Merge branch 'dev' into maxulysse-patch-7

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### 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
@@ -17,6 +18,8 @@
 
 ### General
 
+- Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220))
+
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 
 ### Template

nf_core/pipeline-template/nextflow.config

@@ -286,7 +286,7 @@ validation {
 \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
 

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")

tests/pipelines/test_bump_version.py

@@ -13,12 +13,25 @@ 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")
+        nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "1.1.0")
         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"
+        assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1.0"
+
+        # Check multiqc_config.yml
+        with open(new_pipeline_obj._fp("assets/multiqc_config.yml")) as fh:
+            multiqc_config = yaml.safe_load(fh)
+
+            assert "report_comment" in multiqc_config
+            assert "/releases/tag/1.1.0" in multiqc_config["report_comment"]
+
+        # Check .nf-core.yml
+        with open(new_pipeline_obj._fp(".nf-core.yml")) as fh:
+            nf_core_yml = yaml.safe_load(fh)
+            if nf_core_yml["template"]:
+                assert nf_core_yml["template"]["version"] == "1.1.0"
 
     def test_dev_bump_pipeline_version(self):
         """Test that making a release works with a dev name and a leading v"""
@@ -33,7 +46,7 @@ def test_dev_bump_pipeline_version(self):
     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"
+        version = "25.04.2"
         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()