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1929: local modules use remote format from template #3256

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1929: local modules use remote format from template #3256

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awgymer
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@awgymer awgymer commented Oct 28, 2024

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@awgymer awgymer changed the title fix(1929): more type-gating 1929: local modules use remote format from template Oct 28, 2024
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codecov bot commented Oct 28, 2024 •
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Codecov Report

Attention: Patch coverage is 51.19048% with 41 lines in your changes missing coverage. Please review.

Project coverage is 75.29%. Comparing base (eb4c237) to head (31cffdd).
Report is 9 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/modules/lint/__init__.py 0.00% 13 Missing ⚠️
nf_core/modules/lint/module_tests.py 33.33% 8 Missing ⚠️
nf_core/components/nfcore_component.py 60.00% 6 Missing ⚠️
nf_core/modules/lint/meta_yml.py 33.33% 4 Missing ⚠️
nf_core/components/create.py 81.25% 3 Missing ⚠️
nf_core/modules/lint/environment_yml.py 25.00% 3 Missing ⚠️
...f_core/pipelines/lint/local_component_structure.py 84.61% 2 Missing ⚠️
nf_core/components/lint/__init__.py 66.66% 1 Missing ⚠️
nf_core/subworkflows/lint/subworkflow_tests.py 50.00% 1 Missing ⚠️
Additional details and impacted files

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mirpedrol
mirpedrol reviewed Oct 29, 2024
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nf_core/modules/lint/module_tests.py Outdated
@@ -22,6 +22,8 @@ def module_tests(_, module: NFCoreComponent):
and contains a ``main.nf.test`` and a ``main.nf.test.snap``

"""
if module.nftest_testdir is None or module.nftest_main_nf is None:
raise ValueError()
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don't we want to allow local modules to not have these files?

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Yes, this was my first-pass to get mypy happy so I could run the tests on GitHub yesterday. I am updating the individual lint tests to be a bit more permissive of missing files for local modules.

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awgymer commented Oct 29, 2024

There are currently no tests at all implemented for the linting of local modules or subworkflows 😱

mirpedrol
mirpedrol approved these changes Oct 30, 2024
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The code looks good, but there is a test failing, LGTM once this is fixed 🚀

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@mirpedrol mirpedrol mirpedrol approved these changes

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@awgymer @mirpedrol @nf-core-bot