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Fix normalize_total for dask #2466

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merged 2 commits into from Apr 12, 2023
Merged

Fix normalize_total for dask #2466

merged 2 commits into from Apr 12, 2023

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flying-sheep
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@flying-sheep flying-sheep commented Apr 12, 2023

Fixes #2465

adata.var_names[~gene_subset] will throw an error if gene_subset is an 1D dask array, so we convert it to a numpy array.

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codecov bot commented Apr 12, 2023

Codecov Report

Merging #2466 (9a67bdb) into master (3e3427d) will not change coverage.
The diff coverage is 100.00%.

❗ Current head 9a67bdb differs from pull request most recent head 5bfdac5. Consider uploading reports for the commit 5bfdac5 to get more accurate results

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #2466   +/-   ##
=======================================
  Coverage   71.87%   71.87%           
=======================================
  Files          98       98           
  Lines       11496    11496           
=======================================
  Hits         8263     8263           
  Misses       3233     3233           
Impacted Files Coverage Δ
scanpy/preprocessing/_normalization.py 85.88% <100.00%> (ø)

@flying-sheep flying-sheep merged commit 554b226 into master Apr 12, 2023
6 of 8 checks passed
@flying-sheep flying-sheep deleted the fix-dask-norm branch April 12, 2023 12:46
@flying-sheep flying-sheep mentioned this pull request Aug 4, 2023
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sc.pp.normalize_total does not support dask arrays
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