Add all ruff checks we use in anndata #2761
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #2761 +/- ##
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- Coverage 73.21% 72.46% -0.75%
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Files 111 111
Lines 12246 12418 +172
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+ Hits 8966 8999 +33
- Misses 3280 3419 +139
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flying-sheep
commented
Nov 23, 2023
| tl.pca | ||
| pp.pca |
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I took the liberty to make this more Zen.
It’s the same function, it should be only in one place. (It’s still importable from the other, we can add a deprecation if we want, or just leave it.)
The only places that used to use it from tl are externals, I harmonized all that.
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All changes were automatic, except for:
__all__. Much more uncontroversial than AnnData as scanpy’s public modules were more well defined from the start. There were no ambiguous cases except forsc.getre-exporting"_check_mask","_get_obs_rep", and"_set_obs_rep". But since those aren’t documented, we can decide over their fate at a later date.sc.{pp,tl}.pca. I only needed to create aneighbors/_doc.pyfile for shared neighbors/tools doc parts, and put thepcaimport intoolsin__getattr__(supported since 3.7)with open(p) as f: x = json.loads(f.read())s withx = json.loads(Path(p).read_text())All in all surprisingly easy