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Fix DE tutorial #814

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Merged
Zethson merged 2 commits into from
Jul 5, 2025
Merged

Fix DE tutorial #814

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af6fddd
Fix DE tutorial
Zethson Jul 5, 2025
2527209
Merge branch 'main' of https://github.com/scverse/pertpy into fix/de
Zethson Jul 5, 2025
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.12.1
hooks:
- id: ruff
- id: ruff-check
args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
- id: ruff-format
- repo: https://github.com/pre-commit/pre-commit-hooks
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2 changes: 1 addition & 1 deletion docs/tutorials/notebooks
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Submodule notebooks updated 3 files
+1 −1 .pre-commit-config.yaml
+1 −1 README.md
+381 −369 differential_gene_expression.ipynb
3 changes: 2 additions & 1 deletion pertpy/tools/_perturbation_space/_simple.py
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Expand Up @@ -169,10 +169,11 @@ def compute(

if mode in ps_adata.layers:
ps_adata.X = ps_adata.layers[mode]

for col in original_obs.columns:
if col not in ps_adata.obs.columns:
grouped_values = original_obs.groupby(grouping_cols)[col].first()
ps_adata.obs[col] = grouped_values.values
ps_adata.obs[col] = grouped_values.reindex(ps_adata.obs.index).values

ps_adata.obs[target_col] = ps_adata.obs[target_col].astype("category")

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