Fix Python 3.13 failures in neighborhood enrichment and AnnData test fixture

[Copilot]

The Python 3.13 Actions job failed due to two dependency-compatibility regressions: AnnData(..., dtype=...) in tests and in-place diagonal writes on read-only DataFrame-backed arrays. This PR updates both paths to be compatible with current anndata/numpy behavior while preserving existing semantics.

• Neighborhood enrichment diagonal handling (src/cellcharter/gr/_nhood.py)

  • Replaced np.fill_diagonal(... .values, np.nan) with DataFrame-level masking to avoid mutating potentially read-only backing arrays.
  • Keeps only_inter=True behavior (diagonal set to NaN) unchanged.

• AnnData fixture compatibility (tests/conftest.py)

  • Removed deprecated/unsupported dtype argument from AnnData(...).
  • Moved dtype specification to NumPy array construction (np.array(..., dtype=int)).

• Regression coverage (tests/graph/test_nhood_local.py)

  • Added a focused test that verifies nhood_enrichment(..., only_inter=True, observed_expected=True) returns NaN diagonals for observed/expected/enrichment.

# before
np.fill_diagonal(observed.values, np.nan)

# after
diagonal_mask = np.eye(len(observed), dtype=bool)
observed = observed.mask(diagonal_mask, np.nan)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 67.78%. Comparing base (b605238) to head (ac5800f).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #120      +/-   ##
==========================================
- Coverage   68.00%   67.78%   -0.23%     
==========================================
  Files          23       23              
  Lines        1638     1639       +1     
==========================================
- Hits         1114     1111       -3     
- Misses        524      528       +4     

Files with missing lines	Coverage Δ
src/cellcharter/gr/_nhood.py	94.68% <100.00%> (+0.02%)	⬆️

... and 1 file with indirect coverage changes

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