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refactor: Dropping Jax from scvi-tools#3786

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Ori-Dropping-Jax
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refactor: Dropping Jax from scvi-tools#3786
ori-kron-wis wants to merge 5 commits into
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Ori-Dropping-Jax

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@ori-kron-wis ori-kron-wis self-assigned this Apr 19, 2026
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codecov Bot commented Apr 19, 2026

Codecov Report

❌ Patch coverage is 50.00000% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.69%. Comparing base (c543aa7) to head (7f94ca0).

Files with missing lines Patch % Lines
src/scvi/external/mrvi/_model.py 33.33% 4 Missing ⚠️
src/scvi/model/_utils.py 33.33% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3786      +/-   ##
==========================================
- Coverage   88.52%   84.69%   -3.84%     
==========================================
  Files         237      237              
  Lines       23827    23387     -440     
==========================================
- Hits        21094    19808    -1286     
- Misses       2733     3579     +846     
Flag Coverage Δ
integration 76.19% <50.00%> (+3.58%) ⬆️
nonjax ?

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

Files with missing lines Coverage Δ
src/scvi/__init__.py 100.00% <ø> (ø)
src/scvi/_settings.py 90.26% <ø> (+3.24%) ⬆️
src/scvi/_types.py 100.00% <100.00%> (+7.14%) ⬆️
src/scvi/distributions/__init__.py 100.00% <ø> (+7.69%) ⬆️
src/scvi/distributions/_negative_binomial.py 78.73% <ø> (-1.51%) ⬇️
src/scvi/external/__init__.py 100.00% <ø> (+14.28%) ⬆️
src/scvi/external/mrvi_torch/_model.py 88.30% <ø> (ø)
src/scvi/model/__init__.py 95.65% <ø> (-0.78%) ⬇️
src/scvi/model/base/__init__.py 94.73% <ø> (-1.10%) ⬇️
src/scvi/module/__init__.py 95.23% <ø> (-0.92%) ⬇️
... and 11 more

... and 2 files with indirect coverage changes

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Comment thread src/scvi/model/_utils.py Outdated
Comment thread src/scvi/external/mrvi/_model.py Outdated
@ori-kron-wis ori-kron-wis removed the jax label Apr 19, 2026
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We will need to transform Tangram to Torch before we remove Jax. Afterwards it will also move to scviva-tools @canergen

# Conflicts:
#	.github/workflows/test_linux_nonjax.yml
#	pyproject.toml
#	src/scvi/external/tangram/_model.py
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