Merge branch 'dev' into fix-typos

.github/workflows/update-textual-snapshots.yml

@@ -46,7 +46,7 @@ jobs:
       - name: Run pytest to update snapshots
         id: pytest
         run: |
-          python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes  --durations=0
+          python3 -m pytest tests/pipelines/test_create_app.py --snapshot-update --color=yes  --durations=0
         continue-on-error: true
 
       # indication that the run has finished

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -1,5 +1,27 @@
 # nf-core/tools: Changelog
 
+## v3.0.3dev
+
+### Template
+
+- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223))
+- Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
+- Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225))
+
+### Download
+
+### Linting
+
+### Modules
+
+### Subworkflows
+
+### General
+
+- Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
+- create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229))
+
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 
 ### Template

CONTRIBUTING.md

@@ -153,7 +153,7 @@ 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 the Textual snapshots (run by `tests/pipelines/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/pipeline-template/nextflow.config

@@ -272,7 +272,7 @@ validation {
     defaultIgnoreParams = ["genomes"]
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         {% if is_nfcore -%}
@@ -283,15 +283,15 @@ validation {
 \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[0;35m  {{ 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")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "\n* 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
+    https://github.com/{{ name }}/blob/master/CITATIONS.md
 """{% endif %}
     }{% if is_nfcore %}
     summary {

nf_core/pipeline-template/workflows/pipeline.nf

@@ -47,7 +47,7 @@ workflow {{ short_name|upper }} {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml',
+            name: {% if is_nfcore %}'nf_core_'  + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }

nf_core/pipelines/bump_version.py

@@ -5,9 +5,10 @@
 import logging
 import re
 from pathlib import Path
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import rich.console
+from ruamel.yaml import YAML
 
 import nf_core.utils
 from nf_core.utils import Pipeline
@@ -60,6 +61,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
                     f"/releases/tag/{new_version}",
                 )
             ],
+            yaml_key=["report_comment"],
         )
     if multiqc_current_version != "dev" and multiqc_new_version == "dev":
         update_file_version(
@@ -71,6 +73,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
                     "/tree/dev",
                 )
             ],
+            yaml_key=["report_comment"],
         )
     if multiqc_current_version == "dev" and multiqc_new_version != "dev":
         update_file_version(
@@ -82,6 +85,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
                     f"/releases/tag/{multiqc_new_version}",
                 )
             ],
+            yaml_key=["report_comment"],
         )
     update_file_version(
         Path("assets", "multiqc_config.yml"),
@@ -92,6 +96,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
                 f"/{multiqc_new_version}/",
             ),
         ],
+        yaml_key=["report_comment"],
     )
     # nf-test snap files
     pipeline_name = pipeline_obj.nf_config.get("manifest.name", "").strip(" '\"")
@@ -107,6 +112,20 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
                 )
             ],
         )
+    # .nf-core.yml - pipeline version
+    # update entry: version: 1.0.0dev, but not `nf_core_version`, or `bump_version`
+    update_file_version(
+        ".nf-core.yml",
+        pipeline_obj,
+        [
+            (
+                current_version,
+                new_version,
+            )
+        ],
+        required=False,
+        yaml_key=["template", "version"],
+    )
 
 
 def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
@@ -147,10 +166,11 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
                 # example:
                 # NXF_VER:
                 #   - "20.04.0"
-                rf"- \"{re.escape(current_version)}\"",
-                f'- "{new_version}"',
+                current_version,
+                new_version,
             )
         ],
+        yaml_key=["jobs", "test", "strategy", "matrix", "NXF_VER"],
     )
 
     # README.md - Nextflow version badge
@@ -161,70 +181,128 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:
             (
                 rf"nextflow%20DSL2-%E2%89%A5{re.escape(current_version)}-23aa62.svg",
                 f"nextflow%20DSL2-%E2%89%A5{new_version}-23aa62.svg",
-            ),
-            (
-                # example: 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=20.04.0`)
-                rf"1\.\s*Install\s*\[`Nextflow`\]\(https:\/\/www\.nextflow\.io\/docs\/latest\/getstarted\.html#installation\)\s*\(`>={re.escape(current_version)}`\)",
-                f"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>={new_version}`)",
-            ),
+            )
         ],
     )
 
 
-def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patterns: List[Tuple[str, str]]) -> None:
-    """Updates the version number in a requested file.
+def update_file_version(
+    filename: Union[str, Path],
+    pipeline_obj: Pipeline,
+    patterns: List[Tuple[str, str]],
+    required: bool = True,
+    yaml_key: Optional[List[str]] = None,
+) -> None:
+    """
+    Updates a file with a new version number.
 
