From 075cb21ea5e58805f82629f64e2e23933c5f127c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Sep 2026 16:31:42 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
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Content-Type: text/plain; charset=UTF-8
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.16.2 → v0.16.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.16.2...v0.16.8)
- [github.com/PyCQA/bandit: 1.7.9 → 1.9.4](https://github.com/PyCQA/bandit/compare/1.7.9...1.9.4)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af3eb03..8874b0a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.16.2
+  rev: v0.16.8
   hooks:
     # Run the linter.
     - id: ruff-check
@@ -55,7 +55,7 @@ repos:
 #   - id: codespell
 
 - repo: https://github.com/PyCQA/bandit
-  rev: 1.7.9
+  rev: 1.9.4
   hooks:
     - id: bandit
       args: ["-c", "pyproject.toml"]

From b592bbab4b9bd595d67edd1e6198efa4d7b11759 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 21 Sep 2026 16:33:27 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 README.md | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 41a3463..34c4ec0 100644
--- a/README.md
+++ b/README.md
@@ -52,8 +52,11 @@ sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
 from singlecellexperiment import SingleCellExperiment
 
 tse = SingleCellExperiment(
-    assays={"counts": counts}, row_data=df_gr, col_data=col_data,
-    reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
+    assays={"counts": counts},
+    row_data=df_gr,
+    col_data=col_data,
+    reduced_dims={"tsne": ..., "umap": ...},
+    alternative_experiments={"atac": ...},
 )
 ```