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IO refactor#133

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ilia-kats wants to merge 4 commits intoscverse:mainfrom
ilia-kats:io_refactor
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IO refactor#133
ilia-kats wants to merge 4 commits intoscverse:mainfrom
ilia-kats:io_refactor

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@ilia-kats ilia-kats commented Mar 30, 2026

Switch to AnnData's public API as much as possible.

This now uses read_dispatched to enable custom logic when reading individual modalities. Unfortunately, the same approach was not possible for writing: If we're writing a backed file, only the metadata should be written, while the X should remain intact. Unfortunately, calling write_dispatched on the entire AnnData object first clears the HDF5 group completely, so the X is gone. Therefore, we still need to write the individual modalities by hand.

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codecov bot commented Mar 30, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.46%. Comparing base (5ccf921) to head (6c1353f).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #133      +/-   ##
==========================================
+ Coverage   90.98%   91.46%   +0.48%     
==========================================
  Files          11       10       -1     
  Lines        1797     1746      -51     
==========================================
- Hits         1635     1597      -38     
+ Misses        162      149      -13     
Files with missing lines Coverage Δ
src/mudata/_core/io.py 95.08% <100.00%> (+0.09%) ⬆️
src/mudata/_core/mudata.py 93.12% <100.00%> (-0.01%) ⬇️
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