From 84f47a4e5e2bf3349a1b16d09ecb68c6fc22b9f6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 13 Jul 2026 18:19:04 +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: v2.4.14 → v2.5.3](https://github.com/biomejs/pre-commit/compare/v2.4.14...v2.5.3)
- [github.com/tox-dev/pyproject-fmt: v2.21.1 → v2.25.2](https://github.com/tox-dev/pyproject-fmt/compare/v2.21.1...v2.25.2)
- [github.com/astral-sh/ruff-pre-commit: v0.15.12 → v0.15.21](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.12...v0.15.21)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 40d3ad724..e70f809e8 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: v2.4.14
+    rev: v2.5.3
     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: v2.21.1
+    rev: v2.25.2
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.21
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

From 0bf1b978b132d7a63fe3c83a271e7c3df7bcea73 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 13 Jul 2026 18:23:30 +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 | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2a9967bb3..424fb6230 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -138,10 +138,10 @@ include-package-data = true
 [tool.setuptools_scm]
 
 [tool.hatch]
+version.source = "vcs"
+metadata.allow-direct-references = true
 build.hooks.vcs.version-file = "_version.py"
 build.targets.wheel.packages = [ "src/squidpy" ]
-metadata.allow-direct-references = true
-version.source = "vcs"
 
 [tool.pixi]
 workspace.channels = [ "conda-forge" ]
@@ -187,7 +187,6 @@ lint.select = [
   "UP",  # pyupgrade
   "W",   # pycodestyle
 ]
-# "squidpy/*.py"= ["RST303"]
 lint.ignore = [
   # B008 Do not perform function calls in argument defaults.
   "B008",
@@ -263,20 +262,18 @@ lint.unfixable = [
 # Disallow all relative imports.
 lint.flake8-tidy-imports.ban-relative-imports = "all"
 lint.isort.required-imports = [ "from __future__ import annotations" ]
+# "squidpy/*.py" = [ "RST303" ]
 
 [tool.pytest]
-strict = true
+addopts = [
+  "--ignore=docs",
+]
 filterwarnings = [
   "error::numba.NumbaPerformanceWarning",
   "ignore::UserWarning",
   "ignore::anndata.OldFormatWarning",
   "ignore:.*pkg_resources:DeprecationWarning",
 ]
-python_files = [ "test_*.py" ]
-testpaths = [ "tests/" ]
-addopts = [
-  "--ignore=docs",
-]
 markers = [
   "internet: tests that require internet",
   # the below markers are just there because we import from anndata.tests.helpers,
@@ -284,6 +281,9 @@ markers = [
   "gpu: tests that require GPU",
   "array_api: tests that require array-api-compat",
 ]
+python_files = [ "test_*.py" ]
+strict = true
+testpaths = [ "tests/" ]
 
 [tool.coverage]
 run.branch = true