fname), encoding="latin1") as fh: for line in fh: if "TODO nf-core" in line: line = ( @@ -63,7 +63,7 @@ def pipeline_todos(self, root_dir=None): .strip() ) warned.append(f"TODO string in `{fname}`: _{line}_") - file_paths.append(os.path.join(root, fname)) + file_paths.append(Path(root, fname)) except FileNotFoundError: log.debug(f"Could not open file {fname} in pipeline_todos lint test") diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py index cade9ca3ea..4c16243690 100644 --- a/nf_core/pipelines/lint/readme.py +++ b/nf_core/pipelines/lint/readme.py @@ -1,5 +1,5 @@ -import os import re +from pathlib import Path def readme(self): @@ -29,9 +29,9 @@ def readme(self): failed = [] # Remove field that should be ignored according to the linting config - ignore_configs = self.lint_config.get("readme", []) + ignore_configs = self.lint_config.get("readme", []) if self.lint_config is not None else [] - with open(os.path.join(self.wf_path, "README.md")) as fh: + with open(Path(self.wf_path, "README.md")) as fh: content = fh.read() if "nextflow_badge" not in ignore_configs: From 0a3cb5ffaea2026f55e6291f1f4f1ea73dc3cc4a Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 14:09:35 +0200 Subject: [PATCH 193/574] fix mypy linting --- nf_core/modules/bump_versions.py | 2 +- nf_core/pipelines/create/create.py | 13 +++++++------ tests/pipelines/test_sync.py | 2 +- 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 2d8854e3c0..6546cccc9a 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -76,7 +76,7 @@ def bump_versions( ) # Get list of all modules - _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory) + _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(Path(self.directory)) # Load the .nf-core.yml config _, self.tools_config = nf_core.utils.load_tools_config(self.directory) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index f032db7f69..be07c0c290 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -8,7 +8,7 @@ import re import shutil from pathlib import Path -from typing import Dict, List, Optional, Union +from typing import Dict, List, Optional, Union, cast import git import git.config @@ -21,6 +21,7 @@ from nf_core.pipelines.create.utils import CreateConfig from nf_core.pipelines.create_logo import create_logo from nf_core.pipelines.lint_utils import run_prettier_on_file +from nf_core.utils import LintConfigType log = logging.getLogger(__name__) @@ -57,7 +58,7 @@ def __init__( from_config_file: bool = False, default_branch: Optional[str] = None, is_interactive: bool = False, - ): + ) -> None: if isinstance(template_config, CreateConfig): self.config = template_config elif from_config_file: @@ -418,13 +419,13 @@ def remove_nf_core_in_bug_report_template(self): run_prettier_on_file(bug_report_path) - def fix_linting(self): + def fix_linting(self) -> None: """ Updates the .nf-core.yml with linting configurations for a customized pipeline. """ # Create a lint config - short_name = self.jinja_params["short_name"] + short_name: str = self.jinja_params["short_name"] lint_config: Dict[str, List[str]] = { "files_exist": [ "CODE_OF_CONDUCT.md", @@ -512,7 +513,7 @@ def fix_linting(self): # Add the lint content to the preexisting nf-core config config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir) if config_fn is not None and nf_core_yml is not None: - nf_core_yml.lint = lint_config + nf_core_yml.lint = cast(LintConfigType, lint_config) with open(self.outdir / config_fn, "w") as fh: yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False) @@ -534,7 +535,7 @@ def make_pipeline_logo(self): force=bool(self.force), ) - def git_init_pipeline(self): + def git_init_pipeline(self) -> None: """Initialises the new pipeline as a Git repository and submits first commit. Raises: diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py index b6955e6714..ffbe75510b 100644 --- a/tests/pipelines/test_sync.py +++ b/tests/pipelines/test_sync.py @@ -331,7 +331,7 @@ def test_close_open_template_merge_prs(self, mock_get): @mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post) @mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch) - def test_close_open_pr(self, mock_patch, mock_post): + def test_close_open_pr(self, mock_patch, mock_post) -> None: psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir) psync.inspect_sync_dir() psync.get_wf_config() From b7b45dfab771a2a84ed05d368719f204133ec8a0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 14:09:47 +0200 Subject: [PATCH 194/574] fix circular import --- nf_core/__main__.py | 2 +- nf_core/components/components_utils.py | 16 +++++++++++++--- nf_core/components/info.py | 2 +- nf_core/components/install.py | 2 +- nf_core/modules/modules_json.py | 8 ++------ nf_core/modules/modules_repo.py | 6 +----- nf_core/synced_repo.py | 9 ++++----- tests/modules/test_modules_json.py | 4 ++-- tests/modules/test_update.py | 2 +- tests/subworkflows/test_update.py | 2 +- 10 files changed, 27 insertions(+), 26 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index f33c63e87c..b86f8f4bad 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -52,7 +52,7 @@ subworkflows_test, subworkflows_update, ) -from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE +from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE from nf_core.pipelines.download import DownloadError from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index e4e2ff092b..4e9c0ac601 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -1,16 +1,23 @@ import logging import re from pathlib import Path -from typing import List, Optional, Tuple, Union +from typing import TYPE_CHECKING, List, Optional, Tuple, Union import questionary import rich.prompt +if TYPE_CHECKING: + from nf_core.modules.modules_repo import ModulesRepo + import nf_core.utils -from nf_core.modules.modules_repo import ModulesRepo log = logging.getLogger(__name__) +# Constants for the nf-core/modules repo used throughout the module files +NF_CORE_MODULES_NAME = "nf-core" +NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git" +NF_CORE_MODULES_DEFAULT_BRANCH = "master" + def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]: """ @@ -82,7 +89,10 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P def prompt_component_version_sha( - component_name: str, component_type: str, modules_repo: ModulesRepo, installed_sha: Optional[str] = None + component_name: str, + component_type: str, + modules_repo: "ModulesRepo", + installed_sha: Optional[str] = None, ) -> str: """ Creates an interactive questionary prompt for selecting the module/subworkflow version diff --git a/nf_core/components/info.py b/nf_core/components/info.py index a296fcaccf..55a95593f9 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -15,8 +15,8 @@ import nf_core.utils from nf_core.components.components_command import ComponentCommand +from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE log = logging.getLogger(__name__) diff --git a/nf_core/components/install.py b/nf_core/components/install.py index 8f47913283..f2849f85bc 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -12,11 +12,11 @@ import nf_core.utils from nf_core.components.components_command import ComponentCommand from nf_core.components.components_utils import ( + NF_CORE_MODULES_NAME, get_components_to_install, prompt_component_version_sha, ) from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME log = logging.getLogger(__name__) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 01785c6d65..e9b4aa1025 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -14,12 +14,8 @@ from git.exc import GitCommandError import nf_core.utils -from nf_core.components.components_utils import get_components_to_install -from nf_core.modules.modules_repo import ( - NF_CORE_MODULES_NAME, - NF_CORE_MODULES_REMOTE, - ModulesRepo, -) +from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, get_components_to_install +from nf_core.modules.modules_repo import ModulesRepo from nf_core.pipelines.lint_utils import dump_json_with_prettier from .modules_differ import ModulesDiffer diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index bc92072e3b..5b50205484 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -12,16 +12,12 @@ import nf_core.modules.modules_json import nf_core.modules.modules_utils +from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE from nf_core.synced_repo import RemoteProgressbar, SyncedRepo from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR, load_tools_config log = logging.getLogger(__name__) -# Constants for the nf-core/modules repo used throughout the module files -NF_CORE_MODULES_NAME = "nf-core" -NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git" -NF_CORE_MODULES_DEFAULT_BRANCH = "master" - class ModulesRepo(SyncedRepo): """ diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 8af0ee9a08..8efdd0e488 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -9,15 +9,14 @@ import git from git.exc import GitCommandError +from nf_core.components.components_utils import ( + NF_CORE_MODULES_NAME, + NF_CORE_MODULES_REMOTE, +) from nf_core.utils import load_tools_config log = logging.getLogger(__name__) -# Constants for the nf-core/modules repo used throughout the module files -NF_CORE_MODULES_NAME = "nf-core" -NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git" -NF_CORE_MODULES_DEFAULT_BRANCH = "master" - class RemoteProgressbar(git.RemoteProgress): """ diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py index 845f9c3e34..b2cac99e6d 100644 --- a/tests/modules/test_modules_json.py +++ b/tests/modules/test_modules_json.py @@ -3,13 +3,13 @@ import shutil from pathlib import Path -from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import ( +from nf_core.components.components_utils import ( NF_CORE_MODULES_DEFAULT_BRANCH, NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, ModulesRepo, ) +from nf_core.modules.modules_json import ModulesJson from nf_core.modules.patch import ModulePatch from ..test_modules import TestModules diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py index 1f81eab487..6c8eacc666 100644 --- a/tests/modules/test_update.py +++ b/tests/modules/test_update.py @@ -8,9 +8,9 @@ import yaml import nf_core.utils +from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE from nf_core.modules.install import ModuleInstall from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE from nf_core.modules.patch import ModulePatch from nf_core.modules.update import ModuleUpdate diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py index 7b17a621bc..153038cd1d 100644 --- a/tests/subworkflows/test_update.py +++ b/tests/subworkflows/test_update.py @@ -8,8 +8,8 @@ import yaml import nf_core.utils +from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE from nf_core.modules.modules_json import ModulesJson -from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE from nf_core.modules.update import ModuleUpdate from nf_core.subworkflows.update import SubworkflowUpdate From c6227a7cac8a909e54a46423a9626159ec6589b8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 14:17:18 +0200 Subject: [PATCH 195/574] fix module command imports --- nf_core/commands_modules.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index 3d96d332b0..b93bd7bcb0 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -13,7 +13,7 @@ def modules_list_remote(ctx, keywords, json): """ List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/]. """ - from nf_core.modules import ModuleList + from nf_core.modules.list import ModuleList try: module_list = ModuleList( @@ -33,7 +33,7 @@ def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-b """ List modules installed locally in a pipeline """ - from nf_core.modules import ModuleList + from nf_core.modules.list import ModuleList try: module_list = ModuleList( @@ -55,7 +55,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha): Fetches and installs module files from a remote repo e.g. nf-core/modules. """ - from nf_core.modules import ModuleInstall + from nf_core.modules.install import ModuleInstall try: module_install = ModuleInstall( @@ -93,7 +93,7 @@ def modules_update( Fetches and updates module files from a remote repo e.g. nf-core/modules. """ - from nf_core.modules import ModuleUpdate + from nf_core.modules.update import ModuleUpdate try: module_install = ModuleUpdate( @@ -125,7 +125,7 @@ def modules_patch(ctx, tool, dir, remove): Checks if a module has been modified locally and creates a patch file describing how the module has changed from the remote version """ - from nf_core.modules import ModulePatch + from nf_core.modules.patch import ModulePatch try: module_patch = ModulePatch( @@ -147,7 +147,7 @@ def modules_remove(ctx, dir, tool): """ Remove a module from a pipeline. """ - from nf_core.modules import ModuleRemove + from nf_core.modules.remove import ModuleRemove try: module_remove = ModuleRemove( @@ -194,7 +194,7 @@ def modules_create( elif no_meta: has_meta = False - from nf_core.modules import ModuleCreate + from nf_core.modules.create import ModuleCreate # Run function try: @@ -257,7 +257,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, nf-core/modules repository. """ from nf_core.components.lint import LintExceptionError - from nf_core.modules import ModuleLint + from nf_core.modules.lint import ModuleLint try: module_lint = ModuleLint( @@ -302,7 +302,7 @@ def modules_info(ctx, tool, dir): will print this usage info. If not, usage from the remote modules repo will be shown. """ - from nf_core.modules import ModuleInfo + from nf_core.modules.info import ModuleInfo try: module_info = ModuleInfo( From 847c683d22a44cb20129afb4b63bf94d529badb9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 14:20:10 +0200 Subject: [PATCH 196/574] fix: cannot import name 'NotRequired' --- requirements-dev.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements-dev.txt b/requirements-dev.txt index 82087edcba..aa43ee3fe3 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -14,6 +14,7 @@ types-Markdown types-PyYAML types-requests types-setuptools +typing_extensions >=4.0.0 pytest-asyncio pytest-textual-snapshot==0.4.0 pytest-workflow>=2.0.0 From e7ac7812422e1d76fc67898c72058b6decb23322 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 16:12:12 +0200 Subject: [PATCH 197/574] more dir-> directory conversions --- nf_core/__main__.py | 135 ++++++++++++++++++++-------------- nf_core/commands_pipelines.py | 29 ++++---- 2 files changed, 95 insertions(+), 69 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index b86f8f4bad..91af979586 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -126,7 +126,7 @@ # because they are actually preliminary, but intended program terminations. # (Custom exceptions are cleaner than `sys.exit(1)`, which we used before) def selective_traceback_hook(exctype, value, traceback): - if exctype in {DownloadError}: # extend set as needed + if exctype in {DownloadError, UserWarning}: # extend set as needed log.error(value) else: # print the colored traceback for all other exceptions with rich as usual @@ -278,6 +278,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory [dim]\[default: current working directory][/]", @@ -331,7 +332,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out @click.pass_context def command_pipelines_lint( ctx, - dir, + directory, release, fix, key, @@ -345,7 +346,7 @@ def command_pipelines_lint( """ Check pipeline code against nf-core guidelines. """ - pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) + pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) # nf-core pipelines download @@ -584,6 +585,7 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -610,11 +612,13 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived): @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def command_pipelines_sync( + ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr +): """ Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. """ - pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr) # nf-core pipelines bump-version @@ -624,6 +628,7 @@ def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repositor @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -635,11 +640,11 @@ def command_pipelines_sync(ctx, dir, from_branch, pull_request, github_repositor default=False, help="Bump required nextflow version instead of pipeline version", ) -def command_pipelines_bump_version(ctx, new_version, dir, nextflow): +def command_pipelines_bump_version(ctx, new_version, directory, nextflow): """ Update nf-core pipeline version number with `nf-core pipelines bump-version`. """ - pipelines_bump_version(ctx, new_version, dir, nextflow) + pipelines_bump_version(ctx, new_version, directory, nextflow) # nf-core pipelines create-logo @@ -680,11 +685,11 @@ def command_pipelines_bump_version(ctx, new_version, dir, nextflow): default=False, help="Overwrite any files if they already exist", ) -def command_pipelines_create_logo(logo_text, dir, name, theme, width, format, force): +def command_pipelines_create_logo(logo_text, directory, name, theme, width, format, force): """ Generate a logo with the nf-core logo template. """ - pipelines_create_logo(logo_text, dir, name, theme, width, format, force) + pipelines_create_logo(logo_text, directory, name, theme, width, format, force) # nf-core pipelines schema subcommands @@ -715,6 +720,7 @@ def command_pipelines_schema_validate(pipeline, params): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -735,11 +741,11 @@ def command_pipelines_schema_validate(pipeline, params): default="https://nf-co.re/pipeline_schema_builder", help="Customise the builder URL (for development work)", ) -def command_pipelines_schema_build(dir, no_prompts, web_only, url): +def command_pipelines_schema_build(directory, no_prompts, web_only, url): """ Interactively build a pipeline schema from Nextflow params. """ - pipelines_schema_build(dir, no_prompts, web_only, url) + pipelines_schema_build(directory, no_prompts, web_only, url) # nf-core pipelines schema lint @@ -864,15 +870,16 @@ def command_modules_list_remote(ctx, keywords, json): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def command_modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def command_modules_list_local(ctx, keywords, json, directory): # pylint: disable=redefined-builtin """ List modules installed locally in a pipeline """ - modules_list_local(ctx, keywords, json, dir) + modules_list_local(ctx, keywords, json, directory) # nf-core modules install @@ -882,6 +889,7 @@ def command_modules_list_local(ctx, keywords, json, dir): # pylint: disable=red @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -901,11 +909,11 @@ def command_modules_list_local(ctx, keywords, json, dir): # pylint: disable=red help="Force reinstallation of module if it already exists", ) @click.option("-s", "--sha", type=str, metavar="", help="Install module at commit SHA") -def command_modules_install(ctx, tool, dir, prompt, force, sha): +def command_modules_install(ctx, tool, directory, prompt, force, sha): """ Install DSL2 modules within a pipeline. """ - modules_install(ctx, tool, dir, prompt, force, sha) + modules_install(ctx, tool, directory, prompt, force, sha) # nf-core modules update @@ -992,16 +1000,17 @@ def command_modules_update( @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) @click.option("-r", "--remove", is_flag=True, default=False) -def command_modules_patch(ctx, tool, dir, remove): +def command_modules_patch(ctx, tool, directory, remove): """ Create a patch file for minor changes in a module """ - modules_patch(ctx, tool, dir, remove) + modules_patch(ctx, tool, directory, remove) # nf-core modules remove @@ -1011,15 +1020,16 @@ def command_modules_patch(ctx, tool, dir, remove): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -def command_modules_remove(ctx, dir, tool): +def command_modules_remove(ctx, directory, tool): """ Remove a module from a pipeline. """ - modules_remove(ctx, dir, tool) + modules_remove(ctx, directory, tool) # nf-core modules create @@ -1092,7 +1102,7 @@ def command_modules_remove(ctx, dir, tool): def command_modules_create( ctx, tool, - dir, + directory, author, label, meta, @@ -1109,7 +1119,7 @@ def command_modules_create( modules_create( ctx, tool, - dir, + directory, author, label, meta, @@ -1129,6 +1139,7 @@ def command_modules_create( @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", metavar="", @@ -1154,11 +1165,11 @@ def command_modules_create( default=None, help="Run tests with a specific profile", ) -def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): +def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile): """ Run nf-test for a module. """ - modules_test(ctx, tool, dir, no_prompts, update, once, profile) + modules_test(ctx, tool, directory, no_prompts, update, once, profile) # nf-core modules lint @@ -1168,6 +1179,7 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", metavar="", @@ -1204,11 +1216,11 @@ def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): is_flag=True, help="Fix the module version if a newer version is available", ) -def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): +def command_modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version): """ Lint one or more modules in a directory. """ - modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version) + modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version) # nf-core modules info @@ -1218,15 +1230,16 @@ def command_modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def command_modules_info(ctx, tool, dir): +def command_modules_info(ctx, tool, directory): """ Show developer usage information about a given module. """ - modules_info(ctx, tool, dir) + modules_info(ctx, tool, directory) # nf-core modules bump-versions @@ -1236,18 +1249,19 @@ def command_modules_info(ctx, tool, dir): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", metavar="", ) @click.option("-a", "--all", is_flag=True, help="Run on all modules") @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too") -def command_modules_bump_versions(ctx, tool, dir, all, show_all): +def command_modules_bump_versions(ctx, tool, directory, all, show_all): """ Bump versions for one or more modules in a clone of the nf-core/modules repo. """ - modules_bump_versions(ctx, tool, dir, all, show_all) + modules_bump_versions(ctx, tool, directory, all, show_all) # nf-core subworkflows click command @@ -1313,11 +1327,11 @@ def subworkflows(ctx, git_remote, branch, no_pull): default=False, help="Migrate a module with pytest tests to nf-test", ) -def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): +def command_subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest): """ Create a new subworkflow from the nf-core template. """ - subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest) + subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest) # nf-core subworkflows test @@ -1327,6 +1341,7 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", metavar="", @@ -1352,11 +1367,11 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py default=None, help="Run tests with a specific profile", ) -def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): +def command_subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile): """ Run nf-test for a subworkflow. """ - subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile) + subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile) # nf-core subworkflows list subcommands @@ -1389,15 +1404,16 @@ def command_subworkflows_list_remote(ctx, keywords, json): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def command_subworkflows_list_local(ctx, keywords, json, directory): # pylint: disable=redefined-builtin """ List subworkflows installed locally in a pipeline """ - subworkflows_list_local(ctx, keywords, json, dir) + subworkflows_list_local(ctx, keywords, json, directory) # nf-core subworkflows lint @@ -1407,6 +1423,7 @@ def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disabl @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", metavar="", @@ -1438,11 +1455,11 @@ def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disabl help="Sort lint output by subworkflow or test name.", show_default=True, ) -def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +def command_subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by): """ Lint one or more subworkflows in a directory. """ - subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by) + subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by) # nf-core subworkflows info @@ -1452,15 +1469,16 @@ def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_wa @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: Current working directory][/]", ) -def command_subworkflows_info(ctx, subworkflow, dir): +def command_subworkflows_info(ctx, subworkflow, directory): """ Show developer usage information about a given subworkflow. """ - subworkflows_info(ctx, subworkflow, dir) + subworkflows_info(ctx, subworkflow, directory) # nf-core subworkflows install @@ -1470,6 +1488,7 @@ def command_subworkflows_info(ctx, subworkflow, dir): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -1495,11 +1514,11 @@ def command_subworkflows_info(ctx, subworkflow, dir): metavar="", help="Install subworkflow at commit SHA", ) -def command_subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): +def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha): """ Install DSL2 subworkflow within a pipeline. """ - subworkflows_install(ctx, subworkflow, dir, prompt, force, sha) + subworkflows_install(ctx, subworkflow, directory, prompt, force, sha) # nf-core subworkflows remove @@ -1509,15 +1528,16 @@ def command_subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -def command_subworkflows_remove(ctx, dir, subworkflow): +def command_subworkflows_remove(ctx, directory, subworkflow): """ Remove a subworkflow from a pipeline. """ - subworkflows_remove(ctx, dir, subworkflow) + subworkflows_remove(ctx, directory, subworkflow) # nf-core subworkflows update @@ -1527,6 +1547,7 @@ def command_subworkflows_remove(ctx, dir, subworkflow): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -1587,7 +1608,7 @@ def command_subworkflows_remove(ctx, dir, subworkflow): def command_subworkflows_update( ctx, subworkflow, - dir, + directory, force, prompt, sha, @@ -1601,7 +1622,7 @@ def command_subworkflows_update( Update DSL2 subworkflow within a pipeline. """ subworkflows_update( - ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output + ctx, subworkflow, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output ) @@ -1636,6 +1657,7 @@ def command_schema_validate(pipeline, params): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -1656,14 +1678,14 @@ def command_schema_validate(pipeline, params): default="https://nf-co.re/pipeline_schema_builder", help="Customise the builder URL (for development work)", ) -def command_schema_build(dir, no_prompts, web_only, url): +def command_schema_build(directory, no_prompts, web_only, url): """ Use `nf-core pipelines schema build` instead. """ log.warning( "The `[magenta]nf-core schema build[/]` command is deprecated. Use `[magenta]nf-core pipelines schema build[/]` instead." ) - pipelines_schema_build(dir, no_prompts, web_only, url) + pipelines_schema_build(directory, no_prompts, web_only, url) # nf-core schema lint (deprecated) @@ -1764,14 +1786,14 @@ def command_schema_docs(schema_path, output, format, force, columns): default=False, help="Overwrite any files if they already exist", ) -def command_create_logo(logo_text, dir, name, theme, width, format, force): +def command_create_logo(logo_text, directory, name, theme, width, format, force): """ Use `nf-core pipelines create-logo` instead. """ log.warning( "The `[magenta]nf-core create-logo[/]` command is deprecated. Use `[magenta]nf-core pipelines screate-logo[/]` instead." ) - pipelines_create_logo(logo_text, dir, name, theme, width, format, force) + pipelines_create_logo(logo_text, directory, name, theme, width, format, force) # nf-core sync (deprecated) @@ -1779,6 +1801,7 @@ def command_create_logo(logo_text, dir, name, theme, width, format, force): @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -1805,14 +1828,14 @@ def command_create_logo(logo_text, dir, name, theme, width, format, force): @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def command_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def command_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Use `nf-core pipelines sync` instead. """ log.warning( "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead." ) - pipelines_sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + pipelines_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr) # nf-core bump-version (deprecated) @@ -1822,6 +1845,7 @@ def command_sync(dir, from_branch, pull_request, github_repository, username, te @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", @@ -1833,14 +1857,14 @@ def command_sync(dir, from_branch, pull_request, github_repository, username, te default=False, help="Bump required nextflow version instead of pipeline version", ) -def command_bump_version(ctx, new_version, dir, nextflow): +def command_bump_version(ctx, new_version, directory, nextflow): """ Use `nf-core pipelines bump-version` instead. """ log.warning( "The `[magenta]nf-core bump-version[/]` command is deprecated. Use `[magenta]nf-core pipelines bump-version[/]` instead." ) - pipelines_bump_version(ctx, new_version, dir, nextflow) + pipelines_bump_version(ctx, new_version, directory, nextflow) # nf-core list (deprecated) @@ -2086,6 +2110,7 @@ def command_download( @click.option( "-d", "--dir", + "directory", type=click.Path(exists=True), default=".", help=r"Pipeline directory [dim]\[default: current working directory][/]", @@ -2139,7 +2164,7 @@ def command_download( @click.pass_context def command_lint( ctx, - dir, + directory, release, fix, key, @@ -2156,7 +2181,7 @@ def command_lint( log.warning( "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead." ) - pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) + pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by) # nf-core create (deprecated) diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py index 432a36aaee..c586534b22 100644 --- a/nf_core/commands_pipelines.py +++ b/nf_core/commands_pipelines.py @@ -60,7 +60,7 @@ def pipelines_create(ctx, name, description, author, version, force, outdir, tem # nf-core pipelines bump-version -def pipelines_bump_version(ctx, new_version, dir, nextflow): +def pipelines_bump_version(ctx, new_version, directory, nextflow): """ Update nf-core pipeline version number. @@ -78,10 +78,10 @@ def pipelines_bump_version(ctx, new_version, dir, nextflow): try: # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) + is_pipeline_directory(directory) # Make a pipeline object and load config etc - pipeline_obj = Pipeline(dir) + pipeline_obj = Pipeline(directory) pipeline_obj._load() # Bump the pipeline version number @@ -97,7 +97,7 @@ def pipelines_bump_version(ctx, new_version, dir, nextflow): # nf-core pipelines lint def pipelines_lint( ctx, - dir, + directory, release, fix, key, @@ -123,7 +123,7 @@ def pipelines_lint( # Check if pipeline directory is a pipeline try: - is_pipeline_directory(dir) + is_pipeline_directory(directory) except UserWarning as e: log.error(e) sys.exit(1) @@ -131,7 +131,7 @@ def pipelines_lint( # Run the lint tests! try: lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( - dir, + directory, release, fix, key, @@ -279,7 +279,7 @@ def pipelines_list(ctx, keywords, sort, json, show_archived): # nf-core pipelines sync -def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. @@ -295,12 +295,13 @@ def pipelines_sync(ctx, dir, from_branch, pull_request, github_repository, usern from nf_core.pipelines.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError from nf_core.utils import is_pipeline_directory - # Check if pipeline directory contains necessary files - is_pipeline_directory(dir) - - # Sync the given pipeline dir - sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr) try: + # Check if pipeline directory contains necessary files + is_pipeline_directory(directory) + # Sync the given pipeline dir + sync_obj = PipelineSync( + directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr + ) sync_obj.sync() except (SyncExceptionError, PullRequestExceptionError) as e: log.error(e) @@ -360,7 +361,7 @@ def pipelines_schema_validate(pipeline, params): # nf-core pipelines schema build -def pipelines_schema_build(dir, no_prompts, web_only, url): +def pipelines_schema_build(directory, no_prompts, web_only, url): """ Interactively build a pipeline schema from Nextflow params. @@ -376,7 +377,7 @@ def pipelines_schema_build(dir, no_prompts, web_only, url): try: schema_obj = PipelineSchema() - if schema_obj.build_schema(dir, no_prompts, web_only, url) is False: + if schema_obj.build_schema(directory, no_prompts, web_only, url) is False: sys.exit(1) except (UserWarning, AssertionError) as e: log.error(e) From 5a8ae1240e646413d3c483cb8d67f8d1581495cb Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 16:18:50 +0200 Subject: [PATCH 198/574] fix pydantic warnings --- nf_core/pipelines/create/create.py | 28 ++++++++++++---------------- nf_core/pipelines/sync.py | 2 +- nf_core/utils.py | 8 ++++++-- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index be07c0c290..a2df9aeefc 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -21,7 +21,7 @@ from nf_core.pipelines.create.utils import CreateConfig from nf_core.pipelines.create_logo import create_logo from nf_core.pipelines.lint_utils import run_prettier_on_file -from nf_core.utils import LintConfigType +from nf_core.utils import LintConfigType, NFCoreTemplateConfig log = logging.getLogger(__name__) @@ -111,7 +111,7 @@ def __init__( self.is_interactive = is_interactive self.force = self.config.force if self.config.outdir is None: - self.config.outdir = os.getcwd() + self.config.outdir = str(Path.cwd()) if self.config.outdir == ".": self.outdir = Path(self.config.outdir, self.jinja_params["name_noslash"]).absolute() else: @@ -289,13 +289,13 @@ def render_template(self): log.info("Use -f / --force to overwrite existing files") raise UserWarning(f"Output directory '{self.outdir}' exists!") else: - os.makedirs(self.outdir) + self.outdir.mkdir(parents=True, exist_ok=True) # Run jinja2 for each file in the template folder env = jinja2.Environment( loader=jinja2.PackageLoader("nf_core", "pipeline-template"), keep_trailing_newline=True ) - template_dir = os.path.join(os.path.dirname(nf_core.__file__), "pipeline-template") + template_dir = Path(nf_core.__file__).parent / "pipeline-template" object_attrs = self.jinja_params object_attrs["nf_core_version"] = nf_core.__version__ @@ -310,26 +310,24 @@ def render_template(self): } # Set the paths to skip according to customization - for template_fn_path_obj in template_files: - template_fn_path = str(template_fn_path_obj) - + for template_fn_path in template_files: # Skip files that are in the self.skip_paths list for skip_path in self.skip_paths: - if os.path.relpath(template_fn_path, template_dir).startswith(skip_path): + if str(template_fn_path.relative_to(template_dir)).startswith(skip_path): break else: - if os.path.isdir(template_fn_path): + if template_fn_path.is_dir(): continue - if any([s in template_fn_path for s in ignore_strs]): + if any([s in str(template_fn_path) for s in ignore_strs]): log.debug(f"Ignoring '{template_fn_path}' in jinja2 template creation") continue # Set up vars and directories - template_fn = os.path.relpath(template_fn_path, template_dir) + template_fn = template_fn_path.relative_to(template_dir) output_path = self.outdir / template_fn if template_fn in rename_files: output_path = self.outdir / rename_files[template_fn] - os.makedirs(os.path.dirname(output_path), exist_ok=True) + output_path.parent.mkdir(parents=True, exist_ok=True) try: # Just copy binary files @@ -338,7 +336,7 @@ def render_template(self): # Got this far - render the template log.debug(f"Rendering template file: '{template_fn}'") - j_template = env.get_template(template_fn) + j_template = env.get_template(str(template_fn)) rendered_output = j_template.render(object_attrs) # Write to the pipeline output file @@ -379,9 +377,7 @@ def render_template(self): config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) if config_fn is not None and config_yml is not None: with open(str(config_fn), "w") as fh: - config_yml.template = self.config.model_dump() - # convert posix path to string for yaml dump - config_yml["template"]["outdir"] = str(config_yml["template"]["outdir"]) + config_yml.template = NFCoreTemplateConfig(**self.config.model_dump()) yaml.safe_dump(config_yml.model_dump(), fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index b1da99a626..d044be84e4 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -274,7 +274,7 @@ def make_template_pipeline(self): version=self.wf_config["manifest.version"].strip('"').strip("'"), no_git=True, force=True, - outdir=self.pipeline_dir, + outdir=str(self.pipeline_dir), author=self.wf_config["manifest.author"].strip('"').strip("'"), ).init_pipeline() except Exception as err: diff --git a/nf_core/utils.py b/nf_core/utils.py index 6794cf04fe..0beb8c7366 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1052,6 +1052,12 @@ class NFCoreTemplateConfig(BaseModel): skip_features: Optional[list] = None is_nfcore: Optional[bool] = None + def __getitem__(self, item: str) -> Any: + return getattr(self, item) + + def get(self, item: str, default: Any = None) -> Any: + return getattr(self, item, default) + LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]] @@ -1086,7 +1092,6 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] tools_config = {} config_fn = get_first_available_path(directory, CONFIG_PATHS) - if config_fn is None: depr_path = get_first_available_path(directory, DEPRECATED_CONFIG_PATHS) if depr_path: @@ -1102,7 +1107,6 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] # If the file is empty if tools_config is None: raise AssertionError(f"Config file '{config_fn}' is empty") - # Check for required fields try: nf_core_yaml_config = NFCoreYamlConfig(**tools_config) From ac1ea23974df7182c02a2619a2363010590c1b23 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 16:30:53 +0200 Subject: [PATCH 199/574] fix notrequired not found --- nf_core/modules/modules_json.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index e9b4aa1025..f992271741 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -6,12 +6,13 @@ import shutil import tempfile from pathlib import Path -from typing import Dict, List, NotRequired, Optional, Tuple, TypedDict, Union +from typing import Dict, List, Optional, Tuple, Union import git import questionary import rich.prompt from git.exc import GitCommandError +from typing_extensions import NotRequired, TypedDict # for py<3.11 import nf_core.utils from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, get_components_to_install From 79727c0b430f495468011233ec3b761d275a7be7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 17:28:53 +0200 Subject: [PATCH 200/574] fix pydantic type --- nf_core/pipelines/create/create.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index a2df9aeefc..127b1f607a 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -378,6 +378,7 @@ def render_template(self): if config_fn is not None and config_yml is not None: with open(str(config_fn), "w") as fh: config_yml.template = NFCoreTemplateConfig(**self.config.model_dump()) + config_yml.template.outdir = str(config_yml.template.outdir) yaml.safe_dump(config_yml.model_dump(), fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) From ee67c5fdd7f764f1f16f10f28e75f6f1f45941f5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 17:31:34 +0200 Subject: [PATCH 201/574] fix before model creation --- nf_core/pipelines/create/create.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 127b1f607a..acbe7efd5c 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -377,8 +377,9 @@ def render_template(self): config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) if config_fn is not None and config_yml is not None: with open(str(config_fn), "w") as fh: + self.config.outdir = str(self.config.outdir) config_yml.template = NFCoreTemplateConfig(**self.config.model_dump()) - config_yml.template.outdir = str(config_yml.template.outdir) + yaml.safe_dump(config_yml.model_dump(), fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) From dae348e4de483f5b24f92bcc41ddb1b843f688bf Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 25 Jul 2024 17:33:33 +0200 Subject: [PATCH 202/574] fix modules repo import error --- tests/modules/test_modules_json.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py index b2cac99e6d..0368c146c4 100644 --- a/tests/modules/test_modules_json.py +++ b/tests/modules/test_modules_json.py @@ -7,9 +7,9 @@ NF_CORE_MODULES_DEFAULT_BRANCH, NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, - ModulesRepo, ) from nf_core.modules.modules_json import ModulesJson +from nf_core.modules.modules_repo import ModulesRepo from nf_core.modules.patch import ModulePatch from ..test_modules import TestModules From 9ed6cdcc28d4be17175ae5a4a98f5278949c3db9 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 15:55:30 +0000 Subject: [PATCH 203/574] Update python:3.12-slim Docker digest to 740d94a --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8943b70627..c88abcb1ce 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:f11725aba18c19664a408902103365eaf8013823ffc56270f921d1dc78a198cb +FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 7b4d135569320507bdbfb99ff459aa4d195d9357 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 25 Jul 2024 17:51:32 +0000 Subject: [PATCH 204/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b407f5349a..b27dce4b5c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -53,6 +53,7 @@ - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) +- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From fcc859ef3da2d369c5a5fc7e031d8dcd03d5a72b Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 25 Jul 2024 19:45:20 +0000 Subject: [PATCH 205/574] Update pre-commit hook pre-commit/mirrors-mypy to v1.11.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fc2011cb99..63202e5178 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: alias: ec - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.10.1" + rev: "v1.11.0" hooks: - id: mypy additional_dependencies: From baa1a3c27c9ae947db118f22ba7a3e0b746f9dfd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 25 Jul 2024 20:04:49 +0000 Subject: [PATCH 206/574] Update gitpod/workspace-base Docker digest to f189a41 --- nf_core/gitpod/gitpod.Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 2f458dfc2a..fd0e8bb799 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -1,7 +1,7 @@ # Test build locally before making a PR # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile . -FROM gitpod/workspace-base@sha256:0f3822450f94084f6a62db4a4282d895591f6a55632dc044fe496f98cb79e75c +FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c USER root From b53a4b82436f0313fa5c0896e9edd869c3043084 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 09:30:22 +0200 Subject: [PATCH 207/574] fix incorrect type name --- nf_core/modules/modules_differ.py | 6 +++--- nf_core/modules/modules_json.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index 36d927f084..e310b3bf8b 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -4,7 +4,7 @@ import logging import os from pathlib import Path -from typing import List, Union +from typing import Dict, List, Union from rich.console import Console from rich.syntax import Syntax @@ -296,7 +296,7 @@ def print_diff( console.print(Syntax("".join(diff), "diff", theme="ansi_dark", padding=1)) @staticmethod - def per_file_patch(patch_fn: Union[str, Path]) -> dict[str, List[str]]: + def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]: """ Splits a patch file for several files into one patch per file. @@ -453,7 +453,7 @@ def try_apply_single_patch(file_lines, patch, reverse=False): @staticmethod def try_apply_patch( module: str, repo_path: Union[str, Path], patch_path: Union[str, Path], module_dir: Path, reverse: bool = False - ) -> dict[str, List[str]]: + ) -> Dict[str, List[str]]: """ Try applying a full patch file to a module diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index f992271741..4f3578b02b 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -1000,7 +1000,7 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir): .get("git_sha", None) ) - def get_all_components(self, component_type: str) -> dict[str, List[Tuple[(str, str)]]]: + def get_all_components(self, component_type: str) -> Dict[str, List[Tuple[(str, str)]]]: """ Retrieves all pipeline modules/subworkflows that are reported in the modules.json From bdbdd17a24c8aee70339f22d0bc0994c2f65fe4e Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 11:50:17 +0200 Subject: [PATCH 208/574] fix types --- nf_core/pipelines/create/create.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index acbe7efd5c..5e57d27c3b 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -81,8 +81,11 @@ def __init__( else: raise UserWarning("The template configuration was not provided.") + if self.config.outdir is None: + self.config.outdir = str(Path.cwd()) + self.jinja_params, skip_paths = self.obtain_jinja_params_dict( - self.config.skip_features or [], self.config.outdir + self.config.skip_features or [], Path(self.config.outdir) ) skippable_paths = { @@ -110,8 +113,7 @@ def __init__( self.default_branch = default_branch self.is_interactive = is_interactive self.force = self.config.force - if self.config.outdir is None: - self.config.outdir = str(Path.cwd()) + if self.config.outdir == ".": self.outdir = Path(self.config.outdir, self.jinja_params["name_noslash"]).absolute() else: @@ -184,7 +186,7 @@ def update_config(self, organisation, version, force, outdir): if self.config.is_nfcore is None: self.config.is_nfcore = self.config.org == "nf-core" - def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): + def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Union[str, Path]): """Creates a dictionary of parameters for the new pipeline. Args: @@ -379,7 +381,6 @@ def render_template(self): with open(str(config_fn), "w") as fh: self.config.outdir = str(self.config.outdir) config_yml.template = NFCoreTemplateConfig(**self.config.model_dump()) - yaml.safe_dump(config_yml.model_dump(), fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) From 98c3fb0178a4548fcab1db5055cedd1586f0c915 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 11:54:07 +0200 Subject: [PATCH 209/574] fix type definition for older python version --- nf_core/modules/modules_json.py | 2 +- nf_core/pipelines/lint/modules_json.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 4f3578b02b..9f17add6ae 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -115,7 +115,7 @@ def create(self) -> None: self.dump() def get_component_names_from_repo( - self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, str | List[str]]]]]], directory: Path + self, repos: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Union[str, List[str]]]]]]], directory: Path ) -> List[Tuple[str, List[str], str]]: """ Get component names from repositories in a pipeline. diff --git a/nf_core/pipelines/lint/modules_json.py b/nf_core/pipelines/lint/modules_json.py index 5ce2054036..2b7c266848 100644 --- a/nf_core/pipelines/lint/modules_json.py +++ b/nf_core/pipelines/lint/modules_json.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import Dict, List +from typing import Dict, List, Union from nf_core.modules.modules_json import ModulesJson, ModulesJsonType @@ -19,7 +19,7 @@ def modules_json(self) -> Dict[str, List[str]]: # Load pipeline modules and modules.json _modules_json = ModulesJson(self.wf_path) _modules_json.load() - modules_json_dict: ModulesJsonType | None = _modules_json.modules_json + modules_json_dict: Union[ModulesJsonType, None] = _modules_json.modules_json modules_dir = Path(self.wf_path, "modules") if _modules_json and modules_json_dict is not None: From 7b883eb1f01bac9249428a3821c9a4454dc715ca Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 12:11:41 +0200 Subject: [PATCH 210/574] fix incorrect types and missing cli option names --- nf_core/__main__.py | 6 +++--- nf_core/pipelines/create/create.py | 9 +++++---- nf_core/pipelines/sync.py | 21 +++++++++++---------- 3 files changed, 19 insertions(+), 17 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 91af979586..d0aad63e80 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1036,7 +1036,7 @@ def command_modules_remove(ctx, directory, tool): @modules.command("create") @click.pass_context @click.argument("tool", type=str, required=False, metavar=" or ") -@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="") +@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="") @click.option( "-a", "--author", @@ -1306,7 +1306,7 @@ def subworkflows(ctx, git_remote, branch, no_pull): @subworkflows.command("create") @click.pass_context @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name") -@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="") +@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="") @click.option( "-a", "--author", @@ -1751,7 +1751,7 @@ def command_schema_docs(schema_path, output, format, force, columns): # nf-core create-logo (deprecated) @nf_core_cli.command("create-logo", deprecated=True, hidden=True) @click.argument("logo-text", metavar="") -@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.") +@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.") @click.option( "-n", "--name", diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 5e57d27c3b..15eed46dce 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -278,7 +278,7 @@ def init_pipeline(self): "https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community[/link]" ) - def render_template(self): + def render_template(self) -> None: """Runs Jinja to create a new nf-core pipeline.""" log.info(f"Creating new pipeline: '{self.name}'") @@ -306,7 +306,7 @@ def render_template(self): template_files += list(Path(template_dir).glob("*")) ignore_strs = [".pyc", "__pycache__", ".pyo", ".pyd", ".DS_Store", ".egg"] short_name = self.jinja_params["short_name"] - rename_files = { + rename_files: Dict[str, str] = { "workflows/pipeline.nf": f"workflows/{short_name}.nf", "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf", } @@ -327,8 +327,9 @@ def render_template(self): # Set up vars and directories template_fn = template_fn_path.relative_to(template_dir) output_path = self.outdir / template_fn - if template_fn in rename_files: - output_path = self.outdir / rename_files[template_fn] + + if str(template_fn) in rename_files: + output_path = self.outdir / rename_files[str(template_fn)] output_path.parent.mkdir(parents=True, exist_ok=True) try: diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index d044be84e4..741bdd751a 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -6,6 +6,7 @@ import re import shutil from pathlib import Path +from typing import Dict, Optional, Union import git import questionary @@ -61,24 +62,24 @@ class PipelineSync: def __init__( self, - pipeline_dir, - from_branch=None, - make_pr=False, - gh_repo=None, - gh_username=None, - template_yaml_path=None, - force_pr=False, + pipeline_dir: Union[str, Path], + from_branch: Optional[str] = None, + make_pr: bool = False, + gh_repo: Optional[str] = None, + gh_username: Optional[str] = None, + template_yaml_path: Optional[str] = None, + force_pr: bool = False, ): """Initialise syncing object""" - self.pipeline_dir = Path(pipeline_dir).resolve() + self.pipeline_dir: Path = Path(pipeline_dir).resolve() self.from_branch = from_branch self.original_branch = None self.original_merge_branch = f"nf-core-template-merge-{nf_core.__version__}" self.merge_branch = self.original_merge_branch self.made_changes = False self.make_pr = make_pr - self.gh_pr_returned_data = {} + self.gh_pr_returned_data: Dict = {} self.required_config_vars = ["manifest.name", "manifest.description", "manifest.version", "manifest.author"] self.force_pr = force_pr @@ -87,7 +88,7 @@ def __init__( self.pr_url = "" self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config(self.pipeline_dir) - assert self.config_yml_path is not None # mypy + assert self.config_yml_path is not None and self.config_yml is not None # mypy # Throw deprecation warning if template_yaml_path is set if template_yaml_path is not None: log.warning( From 0fe3910c54251b005a0cbc493de556d865310c1e Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 12:28:30 +0200 Subject: [PATCH 211/574] fix create-logo cli command --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index d0aad63e80..11ab574ccc 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -650,7 +650,7 @@ def command_pipelines_bump_version(ctx, new_version, directory, nextflow): # nf-core pipelines create-logo @pipelines.command("create-logo") @click.argument("logo-text", metavar="") -@click.option("-d", "--dir", type=click.Path(), default=".", help="Directory to save the logo in.") +@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.") @click.option( "-n", "--name", From ce325366e04551b46d109b572e95320c7dc39023 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 14:47:53 +0200 Subject: [PATCH 212/574] add types, include review comments, add pydantic mypy plugin --- .pre-commit-config.yaml | 1 + mypy.ini | 1 + nf_core/components/components_command.py | 6 +++++- nf_core/components/components_utils.py | 2 +- nf_core/components/info.py | 2 +- nf_core/components/lint/__init__.py | 5 +++-- 6 files changed, 12 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bcf7ff65ce..f763fa6658 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -28,3 +28,4 @@ repos: - types-jsonschema - types-Markdown - types-setuptools + - pydantic diff --git a/mypy.ini b/mypy.ini index c48aa5884b..5a95223162 100644 --- a/mypy.ini +++ b/mypy.ini @@ -1,3 +1,4 @@ [mypy] warn_unused_configs = True ignore_missing_imports = true +plugins = pydantic.mypy diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 4440dc32a4..91e14d0606 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -254,7 +254,11 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None: # Update path in modules.json if the file is in the correct format modules_json = ModulesJson(self.directory) modules_json.load() - if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None: + if ( + modules_json.has_git_url_and_modules() + and self.modules_repo.repo_path is not None + and modules_json.modules_json is not None + ): modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][ self.modules_repo.repo_path ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve())) diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 4e9c0ac601..3d64dc1bb6 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -77,7 +77,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P ).unsafe_ask() log.info("To avoid this prompt in the future, add the 'org_path' key to a root '%s' file.", config_fn.name) if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this config now?", default=True): - with open(str(config_fn), "a+") as fh: + with open(config_fn, "a+") as fh: fh.write(f"org_path: {org}\n") log.info(f"Config added to '{config_fn.name}'") diff --git a/nf_core/components/info.py b/nf_core/components/info.py index 55a95593f9..726586b5b7 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -107,7 +107,7 @@ def init_mod_name(self, component): elif self.repo_type == "pipeline": assert self.modules_json is not None # mypy all_components = self.modules_json.get_all_components(self.component_type).get( - self.modules_repo.remote_url, [] + self.modules_repo.remote_url, {} ) components = [ component if directory == self.modules_repo.repo_path else f"{directory}/{component}" diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index e2475ef62c..ddf5e1e165 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -22,6 +22,7 @@ from nf_core.components.nfcore_component import NFCoreComponent from nf_core.modules.modules_json import ModulesJson from nf_core.pipelines.lint_utils import console +from nf_core.utils import LintConfigType from nf_core.utils import plural_s as _s log = logging.getLogger(__name__) @@ -77,8 +78,8 @@ def __init__( self.failed: List[LintResult] = [] self.all_local_components: List[NFCoreComponent] = [] - self.lint_config = None - self.modules_json = None + self.lint_config: Optional[LintConfigType] = None + self.modules_json: Optional[ModulesJson] = None if self.component_type == "modules": self.lint_tests = self.get_all_module_lint_tests(self.repo_type == "pipeline") From 8eeaf28402013b4f54af693f80836de92c8d2cf7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 14:50:35 +0200 Subject: [PATCH 213/574] fix mypy error --- nf_core/modules/lint/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index cea75d8f2e..fcf2d7d066 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -238,7 +238,7 @@ def lint_module( # Otherwise run all the lint tests else: - if self.repo_type == "pipeline" and self.modules_json: + if self.repo_type == "pipeline" and self.modules_json and mod.repo_url: # Set correct sha version = self.modules_json.get_module_version(mod.component_name, mod.repo_url, mod.org) mod.git_sha = version From 95de96b7bddf192cd5ef3ea75218236ec73e02c4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 15:27:31 +0200 Subject: [PATCH 214/574] allow dashes in pipeilne short name (why didn't this fail before?) --- nf_core/pipelines/create/create.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 15eed46dce..dcb6d2c994 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -249,7 +249,7 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un return jinja_params, skip_paths # Check that the pipeline name matches the requirements - if not re.match(r"^[a-z]+$", jinja_params["short_name"]): + if not re.match(r"^[a-z-]+$", jinja_params["short_name"]): if jinja_params["is_nfcore"]: raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.") else: From 1b6f231ebc41665a7cad108fe4fdbc7b38d218f0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 15:27:59 +0200 Subject: [PATCH 215/574] Revert "allow dashes in pipeilne short name (why didn't this fail before?)" This reverts commit 95de96b7bddf192cd5ef3ea75218236ec73e02c4. --- nf_core/pipelines/create/create.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index dcb6d2c994..15eed46dce 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -249,7 +249,7 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un return jinja_params, skip_paths # Check that the pipeline name matches the requirements - if not re.match(r"^[a-z-]+$", jinja_params["short_name"]): + if not re.match(r"^[a-z]+$", jinja_params["short_name"]): if jinja_params["is_nfcore"]: raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.") else: From 5186ac71523c0fe16978c3857325365f02d1093b Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 16:25:41 +0200 Subject: [PATCH 216/574] use path.walk correctly --- nf_core/components/components_command.py | 8 ++++---- nf_core/modules/modules_json.py | 4 ++-- nf_core/pipelines/lint/merge_markers.py | 2 +- nf_core/pipelines/lint/modules_structure.py | 2 +- nf_core/pipelines/lint/pipeline_todos.py | 2 +- nf_core/synced_repo.py | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 91e14d0606..5cde00ef69 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -87,7 +87,7 @@ def get_components_clone_modules(self) -> List[str]: component_base_path = Path(self.directory, self.default_subworkflows_path) return [ str(Path(directory).relative_to(component_base_path)) - for directory, _, files in Path.walk(component_base_path) + for directory, _, files in Path(component_base_path).walk() if "main.nf" in files ] @@ -126,7 +126,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False): + for dir_path, dir_names, filenames in Path(self.directory).walk(top_down=False): if not dir_names and not filenames: try: dir_path.rmdir() @@ -157,7 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]: return [ str(Path(dir_path).relative_to(repo_dir)) - for dir_path, _, files in Path.walk(repo_dir) + for dir_path, _, files in Path(repo_dir).walk() if "main.nf" in files ] @@ -202,7 +202,7 @@ def check_modules_structure(self) -> None: """ if self.repo_type == "pipeline": wrong_location_modules: List[Path] = [] - for directory, _, files in Path.walk(Path(self.directory, "modules")): + for directory, _, files in Path(self.directory, "modules").walk(): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.directory, "modules")) parts = module_path.parts diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 9f17add6ae..3f4fb46f2d 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -134,7 +134,7 @@ def get_component_names_from_repo( repo_url, [ str(component_name.relative_to(directory / modules_repo.repo_path)) - for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path) + for component_name, _, file_names in Path(directory / modules_repo.repo_path).walk() if "main.nf" in file_names ], modules_repo.repo_path, @@ -1189,7 +1189,7 @@ def components_with_repos(): self.modules_dir, modules_repo.repo_path, ) - for dir_name, _, _ in Path.walk(repo_url_path): + for dir_name, _, _ in repo_url_path.walk(): if component_type == "modules": if len(Path(directory).parts) > 1: # The module name is TOOL/SUBTOOL paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py index 208c9f4bcc..4e2f73fb85 100644 --- a/nf_core/pipelines/lint/merge_markers.py +++ b/nf_core/pipelines/lint/merge_markers.py @@ -42,7 +42,7 @@ def merge_markers(self): with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path.walk(self.wf_path, top_down=True): + for root, dirs, files in Path(self.wf_path).walk(top_down=True): # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py index fd29942ed6..34cdc89561 100644 --- a/nf_core/pipelines/lint/modules_structure.py +++ b/nf_core/pipelines/lint/modules_structure.py @@ -19,7 +19,7 @@ def modules_structure(self): modules/nf-core/modules/TOOL/SUBTOOL """ wrong_location_modules = [] - for directory, _, files in Path.walk(Path(self.wf_path, "modules")): + for directory, _, files in Path(self.wf_path, "modules").walk(): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.wf_path, "modules")) parts = module_path.parts diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py index 530d853764..0a21d0d05a 100644 --- a/nf_core/pipelines/lint/pipeline_todos.py +++ b/nf_core/pipelines/lint/pipeline_todos.py @@ -43,7 +43,7 @@ def pipeline_todos(self, root_dir=None): with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path.walk(root_dir, top_down=True): + for root, dirs, files in Path(root_dir).walk(top_down=True): # # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 8efdd0e488..22cdcd1577 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -467,7 +467,7 @@ def get_avail_components( # Module/Subworkflow directories are characterized by having a 'main.nf' file avail_component_names = [ str(Path(dirpath).relative_to(directory)) - for dirpath, _, files in Path.walk(directory) + for dirpath, _, files in Path(directory).walk() if "main.nf" in files ] return avail_component_names From 873398727b6dd8e6a1046f6a91c45bad8fd26825 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 16:37:19 +0200 Subject: [PATCH 217/574] Revert "use path.walk correctly" This reverts commit 5186ac71523c0fe16978c3857325365f02d1093b. --- nf_core/components/components_command.py | 8 ++++---- nf_core/modules/modules_json.py | 4 ++-- nf_core/pipelines/lint/merge_markers.py | 2 +- nf_core/pipelines/lint/modules_structure.py | 2 +- nf_core/pipelines/lint/pipeline_todos.py | 2 +- nf_core/synced_repo.py | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 5cde00ef69..91e14d0606 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -87,7 +87,7 @@ def get_components_clone_modules(self) -> List[str]: component_base_path = Path(self.directory, self.default_subworkflows_path) return [ str(Path(directory).relative_to(component_base_path)) - for directory, _, files in Path(component_base_path).walk() + for directory, _, files in Path.walk(component_base_path) if "main.nf" in files ] @@ -126,7 +126,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in Path(self.directory).walk(top_down=False): + for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False): if not dir_names and not filenames: try: dir_path.rmdir() @@ -157,7 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]: return [ str(Path(dir_path).relative_to(repo_dir)) - for dir_path, _, files in Path(repo_dir).walk() + for dir_path, _, files in Path.walk(repo_dir) if "main.nf" in files ] @@ -202,7 +202,7 @@ def check_modules_structure(self) -> None: """ if self.repo_type == "pipeline": wrong_location_modules: List[Path] = [] - for directory, _, files in Path(self.directory, "modules").walk(): + for directory, _, files in Path.walk(Path(self.directory, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.directory, "modules")) parts = module_path.parts diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 3f4fb46f2d..9f17add6ae 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -134,7 +134,7 @@ def get_component_names_from_repo( repo_url, [ str(component_name.relative_to(directory / modules_repo.repo_path)) - for component_name, _, file_names in Path(directory / modules_repo.repo_path).walk() + for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path) if "main.nf" in file_names ], modules_repo.repo_path, @@ -1189,7 +1189,7 @@ def components_with_repos(): self.modules_dir, modules_repo.repo_path, ) - for dir_name, _, _ in repo_url_path.walk(): + for dir_name, _, _ in Path.walk(repo_url_path): if component_type == "modules": if len(Path(directory).parts) > 1: # The module name is TOOL/SUBTOOL paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py index 4e2f73fb85..208c9f4bcc 100644 --- a/nf_core/pipelines/lint/merge_markers.py +++ b/nf_core/pipelines/lint/merge_markers.py @@ -42,7 +42,7 @@ def merge_markers(self): with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path(self.wf_path).walk(top_down=True): + for root, dirs, files in Path.walk(self.wf_path, top_down=True): # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py index 34cdc89561..fd29942ed6 100644 --- a/nf_core/pipelines/lint/modules_structure.py +++ b/nf_core/pipelines/lint/modules_structure.py @@ -19,7 +19,7 @@ def modules_structure(self): modules/nf-core/modules/TOOL/SUBTOOL """ wrong_location_modules = [] - for directory, _, files in Path(self.wf_path, "modules").walk(): + for directory, _, files in Path.walk(Path(self.wf_path, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.wf_path, "modules")) parts = module_path.parts diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py index 0a21d0d05a..530d853764 100644 --- a/nf_core/pipelines/lint/pipeline_todos.py +++ b/nf_core/pipelines/lint/pipeline_todos.py @@ -43,7 +43,7 @@ def pipeline_todos(self, root_dir=None): with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path(root_dir).walk(top_down=True): # + for root, dirs, files in Path.walk(root_dir, top_down=True): # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 22cdcd1577..8efdd0e488 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -467,7 +467,7 @@ def get_avail_components( # Module/Subworkflow directories are characterized by having a 'main.nf' file avail_component_names = [ str(Path(dirpath).relative_to(directory)) - for dirpath, _, files in Path(directory).walk() + for dirpath, _, files in Path.walk(directory) if "main.nf" in files ] return avail_component_names From 1679594f5a52c0926f7f40800fcf43c445f8515a Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 16:41:59 +0200 Subject: [PATCH 218/574] switch back to os.walk() --- nf_core/components/components_command.py | 13 ++++++------- nf_core/modules/modules_json.py | 4 ++-- nf_core/pipelines/lint/merge_markers.py | 3 ++- nf_core/pipelines/lint/modules_structure.py | 3 ++- nf_core/pipelines/lint/pipeline_todos.py | 3 ++- nf_core/synced_repo.py | 4 +--- 6 files changed, 15 insertions(+), 15 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 91e14d0606..ada8b532e5 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -1,5 +1,6 @@ import logging import mmap +import os import shutil from pathlib import Path from typing import Dict, List, Optional, Union @@ -87,7 +88,7 @@ def get_components_clone_modules(self) -> List[str]: component_base_path = Path(self.directory, self.default_subworkflows_path) return [ str(Path(directory).relative_to(component_base_path)) - for directory, _, files in Path.walk(component_base_path) + for directory, _, files in os.walk(component_base_path) if "main.nf" in files ] @@ -126,10 +127,10 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in Path.walk(Path(self.directory), top_down=False): + for dir_path, dir_names, filenames in os.walk(Path(self.directory), topdown=False): if not dir_names and not filenames: try: - dir_path.rmdir() + Path(dir_path).rmdir() except OSError: pass else: @@ -156,9 +157,7 @@ def components_from_repo(self, install_dir: str) -> List[str]: raise LookupError(f"Nothing installed from {install_dir} in pipeline") return [ - str(Path(dir_path).relative_to(repo_dir)) - for dir_path, _, files in Path.walk(repo_dir) - if "main.nf" in files + str(Path(dir_path).relative_to(repo_dir)) for dir_path, _, files in os.walk(repo_dir) if "main.nf" in files ] def install_component_files( @@ -202,7 +201,7 @@ def check_modules_structure(self) -> None: """ if self.repo_type == "pipeline": wrong_location_modules: List[Path] = [] - for directory, _, files in Path.walk(Path(self.directory, "modules")): + for directory, _, files in os.walk(Path(self.directory, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.directory, "modules")) parts = module_path.parts diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 9f17add6ae..4f86bc8302 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -134,7 +134,7 @@ def get_component_names_from_repo( repo_url, [ str(component_name.relative_to(directory / modules_repo.repo_path)) - for component_name, _, file_names in Path.walk(directory / modules_repo.repo_path) + for component_name, _, file_names in os.walk(directory / modules_repo.repo_path) if "main.nf" in file_names ], modules_repo.repo_path, @@ -1189,7 +1189,7 @@ def components_with_repos(): self.modules_dir, modules_repo.repo_path, ) - for dir_name, _, _ in Path.walk(repo_url_path): + for dir_name, _, _ in os.walk(repo_url_path): if component_type == "modules": if len(Path(directory).parts) > 1: # The module name is TOOL/SUBTOOL paths_in_directory.append(str(Path(*Path(dir_name).parts[-2:]))) diff --git a/nf_core/pipelines/lint/merge_markers.py b/nf_core/pipelines/lint/merge_markers.py index 208c9f4bcc..1c3d70a76f 100644 --- a/nf_core/pipelines/lint/merge_markers.py +++ b/nf_core/pipelines/lint/merge_markers.py @@ -1,5 +1,6 @@ import fnmatch import logging +import os from pathlib import Path import nf_core.utils @@ -42,7 +43,7 @@ def merge_markers(self): with open(Path(self.wf_path, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path.walk(self.wf_path, top_down=True): + for root, dirs, files in os.walk(self.wf_path, topdown=True): # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/pipelines/lint/modules_structure.py b/nf_core/pipelines/lint/modules_structure.py index fd29942ed6..9d9b4c9fc0 100644 --- a/nf_core/pipelines/lint/modules_structure.py +++ b/nf_core/pipelines/lint/modules_structure.py @@ -1,4 +1,5 @@ import logging +import os from pathlib import Path log = logging.getLogger(__name__) @@ -19,7 +20,7 @@ def modules_structure(self): modules/nf-core/modules/TOOL/SUBTOOL """ wrong_location_modules = [] - for directory, _, files in Path.walk(Path(self.wf_path, "modules")): + for directory, _, files in os.walk(Path(self.wf_path, "modules")): if "main.nf" in files: module_path = Path(directory).relative_to(Path(self.wf_path, "modules")) parts = module_path.parts diff --git a/nf_core/pipelines/lint/pipeline_todos.py b/nf_core/pipelines/lint/pipeline_todos.py index 530d853764..0535069f9a 100644 --- a/nf_core/pipelines/lint/pipeline_todos.py +++ b/nf_core/pipelines/lint/pipeline_todos.py @@ -1,5 +1,6 @@ import fnmatch import logging +import os from pathlib import Path log = logging.getLogger(__name__) @@ -43,7 +44,7 @@ def pipeline_todos(self, root_dir=None): with open(Path(root_dir, ".gitignore"), encoding="latin1") as fh: for line in fh: ignore.append(Path(line.strip().rstrip("/")).name) - for root, dirs, files in Path.walk(root_dir, top_down=True): + for root, dirs, files in os.walk(root_dir, topdown=True): # Ignore files for i_base in ignore: i = str(Path(root, i_base)) diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py index 8efdd0e488..e2a76ccaeb 100644 --- a/nf_core/synced_repo.py +++ b/nf_core/synced_repo.py @@ -466,9 +466,7 @@ def get_avail_components( directory = self.subworkflows_dir # Module/Subworkflow directories are characterized by having a 'main.nf' file avail_component_names = [ - str(Path(dirpath).relative_to(directory)) - for dirpath, _, files in Path.walk(directory) - if "main.nf" in files + str(Path(dirpath).relative_to(directory)) for dirpath, _, files in os.walk(directory) if "main.nf" in files ] return avail_component_names From 3c0433e68fc33be6dd35dfbb88b3989e103b6ad6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 22:43:37 +0200 Subject: [PATCH 219/574] fix sync --- nf_core/modules/modules_json.py | 2 +- nf_core/pipelines/create/create.py | 5 ++--- nf_core/pipelines/sync.py | 7 ++----- nf_core/utils.py | 2 ++ 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 4f86bc8302..39d70b7d78 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -133,7 +133,7 @@ def get_component_names_from_repo( components = ( repo_url, [ - str(component_name.relative_to(directory / modules_repo.repo_path)) + str(Path(component_name).relative_to(directory / modules_repo.repo_path)) for component_name, _, file_names in os.walk(directory / modules_repo.repo_path) if "main.nf" in file_names ], diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 15eed46dce..9b64b53446 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -53,7 +53,7 @@ def __init__( no_git: bool = False, force: bool = False, outdir: Optional[Union[Path, str]] = None, - template_config: Optional[Union[str, CreateConfig, Path]] = None, + template_config: Optional[CreateConfig] = None, organisation: str = "nf-core", from_config_file: bool = False, default_branch: Optional[str] = None, @@ -67,7 +67,7 @@ def __init__( _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else Path().cwd()) # Obtain a CreateConfig object from `.nf-core.yml` config file if config_yml is not None and getattr(config_yml, "template", None) is not None: - self.config = CreateConfig(**config_yml["template"]) + self.config = CreateConfig(**config_yml["template"].model_dump()) else: raise UserWarning("The template configuration was not provided in '.nf-core.yml'.") except (FileNotFoundError, UserWarning): @@ -261,7 +261,6 @@ def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Un def init_pipeline(self): """Creates the nf-core pipeline.""" - # Make the new pipeline self.render_template() diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index 741bdd751a..efc7212b4d 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -270,13 +270,10 @@ def make_template_pipeline(self): try: nf_core.pipelines.create.create.PipelineCreate( - name=self.wf_config["manifest.name"].strip('"').strip("'"), - description=self.wf_config["manifest.description"].strip('"').strip("'"), - version=self.wf_config["manifest.version"].strip('"').strip("'"), + outdir=str(self.pipeline_dir), + from_config_file=True, no_git=True, force=True, - outdir=str(self.pipeline_dir), - author=self.wf_config["manifest.author"].strip('"').strip("'"), ).init_pipeline() except Exception as err: # Reset to where you were to prevent git getting messed up. diff --git a/nf_core/utils.py b/nf_core/utils.py index 0beb8c7366..44eafca3cc 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1053,6 +1053,8 @@ class NFCoreTemplateConfig(BaseModel): is_nfcore: Optional[bool] = None def __getitem__(self, item: str) -> Any: + if self is None: + return None return getattr(self, item) def get(self, item: str, default: Any = None) -> Any: From 4d6930be2da27623f5e1644785cb6bcf1a994d74 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 26 Jul 2024 22:46:57 +0200 Subject: [PATCH 220/574] fix types --- nf_core/pipelines/create/create.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 9b64b53446..d5c230e048 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -53,7 +53,7 @@ def __init__( no_git: bool = False, force: bool = False, outdir: Optional[Union[Path, str]] = None, - template_config: Optional[CreateConfig] = None, + template_config: Optional[Union[CreateConfig, str, Path]] = None, organisation: str = "nf-core", from_config_file: bool = False, default_branch: Optional[str] = None, From 26b1cd13c36bc2d1234b8f97e6141bf9c0c82c5c Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 11:44:02 +0200 Subject: [PATCH 221/574] set force true in sync to create a template file --- nf_core/pipelines/sync.