chore: update pre-commit hooks (zarr-developers#3943)

* chore: update pre-commit hooks

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.12](astral-sh/ruff-pre-commit@v0.15.4...v0.15.12)
- [github.com/codespell-project/codespell: v2.4.1 → v2.4.2](codespell-project/codespell@v2.4.1...v2.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.19.1 → v1.20.2](pre-commit/mirrors-mypy@v1.19.1...v1.20.2)
- [github.com/scientific-python/cookie: 2026.03.02 → 2026.04.04](scientific-python/cookie@2026.03.02...2026.04.04)
- [github.com/zizmorcore/zizmor-pre-commit: v1.23.1 → v1.24.1](zizmorcore/zizmor-pre-commit@v1.23.1...v1.24.1)

* chore: fix pre-commit failures

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -11,13 +11,13 @@ default_language_version:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.12
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
@@ -28,7 +28,7 @@ repos:
         exclude: mkdocs.yml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v1.20.2
     hooks:
       - id: mypy
         files: ^(src|tests)/
@@ -47,7 +47,7 @@ repos:
           - hypothesis
           - s3fs
   - repo: https://github.com/scientific-python/cookie
-    rev: 2026.03.02
+    rev: 2026.04.04
     hooks:
       - id: sp-repo-review
   - repo: https://github.com/numpy/numpydoc
@@ -64,7 +64,7 @@ repos:
         types: [python]
         files: ^(src|tests)/
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.23.1
+    rev: v1.24.1
     hooks:
       - id: zizmor
   - repo: https://github.com/twisted/towncrier

src/zarr/core/array.py

@@ -4816,7 +4816,7 @@ def _parse_keep_array_attr(
         if serializer == "keep":
             serializer = "auto"
     # After resolving "keep" above, chunks is never "keep" at this point.
-    chunks_out: ChunksLike | Literal["auto"] = chunks  # type: ignore[assignment]
+    chunks_out: ChunksLike | Literal["auto"] = chunks
     return (
         chunks_out,
         shards,

src/zarr/core/dtype/npy/structured.py

@@ -278,15 +278,16 @@ def _from_json_v2(cls, data: DTypeJSON) -> Self:
             # structured dtypes are constructed directly from a list of lists
             # note that we do not handle the object codec here! this will prevent structured
             # dtypes from containing object dtypes.
+            name = data["name"]
             return cls(
-                fields=tuple(  # type: ignore[misc]
+                fields=tuple(  # type: ignore[str-unpack]
                     (  # type: ignore[misc]
                         f_name,
                         get_data_type_from_json(
                             {"name": f_dtype, "object_codec_id": None}, zarr_format=2
                         ),
                     )
-                    for f_name, f_dtype in data["name"]
+                    for f_name, f_dtype in name
                 )
             )
         msg = f"Invalid JSON representation of {cls.__name__}. Got {data!r}, expected a JSON array of arrays"

src/zarr/storage/_logging.py

@@ -161,7 +161,7 @@ def __repr__(self) -> str:
 
     def __eq__(self, other: object) -> bool:
         with self.log(other):
-            return type(self) is type(other) and self._store.__eq__(other._store)  # type: ignore[attr-defined]
+            return type(self) is type(other) and self._store.__eq__(other._store)
 
     async def get(
         self,

src/zarr/storage/_wrapper.py

@@ -83,7 +83,7 @@ def _check_writable(self) -> None:
         return self._store._check_writable()
 
     def __eq__(self, value: object) -> bool:
-        return type(self) is type(value) and self._store.__eq__(value._store)  # type: ignore[attr-defined]
+        return type(self) is type(value) and self._store.__eq__(value._store)
 
     def __str__(self) -> str:
         return f"wrapping-{self._store}"

tests/test_api.py

@@ -137,7 +137,7 @@ async def test_array_like_creation(
             kwargs["fill_value"] = out_fill
             expect_fill = out_fill
     elif func is zarr.api.asynchronous.open_like:  # type: ignore[comparison-overlap]
-        if out_fill == "keep":
+        if out_fill == "keep":  # type: ignore[unreachable]
             expect_fill = ref_fill
         else:
             kwargs["fill_value"] = out_fill
@@ -161,7 +161,7 @@ async def test_array_like_creation(
     else:
         expect_dtype = ref_arr.dtype  # type: ignore[assignment]
 
