chore: update pre-commit hooks (#3610)

* chore: update pre-commit hooks

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.10](astral-sh/ruff-pre-commit@v0.14.3...v0.14.10)
- [github.com/pre-commit/mirrors-mypy: v1.18.2 → v1.19.1](pre-commit/mirrors-mypy@v1.18.2...v1.19.1)
- [github.com/scientific-python/cookie: 2025.10.20 → 2025.11.21](scientific-python/cookie@2025.10.20...2025.11.21)
- [github.com/numpy/numpydoc: v1.9.0 → v1.10.0](numpy/numpydoc@v1.9.0...v1.10.0)

* update JSON union to include bool

* apply fixes to resolve pre-commit violations

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Davis Bennett <[email protected]>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.3
+    rev: v0.14.10
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -27,7 +27,7 @@ repos:
         exclude: mkdocs.yml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
+    rev: v1.19.1
     hooks:
       - id: mypy
         files: src|tests
@@ -46,7 +46,7 @@ repos:
           - hypothesis
           - s3fs
   - repo: https://github.com/scientific-python/cookie
-    rev: 2025.10.20
+    rev: 2025.11.21
     hooks:
       - id: sp-repo-review
   - repo: https://github.com/pre-commit/pygrep-hooks
@@ -55,7 +55,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: numpydoc-validation
   - repo: https://github.com/twisted/towncrier

pyproject.toml

@@ -395,6 +395,7 @@ ignore_errors = true
 minversion = "7"
 testpaths = ["tests", "docs/user-guide"]
 log_cli_level = "INFO"
+log_level = "INFO"
 xfail_strict = true
 asyncio_mode = "auto"
 asyncio_default_fixture_loop_scope = "function"

src/zarr/_cli/cli.py

@@ -35,7 +35,7 @@ class CLIZarrFormatV3(str, Enum):
     v3 = "v3"
 
 
-@app.command()  # type: ignore[misc]
+@app.command()  # type: ignore[untyped-decorator]
 def migrate(
     zarr_format: Annotated[
         CLIZarrFormatV3,
@@ -120,7 +120,7 @@ def migrate(
         sync(migrate_metadata.remove_metadata(write_store, 2, force=False, dry_run=dry_run))
 
 
-@app.command()  # type: ignore[misc]
+@app.command()  # type: ignore[untyped-decorator]
 def remove_metadata(
     zarr_format: Annotated[
         CLIZarrFormat,
@@ -168,7 +168,7 @@ def remove_metadata(
     )
 
 
-@app.callback()  # type: ignore[misc]
+@app.callback()  # type: ignore[untyped-decorator]
 def main(
     verbose: Annotated[
         bool,

src/zarr/core/common.py

@@ -42,7 +42,7 @@
 ChunkCoords = tuple[int, ...]
 ZarrFormat = Literal[2, 3]
 NodeType = Literal["array", "group"]
-JSON = str | int | float | Mapping[str, "JSON"] | Sequence["JSON"] | None
+JSON = str | int | float | bool | Mapping[str, "JSON"] | Sequence["JSON"] | None
 MemoryOrder = Literal["C", "F"]
 AccessModeLiteral = Literal["r", "r+", "a", "w", "w-"]
 ANY_ACCESS_MODE: Final = "r", "r+", "a", "w", "w-"

tests/test_metadata/test_v2.py

@@ -309,12 +309,13 @@ def test_from_dict_extra_fields() -> None:
 
 
 def test_zstd_checksum() -> None:
+    compressor_config: dict[str, JSON] = {"id": "zstd", "level": 5, "checksum": False}
     arr = zarr.create_array(
         {},
         shape=(10,),
         chunks=(10,),
         dtype="int32",
-        compressors={"id": "zstd", "level": 5, "checksum": False},
+        compressors=compressor_config,
         zarr_format=2,
     )
     metadata = json.loads(