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fix: consistent modularity by using Weighted_Adjacency directly #4113

Merge branch 'main' into pa/graph-upstream
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Codecov / codecov/project succeeded May 11, 2026 in 0s

79.44% (target 75.00%)

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79.44% (target 75.00%)

Details

Codecov Report

❌ Patch coverage is 56.25000% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.44%. Comparing base (30b96bb) to head (d00ebdf).
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/tools/_paga.py 20.00% 4 Missing ⚠️
src/scanpy/neighbors/__init__.py 0.00% 2 Missing ⚠️
src/scanpy/plotting/_tools/paga.py 66.66% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4113      +/-   ##
==========================================
- Coverage   79.60%   79.44%   -0.16%     
==========================================
  Files         119      119              
  Lines       12771    12760      -11     
==========================================
- Hits        10166    10137      -29     
- Misses       2605     2623      +18     
Files with missing lines Coverage Δ
src/scanpy/_utils/__init__.py 73.68% <ø> (-1.44%) ⬇️
src/scanpy/tools/_draw_graph.py 69.01% <100.00%> (ø)
src/scanpy/tools/_leiden.py 92.04% <100.00%> (+0.09%) ⬆️
src/scanpy/tools/_louvain.py 100.00% <ø> (ø)
src/scanpy/plotting/_tools/paga.py 64.32% <66.66%> (+0.06%) ⬆️
src/scanpy/neighbors/__init__.py 81.79% <0.00%> (-0.25%) ⬇️
src/scanpy/tools/_paga.py 32.05% <20.00%> (ø)

... and 5 files with indirect coverage changes