From a86e7b3c0a0e30a2134474ca7d4604412ab6bef4 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 16:31:53 +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 000da3866038023462cd58ca6d6f3f14eabe0a1d 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 16:34:07 +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 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index fcd16aa..7f3b14c 100644
--- a/README.md
+++ b/README.md
@@ -71,7 +71,9 @@ To create a `SummarizedExperiment`,
 from summarizedexperiment import SummarizedExperiment
 
 tse = SummarizedExperiment(
-    assays={"counts": counts}, row_data=row_data, column_data=col_data,
+    assays={"counts": counts},
+    row_data=row_data,
+    column_data=col_data,
     metadata={"seq_platform": "Illumina NovaSeq 6000"},
 )
 ```
@@ -93,8 +95,10 @@ from summarizedexperiment import RangedSummarizedExperiment
 from genomicranges import GenomicRanges
 
 trse = RangedSummarizedExperiment(
-    assays={"counts": counts}, row_data=row_data,
-    row_ranges=GenomicRanges.from_pandas(row_data.to_pandas()), column_data=col_data
+    assays={"counts": counts},
+    row_data=row_data,
+    row_ranges=GenomicRanges.from_pandas(row_data.to_pandas()),
+    column_data=col_data,
 )
 ```