From 64c978239dc2fbccb7975aca6a89fc1918761653 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 19:40:49 +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: v2.3.10 → v2.5.5](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.5.5)
- [github.com/tox-dev/pyproject-fmt: v2.11.1 → v2.26.0](https://github.com/tox-dev/pyproject-fmt/compare/v2.11.1...v2.26.0)
- [github.com/astral-sh/ruff-pre-commit: v0.14.11 → v0.16.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.11...v0.16.0)
---
 .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 2bf7d5a..0d09492 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: v2.3.10
+    rev: v2.5.5
     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: v2.11.1
+    rev: v2.26.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.11
+    rev: v0.16.0
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

From b9bc119f0f9b9cd210a7d20f576a237c942f9747 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 Jul 2026 19:41:45 +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 | 60 ++++++++++++++++++++------------------------------
 1 file changed, 24 insertions(+), 36 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f1e87ae..2c4c91b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,43 +58,31 @@ urls.Documentation = "https://mapqc.readthedocs.io/"
 urls.Homepage = "https://github.com/theislab/mapqc"
 urls.Source = "https://github.com/theislab/mapqc"
 
-[tool.hatch.envs.default]
-installer = "uv"
-features = [ "dev" ]
-
-[tool.hatch.envs.docs]
-features = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
-scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
-scripts.clean = "git clean -fdX -- {args:docs}"
-
-# Test the lowest and highest supported Python versions with normal deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "stable" ]
-python = [ "3.10", "3.13" ]
-
-# Test the newest supported Python version also with pre-release deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.13" ]
-
-[tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+envs.default.installer = "uv"
+envs.default.features = [ "dev" ]
+envs.docs.features = [ "doc" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
+envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
+envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.hatch-test.features = [ "dev", "test" ]
+envs.hatch-test.matrix = [
+  # Test the lowest and highest supported Python versions with normal deps
+  { deps = [ "stable" ], python = [ "3.10", "3.13" ] },
+  # Test the newest supported Python version also with pre-release deps
+  { deps = [ "pre" ], python = [ "3.13" ] },
+]
 # If the matrix variable `deps` is set to "pre",
 # set the environment variable `UV_PRERELEASE` to "allow".
-matrix.deps.env-vars = [
-  { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
+envs.hatch-test.overrides.matrix.deps.env-vars = [
+  { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -128,19 +116,19 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
-testpaths = [ "tests" ]
-xfail_strict = true
-addopts = [
+[tool.pytest]
+ini_options.testpaths = [ "tests" ]
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+ini_options.xfail_strict = true
 
-[tool.coverage.run]
-source = [ "mapqc" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "mapqc" ]
 
 [tool.cruft]
 skip = [