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@flying-sheep flying-sheep commented Nov 14, 2025

I double-checked everything in #2578 and mostly winged it for the rest.

Would be nice if one of you could take a look if I mis-specified something.

  • I didn’t check if some flavors of highly_variable_genes supports only CSR. Any idea?
  • I tried to document things that implicitly convert to csr as “not supporting csc”, except when that’s conditional (i.e sc.pp.scale supports CSC if you don’t specify mask_obs, so that’s detailed in mask_obs).

@flying-sheep flying-sheep added this to the 1.12.0 milestone Nov 14, 2025
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codecov bot commented Nov 14, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.90%. Comparing base (508f857) to head (153929c).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3895      +/-   ##
==========================================
+ Coverage   76.82%   76.90%   +0.07%     
==========================================
  Files         116      117       +1     
  Lines       12398    12440      +42     
==========================================
+ Hits         9525     9567      +42     
  Misses       2873     2873              
Flag Coverage Δ
hatch-test.pre 76.90% <100.00%> (+0.07%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
src/scanpy/_utils/_docs.py 100.00% <100.00%> (ø)
...c/scanpy/experimental/pp/_highly_variable_genes.py 18.44% <ø> (ø)
src/scanpy/get/_aggregated.py 92.78% <ø> (ø)
src/scanpy/neighbors/__init__.py 80.05% <ø> (ø)
src/scanpy/preprocessing/_combat.py 88.46% <ø> (ø)
src/scanpy/preprocessing/_highly_variable_genes.py 94.71% <ø> (ø)
src/scanpy/preprocessing/_normalization.py 94.66% <ø> (ø)
src/scanpy/preprocessing/_pca/__init__.py 90.65% <ø> (ø)
src/scanpy/preprocessing/_qc.py 95.83% <ø> (ø)
src/scanpy/preprocessing/_scale.py 91.20% <ø> (ø)
... and 15 more

@flying-sheep flying-sheep marked this pull request as ready for review November 17, 2025 11:27
@flying-sheep flying-sheep changed the title docs: add array-types directive docs: document array type support Nov 17, 2025
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Document dask support for highly variable genes

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