ci: pre-commit autoupdate (#156)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A. <flying-sheep@web.de>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
   - id: trailing-whitespace
   - id: no-commit-to-branch
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.2
+  rev: v0.15.4
   hooks:
   - id: ruff-check
     args: [--fix, --exit-non-zero-on-fix]
@@ -21,10 +21,6 @@ repos:
   rev: v2.4.4
   hooks:
   - id: biome-format
-- repo: https://github.com/H4rryK4ne/update-mypy-hook
-  rev: v0.3.0
-  hooks:
-  - id: update-mypy-hook
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v1.19.1
   hooks:
@@ -33,77 +29,20 @@ repos:
     pass_filenames: false
     language_version: '3.13'
     additional_dependencies:
-    - alabaster==1.0.0
-    - anndata==0.12.8
-    - array-api-compat==1.13.0
-    - babel==2.18.0
-    - certifi==2026.1.4
-    - cffi==2.0.0
-    - charset-normalizer==3.4.4
-    - click==8.3.1
-    - cloudpickle==3.1.2
-    - colorama==0.4.6 ; sys_platform == 'win32'
-    - coverage==7.13.4
-    - dask==2026.1.2
-    - docutils==0.22.4
-    - donfig==0.8.1.post1
-    - execnet==2.1.2
-    - fsspec==2026.2.0
-    - google-crc32c==1.8.0
-    - h5py==3.15.1
-    - idna==3.11
-    - imagesize==1.4.1
-    - iniconfig==2.3.0
-    - jinja2==3.1.6
-    - joblib==1.5.3
-    - legacy-api-wrap==1.5
-    - llvmlite==0.46.0
-    - locket==1.0.0
-    - markdown-it-py==4.0.0
-    - markupsafe==3.0.3
-    - mdurl==0.1.2
-    - natsort==8.4.0
-    - numba==0.63.1
-    - numcodecs==0.16.5
-    - numpy==2.3.5
-    - numpy-typing-compat==20251206.2.3
-    - optype==0.15.0
-    - packaging==26.0
-    - pandas==2.3.3
-    - partd==1.4.2
-    - pluggy==1.6.0
-    - pycparser==3.0 ; implementation_name != 'PyPy'
-    - pygments==2.19.2
-    - pytest==9.0.2
-    - pytest-codspeed==4.3.0
-    - pytest-doctestplus==1.7.1
-    - pytest-xdist==3.8.0
-    - python-dateutil==2.9.0.post0
-    - pytz==2025.2
-    - pyyaml==6.0.3
-    - requests==2.32.5
-    - rich==14.3.2
-    - roman-numerals==4.1.0
-    - scikit-learn==1.8.0
-    - scipy==1.17.0
-    - scipy-stubs==1.17.0.2
-    - six==1.17.0
-    - snowballstemmer==3.0.1
-    - sphinx==9.1.0
-    - sphinxcontrib-applehelp==2.0.0
-    - sphinxcontrib-devhelp==2.0.0
-    - sphinxcontrib-htmlhelp==2.1.0
-    - sphinxcontrib-jsmath==1.0.1
-    - sphinxcontrib-qthelp==2.0.0
-    - sphinxcontrib-serializinghtml==2.0.0
-    - threadpoolctl==3.6.0
-    - toolz==1.1.0
-    - types-docutils==0.22.3.20251115
-    - tzdata==2025.3
-    - urllib3==2.6.3
-    - zarr==3.1.5
+    - anndata>=0.12
+    - array-api-compat>=1.13
+    - dask>=2026.1
+    - h5py>=3.15
+    - numba>=0.63
+    - packaging>=26
+    - pytest>=9
+    - pytest-codspeed>=4.3
+    - scikit-learn>=1.8
+    - scipy-stubs>=1.17
+    - sphinx>=9
+    - types-docutils>=0.22
+    - zarr>=3.1
 ci:
   autoupdate_commit_msg: 'ci: pre-commit autoupdate'
   skip:
   - mypy  # too big
-  - update-mypy-hook  # offline?

pyproject.toml

@@ -48,15 +48,6 @@ doc = [
   "sphinx>=9.0.1",
   "sphinx-autofixture>=0.4.1",
 ]
-# for update-mypy-hook
-mypy = [
-  "fast-array-utils[full]",
-  "scipy-stubs",
-  # TODO: replace sphinx with this: { include-group = "doc" },
-  "sphinx",
-  "types-docutils",
-  { include-group = "test" },
-]
 test-min = [
   "coverage[toml]",
   "fast-array-utils[sparse,testing]", # include sparse for testing numba-less to_dense

src/testing/fast_array_utils/_array_type.py

@@ -317,7 +317,7 @@ def _to_scipy_sparse(
             x = to_dense(x, to_cpu_memory=True)
 
         cls = cast("type[types.CSBase]", cls or self.cls)
-        return cls(x, dtype=dtype)  # type: ignore[arg-type]
+        return cls(x, dtype=dtype)  # type: ignore[arg-type,misc]
 
     def _to_cupy_array(self, x: ArrayLike | Array, /, *, dtype: DTypeLike | None = None) -> types.CupyArray:
         import cupy as cu