     Args:
-        filename (str): File to scan.
-        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.
-
-    Raises:
-        ValueError, if the version number cannot be found.
+        filename (str): The name of the file to update.
+        pipeline_obj (nf_core.utils.Pipeline): A `Pipeline` object that holds information
+            about the pipeline contents.
+        patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to
+            match and the replacement strings.
+        required (bool, optional): Whether the file is required to exist. Defaults to `True`.
+        yaml_key (Optional[List[str]], optional): The YAML key to update. Defaults to `None`.
     """
-    # Load the file
-    fn = pipeline_obj._fp(filename)
-    content = ""
-    try:
-        with open(fn) as fh:
-            content = fh.read()
-    except FileNotFoundError:
+    fn: Path = pipeline_obj._fp(filename)
+
+    if not fn.exists():
         log.warning(f"File not found: '{fn}'")
         return
 
-    replacements = []
-    for pattern in patterns:
-        found_match = False
+    if yaml_key:
+        update_yaml_file(fn, patterns, yaml_key, required)
+    else:
+        update_text_file(fn, patterns, required)
 
-        newcontent = []
-        for line in content.splitlines():
-            # Match the pattern
-            matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line)
-            if matches_pattern:
-                found_match = True
 
-                # Replace the match
-                newline = re.sub(pattern[0], pattern[1], line)
-                newcontent.append(newline)
+def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[str], required: bool):
+    """
+    Updates a YAML file with a new version number.
 
-                # Save for logging
-                replacements.append((line, newline))
+    Args:
+        fn (Path): The name of the file to update.
+        patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to
+            match and the replacement strings.
+        yaml_key (List[str]): The YAML key to update.
+        required (bool): Whether the file is required to exist.
+    """
+    yaml = YAML()
+    yaml.preserve_quotes = True
+    with open(fn) as file:
+        yaml_content = yaml.load(file)
+
+    try:
+        target = yaml_content
+        for key in yaml_key[:-1]:
+            target = target[key]
 
-            # No match, keep line as it is
+        last_key = yaml_key[-1]
+        current_value = target[last_key]
+
+        new_value = current_value
+        for pattern, replacement in patterns:
+            # check if current value is list
+            if isinstance(current_value, list):
+                new_value = [re.sub(pattern, replacement, item) for item in current_value]
             else:
-                newcontent.append(line)
+                new_value = re.sub(pattern, replacement, current_value)
 
-        if found_match:
-            content = "\n".join(newcontent) + "\n"
-        else:
-            log.error(f"Could not find version number in {filename}: `{pattern}`")
+        if new_value != current_value:
+            target[last_key] = new_value
+            with open(fn, "w") as file:
+                yaml.dump(yaml_content, file)
+            log.info(f"Updated version in YAML file '{fn}'")
+            log_change(str(current_value), str(new_value))
+    except KeyError as e:
+        handle_error(f"Could not find key {e} in the YAML structure of {fn}", required)
 
-    log.info(f"Updated version in '{filename}'")
-    for replacement in replacements:
-        stderr.print(f"          [red] - {replacement[0].strip()}", highlight=False)
-        stderr.print(f"          [green] + {replacement[1].strip()}", highlight=False)
-    stderr.print("\n")
 
-    with open(fn, "w") as fh:
-        fh.write(content)
+def update_text_file(fn: Path, patterns: List[Tuple[str, str]], required: bool):
+    """
+    Updates a text file with a new version number.
+
+    Args:
+        fn (Path): The name of the file to update.
+        patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to
+            match and the replacement strings.
+        required (bool): Whether the file is required to exist.
+    """
+    with open(fn) as file:
+        content = file.read()
+
+    updated = False
+    for pattern, replacement in patterns:
+        new_content, count = re.subn(pattern, replacement, content)
+        if count > 0:
+            log_change(content, new_content)
+            content = new_content
+            updated = True
+            log.info(f"Updated version in '{fn}'")
+            log.debug(f"Replaced pattern '{pattern}' with '{replacement}' {count} times")
+        elif required:
+            handle_error(f"Could not find version number in {fn}: `{pattern}`", required)
+
+    if updated:
+        with open(fn, "w") as file:
+            file.write(content)
+
+
+def handle_error(message: str, required: bool):
+    if required:
+        raise ValueError(message)
+    else:
+        log.info(message)
+
+
+def log_change(old_content: str, new_content: str):
+    old_lines = old_content.splitlines()
+    new_lines = new_content.splitlines()
+
+    for old_line, new_line in zip(old_lines, new_lines):
+        if old_line != new_line:
+            stderr.print(f"          [red] - {old_line.strip()}", highlight=False)
+            stderr.print(f"          [green] + {new_line.strip()}", highlight=False)
+
+    stderr.print("\n")

nf_core/pipelines/create/__init__.py

@@ -1,14 +1,11 @@
 """A Textual app to create a pipeline."""
 
 import logging
-from pathlib import Path
 
 import click
-import yaml
 from textual.app import App
-from textual.widgets import Button
+from textual.widgets import Button, Switch
 
-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
@@ -46,6 +43,7 @@ class PipelineCreateApp(App[utils.CreateConfig]):
     BINDINGS = [
         ("d", "toggle_dark", "Toggle dark mode"),
         ("q", "quit", "Quit"),
+        ("a", "toggle_all", "Toggle all"),
     ]
     SCREENS = {
         "welcome": WelcomeScreen(),
@@ -105,3 +103,14 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
     def action_toggle_dark(self) -> None:
         """An action to toggle dark mode."""
         self.dark: bool = not self.dark
+
+    def action_toggle_all(self) -> None:
+        """An action to toggle all Switches."""
+        switches = self.query(Switch)
+        if not switches:
+            return  # No Switches widgets found
+        # Determine the new state based on the first switch
+        new_state = not switches.first().value if switches.first() else True
+        for switch in switches:
+            switch.value = new_state
+        self.refresh()