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scverse / scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data
http://scvi-tools.org/
BSD 3-Clause "New" or "Revised" License
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Update to ruff rules. Changed code to pass these tests #2956

Closed canergen closed 2 months ago

canergen commented 2 months ago

Added rules:

"PT", # pytest style
"NPY", # numpy formatting
"TCH", # flake8-type-checking
"FA", # flake8-future-annotations
canergen commented 2 months ago

@ori-kron-wis future imports all corrected. We can think about adding NPY002 (random generator), PT011 (raise ValueError not allowed). TD TODO rules, which require every TODO to have an issue, author and restructures TODO (I'm not in favor of doing it before we haven't cleaned up the TODOS).

ori-kron-wis commented 2 months ago

Following the merging of https://github.com/scverse/scvi-tools/pull/2970, and major code base change needed for it and for the updated ruff rules, we close this PR and reOpen it from scratch