-    new_arr = await func(ref_arr, path="foo", zarr_format=zarr_format, **kwargs)  # type: ignore[call-arg]
+    new_arr = await func(ref_arr, path="foo", zarr_format=zarr_format, **kwargs)
     assert new_arr.shape == expect_shape
     assert new_arr.chunks == expect_chunks
     assert new_arr.dtype == expect_dtype
@@ -187,7 +187,7 @@ def test_create_array(store: Store, zarr_format: ZarrFormat) -> None:
     array_w[:] = data_val
     assert array_w.shape == shape
     assert array_w.attrs == attrs
-    assert np.array_equal(array_w[:], np.zeros(shape, dtype=array_w.dtype) + data_val)
+    assert np.array_equal(array_w[:], np.zeros(shape, dtype=array_w.dtype) + data_val)  # type: ignore[unreachable]
 
 
 @pytest.mark.parametrize("write_empty_chunks", [True, False])
@@ -326,7 +326,7 @@ async def test_create_group(store: Store, zarr_format: ZarrFormat) -> None:
     node = create_group(store, path=path, attributes=attrs, zarr_format=zarr_format)
     assert isinstance(node, Group)
     assert node.attrs == attrs
-    assert node.metadata.zarr_format == zarr_format
+    assert node.metadata.zarr_format == zarr_format  # type: ignore[unreachable]
 
 
 async def test_open_group(memory_store: MemoryStore) -> None:

tests/test_array.py

@@ -1770,7 +1770,7 @@ async def test_from_array(
     assert result.fill_value == new_fill_value
     assert result.dtype == src_dtype
     assert result.attrs == new_attributes
-    assert result.chunks == new_chunks
+    assert result.chunks == new_chunks  # type: ignore[unreachable]
 
 
 @pytest.mark.parametrize("store", ["local"], indirect=True)

tests/test_codecs/test_numcodecs.py

@@ -85,7 +85,7 @@ def test_is_numcodec_cls() -> None:
 
 @pytest.mark.parametrize("codec_cls", ALL_CODECS)
 def test_get_codec_class(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None:
-    assert get_codec_class(codec_cls.codec_name) == codec_cls  # type: ignore[comparison-overlap]
+    assert get_codec_class(codec_cls.codec_name) == codec_cls  # type: ignore[comparison-overlap,misc]
 
 
 @pytest.mark.parametrize("codec_class", ALL_CODECS)
@@ -240,7 +240,7 @@ def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec
     try:
         codec_class()._codec  # noqa: B018
     except UnknownCodecError as e:  # pragma: no cover
-        pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}")
+        pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}")  # type: ignore[misc]
 
     data = np.linspace(0, 10, 256, dtype="float32").reshape((16, 16))
 
@@ -265,11 +265,11 @@ def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCo
         codec_class()._codec  # noqa: B018
     except ValueError as e:  # pragma: no cover
         if "codec not available" in str(e):
-            pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
+            pytest.xfail(f"{codec_class.codec_name} is not available: {e}")  # type: ignore[misc]
         else:
             raise
     except ImportError as e:  # pragma: no cover
-        pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
+        pytest.xfail(f"{codec_class.codec_name} is not available: {e}")  # type: ignore[misc]
 
     data = np.arange(0, 256, dtype="float32").reshape((16, 16))
 
@@ -347,7 +347,7 @@ def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None:
     try:
         codec = codec_cls()
     except UnknownCodecError as e:  # pragma: no cover
-        pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}")
+        pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}")  # type: ignore[misc]
 
     expected = codec