Add version check in snapshot file

CHANGELOG.md

@@ -15,6 +15,7 @@
 ### Linting
 
 - Only match assignments of params in `main.nf` and not references like `params.aligner == <something>` ([#2833](https://github.com/nf-core/tools/pull/2833))
+- Include test for presence of versions in snapshot ([#2888](https://github.com/nf-core/tools/pull/2888))
 
 ### Download
 

nf_core/modules/lint/module_tests.py

@@ -107,6 +107,22 @@ def module_tests(_, module: NFCoreComponent):
                                             snap_file,
                                         )
                                     )
+                                if "versions" in str(snap_content[test_name]):
+                                    module.passed.append(
+                                        (
+                                            "test_snap_versions",
+                                            "versions found in snapshot file",
+                                            snap_file,
+                                        )
+                                    )
+                                else:
+                                    module.failed.append(
+                                        (
+                                            "test_snap_versions",
+                                            "versions not found in snapshot file",
+                                            snap_file,
+                                        )
+                                    )
                         except json.decoder.JSONDecodeError as e:
                             module.failed.append(
                                 (

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -114,6 +114,22 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                                             snap_file,
                                         )
                                     )
+                                if "versions" in str(snap_content[test_name]):
+                                    subworkflow.passed.append(
+                                        (
+                                            "test_snap_versions",
+                                            "versions found in snapshot file",
+                                            snap_file,
+                                        )
+                                    )
+                                else:
+                                    subworkflow.warned.append(
+                                        (
+                                            "test_snap_versions",
+                                            "versions not found in snapshot file",
+                                            snap_file,
+                                        )
+                                    )
                         except json.decoder.JSONDecodeError as e:
                             subworkflow.failed.append(
                                 (

tests/modules/lint.py

@@ -642,3 +642,24 @@ def test_nftest_failing_linting(self):
     assert module_lint.failed[2].lint_test == "test_main_tags"
     assert "kallisto/index" in module_lint.failed[2].message
     assert module_lint.failed[3].lint_test == "test_tags_yml"
+
+
+def test_modules_absent_version(self):
+    """Test linting a nf-test module if the versions is absent in the snapshot file `"""
+    with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap")) as fh:
+        content = fh.read()
+        new_content = content.replace("versions", "foo")
+    with open(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap"), "w"
+    ) as fh:
+        fh.write(new_content)
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=False, module="bpipe/test")
+    with open(
+        Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap"), "w"
+    ) as fh:
+        fh.write(content)
+    assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) >= 0
+    assert len(module_lint.warned) >= 0
+    assert module_lint.failed[0].lint_test == "test_snap_versions"

tests/subworkflows/lint.py

@@ -181,3 +181,22 @@ def test_subworkflows_lint_capitalization_fail(self):
 
     # cleanup
     self.subworkflow_remove.remove("bam_stats_samtools", force=True)
+
+
+def test_subworkflows_absent_version(self):
+    """Test linting a nf-test module if the versions is absent in the snapshot file `"""
+    self.subworkflow_install.install("fastq_align_dna")
+    with open(Path(self.pipeline_dir, "subworkflows", "nf-core", "fastq_align_dna", "test", "main.nf.test.snap")) as fh:
+        content = fh.read()
+        new_content = content.replace("versions", "foo")
+    with open(
+        Path(self.pipeline_dir, "subworkflows", "nf-core", "fastq_align_dna", "test", "main.nf.test.snap"), "w"
+    ) as fh:
+        fh.write(new_content)
+
+    subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.pipeline_dir)
+    subworkflow_lint.lint(print_results=False, subworkflow="fastq_align_dna")
+    assert len(subworkflow_lint.failed) == 0
+    assert len(subworkflow_lint.passed) > 0
+    assert len(subworkflow_lint.warned) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+    assert any([x.lint_test == "test_snap_versions" for x in subworkflow_lint.warned])

tests/test_modules.py

@@ -179,6 +179,7 @@ def test_modulesrepo_class(self):
         test_modules_install_trimgalore_twice,
     )
     from .modules.lint import (  # type: ignore[misc]
+        test_modules_absent_version,
         test_modules_environment_yml_file_doesnt_exists,
         test_modules_environment_yml_file_name_mismatch,
         test_modules_environment_yml_file_not_array,

tests/test_subworkflows.py

@@ -119,6 +119,7 @@ def tearDown(self):
         test_subworkflows_install_tracking_added_super_subworkflow,
     )
     from .subworkflows.lint import (  # type: ignore[misc]
+        test_subworkflows_absent_version,
         test_subworkflows_lint,
         test_subworkflows_lint_capitalization_fail,
         test_subworkflows_lint_empty,