fix: check H5AD lock before overwrite

[stanbot8]

Summary

HDF5 can truncate a live H5AD target before it reports a lock failure (h5py issue 1864, HDF5 issue HDFFV-11230). This change opens an existing HDF5 target with r+ before the truncate-mode open. An active reader blocks the overwrite before truncation. Closes #522.

Design

The check changes less code. It does not need a temporary copy.

The implementation changes src/anndata/_io/h5ad.py. The design follows the reported truncation reproducer, the requested overwrite behavior, and the HDF5 lock analysis.

Limitations

• A reader can open after the check, so the reader-open race remains.
• HDF5 file locking must be enabled.
• Writes remain non-atomic.
• Concurrent writers are not serialized.

Tests

• The Windows baseline changed a 20,480-byte file to an empty file.
• The Scanpy reproducer preserved the file and the reader.
• Current Windows and Linux dependencies passed.
• Minimum Linux dependencies passed.
• Three readers survived ten blocked writes. A retry passed after they closed.
• All 11 CI matrix test commands passed. The report upload failed in the fork.

The benchmark and codespell checks passed.

Commands

pytest -q tests/test_readwrite.py -k 'test_write_h5ad_open_elsewhere'

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.87%. Comparing base (b2e6177) to head (8c23e3e).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2569      +/-   ##
==========================================
- Coverage   87.81%   85.87%   -1.95%     
==========================================
  Files          49       49              
  Lines        7799     7802       +3     
==========================================
- Hits         6849     6700     -149     
- Misses        950     1102     +152     

Files with missing lines	Coverage Δ
src/anndata/_io/h5ad.py	93.39% <100.00%> (+0.09%)	⬆️

... and 8 files with indirect coverage changes

[stanbot8]

Superseded by #2570. The replacement writes a complete temporary file before it replaces the target. This design removes the reader-open race that remains in this preflight check.