diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 40d3ad724..eda29b628 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: v2.5.0
     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: v2.25.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.12
+    rev: v0.15.18
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
diff --git a/pyproject.toml b/pyproject.toml
index 418135298..a0e5a6279 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -134,10 +134,10 @@ 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" ]
@@ -183,7 +183,6 @@ lint.select = [
   "UP",  # pyupgrade
   "W",   # pycodestyle
 ]
-# "squidpy/*.py"= ["RST303"]
 lint.ignore = [
   # B008 Do not perform function calls in argument defaults.
   "B008",
@@ -259,20 +258,18 @@ 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,
@@ -280,6 +277,9 @@ 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