Merge pull request #2874 from nf-core/2741-add-the-template-version-t…

…o-the-pipeline-nf-coreyml-file

Add nf_core_version to .nf-core.yml

CHANGELOG.md

@@ -53,6 +53,7 @@
 - Fix topic extraction step for hashtags in toots ([#2810](https://github.com/nf-core/tools/pull/2810))
 - Update modules and subworkflows in the template ([#2811](https://github.com/nf-core/tools/pull/2811))
 - Unpin setup-nextflow and action-tower-launch ([#2806](https://github.com/nf-core/tools/pull/2806))
+- Add nf-core-version to `.nf-core.yml` ([#2874](https://github.com/nf-core/tools/pull/2874))
 
 ### Download
 

docs/api/_src/pipeline_lint_tests/nfcore_yml.md

@@ -0,0 +1,5 @@
+# nfcore_yml
+
+```{eval-rst}
+.. automethod:: nf_core.lint.PipelineLint.nfcore_yml
+```

nf_core/lint/__init__.py

@@ -206,6 +206,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     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,
     )
@@ -264,6 +265,7 @@ def _get_all_lint_tests(release_mode):
             "modules_json",
             "multiqc_config",
             "modules_structure",
+            "nfcore_yml",
         ] + (["version_consistency"] if release_mode else [])
 
     def _load(self):

nf_core/lint/nfcore_yml.py

@@ -0,0 +1,75 @@
+import re
+from pathlib import Path
+from typing import Dict, List
+
+from nf_core import __version__
+
+REPOSITORY_TYPES = ["pipeline", "modules"]
+
+
+def nfcore_yml(self) -> Dict[str, List[str]]:
+    """Repository ``.nf-core.yml`` tests
+
+    The ``.nf-core.yml`` contains metadata for nf-core tools to correctly apply its features.
+
+    * repository type:
+
+        * Check that the repository type is set.
+
+    * nf core version:
+
+         * Check if the nf-core version is set to the latest version.
+
+    """
+    passed: List[str] = []
+    warned: List[str] = []
+    failed: List[str] = []
+    ignored: List[str] = []
+
+    # Remove field that should be ignored according to the linting config
+    ignore_configs = self.lint_config.get(".nf-core", [])
+
+    try:
+        with open(Path(self.wf_path, ".nf-core.yml")) as fh:
+            content = fh.read()
+    except FileNotFoundError:
+        with open(Path(self.wf_path, ".nf-core.yaml")) as fh:
+            content = fh.read()
+
+    if "repository_type" not in ignore_configs:
+        # Check that the repository type is set in the .nf-core.yml
+        repo_type_re = r"repository_type: (.+)"
+        match = re.search(repo_type_re, content)
+        if match:
+            repo_type = match.group(1)
+            if repo_type not in REPOSITORY_TYPES:
+                failed.append(
+                    f"Repository type in `.nf-core.yml` is not valid. "
+                    f"Should be one of `[{', '.join(REPOSITORY_TYPES)}]` but was `{repo_type}`"
+                )
+            else:
+                passed.append(f"Repository type in `.nf-core.yml` is valid: `{repo_type}`")
+        else:
+            warned.append("Repository type not set in `.nf-core.yml`")
+    else:
+        ignored.append("`.nf-core.yml` variable ignored 'repository_type'")
+
+    if "nf_core_version" not in ignore_configs:
+        # Check that the nf-core version is set in the .nf-core.yml
+        nf_core_version_re = r"nf_core_version: (.+)"
+        match = re.search(nf_core_version_re, content)
+        if match:
+            nf_core_version = match.group(1).strip('"')
+            if nf_core_version != __version__ and "dev" not in nf_core_version:
+                warned.append(
+                    f"nf-core version in `.nf-core.yml` is not set to the latest version. "
+                    f"Should be `{__version__}` but was `{nf_core_version}`"
+                )
+            else:
+                passed.append(f"nf-core version in `.nf-core.yml` is set to the latest version: `{nf_core_version}`")
+        else:
+            warned.append("nf-core version not set in `.nf-core.yml`")
+    else:
+        ignored.append("`.nf-core.yml` variable ignored 'nf_core_version'")
+
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

nf_core/pipeline-template/.nf-core.yml

@@ -1 +1,2 @@
 repository_type: pipeline
+nf_core_version: "{{ nf_core_version }}"

tests/lint/nfcore_yml.py

@@ -0,0 +1,53 @@
+import re
+from pathlib import Path
+
+import nf_core.create
+import nf_core.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.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.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

tests/test_lint.py

@@ -233,6 +233,11 @@ 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]
+        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,