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Removes tags.yml from module and subworkflow template #2995

Merged
merged 6 commits into from
Jun 21, 2024
Merged

Removes tags.yml from module and subworkflow template #2995

merged 6 commits into from
Jun 21, 2024
+613 −285

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adamrtalbot
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@adamrtalbot adamrtalbot commented May 22, 2024 •
edited

tags.yml is no longer needed with newer testing workflows. This PR removes the file from the module and subworkflow templates and updates the linting tests to reflect this.

Note I've left tags in the templates because they're still useful.

Related to #2881

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

@adamrtalbot
Removes tags.yml from module and subworkflow template
33179ea 
tags.yml is no longer needed with newer testing workflows. This PR removes the file from the module and subworkflow templates and updates the linting tests to reflect this.

Related to nf-core#2881
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My ruff seems to lint differently to the default one, it's passing all pre-commits and linting but the code seems completely changed?

mirpedrol
mirpedrol reviewed May 22, 2024
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nf_core/subworkflows/lint/subworkflow_tests.py Outdated
Comment on lines 224 to 233
if not is_pytest:
old_test_dir = Path(subworkflow.base_dir, "tests", "subworkflows", subworkflow.component_name)
if old_test_dir.is_dir():
subworkflow.failed.append(("test_old_test_dir", "old test directory exists", old_test_dir))
else:
subworkflow.passed.append(("test_old_test_dir", "old test directory does not exist", old_test_dir))
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These lines should be kept, it's testing that a subworkflow with nf-test doesn't have a directory with pytests

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Done!

tests/modules/lint.py Outdated
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The deleted tests should be removed from tests/test_modules.py, and the same from subworkflows

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done!

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@nf-core-bot fix linting please!

mirpedrol
mirpedrol approved these changes May 22, 2024
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LGTM once tests pass :)
Are we planning to do a bulk PR to the models repo removing all tags.yml files? Otherwise we could keep a listing test throwing a warning, advising to remove this file.

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@nf-core-bot fix linting please!

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Are we planning to do a bulk PR to the models repo removing all tags.yml files? Otherwise we could keep a listing test throwing a warning, advising to remove this file.

I hadn't thought this far ahead, perhaps a warning would be better so we can do it piecemeal.

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@mirpedrol can you see what's wrong with the tests here? I'm getting a lot of import errors on my laptop which don't seem to match the errors on Github.

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@adamrtalbot the tests which are failing now are also failing on the dev branch, I am working on finding what broke them, but it's not related to this PR

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codecov bot commented May 23, 2024

Codecov Report

Attention: Patch coverage is 63.15789% with 7 lines in your changes are missing coverage. Please review.

Project coverage is 76.03%. Comparing base (4ebbbb0) to head (03e78f9).

Files Patch % Lines
nf_core/modules/lint/module_tests.py 50.00% 4 Missing ⚠️
nf_core/subworkflows/lint/subworkflow_tests.py 62.50% 3 Missing ⚠️
Additional details and impacted files

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@adamrtalbot all green now ✅

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@mirpedrol still unrelated failed tests. Any ideas?

@adamrtalbot adamrtalbot merged commit 200493c into nf-core:dev Jun 21, 2024
33 of 35 checks passed
@adamrtalbot adamrtalbot deleted the remove_tags.yml branch June 21, 2024 15:54
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