Pipeline version consistency check

nf_core/pipelines/lint/version_consistency.py

@@ -7,14 +7,15 @@ def version_consistency(self):
     .. note:: This test only runs when the ``--release`` flag is set for ``nf-core pipelines lint``,
               or ``$GITHUB_REF`` is equal to ``main``.
 
-    This lint fetches the pipeline version number from three possible locations:
+    This lint fetches the pipeline version number from four possible locations:
 
     * The pipeline config, ``manifest.version``
     * The docker container in the pipeline config, ``process.container``
 
         Some pipelines may not have this set on a pipeline level. If it is not found, it is ignored.
 
     * ``$GITHUB_REF``, if it looks like a release tag (``refs/tags/<something>``)
+    * The YAML file .nf-core.yml
 
     The test then checks that:
 
@@ -45,6 +46,10 @@ def version_consistency(self):
     ):
         versions["GITHUB_REF"] = os.path.basename(os.environ["GITHUB_REF"].strip(" '\""))
 
+    # Get version from the .nf-core.yml template
+    if self.nf_config.get("config_yml.template.version", ""):
+        versions["nfcore_yml.version"] = self.nf_config.get("config_yml.template.version", "").strip(" '\"")
+
     # Check if they are all numeric
     for v_type, version in versions.items():
         if not version.replace(".", "").isdigit():
@@ -57,7 +62,7 @@ def version_consistency(self):
                 ", ".join([f"{k} = {v}" for k, v in versions.items()])
             )
         )
-
-    passed.append("Version tags are numeric and consistent between container, release tag and config.")
+    else:
+        passed.append("Version tags are consistent between container, release tag, config and .nf-core.yml.")
 
     return {"passed": passed, "failed": failed}

tests/pipelines/lint/test_version_consistency.py

@@ -5,15 +5,71 @@
 
 
 class TestLintVersionConsistency(TestLint):
-    def test_version_consistency(self):
-        """Tests that config variable existence test fails with bad pipeline name"""
+    def test_version_consistency_pass(self):
+        """Tests that pipeline version consistency test passes with good 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()
+
+        # Set the version numbers to be consistent
+        lint_obj.nf_config["manifest.version"] = "1.0.0"
+        lint_obj.nf_config["config_yml.template.version"] = "1.0.0"
+
+        result = lint_obj.version_consistency()
+        assert result["passed"] == [
+            "Version tags are consistent between container, release tag, config and .nf-core.yml."
+        ]
+        assert result["failed"] == []
+
+    def test_version_consistency_not_numeric(self):
+        """Tests that pipeline version consistency test fails with non-numeric version numbers"""
         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."
+            "Version tags are consistent between container, release tag, config and .nf-core.yml."
         ]
         assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"]
+
+    def test_version_consistency_container_not_consistent(self):
+        """Tests that pipeline version consistency test fails with inconsistent version numbers"""
+        new_pipeline = self._make_pipeline_copy()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj.nextflow_config()
+
+        # Set a bad version number for the container
+        lint_obj.nf_config["process.container"] = "nfcore/pipeline:latest"
+        # Set the version numbers to be consistent
+        lint_obj.nf_config["manifest.version"] = "1.0.0"
+        lint_obj.nf_config["config_yml.template.version"] = "1.0.0"
+
+        result = lint_obj.version_consistency()
+        assert len(result["passed"]) == 0
+        assert result["failed"] == [
+            "process.container was not numeric: latest!",
+            "The versioning is not consistent between container, release tag and config. Found manifest.version = 1.0.0, process.container = latest, nfcore_yml.version = 1.0.0",
+        ]
+
+    def test_version_consistency_yml_not_consistent(self):
+        """Tests that pipeline version consistency test fails with inconsistent version numbers"""
+        new_pipeline = self._make_pipeline_copy()
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj.nextflow_config()
+
+        # Set a bad version number for the YAML file
+        lint_obj.nf_config["config_yml.template.version"] = "0.0.0"
+        # Set the version numbers to be consistent
+        lint_obj.nf_config["process.container"] = "nfcore/pipeline:1.0.0"
+        lint_obj.nf_config["manifest.version"] = "1.0.0"
+
+        result = lint_obj.version_consistency()
+        assert len(result["passed"]) == 0
+        assert result["failed"] == [
+            "The versioning is not consistent between container, release tag and config. Found manifest.version = 1.0.0, process.container = 1.0.0, nfcore_yml.version = 0.0.0",
+        ]