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feat: add counts to pbmc68k_reduced - #4269

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flying-sheep merged 7 commits into
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pbmc68k-counts
Jul 30, 2026
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feat: add counts to pbmc68k_reduced#4269
flying-sheep merged 7 commits into
mainfrom
pbmc68k-counts

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@flying-sheep

@flying-sheep flying-sheep commented Jul 28, 2026

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Beyond time to actually have some raw count data.

TODO:

  • move into dataset, maybe remove log_counts layer.
  • maybe patch single mismatched number: we have 4.02, original (adata['AACTCACTGGGTGA-5', 'FTL']) could be restored via adata.X[357, 715] = 4.019 (4.0195003... is at the rounding boundary).
  • remove version guards superseded by bumped versions

  • Closes #
  • Tests included or not required because:

@codecov

codecov Bot commented Jul 28, 2026

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Codecov Report

❌ Patch coverage is 95.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.10%. Comparing base (0a3ed86) to head (b0f97f8).
⚠️ Report is 2 commits behind head on main.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/datasets/_datasets.py 92.85% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4269      +/-   ##
==========================================
+ Coverage   79.04%   79.10%   +0.06%     
==========================================
  Files         128      128              
  Lines       13412    13398      -14     
==========================================
- Hits        10602    10599       -3     
+ Misses       2810     2799      -11     
Flag Coverage Δ
hatch-test.low-vers 77.34% <95.00%> (+0.09%) ⬆️
hatch-test.pre 78.98% <95.00%> (+0.06%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/__init__.py 100.00% <100.00%> (+3.44%) ⬆️
src/scanpy/preprocessing/_pca/_compat.py 100.00% <100.00%> (ø)
src/scanpy/readwrite.py 82.60% <100.00%> (+1.57%) ⬆️
src/scanpy/tools/_louvain.py 100.00% <ø> (ø)
src/scanpy/datasets/_datasets.py 91.50% <92.85%> (+1.22%) ⬆️

... and 2 files with indirect coverage changes

@flying-sheep flying-sheep added this to the 1.13.0 milestone Jul 28, 2026
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flying-sheep marked this pull request as ready for review July 30, 2026 07:28
@flying-sheep
flying-sheep merged commit 4307278 into main Jul 30, 2026
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@flying-sheep
flying-sheep deleted the pbmc68k-counts branch July 30, 2026 11:37
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