chore: type check update

.github/dependabot.yml

@@ -1,5 +1,16 @@
 version: 2
 updates:
+  - package-ecosystem: pre-commit
+    directory: /
+    labels:
+      - run-gpu-ci
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns: ["*"]
   - package-ecosystem: github-actions
     directory: /
     labels:

.github/workflows/autofix.yml

@@ -0,0 +1,26 @@
+# 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@v10.1.0
+        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@v1.3.4
+        if: '!cancelled()'

.github/workflows/ci-gpu.yml

@@ -25,7 +25,7 @@ jobs:
     steps:
       - uses: flying-sheep/check@v1
         with:
-          success: ${{ github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'run-gpu-ci') || github.event.pull_request.user.login == 'pre-commit-ci[bot]' }}
+          success: ${{ github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'run-gpu-ci') }}
   test:
     name: All Tests
     needs: check

.github/workflows/ci.yml

@@ -106,15 +106,6 @@ jobs:
       - run: python -c 'import fast_array_utils as fau; print(fau.__all__)'
       - run: uv pip install --system -e .[testing]
       - run: python -c 'import testing.fast_array_utils as tfau; print(tfau.ArrayType("numpy", "ndarray"))'
-  check:
-    name: Static Checks
-    runs-on: ubuntu-latest
-    env:
-      SKIP: no-commit-to-branch  # this CI runs on the main branch
-    steps:
-      - uses: actions/checkout@v7
-        with: { fetch-depth: 0, filter: "blob:none" }
-      - uses: j178/prek-action@v3.0.0
   pass:
     name: All Checks
     if: always()
@@ -123,7 +114,6 @@ jobs:
       - test
       - bench
       - import
-      - check
     runs-on: ubuntu-latest
     steps:
       - uses: re-actors/alls-green@release/v1

.pre-commit-config.yaml

@@ -3,7 +3,9 @@ repos:
   rev: v6.0.0
   hooks:
   - id: end-of-file-fixer
+    groups: [format]
   - id: trailing-whitespace
+    groups: [format]
   - id: no-commit-to-branch
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.16.8
@@ -13,37 +15,24 @@ repos:
   - id: ruff-check
     args: [--preview, --select=CPY]
   - id: ruff-format
+    groups: [format]
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: v2.29.4
   hooks:
   - id: pyproject-fmt
+    groups: [format]
 - repo: https://github.com/biomejs/pre-commit
   rev: v2.5.14
   hooks:
   - id: biome-format
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v2.3.1
+    groups: [format]
+- repo: local
   hooks:
   - id: mypy
-    args: [--config-file=pyproject.toml, .]
+    name: mypy
+    entry: hatch check types
+    language: system
+    types_or: [python, pyi]
+    require_serial: true
     pass_filenames: false
-    additional_dependencies:
-    - anndata>=0.12
-    - array-api-compat>=1.13,!=1.15.0 # https://github.com/data-apis/array-api-compat/issues/436
-    - dask>=2026.1
-    - h5py>=3.15
-    - jax>=0.10
-    - numba>=0.63
-    - packaging>=26
-    - pytest>=9
-    - pytest-codspeed>=4.3
-    - scikit-learn>=1.8
-    - scipy-stubs>=1.17
-    - sphinx>=9
-    - types-array-api>=1.3
-    - types-docutils>=0.22
-    - zarr>=3.1
-ci:
-  autoupdate_commit_msg: 'ci: pre-commit autoupdate'
-  skip:
-  - mypy  # too big
+    groups: [typecheck]

pyproject.toml

@@ -60,6 +60,12 @@ test-min = [
   "pytest-doctestplus",
   "pytest-xdist",
 ]
+typecheck = [
+  "array-api-compat!=1.15", # https://github.com/data-apis/array-api-compat/issues/436
+  "mypy",
+  "scipy-stubs",
+  "sphinx",
+]
 
 [tool.hatch]
 version.source = "vcs"
@@ -75,6 +81,14 @@ envs.docs.scripts.build = "sphinx-build -M html docs docs/_build"
 envs.docs.scripts.clean = "git clean -fdX 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", "test" ]
 envs.hatch-test.extra-dependencies = [ "ipycytoscape", "ipykernel" ]
 envs.hatch-test.env-vars.CODSPEED_PROFILE_FOLDER = "test-data/codspeed"
 envs.hatch-test.matrix = [
@@ -140,6 +154,7 @@ lint.future-annotations = true
 
 [tool.mypy]
 mypy_path = [ "$MYPY_CONFIG_FILE_DIR/typings", "$MYPY_CONFIG_FILE_DIR/src" ]
+files = [ "." ]
 explicit_package_bases = true
 # https://github.com/dask/dask/issues/8853
 implicit_reexport = true

typings/numba/__init__.pyi

@@ -1,42 +1,10 @@
 # SPDX-License-Identifier: MPL-2.0
-from collections.abc import Callable, Iterable
-from typing import Literal, SupportsIndex, overload
+from collections.abc import Iterable
+from typing import SupportsIndex, overload
 
 from .core import config as config
-from .core.types import Type
+from .core.decorators import njit as njit
 
-type __Signature = str | Type
-type _Signature = str | Type | tuple[__Signature, ...]
-
-# https://numba.readthedocs.io/en/stable/reference/jit-compilation.html#numba.jit
-@overload
-def njit[F: Callable[..., object]](
-    f: F,
-    *,
-    nopython: bool = True,
-    nogil: bool = False,
-    cache: bool = False,
-    forceobj: bool = False,
-    parallel: bool = False,
-    error_model: Literal["python", "numpy"] = "python",
-    fastmath: bool = False,
-    locals: dict[str, object] = {},
-    boundscheck: bool = False,
-) -> F: ...
-@overload
-def njit[F: Callable[..., object]](
-    signature: _Signature | list[_Signature] | None = None,
-    *,
-    nopython: bool = True,
-    nogil: bool = False,
-    cache: bool = False,
-    forceobj: bool = False,
-    parallel: bool = False,
-    error_model: Literal["python", "numpy"] = "python",
-    fastmath: bool = False,
-    locals: dict[str, object] = {},
-    boundscheck: bool = False,
-) -> Callable[[F], F]: ...
 @overload
 def prange(stop: SupportsIndex, /) -> Iterable[int]: ...
 @overload