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index efc7212b4d..fced35dc20 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -263,8 +263,12 @@ def make_template_pipeline(self): logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR) assert self.config_yml_path is not None assert self.config_yml is not None + # Re-write the template yaml info from .nf-core.yml config - if getattr(self.config_yml, "template", None) is not None: + if self.config_yml.template is not None: + # Set force true in config to overwrite existing files + + self.config_yml.template.force = True with open(self.config_yml_path, "w") as config_path: yaml.safe_dump(self.config_yml.model_dump(), config_path) @@ -275,6 +279,14 @@ def make_template_pipeline(self): no_git=True, force=True, ).init_pipeline() + + # set force to false to avoid overwriting files in the future + if self.config_yml.template is not None: + # Set force true in config to overwrite existing files + self.config_yml.template.force = False + with open(self.config_yml_path, "w") as config_path: + yaml.safe_dump(self.config_yml.model_dump(), config_path) + except Exception as err: # Reset to where you were to prevent git getting messed up. self.repo.git.reset("--hard") From 59a3eb38c2f7603ed63c73ea6c1589a9b73a95c1 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 12:33:14 +0200 Subject: [PATCH 222/574] fix missing initialization in download.py --- nf_core/pipelines/download.py | 10 ++++++---- nf_core/utils.py | 14 ++++++++------ 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 797909636c..704fe91b2f 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -11,7 +11,7 @@ import textwrap from datetime import datetime from pathlib import Path -from typing import List, Optional, Tuple +from typing import Any, Dict, List, Optional, Tuple from zipfile import ZipFile import git @@ -24,6 +24,7 @@ from packaging.version import Version import nf_core +import nf_core.modules.modules_utils import nf_core.pipelines.list import nf_core.utils from nf_core.synced_repo import RemoteProgressbar, SyncedRepo @@ -131,6 +132,7 @@ def __init__( self.compress_type = compress_type self.force = force self.platform = platform + self.fullname: Optional[str] = None # if flag is not specified, do not assume deliberate choice and prompt config inclusion interactively. # this implies that non-interactive "no" choice is only possible implicitly (e.g. with --platform or if prompt is suppressed by !stderr.is_interactive). # only alternative would have been to make it a parameter with argument, e.g. -d="yes" or -d="no". @@ -161,8 +163,8 @@ def __init__( # allows to specify a container library / registry or a respective mirror to download images from self.parallel_downloads = parallel_downloads - self.wf_revisions = {} - self.wf_branches = {} + self.wf_revisions = [] + self.wf_branches: Dict[str, Any] = {} self.wf_sha = {} self.wf_download_url = {} self.nf_config = {} @@ -339,7 +341,7 @@ def prompt_pipeline_name(self): stderr.print("Specify the name of a nf-core pipeline or a GitHub repository name (user/repo).") self.pipeline = nf_core.utils.prompt_remote_pipeline_name(self.wfs) - def prompt_revision(self): + def prompt_revision(self) -> None: """ Prompt for pipeline revision / branch Prompt user for revision tag if '--revision' was not set diff --git a/nf_core/utils.py b/nf_core/utils.py index 44eafca3cc..80324fc9a8 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -903,7 +903,9 @@ def prompt_remote_pipeline_name(wfs): raise AssertionError(f"Not able to find pipeline '{pipeline}'") -def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False): +def prompt_pipeline_release_branch( + wf_releases: List[Dict[str, Any]], wf_branches: Dict[str, Any], multiple: bool = False +) -> tuple[Any, list[str]]: """Prompt for pipeline release / branch Args: @@ -912,18 +914,18 @@ def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False): multiple (bool): Allow selection of multiple releases & branches (for Seqera Platform) Returns: - choice (str): Selected release / branch name + choice (questionary.Choice or bool): Selected release / branch or False if no releases / branches available """ # Prompt user for release tag, tag_set will contain all available. - choices = [] - tag_set = [] + choices: List[questionary.Choice] = [] + tag_set: List[str] = [] # Releases if len(wf_releases) > 0: for tag in map(lambda release: release.get("tag_name"), wf_releases): tag_display = [("fg:ansiblue", f"{tag} "), ("class:choice-default", "[release]")] choices.append(questionary.Choice(title=tag_display, value=tag)) - tag_set.append(tag) + tag_set.append(str(tag)) # Branches for branch in wf_branches.keys(): @@ -932,7 +934,7 @@ def prompt_pipeline_release_branch(wf_releases, wf_branches, multiple=False): tag_set.append(branch) if len(choices) == 0: - return False + return [], [] if multiple: return ( From fec536fd1ece3ce042a7fa32c9f05a7ddaa6ad06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 29 Jul 2024 13:35:40 +0200 Subject: [PATCH 223/574] Apply suggestions from code review --- CHANGELOG.md | 2 +- nf_core/commands_pipelines.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c47c1b887..15e92781cb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) -- Rrestructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) +- Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) ### Download diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py index c586534b22..4b6fa75f3e 100644 --- a/nf_core/commands_pipelines.py +++ b/nf_core/commands_pipelines.py @@ -284,7 +284,7 @@ def pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template. To keep nf-core pipelines up to date with improvements in the main - template, we use a method of w that uses a special + template, we use a method of synchronisation that uses a special git branch called [cyan i]TEMPLATE[/]. This command updates the [cyan i]TEMPLATE[/] branch with the latest version of From 7f03f9e807c537c448f75d69002625b0768b4931 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:12:24 +0200 Subject: [PATCH 224/574] fix mypy warnings --- nf_core/pipelines/create/utils.py | 12 +++++++++--- nf_core/pipelines/create_logo.py | 6 +++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 88994c9361..e62ef328e4 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -124,10 +124,16 @@ def compose(self) -> ComposeResult: @on(Input.Submitted) def show_invalid_reasons(self, event: Union[Input.Changed, Input.Submitted]) -> None: """Validate the text input and show errors if invalid.""" - if not event.validation_result.is_valid: - self.query_one(".validation_msg").update("\n".join(event.validation_result.failure_descriptions)) + val_msg = self.query_one(".validation_msg") + if not isinstance(val_msg, Static): + raise ValueError("Validation message not found.") + + if event.validation_result is not None and not event.validation_result.is_valid: + # check that val_msg is instance of Static + if isinstance(val_msg, Static): + val_msg.update("\n".join(event.validation_result.failure_descriptions)) else: - self.query_one(".validation_msg").update("") + val_msg.update("") class ValidateConfig(Validator): diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py index f49e98e93c..6619b910b5 100644 --- a/nf_core/pipelines/create_logo.py +++ b/nf_core/pipelines/create_logo.py @@ -1,6 +1,6 @@ import logging from pathlib import Path -from typing import Union +from typing import Optional, Union from PIL import Image, ImageDraw, ImageFont @@ -59,11 +59,11 @@ def create_logo( return logo_path # cache file cache_path = Path(NFCORE_CACHE_DIR, "logo", cache_name) - img = None + img: Optional[Image.Image] = None if cache_path.is_file(): log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.") img = Image.open(str(cache_path)) - if not img: + if img is None: log.debug(f"Creating logo for {text}") # make sure the figure fits the text From a4c829fb909f060f3c5d35486a7b293c2161757f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 29 Jul 2024 12:40:04 +0200 Subject: [PATCH 225/574] add option to skip code linters --- .../create-test-lint-wf-template.yml | 5 + nf_core/pipeline-template/.gitpod.yml | 3 +- nf_core/pipelines/create/create.py | 8 + nf_core/pipelines/create/custompipeline.py | 16 + tests/__snapshots__/test_create_app.ambr | 511 +++++++++--------- tests/data/pipeline_create_template_skip.yml | 1 + tests/test_create.py | 14 +- 7 files changed, 296 insertions(+), 262 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index b823ca72d8..cfa0a50079 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -41,6 +41,7 @@ jobs: - "template_skip_github_badges.yml" - "template_skip_igenomes.yml" - "template_skip_ci.yml" + - "template_skip_code_linters.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -102,6 +103,10 @@ jobs: run: | printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml + - name: Create template skip code_linters + run: | + printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 105a1821a1..30e85ed977 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -10,8 +10,9 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack + #{%- if code_linters -%} - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files + - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %} - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors # - nextflow.nextflow # Nextflow syntax highlighting diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 27ca8ac847..42e4a6ad7b 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -94,6 +94,13 @@ def __init__( ".github/workflows/awstest.yml", ".github/workflows/release-announcements.yml", ], + "code_linters": [ + ".editorconfig", + ".pre-commit-config.yaml", + ".prettierignore", + ".prettierrc.yml", + ".github/workflows/fix-linting.yml", + ], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -202,6 +209,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "github_badges": {"file": False, "content": True}, "igenomes": {"file": True, "content": True}, "nf_core_configs": {"file": False, "content": True}, + "code_linters": {"file": True, "content": True}, } # Set the parameters for the jinja template diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 7d460db65d..7a94ab228a 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -41,6 +41,16 @@ For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs) """ +markdown_code_linters = """ +Pipelines include code linters, these linters will check the formatting of your code. +Linters will check JSON, YAML, Python and others. +The available code linters are: + +- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. +- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces. +- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -80,6 +90,12 @@ def compose(self) -> ComposeResult: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions", "nf_core_configs", ), + PipelineFeature( + markdown_code_linters, + "Use code linters", + "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", + "code_linters", + ), classes="features-container", ) yield Center( diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 2ad0772587..5e5b005de0 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2971485804-matrix { + .terminal-2778615119-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2971485804-title { + .terminal-2778615119-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2971485804-r1 { fill: #c5c8c6 } - .terminal-2971485804-r2 { fill: #e3e3e3 } - .terminal-2971485804-r3 { fill: #989898 } - .terminal-2971485804-r4 { fill: #e1e1e1 } - .terminal-2971485804-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2971485804-r6 { fill: #1e1e1e } - .terminal-2971485804-r7 { fill: #0178d4 } - .terminal-2971485804-r8 { fill: #454a50 } - .terminal-2971485804-r9 { fill: #e2e2e2 } - .terminal-2971485804-r10 { fill: #808080 } - .terminal-2971485804-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2971485804-r12 { fill: #000000 } - .terminal-2971485804-r13 { fill: #e4e4e4 } - .terminal-2971485804-r14 { fill: #14191f } - .terminal-2971485804-r15 { fill: #507bb3 } - .terminal-2971485804-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2971485804-r17 { fill: #001541 } - .terminal-2971485804-r18 { fill: #7ae998 } - .terminal-2971485804-r19 { fill: #0a180e;font-weight: bold } - .terminal-2971485804-r20 { fill: #008139 } - .terminal-2971485804-r21 { fill: #fea62b;font-weight: bold } - .terminal-2971485804-r22 { fill: #a7a9ab } - .terminal-2971485804-r23 { fill: #e2e3e3 } + .terminal-2778615119-r1 { fill: #c5c8c6 } + .terminal-2778615119-r2 { fill: #e3e3e3 } + .terminal-2778615119-r3 { fill: #989898 } + .terminal-2778615119-r4 { fill: #e1e1e1 } + .terminal-2778615119-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2778615119-r6 { fill: #1e1e1e } + .terminal-2778615119-r7 { fill: #0178d4 } + .terminal-2778615119-r8 { fill: #454a50 } + .terminal-2778615119-r9 { fill: #e2e2e2 } + .terminal-2778615119-r10 { fill: #808080 } + .terminal-2778615119-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-2778615119-r12 { fill: #000000 } + .terminal-2778615119-r13 { fill: #e4e4e4 } + .terminal-2778615119-r14 { fill: #14191f } + .terminal-2778615119-r15 { fill: #507bb3 } + .terminal-2778615119-r16 { fill: #dde6ed;font-weight: bold } + .terminal-2778615119-r17 { fill: #001541 } + .terminal-2778615119-r18 { fill: #7ae998 } + .terminal-2778615119-r19 { fill: #0a180e;font-weight: bold } + .terminal-2778615119-r20 { fill: #008139 } + .terminal-2778615119-r21 { fill: #fea62b;font-weight: bold } + .terminal-2778615119-r22 { fill: #a7a9ab } + .terminal-2778615119-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing▄▄ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,255 @@ font-weight: 700; } - .terminal-1445899181-matrix { + .terminal-763408100-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1445899181-title { + .terminal-763408100-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1445899181-r1 { fill: #c5c8c6 } - .terminal-1445899181-r2 { fill: #e3e3e3 } - .terminal-1445899181-r3 { fill: #989898 } - .terminal-1445899181-r4 { fill: #e1e1e1 } - .terminal-1445899181-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1445899181-r6 { fill: #1e1e1e } - .terminal-1445899181-r7 { fill: #507bb3 } - .terminal-1445899181-r8 { fill: #e2e2e2 } - .terminal-1445899181-r9 { fill: #808080 } - .terminal-1445899181-r10 { fill: #dde6ed;font-weight: bold } - .terminal-1445899181-r11 { fill: #001541 } - .terminal-1445899181-r12 { fill: #454a50 } - .terminal-1445899181-r13 { fill: #7ae998 } - .terminal-1445899181-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-1445899181-r15 { fill: #0a180e;font-weight: bold } - .terminal-1445899181-r16 { fill: #000000 } - .terminal-1445899181-r17 { fill: #008139 } - .terminal-1445899181-r18 { fill: #fea62b;font-weight: bold } - .terminal-1445899181-r19 { fill: #a7a9ab } - .terminal-1445899181-r20 { fill: #e2e3e3 } + .terminal-763408100-r1 { fill: #c5c8c6 } + .terminal-763408100-r2 { fill: #e3e3e3 } + .terminal-763408100-r3 { fill: #989898 } + .terminal-763408100-r4 { fill: #e1e1e1 } + .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } + .terminal-763408100-r6 { fill: #1e1e1e } + .terminal-763408100-r7 { fill: #507bb3 } + .terminal-763408100-r8 { fill: #e2e2e2 } + .terminal-763408100-r9 { fill: #808080 } + .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } + .terminal-763408100-r11 { fill: #001541 } + .terminal-763408100-r12 { fill: #14191f } + .terminal-763408100-r13 { fill: #454a50 } + .terminal-763408100-r14 { fill: #7ae998 } + .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } + .terminal-763408100-r17 { fill: #000000 } + .terminal-763408100-r18 { fill: #008139 } + .terminal-763408100-r19 { fill: #fea62b;font-weight: bold } + .terminal-763408100-r20 { fill: #a7a9ab } + .terminal-763408100-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI tests        The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for  - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file  Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include GitHub - badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles containing - custom parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different ▁▁ + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index ed498cb732..d9ef405c51 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -11,3 +11,4 @@ skip_features: - github_badges - igenomes - nf_core_configs + - code_linters diff --git a/tests/test_create.py b/tests/test_create.py index 313b6f5354..896a8e7ad6 100644 --- a/tests/test_create.py +++ b/tests/test_create.py @@ -106,14 +106,16 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path): pipeline.init_pipeline() # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input - assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml")) - assert os.path.exists(os.path.join(pipeline.outdir, ".nf-core.yml")) - with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh: + assert not os.path.exists(Path(pipeline.outdir / "pipeline_template.yml")) + assert os.path.exists(Path(pipeline.outdir / ".nf-core.yml")) + with open(Path(pipeline.outdir / ".nf-core.yml")) as fh: nfcore_yml = yaml.safe_load(fh) assert "template" in nfcore_yml assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items() # Check that some of the skipped files are not present - assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md")) - assert not os.path.exists(os.path.join(pipeline.outdir, ".github")) - assert not os.path.exists(os.path.join(pipeline.outdir, "conf", "igenomes.config")) + assert not os.path.exists(Path(pipeline.outdir / "CODE_OF_CONDUCT.md")) + assert not os.path.exists(Path(pipeline.outdir / ".github")) + assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config")) + assert not os.path.exists(Path(pipeline.outdir / ".editorconfig")) + assert not os.path.exists(Path(pipeline.outdir / ".editorconfig")) From d2020f511c0f5992b6919e6832d3bcd5cd3bfe75 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:19:36 +0200 Subject: [PATCH 226/574] set default value for self.directory and more dir->directory switches --- nf_core/commands_modules.py | 38 ++++++++++++------------ nf_core/commands_subworkflows.py | 34 ++++++++++----------- nf_core/components/components_command.py | 12 ++++---- nf_core/components/list.py | 4 ++- nf_core/modules/list.py | 11 ++++++- nf_core/subworkflows/list.py | 11 ++++++- tests/modules/test_list.py | 18 +++++------ tests/subworkflows/test_list.py | 2 +- 8 files changed, 73 insertions(+), 57 deletions(-) diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index b93bd7bcb0..a889305055 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -17,7 +17,7 @@ def modules_list_remote(ctx, keywords, json): try: module_list = ModuleList( - None, + ".", True, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -29,7 +29,7 @@ def modules_list_remote(ctx, keywords, json): sys.exit(1) -def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def modules_list_local(ctx, keywords, json, directory): # pylint: disable=redefined-builtin """ List modules installed locally in a pipeline """ @@ -37,7 +37,7 @@ def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-b try: module_list = ModuleList( - dir, + directory, False, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -49,7 +49,7 @@ def modules_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-b sys.exit(1) -def modules_install(ctx, tool, dir, prompt, force, sha): +def modules_install(ctx, tool, directory, prompt, force, sha): """ Install DSL2 modules within a pipeline. @@ -59,7 +59,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha): try: module_install = ModuleInstall( - dir, + directory, force, prompt, sha, @@ -118,7 +118,7 @@ def modules_update( sys.exit(1) -def modules_patch(ctx, tool, dir, remove): +def modules_patch(ctx, tool, directory, remove): """ Create a patch file for minor changes in a module @@ -129,7 +129,7 @@ def modules_patch(ctx, tool, dir, remove): try: module_patch = ModulePatch( - dir, + directory, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], @@ -143,7 +143,7 @@ def modules_patch(ctx, tool, dir, remove): sys.exit(1) -def modules_remove(ctx, dir, tool): +def modules_remove(ctx, directory, tool): """ Remove a module from a pipeline. """ @@ -151,7 +151,7 @@ def modules_remove(ctx, dir, tool): try: module_remove = ModuleRemove( - dir, + directory, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], @@ -165,7 +165,7 @@ def modules_remove(ctx, dir, tool): def modules_create( ctx, tool, - dir, + directory, author, label, meta, @@ -199,7 +199,7 @@ def modules_create( # Run function try: module_create = ModuleCreate( - dir, + directory, tool, author, label, @@ -219,7 +219,7 @@ def modules_create( sys.exit(1) -def modules_test(ctx, tool, dir, no_prompts, update, once, profile): +def modules_test(ctx, tool, directory, no_prompts, update, once, profile): """ Run nf-test for a module. @@ -231,7 +231,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile): module_tester = ComponentsTest( component_type="modules", component_name=tool, - directory=dir, + directory=directory, no_prompts=no_prompts, update=update, once=once, @@ -246,7 +246,7 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile): sys.exit(1) -def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): +def modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version): """ Lint one or more modules in a directory. @@ -261,7 +261,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, try: module_lint = ModuleLint( - dir, + directory, fail_warned=fail_warned, registry=ctx.params["registry"], remote_url=ctx.obj["modules_repo_url"], @@ -290,7 +290,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sys.exit(1) -def modules_info(ctx, tool, dir): +def modules_info(ctx, tool, directory): """ Show developer usage information about a given module. @@ -306,7 +306,7 @@ def modules_info(ctx, tool, dir): try: module_info = ModuleInfo( - dir, + directory, tool, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -318,7 +318,7 @@ def modules_info(ctx, tool, dir): sys.exit(1) -def modules_bump_versions(ctx, tool, dir, all, show_all): +def modules_bump_versions(ctx, tool, directory, all, show_all): """ Bump versions for one or more modules in a clone of the nf-core/modules repo. @@ -328,7 +328,7 @@ def modules_bump_versions(ctx, tool, dir, all, show_all): try: version_bumper = ModuleVersionBumper( - dir, + directory, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index a3abce3f85..36fd998a68 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -10,7 +10,7 @@ stdout = rich.console.Console(force_terminal=rich_force_colors()) -def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): +def subworkflows_create(ctx, subworkflow, directory, author, force, migrate_pytest): """ Create a new subworkflow from the nf-core template. @@ -24,7 +24,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): # Run function try: - subworkflow_create = SubworkflowCreate(dir, subworkflow, author, force, migrate_pytest) + subworkflow_create = SubworkflowCreate(directory, subworkflow, author, force, migrate_pytest) subworkflow_create.create() except UserWarning as e: log.critical(e) @@ -34,7 +34,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): sys.exit(1) -def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): +def subworkflows_test(ctx, subworkflow, directory, no_prompts, update, once, profile): """ Run nf-test for a subworkflow. @@ -46,7 +46,7 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): sw_tester = ComponentsTest( component_type="subworkflows", component_name=subworkflow, - directory=dir, + directory=directory, no_prompts=no_prompts, update=update, once=once, @@ -69,7 +69,7 @@ def subworkflows_list_remote(ctx, keywords, json): try: subworkflow_list = SubworkflowList( - None, + ".", True, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -82,7 +82,7 @@ def subworkflows_list_remote(ctx, keywords, json): sys.exit(1) -def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefined-builtin +def subworkflows_list_local(ctx, keywords, json, directory): # pylint: disable=redefined-builtin """ List subworkflows installed locally in a pipeline """ @@ -90,7 +90,7 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi try: subworkflow_list = SubworkflowList( - dir, + directory, False, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -102,7 +102,7 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi sys.exit(1) -def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +def subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by): """ Lint one or more subworkflows in a directory. @@ -117,7 +117,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo try: subworkflow_lint = SubworkflowLint( - dir, + directory, fail_warned=fail_warned, registry=ctx.params["registry"], remote_url=ctx.obj["modules_repo_url"], @@ -145,7 +145,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo sys.exit(1) -def subworkflows_info(ctx, subworkflow, dir): +def subworkflows_info(ctx, subworkflow, directory): """ Show developer usage information about a given subworkflow. @@ -161,7 +161,7 @@ def subworkflows_info(ctx, subworkflow, dir): try: subworkflow_info = SubworkflowInfo( - dir, + directory, subworkflow, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], @@ -173,7 +173,7 @@ def subworkflows_info(ctx, subworkflow, dir): sys.exit(1) -def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): +def subworkflows_install(ctx, subworkflow, directory, prompt, force, sha): """ Install DSL2 subworkflow within a pipeline. @@ -183,7 +183,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): try: subworkflow_install = SubworkflowInstall( - dir, + directory, force, prompt, sha, @@ -199,7 +199,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha): sys.exit(1) -def subworkflows_remove(ctx, dir, subworkflow): +def subworkflows_remove(ctx, directory, subworkflow): """ Remove a subworkflow from a pipeline. """ @@ -207,7 +207,7 @@ def subworkflows_remove(ctx, dir, subworkflow): try: module_remove = SubworkflowRemove( - dir, + directory, ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], @@ -221,7 +221,7 @@ def subworkflows_remove(ctx, dir, subworkflow): def subworkflows_update( ctx, subworkflow, - dir, + directory, force, prompt, sha, @@ -240,7 +240,7 @@ def subworkflows_update( try: subworkflow_install = SubworkflowUpdate( - dir, + directory, force, prompt, sha, diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index ada8b532e5..69f067f8fe 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -22,9 +22,7 @@ class ComponentCommand: def __init__( self, component_type: str, - directory: Union[ - str, Path - ], # TODO: This is actually None sometimes (e.g. in test_modules_list_remote), need to rewrite the logic here to handle these cases elegantly, for example setting a default path + directory: Union[str, Path] = ".", remote_url: Optional[str] = None, branch: Optional[str] = None, no_pull: bool = False, @@ -34,11 +32,11 @@ def __init__( """ Initialise the ComponentClass object """ - self.component_type = component_type - self.directory = directory + self.component_type: str = component_type + self.directory: Path = Path(directory) self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) - self.hide_progress = hide_progress - self.no_prompts = no_prompts + self.hide_progress: bool = hide_progress + self.no_prompts: bool = no_prompts self._configure_repo_and_paths() def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: diff --git a/nf_core/components/list.py b/nf_core/components/list.py index 0a6b654467..ded035c897 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -25,7 +25,9 @@ def __init__( super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.remote = remote - def list_components(self, keywords: Optional[List[str]] = None, print_json=False) -> Union[rich.table.Table, str]: + def list_components( + self, keywords: Optional[List[str]] = None, print_json: bool = False + ) -> Union[rich.table.Table, str]: keywords = keywords or [] """ Get available modules/subworkflows names from GitHub tree for repo diff --git a/nf_core/modules/list.py b/nf_core/modules/list.py index c7dc943f9e..68da570f67 100644 --- a/nf_core/modules/list.py +++ b/nf_core/modules/list.py @@ -1,4 +1,6 @@ import logging +from pathlib import Path +from typing import Optional, Union from nf_core.components.list import ComponentList @@ -6,5 +8,12 @@ class ModuleList(ComponentList): - def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False): + def __init__( + self, + pipeline_dir: Union[str, Path] = ".", + remote: bool = True, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + ): super().__init__("modules", pipeline_dir, remote, remote_url, branch, no_pull) diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py index ddf144ee00..9e84d6cbe0 100644 --- a/nf_core/subworkflows/list.py +++ b/nf_core/subworkflows/list.py @@ -1,4 +1,6 @@ import logging +from pathlib import Path +from typing import Optional, Union from nf_core.components.list import ComponentList @@ -6,5 +8,12 @@ class SubworkflowList(ComponentList): - def __init__(self, pipeline_dir, remote=True, remote_url=None, branch=None, no_pull=False): + def __init__( + self, + pipeline_dir: Union[str, Path] = ".", + remote: bool = True, + remote_url: Optional[str] = None, + branch: Optional[str] = None, + no_pull: bool = False, + ) -> None: super().__init__("subworkflows", pipeline_dir, remote, remote_url, branch, no_pull) diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py index fdbb61f69e..a170f6d6fc 100644 --- a/tests/modules/test_list.py +++ b/tests/modules/test_list.py @@ -13,7 +13,7 @@ class TestModulesCreate(TestModules): def test_modules_list_remote(self): """Test listing available modules""" - mods_list = nf_core.modules.list.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(remote=True) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -22,9 +22,7 @@ def test_modules_list_remote(self): def test_modules_list_remote_gitlab(self): """Test listing the modules in the remote gitlab repo""" - mods_list = nf_core.modules.list.ModuleList( - None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH - ) + mods_list = nf_core.modules.list.ModuleList(remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -64,22 +62,22 @@ def test_modules_install_gitlab_and_list_pipeline(self): def test_modules_list_local_json(self): """Test listing locally installed modules as JSON""" mods_list = nf_core.modules.list.ModuleList(self.pipeline_dir, remote=False) - listed_mods = mods_list.list_components(print_json=True) + listed_mods = str(mods_list.list_components(print_json=True)) listed_mods = json.loads(listed_mods) assert "fastqc" in listed_mods assert "multiqc" in listed_mods def test_modules_list_remote_json(self): """Test listing available modules as JSON""" - mods_list = nf_core.modules.list.ModuleList(None, remote=True) - listed_mods = mods_list.list_components(print_json=True) + mods_list = nf_core.modules.list.ModuleList(remote=True) + listed_mods: str = str(mods_list.list_components(print_json=True)) listed_mods = json.loads(listed_mods) assert "fastqc" in listed_mods assert "multiqc" in listed_mods def test_modules_list_with_one_keyword(self): """Test listing available modules with one keyword""" - mods_list = nf_core.modules.list.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(remote=True) listed_mods = mods_list.list_components(keywords=["qc"]) console = Console(record=True) console.print(listed_mods) @@ -88,7 +86,7 @@ def test_modules_list_with_one_keyword(self): def test_modules_list_with_keywords(self): """Test listing available modules with multiple keywords""" - mods_list = nf_core.modules.list.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(remote=True) listed_mods = mods_list.list_components(keywords=["fastq", "qc"]) console = Console(record=True) console.print(listed_mods) @@ -97,7 +95,7 @@ def test_modules_list_with_keywords(self): def test_modules_list_with_unused_keyword(self): """Test listing available modules with an unused keyword""" - mods_list = nf_core.modules.list.ModuleList(None, remote=True) + mods_list = nf_core.modules.list.ModuleList(remote=True) with self.assertLogs(level="INFO") as log: listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"]) self.assertIn("No available", log.output[0]) diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py index 5e4e6feb0a..aa1c4de7af 100644 --- a/tests/subworkflows/test_list.py +++ b/tests/subworkflows/test_list.py @@ -9,7 +9,7 @@ class TestSubworkflowsList(TestSubworkflows): def test_subworkflows_list_remote(self): """Test listing available subworkflows""" - subworkflows_list = nf_core.subworkflows.SubworkflowList(None, remote=True) + subworkflows_list = nf_core.subworkflows.SubworkflowList(remote=True) listed_subworkflows = subworkflows_list.list_components() console = Console(record=True) console.print(listed_subworkflows) From ebdb3981fec56235822f07d19dca7bc2c206e7ee Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:26:37 +0200 Subject: [PATCH 227/574] remove unnecessary checks --- nf_core/components/components_command.py | 2 +- nf_core/components/components_utils.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 69f067f8fe..7d43b387fc 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -94,7 +94,7 @@ def has_valid_directory(self) -> bool: """Check that we were given a pipeline or clone of nf-core/modules""" if self.repo_type == "modules": return True - if self.directory is None or not Path(self.directory).exists(): + if not Path(self.directory).exists(): log.error(f"Could not find directory: {self.directory}") return False main_nf = Path(self.directory, "main.nf") diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 3d64dc1bb6..632ae7b2aa 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -26,7 +26,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P """ # Verify that the pipeline dir exists - if directory is None or not Path(directory).is_dir(): + if not Path(directory).is_dir(): raise UserWarning(f"Could not find directory: {directory}") # Try to find the root directory From 15a9071886fda734d182a2ae10a2dd78074c3d48 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:33:20 +0200 Subject: [PATCH 228/574] remove unnecessary Path conversions --- nf_core/components/components_command.py | 12 +++++------- nf_core/components/components_test.py | 2 +- nf_core/components/lint/__init__.py | 12 +++++------- nf_core/modules/bump_versions.py | 2 +- 4 files changed, 12 insertions(+), 16 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 7d43b387fc..4e739fd6b8 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -49,9 +49,7 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ try: if self.directory: - self.directory, self.repo_type, self.org = get_repo_info( - Path(self.directory), use_prompt=not self.no_prompts - ) + self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts) else: self.repo_type = None self.org = "" @@ -94,13 +92,13 @@ def has_valid_directory(self) -> bool: """Check that we were given a pipeline or clone of nf-core/modules""" if self.repo_type == "modules": return True - if not Path(self.directory).exists(): + if not self.directory.exists(): log.error(f"Could not find directory: {self.directory}") return False main_nf = Path(self.directory, "main.nf") nf_config = Path(self.directory, "nextflow.config") if not main_nf.exists() and not nf_config.exists(): - if Path(self.directory).resolve().parts[-1].startswith("nf-core"): + if self.directory.resolve().parts[-1].startswith("nf-core"): raise UserWarning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") log.warning(f"Could not find a 'main.nf' or 'nextflow.config' file in '{self.directory}'") return True @@ -125,7 +123,7 @@ def clear_component_dir(self, component_name: str, component_dir: Union[str, Pat try: shutil.rmtree(component_dir) # remove all empty directories - for dir_path, dir_names, filenames in os.walk(Path(self.directory), topdown=False): + for dir_path, dir_names, filenames in os.walk(self.directory, topdown=False): if not dir_names and not filenames: try: Path(dir_path).rmdir() @@ -258,7 +256,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None: ): modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][ self.modules_repo.repo_path - ][module_name]["patch"] = str(patch_path.relative_to(Path(self.directory).resolve())) + ][module_name]["patch"] = str(patch_path.relative_to(self.directory.resolve())) modules_json.dump() def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[str, Union[int, str]]]]: diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py index f9b891004a..57c0034ba4 100644 --- a/nf_core/components/components_test.py +++ b/nf_core/components/components_test.py @@ -93,7 +93,7 @@ def run(self) -> None: os.environ["NFT_DIFF_ARGS"] = ( "--line-numbers --expand-tabs=2" # taken from https://code.askimed.com/nf-test/docs/assertions/snapshots/#snapshot-differences ) - with nf_core.utils.set_wd(Path(self.directory)): + with nf_core.utils.set_wd(self.directory): self.check_snapshot_stability() if len(self.errors) > 0: errors = "\n - ".join(self.errors) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index ddf5e1e165..be6b225a0a 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -104,7 +104,7 @@ def __init__( repo_url, Path(self.directory, self.component_type, org, comp), self.repo_type, - Path(self.directory), + self.directory, self.component_type, ) ) @@ -121,20 +121,20 @@ def __init__( None, Path(local_component_dir, comp), self.repo_type, - Path(self.directory), + self.directory, self.component_type, remote_component=False, ) for comp in self.get_local_components() ] - self.config = nf_core.utils.fetch_wf_config(Path(self.directory), cache_config=True) + self.config = nf_core.utils.fetch_wf_config(self.directory, cache_config=True) elif self.repo_type == "modules": component_dir = Path( self.directory, self.default_modules_path if self.component_type == "modules" else self.default_subworkflows_path, ) self.all_remote_components = [ - NFCoreComponent(m, None, component_dir / m, self.repo_type, Path(self.directory), self.component_type) + NFCoreComponent(m, None, component_dir / m, self.repo_type, self.directory, self.component_type) for m in self.get_components_clone_modules() ] self.all_local_components = [] @@ -142,9 +142,7 @@ def __init__( raise LookupError(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? - self.config = nf_core.utils.fetch_wf_config( - Path(self.directory).joinpath("tests", "config"), cache_config=True - ) + self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) if registry is None: self.registry = self.config.get("docker.registry", "quay.io") diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 6546cccc9a..2d8854e3c0 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -76,7 +76,7 @@ def bump_versions( ) # Get list of all modules - _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(Path(self.directory)) + _, nfcore_modules = nf_core.modules.modules_utils.get_installed_modules(self.directory) # Load the .nf-core.yml config _, self.tools_config = nf_core.utils.load_tools_config(self.directory) From fa00b1b61e0315177bee09c3d2e8f486cd4ae86e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:42:13 +0200 Subject: [PATCH 229/574] fix types for 3.8 --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 80324fc9a8..86ed09555c 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -905,7 +905,7 @@ def prompt_remote_pipeline_name(wfs): def prompt_pipeline_release_branch( wf_releases: List[Dict[str, Any]], wf_branches: Dict[str, Any], multiple: bool = False -) -> tuple[Any, list[str]]: +) -> Tuple[Any, List[str]]: """Prompt for pipeline release / branch Args: From e7f06bea17e9c29bb40a1b7f8e54818ab308a264 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:46:10 +0200 Subject: [PATCH 230/574] limit `component` to type string --- nf_core/components/install.py | 9 +++++---- nf_core/modules/modules_json.py | 14 ++++++-------- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/nf_core/components/install.py b/nf_core/components/install.py index f2849f85bc..9b42ba77db 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -1,7 +1,10 @@ import logging import os from pathlib import Path -from typing import List, Optional, Union +from typing import TYPE_CHECKING, List, Optional, Union + +if TYPE_CHECKING: + from nf_core.modules.modules_repo import ModulesRepo import questionary from rich.console import Console @@ -180,9 +183,7 @@ def install_included_components(self, subworkflow_dir): self.component_type = original_component_type self.installed_by = original_installed - def collect_and_verify_name( - self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo" - ) -> str: + def collect_and_verify_name(self, component: Optional[str], modules_repo: ModulesRepo) -> str: """ Collect component name. Check that the supplied name is an available module/subworkflow. diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 39d70b7d78..ff4922dc02 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -355,7 +355,7 @@ def determine_branches_and_shas( # Clean up the modules/subworkflows we were unable to find the sha for for component in sb_local: - log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, str(component))}' to 'local' directory") + log.debug(f"Moving {component_type[:-1]} '{Path(install_dir, component)}' to 'local' directory") self.move_component_to_local(component_type, component, str(install_dir)) for component in dead_components: @@ -398,13 +398,13 @@ def find_correct_commit_sha( return commit_sha return None - def move_component_to_local(self, component_type: str, component: Union[str, Path], repo_name: str): + def move_component_to_local(self, component_type: str, component: str, repo_name: str): """ Move a module/subworkflow to the 'local' directory Args: component_type (str): The type of component, either 'modules' or 'subworkflows' - component (Union[str,Path]): The name of the module/subworkflow + component (str): The name of the module/subworkflow repo_name (str): The name of the repository the module resides in """ if component_type == "modules": @@ -418,7 +418,7 @@ def move_component_to_local(self, component_type: str, component: Union[str, Pat if not local_dir.exists(): local_dir.mkdir() - to_name = str(component) + to_name = component # Check if there is already a subdirectory with the name while (local_dir / to_name).exists(): # Add a time suffix to the path to make it unique @@ -1086,9 +1086,7 @@ def get_installed_by_entries(self, component_type, name): return installed_by_entries - def get_component_branch( - self, component_type: str, component: Union[str, Path], repo_url: str, install_dir: str - ) -> str: + def get_component_branch(self, component_type: str, component: str, repo_url: str, install_dir: str) -> str: """ Gets the branch from which the module/subworkflow was installed @@ -1101,7 +1099,7 @@ def get_component_branch( self.load() assert self.modules_json is not None # mypy try: - branch = self.modules_json["repos"][repo_url][component_type][install_dir][str(component)]["branch"] + branch = self.modules_json["repos"][repo_url][component_type][install_dir][component]["branch"] except (KeyError, TypeError): branch = None if branch is None: From ae7d912369630daaf2e43ddcd636bdb8d8cfb2d4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 14:59:04 +0200 Subject: [PATCH 231/574] handle more type warnings --- nf_core/modules/modules_json.py | 10 ++++++++-- nf_core/modules/modules_repo.py | 2 +- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index ff4922dc02..19649a57cd 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -42,7 +42,7 @@ class ModulesJson: An object for handling a 'modules.json' file in a pipeline """ - def __init__(self, pipeline_dir: Union[str, Path]): + def __init__(self, pipeline_dir: Union[str, Path]) -> None: """ Initialise the object. @@ -130,6 +130,10 @@ def get_component_names_from_repo( names = [] for repo_url in repos: modules_repo = ModulesRepo(repo_url) + if modules_repo is None: + raise UserWarning(f"Could not find module repository for '{repo_url}' in '{directory}'") + if modules_repo.repo_path is None: + raise UserWarning(f"Could not find module repository path for '{repo_url}' in '{directory}'") components = ( repo_url, [ @@ -195,6 +199,8 @@ def get_pipeline_module_repositories( # Verify that there is a directory corresponding the remote nrepo_name = ModulesRepo(nrepo_remote).repo_path + if nrepo_name is None: + raise UserWarning(f"Could not find the repository name for '{nrepo_remote}'") if not (directory / nrepo_name).exists(): log.info( "The provided remote does not seem to correspond to a local directory. " @@ -416,7 +422,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name current_path = directory / repo_name / component local_dir = directory / "local" if not local_dir.exists(): - local_dir.mkdir() + local_dir.mkdir(parents=True) to_name = component # Check if there is already a subdirectory with the name diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py index 5b50205484..357fc49cc5 100644 --- a/nf_core/modules/modules_repo.py +++ b/nf_core/modules/modules_repo.py @@ -40,7 +40,7 @@ def __init__( branch: Optional[str] = None, no_pull: bool = False, hide_progress: bool = False, - ): + ) -> None: """ Initializes the object and clones the git repository if it is not already present """ From d7587dc1577602ab26d53dd34a438aedfb4c8a1e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 16:18:32 +0200 Subject: [PATCH 232/574] fix import errors, handle outdir as string --- nf_core/components/info.py | 17 +++++++++-------- nf_core/components/install.py | 10 +++++----- nf_core/pipelines/create/create.py | 3 +-- nf_core/utils.py | 12 ++++++++++-- 4 files changed, 25 insertions(+), 17 deletions(-) diff --git a/nf_core/components/info.py b/nf_core/components/info.py index 726586b5b7..98f8be5272 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -1,7 +1,7 @@ import logging import os from pathlib import Path -from typing import Dict, Optional, Union +from typing import Dict, List, Optional, Tuple, Union import questionary import yaml @@ -83,14 +83,14 @@ def __init__( self.modules_json = None self.component = self.init_mod_name(component_name) - def _configure_repo_and_paths(self, nf_dir_req=False): + def _configure_repo_and_paths(self, nf_dir_req=False) -> None: """ Override the default with nf_dir_req set to False to allow info to be run from anywhere and still return remote info """ return super()._configure_repo_and_paths(nf_dir_req) - def init_mod_name(self, component): + def init_mod_name(self, component: Optional[str]) -> str: """ Makes sure that we have a module/subworkflow name before proceeding. @@ -106,9 +106,10 @@ def init_mod_name(self, component): components = self.get_components_clone_modules() elif self.repo_type == "pipeline": assert self.modules_json is not None # mypy - all_components = self.modules_json.get_all_components(self.component_type).get( - self.modules_repo.remote_url, {} - ) + all_components: List[Tuple[str, str]] = self.modules_json.get_all_components( + self.component_type + ).get(self.modules_repo.remote_url, []) + components = [ component if directory == self.modules_repo.repo_path else f"{directory}/{component}" for directory, component in all_components @@ -169,7 +170,7 @@ def get_component_info(self): return self.generate_component_info_help() - def get_local_yaml(self): + def get_local_yaml(self) -> Optional[Dict]: """Attempt to get the meta.yml file from a locally installed module/subworkflow. Returns: @@ -316,7 +317,7 @@ def generate_component_info_help(self): ) # Print include statement - if self.local_path: + if self.local_path and self.modules_repo.repo_path is not None: install_folder = Path(self.directory, self.component_type, self.modules_repo.repo_path) component_name = "_".join(self.component.upper().split("/")) renderables.append( diff --git a/nf_core/components/install.py b/nf_core/components/install.py index 9b42ba77db..a7be737bf9 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -1,16 +1,14 @@ import logging import os from pathlib import Path -from typing import TYPE_CHECKING, List, Optional, Union - -if TYPE_CHECKING: - from nf_core.modules.modules_repo import ModulesRepo +from typing import List, Optional, Union import questionary from rich.console import Console from rich.syntax import Syntax import nf_core.components +import nf_core.modules.modules_repo import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.components_command import ComponentCommand @@ -183,7 +181,9 @@ def install_included_components(self, subworkflow_dir): self.component_type = original_component_type self.installed_by = original_installed - def collect_and_verify_name(self, component: Optional[str], modules_repo: ModulesRepo) -> str: + def collect_and_verify_name( + self, component: Optional[str], modules_repo: "nf_core.modules.modules_repo.ModulesRepo" + ) -> str: """ Collect component name. Check that the supplied name is an available module/subworkflow. diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index d5c230e048..899507847e 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -83,9 +83,8 @@ def __init__( if self.config.outdir is None: self.config.outdir = str(Path.cwd()) - self.jinja_params, skip_paths = self.obtain_jinja_params_dict( - self.config.skip_features or [], Path(self.config.outdir) + self.config.skip_features or [], str(self.config.outdir) ) skippable_paths = { diff --git a/nf_core/utils.py b/nf_core/utils.py index 86ed09555c..c1cc7c1301 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -30,7 +30,7 @@ import rich.markup import yaml from packaging.version import Version -from pydantic import BaseModel, ValidationError +from pydantic import BaseModel, ValidationError, field_validator from rich.live import Live from rich.spinner import Spinner @@ -1050,10 +1050,18 @@ class NFCoreTemplateConfig(BaseModel): author: Optional[str] = None version: Optional[str] = None force: Optional[bool] = None - outdir: Optional[str] = None + outdir: Optional[Union[str, Path]] = None skip_features: Optional[list] = None is_nfcore: Optional[bool] = None + # convert outdir to str + @field_validator("outdir") + @classmethod + def outdir_to_str(cls, v: Optional[Union[str, Path]]) -> Optional[str]: + if v is not None: + v = str(v) + return v + def __getitem__(self, item: str) -> Any: if self is None: return None From a4cf066e3a041be2b05fa67c661f408644bd5327 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 29 Jul 2024 16:41:19 +0200 Subject: [PATCH 233/574] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/custompipeline.py | 4 ++-- tests/test_create.py | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 7a94ab228a..0925fb5bab 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -42,8 +42,8 @@ """ markdown_code_linters = """ -Pipelines include code linters, these linters will check the formatting of your code. -Linters will check JSON, YAML, Python and others. +Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. +Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. The available code linters are: - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. diff --git a/tests/test_create.py b/tests/test_create.py index 896a8e7ad6..b4ac89c7de 100644 --- a/tests/test_create.py +++ b/tests/test_create.py @@ -118,4 +118,3 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path): assert not os.path.exists(Path(pipeline.outdir / ".github")) assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config")) assert not os.path.exists(Path(pipeline.outdir / ".editorconfig")) - assert not os.path.exists(Path(pipeline.outdir / ".editorconfig")) From 419242b931ff228fee0babf63d50313b2fbd6ee9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 29 Jul 2024 16:46:46 +0200 Subject: [PATCH 234/574] use pathlib instead of os.path --- tests/test_create.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/test_create.py b/tests/test_create.py index b4ac89c7de..920a0f4750 100644 --- a/tests/test_create.py +++ b/tests/test_create.py @@ -106,15 +106,15 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path): pipeline.init_pipeline() # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input - assert not os.path.exists(Path(pipeline.outdir / "pipeline_template.yml")) - assert os.path.exists(Path(pipeline.outdir / ".nf-core.yml")) - with open(Path(pipeline.outdir / ".nf-core.yml")) as fh: + assert not (pipeline.outdir / "pipeline_template.yml").exists() + assert (pipeline.outdir / ".nf-core.yml").exists() + with open(pipeline.outdir / ".nf-core.yml") as fh: nfcore_yml = yaml.safe_load(fh) assert "template" in nfcore_yml assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items() # Check that some of the skipped files are not present - assert not os.path.exists(Path(pipeline.outdir / "CODE_OF_CONDUCT.md")) - assert not os.path.exists(Path(pipeline.outdir / ".github")) - assert not os.path.exists(Path(pipeline.outdir / "conf" / "igenomes.config")) - assert not os.path.exists(Path(pipeline.outdir / ".editorconfig")) + assert not (pipeline.outdir / "CODE_OF_CONDUCT.md").exists() + assert not (pipeline.outdir / ".github").exists() + assert not (pipeline.outdir / "conf" / "igenomes.config").exists() + assert not (pipeline.outdir / ".editorconfig").exists() From f5e865086bda88e28523f0757bf4e71366b228ad Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 29 Jul 2024 16:48:44 +0200 Subject: [PATCH 235/574] update chagelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b27dce4b5c..8eae70a311 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) +- add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) ### Linting From 5979b9d1f4ee8fa157eb1798ec3a7226238f00cb Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 17:24:52 +0200 Subject: [PATCH 236/574] add error message and resolve circular import --- nf_core/components/components_utils.py | 2 +- nf_core/components/install.py | 13 +++++++++---- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 632ae7b2aa..9289d90004 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -63,7 +63,7 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P # Check if it's a valid answer if repo_type not in ["pipeline", "modules"]: - raise UserWarning(f"Invalid repository type: '{repo_type}'") + raise UserWarning(f"Invalid repository type: '{repo_type}', must be 'pipeline' or 'modules'") org: str = "" # Check for org if modules repo if repo_type == "modules": diff --git a/nf_core/components/install.py b/nf_core/components/install.py index a7be737bf9..6130a4cf72 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -8,7 +8,6 @@ from rich.syntax import Syntax import nf_core.components -import nf_core.modules.modules_repo import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.components_command import ComponentCommand @@ -69,12 +68,18 @@ def install(self, component: str, silent: bool = False) -> bool: # Verify SHA if not self.modules_repo.verify_sha(self.prompt, self.sha): + err_msg = f"SHA '{self.sha}' is not a valid commit SHA for the repository '{self.modules_repo.remote_url}'" + log.error(err_msg) return False # verify self.modules_repo entries: if self.modules_repo is None: + err_msg = "Could not find a valid modules repository." + log.error(err_msg) return False if self.modules_repo.repo_path is None: + err_msg = "Could not find a valid modules repository path." + log.error(err_msg) return False # Check and verify component name @@ -200,10 +205,10 @@ def collect_and_verify_name( # Check that the supplied name is an available module/subworkflow if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha): - log.error( - f"{self.component_type[:-1].title()} '{component}' not found in list of available {self.component_type}." - ) log.info(f"Use the command 'nf-core {self.component_type} list' to view available software") + raise SystemError( + f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}" + ) if not modules_repo.component_exists(component, self.component_type, commit=self.sha): warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})" From 24a3ece90f28b9efe1336a5768b55dc6dc62b184 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 17:45:45 +0200 Subject: [PATCH 237/574] actually test installation with a correct subworkflow --- tests/subworkflows/test_install.py | 46 ++++++++++++++++-------------- 1 file changed, 25 insertions(+), 21 deletions(-) diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py index af1ad92415..e6ba9439a4 100644 --- a/tests/subworkflows/test_install.py +++ b/tests/subworkflows/test_install.py @@ -17,26 +17,6 @@ class TestSubworkflowsInstall(TestSubworkflows): - def test_subworkflow_install_nopipeline(self): - """Test installing a subworkflow - no pipeline given""" - assert self.subworkflow_install.directory is not None - self.subworkflow_install.directory = Path("non_existent_dir") - assert self.subworkflow_install.install("foo") is False - - @with_temporary_folder - def test_subworkflows_install_emptypipeline(self, tmpdir): - """Test installing a subworkflow - empty dir given""" - - Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True) - self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe") - with pytest.raises(UserWarning) as excinfo: - self.subworkflow_install.install("foo") - assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) - - def test_subworkflows_install_nosubworkflow(self): - """Test installing a subworkflow - unrecognised subworkflow given""" - assert self.subworkflow_install.install("foo") is False - def test_subworkflows_install_bam_sort_stats_samtools(self): """Test installing a subworkflow - bam_sort_stats_samtools""" assert self.subworkflow_install.install("bam_sort_stats_samtools") is not False @@ -57,6 +37,28 @@ def test_subworkflows_install_bam_sort_stats_samtools(self): assert samtools_idxstats_path.exists() assert samtools_flagstat_path.exists() + def test_subworkflow_install_nopipeline(self): + """Test installing a subworkflow - no pipeline given""" + assert self.subworkflow_install.directory is not None + self.subworkflow_install.directory = Path("non_existent_dir") + assert self.subworkflow_install.install("bam_stats_samtools") is False + + @with_temporary_folder + def test_subworkflows_install_emptypipeline(self, tmpdir): + """Test installing a subworkflow - empty dir given""" + + Path(tmpdir, "nf-core-pipe").mkdir(exist_ok=True) + self.subworkflow_install.directory = Path(tmpdir, "nf-core-pipe") + with pytest.raises(UserWarning) as excinfo: + self.subworkflow_install.install("bam_stats_samtools") + assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) + + def test_subworkflows_install_nosubworkflow(self): + """Test installing a subworkflow - unrecognised subworkflow given""" + with pytest.raises(SystemError) as excinfo: + self.subworkflow_install.install("foo") + assert "Subworkflow 'foo' not found in available subworkflows" in str(excinfo.value) + def test_subworkflows_install_bam_sort_stats_samtools_twice(self): """Test installing a subworkflow - bam_sort_stats_samtools already there""" self.subworkflow_install.install("bam_sort_stats_samtools") @@ -76,7 +78,9 @@ def test_subworkflows_install_different_branch_fail(self): """Test installing a subworkflow from a different branch""" install_obj = SubworkflowInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) # The bam_stats_samtools subworkflow does not exists in the branch-test branch - assert install_obj.install("bam_stats_samtools") is False + with pytest.raises(Exception) as excinfo: + install_obj.install("bam_stats_samtools") + assert "Subworkflow 'bam_stats_samtools' not found in available subworkflows" in str(excinfo.value) def test_subworkflows_install_tracking(self): """Test installing a subworkflow and finding the correct entries in installed_by section of modules.json""" From 05def5932e12de9aa8fa2d07d763a54cd552038c Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 22:21:13 +0200 Subject: [PATCH 238/574] fix list and info command --- nf_core/components/components_command.py | 10 ++++------ nf_core/components/lint/__init__.py | 21 +++++++++++++++------ nf_core/components/list.py | 2 +- nf_core/modules/bump_versions.py | 13 ++++++++----- nf_core/subworkflows/list.py | 2 +- nf_core/utils.py | 2 ++ tests/subworkflows/test_list.py | 2 +- 7 files changed, 32 insertions(+), 20 deletions(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index 4e739fd6b8..bff2467383 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -37,6 +37,8 @@ def __init__( self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) self.hide_progress: bool = hide_progress self.no_prompts: bool = no_prompts + self.repo_type: Optional[str] = None + self.org: str = "" self._configure_repo_and_paths() def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: @@ -50,15 +52,11 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: try: if self.directory: self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts) - else: - self.repo_type = None - self.org = "" - except UserWarning: if nf_dir_req: raise - self.repo_type = None - self.org = "" + except FileNotFoundError: + raise self.default_modules_path = Path("modules", self.org) self.default_tests_path = Path("tests", "modules", self.org) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index be6b225a0a..d0f6685365 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -86,6 +86,11 @@ def __init__( else: self.lint_tests = self.get_all_subworkflow_lint_tests(self.repo_type == "pipeline") + if self.repo_type is None: + raise LookupError( + "Could not determine repository type. Please check the repository type in the nf-core.yml" + ) + if self.repo_type == "pipeline": modules_json = ModulesJson(self.directory) modules_json.check_up_to_date() @@ -128,6 +133,8 @@ def __init__( for comp in self.get_local_components() ] self.config = nf_core.utils.fetch_wf_config(self.directory, cache_config=True) + self._set_registry(registry) + elif self.repo_type == "modules": component_dir = Path( self.directory, @@ -143,16 +150,18 @@ def __init__( # This could be better, perhaps glob for all nextflow.config files in? self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) - - if registry is None: - self.registry = self.config.get("docker.registry", "quay.io") - else: - self.registry = registry - log.debug(f"Registry set to {self.registry}") + self._set_registry(registry) def __repr__(self) -> str: return f"ComponentLint({self.component_type}, {self.directory})" + def _set_registry(self, registry) -> None: + if registry is None: + self.registry = self.config.get("docker.registry", "quay.io") + else: + self.registry = registry + log.debug(f"Registry set to {self.registry}") + @staticmethod def get_all_module_lint_tests(is_pipeline): if is_pipeline: diff --git a/nf_core/components/list.py b/nf_core/components/list.py index ded035c897..65a28db716 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -16,7 +16,7 @@ class ComponentList(ComponentCommand): def __init__( self, component_type: str, - pipeline_dir: Union[str, Path], + pipeline_dir: Union[str, Path] = ".", remote: bool = True, remote_url: Optional[str] = None, branch: Optional[str] = None, diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 2d8854e3c0..d98eac7cd6 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -245,12 +245,15 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: fh.write(content) # change version in environment.yml - with open(str(module.environment_yml)) as fh: + if not module.environment_yml: + log.error(f"Could not read `environment.yml` of {module.component_name} module.") + return False + with open(module.environment_yml) as fh: env_yml = yaml.safe_load(fh) env_yml["dependencies"][0] = re.sub( bioconda_packages[0], f"bioconda::{bioconda_tool_name}={last_ver}", env_yml["dependencies"][0] ) - with open(str(module.environment_yml), "w") as fh: + with open(module.environment_yml, "w") as fh: yaml.dump(env_yml, fh, default_flow_style=False, Dumper=custom_yaml_dumper()) self.updated.append( @@ -271,11 +274,11 @@ def get_bioconda_version(self, module: NFCoreComponent) -> List[str]: """ # Check whether file exists and load it bioconda_packages = [] - try: - with open(str(module.environment_yml)) as fh: + if module.environment_yml is not None and module.environment_yml.exists(): + with open(module.environment_yml) as fh: env_yml = yaml.safe_load(fh) bioconda_packages = env_yml.get("dependencies", []) - except FileNotFoundError: + else: log.error(f"Could not read `environment.yml` of {module.component_name} module.") return bioconda_packages diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py index 9e84d6cbe0..5f849a1f9c 100644 --- a/nf_core/subworkflows/list.py +++ b/nf_core/subworkflows/list.py @@ -10,7 +10,7 @@ class SubworkflowList(ComponentList): def __init__( self, - pipeline_dir: Union[str, Path] = ".", + pipeline_dir: Union[str, Path], remote: bool = True, remote_url: Optional[str] = None, branch: Optional[str] = None, diff --git a/nf_core/utils.py b/nf_core/utils.py index c1cc7c1301..a95eea4b69 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1113,6 +1113,8 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] else: log.debug(f"Could not find a config file in the directory '{directory}'") return Path(directory, CONFIG_PATHS[0]), None + if not Path(config_fn).is_file(): + raise FileNotFoundError(f"No `.nf-core.yml` file found in the directory '{directory}'") with open(str(config_fn)) as fh: tools_config = yaml.safe_load(fh) diff --git a/tests/subworkflows/test_list.py b/tests/subworkflows/test_list.py index aa1c4de7af..1ae8f5fff6 100644 --- a/tests/subworkflows/test_list.py +++ b/tests/subworkflows/test_list.py @@ -19,7 +19,7 @@ def test_subworkflows_list_remote(self): def test_subworkflows_list_remote_gitlab(self): """Test listing the subworkflows in the remote gitlab repo""" subworkflows_list = nf_core.subworkflows.SubworkflowList( - None, remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH + remote=True, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH ) listed_subworkflows = subworkflows_list.list_components() console = Console(record=True) From cce51e3cb06c2e9fbb320ffde026572327eac052 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 29 Jul 2024 22:35:58 +0200 Subject: [PATCH 239/574] add migrate_pytest option to `nf-core test` command --- nf_core/__main__.py | 20 ++++++++++--- nf_core/commands_modules.py | 50 +++++++++++++++++++++----------- nf_core/commands_subworkflows.py | 39 +++++++++++++------------ 3 files changed, 70 insertions(+), 39 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 3da153ee1f..00ae8e2a1f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1154,11 +1154,17 @@ def command_modules_create( default=None, help="Run tests with a specific profile", ) -def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile): +@click.option( + "--migrate-pytest", + is_flag=True, + default=False, + help="Migrate a module with pytest tests to nf-test", +) +def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest): """ Run nf-test for a module. """ - modules_test(ctx, tool, dir, no_prompts, update, once, profile) + modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest) # nf-core modules lint @@ -1352,11 +1358,17 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py default=None, help="Run tests with a specific profile", ) -def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): +@click.option( + "--migrate-pytest", + is_flag=True, + default=False, + help="Migrate a subworkflow with pytest tests to nf-test", +) +def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest): """ Run nf-test for a subworkflow. """ - subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile) + subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest) # nf-core subworkflows list subcommands diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index 3d96d332b0..c65c42d41a 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -219,7 +219,7 @@ def modules_create( sys.exit(1) -def modules_test(ctx, tool, dir, no_prompts, update, once, profile): +def modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest): """ Run nf-test for a module. @@ -227,23 +227,39 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile): """ from nf_core.components.components_test import ComponentsTest - try: - module_tester = ComponentsTest( - component_type="modules", - component_name=tool, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, + if migrate_pytest: + modules_create( + ctx, + tool, + dir, + author="", + label="", + meta=True, + no_meta=False, + force=False, + conda_name=None, + conda_package_version=None, + empty_template=False, + migrate_pytest=migrate_pytest, ) - module_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + else: + try: + module_tester = ComponentsTest( + component_type="modules", + component_name=tool, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + module_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index a3abce3f85..8c3be2bb46 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -34,7 +34,7 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest): sys.exit(1) -def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): +def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest): """ Run nf-test for a subworkflow. @@ -42,23 +42,26 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile): """ from nf_core.components.components_test import ComponentsTest - try: - sw_tester = ComponentsTest( - component_type="subworkflows", - component_name=subworkflow, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, - ) - sw_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + if migrate_pytest: + subworkflows_create(ctx, subworkflow, dir, None, False, True) + else: + try: + sw_tester = ComponentsTest( + component_type="subworkflows", + component_name=subworkflow, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + sw_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) def subworkflows_list_remote(ctx, keywords, json): From 640ce03ab4f687e744f2631ba11971db576d7135 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 29 Jul 2024 20:39:02 +0000 Subject: [PATCH 240/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b27dce4b5c..49a58ff6bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -54,6 +54,7 @@ - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) +- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 2d4d0799d9827797c82059d187a16932f08c8af2 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 30 Jul 2024 18:43:15 +1200 Subject: [PATCH 241/574] Added process_high_memory to create/lint list --- nf_core/components/create.py | 1 + nf_core/modules/lint/main_nf.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/components/create.py b/nf_core/components/create.py index 5d6c411bdc..bae6487925 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -236,6 +236,7 @@ def _get_module_structure_components(self): "process_medium", "process_high", "process_long", + "process_high_memory", ] if self.process_label is None: log.info( diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 81308ba5c5..5477ee9db9 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -423,7 +423,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): def check_process_labels(self, lines): - correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long"] + correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long", "process_high_memory"] all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")] bad_labels = [] good_labels = [] From 423af01f9bd41b644280668a31b229cace850406 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 30 Jul 2024 18:48:51 +1200 Subject: [PATCH 242/574] Updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b27dce4b5c..a56abe0acb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976)) - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) +- Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086)) ### Download From c18d9cdbb3071dad0c221bd07e299f0909263149 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 30 Jul 2024 18:51:48 +1200 Subject: [PATCH 243/574] Fixed linting --- nf_core/modules/lint/main_nf.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 5477ee9db9..883d2bb3e0 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -423,7 +423,14 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): def check_process_labels(self, lines): - correct_process_labels = ["process_single", "process_low", "process_medium", "process_high", "process_long", "process_high_memory"] + correct_process_labels = [ + "process_single", + "process_low", + "process_medium", + "process_high", + "process_long", + "process_high_memory", + ] all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")] bad_labels = [] good_labels = [] From 8de38715468b084a00a9627c89c5e1ec77bf52f4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 09:21:01 +0200 Subject: [PATCH 244/574] exclude click from rich traceback --- nf_core/pipelines/create/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index 56e25bf1d5..1dd9902fb1 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -2,6 +2,7 @@ import logging +import click from textual.app import App from textual.widgets import Button @@ -23,6 +24,7 @@ show_time=False, show_path=False, markup=True, + tracebacks_suppress=[click], ) logging.basicConfig( level="INFO", From 8fe4be6520995812a8d819b3cfe213055d8f6864 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 10:16:43 +0200 Subject: [PATCH 245/574] give nicer message on install failure, fix install test --- nf_core/__main__.py | 2 +- nf_core/components/install.py | 21 +++++++++++++++++---- tests/modules/test_install.py | 4 +++- 3 files changed, 21 insertions(+), 6 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 11ab574ccc..1e5cb210a5 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -126,7 +126,7 @@ # because they are actually preliminary, but intended program terminations. # (Custom exceptions are cleaner than `sys.exit(1)`, which we used before) def selective_traceback_hook(exctype, value, traceback): - if exctype in {DownloadError, UserWarning}: # extend set as needed + if exctype in {DownloadError, UserWarning, ValueError}: # extend set as needed log.error(value) else: # print the colored traceback for all other exceptions with rich as usual diff --git a/nf_core/components/install.py b/nf_core/components/install.py index 6130a4cf72..5bdcd1ebd6 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -4,7 +4,10 @@ from typing import List, Optional, Union import questionary +from rich import print from rich.console import Console +from rich.markdown import Markdown +from rich.panel import Panel from rich.syntax import Syntax import nf_core.components @@ -160,7 +163,7 @@ def install(self, component: str, silent: bool = False) -> bool: ) if self.component_type == "subworkflows": subworkflow_config = Path(install_folder, component, "nextflow.config").relative_to(self.directory) - if os.path.isfile(subworkflow_config): + if subworkflow_config.is_file(): log.info("Add the following config statement to use this subworkflow:") Console().print( Syntax(f"includeConfig '{subworkflow_config}'", "groovy", theme="ansi_dark", padding=1) @@ -205,11 +208,21 @@ def collect_and_verify_name( # Check that the supplied name is an available module/subworkflow if component and component not in modules_repo.get_avail_components(self.component_type, commit=self.sha): - log.info(f"Use the command 'nf-core {self.component_type} list' to view available software") - raise SystemError( - f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}" + log.error(f"{self.component_type[:-1].title()} '{component}' not found in available {self.component_type}") + print( + Panel( + Markdown( + f"Use the command `nf-core {self.component_type} list` to view available {self.component_type}." + ), + title="info", + title_align="left", + style="blue", + padding=1, + ) ) + raise ValueError + if not modules_repo.component_exists(component, self.component_type, commit=self.sha): warn_msg = f"{self.component_type[:-1].title()} '{component}' not found in remote '{modules_repo.remote_url}' ({modules_repo.branch})" log.warning(warn_msg) diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py index 8f7ac0a1dc..5f45d1b5b4 100644 --- a/tests/modules/test_install.py +++ b/tests/modules/test_install.py @@ -55,7 +55,9 @@ def test_modules_install_different_branch_fail(self): """Test installing a module from a different branch""" install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH) # The FastQC module does not exists in the branch-test branch - assert install_obj.install("fastqc") is False + with pytest.raises(Exception) as excinfo: + install_obj.install("fastqc") + assert "Module 'fastqc' not found in available module" in str(excinfo.value) def test_modules_install_different_branch_succeed(self): """Test installing a module from a different branch""" From 6bc7361043ffe2e34685383a8b5af6fef6f4b36f Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 10:48:56 +0200 Subject: [PATCH 246/574] use self.registry --- nf_core/modules/lint/__init__.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index fcf2d7d066..b75f7e7570 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -200,13 +200,12 @@ def lint_modules( for mod in modules: progress_bar.update(lint_progress, advance=1, test_name=mod.component_name) - self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version) + self.lint_module(mod, progress_bar, local=local, fix_version=fix_version) def lint_module( self, mod: NFCoreComponent, progress_bar: rich.progress.Progress, - registry: str, local: bool = False, fix_version: bool = False, ): @@ -228,7 +227,7 @@ def lint_module( # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class # Only check the main script in case of a local module if local: - self.main_nf(mod, fix_version, registry, progress_bar) + self.main_nf(mod, fix_version, self.registry, progress_bar) self.passed += [LintResult(mod, *m) for m in mod.passed] warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)] if not self.fail_warned: @@ -245,7 +244,7 @@ def lint_module( for test_name in self.lint_tests: if test_name == "main_nf": - getattr(self, test_name)(mod, fix_version, registry, progress_bar) + getattr(self, test_name)(mod, fix_version, self.registry, progress_bar) else: getattr(self, test_name)(mod) From e4717cccccce91402535bd9ff49a619ee81ff323 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 10:53:39 +0200 Subject: [PATCH 247/574] move subworkflows main_nf linting closer to the modules version --- nf_core/subworkflows/lint/main_nf.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py index edca32bf30..3ad3f34864 100644 --- a/nf_core/subworkflows/lint/main_nf.py +++ b/nf_core/subworkflows/lint/main_nf.py @@ -31,8 +31,9 @@ def main_nf(_, subworkflow: NFCoreComponent) -> Tuple[List[str], List[str]]: outputs: List[str] = [] # Read the lines directly from the subworkflow - lines = None - if lines is None: + lines: List[str] = [] + + if len(lines) == 0: try: # Check whether file exists and load it with open(subworkflow.main_nf) as fh: From b022862f0c1bce3dbc0188f4aa3135e2b8a71812 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 14:49:54 +0200 Subject: [PATCH 248/574] fix handling of missing dir in list command --- nf_core/components/components_command.py | 2 ++ nf_core/components/list.py | 11 ++++++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/nf_core/components/components_command.py b/nf_core/components/components_command.py index bff2467383..f25fb33a6f 100644 --- a/nf_core/components/components_command.py +++ b/nf_core/components/components_command.py @@ -51,6 +51,8 @@ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: """ try: if self.directory: + if self.directory == Path(".") and not nf_dir_req: + self.no_prompts = True self.directory, self.repo_type, self.org = get_repo_info(self.directory, use_prompt=not self.no_prompts) except UserWarning: if nf_dir_req: diff --git a/nf_core/components/list.py b/nf_core/components/list.py index 65a28db716..05a8f71120 100644 --- a/nf_core/components/list.py +++ b/nf_core/components/list.py @@ -22,8 +22,17 @@ def __init__( branch: Optional[str] = None, no_pull: bool = False, ) -> None: - super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) self.remote = remote + super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) + + def _configure_repo_and_paths(self, nf_dir_req=True) -> None: + """ + Override the default with nf_dir_req set to False to allow + info to be run from anywhere and still return remote info + """ + if self.remote: + nf_dir_req = False + return super()._configure_repo_and_paths(nf_dir_req) def list_components( self, keywords: Optional[List[str]] = None, print_json: bool = False From e9bf654aec84fc749b915e5e834e45ec2d035deb Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 14:50:52 +0200 Subject: [PATCH 249/574] remove unnecessary string conversion --- nf_core/components/create.py | 2 +- nf_core/components/nfcore_component.py | 4 ++-- nf_core/modules/lint/environment_yml.py | 2 +- nf_core/modules/lint/meta_yml.py | 4 ++-- nf_core/modules/lint/module_tests.py | 1 + nf_core/modules/modules_differ.py | 2 +- nf_core/pipelines/create_logo.py | 4 ++-- nf_core/utils.py | 2 +- 8 files changed, 11 insertions(+), 10 deletions(-) diff --git a/nf_core/components/create.py b/nf_core/components/create.py index fdcf402b47..c9af6d1adb 100644 --- a/nf_core/components/create.py +++ b/nf_core/components/create.py @@ -290,7 +290,7 @@ def _render_template(self) -> Optional[bool]: # Write output to the target file log.debug(f"Writing output to: '{dest_fn}'") dest_fn.parent.mkdir(exist_ok=True, parents=True) - with open(str(dest_fn), "w") as fh: + with open(dest_fn, "w") as fh: log.debug(f"Writing output to: '{dest_fn}'") fh.write(rendered_output) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 129871d68c..db3196be91 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -163,7 +163,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" inputs: List[str] = [] - with open(str(self.main_nf)) as f: + with open(self.main_nf) as f: data = f.read() # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo # regex matches: @@ -191,7 +191,7 @@ def get_inputs_from_main_nf(self) -> None: def get_outputs_from_main_nf(self): outputs = [] - with open(str(self.main_nf)) as f: + with open(self.main_nf) as f: data = f.read() # get output values from main.nf after "output:". the names are always after "emit:" if "output:" not in data: diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index e34b9d5856..341b9cd730 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -25,7 +25,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) if module.environment_yml is None: raise LintExceptionError("Module does not have an `environment.yml` file") try: - with open(str(module.environment_yml)) as fh: + with open(module.environment_yml) as fh: env_yml = yaml.safe_load(fh) module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml)) diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 32110b7131..4a0ef6e01e 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -43,7 +43,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None module.get_outputs_from_main_nf() # Check if we have a patch file, get original file in that case meta_yaml = None - if module.is_patched: + if module.is_patched and module_lint_object.modules_repo.repo_path is not None: lines = ModulesDiffer.try_apply_patch( module.component_name, module_lint_object.modules_repo.repo_path, @@ -57,7 +57,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None raise LintExceptionError("Module does not have a `meta.yml` file") if meta_yaml is None: try: - with open(str(module.meta_yml)) as fh: + with open(module.meta_yml) as fh: meta_yaml = yaml.safe_load(fh) module.passed.append(("meta_yml_exists", "Module `meta.yml` exists", module.meta_yml)) except FileNotFoundError: diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 9301db81ee..6722c12129 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -73,6 +73,7 @@ def module_tests(_, module: NFCoreComponent): with open(module.nftest_main_nf) as fh: if "snapshot(" in fh.read(): snap_file = module.nftest_testdir / "main.nf.test.snap" + if snap_file.is_file(): module.passed.append( ( diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index e310b3bf8b..f6b334eb6d 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -307,7 +307,7 @@ def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]: dict[str, str]: A dictionary indexed by the filenames with the file patches as values """ - with open(str(patch_fn)) as fh: + with open(patch_fn) as fh: lines = fh.readlines() patches = {} diff --git a/nf_core/pipelines/create_logo.py b/nf_core/pipelines/create_logo.py index 6619b910b5..c54d8f2085 100644 --- a/nf_core/pipelines/create_logo.py +++ b/nf_core/pipelines/create_logo.py @@ -62,7 +62,7 @@ def create_logo( img: Optional[Image.Image] = None if cache_path.is_file(): log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.") - img = Image.open(str(cache_path)) + img = Image.open(cache_path) if img is None: log.debug(f"Creating logo for {text}") @@ -81,7 +81,7 @@ def create_logo( template_fn = "nf-core-repo-logo-base-darkbg.png" template_path = assets / template_fn - img = Image.open(str(template_path)) + img = Image.open(template_path) # get the height of the template image height = img.size[1] diff --git a/nf_core/utils.py b/nf_core/utils.py index a95eea4b69..c12ec191fb 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1115,7 +1115,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] return Path(directory, CONFIG_PATHS[0]), None if not Path(config_fn).is_file(): raise FileNotFoundError(f"No `.nf-core.yml` file found in the directory '{directory}'") - with open(str(config_fn)) as fh: + with open(config_fn) as fh: tools_config = yaml.safe_load(fh) # If the file is empty From d4c06cb17fce07eedf00b2104e5be6fc5fc5548c Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 14:51:05 +0200 Subject: [PATCH 250/574] fix tests --- nf_core/modules/lint/main_nf.py | 9 +++++---- nf_core/pipelines/refgenie.py | 14 +++++++++----- tests/modules/test_install.py | 15 ++++++--------- tests/modules/test_list.py | 6 +++--- tests/pipelines/test_params_file.py | 18 +++++++++--------- tests/subworkflows/test_install.py | 5 +++-- 6 files changed, 35 insertions(+), 32 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 985a92fa1f..358d6a75a4 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -43,8 +43,8 @@ def main_nf( of ``software`` and ``prefix`` """ - inputs = [] - outputs = [] + inputs: List[str] = [] + outputs: List[str] = [] # Check if we have a patch file affecting the 'main.nf' file # otherwise read the lines directly from the module @@ -58,7 +58,7 @@ def main_nf( reverse=True, ).get("main.nf", [""]) - if not lines: + if len(lines) == 0: try: # Check whether file exists and load it with open(module.main_nf) as fh: @@ -66,9 +66,10 @@ def main_nf( module.passed.append(("main_nf_exists", "Module file exists", module.main_nf)) except FileNotFoundError: module.failed.append(("main_nf_exists", "Module file does not exist", module.main_nf)) + raise FileNotFoundError(f"Module file does not exist: {module.main_nf}") deprecated_i = ["initOptions", "saveFiles", "getSoftwareName", "getProcessName", "publishDir"] - if lines is not None: + if len(lines) > 0: lines_j = "\n".join(lines) else: lines_j = "" diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py index 19ef4b5121..f2eb09f330 100644 --- a/nf_core/pipelines/refgenie.py +++ b/nf_core/pipelines/refgenie.py @@ -181,14 +181,18 @@ def update_config(rgc): log.info("Could not determine path to 'refgenie_genomes.config' file.") return False + if refgenie_genomes_config_file is None: + log.info("Could not determine path to 'refgenie_genomes.config' file.") + return False + # Save the updated genome config - try: - with open(str(refgenie_genomes_config_file), "w+") as fh: - fh.write(refgenie_genomes) - log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}") - except FileNotFoundError: + if not Path(refgenie_genomes_config_file).is_file(): log.warning(f"Could not write to {refgenie_genomes_config_file}") return False + else: + with open(refgenie_genomes_config_file, "w+") as fh: + fh.write(refgenie_genomes) + log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}") # Add include statement to NXF_HOME/config if nxf_home: diff --git a/tests/modules/test_install.py b/tests/modules/test_install.py index 5f45d1b5b4..92d30a494f 100644 --- a/tests/modules/test_install.py +++ b/tests/modules/test_install.py @@ -1,4 +1,3 @@ -import os from pathlib import Path import pytest @@ -17,30 +16,28 @@ class TestModulesCreate(TestModules): - def test_modules_install_nopipeline(self): - """Test installing a module - no pipeline given""" - self.pipeline_dir = None - assert self.mods_install.install("foo") is False - @with_temporary_folder def test_modules_install_emptypipeline(self, tmpdir): """Test installing a module - empty dir given""" Path(tmpdir, "nf-core-pipe").mkdir() self.mods_install.directory = Path(tmpdir, "nf-core-pipe") with pytest.raises(UserWarning) as excinfo: - self.mods_install.install("foo") + self.mods_install.install("fastp") assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value) def test_modules_install_nomodule(self): """Test installing a module - unrecognised module given""" - assert self.mods_install.install("foo") is False + with pytest.raises(ValueError) as excinfo: + self.mods_install.install("foo") + assert excinfo.typename == "ValueError" + assert "Module 'foo' not found in available modules" in self.caplog.text def test_modules_install_trimgalore(self): """Test installing a module - TrimGalore!""" assert self.mods_install.install("trimgalore") is not False assert self.mods_install.directory is not None module_path = Path(self.mods_install.directory, "modules", "nf-core", "trimgalore") - assert os.path.exists(module_path) + assert module_path.exists() def test_modules_install_trimgalore_twice(self): """Test installing a module - TrimGalore! already there""" diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py index a170f6d6fc..282f044c1b 100644 --- a/tests/modules/test_list.py +++ b/tests/modules/test_list.py @@ -10,10 +10,10 @@ from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL -class TestModulesCreate(TestModules): +class TestModulesList(TestModules): def test_modules_list_remote(self): """Test listing available modules""" - mods_list = nf_core.modules.list.ModuleList(remote=True) + mods_list = nf_core.modules.list.ModuleList() listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) @@ -22,7 +22,7 @@ def test_modules_list_remote(self): def test_modules_list_remote_gitlab(self): """Test listing the modules in the remote gitlab repo""" - mods_list = nf_core.modules.list.ModuleList(remote=True, remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) + mods_list = nf_core.modules.list.ModuleList(remote_url=GITLAB_URL, branch=GITLAB_DEFAULT_BRANCH) listed_mods = mods_list.list_components() console = Console(record=True) console.print(listed_mods) diff --git a/tests/pipelines/test_params_file.py b/tests/pipelines/test_params_file.py index 7e3e4b4f42..22a6182acd 100644 --- a/tests/pipelines/test_params_file.py +++ b/tests/pipelines/test_params_file.py @@ -20,15 +20,15 @@ def setup_class(cls): # Create a test pipeline in temp directory cls.tmp_dir = tempfile.mkdtemp() - cls.template_dir = os.path.join(cls.tmp_dir, "wf") + cls.template_dir = Path(cls.tmp_dir, "wf") create_obj = nf_core.pipelines.create.create.PipelineCreate( "testpipeline", "a description", "Me", outdir=cls.template_dir, no_git=True ) create_obj.init_pipeline() - cls.template_schema = os.path.join(cls.template_dir, "nextflow_schema.json") + cls.template_schema = Path(cls.template_dir, "nextflow_schema.json") cls.params_template_builder = ParamsFileBuilder(cls.template_dir) - cls.invalid_template_schema = os.path.join(cls.template_dir, "nextflow_schema_invalid.json") + cls.invalid_template_schema = Path(cls.template_dir, "nextflow_schema_invalid.json") # Remove the allOf section to make the schema invalid with open(cls.template_schema) as fh: @@ -40,14 +40,14 @@ def setup_class(cls): @classmethod def teardown_class(cls): - if os.path.exists(cls.tmp_dir): + if Path(cls.tmp_dir).exists(): shutil.rmtree(cls.tmp_dir) def test_build_template(self): - outfile = os.path.join(self.tmp_dir, "params-file.yml") - self.params_template_builder.write_params_file(outfile) + outfile = Path(self.tmp_dir, "params-file.yml") + self.params_template_builder.write_params_file(str(outfile)) - assert os.path.exists(outfile) + assert outfile.exists() with open(outfile) as fh: out = fh.read() @@ -56,9 +56,9 @@ def test_build_template(self): def test_build_template_invalid_schema(self, caplog): """Build a schema from a template""" - outfile = os.path.join(self.tmp_dir, "params-file-invalid.yml") + outfile = Path(self.tmp_dir, "params-file-invalid.yml") builder = ParamsFileBuilder(self.invalid_template_schema) - res = builder.write_params_file(outfile) + res = builder.write_params_file(str(outfile)) assert res is False assert "Pipeline schema file is invalid" in caplog.text diff --git a/tests/subworkflows/test_install.py b/tests/subworkflows/test_install.py index e6ba9439a4..00ba888414 100644 --- a/tests/subworkflows/test_install.py +++ b/tests/subworkflows/test_install.py @@ -55,9 +55,10 @@ def test_subworkflows_install_emptypipeline(self, tmpdir): def test_subworkflows_install_nosubworkflow(self): """Test installing a subworkflow - unrecognised subworkflow given""" - with pytest.raises(SystemError) as excinfo: + with pytest.raises(ValueError) as excinfo: self.subworkflow_install.install("foo") - assert "Subworkflow 'foo' not found in available subworkflows" in str(excinfo.value) + assert excinfo.typename == "ValueError" + assert "Subworkflow 'foo' not found in available subworkflows" in self.caplog.text def test_subworkflows_install_bam_sort_stats_samtools_twice(self): """Test installing a subworkflow - bam_sort_stats_samtools already there""" From d57c815b83213154179be3b3e390557a6404d3b5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 15:30:46 +0200 Subject: [PATCH 251/574] add type hints to utils functions --- nf_core/components/update.py | 4 +-- nf_core/modules/modules_json.py | 2 +- nf_core/pipelines/download.py | 2 +- nf_core/utils.py | 48 ++++++++++++++++----------------- tests/modules/test_list.py | 2 +- 5 files changed, 29 insertions(+), 29 deletions(-) diff --git a/nf_core/components/update.py b/nf_core/components/update.py index eb15f976bf..3e4694adc8 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -755,7 +755,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path config_files = [f for f in pipeline_files if str(f).endswith(".config")] for config_file in config_files: log.debug(f"Moving '{component}/{config_file}' to updated component") - shutil.move(pipeline_path / config_file, temp_component_dir / config_file) + shutil.move(str(pipeline_path / config_file), temp_component_dir / config_file) files.append(temp_component_dir / config_file) else: @@ -772,7 +772,7 @@ def move_files_from_tmp_dir(self, component: str, install_folder: str, repo_path log.debug(f"Moving '{file}' to updated component") dest = Path(pipeline_path, file) dest.parent.mkdir(parents=True, exist_ok=True) - shutil.move(path, dest) + shutil.move(str(path), dest) log.info(f"Updating '{repo_path}/{component}'") log.debug(f"Updating {self.component_type[:-1]} '{component}' to {new_version} from {repo_path}") diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 19649a57cd..536589d81e 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -430,7 +430,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name # Add a time suffix to the path to make it unique # (do it again and again if it didn't work out...) to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}" - shutil.move(current_path, local_dir / to_name) + shutil.move(str(current_path), local_dir / to_name) def unsynced_components(self) -> Tuple[List[str], List[str], dict]: """ diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 704fe91b2f..97453b127e 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -1388,7 +1388,7 @@ def singularity_pull_image( # where the output of 'singularity pull' is first generated before being copied to the NXF_SINGULARITY_CACHDIR. # if not defined by the Singularity administrators, then use the temporary directory to avoid storing the images in the work directory. if os.environ.get("SINGULARITY_CACHEDIR") is None: - os.environ["SINGULARITY_CACHEDIR"] = NFCORE_CACHE_DIR + os.environ["SINGULARITY_CACHEDIR"] = str(NFCORE_CACHE_DIR) # Sometimes, container still contain an explicit library specification, which # resulted in attempted pulls e.g. from docker://quay.io/quay.io/qiime2/core:2022.11 diff --git a/nf_core/utils.py b/nf_core/utils.py index c12ec191fb..ea850a5d24 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -19,7 +19,7 @@ import time from contextlib import contextmanager from pathlib import Path -from typing import Any, Dict, Generator, List, Optional, Tuple, Union +from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union import git import prompt_toolkit.styles @@ -66,11 +66,11 @@ ] ) -NFCORE_CACHE_DIR = os.path.join( - os.environ.get("XDG_CACHE_HOME", os.path.join(os.getenv("HOME") or "", ".cache")), +NFCORE_CACHE_DIR = Path( + os.environ.get("XDG_CACHE_HOME", Path(os.getenv("HOME") or "", ".cache")), "nfcore", ) -NFCORE_DIR = os.path.join(os.environ.get("XDG_CONFIG_HOME", os.path.join(os.getenv("HOME") or "", ".config")), "nfcore") +NFCORE_DIR = Path(os.environ.get("XDG_CONFIG_HOME", os.path.join(os.getenv("HOME") or "", ".config")), "nfcore") def fetch_remote_version(source_url): @@ -358,17 +358,17 @@ def run_cmd(executable: str, cmd: str) -> Union[Tuple[bytes, bytes], None]: ) -def setup_nfcore_dir(): +def setup_nfcore_dir() -> bool: """Creates a directory for files that need to be kept between sessions Currently only used for keeping local copies of modules repos """ - if not os.path.exists(NFCORE_DIR): - os.makedirs(NFCORE_DIR) - return True + if not NFCORE_DIR.exists(): + NFCORE_DIR.mkdir(parents=True) + return True -def setup_requests_cachedir() -> dict: +def setup_requests_cachedir() -> Dict[str, Union[Path, datetime.timedelta, str]]: """Sets up local caching for faster remote HTTP requests. Caching directory will be set up in the user's home directory under @@ -377,10 +377,10 @@ def setup_requests_cachedir() -> dict: Uses requests_cache monkey patching. Also returns the config dict so that we can use the same setup with a Session. """ - pyversion = ".".join(str(v) for v in sys.version_info[0:3]) - cachedir = setup_nfcore_cachedir(f"cache_{pyversion}") - config = { - "cache_name": os.path.join(cachedir, "github_info"), + pyversion: str = ".".join(str(v) for v in sys.version_info[0:3]) + cachedir: Path = setup_nfcore_cachedir(f"cache_{pyversion}") + config: Dict[str, Union[Path, datetime.timedelta, str]] = { + "cache_name": Path(cachedir, "github_info"), "expire_after": datetime.timedelta(hours=1), "backend": "sqlite", } @@ -403,7 +403,7 @@ def setup_nfcore_cachedir(cache_fn: Union[str, Path]) -> Path: return cachedir -def wait_cli_function(poll_func, refresh_per_second=20): +def wait_cli_function(poll_func: Callable[[], bool], refresh_per_second: int = 20) -> None: """ Display a command-line spinner while calling a function repeatedly. @@ -427,7 +427,7 @@ def wait_cli_function(poll_func, refresh_per_second=20): raise AssertionError("Cancelled!") -def poll_nfcore_web_api(api_url, post_data=None): +def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict: """ Poll the nf-core website API @@ -448,7 +448,7 @@ def poll_nfcore_web_api(api_url, post_data=None): raise AssertionError(f"Could not connect to URL: {api_url}") else: if response.status_code != 200 and response.status_code != 301: - log.debug(f"Response content:\n{response.content}") + log.debug(f"Response content:\n{response.content.decode()}") raise AssertionError( f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)" ) @@ -460,7 +460,7 @@ def poll_nfcore_web_api(api_url, post_data=None): if "status" not in web_response: raise AssertionError() except (json.decoder.JSONDecodeError, AssertionError, TypeError): - log.debug(f"Response content:\n{response.content}") + log.debug(f"Response content:\n{response.content.decode()}") raise AssertionError( f"nf-core website API results response not recognised: {api_url}\n " "See verbose log for full response" @@ -476,14 +476,14 @@ class GitHubAPISession(requests_cache.CachedSession): such as automatically setting up GitHub authentication if we can. """ - def __init__(self): # pylint: disable=super-init-not-called - self.auth_mode = None - self.return_ok = [200, 201] - self.return_retry = [403] - self.return_unauthorised = [401] - self.has_init = False + def __init__(self) -> None: + self.auth_mode: Optional[str] = None + self.return_ok: List[int] = [200, 201] + self.return_retry: List[int] = [403] + self.return_unauthorised: List[int] = [401] + self.has_init: bool = False - def lazy_init(self): + def lazy_init(self) -> None: """ Initialise the object. diff --git a/tests/modules/test_list.py b/tests/modules/test_list.py index 282f044c1b..3e92a33ab4 100644 --- a/tests/modules/test_list.py +++ b/tests/modules/test_list.py @@ -67,7 +67,7 @@ def test_modules_list_local_json(self): assert "fastqc" in listed_mods assert "multiqc" in listed_mods - def test_modules_list_remote_json(self): + def test_modules_list_remote_json(self) -> None: """Test listing available modules as JSON""" mods_list = nf_core.modules.list.ModuleList(remote=True) listed_mods: str = str(mods_list.list_components(print_json=True)) From 495e05acc406b64e1d21e008aed92b443c5fb40e Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 15:46:39 +0200 Subject: [PATCH 252/574] fix refgenie tests --- nf_core/pipelines/refgenie.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipelines/refgenie.py b/nf_core/pipelines/refgenie.py index f2eb09f330..426ca5eb7d 100644 --- a/nf_core/pipelines/refgenie.py +++ b/nf_core/pipelines/refgenie.py @@ -186,13 +186,13 @@ def update_config(rgc): return False # Save the updated genome config - if not Path(refgenie_genomes_config_file).is_file(): - log.warning(f"Could not write to {refgenie_genomes_config_file}") - return False - else: + try: with open(refgenie_genomes_config_file, "w+") as fh: fh.write(refgenie_genomes) log.info(f"Updated nf-core genomes config: {refgenie_genomes_config_file}") + except FileNotFoundError: + log.info(f"Could not write to {refgenie_genomes_config_file}") + return False # Add include statement to NXF_HOME/config if nxf_home: From 4c07bdfef5542de71954dbaedba6293e71bfcc9d Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 30 Jul 2024 15:57:15 +0200 Subject: [PATCH 253/574] fix tests --- nf_core/subworkflows/list.py | 2 +- nf_core/utils.py | 10 ++++++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/nf_core/subworkflows/list.py b/nf_core/subworkflows/list.py index 5f849a1f9c..9e84d6cbe0 100644 --- a/nf_core/subworkflows/list.py +++ b/nf_core/subworkflows/list.py @@ -10,7 +10,7 @@ class SubworkflowList(ComponentList): def __init__( self, - pipeline_dir: Union[str, Path], + pipeline_dir: Union[str, Path] = ".", remote: bool = True, remote_url: Optional[str] = None, branch: Optional[str] = None, diff --git a/nf_core/utils.py b/nf_core/utils.py index ea850a5d24..48b7eae294 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -448,7 +448,10 @@ def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict: raise AssertionError(f"Could not connect to URL: {api_url}") else: if response.status_code != 200 and response.status_code != 301: - log.debug(f"Response content:\n{response.content.decode()}") + response_content = response.content + if isinstance(response_content, bytes): + response_content = response_content.decode() + log.debug(f"Response content:\n{response_content}") raise AssertionError( f"Could not access remote API results: {api_url} (HTML {response.status_code} Error)" ) @@ -460,7 +463,10 @@ def poll_nfcore_web_api(api_url: str, post_data: Optional[Dict] = None) -> Dict: if "status" not in web_response: raise AssertionError() except (json.decoder.JSONDecodeError, AssertionError, TypeError): - log.debug(f"Response content:\n{response.content.decode()}") + response_content = response.content + if isinstance(response_content, bytes): + response_content = response_content.decode() + log.debug(f"Response content:\n{response_content}") raise AssertionError( f"nf-core website API results response not recognised: {api_url}\n " "See verbose log for full response" From c9f86ca5e841cdda6660803ade89919b538efc92 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 1 Aug 2024 00:15:29 +0000 Subject: [PATCH 254/574] Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 63202e5178..879bc15c01 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: alias: ec - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.11.0" + rev: "v1.11.1" hooks: - id: mypy additional_dependencies: From 6f0345f445e97ade328b32b1c059788898ec208a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 1 Aug 2024 00:16:33 +0000 Subject: [PATCH 255/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a56abe0acb..ec033ff1ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -55,6 +55,7 @@ - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) +- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 38ea56804aad6a0bd4492b55e164af42f1bac758 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 2 Aug 2024 10:10:19 +0200 Subject: [PATCH 256/574] allow numbers in custom pipeline name --- nf_core/pipelines/create/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index c15d61e266..a360b5f3a9 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -65,7 +65,7 @@ def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str: if not re.match(r"^[a-z]+$", v): raise ValueError("Must be lowercase without punctuation.") else: - if not re.match(r"^[a-zA-Z-_]+$", v): + if not re.match(r"^[a-zA-Z-_0-9]+$", v): raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.") return v From 8a781b8bcb3f5bc40e67819ee3e03fe774e14a9a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 2 Aug 2024 08:12:16 +0000 Subject: [PATCH 257/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ec033ff1ee..b6cd12d551 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -56,6 +56,7 @@ - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) +- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 7ea871858fbcb263c65de4527fa4644f0ee007fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 2 Aug 2024 10:24:58 +0200 Subject: [PATCH 258/574] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49a58ff6bf..12001d56ef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -54,7 +54,7 @@ - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) -- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) +- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From cbee6d06bb0fbaa2a76d6e7f7c2a842e0a81ec54 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 2 Aug 2024 12:03:07 +0200 Subject: [PATCH 259/574] allow module lables between double quotes --- nf_core/modules/lint/main_nf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 883d2bb3e0..2762dd22d5 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -437,7 +437,7 @@ def check_process_labels(self, lines): if len(all_labels) > 0: for label in all_labels: try: - label = re.match(r"^label\s+'?([a-zA-Z0-9_-]+)'?$", label).group(1) + label = re.match(r"^label\s+'?\"?([a-zA-Z0-9_-]+)'?\"?$", label).group(1) except AttributeError: self.warned.append( ( From 086302e209fa56fd869aae3590e7d1bae780c3fa Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 2 Aug 2024 12:48:00 +0200 Subject: [PATCH 260/574] allow multiline module input tuple --- nf_core/modules/lint/main_nf.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index 883d2bb3e0..ed3d93e2ca 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -81,6 +81,7 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar): script_lines = [] shell_lines = [] when_lines = [] + lines = iter(lines) for line in lines: if re.search(r"^\s*process\s*\w*\s*{", line) and state == "module": state = "process" @@ -104,6 +105,13 @@ def main_nf(module_lint_object, module, fix_version, registry, progress_bar): if state == "process" and not _is_empty(line): process_lines.append(line) if state == "input" and not _is_empty(line): + # allow multiline tuples + if "tuple" in line and line.count("(") <= 1: + joint_tuple = line + while re.sub(r"\s", "", line) != ")": + joint_tuple = joint_tuple + line + line = next(lines) + line = joint_tuple inputs.extend(_parse_input(module, line)) if state == "output" and not _is_empty(line): outputs += _parse_output(module, line) From 5b7425368135301c53f664262133bf84981cbdd9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 2 Aug 2024 15:34:20 +0200 Subject: [PATCH 261/574] Update nf_core/pipelines/create/utils.py Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- nf_core/pipelines/create/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index a360b5f3a9..c387960c39 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -65,7 +65,7 @@ def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str: if not re.match(r"^[a-z]+$", v): raise ValueError("Must be lowercase without punctuation.") else: - if not re.match(r"^[a-zA-Z-_0-9]+$", v): + if not re.match(r"^[-\w]+$", v): raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.") return v From 4f755380032ce01d6b1222036ae68172976e40f5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 5 Aug 2024 08:27:26 +0200 Subject: [PATCH 262/574] update ruff --- .github/workflows/changelog.py | 9 +++++---- .pre-commit-config.yaml | 2 +- nf_core/modules/modules_differ.py | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/changelog.py b/.github/workflows/changelog.py index 471665e4b1..24130e65c4 100644 --- a/.github/workflows/changelog.py +++ b/.github/workflows/changelog.py @@ -1,3 +1,4 @@ +#! /usr/bin/env python3 """ Taken from https://github.com/MultiQC/MultiQC/blob/main/.github/workflows/changelog.py and updated for nf-core @@ -18,7 +19,7 @@ import re import sys from pathlib import Path -from typing import List +from typing import List, Tuple REPO_URL = "https://github.com/nf-core/tools" @@ -32,7 +33,7 @@ assert pr_number, pr_number # Trim the PR number added when GitHub squashes commits, e.g. "Template: Updated (#2026)" -pr_title = pr_title.removesuffix(f" (#{pr_number})") +pr_title = pr_title.removesuffix(f" (#{pr_number})") # type: ignore changelog_path = workspace_path / "CHANGELOG.md" @@ -50,7 +51,7 @@ sys.exit(0) -def _determine_change_type(pr_title) -> tuple[str, str]: +def _determine_change_type(pr_title) -> Tuple[str, str]: """ Determine the type of the PR: Template, Download, Linting, Modules, Subworkflows, or General Returns a tuple of the section name and the module info. @@ -85,7 +86,7 @@ def _determine_change_type(pr_title) -> tuple[str, str]: pr_link = f"([#{pr_number}]({REPO_URL}/pull/{pr_number}))" # Handle manual changelog entries through comments. -if comment := comment.removeprefix("@nf-core-bot changelog").strip(): +if comment := comment.removeprefix("@nf-core-bot changelog").strip(): # type: ignore print(f"Adding manual changelog entry: {comment}") pr_title = comment new_lines = [ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f763fa6658..c83cb5a4b7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.1 + rev: v0.5.6 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix diff --git a/nf_core/modules/modules_differ.py b/nf_core/modules/modules_differ.py index f6b334eb6d..b6d7f0d0fa 100644 --- a/nf_core/modules/modules_differ.py +++ b/nf_core/modules/modules_differ.py @@ -312,7 +312,7 @@ def per_file_patch(patch_fn: Union[str, Path]) -> Dict[str, List[str]]: patches = {} i = 0 - patch_lines: list[str] = [] + patch_lines: List[str] = [] key = "preamble" while i < len(lines): line = lines[i] From f4323602f8481460aea48c973c22e6b79dde6fae Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 13:13:33 +0200 Subject: [PATCH 263/574] add option to exclude gitpod for custom pipeline template --- .github/workflows/create-test-lint-wf-template.yml | 5 +++++ nf_core/pipeline-template/nextflow.config | 2 ++ nf_core/pipelines/create/create.py | 2 ++ nf_core/pipelines/create/custompipeline.py | 13 +++++++++++++ tests/data/pipeline_create_template_skip.yml | 1 + 5 files changed, 23 insertions(+) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index cfa0a50079..8a893ce9f0 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -42,6 +42,7 @@ jobs: - "template_skip_igenomes.yml" - "template_skip_ci.yml" - "template_skip_code_linters.yml" + - "template_skip_gitpod.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -107,6 +108,10 @@ jobs: run: | printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml + - name: Create template skip gitpod + run: | + printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..8a6ca6b327 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -178,11 +178,13 @@ profiles { wave.freeze = true wave.strategy = 'conda,container' } + {%- if gitpod %} gitpod { executor.name = 'local' executor.cpus = 4 executor.memory = 8.GB } + {%- endif %} test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 42e4a6ad7b..8f279df190 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,6 +101,7 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], + "gitpod": [".gitpod.yml"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "igenomes": {"file": True, "content": True}, "nf_core_configs": {"file": False, "content": True}, "code_linters": {"file": True, "content": True}, + "gitpod": {"file": True, "content": True}, } # Set the parameters for the jinja template diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 0925fb5bab..e839042187 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -51,6 +51,13 @@ - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). """ +markdown_gitpod = """ +Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. + +Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. +This is useful to have all the tools ready for pipeline development. +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -96,6 +103,12 @@ def compose(self) -> ComposeResult: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", "code_linters", ), + PipelineFeature( + markdown_gitpod, + "Include a gitpod environment", + "Include the configuration required to use Gitpod.", + "gitpod", + ), classes="features-container", ) yield Center( diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index d9ef405c51..c18d810cd9 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -12,3 +12,4 @@ skip_features: - igenomes - nf_core_configs - code_linters + - gitpod From 997468d81855989fdd95c04e38955ee594bf6335 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 5 Aug 2024 11:15:26 +0000 Subject: [PATCH 264/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aea91cb51a..df11c64169 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) +- add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) ### Linting From 51f37561bf9555202803c23494959f8cec7e1ae3 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 15:27:13 +0200 Subject: [PATCH 265/574] add option to exclude citations for custom pipeline template --- .../create-test-lint-wf-template.yml | 5 + nf_core/pipeline-template/nextflow.config | 3 +- .../pipeline-template/nextflow_schema.json | 4 +- .../pipeline-template/workflows/pipeline.nf | 4 + nf_core/pipelines/create/create.py | 2 + nf_core/pipelines/create/custompipeline.py | 13 + tests/__snapshots__/test_create_app.ambr | 511 +++++++++--------- tests/data/pipeline_create_template_skip.yml | 1 + 8 files changed, 284 insertions(+), 259 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index cfa0a50079..818c206167 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -42,6 +42,7 @@ jobs: - "template_skip_igenomes.yml" - "template_skip_ci.yml" - "template_skip_code_linters.yml" + - "template_skip_citations.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -107,6 +108,10 @@ jobs: run: | printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml + - name: Create template skip citations + run: | + printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..f622205a12 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -25,7 +25,8 @@ params { multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + {%- if citations %} + multiqc_methods_description = null{% endif %} // Boilerplate options outdir = null diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 18bad71b76..0bd4443675 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -234,12 +234,12 @@ "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", "fa_icon": "fas fa-image", "hidden": true - }, + },{% if citations %} "multiqc_methods_description": { "type": "string", "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" - }, + },{% endif %} "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index de0f21fe38..765b97c68e 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -63,21 +63,25 @@ workflow {{ short_name|upper }} { workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + {%- if citations %} ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) + {%- endif %} ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + {%- if citations %} ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( name: 'methods_description_mqc.yaml', sort: true ) ) + {%- endif %} MULTIQC ( ch_multiqc_files.collect(), diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 42e4a6ad7b..86ca1763fc 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,6 +101,7 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], + "citations": ["CITATIONS.md", "assets/methods_description_template.yml"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -210,6 +211,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "igenomes": {"file": True, "content": True}, "nf_core_configs": {"file": False, "content": True}, "code_linters": {"file": True, "content": True}, + "citations": {"file": True, "content": True}, } # Set the parameters for the jinja template diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 0925fb5bab..1dd6134848 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -51,6 +51,13 @@ - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). """ +markdown_citations = """ +If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. + +Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline, +and the logics to add this section to the output MultiQC report (if the report is generated). +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -96,6 +103,12 @@ def compose(self) -> ComposeResult: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", "code_linters", ), + PipelineFeature( + markdown_citations, + "Include citations", + "Include a CITATIONS.md file to add pipeline tools citations.", + "citations", + ), classes="features-container", ) yield Center( diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 5e5b005de0..531ea098bf 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2778615119-matrix { + .terminal-4194849765-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2778615119-title { + .terminal-4194849765-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2778615119-r1 { fill: #c5c8c6 } - .terminal-2778615119-r2 { fill: #e3e3e3 } - .terminal-2778615119-r3 { fill: #989898 } - .terminal-2778615119-r4 { fill: #e1e1e1 } - .terminal-2778615119-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2778615119-r6 { fill: #1e1e1e } - .terminal-2778615119-r7 { fill: #0178d4 } - .terminal-2778615119-r8 { fill: #454a50 } - .terminal-2778615119-r9 { fill: #e2e2e2 } - .terminal-2778615119-r10 { fill: #808080 } - .terminal-2778615119-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2778615119-r12 { fill: #000000 } - .terminal-2778615119-r13 { fill: #e4e4e4 } - .terminal-2778615119-r14 { fill: #14191f } - .terminal-2778615119-r15 { fill: #507bb3 } - .terminal-2778615119-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2778615119-r17 { fill: #001541 } - .terminal-2778615119-r18 { fill: #7ae998 } - .terminal-2778615119-r19 { fill: #0a180e;font-weight: bold } - .terminal-2778615119-r20 { fill: #008139 } - .terminal-2778615119-r21 { fill: #fea62b;font-weight: bold } - .terminal-2778615119-r22 { fill: #a7a9ab } - .terminal-2778615119-r23 { fill: #e2e3e3 } + .terminal-4194849765-r1 { fill: #c5c8c6 } + .terminal-4194849765-r2 { fill: #e3e3e3 } + .terminal-4194849765-r3 { fill: #989898 } + .terminal-4194849765-r4 { fill: #e1e1e1 } + .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } + .terminal-4194849765-r6 { fill: #1e1e1e } + .terminal-4194849765-r7 { fill: #0178d4 } + .terminal-4194849765-r8 { fill: #454a50 } + .terminal-4194849765-r9 { fill: #e2e2e2 } + .terminal-4194849765-r10 { fill: #808080 } + .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-4194849765-r12 { fill: #000000 } + .terminal-4194849765-r13 { fill: #e4e4e4 } + .terminal-4194849765-r14 { fill: #14191f } + .terminal-4194849765-r15 { fill: #507bb3 } + .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } + .terminal-4194849765-r17 { fill: #001541 } + .terminal-4194849765-r18 { fill: #7ae998 } + .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } + .terminal-4194849765-r20 { fill: #008139 } + .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } + .terminal-4194849765-r22 { fill: #a7a9ab } + .terminal-4194849765-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + ▃▃ + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,254 @@ font-weight: 700; } - .terminal-763408100-matrix { + .terminal-423998432-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-763408100-title { + .terminal-423998432-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-763408100-r1 { fill: #c5c8c6 } - .terminal-763408100-r2 { fill: #e3e3e3 } - .terminal-763408100-r3 { fill: #989898 } - .terminal-763408100-r4 { fill: #e1e1e1 } - .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } - .terminal-763408100-r6 { fill: #1e1e1e } - .terminal-763408100-r7 { fill: #507bb3 } - .terminal-763408100-r8 { fill: #e2e2e2 } - .terminal-763408100-r9 { fill: #808080 } - .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } - .terminal-763408100-r11 { fill: #001541 } - .terminal-763408100-r12 { fill: #14191f } - .terminal-763408100-r13 { fill: #454a50 } - .terminal-763408100-r14 { fill: #7ae998 } - .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different ▁▁ - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index d9ef405c51..06e01cc7f2 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -12,3 +12,4 @@ skip_features: - igenomes - nf_core_configs - code_linters + - citations From 74bd318ef0785108f122bc1f14f4d9d668f57b35 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 5 Aug 2024 13:29:41 +0000 Subject: [PATCH 266/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aea91cb51a..a723bd3283 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) +- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) ### Linting From ed4554d7c4a37341a034bb227c4a02953a88ce05 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 15:32:04 +0200 Subject: [PATCH 267/574] update snapshots --- tests/__snapshots__/test_create_app.ambr | 511 +++++++++++------------ 1 file changed, 255 insertions(+), 256 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 5e5b005de0..531ea098bf 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + ▃▃ + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,254 @@ font-weight: 700; } - .terminal-763408100-matrix { + .terminal-423998432-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-763408100-title { + .terminal-423998432-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-763408100-r1 { fill: #c5c8c6 } - .terminal-763408100-r2 { fill: #e3e3e3 } - .terminal-763408100-r3 { fill: #989898 } - .terminal-763408100-r4 { fill: #e1e1e1 } - .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } - .terminal-763408100-r6 { fill: #1e1e1e } - .terminal-763408100-r7 { fill: #507bb3 } - .terminal-763408100-r8 { fill: #e2e2e2 } - .terminal-763408100-r9 { fill: #808080 } - .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } - .terminal-763408100-r11 { fill: #001541 } - .terminal-763408100-r12 { fill: #14191f } - .terminal-763408100-r13 { fill: #454a50 } - .terminal-763408100-r14 { fill: #7ae998 } - .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different ▁▁ - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 9182530d2a4356fa2924798b5aa2025fed793dd0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 5 Aug 2024 16:13:37 +0200 Subject: [PATCH 268/574] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/custompipeline.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 1dd6134848..d5bcf04bc7 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -54,7 +54,7 @@ markdown_citations = """ If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. -Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to describe a Materials & Methods section describing the tools used in the pieline, +Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, and the logics to add this section to the output MultiQC report (if the report is generated). """ @@ -106,7 +106,7 @@ def compose(self) -> ComposeResult: PipelineFeature( markdown_citations, "Include citations", - "Include a CITATIONS.md file to add pipeline tools citations.", + "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).", "citations", ), classes="features-container", From b0d07609507ef60ba79179e810b0cac1f308108a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 16:23:54 +0200 Subject: [PATCH 269/574] exclude content of CITATIONS.md instead of the whole file --- nf_core/pipeline-template/CITATIONS.md | 3 +++ nf_core/pipeline-template/README.md | 4 ++-- .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 2 ++ nf_core/pipeline-template/workflows/pipeline.nf | 2 +- nf_core/pipelines/create/create.py | 2 +- 5 files changed, 9 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 6edf8f620c..c0c0729277 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -8,6 +8,8 @@ > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. +{%- if citations %} + ## Pipeline tools - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) @@ -39,3 +41,4 @@ - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. + > {%- endif %} diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index feece399b5..4efa88d5f6 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -116,10 +116,10 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - +{% if citations %} An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. - +{% endif %} {% if is_nfcore -%} You can cite the `nf-core` publication as follows: diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index a4bfb9f8be..0c2e1d8b0a 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -207,6 +207,7 @@ def genomeExistsError() { } {%- endif %} +{%- if citations %} // // Generate methods description for MultiQC // @@ -270,3 +271,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } +{% endif %} diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 765b97c68e..8ce3637e4e 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -9,7 +9,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' +{% if citations %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 86ca1763fc..3adeec60b7 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,7 +101,7 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], - "citations": ["CITATIONS.md", "assets/methods_description_template.yml"], + "citations": ["assets/methods_description_template.yml"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) From 138ecb793ab57f34b7fb124a81df04512f0b36fd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 5 Aug 2024 16:58:50 +0200 Subject: [PATCH 270/574] update snapshot --- tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++----------- 1 file changed, 256 insertions(+), 255 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 531ea098bf..940a875839 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-4194849765-matrix { + .terminal-2433570258-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4194849765-title { + .terminal-2433570258-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4194849765-r1 { fill: #c5c8c6 } - .terminal-4194849765-r2 { fill: #e3e3e3 } - .terminal-4194849765-r3 { fill: #989898 } - .terminal-4194849765-r4 { fill: #e1e1e1 } - .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4194849765-r6 { fill: #1e1e1e } - .terminal-4194849765-r7 { fill: #0178d4 } - .terminal-4194849765-r8 { fill: #454a50 } - .terminal-4194849765-r9 { fill: #e2e2e2 } - .terminal-4194849765-r10 { fill: #808080 } - .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-4194849765-r12 { fill: #000000 } - .terminal-4194849765-r13 { fill: #e4e4e4 } - .terminal-4194849765-r14 { fill: #14191f } - .terminal-4194849765-r15 { fill: #507bb3 } - .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } - .terminal-4194849765-r17 { fill: #001541 } - .terminal-4194849765-r18 { fill: #7ae998 } - .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } - .terminal-4194849765-r20 { fill: #008139 } - .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } - .terminal-4194849765-r22 { fill: #a7a9ab } - .terminal-4194849765-r23 { fill: #e2e3e3 } + .terminal-2433570258-r1 { fill: #c5c8c6 } + .terminal-2433570258-r2 { fill: #e3e3e3 } + .terminal-2433570258-r3 { fill: #989898 } + .terminal-2433570258-r4 { fill: #e1e1e1 } + .terminal-2433570258-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2433570258-r6 { fill: #1e1e1e } + .terminal-2433570258-r7 { fill: #0178d4 } + .terminal-2433570258-r8 { fill: #454a50 } + .terminal-2433570258-r9 { fill: #e2e2e2 } + .terminal-2433570258-r10 { fill: #808080 } + .terminal-2433570258-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-2433570258-r12 { fill: #000000 } + .terminal-2433570258-r13 { fill: #e4e4e4 } + .terminal-2433570258-r14 { fill: #14191f } + .terminal-2433570258-r15 { fill: #507bb3 } + .terminal-2433570258-r16 { fill: #dde6ed;font-weight: bold } + .terminal-2433570258-r17 { fill: #001541 } + .terminal-2433570258-r18 { fill: #7ae998 } + .terminal-2433570258-r19 { fill: #0a180e;font-weight: bold } + .terminal-2433570258-r20 { fill: #008139 } + .terminal-2433570258-r21 { fill: #fea62b;font-weight: bold } + .terminal-2433570258-r22 { fill: #a7a9ab } + .terminal-2433570258-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - ▃▃ - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + ▃▃ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,255 @@ font-weight: 700; } - .terminal-423998432-matrix { + .terminal-1630976143-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-423998432-title { + .terminal-1630976143-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-423998432-r1 { fill: #c5c8c6 } - .terminal-423998432-r2 { fill: #e3e3e3 } - .terminal-423998432-r3 { fill: #989898 } - .terminal-423998432-r4 { fill: #e1e1e1 } - .terminal-423998432-r5 { fill: #4ebf71;font-weight: bold } - .terminal-423998432-r6 { fill: #1e1e1e } - .terminal-423998432-r7 { fill: #507bb3 } - .terminal-423998432-r8 { fill: #e2e2e2 } - .terminal-423998432-r9 { fill: #808080 } - .terminal-423998432-r10 { fill: #dde6ed;font-weight: bold } - .terminal-423998432-r11 { fill: #001541 } - .terminal-423998432-r12 { fill: #454a50 } - .terminal-423998432-r13 { fill: #7ae998 } - .terminal-423998432-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-423998432-r15 { fill: #0a180e;font-weight: bold } - .terminal-423998432-r16 { fill: #000000 } - .terminal-423998432-r17 { fill: #008139 } - .terminal-423998432-r18 { fill: #fea62b;font-weight: bold } - .terminal-423998432-r19 { fill: #a7a9ab } - .terminal-423998432-r20 { fill: #e2e3e3 } + .terminal-1630976143-r1 { fill: #c5c8c6 } + .terminal-1630976143-r2 { fill: #e3e3e3 } + .terminal-1630976143-r3 { fill: #989898 } + .terminal-1630976143-r4 { fill: #e1e1e1 } + .terminal-1630976143-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1630976143-r6 { fill: #1e1e1e } + .terminal-1630976143-r7 { fill: #507bb3 } + .terminal-1630976143-r8 { fill: #e2e2e2 } + .terminal-1630976143-r9 { fill: #808080 } + .terminal-1630976143-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1630976143-r11 { fill: #001541 } + .terminal-1630976143-r12 { fill: #14191f } + .terminal-1630976143-r13 { fill: #454a50 } + .terminal-1630976143-r14 { fill: #7ae998 } + .terminal-1630976143-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1630976143-r16 { fill: #0a180e;font-weight: bold } + .terminal-1630976143-r17 { fill: #000000 } + .terminal-1630976143-r18 { fill: #008139 } + .terminal-1630976143-r19 { fill: #fea62b;font-weight: bold } + .terminal-1630976143-r20 { fill: #a7a9ab } + .terminal-1630976143-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles ▆▆ + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From d94d1d065001885e2a4b58bf55d1cd5fb352f5b9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 6 Aug 2024 10:28:23 +0200 Subject: [PATCH 271/574] add bot action to update textual snapshots --- .github/workflows/regenerate-snapshots.yml | 92 ++++++++++++++++++++++ CONTRIBUTING.md | 21 +++++ 2 files changed, 113 insertions(+) create mode 100644 .github/workflows/regenerate-snapshots.yml diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/regenerate-snapshots.yml new file mode 100644 index 0000000000..d05505a953 --- /dev/null +++ b/.github/workflows/regenerate-snapshots.yml @@ -0,0 +1,92 @@ +name: Regenerate Textual snapshots from a comment +on: + issue_comment: + types: [created] + +jobs: + regenerate-snapshots: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot regenerate snapshots') && + github.repository == 'nf-core/tools' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # indication that the command is running + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + # Install dependencies and run pytest + - name: Set up Python + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + + - name: Install dependencies + run: | + python -m pip install --upgrade pip -r requirements-dev.txt + pip install -e . + + - name: Run pytest to regenerate snapshots + id: pytest + run: | + python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --cov --durations=0 + continue-on-error: true + + # indication that the run has finished + - name: react if finished succesfully + if: steps.pytest.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" + + - name: Commit & push changes + id: commit-and-push + if: steps.pytest.outcome == 'failure' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Update Textual snapshots" + git push + + - name: react if snapshots were updated + id: react-if-updated + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if snapshots were not updated + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if snapshots were not updated + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to update the snapshots, but it didn't work. Please update them manually. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 2b2dfc1bed..cc81fa3f48 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -125,3 +125,24 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) + +## nf-core-bot + +nf-core has a bot which you can use to perform certain actions on a PR. + +- Fix linting: + +If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words `@nf-core-bot fix linting`. The bot will try to fix the linting, push to your branch, and react to the comment if the fix was successful or not. + +- Update the `CHANGELOG.md`: + +The nf-core-bot runs automatically on every PR updating the `CHANGELOG.md` if it was not updated. It will add the new change using the title of your PR. +If the action didn't run automatically, or you want to provide a different title, you can post a comment with `@nf-core-bot changelog`, optionally followed by the description that you want to add to the changelog. + +- Update Textual snapshots: + +If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact. +If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`. + +> [!WARNING] +> Please always check this report to make sure that the changes are expected. From c76a2ba95adef683e8fa197258472cf6deb36b8d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 6 Aug 2024 08:31:24 +0000 Subject: [PATCH 272/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aea91cb51a..013e8a5d45 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,7 @@ - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) +- Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From d07f3ffbc0a490a7813897ab14f969a079cef70d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 6 Aug 2024 10:49:42 +0200 Subject: [PATCH 273/574] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .github/workflows/regenerate-snapshots.yml | 5 +++-- CONTRIBUTING.md | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/regenerate-snapshots.yml index d05505a953..8fcc9b6f1b 100644 --- a/.github/workflows/regenerate-snapshots.yml +++ b/.github/workflows/regenerate-snapshots.yml @@ -8,7 +8,7 @@ jobs: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot regenerate snapshots') && + contains(github.event.comment.body, '@nf-core-bot update snapshots') && github.repository == 'nf-core/tools' runs-on: ubuntu-latest steps: @@ -36,6 +36,7 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" + cache: "pip" - name: Install dependencies run: | @@ -45,7 +46,7 @@ jobs: - name: Run pytest to regenerate snapshots id: pytest run: | - python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --cov --durations=0 + python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --durations=0 continue-on-error: true # indication that the run has finished diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index cc81fa3f48..3ad9e57243 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -145,4 +145,4 @@ If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`. > [!WARNING] -> Please always check this report to make sure that the changes are expected. +> Please always check the HTML report to make sure that the changes are expected. From 346344f55d47d8bd20fd7344eaff799079f6b3cc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 6 Aug 2024 10:54:39 +0200 Subject: [PATCH 274/574] rename regenerae-snapshots to update-textual-snapshots --- ...shots.yml => update-textual-snapshots.yml} | 6 ++--- CONTRIBUTING.md | 22 ++++++++++++++++--- 2 files changed, 22 insertions(+), 6 deletions(-) rename .github/workflows/{regenerate-snapshots.yml => update-textual-snapshots.yml} (96%) diff --git a/.github/workflows/regenerate-snapshots.yml b/.github/workflows/update-textual-snapshots.yml similarity index 96% rename from .github/workflows/regenerate-snapshots.yml rename to .github/workflows/update-textual-snapshots.yml index 8fcc9b6f1b..fb936762f8 100644 --- a/.github/workflows/regenerate-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -1,10 +1,10 @@ -name: Regenerate Textual snapshots from a comment +name: Update Textual snapshots from a comment on: issue_comment: types: [created] jobs: - regenerate-snapshots: + update-snapshots: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && @@ -43,7 +43,7 @@ jobs: python -m pip install --upgrade pip -r requirements-dev.txt pip install -e . - - name: Run pytest to regenerate snapshots + - name: Run pytest to update snapshots id: pytest run: | python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --durations=0 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3ad9e57243..f9773296c1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -132,17 +132,33 @@ nf-core has a bot which you can use to perform certain actions on a PR. - Fix linting: -If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words `@nf-core-bot fix linting`. The bot will try to fix the linting, push to your branch, and react to the comment if the fix was successful or not. +If the linting tests is failing on a PR to nf-core/tools, you can post a comment with the magic words: + +``` +@nf-core-bot fix linting +``` + +The bot will try to fix the linting, push to your branch, and react to the comment when it starts running (👀) and if the fix was successful (👍🏻) or not (😕). - Update the `CHANGELOG.md`: The nf-core-bot runs automatically on every PR updating the `CHANGELOG.md` if it was not updated. It will add the new change using the title of your PR. -If the action didn't run automatically, or you want to provide a different title, you can post a comment with `@nf-core-bot changelog`, optionally followed by the description that you want to add to the changelog. +If the action didn't run automatically, or you want to provide a different title, you can post a comment with: + +``` +@nf-core-bot changelog +``` + +Optionally followed by the description that you want to add to the changelog. - Update Textual snapshots: If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact. -If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words `@nf-core-bot regenerate snapshots`. +If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words: + +``` +@nf-core-bot update snapshots +``` > [!WARNING] > Please always check the HTML report to make sure that the changes are expected. From 6144d0f1ab8b9440623bfa586de61c75ee240569 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 6 Aug 2024 14:48:57 +0200 Subject: [PATCH 275/574] add option to exclude multiqc from pipeline template --- .../create-test-lint-wf-template.yml | 5 ++ .prettierignore | 2 + .../pipeline-template/.github/CONTRIBUTING.md | 2 + nf_core/pipeline-template/CITATIONS.md | 5 +- nf_core/pipeline-template/README.md | 2 +- .../assets/sendmail_template.txt | 2 + nf_core/pipeline-template/conf/modules.config | 2 + nf_core/pipeline-template/docs/output.md | 8 ++- nf_core/pipeline-template/docs/usage.md | 2 +- nf_core/pipeline-template/main.nf | 6 +- nf_core/pipeline-template/modules.json | 3 +- nf_core/pipeline-template/nextflow.config | 2 + .../pipeline-template/nextflow_schema.json | 7 ++- .../utils_nfcore_pipeline_pipeline/main.nf | 9 ++- nf_core/pipeline-template/tower.yml | 2 + .../pipeline-template/workflows/pipeline.nf | 15 ++--- nf_core/pipelines/create/create.py | 62 ++++++++++++------- nf_core/pipelines/create/custompipeline.py | 8 ++- nf_core/pipelines/create/nfcorepipeline.py | 8 ++- nf_core/pipelines/create/utils.py | 6 ++ 20 files changed, 111 insertions(+), 47 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index cfa0a50079..0bc32d8e41 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -42,6 +42,7 @@ jobs: - "template_skip_igenomes.yml" - "template_skip_ci.yml" - "template_skip_code_linters.yml" + - "template_skip_multiqc.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -107,6 +108,10 @@ jobs: run: | printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml + - name: Create template skip multiqc + run: | + printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/.prettierignore b/.prettierignore index 2a445d487f..059007ab03 100644 --- a/.prettierignore +++ b/.prettierignore @@ -5,6 +5,8 @@ docs/api/_build testing nf_core/module-template/meta.yml nf_core/pipeline-template/nextflow_schema.json +nf_core/pipeline-template/modules.json +nf_core/pipeline-template/tower.yml # don't run on things handled by ruff *.py *.pyc diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index e22a664250..2d6ecc174a 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -87,8 +87,10 @@ If you wish to contribute a new step, please use the following coding standards: 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. + {%- if multiqc %} 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. + {% endif %} ### Default values diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 6edf8f620c..22f5da4e70 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -14,9 +14,10 @@ > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> {%- endif %} ## Software packaging/containerisation tools diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index feece399b5..a9c913d6e2 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -45,7 +45,7 @@ 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) + {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %} ## Usage diff --git a/nf_core/pipeline-template/assets/sendmail_template.txt b/nf_core/pipeline-template/assets/sendmail_template.txt index 3e59cd2d6d..5257815f7c 100644 --- a/nf_core/pipeline-template/assets/sendmail_template.txt +++ b/nf_core/pipeline-template/assets/sendmail_template.txt @@ -26,6 +26,7 @@ Content-Disposition: inline; filename="{{ name_noslash }}_logo_light.png" join( '\n' ) %> <% +{%- if multiqc %} if (mqcFile){ def mqcFileObj = new File("$mqcFile") if (mqcFileObj.length() < mqcMaxSize){ @@ -48,6 +49,7 @@ ${mqcFileObj. join( '\n' )} """ }} +{%- endif %} %> --nfcoremimeboundary-- diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config index d203d2b6e6..84972d8e24 100644 --- a/nf_core/pipeline-template/conf/modules.config +++ b/nf_core/pipeline-template/conf/modules.config @@ -22,6 +22,7 @@ process { ext.args = '--quiet' } + {%- if multiqc %} withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ @@ -30,5 +31,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + {%- endif %} } diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 53b0e242e5..e27ff99598 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -2,7 +2,7 @@ ## Introduction -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. +This document describes the output produced by the pipeline. {% if multiqc %}Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.{% endif %} The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. @@ -13,7 +13,7 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - [FastQC](#fastqc) - Raw read QC -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline + {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %} - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -36,8 +36,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) :::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +The FastQC plots {% if multiqc %}displayed in the MultiQC report{% endif %} shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. ::: +{% if multiqc %} ### MultiQC @@ -54,6 +55,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . +{% endif %} ### Pipeline information diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index bf637219f8..1dc033eea5 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -114,7 +114,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %} To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index c13a0d24e1..fddfc5489e 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -56,10 +56,10 @@ workflow {{ prefix_nodash|upper }}_{{ short_name|upper }} { {{ short_name|upper }} ( samplesheet ) - +{%- if multiqc %} emit: multiqc_report = {{ short_name|upper }}.out.multiqc_report // channel: /path/to/multiqc_report.html - +{%- endif %} } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -101,7 +101,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - {{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report + {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %} ) } diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 9137c59675..eb9391b29a 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -9,12 +9,13 @@ "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] - }, + }{%- if multiqc %}, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } + {%- endif %} } }, "subworkflows": { diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 2e6a56b001..07c04d7b4c 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -20,12 +20,14 @@ params { igenomes_ignore = false {%- endif %} + {%- if multiqc %} // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' multiqc_methods_description = null + {%- endif %} // Boilerplate options outdir = null diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 18bad71b76..1815f57ef0 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -35,12 +35,13 @@ "fa_icon": "fas fa-envelope", "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" - }, + }{% if multiqc %}, "multiqc_title": { "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" } + {% endif %} } }, {%- if igenomes %} @@ -201,6 +202,7 @@ "fa_icon": "fas fa-remove-format", "hidden": true }, + {%- if multiqc %} "max_multiqc_email_size": { "type": "string", "description": "File size limit when attaching MultiQC reports to summary emails.", @@ -209,6 +211,7 @@ "fa_icon": "fas fa-file-upload", "hidden": true }, + {% endif %} "monochrome_logs": { "type": "boolean", "description": "Do not use coloured log outputs.", @@ -222,6 +225,7 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, + {%- if multiqc %} "multiqc_config": { "type": "string", "format": "file-path", @@ -240,6 +244,7 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, + {%- endif %} "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index a4bfb9f8be..7c5b7b2213 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -123,7 +123,7 @@ workflow PIPELINE_COMPLETION { outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications - multiqc_report // string: Path to MultiQC report + {% if multiqc %}multiqc_report // string: Path to MultiQC report{% endif %} main: @@ -134,7 +134,11 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { + {%- if multiqc %} completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + {%- else %} + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, []) + {%- endif %} } completionSummary(monochrome_logs) @@ -206,7 +210,7 @@ def genomeExistsError() { } } {%- endif %} - +{%- if multiqc %} // // Generate methods description for MultiQC // @@ -270,3 +274,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } +{% endif %} diff --git a/nf_core/pipeline-template/tower.yml b/nf_core/pipeline-template/tower.yml index 787aedfe92..2ddbef770e 100644 --- a/nf_core/pipeline-template/tower.yml +++ b/nf_core/pipeline-template/tower.yml @@ -1,5 +1,7 @@ reports: + {%- if multiqc %} multiqc_report.html: display: "MultiQC HTML report" + {%- endif %} samplesheet.csv: display: "Auto-created samplesheet with collated metadata and FASTQ paths" diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index de0f21fe38..eb56cb9235 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -5,11 +5,11 @@ */ include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' +{% if multiqc %}include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endif %} include { paramsSummaryMap } from 'plugin/nf-validation' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +{% if multiqc %}include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %} include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' +{% if multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -25,7 +25,7 @@ workflow {{ short_name|upper }} { main: ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %} // // MODULE: Run FastQC @@ -33,7 +33,7 @@ workflow {{ short_name|upper }} { FASTQC ( ch_samplesheet ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) + {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %} ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // @@ -47,6 +47,7 @@ workflow {{ short_name|upper }} { newLine: true ).set { ch_collated_versions } +{% if multiqc %} // // MODULE: MultiQC // @@ -85,9 +86,9 @@ workflow {{ short_name|upper }} { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - +{% endif %} emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + {%- if multiqc %}multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html{% endif %} versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 42e4a6ad7b..386ddd3bd9 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -101,6 +101,11 @@ def __init__( ".prettierrc.yml", ".github/workflows/fix-linting.yml", ], + "multiqc": [ + "assets/multiqc_config.yml", + "assets/methods_description_template.yml", + "modules/nf-core/multiqc/", + ], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -210,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "igenomes": {"file": True, "content": True}, "nf_core_configs": {"file": False, "content": True}, "code_linters": {"file": True, "content": True}, + "multiqc": {"file": True, "content": True}, } # Set the parameters for the jinja template @@ -374,8 +380,8 @@ def render_template(self): # in the github bug report template self.remove_nf_core_in_bug_report_template() - # Update the .nf-core.yml with linting configurations - self.fix_linting() + # Update the .nf-core.yml with linting configurations + self.fix_linting() if self.config: config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) @@ -425,28 +431,31 @@ def fix_linting(self): """ # Create a lint config short_name = self.jinja_params["short_name"] - lint_config = { - "files_exist": [ - "CODE_OF_CONDUCT.md", - f"assets/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_dark.png", - ".github/ISSUE_TEMPLATE/config.yml", - ".github/workflows/awstest.yml", - ".github/workflows/awsfulltest.yml", - ], - "files_unchanged": [ - "CODE_OF_CONDUCT.md", - f"assets/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_dark.png", - ], - "nextflow_config": [ - "manifest.name", - "manifest.homePage", - ], - "multiqc_config": ["report_comment"], - } + if not self.config.is_nfcore: + lint_config = { + "files_exist": [ + "CODE_OF_CONDUCT.md", + f"assets/nf-core-{short_name}_logo_light.png", + f"docs/images/nf-core-{short_name}_logo_light.png", + f"docs/images/nf-core-{short_name}_logo_dark.png", + ".github/ISSUE_TEMPLATE/config.yml", + ".github/workflows/awstest.yml", + ".github/workflows/awsfulltest.yml", + ], + "files_unchanged": [ + "CODE_OF_CONDUCT.md", + f"assets/nf-core-{short_name}_logo_light.png", + f"docs/images/nf-core-{short_name}_logo_light.png", + f"docs/images/nf-core-{short_name}_logo_dark.png", + ], + "nextflow_config": [ + "manifest.name", + "manifest.homePage", + ], + "multiqc_config": ["report_comment"], + } + else: + lint_config = {"files_exist": [], "files_unchanged": []} # Add GitHub hosting specific configurations if not self.jinja_params["github"]: @@ -505,6 +514,11 @@ def fix_linting(self): if not self.jinja_params["github_badges"] or not self.jinja_params["github"]: lint_config["readme"] = ["nextflow_badge"] + # Add multiqc specific configurations + if not self.jinja_params["multiqc"]: + lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) + lint_config["multiqc_config"] = ["report_comment"] + # If the pipeline is not nf-core if not self.config.is_nfcore: lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"]) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 0925fb5bab..0ddd6533b1 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -6,7 +6,7 @@ from textual.screen import Screen from textual.widgets import Button, Footer, Header, Markdown, Switch -from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes +from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc markdown_ci = """ Nf-core provides a set of Continuous Integration (CI) tests for Github. @@ -96,6 +96,12 @@ def compose(self) -> ComposeResult: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", "code_linters", ), + PipelineFeature( + markdown_multiqc, + "Use multiqc", + "The pipeline will include the MultiQC module which generates an HTML report for quality control.", + "multiqc", + ), classes="features-container", ) yield Center( diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py index 49cc1f8f86..8319cb044c 100644 --- a/nf_core/pipelines/create/nfcorepipeline.py +++ b/nf_core/pipelines/create/nfcorepipeline.py @@ -6,7 +6,7 @@ from textual.screen import Screen from textual.widgets import Button, Footer, Header, Markdown, Switch -from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes +from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc class NfcorePipeline(Screen): @@ -29,6 +29,12 @@ def compose(self) -> ComposeResult: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes", "igenomes", ), + PipelineFeature( + markdown_multiqc, + "Use multiqc", + "The pipeline will include the MultiQC module which generates an HTML report for quality control.", + "multiqc", + ), classes="features-container", ) yield Center( diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index c387960c39..43094ab531 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -259,3 +259,9 @@ def remove_hide_class(app, widget_id: str) -> None: For more information about reference genomes in nf-core pipelines, see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes). """ + +markdown_multiqc = """ +MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. + +The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. +""" From dcc4214f65009f9a94a6a3dd70543567d7016ccd Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 6 Aug 2024 12:50:57 +0000 Subject: [PATCH 276/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aea91cb51a..5256acf3de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) +- add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) ### Linting From a2d6b447f4bb0f11d184d576602dcaf964ccd9b9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 08:31:00 +0200 Subject: [PATCH 277/574] fix tests --- nf_core/pipelines/create/create.py | 13 +- tests/__snapshots__/test_create_app.ambr | 764 +++++++++++------------ 2 files changed, 392 insertions(+), 385 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 386ddd3bd9..86e104aa55 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -455,7 +455,7 @@ def fix_linting(self): "multiqc_config": ["report_comment"], } else: - lint_config = {"files_exist": [], "files_unchanged": []} + lint_config = {} # Add GitHub hosting specific configurations if not self.jinja_params["github"]: @@ -516,8 +516,15 @@ def fix_linting(self): # Add multiqc specific configurations if not self.jinja_params["multiqc"]: - lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) - lint_config["multiqc_config"] = ["report_comment"] + try: + lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) + except KeyError: + lint_config["files_unchanged"] = [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"] + try: + lint_config["files_exist"].extend(["assets/multiqc_config.yml"]) + except KeyError: + lint_config["files_exist"] = ["assets/multiqc_config.yml"] + lint_config["multiqc_config"] = False # If the pipeline is not nf-core if not self.config.is_nfcore: diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 5e5b005de0..6c93216bea 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2778615119-matrix { + .terminal-4132131606-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2778615119-title { + .terminal-4132131606-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2778615119-r1 { fill: #c5c8c6 } - .terminal-2778615119-r2 { fill: #e3e3e3 } - .terminal-2778615119-r3 { fill: #989898 } - .terminal-2778615119-r4 { fill: #e1e1e1 } - .terminal-2778615119-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2778615119-r6 { fill: #1e1e1e } - .terminal-2778615119-r7 { fill: #0178d4 } - .terminal-2778615119-r8 { fill: #454a50 } - .terminal-2778615119-r9 { fill: #e2e2e2 } - .terminal-2778615119-r10 { fill: #808080 } - .terminal-2778615119-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2778615119-r12 { fill: #000000 } - .terminal-2778615119-r13 { fill: #e4e4e4 } - .terminal-2778615119-r14 { fill: #14191f } - .terminal-2778615119-r15 { fill: #507bb3 } - .terminal-2778615119-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2778615119-r17 { fill: #001541 } - .terminal-2778615119-r18 { fill: #7ae998 } - .terminal-2778615119-r19 { fill: #0a180e;font-weight: bold } - .terminal-2778615119-r20 { fill: #008139 } - .terminal-2778615119-r21 { fill: #fea62b;font-weight: bold } - .terminal-2778615119-r22 { fill: #a7a9ab } - .terminal-2778615119-r23 { fill: #e2e3e3 } + .terminal-4132131606-r1 { fill: #c5c8c6 } + .terminal-4132131606-r2 { fill: #e3e3e3 } + .terminal-4132131606-r3 { fill: #989898 } + .terminal-4132131606-r4 { fill: #e1e1e1 } + .terminal-4132131606-r5 { fill: #4ebf71;font-weight: bold } + .terminal-4132131606-r6 { fill: #1e1e1e } + .terminal-4132131606-r7 { fill: #0178d4 } + .terminal-4132131606-r8 { fill: #454a50 } + .terminal-4132131606-r9 { fill: #e2e2e2 } + .terminal-4132131606-r10 { fill: #808080 } + .terminal-4132131606-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-4132131606-r12 { fill: #000000 } + .terminal-4132131606-r13 { fill: #e4e4e4 } + .terminal-4132131606-r14 { fill: #14191f } + .terminal-4132131606-r15 { fill: #507bb3 } + .terminal-4132131606-r16 { fill: #dde6ed;font-weight: bold } + .terminal-4132131606-r17 { fill: #001541 } + .terminal-4132131606-r18 { fill: #7ae998 } + .terminal-4132131606-r19 { fill: #0a180e;font-weight: bold } + .terminal-4132131606-r20 { fill: #008139 } + .terminal-4132131606-r21 { fill: #fea62b;font-weight: bold } + .terminal-4132131606-r22 { fill: #a7a9ab } + .terminal-4132131606-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-763408100-matrix { + .terminal-2850535557-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-763408100-title { + .terminal-2850535557-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-763408100-r1 { fill: #c5c8c6 } - .terminal-763408100-r2 { fill: #e3e3e3 } - .terminal-763408100-r3 { fill: #989898 } - .terminal-763408100-r4 { fill: #e1e1e1 } - .