feat: Add lint check for version snapshot content validation

Add new lint check `test_snap_version_content` to ensure version information
in test snapshots contains actual content instead of MD5/SHA hash values.
This addresses the issue where version snapshots were storing hash values
like "versions.yml:md5,949da9c6297b613b50e24c421576f3f1" instead of
actual version content like {"ALE": {"ale": "20180904"}}.

Changes:
- Add version content validation in module_tests.py with regex patterns
- Add comprehensive tests for both invalid (hash) and valid (content) cases
- Add pytest issue marker support for linking tests to GitHub issues
- Update pyproject.toml with new pytest marker configuration

Fixes: nf-core/modules#6505

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

nf_core/modules/lint/module_tests.py

@@ -170,6 +170,36 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False):
                                         snap_file,
                                     )
                                 )
+                                # Check if version content is actual content vs MD5 hash
+                                # Related to: https://github.com/nf-core/modules/issues/6505
+                                # Ensures version snapshots contain actual content instead of hash values
+                                version_content_valid = True
+                                version_hash_patterns = [
+                                    r"versions\.yml:md5,[\da-f]+",  # MD5 hash pattern
+                                    r"versions\.yml:sha[\d]*,[\da-f]+",  # SHA hash pattern
+                                ]
+
+                                for pattern in version_hash_patterns:
+                                    if re.search(pattern, str(snap_content[test_name])):
+                                        version_content_valid = False
+                                        break
+
+                                if version_content_valid:
+                                    module.passed.append(
+                                        (
+                                            "test_snap_version_content",
+                                            "version information contains actual content instead of hash",
+                                            snap_file,
+                                        )
+                                    )
+                                else:
+                                    module.failed.append(
+                                        (
+                                            "test_snap_version_content",
+                                            "version information should contain actual content, not MD5/SHA hash",
+                                            snap_file,
+                                        )
+                                    )
                             else:
                                 module.failed.append(
                                     (

pyproject.toml

@@ -3,7 +3,10 @@ build-backend = "setuptools.build_meta"
 requires = ["setuptools>=40.6.0", "wheel"]
 
 [tool.pytest.ini_options]
-markers = ["datafiles: load datafiles"]
+markers = [
+    "datafiles: load datafiles",
+    "issue: mark test with related issue URL"
+]
 testpaths = ["tests"]
 python_files = ["test_*.py"]
 norecursedirs = [

tests/modules/lint/test_module_tests.py

@@ -1,6 +1,7 @@
 import json
 from pathlib import Path
 
+import pytest
 from git.repo import Repo
 
 import nf_core.modules.lint
@@ -194,22 +195,94 @@ def test_modules_empty_file_in_stub_snapshot(self):
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
-        
+
         # Check for test_snap_md5sum in passed tests (handle both tuple and LintResult formats)
         found_test = False
         for x in module_lint.passed:
             test_name = None
-            if hasattr(x, 'lint_test'):
+            if hasattr(x, "lint_test"):
                 test_name = x.lint_test
             elif isinstance(x, tuple) and len(x) > 0:
                 test_name = x[0]
-            
+
             if test_name == "test_snap_md5sum":
                 found_test = True
                 break
-        
+
         assert found_test, "test_snap_md5sum not found in passed tests"
 
         # reset the file
         with open(snap_file, "w") as fh:
             fh.write(content)
+
+    @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505")
+    def test_modules_version_snapshot_content_md5_hash(self):
+        """Test linting a nf-test module with version information as MD5 hash instead of actual content, which should fail.
+
+        Related to: https://github.com/nf-core/modules/issues/6505
+        Fixed in: https://github.com/nf-core/tools/pull/3676
+        """
+        snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap"
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+
+        # Add a version entry with MD5 hash format (the old way that should be flagged)
+        snap["my test"]["content"][0]["versions"] = "versions.yml:md5,949da9c6297b613b50e24c421576f3f1"
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+
+        # Should fail because version is using MD5 hash instead of actual content
+        # Filter for only our specific test
+        version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"]
+        assert len(version_content_failures) == 1, (
+            f"Expected 1 test_snap_version_content failure, got {len(version_content_failures)}"
+        )
+        assert version_content_failures[0].lint_test == "test_snap_version_content"
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)
+
+    @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505")
+    def test_modules_version_snapshot_content_valid(self):
+        """Test linting a nf-test module with version information as actual content, which should pass.
+
+        Related to: https://github.com/nf-core/modules/issues/6505
+        Fixed in: https://github.com/nf-core/tools/pull/3676
+        """
+        snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap"
+        snap = json.load(snap_file.open())
+        content = snap_file.read_text()
+
+        # Add a version entry with actual content (the new way that should pass)
+        snap["my test"]["content"][0]["versions"] = {"ALE": {"ale": "20180904"}}
+
+        with open(snap_file, "w") as fh:
+            json.dump(snap, fh)
+
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
+        module_lint.lint(print_results=False, module="bpipe/test")
+
+        # Should pass because version contains actual content
+        # Filter for only our specific test
+        version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"]
+        assert len(version_content_failures) == 0, (
+            f"Expected 0 test_snap_version_content failures, got {len(version_content_failures)}"
+        )
+
+        # Check for test_snap_version_content in passed tests
+        version_content_passed = [
+            x
+            for x in module_lint.passed
+            if (hasattr(x, "lint_test") and x.lint_test == "test_snap_version_content")
+            or (isinstance(x, tuple) and len(x) > 0 and x[0] == "test_snap_version_content")
+        ]
+        assert len(version_content_passed) > 0, "test_snap_version_content not found in passed tests"
+
+        # reset the file
+        with open(snap_file, "w") as fh:
+            fh.write(content)