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fix: handle all-zero genes in seurat_v3#3980

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flying-sheep merged 3 commits into
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pa/fix-loess
Feb 17, 2026
Merged

fix: handle all-zero genes in seurat_v3#3980
flying-sheep merged 3 commits into
mainfrom
pa/fix-loess

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codecov Bot commented Feb 17, 2026

Codecov Report

❌ Patch coverage is 24.44444% with 34 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.28%. Comparing base (4a90f6f) to head (b2bcae9).
⚠️ Report is 61 commits behind head on main.

Files with missing lines Patch % Lines
src/scanpy/queries/_queries.py 0.00% 4 Missing ⚠️
src/scanpy/external/exporting.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_bbknn.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_dca.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_harmony_integrate.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_magic.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_mnn_correct.py 0.00% 2 Missing ⚠️
src/scanpy/external/pp/_scanorama_integrate.py 0.00% 2 Missing ⚠️
src/scanpy/external/tl/_harmony_timeseries.py 0.00% 2 Missing ⚠️
src/scanpy/external/tl/_palantir.py 33.33% 2 Missing ⚠️
... and 6 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3980      +/-   ##
==========================================
- Coverage   78.32%   78.28%   -0.05%     
==========================================
  Files         117      117              
  Lines       12634    12635       +1     
==========================================
- Hits         9896     9891       -5     
- Misses       2738     2744       +6     
Flag Coverage Δ
hatch-test.low-vers 77.57% <24.44%> (+<0.01%) ⬆️
hatch-test.pre 77.22% <24.44%> (-0.05%) ⬇️

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

Files with missing lines Coverage Δ
src/scanpy/_compat.py 71.59% <100.00%> (+0.32%) ⬆️
src/scanpy/metrics/_metrics.py 97.18% <ø> (ø)
src/scanpy/plotting/_utils.py 78.90% <100.00%> (ø)
src/scanpy/preprocessing/_scrublet/__init__.py 96.84% <ø> (ø)
src/scanpy/external/exporting.py 13.38% <0.00%> (ø)
src/scanpy/external/pp/_bbknn.py 53.84% <0.00%> (ø)
src/scanpy/external/pp/_dca.py 50.00% <0.00%> (ø)
src/scanpy/external/pp/_harmony_integrate.py 50.00% <0.00%> (ø)
src/scanpy/external/pp/_magic.py 26.19% <0.00%> (ø)
src/scanpy/external/pp/_mnn_correct.py 22.22% <0.00%> (ø)
... and 10 more

... and 1 file with indirect coverage changes

Base automatically changed from pa/import-msgs to main February 17, 2026 10:25
@flying-sheep flying-sheep added this to the 1.12.1 milestone Feb 17, 2026
@flying-sheep flying-sheep merged commit b1e7c59 into main Feb 17, 2026
14 of 15 checks passed
@flying-sheep flying-sheep deleted the pa/fix-loess branch February 17, 2026 10:31
meeseeksmachine pushed a commit to meeseeksmachine/scanpy that referenced this pull request Feb 17, 2026
flying-sheep added a commit that referenced this pull request Feb 17, 2026
…rat_v3) (#3982)

Co-authored-by: Philipp A <flying-sheep@web.de>
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Segfault in highly_variable_genes() with flavor="seurat_v3"

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