[pre-commit.ci] pre-commit autoupdate (#105)

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

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -6,29 +6,29 @@ repos:
       - id: trailing-whitespace
       - id: no-commit-to-branch
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.13
+    rev: v0.12.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --exit-non-zero-on-fix]
-      - id: ruff
+      - id: ruff-check
         args: [--preview, --select=CPY]
       - id: ruff-format
   - repo: https://github.com/tox-dev/pyproject-fmt
     rev: v2.6.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
+    rev: v2.1.1
     hooks:
       - id: biome-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         args: [--config-file=pyproject.toml]
         additional_dependencies:
           - pytest
-          - pytest-codspeed
+          - pytest-codspeed!=4.0.0  # https://github.com/CodSpeedHQ/pytest-codspeed/pull/84
           - numba
           - numpy
           - scipy-stubs

biome.jsonc

@@ -1,9 +1,9 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.1.1/schema.json",
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": {
                     "trailingCommas": "all",

pyproject.toml

@@ -121,6 +121,7 @@ lint.ignore = [
   "D213",    # prefer docstring summary on first line
   "FIX002",  # “TODO” comments
   "N812",    # lowercase imports are fine
+  "PLC0415", # we rely heavily on non-top-level imports
   "PLR0913", # having many (kw)args is fine
   "Q",       # handled by formatter
   "S101",    # asserts are fine

src/testing/fast_array_utils/_array_type.py

@@ -294,7 +294,7 @@ def _to_cs_dataset(self, x: ArrayLike | Array, /, *, dtype: DTypeLike | None = N
         else:
             raise NotImplementedError
 
-        cls = csr_array if self.cls is types.CSRDataset else csc_array
+        cls = cast("type[types.csr_array[Any, tuple[int, int]] | types.csc_array]", csr_array if self.cls is types.CSRDataset else csc_array)
         x_sparse = self._to_scipy_sparse(x, dtype=dtype, cls=cls)
         anndata.io.write_elem(grp, "/", x_sparse)
         return anndata.io.sparse_dataset(grp)

tests/test_stats.py

@@ -121,7 +121,7 @@ def test_ndim_error(array_type: ArrayType[Array], func: StatFun, ndim: Literal[1
 
 @pytest.mark.array_type(skip=ATS_SPARSE_DS)
 def test_sum(
-    array_type: ArrayType[Array],
+    array_type: ArrayType[CpuArray | GpuArray | DiskArray | types.DaskArray],
     dtype_in: type[DTypeIn],
     dtype_arg: type[DTypeOut] | None,
     axis: Literal[0, 1, None],
@@ -261,6 +261,7 @@ def test_mean_var_sparse_32(array_type: ArrayType[types.CSArray]) -> None:
     ],
 )
 def test_is_constant(
+    *,
     array_type: ArrayType[CpuArray | types.DaskArray],
     axis: Literal[0, 1, None],
     expected: bool | list[bool],