fix: copy connectivities before passing to umap-learn

[nbjustice]

• Closes sc.tl.umap() silently mutates adata.obsp['connectivities'] via shared sparse buffer #4028
• Tests included
• Release notes included

Summary

sc.tl.umap() passes neighbors["connectivities"].tocoo() to umap-learn's simplicial_set_embedding() without copying. Since csr_matrix.tocoo() defaults to copy=False, the COO and CSR matrices share the same data buffer. umap-learn then zeroes out small edge weights in-place, which silently corrupts adata.obsp['connectivities'].

Fix: .tocoo() → .tocoo(copy=True)

Test plan

• Added test_umap_preserves_connectivities asserting data values, nnz count, no explicit zeros, and embedding is still produced
• Verified test fails without the fix and passes with it
• All existing UMAP tests pass

[flying-sheep]

thank you, this looks wonderful!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.50%. Comparing base (1fbe008) to head (b446f41).
⚠️ Report is 3 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4031   +/-   ##
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  Coverage   78.50%   78.50%           
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  Files         117      117           
  Lines       12740    12740           
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  Hits        10001    10001           
  Misses       2739     2739           

Flag	Coverage Δ
hatch-test.low-vers	77.79% <ø> (ø)
hatch-test.pre	77.45% <ø> (ø)

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Files with missing lines	Coverage Δ
src/scanpy/tools/_umap.py	72.30% <ø> (ø)