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } - .terminal-763408100-r6 { fill: #1e1e1e } - .terminal-763408100-r7 { fill: #507bb3 } - .terminal-763408100-r8 { fill: #e2e2e2 } - .terminal-763408100-r9 { fill: #808080 } - .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } - .terminal-763408100-r11 { fill: #001541 } - .terminal-763408100-r12 { fill: #14191f } - .terminal-763408100-r13 { fill: #454a50 } - .terminal-763408100-r14 { fill: #7ae998 } - .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } - .terminal-763408100-r17 { fill: #000000 } - .terminal-763408100-r18 { fill: #008139 } - .terminal-763408100-r19 { fill: #fea62b;font-weight: bold } - .terminal-763408100-r20 { fill: #a7a9ab } - .terminal-763408100-r21 { fill: #e2e3e3 } + .terminal-2850535557-r1 { fill: #c5c8c6 } + .terminal-2850535557-r2 { fill: #e3e3e3 } + .terminal-2850535557-r3 { fill: #989898 } + .terminal-2850535557-r4 { fill: #e1e1e1 } + .terminal-2850535557-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2850535557-r6 { fill: #1e1e1e } + .terminal-2850535557-r7 { fill: #507bb3 } + .terminal-2850535557-r8 { fill: #e2e2e2 } + .terminal-2850535557-r9 { fill: #808080 } + .terminal-2850535557-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2850535557-r11 { fill: #001541 } + .terminal-2850535557-r12 { fill: #14191f } + .terminal-2850535557-r13 { fill: #454a50 } + .terminal-2850535557-r14 { fill: #7ae998 } + .terminal-2850535557-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-2850535557-r16 { fill: #0a180e;font-weight: bold } + .terminal-2850535557-r17 { fill: #000000 } + .terminal-2850535557-r18 { fill: #008139 } + .terminal-2850535557-r19 { fill: #fea62b;font-weight: bold } + .terminal-2850535557-r20 { fill: #a7a9ab } + .terminal-2850535557-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different ▁▁ - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles ▁▁ + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2511,254 +2511,254 @@ font-weight: 700; } - .terminal-388991162-matrix { + .terminal-157696122-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-388991162-title { + .terminal-157696122-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-388991162-r1 { fill: #c5c8c6 } - .terminal-388991162-r2 { fill: #e3e3e3 } - .terminal-388991162-r3 { fill: #989898 } - .terminal-388991162-r4 { fill: #e1e1e1 } - .terminal-388991162-r5 { fill: #4ebf71;font-weight: bold } - .terminal-388991162-r6 { fill: #1e1e1e } - .terminal-388991162-r7 { fill: #507bb3 } - .terminal-388991162-r8 { fill: #e2e2e2 } - .terminal-388991162-r9 { fill: #808080 } - .terminal-388991162-r10 { fill: #dde6ed;font-weight: bold } - .terminal-388991162-r11 { fill: #001541 } - .terminal-388991162-r12 { fill: #454a50 } - .terminal-388991162-r13 { fill: #7ae998 } - .terminal-388991162-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-388991162-r15 { fill: #0a180e;font-weight: bold } - .terminal-388991162-r16 { fill: #000000 } - .terminal-388991162-r17 { fill: #008139 } - .terminal-388991162-r18 { fill: #fea62b;font-weight: bold } - .terminal-388991162-r19 { fill: #a7a9ab } - .terminal-388991162-r20 { fill: #e2e3e3 } + .terminal-157696122-r1 { fill: #c5c8c6 } + .terminal-157696122-r2 { fill: #e3e3e3 } + .terminal-157696122-r3 { fill: #989898 } + .terminal-157696122-r4 { fill: #e1e1e1 } + .terminal-157696122-r5 { fill: #4ebf71;font-weight: bold } + .terminal-157696122-r6 { fill: #1e1e1e } + .terminal-157696122-r7 { fill: #507bb3 } + .terminal-157696122-r8 { fill: #e2e2e2 } + .terminal-157696122-r9 { fill: #808080 } + .terminal-157696122-r10 { fill: #dde6ed;font-weight: bold } + .terminal-157696122-r11 { fill: #001541 } + .terminal-157696122-r12 { fill: #454a50 } + .terminal-157696122-r13 { fill: #7ae998 } + .terminal-157696122-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-157696122-r15 { fill: #0a180e;font-weight: bold } + .terminal-157696122-r16 { fill: #000000 } + .terminal-157696122-r17 { fill: #008139 } + .terminal-157696122-r18 { fill: #fea62b;font-weight: bold } + .terminal-157696122-r19 { fill: #a7a9ab } + .terminal-157696122-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from iGenomes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use multiqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the MultiQC▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which  + generates an HTML  + report for quality  + control. + + + + + + + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 88a354fa73a657570496fd9cc6343d7e75aeaba7 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 09:29:48 +0200 Subject: [PATCH 278/574] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 511 ++++++++++++----------- 1 file changed, 256 insertions(+), 255 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index ed597e46b6..57e4258ef8 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-4194849765-matrix { + .terminal-3843971496-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4194849765-title { + .terminal-3843971496-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4194849765-r1 { fill: #c5c8c6 } - .terminal-4194849765-r2 { fill: #e3e3e3 } - .terminal-4194849765-r3 { fill: #989898 } - .terminal-4194849765-r4 { fill: #e1e1e1 } - .terminal-4194849765-r5 { fill: #4ebf71;font-weight: bold } - .terminal-4194849765-r6 { fill: #1e1e1e } - .terminal-4194849765-r7 { fill: #0178d4 } - .terminal-4194849765-r8 { fill: #454a50 } - .terminal-4194849765-r9 { fill: #e2e2e2 } - .terminal-4194849765-r10 { fill: #808080 } - .terminal-4194849765-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-4194849765-r12 { fill: #000000 } - .terminal-4194849765-r13 { fill: #e4e4e4 } - .terminal-4194849765-r14 { fill: #14191f } - .terminal-4194849765-r15 { fill: #507bb3 } - .terminal-4194849765-r16 { fill: #dde6ed;font-weight: bold } - .terminal-4194849765-r17 { fill: #001541 } - .terminal-4194849765-r18 { fill: #7ae998 } - .terminal-4194849765-r19 { fill: #0a180e;font-weight: bold } - .terminal-4194849765-r20 { fill: #008139 } - .terminal-4194849765-r21 { fill: #fea62b;font-weight: bold } - .terminal-4194849765-r22 { fill: #a7a9ab } - .terminal-4194849765-r23 { fill: #e2e3e3 } + .terminal-3843971496-r1 { fill: #c5c8c6 } + .terminal-3843971496-r2 { fill: #e3e3e3 } + .terminal-3843971496-r3 { fill: #989898 } + .terminal-3843971496-r4 { fill: #e1e1e1 } + .terminal-3843971496-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3843971496-r6 { fill: #1e1e1e } + .terminal-3843971496-r7 { fill: #0178d4 } + .terminal-3843971496-r8 { fill: #454a50 } + .terminal-3843971496-r9 { fill: #e2e2e2 } + .terminal-3843971496-r10 { fill: #808080 } + .terminal-3843971496-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-3843971496-r12 { fill: #000000 } + .terminal-3843971496-r13 { fill: #e4e4e4 } + .terminal-3843971496-r14 { fill: #14191f } + .terminal-3843971496-r15 { fill: #507bb3 } + .terminal-3843971496-r16 { fill: #dde6ed;font-weight: bold } + .terminal-3843971496-r17 { fill: #001541 } + .terminal-3843971496-r18 { fill: #7ae998 } + .terminal-3843971496-r19 { fill: #0a180e;font-weight: bold } + .terminal-3843971496-r20 { fill: #008139 } + .terminal-3843971496-r21 { fill: #fea62b;font-weight: bold } + .terminal-3843971496-r22 { fill: #a7a9ab } + .terminal-3843971496-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - ▃▃ - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files.▁▁ + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,254 +2233,255 @@ font-weight: 700; } - .terminal-423998432-matrix { + .terminal-1616690770-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-423998432-title { + .terminal-1616690770-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-423998432-r1 { fill: #c5c8c6 } - .terminal-423998432-r2 { fill: #e3e3e3 } - .terminal-423998432-r3 { fill: #989898 } - .terminal-423998432-r4 { fill: #e1e1e1 } - .terminal-423998432-r5 { fill: #4ebf71;font-weight: bold } - .terminal-423998432-r6 { fill: #1e1e1e } - .terminal-423998432-r7 { fill: #507bb3 } - .terminal-423998432-r8 { fill: #e2e2e2 } - .terminal-423998432-r9 { fill: #808080 } - .terminal-423998432-r10 { fill: #dde6ed;font-weight: bold } - .terminal-423998432-r11 { fill: #001541 } - .terminal-423998432-r12 { fill: #454a50 } - .terminal-423998432-r13 { fill: #7ae998 } - .terminal-423998432-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-423998432-r15 { fill: #0a180e;font-weight: bold } - .terminal-423998432-r16 { fill: #000000 } - .terminal-423998432-r17 { fill: #008139 } - .terminal-423998432-r18 { fill: #fea62b;font-weight: bold } - .terminal-423998432-r19 { fill: #a7a9ab } - .terminal-423998432-r20 { fill: #e2e3e3 } + .terminal-1616690770-r1 { fill: #c5c8c6 } + .terminal-1616690770-r2 { fill: #e3e3e3 } + .terminal-1616690770-r3 { fill: #989898 } + .terminal-1616690770-r4 { fill: #e1e1e1 } + .terminal-1616690770-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1616690770-r6 { fill: #1e1e1e } + .terminal-1616690770-r7 { fill: #507bb3 } + .terminal-1616690770-r8 { fill: #e2e2e2 } + .terminal-1616690770-r9 { fill: #808080 } + .terminal-1616690770-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1616690770-r11 { fill: #001541 } + .terminal-1616690770-r12 { fill: #14191f } + .terminal-1616690770-r13 { fill: #454a50 } + .terminal-1616690770-r14 { fill: #7ae998 } + .terminal-1616690770-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1616690770-r16 { fill: #0a180e;font-weight: bold } + .terminal-1616690770-r17 { fill: #000000 } + .terminal-1616690770-r18 { fill: #008139 } + .terminal-1616690770-r19 { fill: #fea62b;font-weight: bold } + .terminal-1616690770-r20 { fill: #a7a9ab } + .terminal-1616690770-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help ▄▄ + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 3c1b1b07bf57aa5ab36fc60d0deb96859053057e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 10:01:49 +0200 Subject: [PATCH 279/574] add multiqc potion to test data --- tests/data/pipeline_create_template_skip.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index 1431114c08..7ae5bba8c4 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -14,3 +14,4 @@ skip_features: - code_linters - citations - gitpod + - multiqc From 2fcfd0e7237ce6c624ce538d902c2c14c6d0dcab Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 10:12:23 +0200 Subject: [PATCH 280/574] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------ 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 51ff46d68d..9aad37cc96 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2778615119-matrix { + .terminal-2285198722-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2778615119-title { + .terminal-2285198722-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2778615119-r1 { fill: #c5c8c6 } - .terminal-2778615119-r2 { fill: #e3e3e3 } - .terminal-2778615119-r3 { fill: #989898 } - .terminal-2778615119-r4 { fill: #e1e1e1 } - .terminal-2778615119-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2778615119-r6 { fill: #1e1e1e } - .terminal-2778615119-r7 { fill: #0178d4 } - .terminal-2778615119-r8 { fill: #454a50 } - .terminal-2778615119-r9 { fill: #e2e2e2 } - .terminal-2778615119-r10 { fill: #808080 } - .terminal-2778615119-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2778615119-r12 { fill: #000000 } - .terminal-2778615119-r13 { fill: #e4e4e4 } - .terminal-2778615119-r14 { fill: #14191f } - .terminal-2778615119-r15 { fill: #507bb3 } - .terminal-2778615119-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2778615119-r17 { fill: #001541 } - .terminal-2778615119-r18 { fill: #7ae998 } - .terminal-2778615119-r19 { fill: #0a180e;font-weight: bold } - .terminal-2778615119-r20 { fill: #008139 } - .terminal-2778615119-r21 { fill: #fea62b;font-weight: bold } - .terminal-2778615119-r22 { fill: #a7a9ab } - .terminal-2778615119-r23 { fill: #e2e3e3 } + .terminal-2285198722-r1 { fill: #c5c8c6 } + .terminal-2285198722-r2 { fill: #e3e3e3 } + .terminal-2285198722-r3 { fill: #989898 } + .terminal-2285198722-r4 { fill: #e1e1e1 } + .terminal-2285198722-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2285198722-r6 { fill: #1e1e1e } + .terminal-2285198722-r7 { fill: #0178d4 } + .terminal-2285198722-r8 { fill: #454a50 } + .terminal-2285198722-r9 { fill: #e2e2e2 } + .terminal-2285198722-r10 { fill: #808080 } + .terminal-2285198722-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-2285198722-r12 { fill: #000000 } + .terminal-2285198722-r13 { fill: #e4e4e4 } + .terminal-2285198722-r14 { fill: #14191f } + .terminal-2285198722-r15 { fill: #507bb3 } + .terminal-2285198722-r16 { fill: #dde6ed;font-weight: bold } + .terminal-2285198722-r17 { fill: #001541 } + .terminal-2285198722-r18 { fill: #7ae998 } + .terminal-2285198722-r19 { fill: #0a180e;font-weight: bold } + .terminal-2285198722-r20 { fill: #008139 } + .terminal-2285198722-r21 { fill: #fea62b;font-weight: bold } + .terminal-2285198722-r22 { fill: #a7a9ab } + .terminal-2285198722-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key,▁▁ + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-763408100-matrix { + .terminal-3802907671-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-763408100-title { + .terminal-3802907671-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-763408100-r1 { fill: #c5c8c6 } - .terminal-763408100-r2 { fill: #e3e3e3 } - .terminal-763408100-r3 { fill: #989898 } - .terminal-763408100-r4 { fill: #e1e1e1 } - .terminal-763408100-r5 { fill: #4ebf71;font-weight: bold } - .terminal-763408100-r6 { fill: #1e1e1e } - .terminal-763408100-r7 { fill: #507bb3 } - .terminal-763408100-r8 { fill: #e2e2e2 } - .terminal-763408100-r9 { fill: #808080 } - .terminal-763408100-r10 { fill: #dde6ed;font-weight: bold } - .terminal-763408100-r11 { fill: #001541 } - .terminal-763408100-r12 { fill: #14191f } - .terminal-763408100-r13 { fill: #454a50 } - .terminal-763408100-r14 { fill: #7ae998 } - .terminal-763408100-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-763408100-r16 { fill: #0a180e;font-weight: bold } - .terminal-763408100-r17 { fill: #000000 } - .terminal-763408100-r18 { fill: #008139 } - .terminal-763408100-r19 { fill: #fea62b;font-weight: bold } - .terminal-763408100-r20 { fill: #a7a9ab } - .terminal-763408100-r21 { fill: #e2e3e3 } + .terminal-3802907671-r1 { fill: #c5c8c6 } + .terminal-3802907671-r2 { fill: #e3e3e3 } + .terminal-3802907671-r3 { fill: #989898 } + .terminal-3802907671-r4 { fill: #e1e1e1 } + .terminal-3802907671-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3802907671-r6 { fill: #1e1e1e } + .terminal-3802907671-r7 { fill: #507bb3 } + .terminal-3802907671-r8 { fill: #e2e2e2 } + .terminal-3802907671-r9 { fill: #808080 } + .terminal-3802907671-r10 { fill: #dde6ed;font-weight: bold } + .terminal-3802907671-r11 { fill: #001541 } + .terminal-3802907671-r12 { fill: #14191f } + .terminal-3802907671-r13 { fill: #454a50 } + .terminal-3802907671-r14 { fill: #7ae998 } + .terminal-3802907671-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-3802907671-r16 { fill: #0a180e;font-weight: bold } + .terminal-3802907671-r17 { fill: #000000 } + .terminal-3802907671-r18 { fill: #008139 } + .terminal-3802907671-r19 { fill: #fea62b;font-weight: bold } + .terminal-3802907671-r20 { fill: #a7a9ab } + .terminal-3802907671-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different ▁▁ - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges▃▃ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 57ed19ae36e40e74dda75f18c008a606f79073af Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 7 Aug 2024 10:46:27 +0200 Subject: [PATCH 281/574] run tests also after pytest-migrate --- nf_core/commands_modules.py | 35 +++++++++++++++++------------------ 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index c65c42d41a..a34e9a519e 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -242,24 +242,23 @@ def modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pyte empty_template=False, migrate_pytest=migrate_pytest, ) - else: - try: - module_tester = ComponentsTest( - component_type="modules", - component_name=tool, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, - ) - module_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + try: + module_tester = ComponentsTest( + component_type="modules", + component_name=tool, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + module_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version): From baae14c03e4feec6ef77caf32c610079dcad419f Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 7 Aug 2024 10:47:39 +0200 Subject: [PATCH 282/574] and the same for subworkflows --- nf_core/commands_subworkflows.py | 35 ++++++++++++++++---------------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index 8c3be2bb46..8b2db3578a 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -44,24 +44,23 @@ def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, if migrate_pytest: subworkflows_create(ctx, subworkflow, dir, None, False, True) - else: - try: - sw_tester = ComponentsTest( - component_type="subworkflows", - component_name=subworkflow, - directory=dir, - no_prompts=no_prompts, - update=update, - once=once, - remote_url=ctx.obj["modules_repo_url"], - branch=ctx.obj["modules_repo_branch"], - verbose=ctx.obj["verbose"], - profile=profile, - ) - sw_tester.run() - except (UserWarning, LookupError) as e: - log.critical(e) - sys.exit(1) + try: + sw_tester = ComponentsTest( + component_type="subworkflows", + component_name=subworkflow, + directory=dir, + no_prompts=no_prompts, + update=update, + once=once, + remote_url=ctx.obj["modules_repo_url"], + branch=ctx.obj["modules_repo_branch"], + verbose=ctx.obj["verbose"], + profile=profile, + ) + sw_tester.run() + except (UserWarning, LookupError) as e: + log.critical(e) + sys.exit(1) def subworkflows_list_remote(ctx, keywords, json): From f9eb2a58d7ad231cd14f971d86b57558d3e67912 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 11:15:59 +0200 Subject: [PATCH 283/574] remove multiqc images from the template docs --- .../docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes .../docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes .../docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes nf_core/pipeline-template/docs/output.md | 11 +---------- 4 files changed, 1 insertion(+), 10 deletions(-) delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_counts.png delete mode 100755 nf_core/pipeline-template/docs/images/mqc_fastqc_quality.png diff --git a/nf_core/pipeline-template/docs/images/mqc_fastqc_adapter.png 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[Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots {% if multiqc %}displayed in the MultiQC report{% endif %} shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: -{% if multiqc %} +{%- if multiqc %} ### MultiQC From 3507b15ee40383a7cccce3975e2d9e9a96266985 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 11:56:01 +0200 Subject: [PATCH 284/574] add option to exclude codespaces from pipeline template --- .github/workflows/create-test-lint-wf-template.yml | 7 +++---- nf_core/pipeline-template/.github/CONTRIBUTING.md | 2 ++ nf_core/pipelines/create/create.py | 6 ++++++ nf_core/pipelines/create/custompipeline.py | 13 +++++++++++++ tests/data/pipeline_create_template_skip.yml | 1 + 5 files changed, 25 insertions(+), 4 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index c4eca40fa6..79c2ba6c89 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,6 +44,7 @@ jobs: - "template_skip_code_linters.yml" - "template_skip_citations.yml" - "template_skip_gitpod.yml" + - "template_skip_codespaces.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -117,11 +118,9 @@ jobs: run: | printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml - # Create a pipeline from the template - - name: create a pipeline from the template ${{ matrix.TEMPLATE }} + - name: Create template skip codespaces run: | - cd create-test-lint-wf - nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }} + printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml - name: run the pipeline run: | diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index e22a664250..3a9cd3bcba 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -116,6 +116,7 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ ### Images and figures For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). +{%- if codespaces %} ## GitHub Codespaces @@ -131,3 +132,4 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) + {% endif %} diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 05a5804ee3..225565dbaf 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -103,6 +103,7 @@ def __init__( ], "citations": ["assets/methods_description_template.yml"], "gitpod": [".gitpod.yml"], + "codespaces": [".devcontainer/devcontainer.json"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -214,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "code_linters": {"file": True, "content": True}, "citations": {"file": True, "content": True}, "gitpod": {"file": True, "content": True}, + "codespaces": {"file": True, "content": True}, } # Set the parameters for the jinja template @@ -509,6 +511,10 @@ def fix_linting(self): if not self.jinja_params["github_badges"] or not self.jinja_params["github"]: lint_config["readme"] = ["nextflow_badge"] + # Add codespaces specific configurations + if not self.jinja_params["codespaces"]: + lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md"]) + # If the pipeline is not nf-core if not self.config.is_nfcore: lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"]) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 5f131a7d84..4c75ff2795 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -65,6 +65,13 @@ This is useful to have all the tools ready for pipeline development. """ +markdown_codespaces = """ +The pipeline will include a devcontainer configuration. +The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. + +Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal. +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -122,6 +129,12 @@ def compose(self) -> ComposeResult: "Include the configuration required to use Gitpod.", "gitpod", ), + PipelineFeature( + markdown_codespaces, + "Include GitHub Codespaces", + "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.", + "codespaces", + ), classes="features-container", ) yield Center( diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index 1431114c08..29a336069f 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -14,3 +14,4 @@ skip_features: - code_linters - citations - gitpod + - codespaces From 26769f2eb5568d56977023a88f142e0d28da7e0f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 12:44:24 +0200 Subject: [PATCH 285/574] add option to exclude changelog from custom pipeline template --- .github/workflows/create-test-lint-wf-template.yml | 5 +++++ nf_core/pipelines/create/create.py | 6 ++++++ nf_core/pipelines/create/custompipeline.py | 11 +++++++++++ tests/data/pipeline_create_template_skip.yml | 1 + 4 files changed, 23 insertions(+) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index c4eca40fa6..b4022d780a 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,6 +44,7 @@ jobs: - "template_skip_code_linters.yml" - "template_skip_citations.yml" - "template_skip_gitpod.yml" + - "template_skip_changelog.yml" runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -117,6 +118,10 @@ jobs: run: | printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml + - name: Create template skip changelog + run: | + printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml + # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 05a5804ee3..27dc729439 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -103,6 +103,7 @@ def __init__( ], "citations": ["assets/methods_description_template.yml"], "gitpod": [".gitpod.yml"], + "changelog": ["CHANGELOG.md"], } # Get list of files we're skipping with the supplied skip keys self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) @@ -214,6 +215,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "code_linters": {"file": True, "content": True}, "citations": {"file": True, "content": True}, "gitpod": {"file": True, "content": True}, + "changelog": {"file": True, "content": False}, } # Set the parameters for the jinja template @@ -509,6 +511,10 @@ def fix_linting(self): if not self.jinja_params["github_badges"] or not self.jinja_params["github"]: lint_config["readme"] = ["nextflow_badge"] + # Add changelog specific configurations + if not self.jinja_params["changelog"]: + lint_config["files_exist"].extend(["CHANGELOG.md"]) + # If the pipeline is not nf-core if not self.config.is_nfcore: lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"]) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 5f131a7d84..c39c26507e 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -65,6 +65,11 @@ This is useful to have all the tools ready for pipeline development. """ +markdown_changelog = """ +Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. +You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ +""" + class CustomPipeline(Screen): """Select if the pipeline will use genomic data.""" @@ -122,6 +127,12 @@ def compose(self) -> ComposeResult: "Include the configuration required to use Gitpod.", "gitpod", ), + PipelineFeature( + markdown_changelog, + "Add a changelog", + "Add a CHANGELOG.md file.", + "changelog", + ), classes="features-container", ) yield Center( diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index 1431114c08..ed0b5ef2ad 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -14,3 +14,4 @@ skip_features: - code_linters - citations - gitpod + - changelog From 4d55d7a3382e85efc8be610a8ed3211969626206 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 7 Aug 2024 11:16:38 +0000 Subject: [PATCH 286/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 765507c4e1..52654b5dee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) +- add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) ### Linting From c0bbca287e39709b35457aa1970f9c745c206c0a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 7 Aug 2024 11:17:25 +0000 Subject: [PATCH 287/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 765507c4e1..8e3dfdda55 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) +- add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105)) ### Linting From 4cf16be72aa114b5062a82abc0fe0dafcc4f1b61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 7 Aug 2024 15:09:55 +0200 Subject: [PATCH 288/574] Update nf_core/pipelines/create/create.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/create.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 908dd962d0..d9051f4165 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -520,14 +520,8 @@ def fix_linting(self): # Add multiqc specific configurations if not self.jinja_params["multiqc"]: - try: - lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) - except KeyError: - lint_config["files_unchanged"] = [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"] - try: - lint_config["files_exist"].extend(["assets/multiqc_config.yml"]) - except KeyError: - lint_config["files_exist"] = ["assets/multiqc_config.yml"] + lint_config.setdefault("files_unchanged", []).extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) +lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"]) lint_config["multiqc_config"] = False # If the pipeline is not nf-core From f8d54635e853ecdd948a79d134bdea62c2dbb07a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 15:38:59 +0200 Subject: [PATCH 289/574] fix indentation --- nf_core/pipelines/create/create.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index d9051f4165..684b13f83a 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -520,8 +520,10 @@ def fix_linting(self): # Add multiqc specific configurations if not self.jinja_params["multiqc"]: - lint_config.setdefault("files_unchanged", []).extend([".github/CONTRIBUTING.md", "assets/sendmail_template.txt"]) -lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"]) + lint_config.setdefault("files_unchanged", []).extend( + [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"] + ) + lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"]) lint_config["multiqc_config"] = False # If the pipeline is not nf-core From 8b196cd9a2601e9f05270bbd4bac629cc0b8c823 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 16:12:04 +0200 Subject: [PATCH 290/574] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------ 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 9aad37cc96..231c038c66 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2285198722-matrix { + .terminal-1308777655-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2285198722-title { + .terminal-1308777655-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2285198722-r1 { fill: #c5c8c6 } - .terminal-2285198722-r2 { fill: #e3e3e3 } - .terminal-2285198722-r3 { fill: #989898 } - .terminal-2285198722-r4 { fill: #e1e1e1 } - .terminal-2285198722-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2285198722-r6 { fill: #1e1e1e } - .terminal-2285198722-r7 { fill: #0178d4 } - .terminal-2285198722-r8 { fill: #454a50 } - .terminal-2285198722-r9 { fill: #e2e2e2 } - .terminal-2285198722-r10 { fill: #808080 } - .terminal-2285198722-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-2285198722-r12 { fill: #000000 } - .terminal-2285198722-r13 { fill: #e4e4e4 } - .terminal-2285198722-r14 { fill: #14191f } - .terminal-2285198722-r15 { fill: #507bb3 } - .terminal-2285198722-r16 { fill: #dde6ed;font-weight: bold } - .terminal-2285198722-r17 { fill: #001541 } - .terminal-2285198722-r18 { fill: #7ae998 } - .terminal-2285198722-r19 { fill: #0a180e;font-weight: bold } - .terminal-2285198722-r20 { fill: #008139 } - .terminal-2285198722-r21 { fill: #fea62b;font-weight: bold } - .terminal-2285198722-r22 { fill: #a7a9ab } - .terminal-2285198722-r23 { fill: #e2e3e3 } + .terminal-1308777655-r1 { fill: #c5c8c6 } + .terminal-1308777655-r2 { fill: #e3e3e3 } + .terminal-1308777655-r3 { fill: #989898 } + .terminal-1308777655-r4 { fill: #e1e1e1 } + .terminal-1308777655-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1308777655-r6 { fill: #1e1e1e } + .terminal-1308777655-r7 { fill: #0178d4 } + .terminal-1308777655-r8 { fill: #454a50 } + .terminal-1308777655-r9 { fill: #e2e2e2 } + .terminal-1308777655-r10 { fill: #808080 } + .terminal-1308777655-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-1308777655-r12 { fill: #000000 } + .terminal-1308777655-r13 { fill: #e4e4e4 } + .terminal-1308777655-r14 { fill: #14191f } + .terminal-1308777655-r15 { fill: #507bb3 } + .terminal-1308777655-r16 { fill: #dde6ed;font-weight: bold } + .terminal-1308777655-r17 { fill: #001541 } + .terminal-1308777655-r18 { fill: #7ae998 } + .terminal-1308777655-r19 { fill: #0a180e;font-weight: bold } + .terminal-1308777655-r20 { fill: #008139 } + .terminal-1308777655-r21 { fill: #fea62b;font-weight: bold } + .terminal-1308777655-r22 { fill: #a7a9ab } + .terminal-1308777655-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key,▁▁ - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files. + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-3802907671-matrix { + .terminal-557041160-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3802907671-title { + .terminal-557041160-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3802907671-r1 { fill: #c5c8c6 } - .terminal-3802907671-r2 { fill: #e3e3e3 } - .terminal-3802907671-r3 { fill: #989898 } - .terminal-3802907671-r4 { fill: #e1e1e1 } - .terminal-3802907671-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3802907671-r6 { fill: #1e1e1e } - .terminal-3802907671-r7 { fill: #507bb3 } - .terminal-3802907671-r8 { fill: #e2e2e2 } - .terminal-3802907671-r9 { fill: #808080 } - .terminal-3802907671-r10 { fill: #dde6ed;font-weight: bold } - .terminal-3802907671-r11 { fill: #001541 } - .terminal-3802907671-r12 { fill: #14191f } - .terminal-3802907671-r13 { fill: #454a50 } - .terminal-3802907671-r14 { fill: #7ae998 } - .terminal-3802907671-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-3802907671-r16 { fill: #0a180e;font-weight: bold } - .terminal-3802907671-r17 { fill: #000000 } - .terminal-3802907671-r18 { fill: #008139 } - .terminal-3802907671-r19 { fill: #fea62b;font-weight: bold } - .terminal-3802907671-r20 { fill: #a7a9ab } - .terminal-3802907671-r21 { fill: #e2e3e3 } + .terminal-557041160-r1 { fill: #c5c8c6 } + .terminal-557041160-r2 { fill: #e3e3e3 } + .terminal-557041160-r3 { fill: #989898 } + .terminal-557041160-r4 { fill: #e1e1e1 } + .terminal-557041160-r5 { fill: #4ebf71;font-weight: bold } + .terminal-557041160-r6 { fill: #1e1e1e } + .terminal-557041160-r7 { fill: #507bb3 } + .terminal-557041160-r8 { fill: #e2e2e2 } + .terminal-557041160-r9 { fill: #808080 } + .terminal-557041160-r10 { fill: #dde6ed;font-weight: bold } + .terminal-557041160-r11 { fill: #001541 } + .terminal-557041160-r12 { fill: #14191f } + .terminal-557041160-r13 { fill: #454a50 } + .terminal-557041160-r14 { fill: #7ae998 } + .terminal-557041160-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-557041160-r16 { fill: #0a180e;font-weight: bold } + .terminal-557041160-r17 { fill: #000000 } + .terminal-557041160-r18 { fill: #008139 } + .terminal-557041160-r19 { fill: #fea62b;font-weight: bold } + .terminal-557041160-r20 { fill: #a7a9ab } + .terminal-557041160-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges▃▃ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include ▅▅ + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 1aec52881d806646565b336ce663bcf8366cad9f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 16:31:46 +0200 Subject: [PATCH 291/574] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 512 +++++++++++------------ 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index 231c038c66..f2c1c45c45 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-1308777655-matrix { + .terminal-463758155-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1308777655-title { + .terminal-463758155-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1308777655-r1 { fill: #c5c8c6 } - .terminal-1308777655-r2 { fill: #e3e3e3 } - .terminal-1308777655-r3 { fill: #989898 } - .terminal-1308777655-r4 { fill: #e1e1e1 } - .terminal-1308777655-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1308777655-r6 { fill: #1e1e1e } - .terminal-1308777655-r7 { fill: #0178d4 } - .terminal-1308777655-r8 { fill: #454a50 } - .terminal-1308777655-r9 { fill: #e2e2e2 } - .terminal-1308777655-r10 { fill: #808080 } - .terminal-1308777655-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-1308777655-r12 { fill: #000000 } - .terminal-1308777655-r13 { fill: #e4e4e4 } - .terminal-1308777655-r14 { fill: #14191f } - .terminal-1308777655-r15 { fill: #507bb3 } - .terminal-1308777655-r16 { fill: #dde6ed;font-weight: bold } - .terminal-1308777655-r17 { fill: #001541 } - .terminal-1308777655-r18 { fill: #7ae998 } - .terminal-1308777655-r19 { fill: #0a180e;font-weight: bold } - .terminal-1308777655-r20 { fill: #008139 } - .terminal-1308777655-r21 { fill: #fea62b;font-weight: bold } - .terminal-1308777655-r22 { fill: #a7a9ab } - .terminal-1308777655-r23 { fill: #e2e3e3 } + .terminal-463758155-r1 { fill: #c5c8c6 } + .terminal-463758155-r2 { fill: #e3e3e3 } + .terminal-463758155-r3 { fill: #989898 } + .terminal-463758155-r4 { fill: #e1e1e1 } + .terminal-463758155-r5 { fill: #4ebf71;font-weight: bold } + .terminal-463758155-r6 { fill: #1e1e1e } + .terminal-463758155-r7 { fill: #0178d4 } + .terminal-463758155-r8 { fill: #454a50 } + .terminal-463758155-r9 { fill: #e2e2e2 } + .terminal-463758155-r10 { fill: #808080 } + .terminal-463758155-r11 { fill: #e2e3e3;font-weight: bold } + .terminal-463758155-r12 { fill: #000000 } + .terminal-463758155-r13 { fill: #e4e4e4 } + .terminal-463758155-r14 { fill: #14191f } + .terminal-463758155-r15 { fill: #507bb3 } + .terminal-463758155-r16 { fill: #dde6ed;font-weight: bold } + .terminal-463758155-r17 { fill: #001541 } + .terminal-463758155-r18 { fill: #7ae998 } + .terminal-463758155-r19 { fill: #0a180e;font-weight: bold } + .terminal-463758155-r20 { fill: #008139 } + .terminal-463758155-r21 { fill: #fea62b;font-weight: bold } + .terminal-463758155-r22 { fill: #a7a9ab } + .terminal-463758155-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files. - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Hide help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common  + reference genome files. + + By selecting this option, your pipeline will include a configuration + file specifying the paths to these files.▂▂ + + The required code to use these files will also be included in the  + template. When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference ▂▂ + files. + + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-557041160-matrix { + .terminal-2213530577-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-557041160-title { + .terminal-2213530577-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-557041160-r1 { fill: #c5c8c6 } - .terminal-557041160-r2 { fill: #e3e3e3 } - .terminal-557041160-r3 { fill: #989898 } - .terminal-557041160-r4 { fill: #e1e1e1 } - .terminal-557041160-r5 { fill: #4ebf71;font-weight: bold } - .terminal-557041160-r6 { fill: #1e1e1e } - .terminal-557041160-r7 { fill: #507bb3 } - .terminal-557041160-r8 { fill: #e2e2e2 } - .terminal-557041160-r9 { fill: #808080 } - .terminal-557041160-r10 { fill: #dde6ed;font-weight: bold } - .terminal-557041160-r11 { fill: #001541 } - .terminal-557041160-r12 { fill: #14191f } - .terminal-557041160-r13 { fill: #454a50 } - .terminal-557041160-r14 { fill: #7ae998 } - .terminal-557041160-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-557041160-r16 { fill: #0a180e;font-weight: bold } - .terminal-557041160-r17 { fill: #000000 } - .terminal-557041160-r18 { fill: #008139 } - .terminal-557041160-r19 { fill: #fea62b;font-weight: bold } - .terminal-557041160-r20 { fill: #a7a9ab } - .terminal-557041160-r21 { fill: #e2e3e3 } + .terminal-2213530577-r1 { fill: #c5c8c6 } + .terminal-2213530577-r2 { fill: #e3e3e3 } + .terminal-2213530577-r3 { fill: #989898 } + .terminal-2213530577-r4 { fill: #e1e1e1 } + .terminal-2213530577-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2213530577-r6 { fill: #1e1e1e } + .terminal-2213530577-r7 { fill: #507bb3 } + .terminal-2213530577-r8 { fill: #e2e2e2 } + .terminal-2213530577-r9 { fill: #808080 } + .terminal-2213530577-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2213530577-r11 { fill: #001541 } + .terminal-2213530577-r12 { fill: #14191f } + .terminal-2213530577-r13 { fill: #454a50 } + .terminal-2213530577-r14 { fill: #7ae998 } + .terminal-2213530577-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-2213530577-r16 { fill: #0a180e;font-weight: bold } + .terminal-2213530577-r17 { fill: #000000 } + .terminal-2213530577-r18 { fill: #008139 } + .terminal-2213530577-r19 { fill: #fea62b;font-weight: bold } + .terminal-2213530577-r20 { fill: #a7a9ab } + .terminal-2213530577-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include ▅▅ - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + use a copy of the  + most common  + reference genome  + files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + GitHub actions for + Continuous  + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▆▆ + ▊▎        Add Github badgesThe README.md file Show help  + ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + will include  + GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration         The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + configuration  + profiles  + containing custom  + parameters  + requried to run  + nf-core pipelines  + at different  + institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 19590c3b8aefea9943ba8380e6ece16e9ccf1c67 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 7 Aug 2024 16:52:04 +0200 Subject: [PATCH 292/574] don't remove creating a pipeline to test it :no_mouth: --- .github/workflows/create-test-lint-wf-template.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index f35016197a..dbe143fda6 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -132,6 +132,12 @@ jobs: run: | printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml + # Create a pipeline from the template + - name: create a pipeline from the template ${{ matrix.TEMPLATE }} + run: | + cd create-test-lint-wf + nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }} + - name: run the pipeline run: | cd create-test-lint-wf From 8acb9c4856cddac922536682a2873946ef8aa56b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 8 Aug 2024 13:32:08 +0200 Subject: [PATCH 293/574] handle template features with a yaml file --- .../create-test-lint-wf-template.yml | 78 +++---- .prettierignore | 1 + nf_core/pipelines/create/create.py | 200 ++++------------ nf_core/pipelines/create/templatefeatures.yml | 213 ++++++++++++++++++ tests/data/pipeline_create_template_skip.yml | 13 +- tests/test_create.py | 18 +- 6 files changed, 297 insertions(+), 226 deletions(-) create mode 100644 nf_core/pipelines/create/templatefeatures.yml diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index dbe143fda6..d4ff3fc557 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -31,31 +31,41 @@ env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: + install-yq: + name: Install yq + runs-on: ubuntu-latest + steps: + - name: 🏗 Set up yq + uses: frenck/action-setup-yq@v1 + + prepare-matrix: + name: Retrieve all template features + runs-on: ubuntu-latest + outputs: + all_features: ${{ steps.create_matrix.outputs.matrix }} + steps: + - name: checkout + uses: actions/checkout@v3 + - name: Create Matrix + id: create_matrix + run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT + RunTestWorkflow: runs-on: ${{ matrix.runner }} env: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: - - "template_skip_github_badges.yml" - - "template_skip_igenomes.yml" - - "template_skip_ci.yml" - - "template_skip_code_linters.yml" - - "template_skip_citations.yml" - - "template_skip_gitpod.yml" - - "template_skip_codespaces.yml" - - "template_skip_multiqc.yml" - - "template_skip_changelog.yml" + TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} profile: ["self_hosted_runner"] include: - - TEMPLATE: "template_skip_all.yml" + - TEMPLATE: all runner: ubuntu-latest profile: "docker" - - TEMPLATE: "template_skip_nf_core_configs.yml" + - TEMPLATE: nf_core_configs runner: ubuntu-latest profile: "docker" fail-fast: false @@ -90,53 +100,17 @@ jobs: run: | mkdir create-test-lint-wf export NXF_WORK=$(pwd) - printf "org: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml - - - name: Create template skip github_badges - run: | - printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml - - - name: Create template skip igenomes - run: | - printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml - - - name: Create template skip ci - run: | - printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml - - - name: Create template skip nf_core_configs - run: | - printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml - - - name: Create template skip code_linters - run: | - printf "org: my-prefix\nskip: code_linters" > create-test-lint-wf/template_skip_code_linters.yml - - - name: Create template skip citations - run: | - printf "org: my-prefix\nskip: citations" > create-test-lint-wf/template_skip_citations.yml - - - name: Create template skip gitpod - run: | - printf "org: my-prefix\nskip: gitpod" > create-test-lint-wf/template_skip_gitpod.yml - - - name: Create template skip multiqc - run: | - printf "org: my-prefix\nskip: multiqc" > create-test-lint-wf/template_skip_multiqc.yml - - - name: Create template skip changelog - run: | - printf "org: my-prefix\nskip: changelog" > create-test-lint-wf/template_skip_changelog.yml + printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml - - name: Create template skip codespaces + - name: Create template skip {{ matrix.TEMPLATE }} run: | - printf "org: my-prefix\nskip: codespaces" > create-test-lint-wf/template_skip_codespaces.yml + printf "org: my-prefix\nskip: {{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} run: | cd create-test-lint-wf - nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }} + nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml - name: run the pipeline run: | diff --git a/.prettierignore b/.prettierignore index 059007ab03..9387ee9509 100644 --- a/.prettierignore +++ b/.prettierignore @@ -7,6 +7,7 @@ nf_core/module-template/meta.yml nf_core/pipeline-template/nextflow_schema.json nf_core/pipeline-template/modules.json nf_core/pipeline-template/tower.yml +tests/data/pipeline_create_template_skip.yml # don't run on things handled by ruff *.py *.pyc diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index b04b28c473..db0833c68e 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -76,43 +76,26 @@ def __init__( else: raise UserWarning("The template configuration was not provided.") - self.jinja_params, skip_paths = self.obtain_jinja_params_dict( + # Read features yaml file + features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" + with open(features_yml_path) as fh: + self.template_features_yml = yaml.safe_load(fh) + + self.jinja_params, self.skip_areas = self.obtain_jinja_params_dict( self.config.skip_features or [], self.config.outdir ) - skippable_paths = { - "github": [ - ".github/", - ".gitignore", - ], - "ci": [".github/workflows/"], - "igenomes": ["conf/igenomes.config"], - "is_nfcore": [ - ".github/ISSUE_TEMPLATE/config", - "CODE_OF_CONDUCT.md", - ".github/workflows/awsfulltest.yml", - ".github/workflows/awstest.yml", - ".github/workflows/release-announcements.yml", - ], - "code_linters": [ - ".editorconfig", - ".pre-commit-config.yaml", - ".prettierignore", - ".prettierrc.yml", - ".github/workflows/fix-linting.yml", - ], - "citations": ["assets/methods_description_template.yml"], - "gitpod": [".gitpod.yml"], - "codespaces": [".devcontainer/devcontainer.json"], - "multiqc": [ - "assets/multiqc_config.yml", - "assets/methods_description_template.yml", - "modules/nf-core/multiqc/", - ], - "changelog": ["CHANGELOG.md"], - } + # format strings in features yaml + short_name = self.jinja_params["short_name"] + env = jinja2.Environment(loader=jinja2.PackageLoader("nf_core", "pipelines"), keep_trailing_newline=True) + features_template = env.get_template( + str(features_yml_path.relative_to(Path(nf_core.__file__).parent / "pipelines")) + ) + rendered_features = features_template.render({"short_name": short_name}) + self.template_features_yml = yaml.safe_load(rendered_features) + # Get list of files we're skipping with the supplied skip keys - self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k]) + self.skip_paths = set(sp for k in self.skip_areas for sp in self.template_features_yml[k]["skippable_paths"]) # Set convenience variables self.name = self.config.name @@ -205,43 +188,27 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): Returns: jinja_params (dict): Dictionary of template areas to skip with values true/false. - skip_paths (list): List of template areas which contain paths to skip. + skip_areas (list): List of template areas which contain paths to skip. """ # Try reading config file _, config_yml = nf_core.utils.load_tools_config(pipeline_dir) - # Define the different template areas, and what actions to take for each - # if they are skipped - template_areas = { - "github": {"file": True, "content": False}, - "ci": {"file": True, "content": False}, - "github_badges": {"file": False, "content": True}, - "igenomes": {"file": True, "content": True}, - "nf_core_configs": {"file": False, "content": True}, - "code_linters": {"file": True, "content": True}, - "citations": {"file": True, "content": True}, - "gitpod": {"file": True, "content": True}, - "codespaces": {"file": True, "content": True}, - "multiqc": {"file": True, "content": True}, - "changelog": {"file": True, "content": False}, - } - # Set the parameters for the jinja template jinja_params = self.config.model_dump() # Add template areas to jinja params and create list of areas with paths to skip - skip_paths = [] - for t_area in template_areas: + skip_areas = [] + for t_area in self.template_features_yml.keys(): if t_area in features_to_skip: - if template_areas[t_area]["file"]: - skip_paths.append(t_area) + if self.template_features_yml[t_area]["skippable_paths"]: + skip_areas.append(t_area) jinja_params[t_area] = False else: jinja_params[t_area] = True # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files - if not jinja_params["is_nfcore"]: - skip_paths.append("is_nfcore") + if not self.config.is_nfcore: + skip_areas.append("is_nfcore") # Set the last parameters based on the ones provided jinja_params["short_name"] = ( @@ -259,7 +226,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): and "nextflow_config" in config_yml["lint"] and "manifest.name" in config_yml["lint"]["nextflow_config"] ): - return jinja_params, skip_paths + return jinja_params, skip_areas # Check that the pipeline name matches the requirements if not re.match(r"^[a-z]+$", jinja_params["short_name"]): @@ -270,7 +237,7 @@ def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir): "Your workflow name is not lowercase without punctuation. This may cause Nextflow errors.\nConsider changing the name to avoid special characters." ) - return jinja_params, skip_paths + return jinja_params, skip_areas def init_pipeline(self): """Creates the nf-core pipeline.""" @@ -438,109 +405,20 @@ def fix_linting(self): for a customized pipeline. """ # Create a lint config - short_name = self.jinja_params["short_name"] - if not self.config.is_nfcore: - lint_config = { - "files_exist": [ - "CODE_OF_CONDUCT.md", - f"assets/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_dark.png", - ".github/ISSUE_TEMPLATE/config.yml", - ".github/workflows/awstest.yml", - ".github/workflows/awsfulltest.yml", - ], - "files_unchanged": [ - "CODE_OF_CONDUCT.md", - f"assets/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_light.png", - f"docs/images/nf-core-{short_name}_logo_dark.png", - ], - "nextflow_config": [ - "manifest.name", - "manifest.homePage", - ], - "multiqc_config": ["report_comment"], - } - else: - lint_config = {} - - # Add GitHub hosting specific configurations - if not self.jinja_params["github"]: - lint_config["files_exist"].extend( - [ - ".github/ISSUE_TEMPLATE/bug_report.yml", - ".github/ISSUE_TEMPLATE/feature_request.yml", - ".github/PULL_REQUEST_TEMPLATE.md", - ".github/CONTRIBUTING.md", - ".github/.dockstore.yml", - ".gitignore", - ] - ) - lint_config["files_unchanged"].extend( - [ - ".github/ISSUE_TEMPLATE/bug_report.yml", - ".github/ISSUE_TEMPLATE/config.yml", - ".github/ISSUE_TEMPLATE/feature_request.yml", - ".github/PULL_REQUEST_TEMPLATE.md", - ".github/workflows/branch.yml", - ".github/workflows/linting_comment.yml", - ".github/workflows/linting.yml", - ".github/CONTRIBUTING.md", - ".github/.dockstore.yml", - ] - ) - - # Add CI specific configurations - if not self.jinja_params["ci"]: - lint_config["files_exist"].extend( - [ - ".github/workflows/branch.yml", - ".github/workflows/ci.yml", - ".github/workflows/linting_comment.yml", - ".github/workflows/linting.yml", - ] - ) - - # Add custom config specific configurations - if not self.jinja_params["nf_core_configs"]: - lint_config["files_exist"].extend(["conf/igenomes.config"]) - lint_config["nextflow_config"].extend( - [ - "process.cpus", - "process.memory", - "process.time", - "custom_config", - ] - ) - - # Add igenomes specific configurations - if not self.jinja_params["igenomes"]: - lint_config["files_exist"].extend(["conf/igenomes.config"]) - - # Add github badges specific configurations - if not self.jinja_params["github_badges"] or not self.jinja_params["github"]: - lint_config["readme"] = ["nextflow_badge"] - - # Add codespaces specific configurations - if not self.jinja_params["codespaces"]: - lint_config["files_unchanged"].extend([".github/CONTRIBUTING.md"]) - - # Add multiqc specific configurations - if not self.jinja_params["multiqc"]: - lint_config.setdefault("files_unchanged", []).extend( - [".github/CONTRIBUTING.md", "assets/sendmail_template.txt"] - ) - lint_config.setdefault("files_exist", []).extend(["assets/multiqc_config.yml"]) - lint_config["multiqc_config"] = False - - # Add changelog specific configurations - if not self.jinja_params["changelog"]: - lint_config["files_exist"].extend(["CHANGELOG.md"]) - - # If the pipeline is not nf-core - if not self.config.is_nfcore: - lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"]) + lint_config = {} + for area in self.skip_areas: + try: + for lint_test in self.template_features_yml[area]["linting"]: + if not lint_config[lint_test]: + pass + if self.template_features_yml[area]["linting"][lint_test]: + lint_config.setdefault(lint_test, []).extend( + self.template_features_yml[area]["linting"][lint_test] + ) + else: + lint_config[lint_test] = False + except KeyError: + pass # Areas without linting # Add the lint content to the preexisting nf-core config config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml new file mode 100644 index 0000000000..843203c7f8 --- /dev/null +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -0,0 +1,213 @@ +github: + skippable_paths: + - ".github/" + - ".gitignore" + short_description: "" + description: "" + help: "" + linting: + files_exist: + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".github/ISSUE_TEMPLATE/feature_request.yml" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/CONTRIBUTING.md" + - ".github/.dockstore.yml" + - ".gitignore" + files_unchanged: + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/ISSUE_TEMPLATE/feature_request.yml" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/branch.yml" + - ".github/workflows/linting_comment.yml" + - ".github/workflows/linting.yml" + - ".github/CONTRIBUTING.md" + - ".github/.dockstore.yml" + readme: + - "nextflow_badge" +ci: + skippable_paths: + - ".github/workflows/" + short_description: "Add Github CI tests" + description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing" + help: | + Nf-core provides a set of Continuous Integration (CI) tests for Github. + When you open a pull request (PR) on your pipeline repository, these tests will run automatically. + + There are different types of tests: + * Linting tests check that your code is formatted correctly and that it adheres to nf-core standards + For code linting they will use [prettier](https://prettier.io/). + * Pipeline tests run your pipeline on a small dataset to check that it works + These tests are run with a small test dataset on GitHub and a larger test dataset on AWS + * Marking old issues as stale + linting: + files_exist: + - ".github/workflows/branch.yml" + - ".github/workflows/ci.yml" + - ".github/workflows/linting_comment.yml" + - ".github/workflows/linting.yml" +igenomes: + skippable_paths: + - "conf/igenomes.config" + short_description: "Use reference genomes" + description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes" + help: | + Nf-core pipelines are configured to use a copy of the most common reference genome files. + + By selecting this option, your pipeline will include a configuration file specifying the paths to these files. + + The required code to use these files will also be included in the template. + When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference files. + + For more information about reference genomes in nf-core pipelines, + see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes). + linting: + files_exist: + - "conf/igenomes.config" +github_badges: + skippable_paths: False + short_description: "Add Github badges" + description: "The README.md file of the pipeline will include GitHub badges" + help: | + The pipeline `README.md` will include badges for: + * AWS CI Tests + * Zenodo DOI + * Nextflow + * Conda + * Docker + * Singularity + * Launching on Nextflow Tower + linting: + readme: + - "nextflow_badge" +nf_core_configs: + skippable_paths: False + short_description: "Add configuration files" + description: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions" + help: | + Nf-core has a repository with a collection of configuration profiles. + + Those config files define a set of parameters which are specific to compute environments at different Institutions. + They can be used within all nf-core pipelines. + If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation. + + For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs) + linting: + files_exist: + - "conf/igenomes.config" + nextflow_config: + - "process.cpus" + - "process.memory" + - "process.time" + - "custom_config" +is_nfcore: + skippable_paths: + - ".github/ISSUE_TEMPLATE/config" + - "CODE_OF_CONDUCT.md" + - ".github/workflows/awsfulltest.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/release-announcements.yml" + short_description: "" + description: "" + help: "" + linting: + files_exist: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_dark.png" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/awsfulltest.yml" + files_unchanged: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_dark.png" + - ".github/ISSUE_TEMPLATE/bug_report.yml" + nextflow_config: + - "manifest.name" + - "manifest.homePage" + multiqc_config: + - "report_comment" +code_linters: + skippable_paths: + - ".editorconfig" + - ".pre-commit-config.yaml" + - ".prettierignore" + - ".prettierrc.yml" + - ".github/workflows/fix-linting.yml" + short_description: "Use code linters" + description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." + help: | + Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. + Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. + The available code linters are: + + - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. + - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces. + - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). +citations: + skippable_paths: + - "assets/methods_description_template.yml" + short_description: "Include citations" + description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." + help: | + If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. + + Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, + and the logics to add this section to the output MultiQC report (if the report is generated). +gitpod: + skippable_paths: + - ".gitpod.yml" + short_description: "Include a gitpod environment" + description: "Include the configuration required to use Gitpod." + help: | + Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. + + Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. + This is useful to have all the tools ready for pipeline development. +codespaces: + skippable_paths: + - ".devcontainer/devcontainer.json" + short_description: "Include GitHub Codespaces" + description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed." + help: | + The pipeline will include a devcontainer configuration. + The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. + + Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal. + linting: + files_unchanged: + - ".github/CONTRIBUTING.md" +multiqc: + skippable_paths: + - "assets/multiqc_config.yml" + - "assets/methods_description_template.yml" + - "modules/nf-core/multiqc/" + short_description: "Use multiqc" + description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." + help: | + MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. + + The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. + linting: + files_unchanged: + - ".github/CONTRIBUTING.md" + - "assets/sendmail_template.txt" + files_exist: + - "assets/multiqc_config.yml" + multiqc_config: False +changelog: + skippable_paths: + - "CHANGELOG.md" + short_description: "Add a changelog" + description: "Add a CHANGELOG.md file." + help: | + Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. + + You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ + linting: + files_exist: + - "CHANGELOG.md" diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml index 21cdc0c3d5..3ab8f69eca 100644 --- a/tests/data/pipeline_create_template_skip.yml +++ b/tests/data/pipeline_create_template_skip.yml @@ -5,15 +5,4 @@ version: 1.0.0 force: True org: testprefix is_nfcore: False -skip_features: - - github - - ci - - github_badges - - igenomes - - nf_core_configs - - code_linters - - citations - - gitpod - - codespaces - - multiqc - - changelog +skip_features: {{ all_features }} diff --git a/tests/test_create.py b/tests/test_create.py index 920a0f4750..92f7f2a9d9 100644 --- a/tests/test_create.py +++ b/tests/test_create.py @@ -5,6 +5,7 @@ from pathlib import Path import git +import jinja2 import yaml import nf_core.pipelines.create.create @@ -98,9 +99,24 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path): @with_temporary_folder def test_pipeline_creation_with_yml_skip(self, tmp_path): + # Update pipeline_create_template_skip.yml file + features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" + with open(features_yml_path) as fh: + template_features_yml = yaml.safe_load(fh) + all_features = list(template_features_yml.keys()) + all_features.remove("is_nfcore") + env = jinja2.Environment(loader=jinja2.PackageLoader("tests", "data"), keep_trailing_newline=True) + skip_template = env.get_template( + str(PIPELINE_TEMPLATE_YML_SKIP.relative_to(Path(nf_core.__file__).parent.parent / "tests" / "data")) + ) + rendered_content = skip_template.render({"all_features": all_features}) + rendered_yaml = Path(tmp_path) / "pipeline_create_template_skip.yml" + with open(rendered_yaml, "w") as fh: + fh.write(rendered_content) + pipeline = nf_core.pipelines.create.create.PipelineCreate( outdir=tmp_path, - template_config=PIPELINE_TEMPLATE_YML_SKIP, + template_config=rendered_yaml, default_branch=self.default_branch, ) pipeline.init_pipeline() From 637317a3422f39d3f98fe2aafcc4efc6d0a88a80 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 8 Aug 2024 14:23:01 +0000 Subject: [PATCH 294/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 609c3aea06..c1e07f3bff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105)) - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) +- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) ### Linting From efff9eada0641bc4ee42cf73f2c6943182f00886 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 9 Aug 2024 10:30:55 +0200 Subject: [PATCH 295/574] use template features yaml file to generate textual layout --- nf_core/pipelines/create/__init__.py | 8 + nf_core/pipelines/create/custompipeline.py | 142 ++---------------- nf_core/pipelines/create/nfcorepipeline.py | 25 ++- nf_core/pipelines/create/templatefeatures.yml | 24 +++ nf_core/pipelines/create/utils.py | 21 --- 5 files changed, 50 insertions(+), 170 deletions(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index 56e25bf1d5..ae766b4e26 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -1,10 +1,13 @@ """A Textual app to create a pipeline.""" import logging +from pathlib import Path +import yaml from textual.app import App from textual.widgets import Button +import nf_core from nf_core.pipelines.create import utils from nf_core.pipelines.create.basicdetails import BasicDetails from nf_core.pipelines.create.custompipeline import CustomPipeline @@ -66,6 +69,11 @@ class PipelineCreateApp(App[utils.CreateConfig]): # Logging state LOGGING_STATE = None + # Template features + features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" + with open(features_yml_path) as fh: + template_features_yml = yaml.safe_load(fh) + def on_mount(self) -> None: self.push_screen("welcome") diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 96b6df5062..fdb7a46d28 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -6,76 +6,7 @@ from textual.screen import Screen from textual.widgets import Button, Footer, Header, Markdown, Switch -from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc - -markdown_ci = """ -Nf-core provides a set of Continuous Integration (CI) tests for Github. -When you open a pull request (PR) on your pipeline repository, these tests will run automatically. - -There are different types of tests: -* Linting tests check that your code is formatted correctly and that it adheres to nf-core standards - For code linting they will use [prettier](https://prettier.io/). -* Pipeline tests run your pipeline on a small dataset to check that it works - These tests are run with a small test dataset on GitHub and a larger test dataset on AWS -* Marking old issues as stale -""" - -markdown_badges = """ -The pipeline `README.md` will include badges for: -* AWS CI Tests -* Zenodo DOI -* Nextflow -* Conda -* Docker -* Singularity -* Launching on Nextflow Tower -""" - -markdown_configuration = """ -Nf-core has a repository with a collection of configuration profiles. - -Those config files define a set of parameters which are specific to compute environments at different Institutions. -They can be used within all nf-core pipelines. -If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation. - -For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs) -""" - -markdown_code_linters = """ -Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. -Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. -The available code linters are: - -- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. -- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces. -- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). -""" - -markdown_citations = """ -If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. - -Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, -and the logics to add this section to the output MultiQC report (if the report is generated). -""" - -markdown_gitpod = """ -Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. - -Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. -This is useful to have all the tools ready for pipeline development. -""" - -markdown_codespaces = """ -The pipeline will include a devcontainer configuration. -The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. - -Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal. -""" - -markdown_changelog = """ -Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. -You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ -""" +from nf_core.pipelines.create.utils import PipelineFeature class CustomPipeline(Screen): @@ -91,75 +22,20 @@ def compose(self) -> ComposeResult: """ ) ) - yield ScrollableContainer( - PipelineFeature( - markdown_genomes, - "Use reference genomes", - "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes", - "igenomes", - ), - PipelineFeature( - markdown_ci, - "Add Github CI tests", - "The pipeline will include several GitHub actions for Continuous Integration (CI) testing", - "ci", - ), - PipelineFeature( - markdown_badges, - "Add Github badges", - "The README.md file of the pipeline will include GitHub badges", - "github_badges", - ), - PipelineFeature( - markdown_configuration, - "Add configuration files", - "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions", - "nf_core_configs", - ), - PipelineFeature( - markdown_code_linters, - "Use code linters", - "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.", - "code_linters", - ), - PipelineFeature( - markdown_citations, - "Include citations", - "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).", - "citations", - ), - PipelineFeature( - markdown_gitpod, - "Include a gitpod environment", - "Include the configuration required to use Gitpod.", - "gitpod", - ), - PipelineFeature( - markdown_codespaces, - "Include GitHub Codespaces", - "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.", - "codespaces", - ), - PipelineFeature( - markdown_multiqc, - "Use multiqc", - "The pipeline will include the MultiQC module which generates an HTML report for quality control.", - "multiqc", - ), - PipelineFeature( - markdown_changelog, - "Add a changelog", - "Add a CHANGELOG.md file.", - "changelog", - ), - classes="features-container", - ) + yield ScrollableContainer(id="features") yield Center( Button("Back", id="back", variant="default"), Button("Continue", id="continue", variant="success"), classes="cta", ) + def on_mount(self) -> None: + for name, feature in self.parent.template_features_yml.items(): + if feature["custom_pipelines"]: + self.query_one("#features").mount( + PipelineFeature(feature["help"], feature["short_description"], feature["description"], name) + ) + @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: """Save fields to the config.""" diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py index 8319cb044c..b6a8231694 100644 --- a/nf_core/pipelines/create/nfcorepipeline.py +++ b/nf_core/pipelines/create/nfcorepipeline.py @@ -6,7 +6,7 @@ from textual.screen import Screen from textual.widgets import Button, Footer, Header, Markdown, Switch -from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes, markdown_multiqc +from nf_core.pipelines.create.utils import PipelineFeature class NfcorePipeline(Screen): @@ -22,27 +22,20 @@ def compose(self) -> ComposeResult: """ ) ) - yield ScrollableContainer( - PipelineFeature( - markdown_genomes, - "Use reference genomes", - "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes", - "igenomes", - ), - PipelineFeature( - markdown_multiqc, - "Use multiqc", - "The pipeline will include the MultiQC module which generates an HTML report for quality control.", - "multiqc", - ), - classes="features-container", - ) + yield ScrollableContainer(id="features") yield Center( Button("Back", id="back", variant="default"), Button("Continue", id="continue", variant="success"), classes="cta", ) + def on_mount(self) -> None: + for name, feature in self.parent.template_features_yml.items(): + if feature["nfcore_pipelines"]: + self.query_one("#features").mount( + PipelineFeature(feature["help"], feature["short_description"], feature["description"], name) + ) + @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: """Save fields to the config.""" diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 843203c7f8..a91887a891 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -25,6 +25,8 @@ github: - ".github/.dockstore.yml" readme: - "nextflow_badge" + nfcore_pipelines: False + custom_pipelines: False ci: skippable_paths: - ".github/workflows/" @@ -46,6 +48,8 @@ ci: - ".github/workflows/ci.yml" - ".github/workflows/linting_comment.yml" - ".github/workflows/linting.yml" + nfcore_pipelines: False + custom_pipelines: True igenomes: skippable_paths: - "conf/igenomes.config" @@ -65,6 +69,8 @@ igenomes: linting: files_exist: - "conf/igenomes.config" + nfcore_pipelines: True + custom_pipelines: True github_badges: skippable_paths: False short_description: "Add Github badges" @@ -81,6 +87,8 @@ github_badges: linting: readme: - "nextflow_badge" + nfcore_pipelines: False + custom_pipelines: True nf_core_configs: skippable_paths: False short_description: "Add configuration files" @@ -101,6 +109,8 @@ nf_core_configs: - "process.memory" - "process.time" - "custom_config" + nfcore_pipelines: False + custom_pipelines: True is_nfcore: skippable_paths: - ".github/ISSUE_TEMPLATE/config" @@ -131,6 +141,8 @@ is_nfcore: - "manifest.homePage" multiqc_config: - "report_comment" + nfcore_pipelines: False + custom_pipelines: False code_linters: skippable_paths: - ".editorconfig" @@ -148,6 +160,8 @@ code_linters: - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces. - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). + nfcore_pipelines: False + custom_pipelines: True citations: skippable_paths: - "assets/methods_description_template.yml" @@ -158,6 +172,8 @@ citations: Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, and the logics to add this section to the output MultiQC report (if the report is generated). + nfcore_pipelines: False + custom_pipelines: True gitpod: skippable_paths: - ".gitpod.yml" @@ -168,6 +184,8 @@ gitpod: Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. This is useful to have all the tools ready for pipeline development. + nfcore_pipelines: False + custom_pipelines: True codespaces: skippable_paths: - ".devcontainer/devcontainer.json" @@ -181,6 +199,8 @@ codespaces: linting: files_unchanged: - ".github/CONTRIBUTING.md" + nfcore_pipelines: False + custom_pipelines: True multiqc: skippable_paths: - "assets/multiqc_config.yml" @@ -199,6 +219,8 @@ multiqc: files_exist: - "assets/multiqc_config.yml" multiqc_config: False + nfcore_pipelines: True + custom_pipelines: True changelog: skippable_paths: - "CHANGELOG.md" @@ -211,3 +233,5 @@ changelog: linting: files_exist: - "CHANGELOG.md" + nfcore_pipelines: False + custom_pipelines: True diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 43094ab531..dba498d181 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -244,24 +244,3 @@ def add_hide_class(app, widget_id: str) -> None: def remove_hide_class(app, widget_id: str) -> None: """Remove class 'hide' to a widget. Display widget.""" app.get_widget_by_id(widget_id).remove_class("hide") - - -## Markdown text to reuse in different screens -markdown_genomes = """ -Nf-core pipelines are configured to use a copy of the most common reference genome files. - -By selecting this option, your pipeline will include a configuration file specifying the paths to these files. - -The required code to use these files will also be included in the template. -When the pipeline user provides an appropriate genome key, -the pipeline will automatically download the required reference files. - -For more information about reference genomes in nf-core pipelines, -see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes). -""" - -markdown_multiqc = """ -MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. - -The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. -""" From 2fa7a033ac1a4d99563e63cdaf76611c223b5da8 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 9 Aug 2024 11:26:29 +0200 Subject: [PATCH 296/574] update textual snapshots --- tests/__snapshots__/test_create_app.ambr | 764 +++++++++++------------ 1 file changed, 382 insertions(+), 382 deletions(-) diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr index f2c1c45c45..f4eb255087 100644 --- a/tests/__snapshots__/test_create_app.ambr +++ b/tests/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-463758155-matrix { + .terminal-3220763577-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-463758155-title { + .terminal-3220763577-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-463758155-r1 { fill: #c5c8c6 } - .terminal-463758155-r2 { fill: #e3e3e3 } - .terminal-463758155-r3 { fill: #989898 } - .terminal-463758155-r4 { fill: #e1e1e1 } - .terminal-463758155-r5 { fill: #4ebf71;font-weight: bold } - .terminal-463758155-r6 { fill: #1e1e1e } - .terminal-463758155-r7 { fill: #0178d4 } - .terminal-463758155-r8 { fill: #454a50 } - .terminal-463758155-r9 { fill: #e2e2e2 } - .terminal-463758155-r10 { fill: #808080 } - .terminal-463758155-r11 { fill: #e2e3e3;font-weight: bold } - .terminal-463758155-r12 { fill: #000000 } - .terminal-463758155-r13 { fill: #e4e4e4 } - .terminal-463758155-r14 { fill: #14191f } - .terminal-463758155-r15 { fill: #507bb3 } - .terminal-463758155-r16 { fill: #dde6ed;font-weight: bold } - .terminal-463758155-r17 { fill: #001541 } - .terminal-463758155-r18 { fill: #7ae998 } - .terminal-463758155-r19 { fill: #0a180e;font-weight: bold } - .terminal-463758155-r20 { fill: #008139 } - .terminal-463758155-r21 { fill: #fea62b;font-weight: bold } - .terminal-463758155-r22 { fill: #a7a9ab } - .terminal-463758155-r23 { fill: #e2e3e3 } + .terminal-3220763577-r1 { fill: #c5c8c6 } + .terminal-3220763577-r2 { fill: #e3e3e3 } + .terminal-3220763577-r3 { fill: #989898 } + .terminal-3220763577-r4 { fill: #e1e1e1 } + .terminal-3220763577-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3220763577-r6 { fill: #1e1e1e } + .terminal-3220763577-r7 { fill: #507bb3 } + .terminal-3220763577-r8 { fill: #e2e2e2 } + .terminal-3220763577-r9 { fill: #808080 } + .terminal-3220763577-r10 { fill: #dde6ed;font-weight: bold } + .terminal-3220763577-r11 { fill: #001541 } + .terminal-3220763577-r12 { fill: #0178d4 } + .terminal-3220763577-r13 { fill: #454a50 } + .terminal-3220763577-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-3220763577-r15 { fill: #000000 } + .terminal-3220763577-r16 { fill: #e4e4e4 } + .terminal-3220763577-r17 { fill: #14191f } + .terminal-3220763577-r18 { fill: #7ae998 } + .terminal-3220763577-r19 { fill: #0a180e;font-weight: bold } + .terminal-3220763577-r20 { fill: #008139 } + .terminal-3220763577-r21 { fill: #fea62b;font-weight: bold } + .terminal-3220763577-r22 { fill: #a7a9ab } + .terminal-3220763577-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Hide help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common  - reference genome files. - - By selecting this option, your pipeline will include a configuration - file specifying the paths to these files.▂▂ - - The required code to use these files will also be included in the  - template. When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference ▂▂ - files. - - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files.▂▂ + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-2213530577-matrix { + .terminal-537214554-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2213530577-title { + .terminal-537214554-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2213530577-r1 { fill: #c5c8c6 } - .terminal-2213530577-r2 { fill: #e3e3e3 } - .terminal-2213530577-r3 { fill: #989898 } - .terminal-2213530577-r4 { fill: #e1e1e1 } - .terminal-2213530577-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2213530577-r6 { fill: #1e1e1e } - .terminal-2213530577-r7 { fill: #507bb3 } - .terminal-2213530577-r8 { fill: #e2e2e2 } - .terminal-2213530577-r9 { fill: #808080 } - .terminal-2213530577-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2213530577-r11 { fill: #001541 } - .terminal-2213530577-r12 { fill: #14191f } - .terminal-2213530577-r13 { fill: #454a50 } - .terminal-2213530577-r14 { fill: #7ae998 } - .terminal-2213530577-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-2213530577-r16 { fill: #0a180e;font-weight: bold } - .terminal-2213530577-r17 { fill: #000000 } - .terminal-2213530577-r18 { fill: #008139 } - .terminal-2213530577-r19 { fill: #fea62b;font-weight: bold } - .terminal-2213530577-r20 { fill: #a7a9ab } - .terminal-2213530577-r21 { fill: #e2e3e3 } + .terminal-537214554-r1 { fill: #c5c8c6 } + .terminal-537214554-r2 { fill: #e3e3e3 } + .terminal-537214554-r3 { fill: #989898 } + .terminal-537214554-r4 { fill: #e1e1e1 } + .terminal-537214554-r5 { fill: #4ebf71;font-weight: bold } + .terminal-537214554-r6 { fill: #1e1e1e } + .terminal-537214554-r7 { fill: #507bb3 } + .terminal-537214554-r8 { fill: #e2e2e2 } + .terminal-537214554-r9 { fill: #808080 } + .terminal-537214554-r10 { fill: #dde6ed;font-weight: bold } + .terminal-537214554-r11 { fill: #001541 } + .terminal-537214554-r12 { fill: #14191f } + .terminal-537214554-r13 { fill: #454a50 } + .terminal-537214554-r14 { fill: #7ae998 } + .terminal-537214554-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-537214554-r16 { fill: #0a180e;font-weight: bold } + .terminal-537214554-r17 { fill: #000000 } + .terminal-537214554-r18 { fill: #008139 } + .terminal-537214554-r19 { fill: #fea62b;font-weight: bold } + .terminal-537214554-r20 { fill: #a7a9ab } + .terminal-537214554-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        testsinclude several ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - GitHub actions for - Continuous  - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▆▆ - ▊▎        Add Github badgesThe README.md file Show help  - ▊▁▁▁▁▁▁▁▁▎of the pipeline ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - will include  - GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration         The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - configuration  - profiles  - containing custom  - parameters  - requried to run  - nf-core pipelines  - at different  - institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help ▇▇ + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2511,254 +2511,254 @@ font-weight: 700; } - .terminal-157696122-matrix { + .terminal-1633351929-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-157696122-title { + .terminal-1633351929-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-157696122-r1 { fill: #c5c8c6 } - .terminal-157696122-r2 { fill: #e3e3e3 } - .terminal-157696122-r3 { fill: #989898 } - .terminal-157696122-r4 { fill: #e1e1e1 } - .terminal-157696122-r5 { fill: #4ebf71;font-weight: bold } - .terminal-157696122-r6 { fill: #1e1e1e } - .terminal-157696122-r7 { fill: #507bb3 } - .terminal-157696122-r8 { fill: #e2e2e2 } - .terminal-157696122-r9 { fill: #808080 } - .terminal-157696122-r10 { fill: #dde6ed;font-weight: bold } - .terminal-157696122-r11 { fill: #001541 } - .terminal-157696122-r12 { fill: #454a50 } - .terminal-157696122-r13 { fill: #7ae998 } - .terminal-157696122-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-157696122-r15 { fill: #0a180e;font-weight: bold } - .terminal-157696122-r16 { fill: #000000 } - .terminal-157696122-r17 { fill: #008139 } - .terminal-157696122-r18 { fill: #fea62b;font-weight: bold } - .terminal-157696122-r19 { fill: #a7a9ab } - .terminal-157696122-r20 { fill: #e2e3e3 } + .terminal-1633351929-r1 { fill: #c5c8c6 } + .terminal-1633351929-r2 { fill: #e3e3e3 } + .terminal-1633351929-r3 { fill: #989898 } + .terminal-1633351929-r4 { fill: #e1e1e1 } + .terminal-1633351929-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1633351929-r6 { fill: #1e1e1e } + .terminal-1633351929-r7 { fill: #507bb3 } + .terminal-1633351929-r8 { fill: #e2e2e2 } + .terminal-1633351929-r9 { fill: #808080 } + .terminal-1633351929-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1633351929-r11 { fill: #001541 } + .terminal-1633351929-r12 { fill: #454a50 } + .terminal-1633351929-r13 { fill: #7ae998 } + .terminal-1633351929-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-1633351929-r15 { fill: #0a180e;font-weight: bold } + .terminal-1633351929-r16 { fill: #000000 } + .terminal-1633351929-r17 { fill: #008139 } + .terminal-1633351929-r18 { fill: #fea62b;font-weight: bold } + .terminal-1633351929-r19 { fill: #a7a9ab } + .terminal-1633351929-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        genomesbe configured to ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - use a copy of the  - most common  - reference genome  - files from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use multiqcThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include the MultiQC▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - module which  - generates an HTML  - report for quality  - control. - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most common + reference genome files  + from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use multiqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which generates  + an HTML report for  + quality control. + + + + + + + + + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From a009e68f594767a90cccd0df0e4fbbbceaf4a3f2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 9 Aug 2024 11:37:18 +0200 Subject: [PATCH 297/574] try reading yaml keys with a list format --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index d4ff3fc557..15582951de 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -48,7 +48,7 @@ jobs: uses: actions/checkout@v3 - name: Create Matrix id: create_matrix - run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT + run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print $2}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} From e36bd7fc6411b68c8b22b17aa783ae9680f4fb2c Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 12 Aug 2024 09:37:06 +0200 Subject: [PATCH 298/574] don't read from json on matrix creation --- .github/workflows/create-test-lint-wf-template.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 15582951de..fd7a494d0d 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -56,7 +56,7 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }} + TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} @@ -68,6 +68,9 @@ jobs: - TEMPLATE: nf_core_configs runner: ubuntu-latest profile: "docker" + exclude: + - TEMPLATE: github + - TEMPLATE: is_nfcore fail-fast: false steps: From d4d231444d9a342624b7fb8c2154ba07424bf34d Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 12 Aug 2024 10:22:26 +0200 Subject: [PATCH 299/574] reset lintconfigtype --- nf_core/utils.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 9b3e56da5f..d0546a5c5e 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -19,7 +19,7 @@ import time from contextlib import contextmanager from pathlib import Path -from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, TypedDict, Union +from typing import Any, Callable, Dict, Generator, List, Optional, Tuple, Union import git import prompt_toolkit.styles @@ -1077,11 +1077,7 @@ def get(self, item: str, default: Any = None) -> Any: return getattr(self, item, default) -class LintConfigType(TypedDict): - files_exist: Optional[Union[List, List[str], List[Dict[str, List[str]]]]] - files_unchanged: Optional[Union[List[str], List[Dict[str, List[str]]]]] - nextflow_config: Optional[Union[List[str], List[Dict[str, List[str]]]]] - multiqc_config: Optional[Union[List[str], bool]] +LintConfigType = Optional[Dict[str, Union[List[str], List[Dict[str, List[str]]], bool]]] class NFCoreYamlConfig(BaseModel): From 78c64c719db446bf84f33137cbce80cd54ee37bc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 11:07:04 +0200 Subject: [PATCH 300/574] apply suggestions from code review by @mashehu --- .../create-test-lint-wf-template.yml | 9 ++---- nf_core/pipelines/create/create.py | 4 ++- nf_core/pipelines/create/custompipeline.py | 2 +- nf_core/pipelines/create/nfcorepipeline.py | 2 +- nf_core/pipelines/create/templatefeatures.yml | 28 +++++++++---------- 5 files changed, 21 insertions(+), 24 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index fd7a494d0d..bd661ce07c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -31,19 +31,14 @@ env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} jobs: - install-yq: - name: Install yq - runs-on: ubuntu-latest - steps: - - name: 🏗 Set up yq - uses: frenck/action-setup-yq@v1 - prepare-matrix: name: Retrieve all template features runs-on: ubuntu-latest outputs: all_features: ${{ steps.create_matrix.outputs.matrix }} steps: + - name: 🏗 Set up yq + uses: frenck/action-setup-yq@v1 - name: checkout uses: actions/checkout@v3 - name: Create Matrix diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 584a4673da..1df6cc3f46 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -185,7 +185,9 @@ def update_config(self, organisation, version, force, outdir): if self.config.is_nfcore is None: self.config.is_nfcore = self.config.org == "nf-core" - def obtain_jinja_params_dict(self, features_to_skip: List[str], pipeline_dir: Union[str, Path]): + def obtain_jinja_params_dict( + self, features_to_skip: List[str], pipeline_dir: Union[str, Path] + ) -> tuple[dict, list[str]]: """Creates a dictionary of parameters for the new pipeline. Args: diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index fdb7a46d28..5debcfee7f 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -33,7 +33,7 @@ def on_mount(self) -> None: for name, feature in self.parent.template_features_yml.items(): if feature["custom_pipelines"]: self.query_one("#features").mount( - PipelineFeature(feature["help"], feature["short_description"], feature["description"], name) + PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name) ) @on(Button.Pressed, "#continue") diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py index b6a8231694..ebb9866986 100644 --- a/nf_core/pipelines/create/nfcorepipeline.py +++ b/nf_core/pipelines/create/nfcorepipeline.py @@ -33,7 +33,7 @@ def on_mount(self) -> None: for name, feature in self.parent.template_features_yml.items(): if feature["nfcore_pipelines"]: self.query_one("#features").mount( - PipelineFeature(feature["help"], feature["short_description"], feature["description"], name) + PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name) ) @on(Button.Pressed, "#continue") diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index a91887a891..48ce200551 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -2,9 +2,9 @@ github: skippable_paths: - ".github/" - ".gitignore" - short_description: "" + short_description: "Skip the creation of a local Git repository." description: "" - help: "" + help_text: "" linting: files_exist: - ".github/ISSUE_TEMPLATE/bug_report.yml" @@ -32,7 +32,7 @@ ci: - ".github/workflows/" short_description: "Add Github CI tests" description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing" - help: | + help_text: | Nf-core provides a set of Continuous Integration (CI) tests for Github. When you open a pull request (PR) on your pipeline repository, these tests will run automatically. @@ -55,7 +55,7 @@ igenomes: - "conf/igenomes.config" short_description: "Use reference genomes" description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes" - help: | + help_text: | Nf-core pipelines are configured to use a copy of the most common reference genome files. By selecting this option, your pipeline will include a configuration file specifying the paths to these files. @@ -75,7 +75,7 @@ github_badges: skippable_paths: False short_description: "Add Github badges" description: "The README.md file of the pipeline will include GitHub badges" - help: | + help_text: | The pipeline `README.md` will include badges for: * AWS CI Tests * Zenodo DOI @@ -93,7 +93,7 @@ nf_core_configs: skippable_paths: False short_description: "Add configuration files" description: "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions" - help: | + help_text: | Nf-core has a repository with a collection of configuration profiles. Those config files define a set of parameters which are specific to compute environments at different Institutions. @@ -118,9 +118,9 @@ is_nfcore: - ".github/workflows/awsfulltest.yml" - ".github/workflows/awstest.yml" - ".github/workflows/release-announcements.yml" - short_description: "" + short_description: "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools." description: "" - help: "" + help_text: "" linting: files_exist: - "CODE_OF_CONDUCT.md" @@ -152,7 +152,7 @@ code_linters: - ".github/workflows/fix-linting.yml" short_description: "Use code linters" description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." - help: | + help_text: | Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. The available code linters are: @@ -167,7 +167,7 @@ citations: - "assets/methods_description_template.yml" short_description: "Include citations" description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." - help: | + help_text: | If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, @@ -179,7 +179,7 @@ gitpod: - ".gitpod.yml" short_description: "Include a gitpod environment" description: "Include the configuration required to use Gitpod." - help: | + help_text: | Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. @@ -191,7 +191,7 @@ codespaces: - ".devcontainer/devcontainer.json" short_description: "Include GitHub Codespaces" description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed." - help: | + help_text: | The pipeline will include a devcontainer configuration. The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. @@ -208,7 +208,7 @@ multiqc: - "modules/nf-core/multiqc/" short_description: "Use multiqc" description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." - help: | + help_text: | MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. @@ -226,7 +226,7 @@ changelog: - "CHANGELOG.md" short_description: "Add a changelog" description: "Add a CHANGELOG.md file." - help: | + help_text: | Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ From bf07bf24a31850250486000c708c7b6e31b60f01 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 11:32:58 +0200 Subject: [PATCH 301/574] load feature yaml file with a utils function --- nf_core/pipelines/create/__init__.py | 4 +--- nf_core/pipelines/create/create.py | 6 ++---- nf_core/pipelines/create/utils.py | 11 +++++++++++ tests/pipelines/test_create.py | 5 ++--- 4 files changed, 16 insertions(+), 10 deletions(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index 1774d0a010..8b0edf34cf 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -72,9 +72,7 @@ class PipelineCreateApp(App[utils.CreateConfig]): LOGGING_STATE = None # Template features - features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" - with open(features_yml_path) as fh: - template_features_yml = yaml.safe_load(fh) + template_features_yml = utils.load_features_yaml() def on_mount(self) -> None: self.push_screen("welcome") diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 1df6cc3f46..b3135435ee 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -18,7 +18,7 @@ import nf_core import nf_core.pipelines.schema import nf_core.utils -from nf_core.pipelines.create.utils import CreateConfig +from nf_core.pipelines.create.utils import CreateConfig, features_yml_path, load_features_yaml from nf_core.pipelines.create_logo import create_logo from nf_core.pipelines.lint_utils import run_prettier_on_file from nf_core.utils import LintConfigType, NFCoreTemplateConfig @@ -82,9 +82,7 @@ def __init__( raise UserWarning("The template configuration was not provided.") # Read features yaml file - features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" - with open(features_yml_path) as fh: - self.template_features_yml = yaml.safe_load(fh) + self.template_features_yml = load_features_yaml() if self.config.outdir is None: self.config.outdir = str(Path.cwd()) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 89cf0ab65a..2e0015ed90 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -5,6 +5,7 @@ from pathlib import Path from typing import Any, Dict, Iterator, Union +import yaml from pydantic import ConfigDict, ValidationError, ValidationInfo, field_validator from rich.logging import RichHandler from textual import on @@ -16,6 +17,7 @@ from textual.widget import Widget from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch +import nf_core from nf_core.utils import NFCoreTemplateConfig # Use ContextVar to define a context on the model initialization @@ -34,6 +36,9 @@ def init_context(value: Dict[str, Any]) -> Iterator[None]: # Define a global variable to store the pipeline type NFCORE_PIPELINE_GLOBAL: bool = True +# YAML file describing template features +features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" + class CreateConfig(NFCoreTemplateConfig): """Pydantic model for the nf-core create config.""" @@ -242,3 +247,9 @@ def add_hide_class(app, widget_id: str) -> None: def remove_hide_class(app, widget_id: str) -> None: """Remove class 'hide' to a widget. Display widget.""" app.get_widget_by_id(widget_id).remove_class("hide") + + +def load_features_yaml() -> dict: + """Load the YAML file describing template features.""" + with open(features_yml_path) as fh: + return yaml.safe_load(fh) diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py index b684a4669e..13fd3b24cd 100644 --- a/tests/pipelines/test_create.py +++ b/tests/pipelines/test_create.py @@ -9,6 +9,7 @@ import yaml import nf_core.pipelines.create.create +from nf_core.pipelines.create.utils import load_features_yaml from ..utils import TEST_DATA_DIR, with_temporary_folder @@ -101,9 +102,7 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path): @with_temporary_folder def test_pipeline_creation_with_yml_skip(self, tmp_path): # Update pipeline_create_template_skip.yml file - features_yml_path = Path(nf_core.__file__).parent / "pipelines" / "create" / "templatefeatures.yml" - with open(features_yml_path) as fh: - template_features_yml = yaml.safe_load(fh) + template_features_yml = load_features_yaml() all_features = list(template_features_yml.keys()) all_features.remove("is_nfcore") env = jinja2.Environment(loader=jinja2.PackageLoader("tests", "data"), keep_trailing_newline=True) From 2c2ec5db394128a947bc874461582e45711648d1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 11:51:26 +0200 Subject: [PATCH 302/574] set force to true when creating a pipeline from the app --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index d0546a5c5e..96c16130ca 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1055,7 +1055,7 @@ class NFCoreTemplateConfig(BaseModel): description: Optional[str] = None author: Optional[str] = None version: Optional[str] = None - force: Optional[bool] = None + force: Optional[bool] = True outdir: Optional[Union[str, Path]] = None skip_features: Optional[list] = None is_nfcore: Optional[bool] = None From 2535b6fc136fc24bef77249f3fc755b344100b9c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 13 Aug 2024 12:16:51 +0200 Subject: [PATCH 303/574] Update nf_core/pipelines/create/utils.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 2e0015ed90..0b72c2bcf5 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -249,7 +249,7 @@ def remove_hide_class(app, widget_id: str) -> None: app.get_widget_by_id(widget_id).remove_class("hide") -def load_features_yaml() -> dict: +def load_features_yaml() -> Dict: """Load the YAML file describing template features.""" with open(features_yml_path) as fh: return yaml.safe_load(fh) From 6af86cf39306c2bf3c9bd4d0f61057fdea24f590 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 12:29:02 +0200 Subject: [PATCH 304/574] fix typing --- nf_core/pipelines/create/create.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index b3135435ee..200507d8a0 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -8,7 +8,7 @@ import re import shutil from pathlib import Path -from typing import Dict, List, Optional, Union, cast +from typing import Dict, List, Optional, Tuple, Union, cast import git import git.config @@ -185,7 +185,7 @@ def update_config(self, organisation, version, force, outdir): def obtain_jinja_params_dict( self, features_to_skip: List[str], pipeline_dir: Union[str, Path] - ) -> tuple[dict, list[str]]: + ) -> Tuple[Dict, List[str]]: """Creates a dictionary of parameters for the new pipeline. Args: From d6459cba0cf3e96e156350e541850afb61409e57 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 17:39:35 +0200 Subject: [PATCH 305/574] add templatefeatures.yml to python package --- MANIFEST.in | 1 + 1 file changed, 1 insertion(+) diff --git a/MANIFEST.in b/MANIFEST.in index 68f115d97f..2bec403804 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -10,3 +10,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png include nf_core/assets/logo/placeholder_logo.svg include nf_core/assets/logo/MavenPro-Bold.ttf include nf_core/pipelines/create/create.tcss +include nf_core/pipelines/create/templatefeatures.yml From f6505c2fea94057e66954f45b4c1ad6e37dc8a77 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 13 Aug 2024 15:41:13 +0000 Subject: [PATCH 306/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 398aee5755..c7095e292e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) +- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) ### Linting From afec8773b56cb813c4de59f882f0c056c9b4d114 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 18:11:41 +0200 Subject: [PATCH 307/574] output matrix elements with double quotes --- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index bd661ce07c..0057bdb2d0 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -35,7 +35,7 @@ jobs: name: Retrieve all template features runs-on: ubuntu-latest outputs: - all_features: ${{ steps.create_matrix.outputs.matrix }} + all_features: ${{ fromJSON(steps.create_matrix.outputs.matrix) }} steps: - name: 🏗 Set up yq uses: frenck/action-setup-yq@v1 @@ -43,7 +43,7 @@ jobs: uses: actions/checkout@v3 - name: Create Matrix id: create_matrix - run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print $2}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT + run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} From c8188130153a4c4192714255b98ecd6fc08155bf Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 18:18:20 +0200 Subject: [PATCH 308/574] don't use fromJSON --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 0057bdb2d0..0c97168f44 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -35,7 +35,7 @@ jobs: name: Retrieve all template features runs-on: ubuntu-latest outputs: - all_features: ${{ fromJSON(steps.create_matrix.outputs.matrix) }} + all_features: ${{ steps.create_matrix.outputs.matrix }} steps: - name: 🏗 Set up yq uses: frenck/action-setup-yq@v1 From aef4895bf7a1a5b50d855399d37635cc088d7abb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 18:23:23 +0200 Subject: [PATCH 309/574] try fromJSON when reading the matrix --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 0c97168f44..c2d61c51c8 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -51,7 +51,7 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }} + TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} From 3464aa45a689e33a64bbf2ac3390772ae3b4d3d0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 18:34:47 +0200 Subject: [PATCH 310/574] surround whole matrix by single quotes --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index c2d61c51c8..e097c0c82a 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -43,7 +43,7 @@ jobs: uses: actions/checkout@v3 - name: Create Matrix id: create_matrix - run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "[" $0 "]"}')" >> $GITHUB_OUTPUT + run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} From 5156d0129ae602af54291742cdd7d107bcb2c129 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 13 Aug 2024 18:42:24 +0200 Subject: [PATCH 311/574] escape double quotes to use a json raw string literal --- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index e097c0c82a..3d3726b820 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -43,7 +43,7 @@ jobs: uses: actions/checkout@v3 - name: Create Matrix id: create_matrix - run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\""$2"\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT + run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\\""\""$2"\\""\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} @@ -51,7 +51,7 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} + TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} From 07858624a4c97c209d5b002a699b1e6d89a6001b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 08:46:14 +0200 Subject: [PATCH 312/574] allow spaces at the betinning of include statements in components --- nf_core/components/components_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 01650a643d..dee4fbf6bb 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -143,7 +143,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str regex = re.compile( r"include(?: *{ *)([a-zA-Z\_0-9]*)(?: *as *)?(?:[a-zA-Z\_0-9]*)?(?: *})(?: *from *)(?:'|\")(.*)(?:'|\")" ) - match = regex.match(line) + match = regex.search(line) if match and len(match.groups()) == 2: name, link = match.groups() if link.startswith("../../../"): From dea1781dfeb402b99a0c1a209928db7c55ff7c5b Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 08:49:56 +0200 Subject: [PATCH 313/574] try simpler yq command --- .github/workflows/create-test-lint-wf-template.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 3d3726b820..cc7f272c64 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -43,7 +43,9 @@ jobs: uses: actions/checkout@v3 - name: Create Matrix id: create_matrix - run: echo "matrix=$(yq 'keys' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml | awk '{print "\\""\""$2"\\""\""}' | paste -sd "," - | awk '{print "'\''[" $0 "]'\''"}')" >> $GITHUB_OUTPUT + run: | + echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml >> $GITHUB_OUTPUT + echo $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} @@ -51,7 +53,7 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: ${{ fromJSON(needs.prepare-matrix.outputs.all_features) }} + TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} From d838c869602c6a08238b7bbc17abdc23046083d6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 14 Aug 2024 06:51:20 +0000 Subject: [PATCH 314/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 609c3aea06..91e32374d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,7 @@ - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) +- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From e19be1d13025b18273f494f86f39d67fc2ba1901 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 08:53:05 +0200 Subject: [PATCH 315/574] add missing parenthesis --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index cc7f272c64..e55f904c7c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,7 +44,7 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml >> $GITHUB_OUTPUT + echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml) >> $GITHUB_OUTPUT echo $GITHUB_OUTPUT RunTestWorkflow: From 7c6281f113cd3cac0a0b570e2c178f3036ae80e2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 08:54:29 +0200 Subject: [PATCH 316/574] and missing closing quote --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index e55f904c7c..fd20b67937 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,7 +44,7 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml) >> $GITHUB_OUTPUT + echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT echo $GITHUB_OUTPUT RunTestWorkflow: From 96c2b0a1a8ec5be01cac80c8f418ffacdbd63eda Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:01:56 +0200 Subject: [PATCH 317/574] remove debugging --- .github/workflows/create-test-lint-wf-template.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index fd20b67937..311c6a0582 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -45,7 +45,6 @@ jobs: id: create_matrix run: | echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT - echo $GITHUB_OUTPUT RunTestWorkflow: runs-on: ${{ matrix.runner }} From 08888ffeea3ca0a1c1f2a607d4614b14a109887d Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:06:12 +0200 Subject: [PATCH 318/574] more debugging --- .github/workflows/create-test-lint-wf-template.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 311c6a0582..d46d8f7d31 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,7 +44,9 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq 'keys | tojson' ${{ github.workspace }}/nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT + echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" + - name: Setup ssh session + uses: Warpbuilds/action-debugger@v1.3 RunTestWorkflow: runs-on: ${{ matrix.runner }} From b564d9f451c48888987d6e9ec24ef8cd49fd60b7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:08:18 +0200 Subject: [PATCH 319/574] add output step back --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index d46d8f7d31..e835a2b30c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -44,7 +44,7 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" + echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT - name: Setup ssh session uses: Warpbuilds/action-debugger@v1.3 From 237f888bdb3a3202291a34b03ea0ef2f9981079f Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:11:31 +0200 Subject: [PATCH 320/574] add `needs` step --- .github/workflows/create-test-lint-wf-template.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index e835a2b30c..4fa41a0d4e 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -45,11 +45,10 @@ jobs: id: create_matrix run: | echo "matrix=$(yq 'keys | tojson(0)' nf_core/pipelines/create/templatefeatures.yml)" >> $GITHUB_OUTPUT - - name: Setup ssh session - uses: Warpbuilds/action-debugger@v1.3 RunTestWorkflow: runs-on: ${{ matrix.runner }} + needs: prepare-matrix env: NXF_ANSI_LOG: false strategy: From d81019f56ba0ebf9ea12c7ed72a80f408e650a51 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:16:20 +0200 Subject: [PATCH 321/574] parse output step --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 4fa41a0d4e..71ea02539e 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -53,7 +53,7 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - TEMPLATE: ${{ needs.prepare-matrix.outputs.all_features }} + TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} runner: # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} From c4a1961e33b23e9eb5f1972b0ab84301770974f7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:18:57 +0200 Subject: [PATCH 322/574] add missing escape character --- .github/workflows/create-test-lint-wf-template.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 71ea02539e..29c3933758 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -40,7 +40,7 @@ jobs: - name: 🏗 Set up yq uses: frenck/action-setup-yq@v1 - name: checkout - uses: actions/checkout@v3 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Create Matrix id: create_matrix run: | @@ -102,9 +102,9 @@ jobs: export NXF_WORK=$(pwd) printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml - - name: Create template skip {{ matrix.TEMPLATE }} + - name: Create template skip ${{ matrix.TEMPLATE }} run: | - printf "org: my-prefix\nskip: {{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml + printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} From d401a40cc25419e50846d8b01abf0e66d36a5ec5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 14 Aug 2024 09:21:06 +0200 Subject: [PATCH 323/574] more escape characters --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 29c3933758..1c5189f549 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -104,7 +104,7 @@ jobs: - name: Create template skip ${{ matrix.TEMPLATE }} run: | - printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_{{ matrix.TEMPLATE }}.yml + printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} From 5936e61cf4d44242167550419e5f4f001b4212e0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 10:08:16 +0200 Subject: [PATCH 324/574] fix creating pipeline from template skip_features --- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- nf_core/pipelines/create/create.py | 2 -- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 1c5189f549..c15783e67b 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -100,11 +100,11 @@ jobs: run: | mkdir create-test-lint-wf export NXF_WORK=$(pwd) - printf "org: my-prefix\nskip: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml + printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml - name: Create template skip ${{ matrix.TEMPLATE }} run: | - printf "org: my-prefix\nskip: ${{ matrix.TEMPLATE }}" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml + printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 200507d8a0..873a2ecb19 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -417,8 +417,6 @@ def fix_linting(self): for area in self.skip_areas: try: for lint_test in self.template_features_yml[area]["linting"]: - if not lint_config[lint_test]: - pass if self.template_features_yml[area]["linting"][lint_test]: lint_config.setdefault(lint_test, []).extend( self.template_features_yml[area]["linting"][lint_test] From 4941833dd1fae5720b4b10c3cdf63bb9dbdd3e6f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 10:23:48 +0200 Subject: [PATCH 325/574] handle linting tests false --- nf_core/pipelines/create/create.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 873a2ecb19..c015a43f73 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -417,12 +417,15 @@ def fix_linting(self): for area in self.skip_areas: try: for lint_test in self.template_features_yml[area]["linting"]: - if self.template_features_yml[area]["linting"][lint_test]: - lint_config.setdefault(lint_test, []).extend( - self.template_features_yml[area]["linting"][lint_test] - ) - else: - lint_config[lint_test] = False + try: + if self.template_features_yml[area]["linting"][lint_test]: + lint_config.setdefault(lint_test, []).extend( + self.template_features_yml[area]["linting"][lint_test] + ) + else: + lint_config[lint_test] = False + except AttributeError: + pass # When linting is False except KeyError: pass # Areas without linting From b474a049e7d4cc1cea8d7006e1a2aeb79b810dcc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 10:33:56 +0200 Subject: [PATCH 326/574] exclude running skip nf_core_configs with self_hosted_runner --- .github/workflows/create-test-lint-wf-template.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index c15783e67b..6b916fb79c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -68,6 +68,9 @@ jobs: exclude: - TEMPLATE: github - TEMPLATE: is_nfcore + - TEMPLATE: nf_core_configs + runner: self-hosted + profile: "self_hosted_runner" fail-fast: false steps: From 442f2f0097226595730dd4e1c9af86696f6c16fb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 11:56:50 +0200 Subject: [PATCH 327/574] fix pipeline skipping nf_core_configs --- .prettierignore | 1 + .../.github/ISSUE_TEMPLATE/bug_report.yml | 2 + nf_core/pipeline-template/nextflow.config | 2 +- .../pipeline-template/nextflow_schema.json | 6 ++- nf_core/pipelines/create/create.py | 46 ++----------------- nf_core/pipelines/create/templatefeatures.yml | 2 + 6 files changed, 15 insertions(+), 44 deletions(-) diff --git a/.prettierignore b/.prettierignore index 9387ee9509..cbe7274a4a 100644 --- a/.prettierignore +++ b/.prettierignore @@ -7,6 +7,7 @@ nf_core/module-template/meta.yml nf_core/pipeline-template/nextflow_schema.json nf_core/pipeline-template/modules.json nf_core/pipeline-template/tower.yml +nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml tests/data/pipeline_create_template_skip.yml # don't run on things handled by ruff *.py diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml index 063690f29f..412f5bd3b3 100644 --- a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,6 +2,7 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: +{%- if is_nfcore %} - type: markdown attributes: value: | @@ -9,6 +10,7 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [{{ name }} pipeline documentation](https://nf-co.re/{{ short_name }}/usage) +{%- endif %} - type: textarea id: description diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 3a7f544805..0469d6cfec 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -41,11 +41,11 @@ params { version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + {%- if nf_core_configs %} // Config options config_profile_name = null config_profile_description = null - {%- if nf_core_configs %} custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 1c52e2298d..4a1a22c3ee 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -77,6 +77,7 @@ } }, {%- endif %} + {%- if nf_core_configs %} "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -125,6 +126,7 @@ } } }, + {%- endif %} "max_job_request_options": { "title": "Max job request options", "type": "object", @@ -289,9 +291,9 @@ {% if igenomes %}{ "$ref": "#/definitions/reference_genome_options" },{% endif %} - { + {% if nf_core_configs %}{ "$ref": "#/definitions/institutional_config_options" - }, + },{% endif %} { "$ref": "#/definitions/max_job_request_options" }, diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index c015a43f73..e3f8dc6973 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -349,17 +349,9 @@ def render_template(self) -> None: template_stat = os.stat(template_fn_path) os.chmod(output_path, template_stat.st_mode) - # Remove all unused parameters in the nextflow schema - if not self.jinja_params["igenomes"] or not self.jinja_params["nf_core_configs"]: - self.update_nextflow_schema() if self.config.is_nfcore: # Make a logo and save it, if it is a nf-core pipeline self.make_pipeline_logo() - else: - if self.jinja_params["github"]: - # Remove field mentioning nf-core docs - # in the github bug report template - self.remove_nf_core_in_bug_report_template() # Update the .nf-core.yml with linting configurations self.fix_linting() @@ -374,38 +366,10 @@ def render_template(self) -> None: log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") run_prettier_on_file(self.outdir / config_fn) - def update_nextflow_schema(self): - """ - Removes unused parameters from the nextflow schema. - """ - schema_path = self.outdir / "nextflow_schema.json" - - schema = nf_core.pipelines.schema.PipelineSchema() - schema.schema_filename = schema_path - schema.no_prompts = True - schema.load_schema() - schema.get_wf_params() - schema.remove_schema_notfound_configs() - schema.save_schema(suppress_logging=True) - run_prettier_on_file(schema_path) - - def remove_nf_core_in_bug_report_template(self): - """ - Remove the field mentioning nf-core documentation - in the github bug report template - """ - bug_report_path = self.outdir / ".github" / "ISSUE_TEMPLATE" / "bug_report.yml" - - with open(bug_report_path) as fh: - contents = yaml.load(fh, Loader=yaml.FullLoader) - - # Remove the first item in the body, which is the information about the docs - contents["body"].pop(0) - - with open(bug_report_path, "w") as fh: - yaml.dump(contents, fh, default_flow_style=False, sort_keys=False) - - run_prettier_on_file(bug_report_path) + # Run prettier on files + for file in self.outdir.iterdir(): + if file.is_file() and file.name.endswith(("yaml", "yml", "json")): + run_prettier_on_file(file) def fix_linting(self): """ @@ -414,7 +378,7 @@ def fix_linting(self): """ # Create a lint config lint_config = {} - for area in self.skip_areas: + for area in (self.config.skip_features or []) + self.skip_areas: try: for lint_test in self.template_features_yml[area]["linting"]: try: diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 48ce200551..ac026c9e20 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -109,6 +109,8 @@ nf_core_configs: - "process.memory" - "process.time" - "custom_config" + - "params.custom_config_version" + - "params.custom_config_base" nfcore_pipelines: False custom_pipelines: True is_nfcore: From c3f669e704de117bff30eb569788669e0f8f26ce Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 12:10:00 +0200 Subject: [PATCH 328/574] fix lint pipeline without code linters --- nf_core/pipelines/create/templatefeatures.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index ac026c9e20..b97bf347ab 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -162,6 +162,11 @@ code_linters: - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. - editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces. - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). + linting: + files_exist: + - ".editorconfig" + - ".prettierignore" + - ".prettierrc.yml" nfcore_pipelines: False custom_pipelines: True citations: From 6da1adc768e9032887422fd475c524b94e0b3bb2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 12:12:01 +0200 Subject: [PATCH 329/574] not run skip nf_core_configs with self_hosted_runner --- .github/workflows/create-test-lint-wf-template.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 6b916fb79c..fc6338ab40 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -69,7 +69,6 @@ jobs: - TEMPLATE: github - TEMPLATE: is_nfcore - TEMPLATE: nf_core_configs - runner: self-hosted profile: "self_hosted_runner" fail-fast: false From 598bd17acc9ebf949c3e56b057629e899c453e26 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 12:20:20 +0200 Subject: [PATCH 330/574] create template with skip all only once --- .github/workflows/create-test-lint-wf-template.yml | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index fc6338ab40..70125a10f3 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -98,15 +98,16 @@ jobs: version: latest-everything # Create template files - - name: Create template skip all (except github) + - name: Create template skip ${{ matrix.TEMPLATE }} run: | mkdir create-test-lint-wf export NXF_WORK=$(pwd) - printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml - - - name: Create template skip ${{ matrix.TEMPLATE }} - run: | - printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml + if [ ${{ matrix.TEMPLATE }} == "all" ] + then + printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml + else + printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml + fi # Create a pipeline from the template - name: create a pipeline from the template ${{ matrix.TEMPLATE }} From c038e81c303926f46cf52daa36ec09a9c95b39e5 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 12:46:58 +0200 Subject: [PATCH 331/574] set is_nfcore false when needed --- nf_core/pipelines/create/create.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index e3f8dc6973..dfdcf07a42 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -218,6 +218,7 @@ def obtain_jinja_params_dict( # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files if not self.config.is_nfcore: skip_areas.append("is_nfcore") + jinja_params["is_nfcore"] = False # Set the last parameters based on the ones provided jinja_params["short_name"] = ( From 95a57cffa77e6b7a0918454acb04433c94cd5284 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 14 Aug 2024 13:33:09 +0200 Subject: [PATCH 332/574] run prettier on the pipeline output directory --- nf_core/pipelines/create/create.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index dfdcf07a42..05b04a5422 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -368,9 +368,7 @@ def render_template(self) -> None: run_prettier_on_file(self.outdir / config_fn) # Run prettier on files - for file in self.outdir.iterdir(): - if file.is_file() and file.name.endswith(("yaml", "yml", "json")): - run_prettier_on_file(file) + run_prettier_on_file(self.outdir) def fix_linting(self): """ From a754fe0845f0e28ae0398625d8132a6047aa991e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 15:07:38 +0200 Subject: [PATCH 333/574] add schema checking for draft 2020-12 --- nf_core/pipelines/lint/schema_lint.py | 32 ++++++++++++++++++++++----- nf_core/pipelines/schema.py | 21 +++++++++++++----- requirements.txt | 2 +- 3 files changed, 44 insertions(+), 11 deletions(-) diff --git a/nf_core/pipelines/lint/schema_lint.py b/nf_core/pipelines/lint/schema_lint.py index 6786c5012d..4007bf8fe5 100644 --- a/nf_core/pipelines/lint/schema_lint.py +++ b/nf_core/pipelines/lint/schema_lint.py @@ -16,26 +16,26 @@ def schema_lint(self): The lint test checks the schema for the following: * Schema should be a valid JSON file - * Schema should adhere to `JSONSchema `_, Draft 7. + * Schema should adhere to `JSONSchema `_, Draft 7 or Draft 2020-12. * Parameters can be described in two places: * As ``properties`` in the top-level schema object - * As ``properties`` within subschemas listed in a top-level ``definitions`` objects + * As ``properties`` within subschemas listed in a top-level ``definitions``(draft 7) or ``$defs``(draft 2020-12) objects * The schema must describe at least one parameter * There must be no duplicate parameter IDs across the schema and definition subschema - * All subschema in ``definitions`` must be referenced in the top-level ``allOf`` key + * All subschema in ``definitions`` or ``$defs`` must be referenced in the top-level ``allOf`` key * The top-level ``allOf`` key must not describe any non-existent definitions * Default parameters in the schema must be valid * Core top-level schema attributes should exist and be set as follows: - * ``$schema``: ``https://json-schema.org/draft-07/schema`` + * ``$schema``: ``https://json-schema.org/draft-07/schema`` or ``https://json-schema.org/draft/2020-12/schema`` * ``$id``: URL to the raw schema file, eg. ``https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json`` * ``title``: ``YOURPIPELINE pipeline parameters`` * ``description``: The pipeline config ``manifest.description`` * That the ``input`` property is defined and has a mimetype. A list of common mimetypes can be found `here `_. - For example, an *extremely* minimal schema could look like this: + For example, an *extremely* minimal schema could look like this (draft 7): .. code-block:: json @@ -57,6 +57,28 @@ def schema_lint(self): "allOf": [{"$ref": "#/definitions/my_first_group"}] } + Or this (draft 2020-12): + + .. code-block:: json + + { + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/YOURPIPELINE/master/nextflow_schema.json", + "title": "YOURPIPELINE pipeline parameters", + "description": "This pipeline is for testing", + "properties": { + "first_param": { "type": "string" } + }, + "$defs": { + "my_first_group": { + "properties": { + "second_param": { "type": "string" } + } + } + }, + "allOf": [{"$ref": "#/$defs/my_first_group"}] + } + .. tip:: You can check your pipeline schema without having to run the entire pipeline lint by running ``nf-core pipelines schema lint`` instead of ``nf-core pipelines lint`` """ diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 7f562bff38..854bddccc0 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -359,11 +359,22 @@ def validate_schema(self, schema=None): """ if schema is None: schema = self.schema - try: - jsonschema.Draft7Validator.check_schema(schema) - log.debug("JSON Schema Draft7 validated") - except jsonschema.exceptions.SchemaError as e: - raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}") + + schema_draft = schema["$schema"] + if schema_draft == "https://json-schema.org/draft-07/schema": + try: + jsonschema.Draft7Validator.check_schema(schema) + log.debug("JSON Schema Draft7 validated") + except jsonschema.exceptions.SchemaError as e: + raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}") + elif schema_draft == "https://json-schema.org/draft/2020-12/schema": + try: + jsonschema.Draft202012Validator.check_schema(schema) + log.debug("JSON Schema Draft2020-12 validated") + except jsonschema.exceptions.SchemaError as e: + raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}") + else: + raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.") param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) diff --git a/requirements.txt b/requirements.txt index fb658be2fb..eba6460f03 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,7 +3,7 @@ filetype GitPython PyGithub jinja2 -jsonschema>=3.0 +jsonschema>=4.0 markdown>=3.3 packaging pillow From 464f16e982337699382e66e3b1da21af4f01dd7a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 15:26:52 +0200 Subject: [PATCH 334/574] update validate schema --- nf_core/pipelines/schema.py | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 854bddccc0..abdad719f6 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -378,17 +378,32 @@ def validate_schema(self, schema=None): param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) - for d_key, d_schema in schema.get("definitions", {}).items(): + schema_defs = dict() + defs_notation = "" + if "$defs" in schema: + schema_defs = schema.get("$defs", {}).items() + defs_notation = "$defs" + elif "definitions" in schema: + schema_defs = schema.get("definitions", {}).items() + defs_notation = "definitions" + elif "defs" in schema: + # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0 + # this line prevents the breakage of schemas created for v2.0.0 + schema_defs = schema.get("defs", {}).items() + defs_notation = "defs" + + for d_key, d_schema in schema_defs: # Check that this definition is mentioned in allOf if "allOf" not in schema: raise AssertionError("Schema has definitions, but no allOf key") in_allOf = False for allOf in schema.get("allOf", []): - if allOf["$ref"] == f"#/definitions/{d_key}": + if allOf["$ref"] == f"#/{defs_notation}/{d_key}": in_allOf = True if not in_allOf: - raise AssertionError(f"Definition subschema `{d_key}` not included in schema `allOf`") + raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`") + # TODO add support for nested parameters for d_param_id in d_schema.get("properties", {}): # Check that we don't have any duplicate parameter IDs in different definitions if d_param_id in param_keys: @@ -398,11 +413,11 @@ def validate_schema(self, schema=None): # Check that everything in allOf exists for allOf in schema.get("allOf", []): - if "definitions" not in schema: - raise AssertionError("Schema has allOf, but no definitions") - def_key = allOf["$ref"][14:] - if def_key not in schema.get("definitions", {}): - raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `definitions`") + _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#//" + if allOf_defs_notation not in schema: + raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}") + if def_key not in schema.get(allOf_defs_notation, {}): + raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`") # Check that the schema describes at least one parameter if num_params == 0: From 6658449cc892021782a22885c3db63c0215254b6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 15:51:27 +0200 Subject: [PATCH 335/574] update more code to support draft 2020-12 --- nf_core/pipelines/schema.py | 55 ++++++++++++++++++++----------------- 1 file changed, 30 insertions(+), 25 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index abdad719f6..398783d5a8 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -116,8 +116,26 @@ def load_schema(self): self.schema = json.load(fh) self.schema_defaults = {} self.schema_params = {} + if "$schema" not in self.schema: + raise AssertionError("Schema missing top-level `$schema` attribute") + self.schema_draft = self.schema["$schema"] + self.defs_notation = self.get_defs_notation() log.debug(f"JSON file loaded: {self.schema_filename}") + def get_defs_notation(self, schema=None): + if schema is None: + schema = self.schema + + if "$defs" in schema: + defs_notation = "$defs" + elif "definitions" in schema: + defs_notation = "definitions" + elif "defs" in schema: + # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0 + # this line prevents the breakage of schemas created for v2.0.0 + defs_notation = "defs" + return defs_notation + def sanitise_param_default(self, param): """ Given a param, ensure that the default value is the correct variable type @@ -168,10 +186,11 @@ def get_schema_defaults(self) -> None: if param["default"] is not None: self.schema_defaults[p_key] = param["default"] + # TODO add support for nested parameters # Grouped schema properties in subschema definitions - for defn_name, definition in self.schema.get("definitions", {}).items(): + for defn_name, definition in self.schema.get(self.defs_notation, {}).items(): for p_key, param in definition.get("properties", {}).items(): - self.schema_params[p_key] = ("definitions", defn_name, "properties", p_key) + self.schema_params[p_key] = (self.defs_notation, defn_name, "properties", p_key) if "default" in param: param = self.sanitise_param_default(param) if param["default"] is not None: @@ -248,13 +267,14 @@ def validate_default_params(self): if self.schema is None: log.error("[red][✗] Pipeline schema not found") try: + # TODO add support for nested parameters # Make copy of schema and remove required flags schema_no_required = copy.deepcopy(self.schema) if "required" in schema_no_required: schema_no_required.pop("required") - for group_key, group in schema_no_required.get("definitions", {}).items(): + for group_key, group in schema_no_required.get(self.defs_notation, {}).items(): if "required" in group: - schema_no_required["definitions"][group_key].pop("required") + schema_no_required[self.defs_notation][group_key].pop("required") jsonschema.validate(self.schema_defaults, schema_no_required) except jsonschema.exceptions.ValidationError as e: raise AssertionError(f"Default parameters are invalid: {e.message}") @@ -360,6 +380,8 @@ def validate_schema(self, schema=None): if schema is None: schema = self.schema + if "$schema" not in schema: + raise AssertionError("Schema missing top-level `$schema` attribute") schema_draft = schema["$schema"] if schema_draft == "https://json-schema.org/draft-07/schema": try: @@ -374,25 +396,14 @@ def validate_schema(self, schema=None): except jsonschema.exceptions.SchemaError as e: raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}") else: - raise AssertionError(f"Unsupported JSON schema draft detected: ${schema_draft}. Use draft 7 or 2020-12 instead.") + raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`") param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) schema_defs = dict() - defs_notation = "" - if "$defs" in schema: - schema_defs = schema.get("$defs", {}).items() - defs_notation = "$defs" - elif "definitions" in schema: - schema_defs = schema.get("definitions", {}).items() - defs_notation = "definitions" - elif "defs" in schema: - # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0 - # this line prevents the breakage of schemas created for v2.0.0 - schema_defs = schema.get("defs", {}).items() - defs_notation = "defs" + defs_notation = self.get_defs_notation(schema) - for d_key, d_schema in schema_defs: + for d_key, d_schema in schema.get(defs_notation, {}).items(): # Check that this definition is mentioned in allOf if "allOf" not in schema: raise AssertionError("Schema has definitions, but no allOf key") @@ -428,7 +439,7 @@ def validate_schema(self, schema=None): def validate_schema_title_description(self, schema=None): """ Extra validation command for linting. - Checks that the schema "$id", "title" and "description" attributes match the piipeline config. + Checks that the schema "$id", "title" and "description" attributes match the pipeline config. """ if schema is None: schema = self.schema @@ -436,12 +447,6 @@ def validate_schema_title_description(self, schema=None): log.debug("Pipeline schema not set - skipping validation of top-level attributes") return None - if "$schema" not in self.schema: - raise AssertionError("Schema missing top-level `$schema` attribute") - schema_attr = "http://json-schema.org/draft-07/schema" - if self.schema["$schema"] != schema_attr: - raise AssertionError(f"Schema `$schema` should be `{schema_attr}`\n Found `{self.schema['$schema']}`") - if self.pipeline_manifest == {}: self.get_wf_params() From 6ecde202d05baa2944f582f0b0835ea73765006b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 16:11:47 +0200 Subject: [PATCH 336/574] fix draft 7 schema using http --- nf_core/pipelines/schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 398783d5a8..e1931b9007 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -383,7 +383,7 @@ def validate_schema(self, schema=None): if "$schema" not in schema: raise AssertionError("Schema missing top-level `$schema` attribute") schema_draft = schema["$schema"] - if schema_draft == "https://json-schema.org/draft-07/schema": + if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema": try: jsonschema.Draft7Validator.check_schema(schema) log.debug("JSON Schema Draft7 validated") From 36fad24c7eda672fce4a885fe2e7d5610b022a9c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 16:18:08 +0200 Subject: [PATCH 337/574] ruff --- nf_core/pipelines/schema.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index e1931b9007..188861fff1 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -400,7 +400,6 @@ def validate_schema(self, schema=None): param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) - schema_defs = dict() defs_notation = self.get_defs_notation(schema) for d_key, d_schema in schema.get(defs_notation, {}).items(): @@ -424,11 +423,11 @@ def validate_schema(self, schema=None): # Check that everything in allOf exists for allOf in schema.get("allOf", []): - _, allOf_defs_notation, def_key = allOf["$ref"].split("/") # "#//" - if allOf_defs_notation not in schema: - raise AssertionError(f"Schema has allOf, but no {allOf_defs_notation}") - if def_key not in schema.get(allOf_defs_notation, {}): - raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allOf_defs_notation}`") + _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#//" + if allof_defs_notation not in schema: + raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}") + if def_key not in schema.get(allof_defs_notation, {}): + raise AssertionError(f"Subschema `{def_key}` found in `allOf` but not `{allof_defs_notation}`") # Check that the schema describes at least one parameter if num_params == 0: From 6777694b20726f333dd8eae416917c3324c3e158 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 16:33:00 +0200 Subject: [PATCH 338/574] fix tests + add draft 2020-12 as default draft --- nf_core/pipelines/schema.py | 2 ++ tests/pipelines/test_schema.py | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 188861fff1..1555a4198d 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -46,6 +46,8 @@ def __init__(self): self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder" self.web_schema_build_web_url = None self.web_schema_build_api_url = None + self.schema_draft = "https://json-schema.org/draft/2020-12/schema" + self.defs_notation = "$defs" def get_schema_path( self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None diff --git a/tests/pipelines/test_schema.py b/tests/pipelines/test_schema.py index 633de3db69..777d959e66 100644 --- a/tests/pipelines/test_schema.py +++ b/tests/pipelines/test_schema.py @@ -175,6 +175,7 @@ def test_validate_schema_fail_duplicate_ids(self): Check that the schema validation fails when we have duplicate IDs in definition subschema """ self.schema_obj.schema = { + "$schema": "http://json-schema.org/draft-07/schema", "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"foo": {}}}}, "allOf": [{"$ref": "#/definitions/groupOne"}, {"$ref": "#/definitions/groupTwo"}], } @@ -187,18 +188,20 @@ def test_validate_schema_fail_missing_def(self): Check that the schema validation fails when we a definition in allOf is not in definitions """ self.schema_obj.schema = { + "$schema": "http://json-schema.org/draft-07/schema", "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}}, "allOf": [{"$ref": "#/definitions/groupOne"}], } with pytest.raises(AssertionError) as exc_info: self.schema_obj.validate_schema(self.schema_obj.schema) - assert exc_info.value.args[0] == "Definition subschema `groupTwo` not included in schema `allOf`" + assert exc_info.value.args[0] == "Definition subschema `#/definitions/groupTwo` not included in schema `allOf`" def test_validate_schema_fail_unexpected_allof(self): """ Check that the schema validation fails when we an unrecognised definition is in allOf """ self.schema_obj.schema = { + "$schema": "http://json-schema.org/draft-07/schema", "definitions": {"groupOne": {"properties": {"foo": {}}}, "groupTwo": {"properties": {"bar": {}}}}, "allOf": [ {"$ref": "#/definitions/groupOne"}, From 0dfd15ded935054fc8d185b5fd36223505441ff7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 16:34:01 +0200 Subject: [PATCH 339/574] fix typo --- nf_core/pipelines/schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 1555a4198d..ba5af51f96 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -413,7 +413,7 @@ def validate_schema(self, schema=None): if allOf["$ref"] == f"#/{defs_notation}/{d_key}": in_allOf = True if not in_allOf: - raise AssertionError(f"Definition subschema `#{defs_notation}/{d_key}` not included in schema `allOf`") + raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`") # TODO add support for nested parameters for d_param_id in d_schema.get("properties", {}): From 7f29f373a82ed1ada16b6b493f10d724a4b879cc Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 16:37:06 +0200 Subject: [PATCH 340/574] ruff --- nf_core/pipelines/schema.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index ba5af51f96..43058d4e6f 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -119,7 +119,7 @@ def load_schema(self): self.schema_defaults = {} self.schema_params = {} if "$schema" not in self.schema: - raise AssertionError("Schema missing top-level `$schema` attribute") + raise AssertionError("Schema missing top-level `$schema` attribute") self.schema_draft = self.schema["$schema"] self.defs_notation = self.get_defs_notation() log.debug(f"JSON file loaded: {self.schema_filename}") @@ -385,7 +385,10 @@ def validate_schema(self, schema=None): if "$schema" not in schema: raise AssertionError("Schema missing top-level `$schema` attribute") schema_draft = schema["$schema"] - if schema_draft == "https://json-schema.org/draft-07/schema" or schema_draft == "http://json-schema.org/draft-07/schema": + if ( + schema_draft == "https://json-schema.org/draft-07/schema" + or schema_draft == "http://json-schema.org/draft-07/schema" + ): try: jsonschema.Draft7Validator.check_schema(schema) log.debug("JSON Schema Draft7 validated") @@ -398,7 +401,9 @@ def validate_schema(self, schema=None): except jsonschema.exceptions.SchemaError as e: raise AssertionError(f"Schema does not validate as Draft 2020-12 JSON Schema:\n {e}") else: - raise AssertionError(f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`") + raise AssertionError( + f"Schema `$schema` should be `https://json-schema.org/draft/2020-12/schema` or `https://json-schema.org/draft-07/schema` \n Found `{schema_draft}`" + ) param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) @@ -425,7 +430,7 @@ def validate_schema(self, schema=None): # Check that everything in allOf exists for allOf in schema.get("allOf", []): - _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#//" + _, allof_defs_notation, def_key = allOf["$ref"].split("/") # "#//" if allof_defs_notation not in schema: raise AssertionError(f"Schema has allOf, but no {allof_defs_notation}") if def_key not in schema.get(allof_defs_notation, {}): From 730c6779779d4e14512df25c043eb02efe6d1659 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 17:34:53 +0200 Subject: [PATCH 341/574] add checks for nf-validation and nf-schema plugin config --- nf_core/pipelines/lint/nextflow_config.py | 33 +++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 96323af94d..8fe933d102 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -336,6 +336,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ) # Check for the availability of the "test" configuration profile by parsing nextflow.config + # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions with open(Path(self.wf_path, "nextflow.config")) as f: content = f.read() @@ -363,6 +364,38 @@ def nextflow_config(self) -> Dict[str, List[str]]: else: failed.append("nextflow.config does not contain configuration profile `test`") + match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE) + if not match_plugins: + failed.append( + "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required" + ) + else: + found_plugins = {} + for line in match_plugins.group(1).split("\n"): + cleaned_line = line.split("//")[0].strip().replace("\"", "'") + if "id" not in line: continue + match_line = re.search(r"\bid\s'([^']+)'", cleaned_line) + if not match_line: + failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}") + continue + plugin = match_line.group(1) + name = plugin.split("@")[0] + version = "" + if "@" in plugin: + version = plugin.split("@")[1] + found_plugins[name] = version + + if len(found_plugins) == 0: + failed.append("nextflow.config contains an empty plugins scope") + elif "nf-validation" in found_plugins and "nf-schema" in found_plugins: + failed.append("nextflow.config contains both nf-validation and nf-schema") + elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "": + failed.append("nextflow.config contains an unpinned version of nf-validation") + elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "": + failed.append("nextflow.config contains an unpinned version of nf-schema") + elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: + failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") + # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json ignore_defaults = [] for item in ignore_configs: From 7fbbff7a412c64ef67417dd60a722d67f6d37647 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 14 Aug 2024 17:39:10 +0200 Subject: [PATCH 342/574] linting fully works now! --- nf_core/pipelines/lint/schema_description.py | 5 +++-- nf_core/pipelines/schema.py | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/nf_core/pipelines/lint/schema_description.py b/nf_core/pipelines/lint/schema_description.py index d617e40949..b586cc5242 100644 --- a/nf_core/pipelines/lint/schema_description.py +++ b/nf_core/pipelines/lint/schema_description.py @@ -36,8 +36,9 @@ def schema_description(self): warned.append(f"Ungrouped param in schema: `{up}`") # Iterate over groups and add warning for parameters without a description - for group_key in self.schema_obj.schema["definitions"].keys(): - group = self.schema_obj.schema["definitions"][group_key] + defs_notation = self.schema_obj.defs_notation + for group_key in self.schema_obj.schema[defs_notation].keys(): + group = self.schema_obj.schema[defs_notation][group_key] for param_key, param in group["properties"].items(): if param_key in ignore_params: ignored.append(f"Ignoring description check for param in schema: `{param_key}`") diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 43058d4e6f..c70332beb2 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -203,7 +203,7 @@ def get_schema_types(self) -> None: for name, param in self.schema.get("properties", {}).items(): if "type" in param: self.schema_types[name] = param["type"] - for _, definition in self.schema.get("definitions", {}).items(): + for _, definition in self.schema.get(self.defs_notation, {}).items(): for name, param in definition.get("properties", {}).items(): if "type" in param: self.schema_types[name] = param["type"] From 1c69f9d84e5c342a54ed733c4497de53ee8c1cea Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 15 Aug 2024 15:37:21 +0200 Subject: [PATCH 343/574] Add a verbose click option --- nf_core/__main__.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 153b8b7e75..7da60180cd 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1136,6 +1136,13 @@ def command_modules_create( @modules.command("test") @click.pass_context @click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.option( + "-v", + "--verbose", + is_flag=True, + default=False, + help="Print verbose output to the console.", +) @click.option( "-d", "--dir", @@ -1171,11 +1178,11 @@ def command_modules_create( default=False, help="Migrate a module with pytest tests to nf-test", ) -def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest): +def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose): """ Run nf-test for a module. """ - modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest) + modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose) # nf-core modules lint From 9f6c1f4710ee10d094b0b9b1e011c891d62e5b8c Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 15 Aug 2024 16:44:24 +0200 Subject: [PATCH 344/574] Overwrite the verbose in ctx in case the user uses it --- nf_core/__main__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 7da60180cd..64956e5f3f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1182,7 +1182,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile """ Run nf-test for a module. """ - modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose) + ctx.obj['verbose'] = verbose + modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest) # nf-core modules lint From 7d873b5a456e6a13f77c4a8a6ff8f947b5eafc04 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 15 Aug 2024 16:44:46 +0200 Subject: [PATCH 345/574] Overwrite the verbose in ctx in case the user uses it --- nf_core/__main__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 64956e5f3f..3b56bda66c 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1182,7 +1182,8 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile """ Run nf-test for a module. """ - ctx.obj['verbose'] = verbose + if verbose: + ctx.obj['verbose'] = verbose modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest) From 22a18a4273bd4db1c2343a90742c1b5b9a3b62eb Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 15 Aug 2024 16:48:05 +0200 Subject: [PATCH 346/574] add matthias' suggestion woops --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 3b56bda66c..23930ccd3c 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1141,7 +1141,7 @@ def command_modules_create( "--verbose", is_flag=True, default=False, - help="Print verbose output to the console.", + help="Print verbose output to the console. Sets `--debug` inside the nf-test command.", ) @click.option( "-d", From 7aead16a057bc0e30344aec26d4e12d9512bfa11 Mon Sep 17 00:00:00 2001 From: laurencekuhl Date: Thu, 15 Aug 2024 17:26:25 +0200 Subject: [PATCH 347/574] Ran pre commit --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 23930ccd3c..0efea13ec9 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1183,7 +1183,7 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile Run nf-test for a module. """ if verbose: - ctx.obj['verbose'] = verbose + ctx.obj["verbose"] = verbose modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest) From e5714d3cccdfce236c6c3ee3878282761d598be2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 04:56:51 +0000 Subject: [PATCH 348/574] Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 815e980270..4f08d8419d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.6 + rev: v0.6.0 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 5da0e06d4f7b55e1ec8851c85380b36dbad7919e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 16 Aug 2024 04:57:40 +0000 Subject: [PATCH 349/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc78a1628a..ddc346b9dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -69,6 +69,7 @@ - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 85461c5e47c7527e4879513e90c7150b19bb9013 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 16 Aug 2024 15:34:04 +0000 Subject: [PATCH 350/574] Update python:3.12-slim Docker digest to 59c7332 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c88abcb1ce..fb1a867937 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:740d94a19218c8dd584b92f804b1158f85b0d241e5215ea26ed2dcade2b9d138 +FROM python:3.12-slim@sha256:59c7332a4a24373861c4a5f0eec2c92b87e3efeb8ddef011744ef9a751b1d11c LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 129858342d0529ef59f1f04f7da0332fec038a1a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Sat, 17 Aug 2024 16:36:57 +0000 Subject: [PATCH 351/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddc346b9dc..0a450a6728 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -70,6 +70,7 @@ - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) +- Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 0838d6bb040b8218493fad13c5fc33fa355b84af Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 19 Aug 2024 14:58:27 +0200 Subject: [PATCH 352/574] warning for nf-validation --- nf_core/pipelines/lint/nextflow_config.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 8fe933d102..84bb492cb0 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -396,6 +396,9 @@ def nextflow_config(self) -> Dict[str, List[str]]: elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") + if "nf-validation" in found_plugins: + warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") + # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json ignore_defaults = [] for item in ignore_configs: From 8559c2d6a18624c5096957e6a941011c8725e580 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 19 Aug 2024 16:54:38 +0200 Subject: [PATCH 353/574] fetch plugin on schema filename setting --- nf_core/pipelines/lint/nextflow_config.py | 1 + nf_core/pipelines/schema.py | 81 +++++++++++++++-------- 2 files changed, 54 insertions(+), 28 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 84bb492cb0..a5b7cf325f 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -364,6 +364,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: else: failed.append("nextflow.config does not contain configuration profile `test`") + # Lint for nf-validation and nf-schema match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE) if not match_plugins: failed.append( diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index c70332beb2..77f421724e 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -5,6 +5,7 @@ import logging import tempfile import webbrowser +import re from pathlib import Path from typing import Union @@ -32,7 +33,7 @@ def __init__(self): self.schema = {} self.pipeline_dir = "" - self.schema_filename = "" + self._schema_filename = "" self.schema_defaults = {} self.schema_types = {} self.schema_params = {} @@ -46,8 +47,46 @@ def __init__(self): self.web_schema_build_url = "https://nf-co.re/pipeline_schema_builder" self.web_schema_build_web_url = None self.web_schema_build_api_url = None - self.schema_draft = "https://json-schema.org/draft/2020-12/schema" - self.defs_notation = "$defs" + self.validation_plugin = None + self.schema_draft = None + self.defs_notation = None + + # Update the validation plugin code everytime the schema gets changed + def set_schema_filename(self, schema: str) -> None: + self._schema_filename = schema + basepath = "/".join(str(schema).split("/")[:-1]) + config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config" + self._update_validation_plugin_from_config(config) + + def get_schema_filename(self) -> str: + return self._schema_filename + + def del_schema_filename(self) -> None: + del self._schema_filename + + schema_filename = property(get_schema_filename, set_schema_filename, del_schema_filename) + + def _update_validation_plugin_from_config(self, config: str) -> None: + plugin = "nf-schema" + with open(Path(config)) as conf: + nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE) + nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE) + config_content = conf.read() + if re.search(nf_validation_pattern, config_content): + plugin = "nf-validation" + elif re.search(nf_schema_pattern, config_content): + plugin = "nf-schema" + else: + log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema") + + self.validation_plugin = plugin + # Previous versions of nf-schema used "defs", but it's advised to use "$defs" + if plugin == "nf-schema": + self.defs_notation = "$defs" + self.schema_draft = "https://json-schema.org/draft/2020-12/schema" + else: + self.defs_notation = "definitions" + self.schema_draft = "https://json-schema.org/draft-07/schema" def get_schema_path( self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None @@ -120,24 +159,8 @@ def load_schema(self): self.schema_params = {} if "$schema" not in self.schema: raise AssertionError("Schema missing top-level `$schema` attribute") - self.schema_draft = self.schema["$schema"] - self.defs_notation = self.get_defs_notation() log.debug(f"JSON file loaded: {self.schema_filename}") - def get_defs_notation(self, schema=None): - if schema is None: - schema = self.schema - - if "$defs" in schema: - defs_notation = "$defs" - elif "definitions" in schema: - defs_notation = "definitions" - elif "defs" in schema: - # nf-schema v2.0.0 only supported defs. this has been changed to $defs in nf-schema v2.1.0 - # this line prevents the breakage of schemas created for v2.0.0 - defs_notation = "defs" - return defs_notation - def sanitise_param_default(self, param): """ Given a param, ensure that the default value is the correct variable type @@ -385,16 +408,15 @@ def validate_schema(self, schema=None): if "$schema" not in schema: raise AssertionError("Schema missing top-level `$schema` attribute") schema_draft = schema["$schema"] - if ( - schema_draft == "https://json-schema.org/draft-07/schema" - or schema_draft == "http://json-schema.org/draft-07/schema" - ): + if self.schema_draft != schema_draft: + raise AssertionError(f"Schema is using the wrong draft: {schema_draft}, should be {self.schema_draft}") + if self.schema_draft == "https://json-schema.org/draft-07/schema": try: jsonschema.Draft7Validator.check_schema(schema) log.debug("JSON Schema Draft7 validated") except jsonschema.exceptions.SchemaError as e: raise AssertionError(f"Schema does not validate as Draft 7 JSON Schema:\n {e}") - elif schema_draft == "https://json-schema.org/draft/2020-12/schema": + elif self.schema_draft == "https://json-schema.org/draft/2020-12/schema": try: jsonschema.Draft202012Validator.check_schema(schema) log.debug("JSON Schema Draft2020-12 validated") @@ -407,18 +429,21 @@ def validate_schema(self, schema=None): param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) - defs_notation = self.get_defs_notation(schema) - for d_key, d_schema in schema.get(defs_notation, {}).items(): + print(self.defs_notation) + + for d_key, d_schema in schema.get(self.defs_notation, {}).items(): + print(d_key) + print(d_schema) # Check that this definition is mentioned in allOf if "allOf" not in schema: raise AssertionError("Schema has definitions, but no allOf key") in_allOf = False for allOf in schema.get("allOf", []): - if allOf["$ref"] == f"#/{defs_notation}/{d_key}": + if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}": in_allOf = True if not in_allOf: - raise AssertionError(f"Definition subschema `#/{defs_notation}/{d_key}` not included in schema `allOf`") + raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`") # TODO add support for nested parameters for d_param_id in d_schema.get("properties", {}): From 0296f7d8fa6c5cc7a8dac62b450a8babcd77bab7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 19 Aug 2024 17:00:33 +0200 Subject: [PATCH 354/574] add a check for defs usage instead of $defs --- nf_core/pipelines/schema.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 77f421724e..9c65f34fde 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -430,11 +430,11 @@ def validate_schema(self, schema=None): param_keys = list(schema.get("properties", {}).keys()) num_params = len(param_keys) - print(self.defs_notation) + # Add a small check for older nf-schema JSON schemas + if "defs" in schema: + raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead') for d_key, d_schema in schema.get(self.defs_notation, {}).items(): - print(d_key) - print(d_schema) # Check that this definition is mentioned in allOf if "allOf" not in schema: raise AssertionError("Schema has definitions, but no allOf key") From 0b8d04f89eb7f348bce87cc93f04d983e48e218f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 19 Aug 2024 17:16:31 +0200 Subject: [PATCH 355/574] change all definitions to self.defs_notation --- nf_core/pipelines/schema.