feat: allow precomputed connectivities in neighbors

[ehsanestaji]

• Closes Compute UMAP from pre-existing distance matrix #2157
• Tests included or not required because: added test_neighbors_connectivities_support_umap
• Release notes not necessary because:

Summary

This adds a connectivities argument to sc.pp.neighbors, allowing callers to provide an externally computed neighborhood graph directly. The graph is stored in .obsp and can be consumed by downstream graph-based tools such as sc.tl.umap without requiring Scanpy to recompute neighbors from adata.

When both distances and connectivities are provided, Scanpy stores the supplied distances alongside the supplied connectivities. When only connectivities is provided, no distances matrix is written.

Testing

• uv run --group test-min pytest tests/test_neighbors.py tests/test_neighbors_key_added.py -q
• uv run --group test-min ruff check src/scanpy/neighbors/__init__.py tests/test_neighbors.py
• uv run --group test-min ruff format --check src/scanpy/neighbors/__init__.py tests/test_neighbors.py
• git diff --check

[ehsanestaji]

Thanks for maintaining Scanpy. The PR validation asks for either a milestone or the no milestone label. I do not have permission to set labels on this repository, so could a maintainer please add the appropriate milestone/label when you have a moment?

[codecov]

Codecov Report

❌ Patch coverage is 97.05882% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 79.70%. Comparing base (6bfd839) to head (8f7731d).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/neighbors/__init__.py	97.05%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4133      +/-   ##
==========================================
+ Coverage   79.61%   79.70%   +0.09%     
==========================================
  Files         120      120              
  Lines       12786    12805      +19     
==========================================
+ Hits        10179    10206      +27     
+ Misses       2607     2599       -8     

Flag	Coverage Δ
hatch-test.low-vers	78.94% <97.05%> (+0.08%)	⬆️
hatch-test.pre	79.56% <97.05%> (+0.08%)	⬆️

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

Files with missing lines	Coverage Δ
src/scanpy/neighbors/__init__.py	84.52% <97.05%> (+2.47%)	⬆️

... and 1 file with indirect coverage changes