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GilsonLabUCSD / pAPRika

Advanced toolkit for binding free energy calculations
BSD 3-Clause "New" or "Revised" License
30 stars 14 forks source link

Fixing GitHub Actions #202

Closed jaketanderson closed 2 days ago

jaketanderson commented 1 week ago

This PR aims to get the lint, ci, and codeql workflows working properly. To do so, it was necessary to introduce logic into devtools/conda-envs/test_env.yaml that says if python 3.9 is being used, enforce jax and jaxlib <= 0.4.28. This is because jax above that version contains str | None type operations, which aren't supported below python 3.10.

Python 3.8 doesn't encounter this issue because it defaults to a jax version way older (~0.4.14) which doesn't contain those type operations (Instead, depending on the version, it will use Optional[str] or simply None as the type hint).

One small thing I noticed while making these changes: https://github.com/GilsonLabUCSD/pAPRika/blob/688cc2c19bb88070e4e9f98aa8e23c92817afb57/setup.py#L37 Is including numpy here necessary? Commenting out this line doesn't cause errors for me.

codecov[bot] commented 1 week ago

Codecov Report

Attention: Patch coverage is 92.85714% with 1 line in your changes missing coverage. Please review.

Project coverage is 81.86%. Comparing base (affc777) to head (f0b31dc). Report is 15 commits behind head on master.

Additional details and impacted files
jaketanderson commented 3 days ago

@slochower @jeff231li if either of you have time in the near future, could you please review this PR? I want to get tests up and running before I make a new release.

jaketanderson commented 2 days ago

Thanks both!