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feat: supporting sparse mode in DataSplitter#3840

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feat/sparse-input-csr
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feat: supporting sparse mode in DataSplitter#3840
ori-kron-wis wants to merge 8 commits into
mainfrom
feat/sparse-input-csr

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@ori-kron-wis ori-kron-wis self-assigned this Jun 11, 2026
@ori-kron-wis ori-kron-wis added cuda tests Run test suite on CUDA on-merge: backport to 1.4.x on-merge: backport to 1.4.x labels Jun 11, 2026

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Comment thread src/scvi/nn/_base_components.py Outdated
Comment thread src/scvi/dataloaders/_data_splitting.py
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codecov Bot commented Jun 11, 2026

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Codecov Report

❌ Patch coverage is 94.23077% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.54%. Comparing base (f52957e) to head (6fcc9ad).

Files with missing lines Patch % Lines
src/scvi/dataloaders/_data_splitting.py 89.47% 2 Missing ⚠️
src/scvi/nn/_base_components.py 94.44% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #3840   +/-   ##
=======================================
  Coverage   88.53%   88.54%           
=======================================
  Files         237      237           
  Lines       23831    23876   +45     
=======================================
+ Hits        21099    21141   +42     
- Misses       2732     2735    +3     
Flag Coverage Δ
cuda 72.66% <94.23%> (+0.03%) ⬆️
integration 72.63% <94.23%> (+0.03%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
src/scvi/data/_utils.py 88.26% <100.00%> (+0.33%) ⬆️
src/scvi/module/_vae.py 96.64% <100.00%> (+0.11%) ⬆️
src/scvi/nn/_base_components.py 94.52% <94.44%> (-0.01%) ⬇️
src/scvi/dataloaders/_data_splitting.py 95.75% <89.47%> (-0.59%) ⬇️
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ori-kron-wis and others added 7 commits June 11, 2026 16:23
Adds a real-SCVI regression test asserting the INPUT_CSR sparse encoder
path matches the dense path across covariate configurations: one-hot
covariate dtype cast, continuous-covariate concat, and embedding batch
representation.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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