Merge pull request #1149 from KevinMenden/lint-modules-json

Lint the `modules.json` for uninstalled modules

CHANGELOG.md

@@ -30,6 +30,7 @@
 * Updated `nf-core modules remove` to remove module entry in `modules.json` if module directory is missing
 * Create extra tempdir as work directory for `nf-core modules create-test-yml` to avoid adding the temporary files to the `test.yml`
 * Refactored passing of command line arguments to `nf-core` commands and subcommands ([#1139](https://github.com/nf-core/tools/issues/1139), [#1140](https://github.com/nf-core/tools/issues/1140))
+* Check for `modules.json` for entries of modules that are not actually installed in the pipeline [[#1141](https://github.com/nf-core/tools/issues/1141)]
 * Added `<keywords>` argument to `nf-core modules list` for filtering the listed modules. ([#1139](https://github.com/nf-core/tools/issues/1139)
 
 #### Sync

docs/api/_src/pipeline_lint_tests/modules_json.rst

@@ -0,0 +1,4 @@
+nextflow_config
+===============
+
+.. automethod:: nf_core.lint.PipelineLint.modules_json

nf_core/lint/__init__.py

@@ -106,6 +106,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .files_exist import files_exist
     from .files_unchanged import files_unchanged
     from .merge_markers import merge_markers
+    from .modules_json import modules_json
     from .nextflow_config import nextflow_config
     from .params_used import params_used
     from .pipeline_name_conventions import pipeline_name_conventions
@@ -154,6 +155,7 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=Fal
             "schema_description",
             "actions_schema_validation",
             "merge_markers",
+            "modules_json",
         ]
         if self.release_mode:
             self.lint_tests.extend(["version_consistency"])

nf_core/lint/modules_json.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+from logging import warn
+from nf_core.modules.modules_command import ModuleCommand
+
+
+def modules_json(self):
+    """Make sure all modules described in the ``modules.json`` file are actually installed
+
+    Every module installed from ``nf-core/modules`` must have an entry in the ``modules.json`` file
+    with an associated version git_sha hash.
+
+    * Failure: If module entries are found in ``modules.json`` for modules that are not installed
+    """
+    passed = []
+    warned = []
+    failed = []
+
+    # Load pipeline modules and modules.json
+    modules_command = ModuleCommand(self.wf_path)
+    modules_json = modules_command.load_modules_json()
+
+    if modules_json:
+        modules_command.get_pipeline_modules()
+
+        all_modules_passed = True
+
+        for key in modules_json["modules"].keys():
+            if not key in modules_command.module_names:
+                failed.append(f"Entry for `{key}` found in `modules.json` but module is not installed in pipeline.")
+                all_modules_passed = False
+
+        if all_modules_passed:
+            passed.append("Only installed modules found in `modules.json`")
+    else:
+        warned.append("Could not open `modules.json` file.")
+
+    return {"passed": passed, "warned": warned, "failed": failed}

tests/lint/modules_json.py

@@ -0,0 +1,9 @@
+import nf_core.lint
+
+
+def test_modules_json_fail(self):
+    self.lint_obj._load()
+    results = self.lint_obj.modules_json()
+    assert len(results.get("warned", [])) == 0
+    assert len(results.get("failed", [])) == 0
+    assert len(results.get("passed", [])) == 1

tests/test_lint.py

@@ -215,6 +215,8 @@ def test_sphinx_rst_files(self):
 
     from lint.version_consistency import test_version_consistency
 
+    from lint.modules_json import test_modules_json_fail
+
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2