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feat: Added support for covariates in JaxSCVI#3717

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ori-kron-wis wants to merge 3 commits intomainfrom
Ori-jaxscvi-covs-support
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feat: Added support for covariates in JaxSCVI#3717
ori-kron-wis wants to merge 3 commits intomainfrom
Ori-jaxscvi-covs-support

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@ori-kron-wis ori-kron-wis self-assigned this Feb 18, 2026
@ori-kron-wis ori-kron-wis added jax on-merge: backport to 1.4.x on-merge: backport to 1.4.x labels Feb 18, 2026
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Reviewed commit: a84de7ba46

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codecov bot commented Feb 18, 2026

Codecov Report

❌ Patch coverage is 50.00000% with 79 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.50%. Comparing base (7901963) to head (0f67d46).

Files with missing lines Patch % Lines
src/scvi/train/_trainingplans.py 24.67% 58 Missing ⚠️
src/scvi/model/base/_jaxmixin.py 48.27% 15 Missing ⚠️
src/scvi/module/_jaxvae.py 93.33% 3 Missing ⚠️
src/scvi/train/_callbacks.py 40.00% 3 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (7901963) and HEAD (0f67d46). Click for more details.

HEAD has 37 uploads less than BASE
Flag BASE (7901963) HEAD (0f67d46)
41 4
Additional details and impacted files
@@             Coverage Diff             @@
##             main    #3717       +/-   ##
===========================================
- Coverage   88.43%   77.50%   -10.94%     
===========================================
  Files         226      226               
  Lines       21909    22057      +148     
===========================================
- Hits        19375    17095     -2280     
- Misses       2534     4962     +2428     
Files with missing lines Coverage Δ
src/scvi/model/_jaxscvi.py 100.00% <100.00%> (ø)
src/scvi/module/_jaxvae.py 97.76% <93.33%> (-1.16%) ⬇️
src/scvi/train/_callbacks.py 80.14% <40.00%> (-1.48%) ⬇️
src/scvi/model/base/_jaxmixin.py 74.62% <48.27%> (-20.11%) ⬇️
src/scvi/train/_trainingplans.py 82.67% <24.67%> (-8.42%) ⬇️

... and 65 files with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

…_samples, batch, latent), but cont_covs, cat_oh, and batch remain 2D (batch, dim). jnp.concatenate requires matching rank, so the

  mismatch causes a failure.
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