Chunked writing of h5py.Dataset and zarr.Array #1624
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1624 +/- ##
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- Coverage 86.74% 83.99% -2.75%
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Files 37 40 +3
Lines 5988 6031 +43
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- Hits 5194 5066 -128
- Misses 794 965 +171
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ilan-gold
reviewed
Aug 29, 2024
src/anndata/_io/specs/methods.py
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| @@ -392,6 +389,46 @@ def write_basic( | |||
| f.create_dataset(k, data=elem, **dataset_kwargs) | |||
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| def _iter_chunks_for_copy(elem, dest): | |||
src/anndata/_io/specs/methods.py
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| def write_chunked_dense_array( | ||
| f: GroupStorageType, | ||
| k: str, | ||
| elem, |
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| elem, | |
| elem: GroupStorageType, |
no?
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ArrayStorageType I think
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| elem, | |
| elem: ArrayStorageType, |
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This PR fixes #1623 by writing backed dense arrays in chunks.
Very open to feedback on the logic of how chunking pattern of writes is selected. Maybe we should prioritize the chunking of the destination array over the chunking of the source array?
cc: @ebezzi
Some proof it works: