Separate for test data generation for compatibility with Biotite >= 1.0 and Numpy >= 2.0; Ruff formatting #16
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…sv.gz required for test; updated pyproject.toml -> consistency with biotite
…or; removed unused .csv files; reworked R script for biophysconnector
padix-key
reviewed
Sep 24, 2024
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Thanks for keeping the package up to date with Biotite. I only would recommend a few changes regarding ruff formatting:
- There is a newer version of
ruffavailable, or is there a specific reason to use an older version? In Biotite I would also update the ruff version soon. - You can also configure ruff as optional dependency in
pyproject.tomlalong with configuration of its rules. Can can adapt the rules from Biotite if you like. - To ensure that correct formatting is also used in subsequent PRs, I think a CI job would be reasonable. Again you could adapt the corresponding job from Biotite for it
…; final Ruff checks and fixes in scripts; added Ruff CI job
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Sure, should be fine now. |
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Last changes for this PR: |
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Yes, I agree, the current pyproject.toml allows also 0.x Biotite versions,
if I am not mistaken.
JHKru ***@***.***> schrieb am Mi., 25. Sept. 2024, 12:01:
… Last changes for this PR:
Regarding the dev vs. regular Poetry dependencies ->
We should remain compatible with biotite < 1.0 and numpy >= 1.25, if I'm
not mistaken.
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Compressed .csv files for tests are now stored separately in test/data, together with the corresponding Python/R
scripts.
This is necessary because ProDy does not support newer Numpy/Scipy versions yet (from #15).
For ProDy/rpy2/bio3d, a separate conda env can be installed from test_create_data_env.yml to rerun these scripts locally.
Additional tests for a multimeric protein were added.$\approx$ 41 MB.
The randomly generated coordinates in
test_interaction.pyhad to be limited to a total number of twelve.In total, the test folder takes up
Ruff was added for formatting.