ci: pre-commit autoupdate (#3901)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A. <flying-sheep@web.de>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.5
+    rev: v0.14.7
     hooks:
     -   id: ruff-check
         args: ["--fix"]
@@ -20,7 +20,7 @@ repos:
         - --sort-by-bibkey
         - --drop=abstract
 -   repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.5
+    rev: v2.3.8
     hooks:
     -   id: biome-format
 -   repo: https://github.com/ComPWA/taplo-pre-commit

pyproject.toml

@@ -68,7 +68,7 @@ dependencies = [
     "numba >=0.60",
     "umap-learn>=0.5.7",
     "pynndescent>=0.5.13",
-    "packaging>=21.3",
+    "packaging>=25",
     "session-info2",
     "legacy-api-wrap>=1.5",                       # for positional API deprecations
     "typing-extensions; python_version < '3.13'",
@@ -89,7 +89,7 @@ scanpy = "scanpy.cli:console_main"
 
 [project.optional-dependencies]
 test-min = [
-    "pytest>=8.2",
+    "pytest",
     "pytest-mock",
     "pytest-cov",           # only for use from VS Code
     "pytest-xdist[psutil]",