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Refactor [WIP]: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools#3908

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Refactor [WIP]: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools#3908
ori-kron-wis wants to merge 6 commits into
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inc all peripheral classes/functions that are no longer used

@ori-kron-wis ori-kron-wis self-assigned this Jul 9, 2026
@ori-kron-wis ori-kron-wis added on-merge: backport to 1.5.x on-merge: backport to 1.5.x cuda tests Run test suite on CUDA labels Jul 9, 2026

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Comment thread docs/tutorials/index_spatial.md
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codecov Bot commented Jul 9, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.54%. Comparing base (c8e16ac) to head (6c45379).

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3908      +/-   ##
==========================================
- Coverage   88.55%   88.54%   -0.01%     
==========================================
  Files         241      241              
  Lines       23722    23712      -10     
==========================================
- Hits        21007    20996      -11     
- Misses       2715     2716       +1     
Flag Coverage Δ
cuda 72.82% <100.00%> (-1.89%) ⬇️
integration 72.80% <100.00%> (-1.88%) ⬇️

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

Files with missing lines Coverage Δ
src/scvi/external/__init__.py 100.00% <ø> (ø)
src/scvi/external/diagvi/_model.py 92.15% <ø> (-0.04%) ⬇️
src/scvi/hub/_template.py 100.00% <ø> (ø)
src/scvi/model/__init__.py 95.45% <ø> (-0.20%) ⬇️
src/scvi/model/_condscvi.py 84.76% <ø> (ø)
src/scvi/model/base/_base_model.py 83.58% <100.00%> (ø)
src/scvi/module/__init__.py 95.00% <ø> (-0.24%) ⬇️
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@ori-kron-wis ori-kron-wis changed the title Refactor: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools Refactor [WIP]: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools Jul 9, 2026
# Conflicts:
#	docs/user_guide/models/diagvi.md
#	src/scvi/external/diagvi/_model.py
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