[pre-commit.ci] pre-commit autoupdate

.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: v2.11.1
+    rev: v2.14.2
     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
         types_or: [python, pyi, jupyter]

pyproject.toml

@@ -28,7 +28,6 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dynamic = [ "version" ]
-
 dependencies = [
   "anndata>=0.10.8",
   "h5py",
@@ -38,7 +37,6 @@ dependencies = [
   # for debug logging (referenced from the issue template)
   "session-info2",
 ]
-
 optional-dependencies.io = [ "fsspec", "zarr" ]
 # https://docs.pypi.org/project_metadata/#project-urls
 urls.Documentation = "https://mudata.readthedocs.io/"
@@ -52,13 +50,11 @@ dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-
 test = [
   "coverage>=7.10",
   "pytest",
   "zarr",
 ]
-
 doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
   "ipykernel",
@@ -76,51 +72,33 @@ doc = [
   "sphinxext-opengraph",
 ]
 
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.build.hooks.vcs]
-version-file = "src/mudata/_version.py"
-
-[tool.hatch.envs.default]
-installer = "uv"
-dependency-groups = [ "dev" ]
-
-[tool.hatch.envs.docs]
-dependency-groups = [ "doc" ]
-scripts.build = "sphinx-build -M html docs docs/_build {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 = [ "3.11", "3.14" ]
-
-# Test the newest supported Python version also with pre-release deps
-[[tool.hatch.envs.hatch-test.matrix]]
-deps = [ "pre" ]
-python = [ "3.14" ]
-
-[tool.hatch.envs.hatch-test]
-dependency-groups = [ "dev", "test" ]
-
-[tool.hatch.envs.hatch-test.overrides]
+[tool.hatch]
+build.hooks.vcs.version-file = "src/mudata/_version.py"
+envs.default.installer = "uv"
+envs.default.dependency-groups = [ "dev" ]
+envs.docs.dependency-groups = [ "doc" ]
+envs.docs.scripts.build = "sphinx-build -M html docs docs/_build {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.dependency-groups = [ "dev", "test" ]
+envs.hatch-test.matrix = [
+  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  { deps = [ "pre" ], python = [ "3.14" ] }
+]
 # 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" ] },
 ]
+version.source = "vcs"
 
 [tool.ruff]
 line-length = 120
 src = [ "src" ]
 extend-include = [ "*.ipynb" ]
-
 format.skip-magic-trailing-comma = true
 format.exclude = [ "*.ipynb" ]
 format.docstring-code-format = true
-
 lint.select = [
   "B",      # flake8-bugbear
   "BLE",    # flake8-blind-except
@@ -135,11 +113,11 @@ lint.select = [
   "W",      # Warning detected by Pycodestyle
 ]
 lint.ignore = [
-  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
-  "D100", # Missing docstring in public module
-  "D104", # Missing docstring in public package
-  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
-  "D107", # Missing docstring in __init__
+  "B008",   # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "D100",   # Missing docstring in public module
+  "D104",   # Missing docstring in public package
+  "D105",   # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107",   # Missing docstring in __init__
   # Disable one in each pair of mutually incompatible rules
   "D203",   # We don’t want a blank line before a class docstring
   "D213",   # <> We want docstrings to start immediately after the opening triple quote
@@ -163,10 +141,10 @@ addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
 
-[tool.coverage.run]
-source = [ "mudata" ]
-patch = [ "subprocess" ]
-omit = [
+[tool.coverage]
+run.source = [ "mudata" ]
+run.patch = [ "subprocess" ]
+run.omit = [
   "**/test_*.py",
 ]