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Update feature branch to match upstream/main
…pdates Re-enable some workflows
…test-linux Chore/ci disable schedule test linux
…com/quadbio/scvi-tools into 2-basic-batch-encoding-like-in-glue
…-in-glue 2 basic batch encoding like in glue
…rs-with-guidance-graph-merge
…nce-graph-merge merge to fix divergent branches
Update test_linux_custom_dataloader.yml
# Conflicts: # pyproject.toml # src/scvi/external/__init__.py
for more information, see https://pre-commit.ci
| # for custom dataloders | ||
| dataloaders = ["lamindb>=1.12.1", "cellxgene-census", "tiledbsoma", "tiledbsoma_ml", "torchdata"] | ||
| # for diagvi | ||
| diagvi = ["torch_geometric", "geomloss"] |
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Do you need geomloss? It doesn't seem to be actively maintained.
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Hi Can, at the moment we rely on geomloss to compute the unbalanced optimal transport loss component. However, we are working on another approach based on POT, which is more actively maintained.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3575 +/- ##
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- Coverage 84.70% 75.18% -9.53%
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Files 225 232 +7
Lines 21637 22603 +966
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- Hits 18327 16993 -1334
- Misses 3310 5610 +2300
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Hey @WinterHannah , what is the status of the PR? Should we expect more commits to it? |
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Hi @ori-kron-wis, I’ll be making a few commits to add documentation and a tutorial. It should take about a week at most! |
Added docstring to every function, removed unnecessary code and comments, restructured parts of the code, fixed semi-supervision and feature imputation, added tests.
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