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Backport PR #3667 on branch 1.11.x ((fix): axis_nnz explicitly drops axis with dask) #3674

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Merged
merged 1 commit into from
Jun 6, 2025
Merged

Backport PR #3667 on branch 1.11.x ((fix): axis_nnz explicitly drops axis with dask) #3674

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1 change: 1 addition & 0 deletions docs/release-notes/3667.bugfix.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Ensure `axis_nnz` calculates its chunk size/shape correctly with `dask` {smaller}`I Gold`
3 changes: 1 addition & 2 deletions src/scanpy/_utils/__init__.py
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Expand Up @@ -733,8 +733,7 @@ def _(X: DaskArray, axis: Literal[0, 1]) -> DaskArray:
partial(axis_nnz, axis=axis),
dtype=np.int64,
meta=np.array([], dtype=np.int64),
drop_axis=0,
chunks=len(X.to_delayed()) * (X.chunksize[int(not axis)],),
drop_axis=axis,
)


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2 changes: 1 addition & 1 deletion tests/test_qc_metrics.py
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Expand Up @@ -37,7 +37,7 @@ def adata() -> AnnData:

def prepare_adata(adata: AnnData) -> AnnData:
if isinstance(adata.X, DaskArray):
adata.X = adata.X.rechunk((100, -1))
adata.X = adata.X.rechunk((10, -1))
adata.var["mito"] = np.concatenate(
(np.ones(100, dtype=bool), np.zeros(900, dtype=bool))
)
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