Merge pull request #2404 from ewels/textual-create

Textual create

.editorconfig

@@ -20,3 +20,11 @@ indent_style = unset
 
 [**/Makefile]
 indent_style = unset
+
+[tests/__snapshots__/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset

.github/actions/create-lint-wf/action.yml

@@ -27,7 +27,7 @@ runs:
       run: |
         mkdir -p create-lint-wf && cd create-lint-wf
         export NXF_WORK=$(pwd)
-        nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        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

.github/workflows/create-test-lint-wf-template.yml

@@ -84,29 +84,29 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
+          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 "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
+          printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
 
       - name: Create template skip igenomes
         run: |
-          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
+          printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
 
       - name: Create template skip ci
         run: |
-          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
+          printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
 
       - name: Create template skip nf_core_configs
         run: |
-          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
+          printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.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 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 ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |

.github/workflows/create-test-wf.yml

@@ -70,7 +70,11 @@ jobs:
         run: |
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+          # echo current directory
+          pwd
+          # echo content of current directory
+          ls -la
           nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact

.github/workflows/pytest.yml

@@ -142,6 +142,13 @@ jobs:
             exit 1
           fi
 
+      - name: Store snapshot report
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        if: always()
+        with:
+          name: Snapshot Report ${{ matrix.test }}
+          path: ./snapshot_report.html
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:

.gitignore

@@ -115,3 +115,6 @@ ENV/
 pip-wheel-metadata
 .vscode
 .*.sw?
+
+# Textual
+snapshot_report.html

MANIFEST.in

@@ -9,3 +9,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
 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

nf_core/__main__.py

@@ -17,7 +17,7 @@
 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.utils import check_if_outdated, rich_force_colors, setup_nfcore_dir
+from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
 
 # Set up logging as the root logger
 # Submodules should all traverse back to this
@@ -45,7 +45,7 @@
         {
             "name": "Commands for developers",
             "commands": [
-                "create",
+                "pipelines",
                 "lint",
                 "modules",
                 "subworkflows",
@@ -56,6 +56,12 @@
             ],
         },
     ],
+    "nf-core pipelines": [
+        {
+            "name": "Pipeline commands",
+            "commands": ["create"],
+        },
+    ],
     "nf-core modules": [
         {
             "name": "For pipelines",
@@ -115,25 +121,11 @@ def run_nf_core():
     # print nf-core header if environment variable is not set
     if os.environ.get("_NF_CORE_COMPLETE") is None:
         # Print nf-core header
-        stderr.print(f"\n[green]{' ' * 42},--.[grey39]/[green],-.", highlight=False)
-        stderr.print(
-            "[blue]          ___     __   __   __   ___     [green]/,-._.--~\\",
-            highlight=False,
-        )
-        stderr.print(
-            r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {",
-            highlight=False,
-        )
-        stderr.print(
-            r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,",
-            highlight=False,
-        )
-        stderr.print(
-            "[green]                                          `._,._,'\n",
-            highlight=False,
-        )
+        stderr.print("\n")
+        for line in nfcore_logo:
+            stderr.print(line, highlight=False)
         stderr.print(
-            f"[grey39]    nf-core/tools version {__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
+            f"\n[grey39]    nf-core/tools version {__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
             highlight=False,
         )
         try:
@@ -494,53 +486,6 @@ def licences(pipeline, json):
         sys.exit(1)
 
 
-# nf-core create
-@nf_core_cli.command()
-@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="1.0dev", 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("--plain", is_flag=True, help="Use the standard nf-core template")
-def create(name, description, author, version, force, outdir, template_yaml, plain):
-    """
-    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.
-    """
-    from nf_core.create import PipelineCreate
-
-    try:
-        create_obj = PipelineCreate(
-            name,
-            description,
-            author,
-            version=version,
-            force=force,
-            outdir=outdir,
-            template_yaml_path=template_yaml,
-            plain=plain,
-        )
-        create_obj.init_pipeline()
-    except UserWarning as e:
-        log.error(e)
-        sys.exit(1)
-
-
 # nf-core lint
 @nf_core_cli.command()
 @click.option(
@@ -658,6 +603,111 @@ def lint(
         sys.exit(1)
 
 
+# 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 create_pipeline(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 create (deprecated)
+@nf_core_cli.command(hidden=True, deprecated=True)
+@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, 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):
+    """
+    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.error(
+        "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
+    )
+    sys.exit(0)
+
+
 # nf-core modules subcommands
 @nf_core_cli.group()
 @click.option(

nf_core/lint/files_unchanged.py

@@ -8,7 +8,7 @@
 
 import yaml
 
-import nf_core.create
+import nf_core.pipelines.create.create
 
 log = logging.getLogger(__name__)
 
@@ -109,7 +109,7 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     ]
 
     # Only show error messages from pipeline creation
-    logging.getLogger("nf_core.create").setLevel(logging.ERROR)
+    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()
@@ -119,16 +119,16 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
         "name": short_name,
         "description": self.nf_config["manifest.description"].strip("\"'"),
         "author": self.nf_config["manifest.author"].strip("\"'"),
-        "prefix": prefix,
+        "org": prefix,
     }
 
     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 = Path(tmp_dir, f"{prefix}-{short_name}")
-    create_obj = nf_core.create.PipelineCreate(
-        None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
+    test_pipeline_dir = os.path.join(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
     )
     create_obj.init_pipeline()
 

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -9,7 +9,7 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 > [!NOTE]
 > If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
@@ -63,7 +63,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 ## Getting help
 

nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md

@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
-      {%- if branded %}
+      {%- 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`).