perf(score_genes): avoid copy-heavy sparse nan mean path

[SID-6921]

• Problem: _sparse_nanmean currently makes sparse copies and eliminate_zeros calls.
• Change: aggregate sums and NaN counts directly via compressed index pointers (csr/csc), no matrix copies.
• Correctness: preserves np.nanmean-equivalent behavior for sparse matrices.
• Tests: expanded test_sparse_nanmean to run on both csr and csc formats.
• Validation command: ANNDATA_ZARR_WRITE_FORMAT=3 python -m pytest tests/test_score_genes.py -k sparse_nanmean -q
• Closes _sparse_nanmean is inefficient #1894

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

This PR optimizes _sparse_nanmean() for compressed sparse matrices and expands unit tests to validate behavior across sparse storage formats.

Changes:

• Reworked _sparse_nanmean() to avoid sparse matrix copies/eliminate_zeros() and compute reductions via indptr-based aggregation.
• Added explicit runtime validation for axis values.
• Extended tests to run _sparse_nanmean() against both CSR and CSC inputs.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
tests/test_score_genes.py	Parameterizes the test to exercise both CSR and CSC matrix formats.
src/scanpy/tools/_score_genes.py	Replaces copy-heavy NaN-mean computation with a pointer-based aggregation approach and adds axis validation.

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[SID-6921]

Maintainers: this PR is failing the metadata gate because I cannot apply labels from a fork. Could you please add the
o milestone\ label (or assign a milestone)? The code checks pass locally.

[codecov]

Codecov Report

❌ Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.60%. Comparing base (2ae768e) to head (0a84825).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/tools/_score_genes.py	85.71%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4159      +/-   ##
==========================================
- Coverage   79.61%   79.60%   -0.02%     
==========================================
  Files         120      120              
  Lines       12786    12790       +4     
==========================================
+ Hits        10180    10181       +1     
- Misses       2606     2609       +3     

Flag	Coverage Δ
hatch-test.low-vers	78.85% <85.71%> (+<0.01%)	⬆️
hatch-test.pre	79.46% <85.71%> (-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/tools/_score_genes.py	86.20% <85.71%> (-1.30%)	⬇️

... and 2 files with indirect coverage changes