chore: cruft update

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "31733e798d89018e590c2586962c153d38057dad",
+  "commit": "9345e6250d37a482c0bed3ecfd2ffb082f123bc3",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -37,7 +37,7 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "31733e798d89018e590c2586962c153d38057dad"
+      "_commit": "9345e6250d37a482c0bed3ecfd2ffb082f123bc3"
     }
   },
   "directory": null

.github/workflows/autofix.yaml

@@ -0,0 +1,29 @@
+# The workflow name is mandated by autofix.ci.
+# It needs to be a dedicated workflow, as autofix.ci times out on long runs.
+name: autofix.ci
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    name: Pre-commit checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+          filter: blob:none
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          enable-cache: true
+      - run: uv tool install hatch
+      - name: Run pre-commit hooks
+        run: uvx prek run --all-files --show-diff-on-failure --color=always
+      - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
+        if: '!cancelled()'

.gitignore

@@ -5,6 +5,7 @@ buck-out/
 
 # Compiled files
 .venv/
+uv.lock
 __pycache__/
 .*cache/
 

.pre-commit-config.yaml

@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.7
+    rev: v2.5.11
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
         groups: [format]
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.27.0
+    rev: v2.29.2
     hooks:
       - id: pyproject-fmt
         groups: [format]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.16.2
+    rev: v0.16.5
     hooks:
       - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
@@ -53,7 +53,7 @@ repos:
         args: [--assume-in-merge]
 
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.29.0
+    rev: v1.30.0
     hooks:
       - id: zizmor
         args: [--no-progress, --fix]

docs/contributing.md

@@ -148,26 +148,28 @@ The `.venv` directory is typically automatically discovered by IDEs such as VS C
 
 ## Code-style
 
-This package uses [pre-commit][]-style hooks to enforce consistent code-styles.
-We recommend running them with [prek][], a fast, drop-in replacement for `pre-commit` that reads the same `.pre-commit-config.yaml`.
+This package uses Git hooks to enforce consistent code-styles.
+They are defined in `.pre-commit-config.yaml` and run with [prek][].
 On every commit, the checks will either automatically fix issues with the code, or raise an error message.
 
-To enable the checks locally, install [prek][] (e.g. with `uv tool install prek`) and run
+To enable the checks locally, run
 
 ```bash
-prek install
+hatch run hatch-check-code:prek install
+# or
+uvx prek install
 ```
 
 in the root of the repository.
 prek will automatically download all dependencies when it is run for the first time.
 
-If you didn’t run the checks locally, the `Pre-commit checks` job of the GitHub Actions CI runs them on your pull request and reports any failures.
+If you didn’t run the checks locally, the `Pre-commit checks` job of the GitHub Actions CI runs them on your pull request,
+pushes the automatic fixes back to your branch, and reports any remaining failures.
 We strongly encourage installing and running the checks locally first to understand their usage.
 
 Finally, most editors have an _autoformat on save_ feature.
 Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
 
-[pre-commit]: https://pre-commit.com/
 [prek]: https://prek.j178.dev/
 [ruff-editors]: https://docs.astral.sh/ruff/integrations/
 [biome-editors]: https://biomejs.dev/guides/integrate-in-editor/

pyproject.toml

@@ -23,6 +23,7 @@ classifiers = [
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
+  "Typing :: Typed",
 ]
 dependencies = [
   "myst-nb>=1.1",
@@ -41,7 +42,6 @@ entry-points."sphinx.html_themes".scverse = "scverse_doc.theme"
 
 [dependency-groups]
 dev = [
-  "prek",
   "twine>=4.0.2",
 ]
 test = [
@@ -60,12 +60,21 @@ doc = [
 typecheck = [ "mypy" ]
 
 [tool.hatch]
+build.targets.sdist.exclude = [ "/docs", "/tests" ]
 envs.default.installer = "uv"
 envs.default.dependency-groups = [ "dev" ]
 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.docs.dependency-groups = [ "doc" ]
+envs.hatch-check-code.dependencies = [ "prek" ]
+envs.hatch-check-code.scripts.lint-check = "echo 'try `hatch check code --fix`'; false"
+envs.hatch-check-code.scripts.lint-fix = "prek run -a --no-group=format --no-group=typecheck"
+envs.hatch-check-fmt.dependencies = [ "prek" ]
+envs.hatch-check-fmt.scripts.format-check = "echo 'try `hatch check fmt --fix`'; false"
+envs.hatch-check-fmt.scripts.format-fix = "prek run -a --group=format --no-group=typecheck"
+envs.hatch-check-types.scripts.check = [ "mypy" ]
+envs.hatch-check-types.dependency-groups = [ "typecheck", "doc", "test" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
   { deps = [ "stable" ], python = [ "3.12", "3.14" ] },
@@ -78,14 +87,6 @@ envs.hatch-test.overrides.matrix.deps.env-vars = [
   { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
 ]
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
-envs.hatch-check-fmt.dependencies = [ "prek" ]
-envs.hatch-check-fmt.scripts.format-check = "echo 'try `hatch check fmt --fix`'; false"
-envs.hatch-check-fmt.scripts.format-fix = "prek run -a --group=format --no-group=typecheck"
-envs.hatch-check-code.dependencies = [ "prek" ]
-envs.hatch-check-code.scripts.lint-check = "echo 'try `hatch check code --fix`'; false"
-envs.hatch-check-code.scripts.lint-fix = "prek run -a --no-group=format --no-group=typecheck"
-envs.hatch-check-types.scripts.check = [ "mypy" ]
-envs.hatch-check-types.dependency-groups = [ "typecheck", "doc", "test" ]
 
 [tool.ruff]
 line-length = 120
@@ -137,11 +138,11 @@ strict = true
 testpaths = [ "tests" ]
 
 [tool.coverage]
+run.source = [ "scverse_doc" ]
 run.omit = [
   "**/test_*.py",
 ]
 run.patch = [ "subprocess" ]
-run.source = [ "scverse_doc" ]
 
 [tool.cruft]
 skip = [