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fix(totalvi): apply protein capture efficiency in posterior predictive samples - #4033

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Ori-4022-totalvi-protein-exp-fix
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Ori-4022-totalvi-protein-exp-fix

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close #4022

@ori-kron-wis ori-kron-wis self-assigned this Sep 23, 2026
@ori-kron-wis ori-kron-wis added the on-merge: backport to 1.5.x on-merge: backport to 1.5.x label Sep 23, 2026
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Codex Review Summary

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Review Status Commit Review trigger
📝 Code Review ✅ Completed 2026-09-23T11:45:25.810015Z 0b0b3a4 PR opened
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💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 0b0b3a40c6

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Comment thread src/scvi/model/_totalvi.py Outdated
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.47%. Comparing base (0aa4d96) to head (a582ed6).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #4033   +/-   ##
=======================================
  Coverage   89.46%   89.47%           
=======================================
  Files         247      247           
  Lines       24389    24390    +1     
=======================================
+ Hits        21820    21822    +2     
+ Misses       2569     2568    -1     
Flag Coverage Δ
integration 75.96% <100.00%> (+<0.01%) ⬆️

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

Files with missing lines Coverage Δ
src/scvi/model/_totalvi.py 87.94% <100.00%> (+0.23%) ⬆️
src/scvi/module/_totalvae.py 89.39% <100.00%> (ø)
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TOTALVI.get_normalized_expression omits learned protein capture efficiency

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