From 2145e68b9a228bd2ad407e481f02ebc69f5d6ef0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Feb 2026 18:33:10 +0000
Subject: [PATCH 1/3] [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 → v2.3.14](https://github.com/biomejs/pre-commit/compare/v2.3.10...v2.3.14)
- [github.com/tox-dev/pyproject-fmt: v2.12.1 → v2.15.0](https://github.com/tox-dev/pyproject-fmt/compare/v2.12.1...v2.15.0)
- [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.15.0)
---
 .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 1767caa..2f9d9c2 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: v2.3.14
     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: v2.12.1
+    rev: v2.15.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.14
+    rev: v0.15.0
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]

From f21be45b89cec6712ef5f688cb040454b59c609d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 9 Feb 2026 18:33:29 +0000
Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 58 ++++++++++++++++++++------------------------------
 1 file changed, 23 insertions(+), 35 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c012016..25ab7f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,33 +59,23 @@ urls.Documentation = "https://anndata-plot.readthedocs.io/"
 urls.Homepage = "https://github.com/scverse/anndata-plot"
 urls.Source = "https://github.com/scverse/anndata-plot"
 
-[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}"
-
-[tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
-
-# 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.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.open = "python -m webbrowser -t docs/_build/html/index.html"
+envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
+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 = [
+envs.hatch-test.overrides.matrix.deps.env-vars = [
   { key = "UV_PRERELEASE", value = "allow", if = [ "pre" ] },
 ]
 
@@ -93,9 +83,7 @@ matrix.deps.env-vars = [
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -129,19 +117,19 @@ 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.xfail_strict = true
+ini_options.addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "anndata_plot" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.omit = [
   "**/test_*.py",
 ]
+run.patch = [ "subprocess" ]
+run.source = [ "anndata_plot" ]
 
 [tool.cruft]
 skip = [

From ba738db98b6ce94c444d3745f4a1c40967296882 Mon Sep 17 00:00:00 2001
From: Phil Schaf <flying-sheep@web.de>
Date: Mon, 9 Feb 2026 19:38:46 +0100
Subject: [PATCH 3/3] no more ini

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 25ab7f4..bb9eefa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -118,9 +118,9 @@ lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
 [tool.pytest]
-ini_options.testpaths = [ "tests" ]
-ini_options.xfail_strict = true
-ini_options.addopts = [
+strict = true
+testpaths = [ "tests" ]
+addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]