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feat: allow use_graph and neighbors_key for metrics#3898

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flying-sheep merged 6 commits into
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pa/use-graph
Dec 19, 2025
Merged

feat: allow use_graph and neighbors_key for metrics#3898
flying-sheep merged 6 commits into
mainfrom
pa/use-graph

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@flying-sheep flying-sheep commented Nov 18, 2025

  • Closes #
  • Tests included or not required because:

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codecov Bot commented Nov 18, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.92%. Comparing base (c4cbb22) to head (cb4f551).
⚠️ Report is 49 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3898      +/-   ##
==========================================
+ Coverage   76.82%   76.92%   +0.09%     
==========================================
  Files         116      116              
  Lines       12398    12407       +9     
==========================================
+ Hits         9525     9544      +19     
+ Misses       2873     2863      -10     
Flag Coverage Δ
hatch-test.pre 76.92% <100.00%> (+0.09%) ⬆️

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

Files with missing lines Coverage Δ
src/scanpy/metrics/_common.py 94.73% <100.00%> (+4.32%) ⬆️
src/scanpy/metrics/_gearys_c.py 100.00% <100.00%> (ø)
src/scanpy/metrics/_morans_i.py 100.00% <100.00%> (ø)
src/scanpy/neighbors/_doc.py 100.00% <100.00%> (ø)
src/scanpy/plotting/_docs.py 100.00% <100.00%> (ø)
src/scanpy/preprocessing/_highly_variable_genes.py 95.03% <ø> (+0.31%) ⬆️

... and 2 files with indirect coverage changes

@flying-sheep flying-sheep added this to the 1.12.0 milestone Nov 18, 2025
@flying-sheep flying-sheep self-assigned this Nov 18, 2025
@flying-sheep flying-sheep marked this pull request as ready for review November 20, 2025 13:09
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@ilan-gold ilan-gold left a comment

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Is the title correct for this PR? An issue for it? It looks good just confused, not sure I'm totally clear

@flying-sheep flying-sheep changed the title feat: allow use_graph for metrics feat: allow use_graph and neighbors_key for metrics Dec 16, 2025
Comment thread src/scanpy/metrics/_common.py
@flying-sheep flying-sheep merged commit 22845a1 into main Dec 19, 2025
16 of 17 checks passed
@flying-sheep flying-sheep deleted the pa/use-graph branch December 19, 2025 08:08
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2 participants