Pipeline version consistency check

nf_core/pipelines/lint/version_consistency.py

@@ -1,4 +1,7 @@
 import os
+from pathlib import Path
+
+from ruamel.yaml import YAML
 
 
 def version_consistency(self):
@@ -7,14 +10,15 @@ 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 +49,12 @@ def version_consistency(self):
     ):
         versions["GITHUB_REF"] = os.path.basename(os.environ["GITHUB_REF"].strip(" '\""))
 
+    # Get version from the .nf-core.yml template
+    yaml = YAML()
+    nfcore_yml = yaml.load(Path(self.wf_path) / ".nf-core.yml")
+    if nfcore_yml["template"] and "version" in nfcore_yml["template"]:
+        versions["nfcore_yml.version"] = nfcore_yml["template"]["version"].strip(" '\"")
+
     # Check if they are all numeric
     for v_type, version in versions.items():
         if not version.replace(".", "").isdigit():
@@ -57,7 +67,7 @@ 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: {}".format(", ".join([f"{k} = {v}" for k, v in versions.items()])))
 
     return {"passed": passed, "failed": failed}

tests/pipelines/lint/test_version_consistency.py

@@ -1,19 +1,82 @@
+import re
+from pathlib import Path
+
+from ruamel.yaml import YAML
+
 import nf_core.pipelines.create.create
 import nf_core.pipelines.lint
+from nf_core.utils import NFCoreYamlConfig
 
 from ..test_lint import TestLint
 
 
 class TestLintVersionConsistency(TestLint):
-    def test_version_consistency(self):
-        """Tests that config variable existence test fails with bad pipeline name"""
-        new_pipeline = self._make_pipeline_copy()
-        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+    def setUp(self) -> None:
+        super().setUp()
+        self.new_pipeline = self._make_pipeline_copy()
+        self.nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
+        self.yaml = YAML()
+        self.nf_core_yml: NFCoreYamlConfig = self.yaml.load(self.nf_core_yml_path)
+
+    def test_version_consistency_pass(self):
+        """Tests that pipeline version consistency test passes with good pipeline version"""
+        # Declare the pipeline version in the .nf-core.yml file
+        self.nf_core_yml["template"]["version"] = "1.0.0"
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
+
+        # Set the version in the nextflow.config file
+        nf_conf_file = Path(self.new_pipeline, "nextflow.config")
+        with open(nf_conf_file) as f:
+            content = f.read()
+            pass_content = re.sub(r"(?m)^(?P<indent>\s*version\s*=\s*)'[^']+'", rf"\g<indent>'{'1.0.0'}'", content)
+        with open(nf_conf_file, "w") as f:
+            f.write(pass_content)
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         lint_obj.load_pipeline_config()
         lint_obj.nextflow_config()
+        # Set the version for the container
+        lint_obj.nf_config["process.container"] = "nfcore/pipeline:1.0.0"
+        result = lint_obj.version_consistency()
+        assert result["passed"] == [
+            "Version tags are consistent: manifest.version = 1.0.0, process.container = 1.0.0, nfcore_yml.version = 1.0.0",
+        ]
+        assert result["failed"] == []
+
+    def test_version_consistency_not_numeric(self):
+        """Tests that pipeline version consistency test fails with non-numeric version numbers"""
+        self.nf_core_yml["template"]["version"] = "1.0.0dev"
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
 
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.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: manifest.version = 1.0.0dev, nfcore_yml.version = 1.0.0dev"
+        ]
+        assert result["failed"] == [
+            "manifest.version was not numeric: 1.0.0dev!",
+            "nfcore_yml.version was not numeric: 1.0.0dev!",
+        ]
+
+    def test_version_consistency_not_consistent(self):
+        """Tests that pipeline version consistency test fails with inconsistent version numbers"""
+        self.nf_core_yml["template"]["version"] = "0.0.0"
+        self.yaml.dump(self.nf_core_yml, self.nf_core_yml_path)
+        nf_conf_file = Path(self.new_pipeline, "nextflow.config")
+        with open(nf_conf_file) as f:
+            content = f.read()
+            fail_content = re.sub(r"(?m)^(?P<indent>\s*version\s*=\s*)'[^']+'", rf"\g<indent>'{'1.0.0'}'", content)
+        with open(nf_conf_file, "w") as f:
+            f.write(fail_content)
+        lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
+        lint_obj.load_pipeline_config()
+        lint_obj.nextflow_config()
+
+        lint_obj.nf_config["process.container"] = "nfcore/pipeline:0.1"
+        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 = 0.1, nfcore_yml.version = 0.0.0",
         ]
-        assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"]