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fix sparse backed data loading #1824

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merged 1 commit into from Dec 14, 2022
Merged

fix sparse backed data loading #1824

merged 1 commit into from Dec 14, 2022

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adamgayoso
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@adamgayoso adamgayoso commented Dec 14, 2022

Backed data currently doesn't work if X is sparse due to a minor bug.

I tested this and it works, with 1200 genes it's about twice as slow to load backed sparse. We can expose setting data loader num_workers to improve speed.

@adamgayoso adamgayoso marked this pull request as ready for review December 14, 2022 20:40
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codecov bot commented Dec 14, 2022

Codecov Report

Base: 90.45% // Head: 90.46% // Increases project coverage by +0.00% 🎉

Coverage data is based on head (c897fad) compared to base (c4c3c22).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1824   +/-   ##
=======================================
  Coverage   90.45%   90.46%           
=======================================
  Files         130      130           
  Lines       10337    10337           
=======================================
+ Hits         9350     9351    +1     
+ Misses        987      986    -1     
Impacted Files Coverage Δ
scvi/__init__.py 87.50% <ø> (ø)
scvi/module/_scanvae.py 79.82% <ø> (ø)
scvi/module/_vaec.py 85.71% <ø> (ø)
scvi/utils/_track.py 72.72% <ø> (ø)
scvi/dataloaders/_anntorchdataset.py 92.64% <100.00%> (+1.47%) ⬆️

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@adamgayoso adamgayoso merged commit 9b8eb8a into main Dec 14, 2022
@adamgayoso adamgayoso deleted the backed branch December 14, 2022 23:06
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2 participants