In modules linting warn about the presence of pytest-workflow files

[edmundmiller]

Description of feature

Then later once we've migrated we can switch it to a failure.

[ejseqera]

Should we subsequently deprecate this logic here below in modules.lint.modules_tests for checking entries in pytest_modules.yml?

    try:
        pytest_yml_path = os.path.join(module.base_dir, "tests", "config", "pytest_modules.yml")
        with open(pytest_yml_path, "r") as fh:pip
            pytest_yml = yaml.safe_load(fh)
            if module.component_name in pytest_yml.keys():
                module.passed.append(("test_pytest_yml", "correct entry in pytest_modules.yml", pytest_yml_path))
            else:
                module.failed.append(("test_pytest_yml", "missing entry in pytest_modules.yml", pytest_yml_path))
    except FileNotFoundError:
        module.failed.append(("test_pytest_yml", "Could not open pytest_modules.yml file", pytest_yml_path))

[edmundmiller]

Yep, exactly!

Or flip the logic around and report in the correct entry and warn/fail that test needs to be migrated over. See nf-core/modules#4151 (review) for the discussion on that we need to update the docs first.

[nvnieuwk]

I've been looking into adding lint action support for nf-test. I think for now we should just check whether or not the tag is in pytest_modules.yml or if the modules/nf-core/<tool>/<subtool>/tests/main.nf.test file exists (at least until the full migration has been done). I'll work on a small POC PR right now

[mirpedrol]

This is done in the dev branch of nf-core/tools, feel free to re-open the issue if you think there is something still missing :)