[python] Prototype Dask-backed to_anndata
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Codecov ReportAttention: Patch coverage is
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- Coverage 89.15% 88.94% -0.22%
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ryan-williams
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to_anndatato_anndata
johnkerl
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Mar 12, 2025
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@ryan-williams this is truly gorgeous.
Several relatively minor things flagged. I've nothing "big" to add.
I defer to @ivirshup who's got the Dask-user context which I lack.
Thank you for your time on this!
| "id": "510dcf31-f0fb-4652-bcfb-abdf4cb6f1e2", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The `X` matrix is a [Dask Array]:\n", |
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It wouldn't hurt to add type(adata.X) as another cell -- just a thought
Co-authored-by: John Kerl <[email protected]>
This was referenced Mar 12, 2025
ryan-williams
commented
Mar 12, 2025
CR: notebook copy fix Co-authored-by: John Kerl <[email protected]>
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Changes
Experiment{,AxisQuery}.to_anndatacan optionally produce an AnnData withXmatrix of typedask.Arrayscipy.sparse.csr_matrix's, produced lazily from slices of the underlyingExperimentorExperimentAxisQuerydaskis introduced as a "dev" dependency (for tests of this code)requirements_spatial.txt, for similar reasonsimport daskonly occurs inside relevant functions and test-cases; this change should be transparent to users.I've also enumerated and reordered the tutorials in tutorials.rst.
sc-64138