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 9c65f34fde..9db9457516 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -235,7 +235,7 @@ def save_schema(self, suppress_logging=False): """Save a pipeline schema to a file""" # Write results to a JSON file num_params = len(self.schema.get("properties", {})) - num_params += sum(len(d.get("properties", {})) for d in self.schema.get("definitions", {}).values()) + num_params += sum(len(d.get("properties", {})) for d in self.schema.get(self.defs_notation, {}).values()) if not suppress_logging: log.info(f"Writing schema with {num_params} params: '{self.schema_filename}'") dump_json_with_prettier(self.schema_filename, self.schema) @@ -321,7 +321,7 @@ def validate_default_params(self): params_ignore = [] # Go over group keys - for group_key, group in schema_no_required.get("definitions", {}).items(): + for group_key, group in schema_no_required.get(self.defs_notation, {}).items(): group_properties = group.get("properties") for param in group_properties: if param in params_ignore: @@ -527,9 +527,9 @@ def check_for_input_mimetype(self): if "input" not in self.schema_params: raise LookupError("Parameter `input` not found in schema") # Check that the input parameter is defined in the right place - if "input" not in self.schema.get("definitions", {}).get("input_output_options", {}).get("properties", {}): + if "input" not in self.schema.get(self.defs_notation, {}).get("input_output_options", {}).get("properties", {}): raise LookupError("Parameter `input` is not defined in the correct subschema (input_output_options)") - input_entry = self.schema["definitions"]["input_output_options"]["properties"]["input"] + input_entry = self.schema[self.defs_notation]["input_output_options"]["properties"]["input"] if "mimetype" not in input_entry: return None mimetype = input_entry["mimetype"] @@ -581,7 +581,7 @@ def schema_to_markdown(self, columns): out = f"# {self.schema['title']}\n\n" out += f"{self.schema['description']}\n" # Grouped parameters - for definition in self.schema.get("definitions", {}).values(): + for definition in self.schema.get(self.defs_notation, {}).values(): out += f"\n## {definition.get('title', {})}\n\n" out += f"{definition.get('description', '')}\n\n" required = definition.get("required", []) @@ -763,15 +763,15 @@ def remove_schema_empty_definitions(self): """ # Identify and remove empty definitions from the schema empty_definitions = [] - for d_key, d_schema in list(self.schema.get("definitions", {}).items()): + for d_key, d_schema in list(self.schema.get(self.defs_notation, {}).items()): if not d_schema.get("properties"): - del self.schema["definitions"][d_key] + del self.schema[self.defs_notation][d_key] empty_definitions.append(d_key) log.warning(f"Removing empty group: '{d_key}'") # Remove "allOf" group with empty definitions from the schema for d_key in empty_definitions: - allOf = {"$ref": f"#/definitions/{d_key}"} + allOf = {"$ref": f"#/{self.defs_notation}/{d_key}"} if allOf in self.schema.get("allOf", []): self.schema["allOf"].remove(allOf) @@ -780,8 +780,8 @@ def remove_schema_empty_definitions(self): del self.schema["allOf"] # If we don't have anything left in "definitions", remove it - if self.schema.get("definitions") == {}: - del self.schema["definitions"] + if self.schema.get(self.defs_notation) == {}: + del self.schema[self.defs_notation] def remove_schema_notfound_configs(self): """ @@ -791,9 +791,9 @@ def remove_schema_notfound_configs(self): # Top-level properties self.schema, params_removed = self.remove_schema_notfound_configs_single_schema(self.schema) # Sub-schemas in definitions - for d_key, definition in self.schema.get("definitions", {}).items(): + for d_key, definition in self.schema.get(self.defs_notation, {}).items(): cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition) - self.schema["definitions"][d_key] = cleaned_schema + self.schema[self.defs_notation][d_key] = cleaned_schema params_removed.extend(p_removed) return params_removed From 544381310c6e5ac57664524f63105441246c34fd Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 19 Aug 2024 18:33:52 +0200 Subject: [PATCH 356/574] migrate template part 1 --- nf_core/pipeline-template/conf/colors.config | 61 ++++++++ nf_core/pipeline-template/nextflow.config | 44 ++++-- .../pipeline-template/nextflow_schema.json | 55 +++---- .../utils_nfcore_pipeline_pipeline/main.nf | 17 +- .../nf-core/utils_nfcore_pipeline/main.nf | 46 ------ .../nf-core/utils_nfvalidation_plugin/main.nf | 25 +-- .../tests/main.nf.test | 145 +----------------- .../tests/nextflow.config | 1 + .../pipeline-template/workflows/pipeline.nf | 2 +- 9 files changed, 130 insertions(+), 266 deletions(-) create mode 100644 nf_core/pipeline-template/conf/colors.config create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config new file mode 100644 index 0000000000..00f2963267 --- /dev/null +++ b/nf_core/pipeline-template/conf/colors.config @@ -0,0 +1,61 @@ +// For now, there is no easy way to set monochromeLogs +colors { + // Reset / Meta + reset = "\033[0m" + bold = "\033[1m" + dim = "\033[2m" + underlined = "\033[4m" + blink = "\033[5m" + reverse = "\033[7m" + hidden = "\033[8m" + + // Regular Colors + black = "\033[0;30m" + red = "\033[0;31m" + green = "\033[0;32m" + yellow = "\033[0;33m" + blue = "\033[0;34m" + purple = "\033[0;35m" + cyan = "\033[0;36m" + white = "\033[0;37m" + + // Bold + bblack = "\033[1;30m" + bred = "\033[1;31m" + bgreen = "\033[1;32m" + byellow = "\033[1;33m" + bblue = "\033[1;34m" + bpurple = "\033[1;35m" + bcyan = "\033[1;36m" + bwhite = "\033[1;37m" + + // Underline + ublack = "\033[4;30m" + ured = "\033[4;31m" + ugreen = "\033[4;32m" + uyellow = "\033[4;33m" + ublue = "\033[4;34m" + upurple = "\033[4;35m" + ucyan = "\033[4;36m" + uwhite = "\033[4;37m" + + // High Intensity + iblack = "\033[0;90m" + ired = "\033[0;91m" + igreen = "\033[0;92m" + iyellow = "\033[0;93m" + iblue = "\033[0;94m" + ipurple = "\033[0;95m" + icyan = "\033[0;96m" + iwhite = "\033[0;97m" + + // Bold High Intensity + biblack = "\033[1;90m" + bired = "\033[1;91m" + bigreen = "\033[1;92m" + biyellow = "\033[1;93m" + biblue = "\033[1;94m" + bipurple = "\033[1;95m" + bicyan = "\033[1;96m" + biwhite = "\033[1;97m" +} \ No newline at end of file diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 0469d6cfec..3d3841ba49 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -38,6 +38,8 @@ params { monochrome_logs = false hook_url = null help = false + helpFull = false + showHidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' @@ -59,10 +61,6 @@ params { max_time = '240.h' // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false validate_params = true } @@ -200,11 +198,6 @@ podman.registry = 'quay.io' singularity.registry = 'quay.io' charliecloud.registry = 'quay.io' -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} - {% if igenomes -%} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -267,6 +260,39 @@ manifest { doi = '' } +// Nextflow plugins +plugins { + id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +includeConfig "conf/colors.config" + +validation { + parametersSchema = "${projectDir}/nextflow_schema.json" + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + beforeText = """ +-${colors.dim}----------------------------------------------------${colors.reset}- + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} +${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} +${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} +${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} +${colors.purple} ${manifest.name} ${manifest.version}${colors.reset} +-${colors.dim}----------------------------------------------------${colors.reset}- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } +} + + // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 4a1a22c3ee..14120bbabc 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/{{ name }}/master/nextflow_schema.json", "title": "{{ name }} pipeline parameters", "description": "{{ description }}", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -73,6 +73,20 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" + }, + "genomes": { + "type": "object", + "description": "An object containing all reference data availabe in igenomes", + "fa_icon": "fas fa-ban", + "hidden": true } } }, @@ -169,12 +183,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -253,27 +261,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -286,19 +273,19 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, {% if igenomes %}{ - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/reference_genome_options" },{% endif %} {% if nf_core_configs %}{ - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/institutional_config_options" },{% endif %} { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/max_job_request_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 72c9be85eb..c83d2ae0cb 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -9,8 +9,8 @@ */ include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' @@ -30,7 +30,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -54,16 +53,8 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, - validate_params, - "nextflow_schema.json" + validate_params ) // @@ -84,7 +75,7 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c3927..a5dcd5f83d 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -61,25 +61,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -157,33 +138,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf index 2585b65d1b..453894a64a 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -8,9 +8,8 @@ ======================================================================================== */ -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' /* ======================================================================================== @@ -21,12 +20,7 @@ include { validateParameters } from 'plugin/nf-validation' workflow UTILS_NFVALIDATION_PLUGIN { take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value main: @@ -37,24 +31,11 @@ workflow UTILS_NFVALIDATION_PLUGIN { post_help_text = post_help_text ?: '' workflow_command = workflow_command ?: '' - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - // // Validate parameters relative to the parameter JSON schema // if (validate_params){ - validateParameters(parameters_schema: schema_filename) + validateParameters() } emit: diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 5784a33f2f..354b817545 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -10,30 +10,21 @@ nextflow_workflow { tag "utils_nfvalidation_plugin" tag "subworkflows/utils_nfvalidation_plugin" + config "./nextflow.config" + test("Should run nothing") { when { params { - monochrome_logs = true test_data = '' } workflow { """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename + input[0] = validate_params """ } } @@ -45,147 +36,19 @@ nextflow_workflow { } } - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - test("Should validate params") { when { params { - monochrome_logs = true test_data = '' outdir = 1 } workflow { """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename + input[0] = validate_params """ } } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config new file mode 100644 index 0000000000..8d047ed59e --- /dev/null +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config @@ -0,0 +1 @@ +validation.monochromeLogs = true \ No newline at end of file diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index d98c392f0c..4bb0913211 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -6,7 +6,7 @@ include { FASTQC } from '../modules/nf-core/fastqc/main' {% if multiqc %}include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endif %} -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' {% if multiqc %}include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %} include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} From 7931c7f658712e15d522531616c3e001849e338b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 12:43:06 +0200 Subject: [PATCH 357/574] add option to exclude license from pipeline template --- nf_core/pipelines/create/templatefeatures.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index b97bf347ab..dc3f072710 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -242,3 +242,18 @@ changelog: - "CHANGELOG.md" nfcore_pipelines: False custom_pipelines: True +license: + skippable_paths: + - "LICENSE" + short_description: "Add a license" + description: "Add the MIT license file." + help_text: | + To protect the copyright of the pipeline, you can add a LICENSE file. + This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT + linting: + files_exist: + - "LICENSE" + files_unchanged: + - "LICENSE" + nfcore_pipelines: False + custom_pipelines: True From 6ff0929c0956b148839c231133b440f5f0cd876a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Aug 2024 10:46:47 +0000 Subject: [PATCH 358/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a450a6728..b530f597bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) +- add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) ### Linting From 78d469fd893a6e1c45aa59330378f213a994fdbf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 20 Aug 2024 12:56:04 +0200 Subject: [PATCH 359/574] Update nf_core/pipelines/create/templatefeatures.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/templatefeatures.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index dc3f072710..a8a6ce5656 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -245,7 +245,7 @@ changelog: license: skippable_paths: - "LICENSE" - short_description: "Add a license" + short_description: "Add a license File" description: "Add the MIT license file." help_text: | To protect the copyright of the pipeline, you can add a LICENSE file. From 34565c1e12ce20cda823e4e92eed6c084501821f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 13:00:04 +0200 Subject: [PATCH 360/574] update textual snapshots --- .../__snapshots__/test_create_app.ambr | 512 +++++++++--------- 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index f4eb255087..66c08faba0 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-3220763577-matrix { + .terminal-2278814444-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3220763577-title { + .terminal-2278814444-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3220763577-r1 { fill: #c5c8c6 } - .terminal-3220763577-r2 { fill: #e3e3e3 } - .terminal-3220763577-r3 { fill: #989898 } - .terminal-3220763577-r4 { fill: #e1e1e1 } - .terminal-3220763577-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3220763577-r6 { fill: #1e1e1e } - .terminal-3220763577-r7 { fill: #507bb3 } - .terminal-3220763577-r8 { fill: #e2e2e2 } - .terminal-3220763577-r9 { fill: #808080 } - .terminal-3220763577-r10 { fill: #dde6ed;font-weight: bold } - .terminal-3220763577-r11 { fill: #001541 } - .terminal-3220763577-r12 { fill: #0178d4 } - .terminal-3220763577-r13 { fill: #454a50 } - .terminal-3220763577-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-3220763577-r15 { fill: #000000 } - .terminal-3220763577-r16 { fill: #e4e4e4 } - .terminal-3220763577-r17 { fill: #14191f } - .terminal-3220763577-r18 { fill: #7ae998 } - .terminal-3220763577-r19 { fill: #0a180e;font-weight: bold } - .terminal-3220763577-r20 { fill: #008139 } - .terminal-3220763577-r21 { fill: #fea62b;font-weight: bold } - .terminal-3220763577-r22 { fill: #a7a9ab } - .terminal-3220763577-r23 { fill: #e2e3e3 } + .terminal-2278814444-r1 { fill: #c5c8c6 } + .terminal-2278814444-r2 { fill: #e3e3e3 } + .terminal-2278814444-r3 { fill: #989898 } + .terminal-2278814444-r4 { fill: #e1e1e1 } + .terminal-2278814444-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2278814444-r6 { fill: #1e1e1e } + .terminal-2278814444-r7 { fill: #507bb3 } + .terminal-2278814444-r8 { fill: #e2e2e2 } + .terminal-2278814444-r9 { fill: #808080 } + .terminal-2278814444-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2278814444-r11 { fill: #001541 } + .terminal-2278814444-r12 { fill: #0178d4 } + .terminal-2278814444-r13 { fill: #454a50 } + .terminal-2278814444-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-2278814444-r15 { fill: #000000 } + .terminal-2278814444-r16 { fill: #e4e4e4 } + .terminal-2278814444-r17 { fill: #14191f } + .terminal-2278814444-r18 { fill: #7ae998 } + .terminal-2278814444-r19 { fill: #0a180e;font-weight: bold } + .terminal-2278814444-r20 { fill: #008139 } + .terminal-2278814444-r21 { fill: #fea62b;font-weight: bold } + .terminal-2278814444-r22 { fill: #a7a9ab } + .terminal-2278814444-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files.▂▂ - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-537214554-matrix { + .terminal-2282176583-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-537214554-title { + .terminal-2282176583-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-537214554-r1 { fill: #c5c8c6 } - .terminal-537214554-r2 { fill: #e3e3e3 } - .terminal-537214554-r3 { fill: #989898 } - .terminal-537214554-r4 { fill: #e1e1e1 } - .terminal-537214554-r5 { fill: #4ebf71;font-weight: bold } - .terminal-537214554-r6 { fill: #1e1e1e } - .terminal-537214554-r7 { fill: #507bb3 } - .terminal-537214554-r8 { fill: #e2e2e2 } - .terminal-537214554-r9 { fill: #808080 } - .terminal-537214554-r10 { fill: #dde6ed;font-weight: bold } - .terminal-537214554-r11 { fill: #001541 } - .terminal-537214554-r12 { fill: #14191f } - .terminal-537214554-r13 { fill: #454a50 } - .terminal-537214554-r14 { fill: #7ae998 } - .terminal-537214554-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-537214554-r16 { fill: #0a180e;font-weight: bold } - .terminal-537214554-r17 { fill: #000000 } - .terminal-537214554-r18 { fill: #008139 } - .terminal-537214554-r19 { fill: #fea62b;font-weight: bold } - .terminal-537214554-r20 { fill: #a7a9ab } - .terminal-537214554-r21 { fill: #e2e3e3 } + .terminal-2282176583-r1 { fill: #c5c8c6 } + .terminal-2282176583-r2 { fill: #e3e3e3 } + .terminal-2282176583-r3 { fill: #989898 } + .terminal-2282176583-r4 { fill: #e1e1e1 } + .terminal-2282176583-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2282176583-r6 { fill: #1e1e1e } + .terminal-2282176583-r7 { fill: #507bb3 } + .terminal-2282176583-r8 { fill: #e2e2e2 } + .terminal-2282176583-r9 { fill: #808080 } + .terminal-2282176583-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2282176583-r11 { fill: #001541 } + .terminal-2282176583-r12 { fill: #14191f } + .terminal-2282176583-r13 { fill: #454a50 } + .terminal-2282176583-r14 { fill: #7ae998 } + .terminal-2282176583-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-2282176583-r16 { fill: #0a180e;font-weight: bold } + .terminal-2282176583-r17 { fill: #000000 } + .terminal-2282176583-r18 { fill: #008139 } + .terminal-2282176583-r19 { fill: #fea62b;font-weight: bold } + .terminal-2282176583-r20 { fill: #a7a9ab } + .terminal-2282176583-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help ▇▇ - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▇▇ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From ceb78a84c90d7955e903f3ffbfa26000d62557fb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 15:11:26 +0200 Subject: [PATCH 361/574] add option to exclude email from pipeline template --- nf_core/pipeline-template/.editorconfig | 2 + nf_core/pipeline-template/.prettierignore | 2 + nf_core/pipeline-template/docs/output.md | 2 +- nf_core/pipeline-template/main.nf | 4 +- nf_core/pipeline-template/nextflow.config | 2 + .../pipeline-template/nextflow_schema.json | 8 +- .../utils_nfcore_pipeline_pipeline/main.nf | 6 + nf_core/pipelines/create/templatefeatures.yml | 18 + .../__snapshots__/test_create_app.ambr | 510 +++++++++--------- 9 files changed, 293 insertions(+), 261 deletions(-) diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig index 72dda289a0..5efa586109 100644 --- a/nf_core/pipeline-template/.editorconfig +++ b/nf_core/pipeline-template/.editorconfig @@ -25,8 +25,10 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset +{%- if email %} [/assets/email*] indent_size = unset +{%- endif %} # ignore python and markdown [*.{py,md}] diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore index 437d763d0c..3b3d5ff08e 100644 --- a/nf_core/pipeline-template/.prettierignore +++ b/nf_core/pipeline-template/.prettierignore @@ -1,4 +1,6 @@ +{%- if email %} email_template.html +{%- endif %} adaptivecard.json slackreport.json .nextflow* diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index edd48b83f4..76195a6825 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -55,7 +55,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. + {% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %} - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`. diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index fddfc5489e..0cf688a7e9 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -20,7 +20,7 @@ include { {{ short_name|upper }} } from './workflows/{{ short_name }}' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' -{% if igenomes %} +{%- if igenomes %} include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline' /* @@ -95,9 +95,11 @@ workflow { // SUBWORKFLOW: Run completion tasks // PIPELINE_COMPLETION ( + {%- if email %} params.email, params.email_on_fail, params.plaintext_email, + {%- endif %} params.outdir, params.monochrome_logs, params.hook_url, diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 0469d6cfec..daa1c5e369 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -32,9 +32,11 @@ params { // Boilerplate options outdir = null publish_dir_mode = 'copy' + {%- if email %} email = null email_on_fail = null plaintext_email = false + {%- endif %} monochrome_logs = false hook_url = null help = false diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 4a1a22c3ee..4a376330bd 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -28,14 +28,14 @@ "format": "directory-path", "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" - }, + }{% if email %}, "email": { "type": "string", "description": "Email address for completion summary.", "fa_icon": "fas fa-envelope", "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" - }{% if multiqc %}, + }{% endif %}{% if multiqc %}, "multiqc_title": { "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", @@ -189,7 +189,7 @@ "fa_icon": "fas fa-copy", "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true - }, + },{% if email %} "email_on_fail": { "type": "string", "description": "Email address for completion summary, only when pipeline fails.", @@ -203,7 +203,7 @@ "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", "hidden": true - }, + },{% endif %} {%- if multiqc %} "max_multiqc_email_size": { "type": "string", diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 72c9be85eb..62ef73d65d 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -12,7 +12,9 @@ include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plu include { paramsSummaryMap } from 'plugin/nf-validation' include { fromSamplesheet } from 'plugin/nf-validation' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +{%- if email %} include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +{%- endif %} include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' @@ -117,9 +119,11 @@ workflow PIPELINE_INITIALISATION { workflow PIPELINE_COMPLETION { take: + {%- if email %} email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML + {% endif %} outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications @@ -133,6 +137,7 @@ workflow PIPELINE_COMPLETION { // Completion email and summary // workflow.onComplete { + {%- if email %} if (email || email_on_fail) { {%- if multiqc %} completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) @@ -140,6 +145,7 @@ workflow PIPELINE_COMPLETION { completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, []) {%- endif %} } + {%- endif %} completionSummary(monochrome_logs) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index a8a6ce5656..5dafd7e312 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -257,3 +257,21 @@ license: - "LICENSE" nfcore_pipelines: False custom_pipelines: True +email: + skippable_paths: + - "assets/email_template.html" + - "assets/sendmail_template.txt" + - "assets/email_template.txt" + short_description: "Enable email updates" + description: "Enable sending emails on pipeline completion." + help_text: | + Enable the option of sending an email which will include pipeline execution reports on pipeline completion. + linting: + files_exist: + - "assets/email_template.html" + - "assets/sendmail_template.txt" + - "assets/email_template.txt" + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index 66c08faba0..f2a0578474 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2278814444-matrix { + .terminal-2220422576-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2278814444-title { + .terminal-2220422576-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2278814444-r1 { fill: #c5c8c6 } - .terminal-2278814444-r2 { fill: #e3e3e3 } - .terminal-2278814444-r3 { fill: #989898 } - .terminal-2278814444-r4 { fill: #e1e1e1 } - .terminal-2278814444-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2278814444-r6 { fill: #1e1e1e } - .terminal-2278814444-r7 { fill: #507bb3 } - .terminal-2278814444-r8 { fill: #e2e2e2 } - .terminal-2278814444-r9 { fill: #808080 } - .terminal-2278814444-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2278814444-r11 { fill: #001541 } - .terminal-2278814444-r12 { fill: #0178d4 } - .terminal-2278814444-r13 { fill: #454a50 } - .terminal-2278814444-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-2278814444-r15 { fill: #000000 } - .terminal-2278814444-r16 { fill: #e4e4e4 } - .terminal-2278814444-r17 { fill: #14191f } - .terminal-2278814444-r18 { fill: #7ae998 } - .terminal-2278814444-r19 { fill: #0a180e;font-weight: bold } - .terminal-2278814444-r20 { fill: #008139 } - .terminal-2278814444-r21 { fill: #fea62b;font-weight: bold } - .terminal-2278814444-r22 { fill: #a7a9ab } - .terminal-2278814444-r23 { fill: #e2e3e3 } + .terminal-2220422576-r1 { fill: #c5c8c6 } + .terminal-2220422576-r2 { fill: #e3e3e3 } + .terminal-2220422576-r3 { fill: #989898 } + .terminal-2220422576-r4 { fill: #e1e1e1 } + .terminal-2220422576-r5 { fill: #4ebf71;font-weight: bold } + .terminal-2220422576-r6 { fill: #1e1e1e } + .terminal-2220422576-r7 { fill: #507bb3 } + .terminal-2220422576-r8 { fill: #e2e2e2 } + .terminal-2220422576-r9 { fill: #808080 } + .terminal-2220422576-r10 { fill: #dde6ed;font-weight: bold } + .terminal-2220422576-r11 { fill: #001541 } + .terminal-2220422576-r12 { fill: #0178d4 } + .terminal-2220422576-r13 { fill: #454a50 } + .terminal-2220422576-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-2220422576-r15 { fill: #000000 } + .terminal-2220422576-r16 { fill: #e4e4e4 } + .terminal-2220422576-r17 { fill: #14191f } + .terminal-2220422576-r18 { fill: #7ae998 } + .terminal-2220422576-r19 { fill: #0a180e;font-weight: bold } + .terminal-2220422576-r20 { fill: #008139 } + .terminal-2220422576-r21 { fill: #fea62b;font-weight: bold } + .terminal-2220422576-r22 { fill: #a7a9ab } + .terminal-2220422576-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - + - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files. - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common reference ▇▇ + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-2282176583-matrix { + .terminal-1370375189-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2282176583-title { + .terminal-1370375189-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2282176583-r1 { fill: #c5c8c6 } - .terminal-2282176583-r2 { fill: #e3e3e3 } - .terminal-2282176583-r3 { fill: #989898 } - .terminal-2282176583-r4 { fill: #e1e1e1 } - .terminal-2282176583-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2282176583-r6 { fill: #1e1e1e } - .terminal-2282176583-r7 { fill: #507bb3 } - .terminal-2282176583-r8 { fill: #e2e2e2 } - .terminal-2282176583-r9 { fill: #808080 } - .terminal-2282176583-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2282176583-r11 { fill: #001541 } - .terminal-2282176583-r12 { fill: #14191f } - .terminal-2282176583-r13 { fill: #454a50 } - .terminal-2282176583-r14 { fill: #7ae998 } - .terminal-2282176583-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-2282176583-r16 { fill: #0a180e;font-weight: bold } - .terminal-2282176583-r17 { fill: #000000 } - .terminal-2282176583-r18 { fill: #008139 } - .terminal-2282176583-r19 { fill: #fea62b;font-weight: bold } - .terminal-2282176583-r20 { fill: #a7a9ab } - .terminal-2282176583-r21 { fill: #e2e3e3 } + .terminal-1370375189-r1 { fill: #c5c8c6 } + .terminal-1370375189-r2 { fill: #e3e3e3 } + .terminal-1370375189-r3 { fill: #989898 } + .terminal-1370375189-r4 { fill: #e1e1e1 } + .terminal-1370375189-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1370375189-r6 { fill: #1e1e1e } + .terminal-1370375189-r7 { fill: #507bb3 } + .terminal-1370375189-r8 { fill: #e2e2e2 } + .terminal-1370375189-r9 { fill: #808080 } + .terminal-1370375189-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1370375189-r11 { fill: #001541 } + .terminal-1370375189-r12 { fill: #14191f } + .terminal-1370375189-r13 { fill: #454a50 } + .terminal-1370375189-r14 { fill: #7ae998 } + .terminal-1370375189-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1370375189-r16 { fill: #0a180e;font-weight: bold } + .terminal-1370375189-r17 { fill: #000000 } + .terminal-1370375189-r18 { fill: #008139 } + .terminal-1370375189-r19 { fill: #fea62b;font-weight: bold } + .terminal-1370375189-r20 { fill: #a7a9ab } + .terminal-1370375189-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▇▇ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges▁▁ + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 1390a6d5e2bb259c6004a845e212abe2b80ff167 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Aug 2024 13:19:14 +0000 Subject: [PATCH 362/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b530f597bc..98fb925338 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) +- add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) ### Linting From 5519c83d5b582af797ff4ae242fa98113bbe847a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 20 Aug 2024 15:24:51 +0200 Subject: [PATCH 363/574] some small updates for the new release --- nf_core/pipeline-template/conf/colors.config | 61 ------------------- nf_core/pipeline-template/modules.json | 4 +- nf_core/pipeline-template/nextflow.config | 22 ++++--- .../nf-core/utils_nfschema_plugin/main.nf | 32 ++++++++++ .../nf-core/utils_nfschema_plugin/meta.yml | 22 +++++++ .../tests/main.nf.test | 27 ++++---- .../tests/nextflow.config | 8 +++ .../tests/nextflow_schema.json | 8 +-- .../nf-core/utils_nfvalidation_plugin/main.nf | 43 ------------- .../utils_nfvalidation_plugin/meta.yml | 44 ------------- .../tests/nextflow.config | 1 - .../utils_nfvalidation_plugin/tests/tags.yml | 2 - 12 files changed, 93 insertions(+), 181 deletions(-) delete mode 100644 nf_core/pipeline-template/conf/colors.config create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/main.nf.test (62%) create mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename nf_core/pipeline-template/subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config delete mode 100644 nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/nf_core/pipeline-template/conf/colors.config b/nf_core/pipeline-template/conf/colors.config deleted file mode 100644 index 00f2963267..0000000000 --- a/nf_core/pipeline-template/conf/colors.config +++ /dev/null @@ -1,61 +0,0 @@ -// For now, there is no easy way to set monochromeLogs -colors { - // Reset / Meta - reset = "\033[0m" - bold = "\033[1m" - dim = "\033[2m" - underlined = "\033[4m" - blink = "\033[5m" - reverse = "\033[7m" - hidden = "\033[8m" - - // Regular Colors - black = "\033[0;30m" - red = "\033[0;31m" - green = "\033[0;32m" - yellow = "\033[0;33m" - blue = "\033[0;34m" - purple = "\033[0;35m" - cyan = "\033[0;36m" - white = "\033[0;37m" - - // Bold - bblack = "\033[1;30m" - bred = "\033[1;31m" - bgreen = "\033[1;32m" - byellow = "\033[1;33m" - bblue = "\033[1;34m" - bpurple = "\033[1;35m" - bcyan = "\033[1;36m" - bwhite = "\033[1;37m" - - // Underline - ublack = "\033[4;30m" - ured = "\033[4;31m" - ugreen = "\033[4;32m" - uyellow = "\033[4;33m" - ublue = "\033[4;34m" - upurple = "\033[4;35m" - ucyan = "\033[4;36m" - uwhite = "\033[4;37m" - - // High Intensity - iblack = "\033[0;90m" - ired = "\033[0;91m" - igreen = "\033[0;92m" - iyellow = "\033[0;93m" - iblue = "\033[0;94m" - ipurple = "\033[0;95m" - icyan = "\033[0;96m" - iwhite = "\033[0;97m" - - // Bold High Intensity - biblack = "\033[1;90m" - bired = "\033[1;91m" - bigreen = "\033[1;92m" - biyellow = "\033[1;93m" - biblue = "\033[1;94m" - bipurple = "\033[1;95m" - bicyan = "\033[1;96m" - biwhite = "\033[1;97m" -} \ No newline at end of file diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index eb9391b29a..1a3b96490d 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -30,9 +30,9 @@ "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85", "installed_by": ["subworkflows"] } } diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 3d3841ba49..346292c980 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -265,22 +265,20 @@ plugins { id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } -includeConfig "conf/colors.config" - validation { parametersSchema = "${projectDir}/nextflow_schema.json" help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " beforeText = """ --${colors.dim}----------------------------------------------------${colors.reset}- - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} -${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} -${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} -${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} -${colors.purple} ${manifest.name} ${manifest.version}${colors.reset} --${colors.dim}----------------------------------------------------${colors.reset}- +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework @@ -290,6 +288,10 @@ ${colors.purple} ${manifest.name} ${manifest.version}${colors.reset} https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText + } } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000000..5d1dc7c928 --- /dev/null +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,32 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + validate_params // boolean: validate the parameters + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + log.info paramsSummaryLog(workflow) + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + validateParameters() + } + + emit: + dummy_emit = true +} + diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000000..90b8cb1898 --- /dev/null +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,22 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test similarity index 62% rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 354b817545..703d3a9b86 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -1,14 +1,14 @@ +// TODO nf-core: Once you have added the required tests, please run the following command to build this file: +// nf-core subworkflows test utils_nfschema_plugin nextflow_workflow { - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" + workflow "UTILS_NFSCHEMA_PLUGIN" + tag "subworkflows" tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" + tag "subworkflows/utils_nfschema_plugin" config "./nextflow.config" @@ -17,13 +17,12 @@ nextflow_workflow { when { params { - test_data = '' + test_data = '' } workflow { """ - validate_params = false - + validate_params = false input[0] = validate_params """ } @@ -41,13 +40,13 @@ nextflow_workflow { when { params { - test_data = '' - outdir = 1 + test_data = '' + outdir = 1 } + workflow { """ - validate_params = true - + validate_params = true input[0] = validate_params """ } @@ -56,7 +55,7 @@ nextflow_workflow { then { assertAll( { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } ) } } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000000..0907ac58f0 --- /dev/null +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c93e..331e0d2f44 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 453894a64a..0000000000 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,43 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsSummaryLog } from 'plugin/nf-schema' -include { validateParameters } from 'plugin/nf-schema' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - validate_params // boolean: validate parameters - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters() - } - - emit: - dummy_emit = true -} diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04f5..0000000000 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config deleted file mode 100644 index 8d047ed59e..0000000000 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow.config +++ /dev/null @@ -1 +0,0 @@ -validation.monochromeLogs = true \ No newline at end of file diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff49..0000000000 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** From 171640b62dddcb81feddced4f674df88c47654ab Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 20 Aug 2024 16:13:59 +0200 Subject: [PATCH 364/574] some more small updates to the template --- nf_core/pipeline-template/nextflow.config | 2 +- .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 346292c980..ef067dcfab 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -255,7 +255,7 @@ manifest { homePage = 'https://github.com/{{ name }}' description = """{{ description }}""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.10.0' version = '{{ version }}' doi = '' } diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index c83d2ae0cb..a994cfd584 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -8,7 +8,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -53,7 +53,7 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - UTILS_NFVALIDATION_PLUGIN ( + UTILS_NFSCHEMA_PLUGIN ( validate_params ) From f72a2c325324dfc21d494d4135ae03da416ee709 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 20 Aug 2024 16:19:19 +0200 Subject: [PATCH 365/574] update pytest test_make_pipeline_schema --- tests/pipelines/test_launch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/pipelines/test_launch.py b/tests/pipelines/test_launch.py index da7618d486..7c6e3d6196 100644 --- a/tests/pipelines/test_launch.py +++ b/tests/pipelines/test_launch.py @@ -60,7 +60,7 @@ def test_make_pipeline_schema(self, tmp_path): Path(test_pipeline_dir, "nextflow_schema.json").unlink() self.launcher = nf_core.pipelines.launch.Launch(test_pipeline_dir, params_out=self.nf_params_fn) self.launcher.get_pipeline_schema() - assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) > 2 + assert len(self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]) >= 2 assert self.launcher.schema_obj.schema["definitions"]["input_output_options"]["properties"]["outdir"] == { "type": "string", "format": "directory-path", From 249b3da383f17ab0beecfeb9e8346619edaf6776 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 20 Aug 2024 16:59:22 +0200 Subject: [PATCH 366/574] update handling of ignored parameters --- .../.github/workflows/ci.yml | 2 +- nf_core/pipeline-template/README.md | 2 +- nf_core/pipelines/lint/nextflow_config.py | 15 +++++-------- nf_core/pipelines/schema.py | 22 ++++++++++++++----- 4 files changed, 23 insertions(+), 18 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index 6b2547765d..63fa99cec8 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "23.10.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 7718d2e5f8..d31dee93f4 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -16,7 +16,7 @@ [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index a5b7cf325f..150a89e102 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -65,14 +65,6 @@ def nextflow_config(self) -> Dict[str, List[str]]: * Should always be set to default value: ``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}`` - * ``params.validationShowHiddenParams`` - - * Determines whether boilerplate params are showed by schema. Set to ``false`` by default - - * ``params.validationSchemaIgnoreParams`` - - * A comma separated string of inputs the schema validation should ignore. - **The following variables throw warnings if missing:** * ``manifest.mainScript``: The filename of the main pipeline script (should be ``main.nf``) @@ -151,8 +143,11 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["process.time"], ["params.outdir"], ["params.input"], - ["params.validationShowHiddenParams"], - ["params.validationSchemaIgnoreParams"], + ["validation.help.enabled"], + ["validation.help.beforeText"], + ["validation.help.afterText"], + ["validation.summary.beforeText"], + ["validation.summary.afterText"] ] # Throw a warning if these are missing config_warn = [ diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 9db9457516..78f4317094 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -50,6 +50,7 @@ def __init__(self): self.validation_plugin = None self.schema_draft = None self.defs_notation = None + self.ignored_params = [] # Update the validation plugin code everytime the schema gets changed def set_schema_filename(self, schema: str) -> None: @@ -69,16 +70,26 @@ def del_schema_filename(self) -> None: def _update_validation_plugin_from_config(self, config: str) -> None: plugin = "nf-schema" with open(Path(config)) as conf: - nf_schema_pattern = re.compile("id\s*[\"']nf-schema", re.MULTILINE) - nf_validation_pattern = re.compile("id\s*[\"']nf-validation", re.MULTILINE) + nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE) + nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE) config_content = conf.read() if re.search(nf_validation_pattern, config_content): plugin = "nf-validation" + self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",") + self.ignored_params.append("validationSchemaIgnoreParams") elif re.search(nf_schema_pattern, config_content): plugin = "nf-schema" + ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE) + ignored_params_match = re.search(ignored_params_pattern, config_content) + ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default + if ignored_params_match and len(ignored_params_match.groups()) == 1: + ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(",")) + self.ignored_params = ignored_params else: log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema") + + self.validation_plugin = plugin # Previous versions of nf-schema used "defs", but it's advised to use "$defs" if plugin == "nf-schema": @@ -845,13 +856,12 @@ def add_schema_found_configs(self): Update defaults if they have changed """ params_added = [] - params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",") - params_ignore.append("validationSchemaIgnoreParams") + for p_key, p_val in self.pipeline_params.items(): s_key = self.schema_params.get(p_key) # Check if key is in schema parameters # Key is in pipeline but not in schema or ignored from schema - if p_key not in self.schema_params and p_key not in params_ignore: + if p_key not in self.schema_params and p_key not in self.ignored_params: if ( self.no_prompts or self.schema_from_scratch @@ -884,7 +894,7 @@ def add_schema_found_configs(self): elif ( s_key and (p_key not in self.schema_defaults) - and (p_key not in params_ignore) + and (p_key not in self.ignored_params) and (p_def := self.build_schema_param(p_val).get("default")) ): if self.no_prompts or Confirm.ask( From af34d0718db98544a8da402952aea87ca778a60e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 20 Aug 2024 17:50:32 +0200 Subject: [PATCH 367/574] update validation plugin fetching --- nf_core/pipeline-template/nextflow.config | 2 +- nf_core/pipelines/schema.py | 58 ++++++++++++----------- 2 files changed, 32 insertions(+), 28 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index ef067dcfab..3a98c40f0a 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -61,7 +61,7 @@ params { max_time = '240.h' // Schema validation default options - validate_params = true + validate_params = true } diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 78f4317094..e9c5556dbb 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -69,35 +69,45 @@ def del_schema_filename(self) -> None: def _update_validation_plugin_from_config(self, config: str) -> None: plugin = "nf-schema" - with open(Path(config)) as conf: - nf_schema_pattern = re.compile(r"id\s*[\"']nf-schema", re.MULTILINE) - nf_validation_pattern = re.compile(r"id\s*[\"']nf-validation", re.MULTILINE) - config_content = conf.read() - if re.search(nf_validation_pattern, config_content): - plugin = "nf-validation" - self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",") - self.ignored_params.append("validationSchemaIgnoreParams") - elif re.search(nf_schema_pattern, config_content): + conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent) + + plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",") + plugin_found = False + for plugin_instance in plugins: + if "nf-schema" in plugin_instance: plugin = "nf-schema" - ignored_params_pattern = re.compile(r"defaultIgnoreParams\s*=\s*\[([^\]]*)\]", re.MULTILINE) - ignored_params_match = re.search(ignored_params_pattern, config_content) - ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default - if ignored_params_match and len(ignored_params_match.groups()) == 1: - ignored_params.extend(ignored_params_match.group(1).replace("\"", "").replace("'", '').replace(" ", "").split(",")) - self.ignored_params = ignored_params - else: - log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema") - + plugin_found = True + break + elif "nf-validation" in plugin_instance: + plugin = "nf-validation" + plugin_found = True + break + + if not plugin_found: + log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema") + + if "nf-validation" in plugins: + plugin = "nf-validation" + elif "nf-schema" in plugins: + plugin = "nf-schema" - self.validation_plugin = plugin # Previous versions of nf-schema used "defs", but it's advised to use "$defs" if plugin == "nf-schema": self.defs_notation = "$defs" + ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default + ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", []) + if len(ignored_params_config) > 0: + ignored_params.extend(ignored_params_config) + self.ignored_params = ignored_params self.schema_draft = "https://json-schema.org/draft/2020-12/schema" + else: self.defs_notation = "definitions" self.schema_draft = "https://json-schema.org/draft-07/schema" + self.get_wf_params() + self.ignored_params = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",") + self.ignored_params.append("validationSchemaIgnoreParams") def get_schema_path( self, path: Union[str, Path], local_only: bool = False, revision: Union[str, None] = None @@ -325,17 +335,11 @@ def validate_default_params(self): if self.pipeline_params == {}: self.get_wf_params() - # Collect parameters to ignore - if "validationSchemaIgnoreParams" in self.pipeline_params: - params_ignore = self.pipeline_params.get("validationSchemaIgnoreParams", "").strip("\"'").split(",") - else: - params_ignore = [] - # Go over group keys for group_key, group in schema_no_required.get(self.defs_notation, {}).items(): group_properties = group.get("properties") for param in group_properties: - if param in params_ignore: + if param in self.ignored_params: continue if param in self.pipeline_params: self.validate_config_default_parameter(param, group_properties[param], self.pipeline_params[param]) @@ -348,7 +352,7 @@ def validate_default_params(self): ungrouped_properties = self.schema.get("properties") if ungrouped_properties: for param in ungrouped_properties: - if param in params_ignore: + if param in self.ignored_params: continue if param in self.pipeline_params: self.validate_config_default_parameter( From e6381b71c67fcc1ecb18c8b3c6e796dd6df0dec7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 21 Aug 2024 10:59:31 +0200 Subject: [PATCH 368/574] update plugin linting --- nf_core/pipelines/lint/nextflow_config.py | 56 ++++++++--------------- 1 file changed, 20 insertions(+), 36 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 150a89e102..bd2f4f768b 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -1,3 +1,4 @@ +import ast import logging import re from pathlib import Path @@ -330,6 +331,25 @@ def nextflow_config(self) -> Dict[str, List[str]]: ) ) + # Lint for plugins + config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\"")) + found_plugins = [] + if len(config_plugins) == 0: + failed.append("nextflow.config contains an empty plugins scope") + for plugin in config_plugins: + if "@" not in plugin: + failed.append(f"Plugin '{plugin}' does not have a pinned version") + found_plugins.append(plugin.split("@")[0]) + + if "nf-validation" in found_plugins and "nf-schema" in found_plugins: + failed.append("nextflow.config contains both nf-validation and nf-schema") + if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: + failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") + + if "nf-validation" in found_plugins: + warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") + + # Check for the availability of the "test" configuration profile by parsing nextflow.config # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions with open(Path(self.wf_path, "nextflow.config")) as f: @@ -359,42 +379,6 @@ def nextflow_config(self) -> Dict[str, List[str]]: else: failed.append("nextflow.config does not contain configuration profile `test`") - # Lint for nf-validation and nf-schema - match_plugins = re.search(r"\bplugins\s*\{([^}]+)}", cleaned_content, re.MULTILINE) - if not match_plugins: - failed.append( - "nextflow.config does not contain `plugins` scope, but `nf-validation` or `nf-schema` plugins are required" - ) - else: - found_plugins = {} - for line in match_plugins.group(1).split("\n"): - cleaned_line = line.split("//")[0].strip().replace("\"", "'") - if "id" not in line: continue - match_line = re.search(r"\bid\s'([^']+)'", cleaned_line) - if not match_line: - failed.append(f"nextflow.config contains an invalid plugins identifier: {cleaned_line}") - continue - plugin = match_line.group(1) - name = plugin.split("@")[0] - version = "" - if "@" in plugin: - version = plugin.split("@")[1] - found_plugins[name] = version - - if len(found_plugins) == 0: - failed.append("nextflow.config contains an empty plugins scope") - elif "nf-validation" in found_plugins and "nf-schema" in found_plugins: - failed.append("nextflow.config contains both nf-validation and nf-schema") - elif "nf-validation" in found_plugins and found_plugins["nf-validation"] == "": - failed.append("nextflow.config contains an unpinned version of nf-validation") - elif "nf-schema" in found_plugins and found_plugins["nf-schema"] == "": - failed.append("nextflow.config contains an unpinned version of nf-schema") - elif "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: - failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") - - if "nf-validation" in found_plugins: - warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") - # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json ignore_defaults = [] for item in ignore_configs: From e66a732e7db6452fb12b0f311762b19bbe7f3418 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 21 Aug 2024 11:01:16 +0200 Subject: [PATCH 369/574] ignore genomes for now --- nf_core/pipeline-template/nextflow.config | 2 +- nf_core/pipeline-template/nextflow_schema.json | 6 ------ 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 3a98c40f0a..bb55678001 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -266,7 +266,7 @@ plugins { } validation { - parametersSchema = "${projectDir}/nextflow_schema.json" + defaultIgnoreParams = ["genomes"] help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 14120bbabc..908d310171 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -81,12 +81,6 @@ "fa_icon": "fas fa-ban", "hidden": true, "default": "s3://ngi-igenomes/igenomes/" - }, - "genomes": { - "type": "object", - "description": "An object containing all reference data availabe in igenomes", - "fa_icon": "fas fa-ban", - "hidden": true } } }, From b6ae8d01dd440558cb3a2af821a04ea8fc89591a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 21 Aug 2024 12:23:52 +0200 Subject: [PATCH 370/574] improve config linting for validation even more --- nf_core/pipelines/lint/nextflow_config.py | 59 ++++++++++++++--------- 1 file changed, 35 insertions(+), 24 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index bd2f4f768b..6e292deb09 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -144,11 +144,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["process.time"], ["params.outdir"], ["params.input"], - ["validation.help.enabled"], - ["validation.help.beforeText"], - ["validation.help.afterText"], - ["validation.summary.beforeText"], - ["validation.summary.afterText"] + ["validation.help.enabled"] ] # Throw a warning if these are missing config_warn = [ @@ -157,6 +153,11 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["trace.file"], ["report.file"], ["dag.file"], + ["validation.help.beforeText"], + ["validation.help.afterText"], + ["validation.help.command"], + ["validation.summary.beforeText"], + ["validation.summary.afterText"] ] # Old depreciated vars - fail if present config_fail_ifdefined = [ @@ -168,6 +169,35 @@ def nextflow_config(self) -> Dict[str, List[str]]: "params.enable_conda", ] + # Lint for plugins + config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\"")) + found_plugins = [] + if len(config_plugins) == 0: + failed.append("nextflow.config contains an empty plugins scope") + for plugin in config_plugins: + if "@" not in plugin: + failed.append(f"Plugin '{plugin}' does not have a pinned version") + found_plugins.append(plugin.split("@")[0]) + + if "nf-validation" in found_plugins and "nf-schema" in found_plugins: + failed.append("nextflow.config contains both nf-validation and nf-schema") + if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: + failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") + + if "nf-schema" in found_plugins: + if self.nf_config.get("validation.help.enabled", "false") == "false": + failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages") + config_fail_ifdefined.extend([ + "params.validationFailUnrecognisedParams", + "params.validationLenientMode", + "params.validationSchemaIgnoreParams", + "params.validationShowHiddenParams" + ]) + + if "nf-validation" in found_plugins: + warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") + + # Remove field that should be ignored according to the linting config ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else [] @@ -331,25 +361,6 @@ def nextflow_config(self) -> Dict[str, List[str]]: ) ) - # Lint for plugins - config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\"")) - found_plugins = [] - if len(config_plugins) == 0: - failed.append("nextflow.config contains an empty plugins scope") - for plugin in config_plugins: - if "@" not in plugin: - failed.append(f"Plugin '{plugin}' does not have a pinned version") - found_plugins.append(plugin.split("@")[0]) - - if "nf-validation" in found_plugins and "nf-schema" in found_plugins: - failed.append("nextflow.config contains both nf-validation and nf-schema") - if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: - failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") - - if "nf-validation" in found_plugins: - warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") - - # Check for the availability of the "test" configuration profile by parsing nextflow.config # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions with open(Path(self.wf_path, "nextflow.config")) as f: From 1ede989be403e25f8b7485503d6a07bb6f20301d Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 21 Aug 2024 11:27:40 +0200 Subject: [PATCH 371/574] add option to exclude adaptivecard and slackreport from pipeline template --- nf_core/pipeline-template/.prettierignore | 4 +++ nf_core/pipeline-template/main.nf | 4 +-- .../utils_nfcore_pipeline_pipeline/main.nf | 6 ++++- nf_core/pipelines/create/templatefeatures.yml | 25 +++++++++++++++++++ 4 files changed, 36 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/.prettierignore b/nf_core/pipeline-template/.prettierignore index 3b3d5ff08e..c8e8ad9e11 100644 --- a/nf_core/pipeline-template/.prettierignore +++ b/nf_core/pipeline-template/.prettierignore @@ -1,8 +1,12 @@ {%- if email %} email_template.html {%- endif %} +{%- if adaptivecard %} adaptivecard.json +{%- endif %} +{%- if slackreport %} slackreport.json +{%- endif %} .nextflow* work/ data/ diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index 0cf688a7e9..7002a9c2d5 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -102,8 +102,8 @@ workflow { {%- endif %} params.outdir, params.monochrome_logs, - params.hook_url, - {%- if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %} + {% if adaptivecard or slackreport %}params.hook_url,{% endif %} + {% if multiqc %}{{ prefix_nodash|upper }}_{{ short_name|upper }}.out.multiqc_report{% endif %} ) } diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 62ef73d65d..3db8f66cb6 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -18,7 +18,9 @@ include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +{%- if adaptivecard or slackreport %} include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +{%- endif %} include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' @@ -126,7 +128,7 @@ workflow PIPELINE_COMPLETION { {% endif %} outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications + {% if adaptivecard or slackreport %}hook_url // string: hook URL for notifications{% endif %} {% if multiqc %}multiqc_report // string: Path to MultiQC report{% endif %} main: @@ -149,9 +151,11 @@ workflow PIPELINE_COMPLETION { completionSummary(monochrome_logs) + {%- if adaptivecard or slackreport %} if (hook_url) { imNotification(summary_params, hook_url) } + {%- endif %} } workflow.onError { diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 5dafd7e312..ff56ee190e 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -275,3 +275,28 @@ email: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True +adaptivecard: + skippable_paths: + - "assets/adaptivecard.json" + short_description: "Add template for status messages" + description: "Enable pipeline status update messages through Microsoft Teams" + help_text: | + This adds an Adaptive Card. A snippets of user interface. + This Adaptive Card is used as a template for pipeline update messages and it is compatible with Microsoft Teams. + linting: + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True +slackreport: + skippable_paths: + - "assets/slackreport.json" + short_description: "Add template for slack status messages" + description: "Enable pipeline status update messages through Slack" + help_text: | + This adds an JSON template used as a template for pipeline update messages in Slack. + linting: + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True From c9adbd5bff432f4370a6901e00a576a687cdc416 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 21 Aug 2024 13:58:07 +0200 Subject: [PATCH 372/574] update textual snapshot --- .../__snapshots__/test_create_app.ambr | 512 +++++++++--------- 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index f2a0578474..ee470c915c 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-2220422576-matrix { + .terminal-3293903238-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2220422576-title { + .terminal-3293903238-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2220422576-r1 { fill: #c5c8c6 } - .terminal-2220422576-r2 { fill: #e3e3e3 } - .terminal-2220422576-r3 { fill: #989898 } - .terminal-2220422576-r4 { fill: #e1e1e1 } - .terminal-2220422576-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2220422576-r6 { fill: #1e1e1e } - .terminal-2220422576-r7 { fill: #507bb3 } - .terminal-2220422576-r8 { fill: #e2e2e2 } - .terminal-2220422576-r9 { fill: #808080 } - .terminal-2220422576-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2220422576-r11 { fill: #001541 } - .terminal-2220422576-r12 { fill: #0178d4 } - .terminal-2220422576-r13 { fill: #454a50 } - .terminal-2220422576-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-2220422576-r15 { fill: #000000 } - .terminal-2220422576-r16 { fill: #e4e4e4 } - .terminal-2220422576-r17 { fill: #14191f } - .terminal-2220422576-r18 { fill: #7ae998 } - .terminal-2220422576-r19 { fill: #0a180e;font-weight: bold } - .terminal-2220422576-r20 { fill: #008139 } - .terminal-2220422576-r21 { fill: #fea62b;font-weight: bold } - .terminal-2220422576-r22 { fill: #a7a9ab } - .terminal-2220422576-r23 { fill: #e2e3e3 } + .terminal-3293903238-r1 { fill: #c5c8c6 } + .terminal-3293903238-r2 { fill: #e3e3e3 } + .terminal-3293903238-r3 { fill: #989898 } + .terminal-3293903238-r4 { fill: #e1e1e1 } + .terminal-3293903238-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3293903238-r6 { fill: #1e1e1e } + .terminal-3293903238-r7 { fill: #507bb3 } + .terminal-3293903238-r8 { fill: #e2e2e2 } + .terminal-3293903238-r9 { fill: #808080 } + .terminal-3293903238-r10 { fill: #dde6ed;font-weight: bold } + .terminal-3293903238-r11 { fill: #001541 } + .terminal-3293903238-r12 { fill: #0178d4 } + .terminal-3293903238-r13 { fill: #454a50 } + .terminal-3293903238-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-3293903238-r15 { fill: #000000 } + .terminal-3293903238-r16 { fill: #14191f } + .terminal-3293903238-r17 { fill: #e4e4e4 } + .terminal-3293903238-r18 { fill: #7ae998 } + .terminal-3293903238-r19 { fill: #0a180e;font-weight: bold } + .terminal-3293903238-r20 { fill: #008139 } + .terminal-3293903238-r21 { fill: #fea62b;font-weight: bold } + .terminal-3293903238-r22 { fill: #a7a9ab } + .terminal-3293903238-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common reference ▇▇ - genome files. - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + ▅▅ + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-1370375189-matrix { + .terminal-2443134963-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1370375189-title { + .terminal-2443134963-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1370375189-r1 { fill: #c5c8c6 } - .terminal-1370375189-r2 { fill: #e3e3e3 } - .terminal-1370375189-r3 { fill: #989898 } - .terminal-1370375189-r4 { fill: #e1e1e1 } - .terminal-1370375189-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1370375189-r6 { fill: #1e1e1e } - .terminal-1370375189-r7 { fill: #507bb3 } - .terminal-1370375189-r8 { fill: #e2e2e2 } - .terminal-1370375189-r9 { fill: #808080 } - .terminal-1370375189-r10 { fill: #dde6ed;font-weight: bold } - .terminal-1370375189-r11 { fill: #001541 } - .terminal-1370375189-r12 { fill: #14191f } - .terminal-1370375189-r13 { fill: #454a50 } - .terminal-1370375189-r14 { fill: #7ae998 } - .terminal-1370375189-r15 { fill: #e2e3e3;font-weight: bold } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges▁▁ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help ▃▃ + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From 1be17370b30fe34adccb5b698d26145e05522e99 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 21 Aug 2024 14:56:37 +0200 Subject: [PATCH 373/574] check plugin includes in pipeline --- nf_core/pipelines/lint/__init__.py | 3 ++ nf_core/pipelines/lint/nextflow_config.py | 4 ++- nf_core/pipelines/lint/plugin_includes.py | 38 +++++++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 nf_core/pipelines/lint/plugin_includes.py diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index ed833d3219..219cdd8f5c 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -45,6 +45,7 @@ from .nfcore_yml import nfcore_yml from .pipeline_name_conventions import pipeline_name_conventions from .pipeline_todos import pipeline_todos +from .plugin_includes import plugin_includes from .readme import readme from .schema_description import schema_description from .schema_lint import schema_lint @@ -92,6 +93,7 @@ class PipelineLint(nf_core.utils.Pipeline): nfcore_yml = nfcore_yml pipeline_name_conventions = pipeline_name_conventions pipeline_todos = pipeline_todos + plugin_includes = plugin_includes readme = readme schema_description = schema_description schema_lint = schema_lint @@ -135,6 +137,7 @@ def _get_all_lint_tests(release_mode): "actions_awsfulltest", "readme", "pipeline_todos", + "plugin_includes", "pipeline_name_conventions", "template_strings", "schema_lint", diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 6e292deb09..a735c5042b 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -170,7 +170,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ] # Lint for plugins - config_plugins = ast.literal_eval(self.nf_config.get("plugins", "").strip("\"")) + config_plugins = ast.literal_eval(self.nf_config.get("plugins", "")) found_plugins = [] if len(config_plugins) == 0: failed.append("nextflow.config contains an empty plugins scope") @@ -185,6 +185,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") if "nf-schema" in found_plugins: + passed.append("Found nf-schema plugin") if self.nf_config.get("validation.help.enabled", "false") == "false": failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages") config_fail_ifdefined.extend([ @@ -195,6 +196,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ]) if "nf-validation" in found_plugins: + passed.append("Found nf-validation plugin") warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py new file mode 100644 index 0000000000..247c4e493b --- /dev/null +++ b/nf_core/pipelines/lint/plugin_includes.py @@ -0,0 +1,38 @@ +import ast +import glob +import logging +import re +from typing import Dict, List + +log = logging.getLogger(__name__) + + +def plugin_includes(self) -> Dict[str, List[str]]: + """Checks the include statements in the all *.nf files for plugin includes + + When nf-schema is used in an nf-core pipeline, the include statements of the plugin + functions have to use nf-schema instead of nf-validation and vice versa + """ + config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))] + validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema" + + passed = [] + warned = [] + failed = [] + ignored = [] + + plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE) + workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")] + test_passed = True + for file in workflow_files: + with open(file, "r") as of: + plugin_includes = re.findall(plugin_include_pattern, of.read()) + for include in plugin_includes: + if include not in ["nf-validation", "nf-schema"]: continue + if include != validation_plugin: + test_passed = False + failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`") + + if test_passed: passed.append("No wrong validation plugin imports have been found") + + return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored} From f7137ca3c6e0240033cb56e690125cfbed54301b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 21 Aug 2024 16:44:58 +0200 Subject: [PATCH 374/574] Apply suggestions from code review --- nf_core/pipelines/create/templatefeatures.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index ff56ee190e..6a5fac358d 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -278,7 +278,7 @@ email: adaptivecard: skippable_paths: - "assets/adaptivecard.json" - short_description: "Add template for status messages" + short_description: "Support Microsoft Teams notifications" description: "Enable pipeline status update messages through Microsoft Teams" help_text: | This adds an Adaptive Card. A snippets of user interface. @@ -291,7 +291,7 @@ adaptivecard: slackreport: skippable_paths: - "assets/slackreport.json" - short_description: "Add template for slack status messages" + short_description: "Support Slack notifications" description: "Enable pipeline status update messages through Slack" help_text: | This adds an JSON template used as a template for pipeline update messages in Slack. From 2f1a4428dc73e15aea2fc001bec4df323700035e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 14:51:07 +0200 Subject: [PATCH 375/574] make nf-schema optional in the template --- .../assets/schema_input.json | 2 +- nf_core/pipeline-template/main.nf | 1 - nf_core/pipeline-template/modules.json | 4 +- nf_core/pipeline-template/nextflow.config | 9 ++-- .../pipeline-template/nextflow_schema.json | 3 +- .../utils_nfcore_pipeline_pipeline/main.nf | 18 +++++--- .../nf-core/utils_nfcore_pipeline/main.nf | 46 +++++++++++++++++++ .../pipeline-template/workflows/pipeline.nf | 2 +- nf_core/pipelines/create/templatefeatures.yml | 10 ++++ nf_core/pipelines/lint/nextflow_config.py | 20 ++++---- 10 files changed, 90 insertions(+), 25 deletions(-) diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json index e76b95fa99..28a468adaf 100644 --- a/nf_core/pipeline-template/assets/schema_input.json +++ b/nf_core/pipeline-template/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/{{ name }}/master/assets/schema_input.json", "title": "{{ name }} pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index fddfc5489e..f644f52afc 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -76,7 +76,6 @@ workflow { // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 1a3b96490d..0a883b60b7 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -29,12 +29,12 @@ "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] - }, + }{% if nf_schema %}, "utils_nfschema_plugin": { "branch": "master", "git_sha": "a3e87febb28bd0461c22a917c5b2c1492053ef85", "installed_by": ["subworkflows"] - } + }{% endif %} } } } diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index bb55678001..4acc34e409 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -37,9 +37,9 @@ params { plaintext_email = false monochrome_logs = false hook_url = null - help = false + {% if nf_schema %}help = false helpFull = false - showHidden = false + showHidden = false{% endif %} version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' @@ -260,13 +260,14 @@ manifest { doi = '' } +{% if nf_schema -%} // Nextflow plugins plugins { id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { - defaultIgnoreParams = ["genomes"] + defaultIgnoreParams = ["genomes", "helpFull", "showHidden", "help-full", "show-hidden"] // The last 4 parameters are here because of a bug in nf-schema. This will be fixed in a later version help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " @@ -293,7 +294,7 @@ validation { afterText = validation.help.afterText } } - +{% endif -%} // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json index 908d310171..c729c370bf 100644 --- a/nf_core/pipeline-template/nextflow_schema.json +++ b/nf_core/pipeline-template/nextflow_schema.json @@ -40,8 +40,7 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" - } - {% endif %} + }{% endif %} } }, {%- if igenomes %} diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index a994cfd584..1fef6912b3 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { samplesheetToList } from 'plugin/nf-schema'{% endif %} include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* ======================================================================================== @@ -50,12 +47,14 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) + {% if nf_schema %} // // Validate parameters and generate parameter summary to stdout // UTILS_NFSCHEMA_PLUGIN ( validate_params ) + {% endif %} // // Check config provided to the pipeline @@ -74,6 +73,7 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + {% if nf_schema %} Channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { @@ -93,6 +93,12 @@ workflow PIPELINE_INITIALISATION { return [ meta, fastqs.flatten() ] } .set { ch_samplesheet } + {% else %} + Channel + .fromPath(params.input) + .splitCsv(header: true, strip: true) + .set { ch_samplesheet } + {% endif %} emit: samplesheet = ch_samplesheet diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a5dcd5f83d..14558c3927 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -61,6 +61,25 @@ def checkProfileProvided(nextflow_cli_args) { } } +// +// Citation string for pipeline +// +def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + temp_doi_ref + "\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + // // Generate workflow version string // @@ -138,6 +157,33 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + // // ANSII colours used for terminal logging // diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 4bb0913211..8d2773820d 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -6,7 +6,7 @@ include { FASTQC } from '../modules/nf-core/fastqc/main' {% if multiqc %}include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endif %} -include { paramsSummaryMap } from 'plugin/nf-schema' +{% if nf_schema %}include { paramsSummaryMap } from 'plugin/nf-schema'{% endif %} {% if multiqc %}include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %} include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' {% if citations or multiqc %}include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'{% endif %} diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index b97bf347ab..7a24b3d91a 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -242,3 +242,13 @@ changelog: - "CHANGELOG.md" nfcore_pipelines: False custom_pipelines: True +nf_schema: + skippable_paths: + - "subworkflows/nf-core/utils_nfschema_plugin" + short_description: "Use nf-schema for this pipeline." + help_text: | + nf-schema is used to validate input parameters based on a JSON schema. + It also provides helper functionality to create help messages, get a summary + of changed parameters and validate and convert a samplesheet to a channel. + nfcore_pipelines: False + custom_pipelines: False diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index a735c5042b..1dfdabaf10 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -143,8 +143,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["process.memory"], ["process.time"], ["params.outdir"], - ["params.input"], - ["validation.help.enabled"] + ["params.input"] ] # Throw a warning if these are missing config_warn = [ @@ -152,12 +151,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["timeline.file"], ["trace.file"], ["report.file"], - ["dag.file"], - ["validation.help.beforeText"], - ["validation.help.afterText"], - ["validation.help.command"], - ["validation.summary.beforeText"], - ["validation.summary.afterText"] + ["dag.file"] ] # Old depreciated vars - fail if present config_fail_ifdefined = [ @@ -188,6 +182,16 @@ def nextflow_config(self) -> Dict[str, List[str]]: passed.append("Found nf-schema plugin") if self.nf_config.get("validation.help.enabled", "false") == "false": failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages") + config_fail.extend([ + ["validation.help.enabled"] + ]) + config_warn.extend([ + ["validation.help.beforeText"], + ["validation.help.afterText"], + ["validation.help.command"], + ["validation.summary.beforeText"], + ["validation.summary.afterText"] + ]) config_fail_ifdefined.extend([ "params.validationFailUnrecognisedParams", "params.validationLenientMode", From 364b54bde2994927d3124bfdf53d97bd1ecc6350 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 15:57:29 +0200 Subject: [PATCH 376/574] small fixes for template without nf-schema --- .../utils_nfcore_pipeline_pipeline/main.nf | 33 ++++++++++--------- .../pipeline-template/workflows/pipeline.nf | 6 ++-- nf_core/pipelines/lint/nextflow_config.py | 6 ++-- nf_core/pipelines/lint/plugin_includes.py | 2 +- 4 files changed, 25 insertions(+), 22 deletions(-) diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index d96f203544..0867a0a4c9 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -77,9 +77,14 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - {% if nf_schema %} - Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + + Channel{% if nf_schema %} + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")){% else %} + .fromPath(params.input) + .splitCsv(header: true, strip: true) + .map { row -> + [[id:row.sample], row.fastq_1, row.fastq_2] + }{% endif %} .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -97,12 +102,6 @@ workflow PIPELINE_INITIALISATION { return [ meta, fastqs.flatten() ] } .set { ch_samplesheet } - {% else %} - Channel - .fromPath(params.input) - .splitCsv(header: true, strip: true) - .set { ch_samplesheet } - {% endif %} emit: samplesheet = ch_samplesheet @@ -130,19 +129,21 @@ workflow PIPELINE_COMPLETION { main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - // // Completion email and summary // workflow.onComplete { {%- if email %} if (email || email_on_fail) { - {%- if multiqc %} - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) - {%- else %} - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, []) - {%- endif %} + completionEmail( + {% if nf_schema %}paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json"){% else %}{}{% endif %}, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + {% if multiqc %}multiqc_report.toList(){% else %}[]{% endif %} + ) } {%- endif %} diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 8d2773820d..ca5de36a61 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -60,9 +60,13 @@ workflow {{ short_name|upper }} { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + {% if nf_schema %} summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + {% endif %} {%- if citations %} ch_multiqc_custom_methods_description = params.multiqc_methods_description ? @@ -72,8 +76,6 @@ workflow {{ short_name|upper }} { methodsDescriptionText(ch_multiqc_custom_methods_description)) {%- endif %} - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) {%- if citations %} ch_multiqc_files = ch_multiqc_files.mix( diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 1dfdabaf10..f5689813a4 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -164,10 +164,10 @@ def nextflow_config(self) -> Dict[str, List[str]]: ] # Lint for plugins - config_plugins = ast.literal_eval(self.nf_config.get("plugins", "")) + config_plugins = ast.literal_eval(self.nf_config.get("plugins", "[]")) found_plugins = [] if len(config_plugins) == 0: - failed.append("nextflow.config contains an empty plugins scope") + warned.append("nextflow.config contains an empty plugins scope") for plugin in config_plugins: if "@" not in plugin: failed.append(f"Plugin '{plugin}' does not have a pinned version") @@ -176,7 +176,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: if "nf-validation" in found_plugins and "nf-schema" in found_plugins: failed.append("nextflow.config contains both nf-validation and nf-schema") if "nf-validation" not in found_plugins and "nf-schema" not in found_plugins: - failed.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") + warned.append("nextflow.config does not contain `nf-validation` or `nf-schema` in the plugins scope") if "nf-schema" in found_plugins: passed.append("Found nf-schema plugin") diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py index 247c4e493b..740c001a11 100644 --- a/nf_core/pipelines/lint/plugin_includes.py +++ b/nf_core/pipelines/lint/plugin_includes.py @@ -13,7 +13,7 @@ def plugin_includes(self) -> Dict[str, List[str]]: When nf-schema is used in an nf-core pipeline, the include statements of the plugin functions have to use nf-schema instead of nf-validation and vice versa """ - config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", ""))] + config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))] validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema" passed = [] From 4e631384906d2c02ab537276f22ea47c3ceb438d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 16:02:58 +0200 Subject: [PATCH 377/574] bump nextflow version --- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-wf.yml | 2 +- .../nf-core/utils_nextflow_pipeline/tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/tests/nextflow.config | 2 +- nf_core/pipelines/lint/readme.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 7e90febb74..f07b31e9de 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -38,7 +38,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "23.10.0" - "latest-everything" steps: - name: go to subdirectory and change nextflow workdir diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index a95a477459..56c6c822a9 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -39,7 +39,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "23.10.0" - "latest-everything" steps: - name: go to working directory diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf6d..0fa4abaf43 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.10.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config index d0a926bf6d..0fa4abaf43 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.10.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/nf_core/pipelines/lint/readme.py b/nf_core/pipelines/lint/readme.py index 4c16243690..1c09104258 100644 --- a/nf_core/pipelines/lint/readme.py +++ b/nf_core/pipelines/lint/readme.py @@ -36,7 +36,7 @@ def readme(self): if "nextflow_badge" not in ignore_configs: # Check that there is a readme badge showing the minimum required version of Nextflow - # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) + # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.10.0-23aa62.svg)](https://www.nextflow.io/) # and that it has the correct version nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)" match = re.search(nf_badge_re, content) From 11efc5547be76f1a6412d049dbfcd10cd337c660 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 16:08:41 +0200 Subject: [PATCH 378/574] update changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98fb925338..b4fcfe8646 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,8 @@ - add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) +- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116)) +- add option to exclude nf-schema from the template ([#3116](https://github.com/nf-core/tools/pull/3116)) ### Linting @@ -26,6 +28,10 @@ - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014)) - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086)) +- Linting will now fail when an unpinned plugin is used ([#3116](https://github.com/nf-core/tools/pull/3116)) +- Linting will now check if the schema is correct for the used validation plugin ([#3116])(https://github.com/nf-core/tools/pull/3116) +- Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(https://github.com/nf-core/tools/pull/3116) +- Full linting for correct use of nf-schema and nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116)) ### Download From 47c3fe324280a54d4cae4227ab7679ac488b1edb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 16:13:04 +0200 Subject: [PATCH 379/574] fix ruff linting --- nf_core/pipelines/lint/nextflow_config.py | 53 +++++++++++------------ nf_core/pipelines/lint/plugin_includes.py | 24 ++++++---- nf_core/pipelines/schema.py | 17 +++++--- 3 files changed, 51 insertions(+), 43 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index f5689813a4..255042ce5a 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -143,16 +143,10 @@ def nextflow_config(self) -> Dict[str, List[str]]: ["process.memory"], ["process.time"], ["params.outdir"], - ["params.input"] + ["params.input"], ] # Throw a warning if these are missing - config_warn = [ - ["manifest.mainScript"], - ["timeline.file"], - ["trace.file"], - ["report.file"], - ["dag.file"] - ] + config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]] # Old depreciated vars - fail if present config_fail_ifdefined = [ "params.nf_required_version", @@ -181,28 +175,33 @@ def nextflow_config(self) -> Dict[str, List[str]]: if "nf-schema" in found_plugins: passed.append("Found nf-schema plugin") if self.nf_config.get("validation.help.enabled", "false") == "false": - failed.append("The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages") - config_fail.extend([ - ["validation.help.enabled"] - ]) - config_warn.extend([ - ["validation.help.beforeText"], - ["validation.help.afterText"], - ["validation.help.command"], - ["validation.summary.beforeText"], - ["validation.summary.afterText"] - ]) - config_fail_ifdefined.extend([ - "params.validationFailUnrecognisedParams", - "params.validationLenientMode", - "params.validationSchemaIgnoreParams", - "params.validationShowHiddenParams" - ]) + failed.append( + "The help message has not been enabled. Set the `validation.help.enabled` configuration option to `true` to enable help messages" + ) + config_fail.extend([["validation.help.enabled"]]) + config_warn.extend( + [ + ["validation.help.beforeText"], + ["validation.help.afterText"], + ["validation.help.command"], + ["validation.summary.beforeText"], + ["validation.summary.afterText"], + ] + ) + config_fail_ifdefined.extend( + [ + "params.validationFailUnrecognisedParams", + "params.validationLenientMode", + "params.validationSchemaIgnoreParams", + "params.validationShowHiddenParams", + ] + ) if "nf-validation" in found_plugins: passed.append("Found nf-validation plugin") - warned.append("nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/") - + warned.append( + "nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/" + ) # Remove field that should be ignored according to the linting config ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else [] diff --git a/nf_core/pipelines/lint/plugin_includes.py b/nf_core/pipelines/lint/plugin_includes.py index 740c001a11..6a57b1d280 100644 --- a/nf_core/pipelines/lint/plugin_includes.py +++ b/nf_core/pipelines/lint/plugin_includes.py @@ -16,23 +16,29 @@ def plugin_includes(self) -> Dict[str, List[str]]: config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))] validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema" - passed = [] - warned = [] - failed = [] - ignored = [] + passed: list[str] = [] + warned: list[str] = [] + failed: list[str] = [] + ignored: list[str] = [] plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE) - workflow_files = [file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/")] + workflow_files = [ + file for file in glob.glob(f"{self.wf_path}/**/*.nf", recursive=True) if not file.startswith("./modules/") + ] test_passed = True for file in workflow_files: - with open(file, "r") as of: + with open(file) as of: plugin_includes = re.findall(plugin_include_pattern, of.read()) for include in plugin_includes: - if include not in ["nf-validation", "nf-schema"]: continue + if include not in ["nf-validation", "nf-schema"]: + continue if include != validation_plugin: test_passed = False - failed.append(f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`") + failed.append( + f"Found a `{include}` plugin import in `{file[2:]}`, but `{validation_plugin}` was used in `nextflow.config`" + ) - if test_passed: passed.append("No wrong validation plugin imports have been found") + if test_passed: + passed.append("No wrong validation plugin imports have been found") return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored} diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index e9c5556dbb..ccbc86645e 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -5,7 +5,6 @@ import logging import tempfile import webbrowser -import re from pathlib import Path from typing import Union @@ -58,10 +57,10 @@ def set_schema_filename(self, schema: str) -> None: basepath = "/".join(str(schema).split("/")[:-1]) config = f"{basepath}/nextflow.config" if basepath != "" else "nextflow.config" self._update_validation_plugin_from_config(config) - + def get_schema_filename(self) -> str: return self._schema_filename - + def del_schema_filename(self) -> None: del self._schema_filename @@ -71,7 +70,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None: plugin = "nf-schema" conf = nf_core.utils.fetch_wf_config(Path(self.schema_filename).parent) - plugins = str(conf.get("plugins", "")).strip("\"").strip("'").strip(" ").split(",") + plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",") plugin_found = False for plugin_instance in plugins: if "nf-schema" in plugin_instance: @@ -95,7 +94,7 @@ def _update_validation_plugin_from_config(self, config: str) -> None: # Previous versions of nf-schema used "defs", but it's advised to use "$defs" if plugin == "nf-schema": self.defs_notation = "$defs" - ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default + ignored_params = ["help", "helpFull", "showHidden"] # Help parameter should be ignored by default ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", []) if len(ignored_params_config) > 0: ignored_params.extend(ignored_params_config) @@ -447,7 +446,9 @@ def validate_schema(self, schema=None): # Add a small check for older nf-schema JSON schemas if "defs" in schema: - raise AssertionError(f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead') + raise AssertionError( + f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead' + ) for d_key, d_schema in schema.get(self.defs_notation, {}).items(): # Check that this definition is mentioned in allOf @@ -458,7 +459,9 @@ def validate_schema(self, schema=None): if allOf["$ref"] == f"#/{self.defs_notation}/{d_key}": in_allOf = True if not in_allOf: - raise AssertionError(f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`") + raise AssertionError( + f"Definition subschema `#/{self.defs_notation}/{d_key}` not included in schema `allOf`" + ) # TODO add support for nested parameters for d_param_id in d_schema.get("properties", {}): From 09bfca2663275c37173ce8018c858164974479f8 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 22 Aug 2024 16:29:39 +0200 Subject: [PATCH 380/574] add a plugin includes test --- tests/pipelines/lint/test_plugin_includes.py | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 tests/pipelines/lint/test_plugin_includes.py diff --git a/tests/pipelines/lint/test_plugin_includes.py b/tests/pipelines/lint/test_plugin_includes.py new file mode 100644 index 0000000000..21e6107c14 --- /dev/null +++ b/tests/pipelines/lint/test_plugin_includes.py @@ -0,0 +1,23 @@ +import nf_core.pipelines.lint + +from ..test_lint import TestLint + +class TestLintNextflowConfig(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + def test_default_values_match(self): + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + result = lint_obj.plugin_includes() + assert len(result["failed"]) == 0 + assert len(result["warned"]) == 0 + + def test_wrong_include(self): + test_path = self.new_pipeline / "test.nf" + with open(test_path, "w") as of: + of.write("include { paramsSummary } from 'plugin/nf-validation'\n") + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + result = lint_obj.plugin_includes() + assert len(result["failed"]) == 1 + assert len(result["warned"]) == 0 \ No newline at end of file From 44dbbf7a2b095144cb954bb1ed09578776979c92 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 23 Aug 2024 09:50:51 +0200 Subject: [PATCH 381/574] update review comments --- nf_core/pipeline-template/nextflow.config | 7 ++++--- nf_core/pipelines/create/templatefeatures.yml | 7 ++++--- nf_core/pipelines/lint/nextflow_config.py | 1 - nf_core/pipelines/schema.py | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index ad800cc55b..3b3183ece1 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -273,6 +273,7 @@ validation { help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + {% if is_nfcore %} beforeText = """ -\033[2m----------------------------------------------------\033[0m- \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m @@ -289,12 +290,12 @@ validation { * Software dependencies https://github.com/${manifest.name}/blob/master/CITATIONS.md -""" - } +"""{% endif %} + }{% if is_nfcore %} summary { beforeText = validation.help.beforeText afterText = validation.help.afterText - } + }[% endif %] } {% endif -%} diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 29b53eb0a7..224bc38266 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -245,13 +245,14 @@ changelog: nf_schema: skippable_paths: - "subworkflows/nf-core/utils_nfschema_plugin" - short_description: "Use nf-schema for this pipeline." + short_description: "Use nf-schema" + description: "Use nf-schema for this pipeline." help_text: | nf-schema is used to validate input parameters based on a JSON schema. It also provides helper functionality to create help messages, get a summary of changed parameters and validate and convert a samplesheet to a channel. - nfcore_pipelines: False - custom_pipelines: False + nfcore_pipelines: True + custom_pipelines: True license: skippable_paths: - "LICENSE" diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 255042ce5a..71eb6f118f 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -367,7 +367,6 @@ def nextflow_config(self) -> Dict[str, List[str]]: ) # Check for the availability of the "test" configuration profile by parsing nextflow.config - # Also check for the presence of nf-validation/nf-schema and check if they have pinned versions with open(Path(self.wf_path, "nextflow.config")) as f: content = f.read() diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index ccbc86645e..04f5ca2ace 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -447,7 +447,7 @@ def validate_schema(self, schema=None): # Add a small check for older nf-schema JSON schemas if "defs" in schema: raise AssertionError( - f'Using "defs" for schema definitions is not supported. Please use {self.defs_notation} instead' + f'Using "defs" for schema definitions is not supported. Please use "{self.defs_notation}" instead' ) for d_key, d_schema in schema.get(self.defs_notation, {}).items(): From ea51814bc2b1549c14605ba66591e7043bb5e4b3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 23 Aug 2024 10:17:15 +0200 Subject: [PATCH 382/574] remove duplicate code --- nf_core/pipelines/schema.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 04f5ca2ace..dbe851415f 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -85,11 +85,6 @@ def _update_validation_plugin_from_config(self, config: str) -> None: if not plugin_found: log.warning("Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema") - if "nf-validation" in plugins: - plugin = "nf-validation" - elif "nf-schema" in plugins: - plugin = "nf-schema" - self.validation_plugin = plugin # Previous versions of nf-schema used "defs", but it's advised to use "$defs" if plugin == "nf-schema": From 113fa4226cbdb471607615cf9c45b61bcfbc55c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 23 Aug 2024 10:06:12 +0000 Subject: [PATCH 383/574] update utils_nextflow_pipeline --- nf_core/pipeline-template/modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index eb9391b29a..8b156083f3 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -22,7 +22,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { From 195fc5168c9810d36f994996d588c219b72b9eef Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 11:35:43 +0000 Subject: [PATCH 384/574] Uncomment nextflow extension and align comments --- .gitpod.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index b2fbb73133..b93095c780 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -11,12 +11,12 @@ tasks: unset JAVA_TOOL_OPTIONS vscode: - extensions: # based on nf-core.nf-core-extensionpack + extensions: - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff From 65f26b1455b5592ec301fb618464372b3a8280da Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 11:44:48 +0000 Subject: [PATCH 385/574] Add Digest comment and remove conda defaults channel --- nf_core/gitpod/gitpod.Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index fd0e8bb799..944222668b 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -1,6 +1,7 @@ # Test build locally before making a PR # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile . +# See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used. FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c USER root @@ -40,9 +41,8 @@ RUN chown -R gitpod:gitpod /opt/conda /usr/src/nf_core # Change user to gitpod USER gitpod -# Install nextflow, nf-core, Mamba, and pytest-workflow -RUN conda config --add channels defaults && \ - conda config --add channels bioconda && \ +# Install nextflow, nf-core, nf-test, and other useful tools +RUN conda config --add channels bioconda && \ conda config --add channels conda-forge && \ conda config --set channel_priority strict && \ conda install --quiet --yes --name base \ From 506491f66e3dd612e726b508ab72e125fd8e31b8 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 12:04:32 +0000 Subject: [PATCH 386/574] Blank JAVA_TOOL_OPTIONS --- nf_core/gitpod/gitpod.Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 944222668b..849729966b 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -63,3 +63,4 @@ RUN nextflow self-update && \ # Setup pdiff for nf-test diffs ENV NFT_DIFF="pdiff" ENV NFT_DIFF_ARGS="--line-numbers --expand-tabs=2" +ENV JAVA_TOOL_OPTIONS= From 411cd22da23380799e7535b7340a5a0e16510bd7 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 12:07:25 +0000 Subject: [PATCH 387/574] Remove unset JAVA_TOOL_OPTIONS --- .gitpod.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index b93095c780..efe193f35f 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -6,9 +6,6 @@ tasks: python -m pip install -r requirements-dev.txt pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: From bc6ecda3aec81e24b858b6e98e62eb30ad13dd0a Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 12:11:13 +0000 Subject: [PATCH 388/574] Remove unset JAVA_TOOL_OPTIONS from pipeline template --- nf_core/pipeline-template/.gitpod.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 30e85ed977..5907fb59c9 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -4,9 +4,6 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack @@ -15,7 +12,7 @@ vscode: - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files{% endif %} - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff From d324760487b25de1f12027699099bc5d649eaf60 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 23 Aug 2024 12:14:18 +0000 Subject: [PATCH 389/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98fb925338..2e13e82f5e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -73,6 +73,7 @@ - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) +- Update gitpod ([#3136](https://github.com/nf-core/tools/pull/3136)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 1bcb70fbfc3b17b3a73dec382a96a20d02108617 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Fri, 23 Aug 2024 14:26:26 +0200 Subject: [PATCH 390/574] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e13e82f5e..aca2e6f200 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -73,7 +73,7 @@ - Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) -- Update gitpod ([#3136](https://github.com/nf-core/tools/pull/3136)) +- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] From 6e018ce6981548fb11ae5f34e3c476305695ad8f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 15:41:07 +0200 Subject: [PATCH 391/574] organise changelog and bump version to 3.0.0dev --- CHANGELOG.md | 55 +++++++++++++++++++++++++++------------------------- setup.py | 2 +- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index aca2e6f200..42cb2a62aa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,18 @@ # nf-core/tools: Changelog -## v2.14.2dev +## v3.0.0dev + +**Highlights** + +- Pipeline commands are renamed from nf-core to nf-core pipelines +- More customisation for pipeline templates +- A Text User Interface app when running nf-core pipelines create +- The pipeline template will come with the nf-schema plugin +- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline +- `nf-core licences` command is deprecated. +- Pipeline linting will run with the used version of the template +- The structure of nf-core/tools pytests has been updated +- The structure of the API docs has been updated ### Template @@ -9,14 +21,13 @@ - Remove deprecated syntax ([#3046](https://github.com/nf-core/tools/pull/3046)) - Use filename in code block for `params.yml` ([#3055](https://github.com/nf-core/tools/pull/3055)) - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072)) +- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084)) - add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101)) - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100)) - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105)) - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103)) - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) -- handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108)) -- add templatefeatures.yml to python package ([#3112](https://github.com/nf-core/tools/pull/3112)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) @@ -27,53 +38,45 @@ - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070)) - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086)) -### Download +### Pipeline create command + +- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) +- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) ### Components - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) +- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) +- Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) ### General -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974)) -- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) - move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983)) - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006)) -- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012)) - README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017)) -- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020)) -- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031)) - Add warning deprecation message to top-level commands ([#3036](https://github.com/nf-core/tools/pull/3036)) -- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) - move pipeline commands to functions to avoid duplication ([#3039](https://github.com/nf-core/tools/pull/3039)) -- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) -- Update python:3.12-slim Docker digest to da2d7af ([#3041](https://github.com/nf-core/tools/pull/3041)) -- Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048)) - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052)) - Add `--limit-output` argument for modules/subworkflow update ([#3047](https://github.com/nf-core/tools/pull/3047)) - update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054)) -- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) - handle new jsonschema error type ([#3061](https://github.com/nf-core/tools/pull/3061)) -- Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071)) - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074)) -- Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079)) -- Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) -- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) -- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102)) -- Components: allow spaces at the betinning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) +- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136)) + +## Version updates + - Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 ([#3122](https://github.com/nf-core/tools/pull/3122)) +- Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982)) - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) -- Update gitpod setup ([#3136](https://github.com/nf-core/tools/pull/3136)) +- Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) +- Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] diff --git a/setup.py b/setup.py index 8f32daa904..45df29b8bc 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "2.14.2dev" +version = "3.0.0dev" with open("README.md") as f: readme = f.read() From 41b2676c8746e92960907c3263f296ea7f606d96 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 15:52:40 +0200 Subject: [PATCH 392/574] more details! :D --- CHANGELOG.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42cb2a62aa..2a3e98f63b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,13 +4,13 @@ **Highlights** -- Pipeline commands are renamed from nf-core to nf-core pipelines -- More customisation for pipeline templates -- A Text User Interface app when running nf-core pipelines create -- The pipeline template will come with the nf-schema plugin -- New command nf-core pipelines rocrate to create a Research Object (RO) crate for a pipeline +- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to match the structure of modules and subworkflows commands. +- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module. +- A new Text User Interface app when running nf-core pipelines create +- The pipeline template will come with the `nf-schema` plugin +- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release. +- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline - `nf-core licences` command is deprecated. -- Pipeline linting will run with the used version of the template - The structure of nf-core/tools pytests has been updated - The structure of the API docs has been updated From 8000e1f5c31e7903ff72bb2453b67ca8db262f67 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 23 Aug 2024 16:04:19 +0200 Subject: [PATCH 393/574] add suggestions from @mashehu --- CHANGELOG.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2a3e98f63b..5590abc04a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,12 +4,12 @@ **Highlights** -- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to match the structure of modules and subworkflows commands. -- More customisation for pipeline templates. The template has been divided into features which can be skipped, making it easier to avoid annoying merge conflicts, for example, for pipeline which don't have a FastQC module. -- A new Text User Interface app when running nf-core pipelines create -- The pipeline template will come with the `nf-schema` plugin -- Pipeline linting will run with the used version of the template to minimise errors in opened PRs with every new tools release. -- New command `nf-core pipelines rocrate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/about_ro_crate) for a pipeline +- Pipeline commands are renamed from `nf-core ` to `nf-core pipelines ` to follow the same command structure as modules and subworkflows commands. +- More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it. +- A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters) +- We replaced nf-validation with nf-schema in the pipeline template +- CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release. +- New command `nf-core pipelines ro-crate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/) for a pipeline - `nf-core licences` command is deprecated. - The structure of nf-core/tools pytests has been updated - The structure of the API docs has been updated From f2b282c696ebfff78ac4e328dca3d9a25b258ec4 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 21 Aug 2024 16:12:58 +0200 Subject: [PATCH 394/574] add option to exclude fastqc from pipeline template --- nf_core/pipeline-template/CITATIONS.md | 7 +++---- nf_core/pipeline-template/README.md | 4 ++-- nf_core/pipeline-template/conf/modules.config | 2 ++ nf_core/pipeline-template/docs/output.md | 9 ++++++--- nf_core/pipeline-template/modules.json | 3 ++- .../local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++-- nf_core/pipeline-template/workflows/pipeline.nf | 4 +++- nf_core/pipelines/create/templatefeatures.yml | 10 ++++++++++ 8 files changed, 30 insertions(+), 13 deletions(-) diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 7cf37e5018..2373f1de7f 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -12,11 +12,10 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +{% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - -{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. > {%- endif %} diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 7718d2e5f8..a618f87bf7 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -44,8 +44,8 @@ workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. --> -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) - {% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %} +{% if fastqc %}1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)){% endif %} +{% if multiqc %}2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)){% endif %} ## Usage diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config index 84972d8e24..078142fad0 100644 --- a/nf_core/pipeline-template/conf/modules.config +++ b/nf_core/pipeline-template/conf/modules.config @@ -18,9 +18,11 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] + {%- if fastqc %} withName: FASTQC { ext.args = '--quiet' } + {%- endif %} {%- if multiqc %} withName: 'MULTIQC' { diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 76195a6825..5e42d50cc5 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -12,10 +12,13 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC - {% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %} +{% if fastqc %}- [FastQC](#fastqc) - Raw read QC{% endif %} +{% if multiqc %}- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline{% endif %} + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +{%- if fastqc %} + ### FastQC
@@ -28,7 +31,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - +{%- endif %} {%- if multiqc %} ### MultiQC diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 8b156083f3..6ab68d0f2a 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -5,11 +5,12 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + {%- if fastqc %} "fastqc": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] - }{%- if multiqc %}, + }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index 3db8f66cb6..fe9e558cfe 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -230,7 +230,7 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "FastQC (Andrews 2010),", + {% if fastqc %}"FastQC (Andrews 2010),",{% endif %} "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -243,7 +243,7 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + {% if fastqc %}"
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ",{% endif %} "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index d98c392f0c..e15d32f977 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { FASTQC } from '../modules/nf-core/fastqc/main' +{% if fastqc %}include { FASTQC } from '../modules/nf-core/fastqc/main'{% endif %} {% if multiqc %}include { MULTIQC } from '../modules/nf-core/multiqc/main'{% endif %} include { paramsSummaryMap } from 'plugin/nf-validation' {% if multiqc %}include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'{% endif %} @@ -27,6 +27,7 @@ workflow {{ short_name|upper }} { ch_versions = Channel.empty() {% if multiqc %}ch_multiqc_files = Channel.empty(){% endif %} + {%- if fastqc %} // // MODULE: Run FastQC // @@ -35,6 +36,7 @@ workflow {{ short_name|upper }} { ) {% if multiqc %}ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}){% endif %} ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + {%- endif %} // // Collate and save software versions diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 6a5fac358d..9fb56d610f 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -228,6 +228,16 @@ multiqc: multiqc_config: False nfcore_pipelines: True custom_pipelines: True +fastqc: + skippable_paths: + - "modules/nf-core/fastqc/" + short_description: "Use fastqc" + description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." + help_text: | + FastQC is a tool which provides quality control checks on raw sequencing data. + The pipeline will include the FastQC module. + nfcore_pipelines: True + custom_pipelines: True changelog: skippable_paths: - "CHANGELOG.md" From e4f685d90e48c9ba0d01312eeae4fb2238afb000 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 21 Aug 2024 14:34:56 +0000 Subject: [PATCH 395/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1527f5ba49..6415612bbf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) +- add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129)) ### Linting From 0e4a7d1393fbe944f39e6c38219c43d02831999a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 11:31:14 +0200 Subject: [PATCH 396/574] don't fail when no nf-core modules installed --- nf_core/components/lint/__init__.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index d0f6685365..0373170cfb 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -114,9 +114,7 @@ def __init__( ) ) if not self.all_remote_components: - raise LookupError( - f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline." - ) + log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") local_component_dir = Path(self.directory, self.component_type, "local") if local_component_dir.exists(): @@ -146,7 +144,7 @@ def __init__( ] self.all_local_components = [] if not self.all_remote_components: - raise LookupError(f"No {self.component_type} in '{self.component_type}' directory") + log.debug(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) From 92618ad8be8362ba5bece5eb82ab44fc08012c21 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 11:46:39 +0200 Subject: [PATCH 397/574] fix versions yaml file name --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index e15d32f977..8c797ede38 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -44,7 +44,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From d437582e632ad7bed1768a684eafdeba13cd16cf Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 12:46:28 +0200 Subject: [PATCH 398/574] udpate bpipe and fix pytests --- nf_core/components/lint/__init__.py | 4 ++-- nf_core/modules/lint/__init__.py | 2 +- tests/modules/test_lint.py | 11 +++++------ tests/subworkflows/test_lint.py | 10 ++++------ tests/test_modules.py | 4 ++-- 5 files changed, 14 insertions(+), 17 deletions(-) diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py index 0373170cfb..c1b1f24cb7 100644 --- a/nf_core/components/lint/__init__.py +++ b/nf_core/components/lint/__init__.py @@ -114,7 +114,7 @@ def __init__( ) ) if not self.all_remote_components: - log.debug(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") + log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.") local_component_dir = Path(self.directory, self.component_type, "local") if local_component_dir.exists(): @@ -144,7 +144,7 @@ def __init__( ] self.all_local_components = [] if not self.all_remote_components: - log.debug(f"No {self.component_type} in '{self.component_type}' directory") + log.warning(f"No {self.component_type} in '{self.component_type}' directory") # This could be better, perhaps glob for all nextflow.config files in? self.config = nf_core.utils.fetch_wf_config(self.directory / "tests" / "config", cache_config=True) diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py index b75f7e7570..017b3965b4 100644 --- a/nf_core/modules/lint/__init__.py +++ b/nf_core/modules/lint/__init__.py @@ -110,7 +110,7 @@ def lint( """ # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class # Prompt for module or all - if module is None and not all_modules: + if module is None and not all_modules and len(self.all_remote_components) > 0: questions = [ { "type": "list", diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index dfe288a6ee..cc7e0565e0 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -2,7 +2,6 @@ from pathlib import Path from typing import Union -import pytest import yaml from git.repo import Repo @@ -191,8 +190,8 @@ def test_modules_lint_empty(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text def test_modules_lint_new_modules(self): """lint a new module""" @@ -206,8 +205,8 @@ def test_modules_lint_no_gitlab(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) self.mods_remove.remove("multiqc", force=True) - with pytest.raises(LookupError): - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text def test_modules_lint_gitlab_modules(self): """Lint modules from a different remote""" @@ -566,7 +565,7 @@ def test_modules_meta_yml_input_mismatch(self): fh.write(main_nf) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2 + assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}" lint_tests = [x.lint_test for x in module_lint.warned] # check that it is there twice: assert lint_tests.count("meta_input_meta_only") == 1 diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py index 2693008707..c8b97fd0b0 100644 --- a/tests/subworkflows/test_lint.py +++ b/tests/subworkflows/test_lint.py @@ -2,8 +2,6 @@ import shutil from pathlib import Path -import pytest - import nf_core.subworkflows from ..test_subworkflows import TestSubworkflows @@ -25,8 +23,8 @@ def test_subworkflows_lint_empty(self): self.subworkflow_remove.remove("utils_nextflow_pipeline", force=True) self.subworkflow_remove.remove("utils_nfcore_pipeline", force=True) self.subworkflow_remove.remove("utils_nfvalidation_plugin", force=True) - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir) + assert "No subworkflows from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text def test_subworkflows_lint_new_subworkflow(self): """lint a new subworkflow""" @@ -39,8 +37,8 @@ def test_subworkflows_lint_new_subworkflow(self): def test_subworkflows_lint_no_gitlab(self): """Test linting a pipeline with no subworkflows installed""" - with pytest.raises(LookupError): - nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No subworkflows from {GITLAB_URL} installed in pipeline" in self.caplog.text def test_subworkflows_lint_gitlab_subworkflows(self): """Lint subworkflows from a different remote""" diff --git a/tests/test_modules.py b/tests/test_modules.py index 9ce74fd4e1..0e16497176 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -44,8 +44,8 @@ def create_modules_repo_dummy(tmp_dir): yaml.dump(nf_core_yml.model_dump(), fh) # mock biocontainers and anaconda response with responses.RequestsMock() as rsps: - mock_anaconda_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") - mock_biocontainers_api_calls(rsps, "bpipe", "0.9.12--hdfd78af_0") + mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") + mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules module_create = nf_core.modules.create.ModuleCreate( root_dir, "bpipe/test", "@author", "process_single", False, False From 9551cdc3467dca4b4cd1bc3d3bf735340b9ee7bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 26 Aug 2024 14:21:37 +0200 Subject: [PATCH 399/574] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipeline-template/conf/modules.config | 2 +- .../subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config index 078142fad0..35e861d9b1 100644 --- a/nf_core/pipeline-template/conf/modules.config +++ b/nf_core/pipeline-template/conf/modules.config @@ -18,7 +18,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - {%- if fastqc %} + {% if fastqc -%} withName: FASTQC { ext.args = '--quiet' } diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index fe9e558cfe..b130b7f88a 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -231,7 +231,7 @@ def toolCitationText() { def citation_text = [ "Tools used in the workflow included:", {% if fastqc %}"FastQC (Andrews 2010),",{% endif %} - "MultiQC (Ewels et al. 2016)", + {% if multiqc %}"MultiQC (Ewels et al. 2016)",{% endif %} "." ].join(' ').trim() @@ -244,7 +244,7 @@ def toolBibliographyText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ {% if fastqc %}"
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ",{% endif %} - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + {% if multiqc %}"
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • "{% endif %} ].join(' ').trim() return reference_text From 9d29e9342b5258b8c08f495d49409761707493c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 26 Aug 2024 12:25:34 +0000 Subject: [PATCH 400/574] update textual snapshots --- .../__snapshots__/test_create_app.ambr | 764 +++++++++--------- .../pytest-0/test_github_details0 | 1 - .../pytest-0/test_github_exit_message0 | 1 - .../pytest-0/test_github_question0 | 1 - .../pytest-1/test_github_details0 | 1 - .../pytest-1/test_github_exit_message0 | 1 - .../pytest-1/test_github_question0 | 1 - 7 files changed, 382 insertions(+), 388 deletions(-) delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_details0 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 delete mode 160000 tmp/pytest-of-gitpod/pytest-0/test_github_question0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_details0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 delete mode 160000 tmp/pytest-of-gitpod/pytest-1/test_github_question0 diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index ee470c915c..f5a19837b6 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-3293903238-matrix { + .terminal-1136262003-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3293903238-title { + .terminal-1136262003-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3293903238-r1 { fill: #c5c8c6 } - .terminal-3293903238-r2 { fill: #e3e3e3 } - .terminal-3293903238-r3 { fill: #989898 } - .terminal-3293903238-r4 { fill: #e1e1e1 } - .terminal-3293903238-r5 { fill: #4ebf71;font-weight: bold } - .terminal-3293903238-r6 { fill: #1e1e1e } - .terminal-3293903238-r7 { fill: #507bb3 } - .terminal-3293903238-r8 { fill: #e2e2e2 } - .terminal-3293903238-r9 { fill: #808080 } - .terminal-3293903238-r10 { fill: #dde6ed;font-weight: bold } - .terminal-3293903238-r11 { fill: #001541 } - .terminal-3293903238-r12 { fill: #0178d4 } - .terminal-3293903238-r13 { fill: #454a50 } - .terminal-3293903238-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-3293903238-r15 { fill: #000000 } - .terminal-3293903238-r16 { fill: #14191f } - .terminal-3293903238-r17 { fill: #e4e4e4 } - .terminal-3293903238-r18 { fill: #7ae998 } - .terminal-3293903238-r19 { fill: #0a180e;font-weight: bold } - .terminal-3293903238-r20 { fill: #008139 } - .terminal-3293903238-r21 { fill: #fea62b;font-weight: bold } - .terminal-3293903238-r22 { fill: #a7a9ab } - .terminal-3293903238-r23 { fill: #e2e3e3 } + .terminal-1136262003-r1 { fill: #c5c8c6 } + .terminal-1136262003-r2 { fill: #e3e3e3 } + .terminal-1136262003-r3 { fill: #989898 } + .terminal-1136262003-r4 { fill: #e1e1e1 } + .terminal-1136262003-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1136262003-r6 { fill: #1e1e1e } + .terminal-1136262003-r7 { fill: #507bb3 } + .terminal-1136262003-r8 { fill: #e2e2e2 } + .terminal-1136262003-r9 { fill: #808080 } + .terminal-1136262003-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1136262003-r11 { fill: #001541 } + .terminal-1136262003-r12 { fill: #0178d4 } + .terminal-1136262003-r13 { fill: #454a50 } + .terminal-1136262003-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-1136262003-r15 { fill: #000000 } + .terminal-1136262003-r16 { fill: #14191f } + .terminal-1136262003-r17 { fill: #e4e4e4 } + .terminal-1136262003-r18 { fill: #7ae998 } + .terminal-1136262003-r19 { fill: #0a180e;font-weight: bold } + .terminal-1136262003-r20 { fill: #008139 } + .terminal-1136262003-r21 { fill: #fea62b;font-weight: bold } + .terminal-1136262003-r22 { fill: #a7a9ab } + .terminal-1136262003-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - ▅▅ - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files. - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes▅▅ + + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-2443134963-matrix { + .terminal-242174438-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2443134963-title { + .terminal-242174438-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2443134963-r1 { fill: #c5c8c6 } - .terminal-2443134963-r2 { fill: #e3e3e3 } - .terminal-2443134963-r3 { fill: #989898 } - .terminal-2443134963-r4 { fill: #e1e1e1 } - .terminal-2443134963-r5 { fill: #4ebf71;font-weight: bold } - .terminal-2443134963-r6 { fill: #1e1e1e } - .terminal-2443134963-r7 { fill: #507bb3 } - .terminal-2443134963-r8 { fill: #e2e2e2 } - .terminal-2443134963-r9 { fill: #808080 } - .terminal-2443134963-r10 { fill: #dde6ed;font-weight: bold } - .terminal-2443134963-r11 { fill: #001541 } - .terminal-2443134963-r12 { fill: #14191f } - .terminal-2443134963-r13 { fill: #454a50 } - .terminal-2443134963-r14 { fill: #7ae998 } - .terminal-2443134963-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-2443134963-r16 { fill: #0a180e;font-weight: bold } - .terminal-2443134963-r17 { fill: #000000 } - .terminal-2443134963-r18 { fill: #008139 } - .terminal-2443134963-r19 { fill: #fea62b;font-weight: bold } - .terminal-2443134963-r20 { fill: #a7a9ab } - .terminal-2443134963-r21 { fill: #e2e3e3 } + .terminal-242174438-r1 { fill: #c5c8c6 } + .terminal-242174438-r2 { fill: #e3e3e3 } + .terminal-242174438-r3 { fill: #989898 } + .terminal-242174438-r4 { fill: #e1e1e1 } + .terminal-242174438-r5 { fill: #4ebf71;font-weight: bold } + .terminal-242174438-r6 { fill: #1e1e1e } + .terminal-242174438-r7 { fill: #507bb3 } + .terminal-242174438-r8 { fill: #e2e2e2 } + .terminal-242174438-r9 { fill: #808080 } + .terminal-242174438-r10 { fill: #dde6ed;font-weight: bold } + .terminal-242174438-r11 { fill: #001541 } + .terminal-242174438-r12 { fill: #14191f } + .terminal-242174438-r13 { fill: #454a50 } + .terminal-242174438-r14 { fill: #7ae998 } + .terminal-242174438-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-242174438-r16 { fill: #0a180e;font-weight: bold } + .terminal-242174438-r17 { fill: #000000 } + .terminal-242174438-r18 { fill: #008139 } + .terminal-242174438-r19 { fill: #fea62b;font-weight: bold } + .terminal-242174438-r20 { fill: #a7a9ab } + .terminal-242174438-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help ▃▃ - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▆▆ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2511,254 +2511,254 @@ font-weight: 700; } - .terminal-1633351929-matrix { + .terminal-1052877418-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1633351929-title { + .terminal-1052877418-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1633351929-r1 { fill: #c5c8c6 } - .terminal-1633351929-r2 { fill: #e3e3e3 } - .terminal-1633351929-r3 { fill: #989898 } - .terminal-1633351929-r4 { fill: #e1e1e1 } - .terminal-1633351929-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1633351929-r6 { fill: #1e1e1e } - .terminal-1633351929-r7 { fill: #507bb3 } - .terminal-1633351929-r8 { fill: #e2e2e2 } - .terminal-1633351929-r9 { fill: #808080 } - .terminal-1633351929-r10 { fill: #dde6ed;font-weight: bold } - .terminal-1633351929-r11 { fill: #001541 } - .terminal-1633351929-r12 { fill: #454a50 } - .terminal-1633351929-r13 { fill: #7ae998 } - .terminal-1633351929-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-1633351929-r15 { fill: #0a180e;font-weight: bold } - .terminal-1633351929-r16 { fill: #000000 } - .terminal-1633351929-r17 { fill: #008139 } - .terminal-1633351929-r18 { fill: #fea62b;font-weight: bold } - .terminal-1633351929-r19 { fill: #a7a9ab } - .terminal-1633351929-r20 { fill: #e2e3e3 } + .terminal-1052877418-r1 { fill: #c5c8c6 } + .terminal-1052877418-r2 { fill: #e3e3e3 } + .terminal-1052877418-r3 { fill: #989898 } + .terminal-1052877418-r4 { fill: #e1e1e1 } + .terminal-1052877418-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1052877418-r6 { fill: #1e1e1e } + .terminal-1052877418-r7 { fill: #507bb3 } + .terminal-1052877418-r8 { fill: #e2e2e2 } + .terminal-1052877418-r9 { fill: #808080 } + .terminal-1052877418-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1052877418-r11 { fill: #001541 } + .terminal-1052877418-r12 { fill: #454a50 } + .terminal-1052877418-r13 { fill: #7ae998 } + .terminal-1052877418-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-1052877418-r15 { fill: #0a180e;font-weight: bold } + .terminal-1052877418-r16 { fill: #000000 } + .terminal-1052877418-r17 { fill: #008139 } + .terminal-1052877418-r18 { fill: #fea62b;font-weight: bold } + .terminal-1052877418-r19 { fill: #a7a9ab } + .terminal-1052877418-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most common - reference genome files  - from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use multiqcThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - module which generates  - an HTML report for  - quality control. - - - - - - - - - - - - - - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most common + reference genome files  + from iGenomes + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use multiqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which generates  + an HTML report for  + quality control. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use fastqcThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + module which performs  + quality control  + analysis of input FASTQ + files. + + + + + + + + + + + + + + + + + + + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 b/tmp/pytest-of-gitpod/pytest-0/test_github_details0 deleted file mode 160000 index ee82f320cb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit ee82f320cb567b302e7328c1cacab94a98dae787 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 deleted file mode 160000 index f7fe48cf9d..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit f7fe48cf9d00ab24581686a6d4226d2e9005c607 diff --git a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 b/tmp/pytest-of-gitpod/pytest-0/test_github_question0 deleted file mode 160000 index dce3324acb..0000000000 --- a/tmp/pytest-of-gitpod/pytest-0/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit dce3324acbbe32f905afae8553e042f39404b37e diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 b/tmp/pytest-of-gitpod/pytest-1/test_github_details0 deleted file mode 160000 index e2638dca91..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_details0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit e2638dca91b137a96b491008b1eeef2bfd791bec diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 b/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 deleted file mode 160000 index 74cda800a8..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_exit_message0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 74cda800a86fd07e93bbf8e00e4890516e3d838d diff --git a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 b/tmp/pytest-of-gitpod/pytest-1/test_github_question0 deleted file mode 160000 index 444ebc5370..0000000000 --- a/tmp/pytest-of-gitpod/pytest-1/test_github_question0 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 444ebc5370bf91ea808f5d65c5788064f0480045 From 52da9e369598bc69ad356b25c38d6c09fed940cf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 21 Aug 2024 15:05:24 +0000 Subject: [PATCH 401/574] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6415612bbf..45d4fc18bd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129)) +- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130)) ### Linting From a8cb9408d16ce47eda65baee2f73354b7566b72e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 26 Aug 2024 14:10:30 +0200 Subject: [PATCH 402/574] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/templatefeatures.yml | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/nf_core/pipelines/create/templatefeatures.yml b/nf_core/pipelines/create/templatefeatures.yml index 9fb56d610f..ab5f262374 100644 --- a/nf_core/pipelines/create/templatefeatures.yml +++ b/nf_core/pipelines/create/templatefeatures.yml @@ -310,3 +310,23 @@ slackreport: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True +documentation: + skippable_paths: + - "docs" + short_description: "Add documentation" + description: "Add documentation to the pipeline" + help_text: | + This will add documentation markdown files where you can describe your pipeline. + It includes: + - docs/README.md: A README file where you can describe the structure of your documentation. + - docs/output.md: A file where you can explain the output generated by the pipeline + - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters. + + These files come with an exemplary documentation structure written. + linting: + files_exist: + - "docs/output.md" + - "docs/README.md" + - "docs/usage.md" + nfcore_pipelines: False + custom_pipelines: True From bcbed0567441c2e5d62f2525da1a2ebebc7d5a23 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 26 Aug 2024 15:55:44 +0200 Subject: [PATCH 403/574] update textual snapshots --- .../__snapshots__/test_create_app.ambr | 512 +++++++++--------- 1 file changed, 256 insertions(+), 256 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app.ambr b/tests/pipelines/__snapshots__/test_create_app.ambr index f5a19837b6..0015728fda 100644 --- a/tests/pipelines/__snapshots__/test_create_app.ambr +++ b/tests/pipelines/__snapshots__/test_create_app.ambr @@ -851,257 +851,257 @@ font-weight: 700; } - .terminal-1136262003-matrix { + .terminal-3611359904-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1136262003-title { + .terminal-3611359904-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1136262003-r1 { fill: #c5c8c6 } - .terminal-1136262003-r2 { fill: #e3e3e3 } - .terminal-1136262003-r3 { fill: #989898 } - .terminal-1136262003-r4 { fill: #e1e1e1 } - .terminal-1136262003-r5 { fill: #4ebf71;font-weight: bold } - .terminal-1136262003-r6 { fill: #1e1e1e } - .terminal-1136262003-r7 { fill: #507bb3 } - .terminal-1136262003-r8 { fill: #e2e2e2 } - .terminal-1136262003-r9 { fill: #808080 } - .terminal-1136262003-r10 { fill: #dde6ed;font-weight: bold } - .terminal-1136262003-r11 { fill: #001541 } - .terminal-1136262003-r12 { fill: #0178d4 } - .terminal-1136262003-r13 { fill: #454a50 } - .terminal-1136262003-r14 { fill: #e2e3e3;font-weight: bold } - .terminal-1136262003-r15 { fill: #000000 } - .terminal-1136262003-r16 { fill: #14191f } - .terminal-1136262003-r17 { fill: #e4e4e4 } - .terminal-1136262003-r18 { fill: #7ae998 } - .terminal-1136262003-r19 { fill: #0a180e;font-weight: bold } - .terminal-1136262003-r20 { fill: #008139 } - .terminal-1136262003-r21 { fill: #fea62b;font-weight: bold } - .terminal-1136262003-r22 { fill: #a7a9ab } - .terminal-1136262003-r23 { fill: #e2e3e3 } + .terminal-3611359904-r1 { fill: #c5c8c6 } + .terminal-3611359904-r2 { fill: #e3e3e3 } + .terminal-3611359904-r3 { fill: #989898 } + .terminal-3611359904-r4 { fill: #e1e1e1 } + .terminal-3611359904-r5 { fill: #4ebf71;font-weight: bold } + .terminal-3611359904-r6 { fill: #1e1e1e } + .terminal-3611359904-r7 { fill: #507bb3 } + .terminal-3611359904-r8 { fill: #e2e2e2 } + .terminal-3611359904-r9 { fill: #808080 } + .terminal-3611359904-r10 { fill: #dde6ed;font-weight: bold } + .terminal-3611359904-r11 { fill: #001541 } + .terminal-3611359904-r12 { fill: #0178d4 } + .terminal-3611359904-r13 { fill: #454a50 } + .terminal-3611359904-r14 { fill: #e2e3e3;font-weight: bold } + .terminal-3611359904-r15 { fill: #000000 } + .terminal-3611359904-r16 { fill: #e4e4e4 } + .terminal-3611359904-r17 { fill: #14191f } + .terminal-3611359904-r18 { fill: #7ae998 } + .terminal-3611359904-r19 { fill: #0a180e;font-weight: bold } + .terminal-3611359904-r20 { fill: #008139 } + .terminal-3611359904-r21 { fill: #fea62b;font-weight: bold } + .terminal-3611359904-r22 { fill: #a7a9ab } + .terminal-3611359904-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes▅▅ - - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files. - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Hide help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + + + Nf-core pipelines are configured to use a copy of the most common reference  + genome files. + + By selecting this option, your pipeline will include a configuration file  + specifying the paths to these files. + + The required code to use these files will also be included in the template.  + When the pipeline user provides an appropriate genome key, the pipeline will + automatically download the required reference files. + ▅▅ + For more information about reference genomes in nf-core pipelines, see the  + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  @@ -2233,255 +2233,255 @@ font-weight: 700; } - .terminal-242174438-matrix { + .terminal-1661160397-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-242174438-title { + .terminal-1661160397-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-242174438-r1 { fill: #c5c8c6 } - .terminal-242174438-r2 { fill: #e3e3e3 } - .terminal-242174438-r3 { fill: #989898 } - .terminal-242174438-r4 { fill: #e1e1e1 } - .terminal-242174438-r5 { fill: #4ebf71;font-weight: bold } - .terminal-242174438-r6 { fill: #1e1e1e } - .terminal-242174438-r7 { fill: #507bb3 } - .terminal-242174438-r8 { fill: #e2e2e2 } - .terminal-242174438-r9 { fill: #808080 } - .terminal-242174438-r10 { fill: #dde6ed;font-weight: bold } - .terminal-242174438-r11 { fill: #001541 } - .terminal-242174438-r12 { fill: #14191f } - .terminal-242174438-r13 { fill: #454a50 } - .terminal-242174438-r14 { fill: #7ae998 } - .terminal-242174438-r15 { fill: #e2e3e3;font-weight: bold } - .terminal-242174438-r16 { fill: #0a180e;font-weight: bold } - .terminal-242174438-r17 { fill: #000000 } - .terminal-242174438-r18 { fill: #008139 } - .terminal-242174438-r19 { fill: #fea62b;font-weight: bold } - .terminal-242174438-r20 { fill: #a7a9ab } - .terminal-242174438-r21 { fill: #e2e3e3 } + .terminal-1661160397-r1 { fill: #c5c8c6 } + .terminal-1661160397-r2 { fill: #e3e3e3 } + .terminal-1661160397-r3 { fill: #989898 } + .terminal-1661160397-r4 { fill: #e1e1e1 } + .terminal-1661160397-r5 { fill: #4ebf71;font-weight: bold } + .terminal-1661160397-r6 { fill: #1e1e1e } + .terminal-1661160397-r7 { fill: #507bb3 } + .terminal-1661160397-r8 { fill: #e2e2e2 } + .terminal-1661160397-r9 { fill: #808080 } + .terminal-1661160397-r10 { fill: #dde6ed;font-weight: bold } + .terminal-1661160397-r11 { fill: #001541 } + .terminal-1661160397-r12 { fill: #14191f } + .terminal-1661160397-r13 { fill: #454a50 } + .terminal-1661160397-r14 { fill: #7ae998 } + .terminal-1661160397-r15 { fill: #e2e3e3;font-weight: bold } + .terminal-1661160397-r16 { fill: #0a180e;font-weight: bold } + .terminal-1661160397-r17 { fill: #000000 } + .terminal-1661160397-r18 { fill: #008139 } + .terminal-1661160397-r19 { fill: #fea62b;font-weight: bold } + .terminal-1661160397-r20 { fill: #a7a9ab } + .terminal-1661160397-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▆▆ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - editor-config and  - prettier. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Include citationsInclude pipeline tools Show help  - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + + Template features + + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github CI testsThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + actions for Continuous + Integration (CI)  + testing + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use reference genomesThe pipeline will be  Show help  + ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + copy of the most  + common reference  + genome files from  + iGenomes + ▃▃ + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add Github badgesThe README.md file of  Show help  + ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + include GitHub badges + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Add configuration The pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + profiles containing  + custom parameters  + requried to run  + nf-core pipelines at  + different institutions + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Use code lintersThe pipeline will  Show help  + ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + and CI tests to lint  + your code: pre-commit, + editor-config and  + prettier. + + ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + ▊▎        Include citationsInclude pipeline tools Show help  + ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +  Back  Continue  + ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +  d Toggle dark mode  q Quit  From d3d6345b5bc1519dd9426b66319043d05d0c2a85 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 22 Aug 2024 10:54:18 +0200 Subject: [PATCH 404/574] add option to exclude test configs from pipeline template --- .../create-test-lint-wf-template.yml | 1 + .../pipeline-template/.github/CONTRIBUTING.md | 7 ++++- .../.github/PULL_REQUEST_TEMPLATE.md | 2 ++ .../.github/workflows/download_pipeline.yml | 4 +-- nf_core/pipeline-template/README.md | 2 +- nf_core/pipeline-template/docs/usage.md | 3 ++ nf_core/pipeline-template/nextflow.config | 4 ++- .../pipeline-template/nextflow_schema.json | 4 +-- nf_core/pipelines/create/templatefeatures.yml | 28 +++++++++++++++++++ 9 files changed, 48 insertions(+), 7 deletions(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 70125a10f3..46f55a4b64 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -70,6 +70,7 @@ jobs: - TEMPLATE: is_nfcore - TEMPLATE: nf_core_configs profile: "self_hosted_runner" + - TEMPLATE: test_config fail-fast: false steps: diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index 5a58501bb2..f331d38673 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -30,16 +30,18 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +{%- if test_config %} You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: ```bash nf-test test --profile debug,test,docker --verbose ``` +{% endif %} When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. -There are typically two types of tests that run: +{% if test_config %}There are typically two types of tests that run:{% endif %} ### Lint tests @@ -48,12 +50,15 @@ To enforce these and ensure that all pipelines stay in sync, we have developed a If any failures or warnings are encountered, please follow the listed URL for more documentation. +{%- if test_config %} + ### Pipeline tests Each `nf-core` pipeline should be set up with a minimal set of test-data. `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. If there are any failures then the automated tests fail. These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. +{%- endif %} ## Patch diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md index dee23ccab1..c96f2dd4c2 100644 --- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md +++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md @@ -20,8 +20,10 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. {%- endif %} - [ ] Make sure your code lints (`nf-core pipelines lint`). + {%- if test_config %} - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). + {%- endif %} - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 99a42d86d2..e7a28e5ac4 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -68,7 +68,7 @@ jobs: --download-configuration - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %} - name: Run the downloaded pipeline (stub) id: stub_run_pipeline @@ -83,4 +83,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %} + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %} diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index a618f87bf7..c8ed828d38 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -50,7 +50,7 @@ ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. {% if test_config %}Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.{% endif %} - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - - GitHub organisationWorkflow name - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - A short description of your pipeline. - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - Name of the main author / authors - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Next  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_basic_details_nfcore - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - - GitHub organisationWorkflow name - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core                                   ▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - A short description of your pipeline. - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - Name of the main author / authors - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Next  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_choose_type - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Choose pipeline type - - - - - Choose "nf-core" if:Choose "Custom" if: - - ● You want your pipeline to be part of the ● Your pipeline will never be part of  - nf-core communitynf-core - ● You think that there's an outside chance ● You want full control over all features  - that it ever could be part of nf-corethat are included from the template  - (including those that are mandatory for  - nf-core). - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  nf-core  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Custom  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - What's the difference? - -   Choosing "nf-core" effectively pre-selects the following template features: - - ● GitHub Actions continuous-integration configuration files: - ▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) - ▪ Code formatting checks with Prettier - ▪ Auto-fix linting functionality using @nf-core-bot - ▪ Marking old issues as stale - ● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_customisation_help - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use a GitHub Create a GitHub  Show help  - ▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - pipeline. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing▄▄ - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Hide help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - - Nf-core pipelines are configured to use a copy of the most common reference  - genome files. - - By selecting this option, your pipeline will include a configuration file  - specifying the paths to these files. - - The required code to use these files will also be included in the template.  - When the pipeline user provides an appropriate genome key, the pipeline will - automatically download the required reference files. - ▅▅ - For more information about reference genomes in nf-core pipelines, see the  - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_final_details - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Final details - - - - - First version of the pipelinePath to the output directory where the  - pipeline will be created - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊1.0.0dev▎▊.                                         ▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Finish  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_github_details - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - -   Now that we have created a new pipeline locally, we can create a new GitHub repository and push    -   the code to it. - - - - - Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - for login. Show  - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - ▊GitHub username▎▊••••••••••••                  ▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - The name of the organisation where the The name of the new GitHub repository - GitHub repo will be cretaed - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core                               ▎▊mypipeline                            ▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - ▌⚠️ You can't create a repository directly in the nf-core organisation. - ▌Please create the pipeline repo to an organisation where you have access or use your user  - ▌account. A core-team member will be able to transfer the repo to nf-core once the development - ▌has started. - - ▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - - ▊▔▔▔▔▔▔▔▔▎Private - ▊▎Select to make the new GitHub repo private. - ▊▁▁▁▁▁▁▁▁▎ - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Create GitHub repo  Finish without creating a repo  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_github_exit_message - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - HowTo create a GitHub repository - - - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - -   If you would like to create the GitHub repository later, you can do it manually by following  -   these steps: - -  1. Create a new GitHub repository -  2. Add the remote to your local repository: - - - cd <pipeline_directory> - git remote add origin git@github.com:<username>/<repo_name>.git - - -  3. Push the code to the remote: - - - git push --all origin - - - ▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Close  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_github_question - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Create GitHub repository - - -   After creating the pipeline template locally, we can create a GitHub repository and push the  -   code to it. - -   Do you want to create a GitHub repository? - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Create GitHub repo  Finish without creating a repo  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_type_custom - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use a GitHub Create a GitHub  Show help  - ▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - pipeline. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github CI testsThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - actions for Continuous - Integration (CI)  - testing - ▃▃ - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most  - common reference  - genome files from  - iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add Github badgesThe README.md file of  Show help  - ▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - include GitHub badges - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Add configuration The pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - profiles containing  - custom parameters  - requried to run  - nf-core pipelines at  - different institutions - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use code lintersThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - and CI tests to lint  - your code: pre-commit, - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_type_nfcore - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Template features - - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use reference genomesThe pipeline will be  Show help  - ▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - copy of the most common - reference genome files  - from iGenomes - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use multiqcThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - module which generates  - an HTML report for  - quality control. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use fastqcThe pipeline will  Show help  - ▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - module which performs  - quality control  - analysis of input FASTQ - files. - - ▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - ▊▎        Use nf-schemaUse the nf-schema  Show help  - ▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - this pipeline. - - - - - - - - - - - - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Continue  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_type_nfcore_validation - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - - Basic details - - - - - GitHub organisationWorkflow name - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊nf-core                                   ▎▊Pipeline Name▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Must be lowercase without  - punctuation. - - - - A short description of your pipeline. - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Description▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - - - Name of the main author / authors - - ▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ - ▊Author(s)▎ - ▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - Value error, Cannot be left empty. - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Back  Next  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- -# name: test_welcome - ''' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core create - - - - - - - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - -                                           ,--./,-. -           ___     __   __   __   ___     /,-._.--~\  -     |\ | |__  __ /  ` /  \ |__) |__         }  { -     | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                           `._,._,' - - - - Welcome to the nf-core pipeline creation wizard - -   This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -   The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    -   pipelines. - - ▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with - ▌the community as early as possible; ideally before you start on your pipeline! See the  - ▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - - ▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -  Let's go!  - ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - -  d Toggle dark mode  q Quit  - - - - - ''' -# --- diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg new file mode 100644 index 0000000000..5c4a15831c --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -0,0 +1,271 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg new file mode 100644 index 0000000000..4445dc68a6 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -0,0 +1,274 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg new file mode 100644 index 0000000000..f32d5271ea --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -0,0 +1,269 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the ● Your pipeline will never be part of  +nf-core communitynf-core +● You think that there's an outside chance ● You want full control over all features  +that it ever could be part of nf-corethat are included from the template  +(including those that are mandatory for  +nf-core). +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +  Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg new file mode 100644 index 0000000000..8969694cbc --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -0,0 +1,275 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing▄▄ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Hide help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + + +Nf-core pipelines are configured to use a copy of the most common reference  +genome files. + +By selecting this option, your pipeline will include a configuration file  +specifying the paths to these files. + +The required code to use these files will also be included in the template.  +When the pipeline user provides an appropriate genome key, the pipeline will +automatically download the required reference files. +▅▅ +For more information about reference genomes in nf-core pipelines, see the  + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg new file mode 100644 index 0000000000..ddd0ff57ec --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -0,0 +1,269 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Final details + + + + +First version of the pipelinePath to the output directory where the  +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg new file mode 100644 index 0000000000..3013b9961e --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -0,0 +1,276 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Create GitHub repository + +  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +  the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +The name of the organisation where the The name of the new GitHub repository +GitHub repo will be cretaed +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user  +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg new file mode 100644 index 0000000000..3612a062c7 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -0,0 +1,272 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +  If you would like to create the GitHub repository later, you can do it manually by following  +  these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg new file mode 100644 index 0000000000..a0ca3d70d1 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -0,0 +1,265 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Create GitHub repository + + +  After creating the pipeline template locally, we can create a GitHub repository and push the  +  code to it. + +  Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg new file mode 100644 index 0000000000..7ff071efa0 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -0,0 +1,273 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing +▃▃ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add configuration The pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +profiles containing  +custom parameters  +requried to run  +nf-core pipelines at  +different institutions + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use code lintersThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +and CI tests to lint  +your code: pre-commit, +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg new file mode 100644 index 0000000000..48b9b91e9d --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -0,0 +1,272 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use multiqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use fastqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + + + + + + + + + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg new file mode 100644 index 0000000000..7e55b2b0f2 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -0,0 +1,273 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg new file mode 100644 index 0000000000..2670307c22 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -0,0 +1,271 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core create + + + + + + + + + + ⭘nf-core create — Create a new pipeline with the nf-core pipeline template + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    +  pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the  +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  + + + From 8d5f898f3114d1b029963af7ed60590b56288175 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 27 Sep 2024 11:51:12 +0200 Subject: [PATCH 526/574] remove code duplication and format components info command --- nf_core/components/info.py | 43 +++++++++++++++++++++++--------------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/nf_core/components/info.py b/nf_core/components/info.py index e4a58d1618..f3e5bf617c 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -229,6 +229,25 @@ def get_remote_yaml(self) -> Optional[dict]: self.remote_location = self.modules_repo.remote_url return yaml.safe_load(file_contents) + def generate_params_table(self, type) -> Table: + "Generate a rich table for inputs and outputs" + table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) + table.add_column(f":inbox_tray: {type}") + table.add_column("Description") + if self.component_type == "modules": + table.add_column("Pattern", justify="right", style="green") + elif self.component_type == "subworkflows": + table.add_column("Structure", justify="right", style="green") + return table + + def get_channel_structure(self, structure: dict) -> str: + "Get the structure of a channel" + structure_str = "" + for key, info in structure.items(): + pattern = f" - {info['pattern']}" if info.get("pattern") else "" + structure_str += f"{key} ({info['type']}{pattern})" + return structure_str + def generate_component_info_help(self): """Take the parsed meta.yml and generate rich help. @@ -277,14 +296,9 @@ def generate_component_info_help(self): # Inputs if self.meta.get("input"): - inputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) - inputs_table.add_column(":inbox_tray: Inputs") - inputs_table.add_column("Description") - if self.component_type == "modules": - inputs_table.add_column("Pattern", justify="right", style="green") - elif self.component_type == "subworkflows": - inputs_table.add_column("Structure", justify="right", style="green") - for input in self.meta["input"]: + inputs_table = self.generate_params_table("Inputs") + for i, input in enumerate(self.meta["input"]): + inputs_table.add_row(f"[italic]input[{i}][/]", "", "") if self.component_type == "modules": for element in input: for key, info in element.items(): @@ -298,23 +312,18 @@ def generate_component_info_help(self): inputs_table.add_row( f"[orange1 on black] {key} [/][dim i]", Markdown(info["description"] if info["description"] else ""), - info.get("structure", ""), + self.get_channel_structure(info["structure"]) if info.get("structure") else "", ) renderables.append(inputs_table) # Outputs if self.meta.get("output"): - outputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) - outputs_table.add_column(":outbox_tray: Outputs") - outputs_table.add_column("Description") - if self.component_type == "modules": - inputs_table.add_column("Pattern", justify="right", style="green") - elif self.component_type == "subworkflows": - inputs_table.add_column("Structure", justify="right", style="green") + outputs_table = self.generate_params_table("Outputs") for output in self.meta["output"]: if self.component_type == "modules": for ch_name, elements in output.items(): + outputs_table.add_row(f"{ch_name}", "", "") for element in elements: for key, info in element.items(): outputs_table.add_row( @@ -327,7 +336,7 @@ def generate_component_info_help(self): outputs_table.add_row( f"[orange1 on black] {key} [/][dim i]", Markdown(info["description"] if info["description"] else ""), - info.get("structure", ""), + self.get_channel_structure(info["structure"]) if info.get("structure") else "", ) renderables.append(outputs_table) From efc11ba691b08b06df1e1631e9416de36a503a02 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 27 Sep 2024 16:35:00 +0200 Subject: [PATCH 527/574] add conf/igenomes_ignored.config to linting --- nf_core/pipelines/create/template_features.