Restore scGen batch-removal tutorial in the docs#1029
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Bump the tutorials submodule to include the restored `scgen_batch_removal.ipynb` and add it to the tools gallery under a new "Batch correction" section. Depends on scverse/pertpy-tutorials#66. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1029 +/- ##
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+ Coverage 77.95% 77.98% +0.02%
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- Hits 5135 5111 -24
+ Misses 1452 1443 -9 🚀 New features to boost your workflow:
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Brings back the scGen batch-removal tutorial and renders it in the docs.
Changes
docs/tutorials/notebookssubmodule to include the restoredscgen_batch_removal.ipynb(Restore scGen batch-removal tutorial pertpy-tutorials#66).notebooks/scgen_batch_removalto the tutorials gallery indocs/tutorials/tools.mdunder a new Batch correction section, so it renders.Context
The batch-removal tutorial was removed from
pertpy-tutorialsin late 2023 (4ef5318). It has been restored and modernized (currentpt.tl.ScgenAPI,kang_2018schema, runs in ~2 min on CPU). The docs build renders stored notebook outputs (nb_execution_mode = "off"), and the notebook's outputs were regenerated with the scGen reproduction fix in #1028.Dependencies / merge order
maincommit (the current pointer is the PR branch commit), then merge.🤖 Generated with Claude Code