Add snakefmt to precommit

kaitj commented 1 year ago

Proposed changes

Updates pyproject.toml to remove settings for pylint. Add settings for snakefmt

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[ ] Bugfix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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[ ] Changes have been tested to ensure that fix is effective or that a feature works.
[x] Changes pass the unit tests
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[x] I have included necessary documentation or comments (as necessary)
[ ] Any dependent changes have been merged and published

Notes

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tkkuehn commented 1 year ago

We should run pre-commit run --all-files, maybe in a separate PR. There will be a lot of changes...

We should also double check that the GH actions check align with the pre-commit hooks, maybe in the same PR. I think if the checks pass pre-commit run --all-files shouldn't want to change anything.

kaitj commented 1 year ago

We should run pre-commit run --all-files, maybe in a separate PR. There will be a lot of changes...

We should also double check that the GH actions check align with the pre-commit hooks, maybe in the same PR. I think if the checks pass pre-commit run --all-files shouldn't want to change anything.

I agree. We can maybe make this a separate issue so we don't forget and hold off until the individual .smk files have been checked over. I've started to run snakefmt as I've gone through and edited those files to try to catch and fix as many errors as possible there.

kaitj commented 1 year ago

See #18 for issue, will merge this in.

khanlab / scattr