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Restore scGen batch-removal tutorial in the docs#1029

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docs/scgen-batch-removal-tutorial
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Restore scGen batch-removal tutorial in the docs#1029
Zethson wants to merge 1 commit into
mainfrom
docs/scgen-batch-removal-tutorial

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@Zethson

@Zethson Zethson commented Jun 26, 2026

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Brings back the scGen batch-removal tutorial and renders it in the docs.

Changes

  • Bumps the docs/tutorials/notebooks submodule to include the restored scgen_batch_removal.ipynb (Restore scGen batch-removal tutorial pertpy-tutorials#66).
  • Adds notebooks/scgen_batch_removal to the tutorials gallery in docs/tutorials/tools.md under a new Batch correction section, so it renders.

Context

The batch-removal tutorial was removed from pertpy-tutorials in late 2023 (4ef5318). It has been restored and modernized (current pt.tl.Scgen API, kang_2018 schema, 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

  1. Merge Restore scGen batch-removal tutorial pertpy-tutorials#66 first.
  2. Re-point this submodule to the resulting main commit (the current pointer is the PR branch commit), then merge.
  3. Best paired with Make JAX scGen reproduce PyTorch scGen #1028 (scGen reproduction fix), which makes the demonstrated results correct.

🤖 Generated with Claude Code

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>
@github-actions github-actions Bot added the chore label Jun 26, 2026
@codecov-commenter

codecov-commenter commented Jun 26, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.98%. Comparing base (473da92) to head (5c35cfe).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1029      +/-   ##
==========================================
+ Coverage   77.95%   77.98%   +0.02%     
==========================================
  Files          50       50              
  Lines        6587     6554      -33     
==========================================
- Hits         5135     5111      -24     
+ Misses       1452     1443       -9     

see 4 files with indirect coverage changes

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2 participants