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chore!: remove use_highly_variable#4039

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flying-sheep wants to merge 6 commits intomainfrom
pa/no-use-highly-variable
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chore!: remove use_highly_variable#4039
flying-sheep wants to merge 6 commits intomainfrom
pa/no-use-highly-variable

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@flying-sheep flying-sheep commented Apr 7, 2026

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codecov bot commented Apr 7, 2026

Codecov Report

❌ Patch coverage is 90.90909% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.49%. Comparing base (dcba591) to head (cc2cfa4).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/tools/_ingest.py 71.42% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4039      +/-   ##
==========================================
- Coverage   78.50%   78.49%   -0.01%     
==========================================
  Files         117      117              
  Lines       12750    12736      -14     
==========================================
- Hits        10009     9997      -12     
+ Misses       2741     2739       -2     
Flag Coverage Δ
hatch-test.low-vers 77.79% <90.90%> (-0.01%) ⬇️
hatch-test.pre 78.37% <90.90%> (-0.01%) ⬇️

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

Files with missing lines Coverage Δ
src/scanpy/experimental/pp/_normalization.py 94.31% <100.00%> (+0.06%) ⬆️
src/scanpy/preprocessing/_docs.py 100.00% <100.00%> (ø)
src/scanpy/preprocessing/_pca/__init__.py 91.51% <100.00%> (+0.45%) ⬆️
src/scanpy/tools/_ingest.py 77.82% <71.42%> (-0.09%) ⬇️

@flying-sheep flying-sheep added this to the 1.13.0 milestone Apr 9, 2026
@flying-sheep flying-sheep marked this pull request as ready for review April 10, 2026 11:24
@flying-sheep flying-sheep requested a review from ilan-gold April 10, 2026 13:08
@flying-sheep flying-sheep linked an issue Apr 10, 2026 that may be closed by this pull request
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1.10 deprecation: use_highly_variable parameter

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