From 463033a00149d7ac2ee3ede5f8da6182b9ff3c0a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 17:08:25 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.5.3 → v2.5.15](https://github.com/biomejs/pre-commit/compare/v2.5.3...v2.5.15)
- [github.com/tox-dev/pyproject-fmt: v2.25.3 → v2.30.3](https://github.com/tox-dev/pyproject-fmt/compare/v2.25.3...v2.30.3)
- [github.com/astral-sh/ruff-pre-commit: v0.15.21 → v0.17.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.21...v0.17.1)
- [github.com/zizmorcore/zizmor-pre-commit: v1.24.1 → v1.31.1](https://github.com/zizmorcore/zizmor-pre-commit/compare/v1.24.1...v1.31.1)
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3a84322..1f0da4b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.3
+    rev: v2.5.15
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.25.3
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.21
+    rev: v0.17.1
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
@@ -38,7 +38,7 @@ repos:
         args: [--assume-in-merge]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.24.1
+    rev: v1.31.1
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]

From a47302ca677b5a3207288c435d59c336d547bd02 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Oct 2026 17:08:39 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

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

diff --git a/pyproject.toml b/pyproject.toml
index 7d80089..3f63fbb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,10 @@ requires = [ "hatchling" ]
 [project]
 name = "cellcharter"
 version = "0.3.8"
-description = "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data."
+description = """\
+  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics \
+  data.\
+  """
 readme = "README.md"
 license = { file = "LICENSE" }
 maintainers = [
@@ -139,11 +142,11 @@ ini_options.filterwarnings = [
 ]
 
 [tool.coverage]
+run.source = [ "cellcharter" ]
 run.omit = [
   "**/test_*.py",
 ]
 run.patch = [ "subprocess" ]
-run.source = [ "cellcharter" ]
 
 [tool.jupytext]
 formats = "ipynb,md"