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Model: DiagVI #3570

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WinterHannah and others added 30 commits May 13, 2025 16:41
@WinterHannah
multi-modal batch VAE
f853803
@WinterHannah
tests
d49fdea
@WinterHannah
batch encoding dual mod VAE
fa358c5
@Marius1311
Merge pull request #9 from quadbio/main
ab7de85 
Update feature branch to match upstream/main
@Marius1311
Re-enable some workflows
ab0e4b4
@Marius1311
Merge pull request #10 from quadbio/chore/gha-spatial-branch-updates
5407a45 
Re-enable some workflows
@Marius1311
ci: comment out schedule trigger in test_linux workflow (resource sav…
92a7975 
…ing)
@Marius1311
Set up simple linting workflow
b10b081
@Marius1311
Fix linter
23282c9
@Marius1311
Modify the linux test workflow, depend on label
ec9b293
@Marius1311
Merge pull request #11 from quadbio/chore/ci-disable-schedule-test-linux
9b53764 
Chore/ci disable schedule test linux
@Marius1311
Merge branch 'feature/spatial' into 2-basic-batch-encoding-like-in-glue
42fb0e3
@WinterHannah
updated tests
c94b551
@WinterHannah
Merge branch '2-basic-batch-encoding-like-in-glue' of https://github.…
4812cb7 
…com/quadbio/scvi-tools into 2-basic-batch-encoding-like-in-glue
@WinterHannah
basemodelclass change
4526520
@WinterHannah
guidance graph and tensorboard
ef923d1
@WinterHannah
add init file
5f3d226
@WinterHannah
logging update
bcb085e
@WinterHannah
incorporated comments
8d7dcc1
@WinterHannah
different parameters for test
043f445
@WinterHannah
Merge pull request #8 from quadbio/2-basic-batch-encoding-like-in-glue
9875704 
2 basic batch encoding like in glue
@WinterHannah
guidance graph
c44b70a
@WinterHannah
Merge branch '3-link-decoders-with-guidance-graph' into 3-link-decode…
a693020 
…rs-with-guidance-graph-merge
@WinterHannah
Merge pull request #12 from quadbio/3-link-decoders-with-guidance-gra…
9a06794 
…ph-merge

merge to fix divergent branches
@WinterHannah
ruff formatting
a4274aa
@WinterHannah
Update test_linux_custom_dataloader.yml
7820ea6
@WinterHannah
Merge pull request #14 from quadbio/feature/spatial
fe9bfaa 
Update test_linux_custom_dataloader.yml
@WinterHannah
update workflow env
33c9b2e
@WinterHannah
fixed tests
194eea1
@WinterHannah
improved edge sampling
0d0dc84
WinterHannah and others added 21 commits August 12, 2025 15:19
@ori-kron-wis ori-kron-wis self-assigned this Oct 21, 2025
@ori-kron-wis ori-kron-wis added the on-merge: backport to 1.4.x on-merge: backport to 1.4.x label Oct 21, 2025
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codecov bot commented Oct 21, 2025 •
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Codecov Report

❌ Patch coverage is 72.13930% with 224 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.11%. Comparing base (7a226a3) to head (84f0cd7).

Files with missing lines Patch % Lines
src/scvi/external/diagvi/_model.py 73.16% 84 Missing ⚠️
src/scvi/external/diagvi/_base_components.py 43.65% 71 Missing ⚠️
src/scvi/external/diagvi/_module.py 70.22% 39 Missing ⚠️
src/scvi/external/diagvi/_utils.py 79.36% 26 Missing ⚠️
src/scvi/external/diagvi/_task.py 96.03% 4 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (7a226a3) and HEAD (84f0cd7). Click for more details.

HEAD has 112 uploads less than BASE
Flag BASE (7a226a3) HEAD (84f0cd7)
115 3
Additional details and impacted files 
@@             Coverage Diff             @@
##             main    #3570       +/-   ##
===========================================
- Coverage   87.33%   74.11%   -13.23%     
===========================================
  Files         224      230        +6     
  Lines       21029    21832      +803     
===========================================
- Hits        18365    16180     -2185     
- Misses       2664     5652     +2988
Files with missing lines Coverage Δ
src/scvi/external/__init__.py 85.71% <100.00%> (+0.42%) ⬆️
src/scvi/external/diagvi/__init__.py 100.00% <100.00%> (ø)
src/scvi/model/base/_base_model.py 77.00% <100.00%> (-5.84%) ⬇️
src/scvi/external/diagvi/_task.py 96.03% <96.03%> (ø)
src/scvi/external/diagvi/_utils.py 79.36% <79.36%> (ø)
src/scvi/external/diagvi/_module.py 70.22% <70.22%> (ø)
src/scvi/external/diagvi/_base_components.py 43.65% <43.65%> (ø)
src/scvi/external/diagvi/_model.py 73.16% <73.16%> (ø)

... and 62 files with indirect coverage changes

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@ori-kron-wis ori-kron-wis changed the title feat: DiagVI Model: DiagVI Oct 22, 2025
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@ori-kron-wis @WinterHannah @Marius1311