ci: pre-commit autoupdate (#3985)

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

@@ -3,7 +3,7 @@ ci:
 
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.1
+    rev: v0.15.2
     hooks:
     -   id: ruff-check
         args: ["--fix"]
@@ -20,11 +20,11 @@ repos:
         - --sort-by-bibkey
         - --drop=abstract
 -   repo: https://github.com/biomejs/pre-commit
-    rev: v2.3.15
+    rev: v2.4.4
     hooks:
     -   id: biome-format
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.16.0
+    rev: v2.16.2
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/pre-commit/pre-commit-hooks

docs/conf.py

@@ -8,6 +8,7 @@
 from datetime import datetime
 from functools import partial
 from importlib.metadata import version as get_version
+from itertools import product
 from pathlib import Path, PurePosixPath
 from typing import TYPE_CHECKING
 
@@ -263,7 +264,10 @@ def setup(app: Sphinx) -> None:
     # https://github.com/pandas-dev/pandas/issues/63810
     "pandas.api.typing.aliases.AnyArrayLike": ("doc", "pandas:reference/aliases"),
     "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
-    "numpy.typing.ArrayLike": ("py:data", "numpy.typing.ArrayLike"),
+    **{
+        f"numpy.{prefix}typing.{name}": ("py:data", f"numpy.typing.{name}")
+        for name, prefix in product(["ArrayLike", "DTypeLike"], ["", "_"])
+    },
 }
 
 nitpick_ignore = [

hatch.toml

@@ -30,7 +30,7 @@ overrides.matrix.deps.env-vars = [
 overrides.matrix.deps.pre-install-commands = [
     { if = [
         "low-vers",
-    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras --all-groups -o ci/scanpy-low-vers.txt" },
+    ], value = "uv run ci/scripts/low-vers.py pyproject.toml --all-extras --groups=test -o ci/scanpy-low-vers.txt" },
 ]
 overrides.matrix.deps.python = [
     { if = [ "low-vers" ], value = "3.12" },

pyproject.toml

@@ -120,6 +120,7 @@ doc = [
     "myst-nb>=1",
     "myst-parser>=2",
     "nbsphinx>=0.9",
+    "numpy>=2.4",                           # type aliases
     "sam-algorithm",
     # TODO: remove necessity for being able to import doc-linked classes
     "scanpy[dask-ml,leiden,paga,plotting]",