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refactor(model): refactor out common minified mode methods #2883

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refactor(model): refactor out common minified mode methods #2883

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codecov bot commented Jul 3, 2024 •
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Codecov Report

Attention: Patch coverage is 85.71429% with 5 lines in your changes missing coverage. Please review.

Project coverage is 84.31%. Comparing base (38e1d65) to head (23c60a5).

Files with missing lines Patch % Lines
src/scvi/model/base/_base_model.py 84.61% 4 Missing ⚠️
src/scvi/model/utils/_minification.py 87.50% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #2883      +/-   ##
==========================================
- Coverage   84.80%   84.31%   -0.50%     
==========================================
  Files         173      173              
  Lines       14797    14768      -29     
==========================================
- Hits        12549    12452      -97     
- Misses       2248     2316      +68
Files with missing lines Coverage Δ
src/scvi/data/_constants.py 100.00% <100.00%> (ø)
src/scvi/model/_scanvi.py 93.24% <ø> (+2.01%) ⬆️
src/scvi/model/_scvi.py 95.91% <ø> (+5.50%) ⬆️
src/scvi/model/utils/_minification.py 90.90% <87.50%> (-1.40%) ⬇️
src/scvi/model/base/_base_model.py 92.26% <84.61%> (-0.68%) ⬇️

... and 5 files with indirect coverage changes

@martinkim0 martinkim0 added the cuda tests Run test suite on CUDA label Jul 11, 2024
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@martinkim0 Was this one ready to merge or are things missing?

@canergen canergen added cuda tests Run test suite on CUDA on-merge: backport to 1.2.x on-merge: backport to 1.2.x and removed cuda tests Run test suite on CUDA labels Jul 30, 2024
@ori-kron-wis ori-kron-wis removed the on-merge: backport to 1.2.x on-merge: backport to 1.2.x label Sep 25, 2024
@ori-kron-wis ori-kron-wis added this to the scvi-tools 1.2 milestone Nov 6, 2024
@ori-kron-wis ori-kron-wis self-assigned this Nov 6, 2024
canergen
canergen reviewed Nov 12, 2024
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src/scvi/model/utils/_minification.py
counts = adata_manager.get_from_registry(REGISTRY_KEYS.X_KEY)
all_zeros = csr_matrix(counts.shape)
return AnnData(
X=counts if keep_count_data else all_zeros,
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Change back to keep all layers

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@martinkim0 @canergen @ori-kron-wis