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index c166429431..6f476cdfbe 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -77,6 +77,7 @@ igenomes: linting: files_exist: - "conf/igenomes.config" + - "conf/igenomes_ignored.config" nfcore_pipelines: True custom_pipelines: True github_badges: From 27093939c2dec3d770a97ea17222ffbe7c2b6934 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 13 Sep 2024 16:46:16 +0200 Subject: [PATCH 528/574] remove try-catch blocks from nextflow.config --- CHANGELOG.md | 1 + nf_core/pipeline-template/nextflow.config | 13 +++---------- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a11aee515..b1c5463a9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ - Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168)) - Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037)) - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176)) +- Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167)) ### Linting diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 39c3521363..dc2aea0b72 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -186,18 +186,11 @@ profiles { {% if nf_core_configs -%} // Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load {{ name }} custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config") -} +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" {% endif -%} // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile From b1df038c263bd8893d7971e0cfe30dac746f86d1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 11:52:34 +0200 Subject: [PATCH 529/574] change the name of tmp pipeline to be consistent with all tests --- tests/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/utils.py b/tests/utils.py index 6f4b73cccc..022b91227f 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -113,7 +113,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: tmp_dir = Path(tempfile.TemporaryDirectory().name) root_repo_dir = Path(__file__).resolve().parent.parent template_dir = root_repo_dir / "nf_core" / "pipeline-template" - pipeline_name = "mypipeline" + pipeline_name = "testpipeline" pipeline_dir = tmp_dir / pipeline_name pipeline_dir.mkdir(parents=True) @@ -123,7 +123,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: org_path="nf-core", lint=None, template=NFCoreTemplateConfig( - name="mypipeline", + name="testpipeline", author="me", description="it is mine", org="nf-core", From 7e738eab0ed726ea21d007822a30e396a62c8ded Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 12:19:46 +0200 Subject: [PATCH 530/574] update nextflow_config linting to include the new includeconfig line --- nf_core/pipelines/lint/nextflow_config.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 14e91cc609..dd45621bc6 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -346,7 +346,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`") # Check that lines for loading custom profiles exist - lines = [ + old_lines = [ r"// Load nf-core custom profiles from different Institutions", r"try {", r'includeConfig "${params.custom_config_base}/nfcore_custom.config"', @@ -354,11 +354,19 @@ def nextflow_config(self) -> Dict[str, List[str]]: r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")', r"}", ] + lines = [ + r"// Load nf-core custom profiles from different Institutions", + r'''includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"''', + ] path = Path(self.wf_path, "nextflow.config") i = 0 with open(path) as f: for line in f: - if lines[i] in line: + if old_lines[i] in line: + i += 1 + if i == len(old_lines): + break + elif lines[i] in line: i += 1 if i == len(lines): break @@ -366,6 +374,12 @@ def nextflow_config(self) -> Dict[str, List[str]]: i = 0 if i == len(lines): passed.append("Lines for loading custom profiles found") + elif i == len(old_lines): + failed.append( + "Old lines for loading custom profiles found. File should contain: ```groovy\n{}".format( + "\n".join(lines) + ) + ) else: lines[2] = f"\t{lines[2]}" lines[4] = f"\t{lines[4]}" From e46779b6b8709af658c43ed5533603db306231e1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:04:28 +0200 Subject: [PATCH 531/574] add test on pipeline release to check that custom configs are included --- nf_core/pipeline-template/nextflow.config | 2 +- nf_core/pipelines/lint/__init__.py | 4 ++- nf_core/pipelines/lint/included_configs.py | 37 ++++++++++++++++++++++ 3 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 nf_core/pipelines/lint/included_configs.py diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index dc2aea0b72..4c816a2a2c 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -190,7 +190,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load {{ name }} custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" {% endif -%} // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index 6d27351b62..8cc7c37cb2 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -37,6 +37,7 @@ from .configs import base_config, modules_config from .files_exist import files_exist from .files_unchanged import files_unchanged +from .included_configs import included_configs from .merge_markers import merge_markers from .modules_json import modules_json from .modules_structure import modules_structure @@ -101,6 +102,7 @@ class PipelineLint(nf_core.utils.Pipeline): system_exit = system_exit template_strings = template_strings version_consistency = version_consistency + included_configs = included_configs def __init__( self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False @@ -152,7 +154,7 @@ def _get_all_lint_tests(release_mode): "base_config", "modules_config", "nfcore_yml", - ] + (["version_consistency"] if release_mode else []) + ] + (["version_consistency", "included_configs"] if release_mode else []) def _load(self) -> bool: """Load information about the pipeline into the PipelineLint object""" diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py new file mode 100644 index 0000000000..9d4eb1f990 --- /dev/null +++ b/nf_core/pipelines/lint/included_configs.py @@ -0,0 +1,37 @@ +from pathlib import Path + + +def included_configs(self): + """Check that the pipeline nextflow.config includes the pipeline custom configs. + + If the include line is uncommented, the test passes. + If the include line is commented, the test fails. + If the include line is missing, the test warns. + + Can be skipped by adding the following to the .nf-core.yml file: + lint: + included_configs: False + """ + passed = [] + failed = [] + warned = [] + + config_file = Path(self.wf_path / "nextflow.config") + + with open(config_file) as fh: + config = fh.read() + print(self.pipeline_name) + if ( + f"// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + in config + ): + failed.append("Pipeline config does not include custom configs. Please uncomment the includeConfig line.") + elif ( + "includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + in config + ): + passed.append("Pipeline config includes custom configs.") + else: + warned.append("Pipeline config does not include custom configs. Please add the includeConfig line.") + + return {"passed": passed, "failed": failed, "warned": warned} From 70b231e9ee4eb1361f5bfb0cc47aec41bc73f849 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:43:28 +0200 Subject: [PATCH 532/574] fix tests by uncommenting includeConfig statements --- .github/actions/create-lint-wf/action.yml | 6 ++++++ .github/workflows/create-lint-wf.yml | 5 +++++ .github/workflows/create-test-lint-wf-template.yml | 5 +++++ nf_core/pipelines/create/template_features.yml | 1 + nf_core/pipelines/lint/included_configs.py | 1 - 5 files changed, 17 insertions(+), 1 deletion(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 8760901db1..7cc6f85d4f 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -53,6 +53,12 @@ runs: run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + shell: bash + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX shell: bash diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 1a3e283d00..190cd01170 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -78,6 +78,11 @@ jobs: run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Run the other nf-core commands - name: nf-core pipelines list run: nf-core --log-file log.txt pipelines list diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 1fb521b4bb..10aeccd297 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -137,6 +137,11 @@ jobs: run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-test-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 6f476cdfbe..55bb3b0b3e 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -120,6 +120,7 @@ nf_core_configs: - "custom_config" - "params.custom_config_version" - "params.custom_config_base" + included_configs: False nfcore_pipelines: False custom_pipelines: True is_nfcore: diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py index 9d4eb1f990..6cfeb3f8a5 100644 --- a/nf_core/pipelines/lint/included_configs.py +++ b/nf_core/pipelines/lint/included_configs.py @@ -20,7 +20,6 @@ def included_configs(self): with open(config_file) as fh: config = fh.read() - print(self.pipeline_name) if ( f"// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" in config From 3a0a8ca33cc876bfb6299ded1b09f1b9cd4e4dcd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:56:51 +0200 Subject: [PATCH 533/574] fix sed commands --- .github/actions/create-lint-wf/action.yml | 2 +- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 7cc6f85d4f..ecd0eef873 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -56,7 +56,7 @@ runs: # Uncomment includeConfig statement - name: uncomment include config shell: bash - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Replace zenodo.XXXXXX to pass readme linting diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 190cd01170..e0b4c67cfc 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -80,7 +80,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Run the other nf-core commands diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 10aeccd297..86d6b3f6b7 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -139,7 +139,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Replace zenodo.XXXXXX to pass readme linting From c779bf4197ae545527cc4251ce27aeb3ee011c3b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:10:19 +0200 Subject: [PATCH 534/574] formatted string --- nf_core/pipelines/lint/included_configs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py index 6cfeb3f8a5..75c4594f41 100644 --- a/nf_core/pipelines/lint/included_configs.py +++ b/nf_core/pipelines/lint/included_configs.py @@ -26,7 +26,7 @@ def included_configs(self): ): failed.append("Pipeline config does not include custom configs. Please uncomment the includeConfig line.") elif ( - "includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + f"includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" in config ): passed.append("Pipeline config includes custom configs.") From d625d923933294b9da93cc63de0b4beccdd35752 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:16:03 +0200 Subject: [PATCH 535/574] test output directory typo --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 86d6b3f6b7..debbf8e691 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -140,7 +140,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; - working-directory: create-lint-wf + working-directory: create-test-lint-wf # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX From 19d21bb91ab2c765406224417db417189ece6af2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:19:38 +0200 Subject: [PATCH 536/574] fix more output directory errors --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index debbf8e691..d8df2f6905 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -139,7 +139,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; + run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-test-lint-wf # Replace zenodo.XXXXXX to pass readme linting From 5f367d18ffa4274ba8eb3084cf94abe6c10e19c2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:32:51 +0200 Subject: [PATCH 537/574] generate API docs --- docs/api/_src/pipeline_lint_tests/included_configs.md | 5 +++++ docs/api/_src/pipeline_lint_tests/index.md | 2 ++ 2 files changed, 7 insertions(+) create mode 100644 docs/api/_src/pipeline_lint_tests/included_configs.md diff --git a/docs/api/_src/pipeline_lint_tests/included_configs.md b/docs/api/_src/pipeline_lint_tests/included_configs.md new file mode 100644 index 0000000000..f68f7da25e --- /dev/null +++ b/docs/api/_src/pipeline_lint_tests/included_configs.md @@ -0,0 +1,5 @@ +# included_configs + + ```{eval-rst} + .. automethod:: nf_core.pipelines.lint.PipelineLint.included_configs + ``` diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md index 3575c08db4..4dd93442d2 100644 --- a/docs/api/_src/pipeline_lint_tests/index.md +++ b/docs/api/_src/pipeline_lint_tests/index.md @@ -7,6 +7,7 @@ - [base_config](./base_config/) - [files_exist](./files_exist/) - [files_unchanged](./files_unchanged/) + - [included_configs](./included_configs/) - [merge_markers](./merge_markers/) - [modules_config](./modules_config/) - [modules_json](./modules_json/) @@ -16,6 +17,7 @@ - [nfcore_yml](./nfcore_yml/) - [pipeline_name_conventions](./pipeline_name_conventions/) - [pipeline_todos](./pipeline_todos/) + - [plugin_includes](./plugin_includes/) - [readme](./readme/) - [schema_description](./schema_description/) - [schema_lint](./schema_lint/) From ae5084038ac5712e12566eb39ebd0aab593942be Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Mon, 23 Sep 2024 19:18:21 +0200 Subject: [PATCH 538/574] Refactor CLI commands for Download. --- nf_core/__main__.py | 20 +++++--------------- nf_core/pipelines/download.py | 6 ++---- 2 files changed, 7 insertions(+), 19 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index c7e927c8c8..9255c53bd1 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -366,26 +366,18 @@ def command_pipelines_lint( help="Archive compression type", ) @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files") -# TODO: Remove this in a future release. Deprecated in March 2024. -@click.option( - "-t", - "--tower", - is_flag=True, - default=False, - hidden=True, - help="Download for Seqera Platform. DEPRECATED: Please use `--platform` instead.", -) @click.option( + "-p", "--platform", is_flag=True, default=False, help="Download for Seqera Platform (formerly Nextflow Tower)", ) @click.option( - "-d", + "-c", "--download-configuration", - is_flag=True, - default=False, + type=click.Choice(["yes", "no"]), + default="no", help="Include configuration profiles in download. Not available with `--platform`", ) @click.option( @@ -420,7 +412,7 @@ def command_pipelines_lint( help="List of images already available in a remote `singularity.cacheDir`.", ) @click.option( - "-p", + "-n", "--parallel-downloads", type=int, default=4, @@ -434,7 +426,6 @@ def command_pipelines_download( outdir, compress, force, - tower, platform, download_configuration, tag, @@ -454,7 +445,6 @@ def command_pipelines_download( outdir, compress, force, - tower, platform, download_configuration, tag, diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 97453b127e..7018dc7b42 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -133,10 +133,8 @@ def __init__( self.force = force self.platform = platform self.fullname: Optional[str] = None - # if flag is not specified, do not assume deliberate choice and prompt config inclusion interactively. - # this implies that non-interactive "no" choice is only possible implicitly (e.g. with --platform or if prompt is suppressed by !stderr.is_interactive). - # only alternative would have been to make it a parameter with argument, e.g. -d="yes" or -d="no". - self.include_configs = True if download_configuration else False if bool(platform) else None + # downloading configs is not supported for Seqera Platform downloads. + self.include_configs = True if download_configuration == "yes" and not bool(platform) else False # Additional tags to add to the downloaded pipeline. This enables to mark particular commits or revisions with # additional tags, e.g. "stable", "testing", "validated", "production" etc. Since this requires a git-repo, it is only # available for the bare / Seqera Platform download. From 95435c9c58cb556a096906bf368549e18de21799 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Mon, 23 Sep 2024 19:55:51 +0200 Subject: [PATCH 539/574] Adapt tests for the new Pipelines Download CLI. --- nf_core/__main__.py | 3 +-- nf_core/commands_pipelines.py | 6 +----- tests/test_cli.py | 4 ++-- 3 files changed, 4 insertions(+), 9 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 9255c53bd1..98673fe1ee 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -2110,8 +2110,7 @@ def command_download( outdir, compress, force, - tower, - platform, + platform or tower, download_configuration, tag, container_system, diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py index 23affb1d27..1186935e52 100644 --- a/nf_core/commands_pipelines.py +++ b/nf_core/commands_pipelines.py @@ -167,7 +167,6 @@ def pipelines_download( outdir, compress, force, - tower, platform, download_configuration, tag, @@ -185,16 +184,13 @@ def pipelines_download( """ from nf_core.pipelines.download import DownloadWorkflow - if tower: - log.warning("[red]The `-t` / `--tower` flag is deprecated. Please use `--platform` instead.[/]") - dl = DownloadWorkflow( pipeline, revision, outdir, compress, force, - tower or platform, # True if either specified + platform, download_configuration, tag, container_system, diff --git a/tests/test_cli.py b/tests/test_cli.py index 026efd1e6a..bea0223f06 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -167,7 +167,7 @@ def test_cli_download(self, mock_dl): "compress": "tar.gz", "force": None, "platform": None, - "download-configuration": None, + "download-configuration": "yes", "tag": "3.12=testing", "container-system": "singularity", "container-library": "quay.io", @@ -188,7 +188,7 @@ def test_cli_download(self, mock_dl): params["compress"], "force" in params, "platform" in params, - "download-configuration" in params, + params["download-configuration"], (params["tag"],), params["container-system"], (params["container-library"],), From 5dea0d032a52cfa2779b487baa5e38aaa5421cd1 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Mon, 23 Sep 2024 20:24:10 +0200 Subject: [PATCH 540/574] Fix GitHub Action in pipeline-template and update Changelog. --- CHANGELOG.md | 11 +++++++++++ nf_core/__main__.py | 2 +- .../.github/workflows/download_pipeline.yml | 2 +- 3 files changed, 13 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a11aee515..bc740a8030 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -70,6 +70,17 @@ - Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077)) +### Download + +- Fully removed already deprecated `-t` / `--tower` flag. +- Refactored the CLI for consistency (short flag is usually second word, e.g. also for `--container-library` etc.): + +| Old parameter | New parameter | +| --------------------------------- | --------------------------------- | +| `-d` / `--download-configuration` | `-c` / `--download-configuration` | +| `-p` / `--parallel-downloads` | `-d` / `--parallel-downloads` | +| new parameter | `-p` / (`--platform`) | + ### General - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 98673fe1ee..e0c1b85e91 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -412,7 +412,7 @@ def command_pipelines_lint( help="List of images already available in a remote `singularity.cacheDir`.", ) @click.option( - "-n", + "-d", "--parallel-downloads", type=int, default=4, diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index e7a28e5ac4..f704609ca8 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -65,7 +65,7 @@ jobs: --container-system 'singularity' \ --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %} From 91e9de554e251236cf9b5683859bdd68284f8fa5 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 1 Oct 2024 11:53:40 +0200 Subject: [PATCH 541/574] skip citations.md from linting --- nf_core/pipelines/create/template_features.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 1b9ff68741..3eb6547265 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -194,6 +194,9 @@ citations: Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, and the logics to add this section to the output MultiQC report (if the report is generated). + linting: + files_exist: + - "CITATIONS.md" nfcore_pipelines: False custom_pipelines: True gitpod: From b75ba51dba493d8171e1bdb10d13b952a82f405b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 1 Oct 2024 16:51:32 +0200 Subject: [PATCH 542/574] fix old nf-core sync command and use the info from .nf-core.yml to sync a pipeline --- nf_core/__main__.py | 5 +++-- nf_core/utils.py | 39 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index e0c1b85e91..08589fc242 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1815,6 +1815,7 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force) # nf-core sync (deprecated) @nf_core_cli.command("sync", hidden=True, deprecated=True) +@click.pass_context @click.option( "-d", "--dir", @@ -1845,14 +1846,14 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force) @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.") @click.option("-u", "--username", type=str, help="GitHub PR: auth username.") @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template") -def command_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr): +def command_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr): """ Use `nf-core pipelines sync` instead. """ log.warning( "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead." ) - pipelines_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr) + pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr) # nf-core bump-version (deprecated) diff --git a/nf_core/utils.py b/nf_core/utils.py index 663efb6b46..7795d0d273 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1136,6 +1136,45 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] error_message += f"\n{error['loc'][0]}: {error['msg']}" raise AssertionError(error_message) + # Retrieve information if template from config file is empty + wf_config = fetch_wf_config(Path(directory)) + config_template_keys = tools_config["template"].keys() if "template" in tools_config else [] + if nf_core_yaml_config.template is None: + # The .nf-core.yml file did not contain template information + nf_core_yaml_config.template = NFCoreTemplateConfig( + org="nf-core", + name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], + description=wf_config["manifest.description"].strip('"').strip("'"), + author=wf_config["manifest.author"].strip('"').strip("'"), + version=wf_config["manifest.version"].strip('"').strip("'"), + outdir=str(directory), + ) + elif "prefix" in config_template_keys or "skip" in config_template_keys: + # The .nf-core.yml file contained the old prefix or skip keys + nf_core_yaml_config.template = NFCoreTemplateConfig( + org=tools_config["template"]["prefix"] + if "prefix" in config_template_keys + else tools_config["template"]["org"] or "nf-core", + name=tools_config["template"]["name"] + if "name" in config_template_keys + else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], + description=tools_config["template"]["description"] + if "description" in config_template_keys + else wf_config["manifest.description"].strip('"').strip("'"), + author=tools_config["template"]["author"] + if "author" in config_template_keys + else wf_config["manifest.author"].strip('"').strip("'"), + version=tools_config["template"]["version"] + if "version" in config_template_keys + else wf_config["manifest.version"].strip('"').strip("'"), + outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory), + skip_features=tools_config["template"]["skip"] + if "skip" in config_template_keys + else tools_config["template"]["skip_features"] + if "skip_features" in config_template_keys + else None, + ) + log.debug("Using config file: %s", config_fn) return config_fn, nf_core_yaml_config From a3468d3527f60b82e8ad85da7ecb43eb968c8475 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 09:33:39 +0200 Subject: [PATCH 543/574] udpate nf-core version and outdir before writing to the template .nf-core.yml --- nf_core/pipelines/create/create.py | 6 +----- nf_core/pipelines/sync.py | 10 ++++++++-- nf_core/utils.py | 10 +++++++++- 3 files changed, 18 insertions(+), 8 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 8e1d46c690..b23dc27e0d 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -182,7 +182,7 @@ def update_config(self, organisation, version, force, outdir): self.config.force = force if force else False if self.config.outdir is None: self.config.outdir = outdir if outdir else "." - if self.config.is_nfcore is None: + if self.config.is_nfcore is None or self.config.is_nfcore == "null": self.config.is_nfcore = self.config.org == "nf-core" def obtain_jinja_params_dict( @@ -363,11 +363,9 @@ def render_template(self) -> None: config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir) if config_fn is not None and config_yml is not None: with open(str(config_fn), "w") as fh: - self.config.outdir = str(self.config.outdir) config_yml.template = NFCoreTemplateConfig(**self.config.model_dump()) yaml.safe_dump(config_yml.model_dump(), fh) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") - run_prettier_on_file(self.outdir / config_fn) # Run prettier on files run_prettier_on_file(self.outdir) @@ -401,8 +399,6 @@ def fix_linting(self): with open(self.outdir / config_fn, "w") as fh: yaml.dump(nf_core_yml.model_dump(), fh, default_flow_style=False, sort_keys=False) - run_prettier_on_file(Path(self.outdir, config_fn)) - def make_pipeline_logo(self): """Fetch a logo for the new pipeline from the nf-core website""" email_logo_path = Path(self.outdir) / "assets" diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index fced35dc20..31152564a7 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -273,17 +273,23 @@ def make_template_pipeline(self): yaml.safe_dump(self.config_yml.model_dump(), config_path) try: - nf_core.pipelines.create.create.PipelineCreate( + pipeline_create_obj = nf_core.pipelines.create.create.PipelineCreate( outdir=str(self.pipeline_dir), from_config_file=True, no_git=True, force=True, - ).init_pipeline() + ) + pipeline_create_obj.init_pipeline() # set force to false to avoid overwriting files in the future if self.config_yml.template is not None: + self.config_yml.template = pipeline_create_obj.config # Set force true in config to overwrite existing files self.config_yml.template.force = False + # Set outdir as the current directory to avoid local info leaking + self.config_yml.template.outdir = "." + # Update nf-core version + self.config_yml.nf_core_version = nf_core.__version__ with open(self.config_yml_path, "w") as config_path: yaml.safe_dump(self.config_yml.model_dump(), config_path) diff --git a/nf_core/utils.py b/nf_core/utils.py index 7795d0d273..7fcb6026fc 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1148,13 +1148,16 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] author=wf_config["manifest.author"].strip('"').strip("'"), version=wf_config["manifest.version"].strip('"').strip("'"), outdir=str(directory), + is_nfcore=True, ) elif "prefix" in config_template_keys or "skip" in config_template_keys: # The .nf-core.yml file contained the old prefix or skip keys nf_core_yaml_config.template = NFCoreTemplateConfig( org=tools_config["template"]["prefix"] if "prefix" in config_template_keys - else tools_config["template"]["org"] or "nf-core", + else tools_config["template"]["org"] + if "org" in config_template_keys + else "nf-core", name=tools_config["template"]["name"] if "name" in config_template_keys else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], @@ -1173,6 +1176,11 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] else tools_config["template"]["skip_features"] if "skip_features" in config_template_keys else None, + is_nfcore=tools_config["template"]["prefix"] == "nf-core" + if "prefix" in config_template_keys + else tools_config["template"]["org"] == "nf-core" + if "org" in config_template_keys + else True, ) log.debug("Using config file: %s", config_fn) From d0a24be2c7da106f45aafd1be763cb772e0a9fa3 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 09:52:14 +0200 Subject: [PATCH 544/574] udpate yaml config only in pipeline repos --- nf_core/utils.py | 93 ++++++++++++++++++++++++------------------------ 1 file changed, 47 insertions(+), 46 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 7fcb6026fc..4e29994ca9 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1136,52 +1136,53 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] error_message += f"\n{error['loc'][0]}: {error['msg']}" raise AssertionError(error_message) - # Retrieve information if template from config file is empty - wf_config = fetch_wf_config(Path(directory)) - config_template_keys = tools_config["template"].keys() if "template" in tools_config else [] - if nf_core_yaml_config.template is None: - # The .nf-core.yml file did not contain template information - nf_core_yaml_config.template = NFCoreTemplateConfig( - org="nf-core", - name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], - description=wf_config["manifest.description"].strip('"').strip("'"), - author=wf_config["manifest.author"].strip('"').strip("'"), - version=wf_config["manifest.version"].strip('"').strip("'"), - outdir=str(directory), - is_nfcore=True, - ) - elif "prefix" in config_template_keys or "skip" in config_template_keys: - # The .nf-core.yml file contained the old prefix or skip keys - nf_core_yaml_config.template = NFCoreTemplateConfig( - org=tools_config["template"]["prefix"] - if "prefix" in config_template_keys - else tools_config["template"]["org"] - if "org" in config_template_keys - else "nf-core", - name=tools_config["template"]["name"] - if "name" in config_template_keys - else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], - description=tools_config["template"]["description"] - if "description" in config_template_keys - else wf_config["manifest.description"].strip('"').strip("'"), - author=tools_config["template"]["author"] - if "author" in config_template_keys - else wf_config["manifest.author"].strip('"').strip("'"), - version=tools_config["template"]["version"] - if "version" in config_template_keys - else wf_config["manifest.version"].strip('"').strip("'"), - outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory), - skip_features=tools_config["template"]["skip"] - if "skip" in config_template_keys - else tools_config["template"]["skip_features"] - if "skip_features" in config_template_keys - else None, - is_nfcore=tools_config["template"]["prefix"] == "nf-core" - if "prefix" in config_template_keys - else tools_config["template"]["org"] == "nf-core" - if "org" in config_template_keys - else True, - ) + if nf_core_yaml_config["repository_type"] == "pipeline": + # Retrieve information if template from config file is empty + wf_config = fetch_wf_config(Path(directory)) + config_template_keys = tools_config["template"].keys() if "template" in tools_config else [] + if nf_core_yaml_config.template is None: + # The .nf-core.yml file did not contain template information + nf_core_yaml_config.template = NFCoreTemplateConfig( + org="nf-core", + name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], + description=wf_config["manifest.description"].strip('"').strip("'"), + author=wf_config["manifest.author"].strip('"').strip("'"), + version=wf_config["manifest.version"].strip('"').strip("'"), + outdir=str(directory), + is_nfcore=True, + ) + elif "prefix" in config_template_keys or "skip" in config_template_keys: + # The .nf-core.yml file contained the old prefix or skip keys + nf_core_yaml_config.template = NFCoreTemplateConfig( + org=tools_config["template"]["prefix"] + if "prefix" in config_template_keys + else tools_config["template"]["org"] + if "org" in config_template_keys + else "nf-core", + name=tools_config["template"]["name"] + if "name" in config_template_keys + else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], + description=tools_config["template"]["description"] + if "description" in config_template_keys + else wf_config["manifest.description"].strip('"').strip("'"), + author=tools_config["template"]["author"] + if "author" in config_template_keys + else wf_config["manifest.author"].strip('"').strip("'"), + version=tools_config["template"]["version"] + if "version" in config_template_keys + else wf_config["manifest.version"].strip('"').strip("'"), + outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory), + skip_features=tools_config["template"]["skip"] + if "skip" in config_template_keys + else tools_config["template"]["skip_features"] + if "skip_features" in config_template_keys + else None, + is_nfcore=tools_config["template"]["prefix"] == "nf-core" + if "prefix" in config_template_keys + else tools_config["template"]["org"] == "nf-core" + if "org" in config_template_keys + else True, + ) log.debug("Using config file: %s", config_fn) return config_fn, nf_core_yaml_config From c95de5d29c6eaf1b3d6757d6bb95b3614850f471 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 09:58:25 +0200 Subject: [PATCH 545/574] fix pytests --- nf_core/utils.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 4e29994ca9..ef24537950 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1139,7 +1139,11 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] if nf_core_yaml_config["repository_type"] == "pipeline": # Retrieve information if template from config file is empty wf_config = fetch_wf_config(Path(directory)) - config_template_keys = tools_config["template"].keys() if "template" in tools_config else [] + config_template_keys = ( + tools_config["template"].keys() + if "template" in tools_config and tools_config["template"] is not None + else [] + ) if nf_core_yaml_config.template is None: # The .nf-core.yml file did not contain template information nf_core_yaml_config.template = NFCoreTemplateConfig( From 0b2e2277014125f601aff76a68afce09d48459be Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 10:57:52 +0200 Subject: [PATCH 546/574] take into account empty directories --- nf_core/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index ef24537950..e5bc42804c 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1136,9 +1136,9 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] error_message += f"\n{error['loc'][0]}: {error['msg']}" raise AssertionError(error_message) - if nf_core_yaml_config["repository_type"] == "pipeline": + wf_config = fetch_wf_config(Path(directory)) + if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config != {}: # Retrieve information if template from config file is empty - wf_config = fetch_wf_config(Path(directory)) config_template_keys = ( tools_config["template"].keys() if "template" in tools_config and tools_config["template"] is not None From b8b0c7b854320f727176bd72749231cc521dd64c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 2 Oct 2024 12:05:58 +0200 Subject: [PATCH 547/574] Update nf_core/utils.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index e5bc42804c..06fd69ebd1 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1137,7 +1137,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] raise AssertionError(error_message) wf_config = fetch_wf_config(Path(directory)) - if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config != {}: + if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config: # Retrieve information if template from config file is empty config_template_keys = ( tools_config["template"].keys() From 1ac4e0645f0ec72524fcff11afa23b425db0f267 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 2 Oct 2024 12:07:20 +0200 Subject: [PATCH 548/574] Update nf_core/utils.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/utils.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 06fd69ebd1..5120519e52 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1139,11 +1139,7 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] wf_config = fetch_wf_config(Path(directory)) if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config: # Retrieve information if template from config file is empty - config_template_keys = ( - tools_config["template"].keys() - if "template" in tools_config and tools_config["template"] is not None - else [] - ) + config_template_keys = tools_config.get('template', {}).keys() if nf_core_yaml_config.template is None: # The .nf-core.yml file did not contain template information nf_core_yaml_config.template = NFCoreTemplateConfig( From 97bc4ea42b5915b9e4db691c598084ba68fe2207 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 12:08:43 +0200 Subject: [PATCH 549/574] update strip commands --- nf_core/pipelines/download.py | 2 +- nf_core/pipelines/schema.py | 4 ++-- nf_core/utils.py | 18 +++++++++--------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/nf_core/pipelines/download.py b/nf_core/pipelines/download.py index 7018dc7b42..b9028d4b3a 100644 --- a/nf_core/pipelines/download.py +++ b/nf_core/pipelines/download.py @@ -746,7 +746,7 @@ def find_container_images(self, workflow_directory: str) -> None: self.nf_config is needed, because we need to restart search over raw input if no proper container matches are found. """ - config_findings.append((k, v.strip('"').strip("'"), self.nf_config, "Nextflow configs")) + config_findings.append((k, v.strip("'\""), self.nf_config, "Nextflow configs")) # rectify the container paths found in the config # Raw config_findings may yield multiple containers, so better create a shallow copy of the list, since length of input and output may be different ?!? diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 95ed5e5b6e..3aec815c76 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -71,7 +71,7 @@ def _update_validation_plugin_from_config(self) -> None: else: conf = nf_core.utils.fetch_wf_config(Path(self.pipeline_dir)) - plugins = str(conf.get("plugins", "")).strip('"').strip("'").strip(" ").split(",") + plugins = str(conf.get("plugins", "")).strip("'\"").strip(" ").split(",") plugin_found = False for plugin_instance in plugins: if "nf-schema" in plugin_instance: @@ -373,7 +373,7 @@ def validate_config_default_parameter(self, param, schema_param, config_default) # If we have a default in the schema, check it matches the config if "default" in schema_param and ( (schema_param["type"] == "boolean" and str(config_default).lower() != str(schema_param["default"]).lower()) - and (str(schema_param["default"]) != str(config_default).strip('"').strip("'")) + and (str(schema_param["default"]) != str(config_default).strip("'\"")) ): # Check that we are not deferring the execution of this parameter in the schema default with squiggly brakcets if schema_param["type"] != "string" or "{" not in schema_param["default"]: diff --git a/nf_core/utils.py b/nf_core/utils.py index 5120519e52..f5444fe02a 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1139,15 +1139,15 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] wf_config = fetch_wf_config(Path(directory)) if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config: # Retrieve information if template from config file is empty - config_template_keys = tools_config.get('template', {}).keys() + config_template_keys = tools_config.get("template", {}).keys() if nf_core_yaml_config.template is None: # The .nf-core.yml file did not contain template information nf_core_yaml_config.template = NFCoreTemplateConfig( org="nf-core", - name=wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], - description=wf_config["manifest.description"].strip('"').strip("'"), - author=wf_config["manifest.author"].strip('"').strip("'"), - version=wf_config["manifest.version"].strip('"').strip("'"), + name=wf_config["manifest.name"].strip("'\"").split("/")[-1], + description=wf_config["manifest.description"].strip("'\""), + author=wf_config["manifest.author"].strip("'\""), + version=wf_config["manifest.version"].strip("'\""), outdir=str(directory), is_nfcore=True, ) @@ -1161,16 +1161,16 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] else "nf-core", name=tools_config["template"]["name"] if "name" in config_template_keys - else wf_config["manifest.name"].strip('"').strip("'").split("/")[-1], + else wf_config["manifest.name"].strip("'\"").split("/")[-1], description=tools_config["template"]["description"] if "description" in config_template_keys - else wf_config["manifest.description"].strip('"').strip("'"), + else wf_config["manifest.description"].strip("'\""), author=tools_config["template"]["author"] if "author" in config_template_keys - else wf_config["manifest.author"].strip('"').strip("'"), + else wf_config["manifest.author"].strip("'\""), version=tools_config["template"]["version"] if "version" in config_template_keys - else wf_config["manifest.version"].strip('"').strip("'"), + else wf_config["manifest.version"].strip("'\""), outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory), skip_features=tools_config["template"]["skip"] if "skip" in config_template_keys From 86f436a0857205d4bdc3e3be4d9823d76ae0fbf9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 12:15:42 +0200 Subject: [PATCH 550/574] apply comments from code review by @mashehu --- nf_core/utils.py | 36 ++++++++---------------------------- 1 file changed, 8 insertions(+), 28 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index f5444fe02a..dd5ca66e89 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1154,34 +1154,14 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] elif "prefix" in config_template_keys or "skip" in config_template_keys: # The .nf-core.yml file contained the old prefix or skip keys nf_core_yaml_config.template = NFCoreTemplateConfig( - org=tools_config["template"]["prefix"] - if "prefix" in config_template_keys - else tools_config["template"]["org"] - if "org" in config_template_keys - else "nf-core", - name=tools_config["template"]["name"] - if "name" in config_template_keys - else wf_config["manifest.name"].strip("'\"").split("/")[-1], - description=tools_config["template"]["description"] - if "description" in config_template_keys - else wf_config["manifest.description"].strip("'\""), - author=tools_config["template"]["author"] - if "author" in config_template_keys - else wf_config["manifest.author"].strip("'\""), - version=tools_config["template"]["version"] - if "version" in config_template_keys - else wf_config["manifest.version"].strip("'\""), - outdir=tools_config["template"]["outdir"] if "outdir" in config_template_keys else str(directory), - skip_features=tools_config["template"]["skip"] - if "skip" in config_template_keys - else tools_config["template"]["skip_features"] - if "skip_features" in config_template_keys - else None, - is_nfcore=tools_config["template"]["prefix"] == "nf-core" - if "prefix" in config_template_keys - else tools_config["template"]["org"] == "nf-core" - if "org" in config_template_keys - else True, + org=tools_config["template"].get("prefix", tools_config["template"].get("org", "nf-core")), + name=tools_config["template"].get("name", wf_config["manifest.name"].strip("'\"").split("/")[-1]), + description=tools_config["template"].get("description", wf_config["manifest.description"].strip("'\"")), + author=tools_config["template"].get("author", wf_config["manifest.author"].strip("'\"")), + version=tools_config["template"].get("version", wf_config["manifest.version"].strip("'\"")), + outdir=tools_config["template"].get("outdir", str(directory)), + skip_features=tools_config["template"].get("skip", tools_config["template"].get("skip_features")), + is_nfcore=tools_config["template"].get("prefix", tools_config["template"].get("org")) == "nf-core", ) log.debug("Using config file: %s", config_fn) From 26299f0082debced834a1d8f6d301a1c3f4d365f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 2 Oct 2024 14:40:03 +0200 Subject: [PATCH 551/574] more code suggestions, thanks @mashehu --- nf_core/utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index dd5ca66e89..3f71de8d1e 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1139,7 +1139,8 @@ def load_tools_config(directory: Union[str, Path] = ".") -> Tuple[Optional[Path] wf_config = fetch_wf_config(Path(directory)) if nf_core_yaml_config["repository_type"] == "pipeline" and wf_config: # Retrieve information if template from config file is empty - config_template_keys = tools_config.get("template", {}).keys() + template = tools_config.get("template") + config_template_keys = template.keys() if template is not None else [] if nf_core_yaml_config.template is None: # The .nf-core.yml file did not contain template information nf_core_yaml_config.template = NFCoreTemplateConfig( From d52969b323c42d20cafb482980ab2a29ebd86efb Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 2 Oct 2024 12:57:44 +0000 Subject: [PATCH 552/574] Update gitpod/workspace-base Docker digest to 2cc134f --- nf_core/gitpod/gitpod.Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index c462c6a47e..2a9fbb0ed6 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -2,7 +2,7 @@ # docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile . # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used. -FROM gitpod/workspace-base@sha256:f189a4195c3861365356f9c1b438ab26fd88e1ff46ce2843afc62861fc982e0c +FROM gitpod/workspace-base@sha256:2cc134fe5bd7d8fdbe44cab294925d4bc6d2d178d94624f4c376584a22d1f7b6 USER root From 93c2def991768265bc35ebc789235f9bf55698d8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 3 Oct 2024 14:57:32 +0200 Subject: [PATCH 553/574] fix running prettier on rendered template --- nf_core/pipelines/create/create.py | 2 +- nf_core/pipelines/lint_utils.py | 30 +++++++++++++++++++++++------- nf_core/pipelines/sync.py | 4 ++-- 3 files changed, 26 insertions(+), 10 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index b23dc27e0d..8ab547c1cc 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -368,7 +368,7 @@ def render_template(self) -> None: log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") # Run prettier on files - run_prettier_on_file(self.outdir) + run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")]) def fix_linting(self): """ diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py index ff65fb0e56..b4c56c6007 100644 --- a/nf_core/pipelines/lint_utils.py +++ b/nf_core/pipelines/lint_utils.py @@ -2,9 +2,10 @@ import logging import subprocess from pathlib import Path -from typing import List +from typing import List, Union import rich +import yaml from rich.console import Console from rich.table import Table @@ -69,7 +70,7 @@ def print_fixes(lint_obj): ) -def run_prettier_on_file(file): +def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None: """Run the pre-commit hook prettier on a file. Args: @@ -80,12 +81,15 @@ def run_prettier_on_file(file): """ nf_core_pre_commit_config = Path(nf_core.__file__).parent / ".pre-commit-prettier-config.yaml" + args = ["pre-commit", "run", "--config", str(nf_core_pre_commit_config), "prettier"] + if isinstance(file, List): + args.extend(["--files", *file]) + else: + args.extend(["--files", str(file)]) + try: - subprocess.run( - ["pre-commit", "run", "--config", nf_core_pre_commit_config, "prettier", "--files", file], - capture_output=True, - check=True, - ) + subprocess.run(args, capture_output=True, check=True) + log.debug(f"${subprocess.STDOUT}") except subprocess.CalledProcessError as e: if ": SyntaxError: " in e.stdout.decode(): log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}") @@ -111,6 +115,18 @@ def dump_json_with_prettier(file_name, file_content): run_prettier_on_file(file_name) +def dump_yaml_with_prettier(file_name: Union[Path, str], file_content: dict) -> None: + """Dump a YAML file and run prettier on it. + + Args: + file_name (Path | str): A file identifier as a string or pathlib.Path. + file_content (dict): Content to dump into the YAML file + """ + with open(file_name, "w") as fh: + yaml.safe_dump(file_content, fh) + run_prettier_on_file(file_name) + + def ignore_file(lint_name: str, file_path: Path, dir_path: Path) -> List[List[str]]: """Ignore a file and add the result to the ignored list. Return the passed, failed, ignored and ignore_configs lists.""" diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index 31152564a7..12b29f15ec 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -21,6 +21,7 @@ import nf_core.pipelines.create.create import nf_core.pipelines.list import nf_core.utils +from nf_core.pipelines.lint_utils import dump_yaml_with_prettier log = logging.getLogger(__name__) @@ -290,8 +291,7 @@ def make_template_pipeline(self): self.config_yml.template.outdir = "." # Update nf-core version self.config_yml.nf_core_version = nf_core.__version__ - with open(self.config_yml_path, "w") as config_path: - yaml.safe_dump(self.config_yml.model_dump(), config_path) + dump_yaml_with_prettier(self.config_yml_path, self.config_yml.model_dump()) except Exception as err: # Reset to where you were to prevent git getting messed up. From 320037f9c88e9b888c92dab64cf7241fbb692688 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 08:55:47 +0200 Subject: [PATCH 554/574] sync: copy modules.json to TEMPLATE branch --- nf_core/pipelines/sync.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index 12b29f15ec..c1dc8768a6 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -18,6 +18,8 @@ from git import GitCommandError, InvalidGitRepositoryError import nf_core +import nf_core.modules +import nf_core.modules.install import nf_core.pipelines.create.create import nf_core.pipelines.list import nf_core.utils @@ -137,6 +139,7 @@ def sync(self): self.checkout_template_branch() self.delete_template_branch_files() self.make_template_pipeline() + self.copy_components_to_template() self.commit_template_changes() if not self.made_changes and self.force_pr: @@ -298,6 +301,16 @@ def make_template_pipeline(self): self.repo.git.reset("--hard") raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{err}") + def copy_components_to_template(self) -> None: + """ + Copy the modules.json file from the current pipeline to the TEMPLATE branch using git checkout + """ + log.info("Copying modules.json to TEMPLATE branch") + try: + self.repo.git.checkout(self.original_branch, "--", "modules.json") + except GitCommandError as e: + raise SyncExceptionError(f"Could not copy modules.json to TEMPLATE branch:\n{e}") + def commit_template_changes(self): """If we have any changes with the new template files, make a git commit""" # Check that we have something to commit From 8192ca6373fc14f5614397a3d1dc986dfc119bd3 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 09:04:58 +0200 Subject: [PATCH 555/574] remove unused imports --- nf_core/pipelines/sync.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index c1dc8768a6..31cd26dd64 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -18,8 +18,6 @@ from git import GitCommandError, InvalidGitRepositoryError import nf_core -import nf_core.modules -import nf_core.modules.install import nf_core.pipelines.create.create import nf_core.pipelines.list import nf_core.utils From 89a41eba2cc8acb212b62a360e8cf2b4d0b19787 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 09:28:44 +0200 Subject: [PATCH 556/574] handle non-existent modules.json file more gracefully --- nf_core/pipelines/sync.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index 31cd26dd64..c6d0218cce 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -307,7 +307,12 @@ def copy_components_to_template(self) -> None: try: self.repo.git.checkout(self.original_branch, "--", "modules.json") except GitCommandError as e: - raise SyncExceptionError(f"Could not copy modules.json to TEMPLATE branch:\n{e}") + # don't raise an error if the file doesn't exist + if "did not match any file(s) known to git" in str(e): + log.info("No modules.json file found in current pipeline - not copying") + return + else: + raise SyncExceptionError(f"Could not copy modules.json to TEMPLATE branch:\n{e}") def commit_template_changes(self): """If we have any changes with the new template files, make a git commit""" From 375fad3df8ea5c235a3dfb9ee44b467cd94fd208 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 4 Oct 2024 11:11:40 +0200 Subject: [PATCH 557/574] fix template new lines --- nf_core/pipeline-template/.editorconfig | 8 ++++---- nf_core/pipeline-template/CITATIONS.md | 6 ++++-- nf_core/pipeline-template/README.md | 2 +- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig index 5145366e50..1db986f5b5 100644 --- a/nf_core/pipeline-template/.editorconfig +++ b/nf_core/pipeline-template/.editorconfig @@ -11,7 +11,7 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 -{%- if modules %} +{% if modules %} # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -25,12 +25,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -{%- endif %} +{% endif %} -{%- if email %} +{% if email %} [/assets/email*] indent_size = unset -{%- endif %} +{% endif %} # ignore python and markdown [*.{py,md}] diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 2373f1de7f..01e97c1413 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -15,10 +15,12 @@ {% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. -> {% endif %} > {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> {% endif %} + +{% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -> {%- endif %} +> {% endif %} ## Software packaging/containerisation tools diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 4331454288..bcf159f465 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -7,7 +7,7 @@ -{%- else %} +{% else %} # {{ name }} From 80cca2fd13ae1d872c31435300f2b68c0db7790c Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 11:29:02 +0200 Subject: [PATCH 558/574] add pydantic autodoc --- docs/api/_src/conf.py | 2 +- docs/api/requirements.txt | 1 + nf_core/utils.py | 20 ++++++++++++++++++++ 3 files changed, 22 insertions(+), 1 deletion(-) diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py index bfdbd7888d..729cf6ba35 100644 --- a/docs/api/_src/conf.py +++ b/docs/api/_src/conf.py @@ -40,7 +40,7 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon"] +extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinxcontrib.autodoc_pydantic"] # Add any paths that contain templates here, relative to this directory. templates_path = ["./_templates"] diff --git a/docs/api/requirements.txt b/docs/api/requirements.txt index abffe30740..1d23f0b27d 100644 --- a/docs/api/requirements.txt +++ b/docs/api/requirements.txt @@ -1,3 +1,4 @@ +autodoc_pydantic Sphinx>=3.3.1 sphinxcontrib-napoleon sphinx-markdown-builder diff --git a/nf_core/utils.py b/nf_core/utils.py index 3f71de8d1e..7e3a4671d8 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1050,15 +1050,26 @@ def get_repo_releases_branches(pipeline, wfs): class NFCoreTemplateConfig(BaseModel): + """Template configuration schema""" + org: Optional[str] = None + """ Organisation name """ name: Optional[str] = None + """ Pipeline name """ description: Optional[str] = None + """ Pipeline description """ author: Optional[str] = None + """ Pipeline author """ version: Optional[str] = None + """ Pipeline version """ force: Optional[bool] = True + """ Force overwrite of existing files """ outdir: Optional[Union[str, Path]] = None + """ Output directory """ skip_features: Optional[list] = None + """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """ is_nfcore: Optional[bool] = None + """ Whether the pipeline is an nf-core pipeline. """ # convert outdir to str @field_validator("outdir") @@ -1081,13 +1092,22 @@ def get(self, item: str, default: Any = None) -> Any: class NFCoreYamlConfig(BaseModel): + """.nf-core.yml configuration file schema""" + repository_type: str + """ Type of repository: pipeline or modules """ nf_core_version: Optional[str] = None + """ Version of nf-core/tools used to create/update the pipeline""" org_path: Optional[str] = None + """ Path to the organisation's nf-core pipelines repository """ lint: Optional[LintConfigType] = None + """ Linting configuration """ template: Optional[NFCoreTemplateConfig] = None + """ Template configuration """ bump_version: Optional[Dict[str, bool]] = None + """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). """ update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None + """ Disable updating specific modules/subworkflows (when repository_type is pipeline).""" def __getitem__(self, item: str) -> Any: return getattr(self, item) From f063bf5db97ef3eb722d22bdd1d382d3943446c7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 11:44:33 +0200 Subject: [PATCH 559/574] render also utils.py docs --- docs/api/_src/api/utils.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/api/_src/api/utils.md diff --git a/docs/api/_src/api/utils.md b/docs/api/_src/api/utils.md new file mode 100644 index 0000000000..1353f97ef5 --- /dev/null +++ b/docs/api/_src/api/utils.md @@ -0,0 +1,9 @@ +# nf_core.utils + +```{eval-rst} +.. automodule:: nf_core.utils + :members: + :undoc-members: + :show-inheritance: + :private-members: +``` From 4ea365085be4e8a9ef4ad8d21dba2c39499d49fd Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 12:00:11 +0200 Subject: [PATCH 560/574] include review comments and links to docs MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/utils.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 7e3a4671d8..068da22def 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1099,15 +1099,15 @@ class NFCoreYamlConfig(BaseModel): nf_core_version: Optional[str] = None """ Version of nf-core/tools used to create/update the pipeline""" org_path: Optional[str] = None - """ Path to the organisation's nf-core pipelines repository """ + """ Path to the organisation's modules repository (used for modules repo_type only) """ lint: Optional[LintConfigType] = None - """ Linting configuration """ + """ Pipeline linting configuration, see https://nf-co.re/docs/nf-core-tools/pipelines/lint#linting-config for examples and documentation """ template: Optional[NFCoreTemplateConfig] = None - """ Template configuration """ + """ Pipeline template configuration """ bump_version: Optional[Dict[str, bool]] = None - """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). """ + """ Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https://nf-co.re/docs/nf-core-tools/modules/bump-versions for more information.""" update: Optional[Dict[str, Union[str, bool, Dict[str, Union[str, Dict[str, Union[str, bool]]]]]]] = None - """ Disable updating specific modules/subworkflows (when repository_type is pipeline).""" + """ Disable updating specific modules/subworkflows (when repository_type is pipeline). See https://nf-co.re/docs/nf-core-tools/modules/update for more information.""" def __getitem__(self, item: str) -> Any: return getattr(self, item) From 46b998b50b0b7625cec269bae7d6182e379788ba Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 12:19:48 +0200 Subject: [PATCH 561/574] install modules in TEMPLATE branch --- nf_core/modules/modules_json.py | 2 +- nf_core/pipelines/sync.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py index 536589d81e..05c64b6dee 100644 --- a/nf_core/modules/modules_json.py +++ b/nf_core/modules/modules_json.py @@ -432,7 +432,7 @@ def move_component_to_local(self, component_type: str, component: str, repo_name to_name += f"-{datetime.datetime.now().strftime('%y%m%d%H%M%S')}" shutil.move(str(current_path), local_dir / to_name) - def unsynced_components(self) -> Tuple[List[str], List[str], dict]: + def unsynced_components(self) -> Tuple[List[str], List[str], Dict]: """ Compute the difference between the modules/subworkflows in the directory and the modules/subworkflows in the 'modules.json' file. This is done by looking at all diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index c6d0218cce..d573f88668 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -18,6 +18,7 @@ from git import GitCommandError, InvalidGitRepositoryError import nf_core +import nf_core.modules.modules_json import nf_core.pipelines.create.create import nf_core.pipelines.list import nf_core.utils @@ -306,6 +307,7 @@ def copy_components_to_template(self) -> None: log.info("Copying modules.json to TEMPLATE branch") try: self.repo.git.checkout(self.original_branch, "--", "modules.json") + nf_core.modules.modules_json.ModulesJson(self.pipeline_dir).check_up_to_date() except GitCommandError as e: # don't raise an error if the file doesn't exist if "did not match any file(s) known to git" in str(e): From fa1a01dfddc12306832a7f1db459833b11e5100f Mon Sep 17 00:00:00 2001 From: mashehu Date: Fri, 4 Oct 2024 15:29:32 +0200 Subject: [PATCH 562/574] remove modules.json copy step in sync --- nf_core/pipelines/sync.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py index d573f88668..12b29f15ec 100644 --- a/nf_core/pipelines/sync.py +++ b/nf_core/pipelines/sync.py @@ -18,7 +18,6 @@ from git import GitCommandError, InvalidGitRepositoryError import nf_core -import nf_core.modules.modules_json import nf_core.pipelines.create.create import nf_core.pipelines.list import nf_core.utils @@ -138,7 +137,6 @@ def sync(self): self.checkout_template_branch() self.delete_template_branch_files() self.make_template_pipeline() - self.copy_components_to_template() self.commit_template_changes() if not self.made_changes and self.force_pr: @@ -300,22 +298,6 @@ def make_template_pipeline(self): self.repo.git.reset("--hard") raise SyncExceptionError(f"Failed to rebuild pipeline from template with error:\n{err}") - def copy_components_to_template(self) -> None: - """ - Copy the modules.json file from the current pipeline to the TEMPLATE branch using git checkout - """ - log.info("Copying modules.json to TEMPLATE branch") - try: - self.repo.git.checkout(self.original_branch, "--", "modules.json") - nf_core.modules.modules_json.ModulesJson(self.pipeline_dir).check_up_to_date() - except GitCommandError as e: - # don't raise an error if the file doesn't exist - if "did not match any file(s) known to git" in str(e): - log.info("No modules.json file found in current pipeline - not copying") - return - else: - raise SyncExceptionError(f"Could not copy modules.json to TEMPLATE branch:\n{e}") - def commit_template_changes(self): """If we have any changes with the new template files, make a git commit""" # Check that we have something to commit From d6cd2738bc16516a6285895207a72c8f61a31d8f Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Thu, 26 Sep 2024 11:50:14 +0200 Subject: [PATCH 563/574] Improve the Github Action to test offline support better. --- .../.github/workflows/download_pipeline.yml | 35 ++++++++++++++++--- 1 file changed, 31 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index f704609ca8..f3936f5e01 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -54,33 +54,60 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "{% raw %}REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %} + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l) + echo "Post-pipeline container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + echo "The number of container images has changed. The pipeline has no support for offline runs!" + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi From ca5eaa5c36f1dd4c64544313545bf854786dd16d Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Thu, 26 Sep 2024 12:09:21 +0200 Subject: [PATCH 564/574] Add raw statements for template and update Singularity version in runner. --- .../.github/workflows/download_pipeline.yml | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index f3936f5e01..406ef3bddf 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -77,7 +79,7 @@ jobs: - name: Count the downloaded number of container images id: count_initial run: | - image_count=$(ls -1 ./singularity_container_images | wc -l) + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Initial container image count: $image_count" echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} @@ -99,15 +101,18 @@ jobs: - name: Count the downloaded number of container images id: count_afterwards run: | - image_count=$(ls -1 ./singularity_container_images | wc -l) - echo "Post-pipeline container image count: $image_count" + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} - name: Compare container image counts run: | + {% raw %} if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - echo "The number of container images has changed. The pipeline has no support for offline runs!" + echo "$(expr ${{ env.IMAGE_COUNT_AFTER }}-${{ env.IMAGE_COUNT_INITIAL }}) additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images exit 1 else echo "The pipeline can be downloaded successfully!" fi + {% endraw %} From 5c39ab8aa0ab0f7ed459ae0566c7e79312e23c50 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Thu, 26 Sep 2024 13:15:15 +0200 Subject: [PATCH 565/574] Fix container image count calculation. --- .../.github/workflows/download_pipeline.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 406ef3bddf..29a9e8b5d4 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -69,7 +69,7 @@ jobs: --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' @@ -109,7 +109,10 @@ jobs: run: | {% raw %} if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - echo "$(expr ${{ env.IMAGE_COUNT_AFTER }}-${{ env.IMAGE_COUNT_INITIAL }}) additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" tree ./singularity_container_images exit 1 else From 8feb89b770ebee56a34d1d419e6fbd44189c0e0f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 4 Oct 2024 14:11:53 +0000 Subject: [PATCH 566/574] chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.6.9 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7cbde0c86b..67aa3204c4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.0 + rev: v0.6.9 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 89961d6d62f7c1c4ba64181efa1169a52eb0e670 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Fri, 4 Oct 2024 16:17:42 +0200 Subject: [PATCH 567/574] Tidy Jinja template markup. --- CHANGELOG.md | 1 + .../.github/workflows/download_pipeline.yml | 7 +++---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 12a0c9911e..717e82a489 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,7 @@ - Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168)) - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176)) - Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167)) +- Extend `download_pipeline.yml` to count pre-downloaded container images. ([#3182](https://github.com/nf-core/tools/pull/3182)) ### Linting diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 29a9e8b5d4..8d70f38966 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -74,7 +74,7 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %} + run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% if test_config %} - name: Count the downloaded number of container images id: count_initial @@ -96,7 +96,7 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}{% endif %} + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results - name: Count the downloaded number of container images id: count_afterwards @@ -107,7 +107,6 @@ jobs: - name: Compare container image counts run: | - {% raw %} if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ env.IMAGE_COUNT_INITIAL }} final_count=${{ env.IMAGE_COUNT_AFTER }} @@ -118,4 +117,4 @@ jobs: else echo "The pipeline can be downloaded successfully!" fi - {% endraw %} + {% endif %}{% endraw %} From 664fbfab163c9b21ef303baa0a34be3965e212a2 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Fri, 4 Oct 2024 16:34:54 +0200 Subject: [PATCH 568/574] The raw statements must not wrap other Jinja markup. --- .../pipeline-template/.github/workflows/download_pipeline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 8d70f38966..29b9947549 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -74,7 +74,7 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% if test_config %} + run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %} - name: Count the downloaded number of container images id: count_initial @@ -117,4 +117,4 @@ jobs: else echo "The pipeline can be downloaded successfully!" fi - {% endif %}{% endraw %} + {% endraw %}{% endif %} From fc9c0010709455a5bbcc70aa51cf21d8d23d5798 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 4 Oct 2024 20:36:21 +0000 Subject: [PATCH 569/574] chore(deps): update python:3.12-slim docker digest to af4e85f --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index fb1a867937..8269e95702 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.12-slim@sha256:59c7332a4a24373861c4a5f0eec2c92b87e3efeb8ddef011744ef9a751b1d11c +FROM python:3.12-slim@sha256:af4e85f1cac90dd3771e47292ea7c8a9830abfabbe4faa5c53f158854c2e819d LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From aa158204e13e42a9f832916ee0a9fc860e409bb1 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 10:00:28 +0200 Subject: [PATCH 570/574] add pipeline name as an optional sync input --- .github/workflows/sync.yml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index 55880e8130..c86d79d788 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -19,6 +19,10 @@ on: description: "Force a PR to be created" type: boolean default: false + pipeline: + description: "Pipeline to sync" + type: string + default: "all" # Cancel if a newer run is started concurrency: @@ -35,6 +39,14 @@ jobs: run: | if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then echo '{"pipeline":["testpipeline"]}' > pipeline_names.json + elif [ "${{ github.event.inputs.pipeline }}" != "all" ]; then + curl -O https://nf-co.re/pipeline_names.json + # check if the pipeline exists + if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then + echo "Pipeline ${{ github.event.inputs.pipeline }} does not exist" + exit 1 + fi + echo '{"pipeline":["${{ github.event.inputs.pipeline }}"]}' > pipeline_names.json else curl -O https://nf-co.re/pipeline_names.json fi From 962f4b3f137866527cecb820eea0daf75aba02d0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 11:01:23 +0200 Subject: [PATCH 571/574] fix for multiqc_config template for released pipelines --- nf_core/pipeline-template/assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index cd4e539b31..e6fd878986 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -3,11 +3,11 @@ report_comment: > This report has been generated by the     {{ name }} analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the documentation.{% endif %} - {%- else %} + {%- else -%} This report has been generated by the {{ name }} analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the documentation.{% endif %} - {% endif %} + {%- endif %} report_section_order: "{{ name_noslash }}-methods-description": order: -1000 From baeb1dfd351b922e34daf61257eb4539c9d4b8e3 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 7 Oct 2024 11:22:32 +0200 Subject: [PATCH 572/574] bump version to 3.0.0 --- .gitpod.yml | 2 +- CHANGELOG.md | 17 ++++++++--------- setup.py | 2 +- 3 files changed, 10 insertions(+), 11 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index efe193f35f..f92457278b 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:dev +image: nfcore/gitpod:latest tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 717e82a489..1904cd99c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/tools: Changelog -## v3.0.0dev +## [v3.0.0 - Titanium Tapir](https://github.com/nf-core/tools/releases/tag/3.0.0) - [2024-10-07] **Highlights** @@ -9,7 +9,6 @@ - A new Text User Interface app when running `nf-core pipelines create` to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters) - We replaced nf-validation with nf-schema in the pipeline template - CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release. -- New command `nf-core pipelines ro-crate` to create a [Research Object (RO) crate](https://www.researchobject.org/ro-crate/) for a pipeline - `nf-core licences` command is deprecated. - The structure of nf-core/tools pytests has been updated - The structure of the API docs has been updated @@ -30,12 +29,12 @@ - add option to exclude changelog from custom pipeline template ([#3104](https://github.com/nf-core/tools/pull/3104)) - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125)) - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126)) -- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116)) - add option to exclude nf-schema from the template ([#3116](https://github.com/nf-core/tools/pull/3116)) - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129)) - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130)) - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133)) - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134)) +- Use nf-schema instead of nf-validation ([#3116](https://github.com/nf-core/tools/pull/3116)) - test pipeline with conda and singularity on PRs to master ([#3149](https://github.com/nf-core/tools/pull/3149)) - run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148)) - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099)) @@ -61,16 +60,16 @@ ### Pipeline create command -- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) -- Create: Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) -- Create app: display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) -- Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) +- Allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008)) +- Mock git cretentials to generate stable textual snapshots ([#3007](https://github.com/nf-core/tools/pull/3007)) +- Display input textbox with equally spaced grid ([#3038](https://github.com/nf-core/tools/pull/3038)) +- Allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094)) ### Components - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) - Add `--migrate_pytest` option to `nf-core test` command ([#3085](https://github.com/nf-core/tools/pull/3085)) -- Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) +- Allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077)) ### Download @@ -88,7 +87,6 @@ - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991)) -- update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) - move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983)) - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003)) - Remove nf-core licences command ([#3012](https://github.com/nf-core/tools/pull/3012)) @@ -112,6 +110,7 @@ - Update python:3.12-slim Docker digest to 59c7332 ([#3124](https://github.com/nf-core/tools/pull/3124)) - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091)) - Update to pytest v8 and move it to dev dependencies ([#3058](https://github.com/nf-core/tools/pull/3058)) +- Update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998)) ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09] diff --git a/setup.py b/setup.py index 45df29b8bc..95a4655306 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.0.0dev" +version = "3.0.0" with open("README.md") as f: readme = f.read() From 0865cd1df778d2c5bbf2e31ddb06f58c4103f3be Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 7 Oct 2024 11:22:55 +0200 Subject: [PATCH 573/574] update nf-core command in sync.yml --- .github/workflows/sync.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index c86d79d788..d453dc9305 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -94,7 +94,7 @@ jobs: run: | git config --global user.email "core@nf-co.re" git config --global user.name "nf-core-bot" - nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync -d nf-core/${{ matrix.pipeline }} \ + nf-core --log-file sync_log_${{ matrix.pipeline }}.txt pipelines sync -d nf-core/${{ matrix.pipeline }} \ --from-branch dev \ --pull-request \ --username nf-core-bot \ From f20f797ce755bdd2647bb951be37d54c2435921b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 7 Oct 2024 11:35:22 +0200 Subject: [PATCH 574/574] fix some more template newlines --- nf_core/pipeline-template/.github/CONTRIBUTING.md | 4 ++-- nf_core/pipeline-template/docs/output.md | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index f331d38673..63cddcb7fc 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -37,7 +37,7 @@ You have the option to test your changes locally by running the pipeline. For re nf-test test --profile debug,test,docker --verbose ``` -{% endif %} +{% endif -%} When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -95,7 +95,7 @@ If you wish to contribute a new step, please use the following coding standards: {%- if multiqc %} 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - {% endif %} + {%- endif %} ### Default values diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 5e42d50cc5..083c46ecda 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -58,7 +58,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - {% if email %}- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %} + {%- if email %} + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %} - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`.