Merge pull request #270 from will-moore/pre-commit-ci-update-config

Pre commit ci update config

.pre-commit-config.yaml

@@ -12,20 +12,20 @@ repos:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.3.0
     hooks:
       - id: black
         args: [--target-version=py36]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.0
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args:
           - --py36-plus
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
         exclude: .bumpversion.cfg
@@ -45,7 +45,7 @@ repos:
           - --autofix
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
         additional_dependencies: [
@@ -64,12 +64,12 @@ repos:
         ]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.1.1
     hooks:
       - id: mypy
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.1.1
     hooks:
       - id: mypy
         args: [
@@ -79,7 +79,7 @@ repos:
         exclude: tests/|setup.py
 
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.28.0
+    rev: v1.30.0
     hooks:
       - id: yamllint
         # args: [--config-data=relaxed]

ome_zarr/axes.py

@@ -97,7 +97,6 @@ def _get_names(self) -> List[str]:
         return axes_names
 
     def _validate_03(self) -> None:
-
         val_axes = tuple(self._get_names())
         if len(val_axes) == 2:
             if val_axes != ("y", "x"):

ome_zarr/cli.py

@@ -73,7 +73,7 @@ def csv_to_labels(args: argparse.Namespace) -> None:
     csv_to_zarr(args.csv_path, args.csv_id, args.csv_keys, args.zarr_path, args.zarr_id)
 
 
-def main(args: List[str] = None) -> None:
+def main(args: List[str]) -> None:
     """Run appropriate function with argparse arguments, handling errors."""
     parser = argparse.ArgumentParser()
     parser.add_argument(

ome_zarr/csv.py

@@ -126,7 +126,6 @@ def dict_to_zarr(
         labels_paths.append(os.path.join(zarr_path, "labels", "0"))
 
     for path_to_labels in labels_paths:
-
         label_group = zarr_open(path_to_labels)
         attrs = label_group.attrs.asdict()
         properties = attrs.get("image-label", {}).get("properties")

ome_zarr/data.py

@@ -1,6 +1,6 @@
 """Functions for generating synthetic data."""
 from random import randrange
-from typing import Callable, List, Tuple, Union
+from typing import Callable, List, Optional, Tuple, Union
 
 import numpy as np
 import zarr
@@ -103,7 +103,7 @@ def create_zarr(
     method: Callable[..., Tuple[List, List]] = coins,
     label_name: str = "coins",
     fmt: Format = CurrentFormat(),
-    chunks: Union[Tuple, List] = None,
+    chunks: Optional[Union[Tuple, List]] = None,
 ) -> zarr.Group:
     """Generate a synthetic image pyramid with labels."""
     pyramid, labels = method()
@@ -170,7 +170,6 @@ def create_zarr(
     grp.attrs["omero"] = image_data
 
     if labels:
-
         labels_grp = grp.create_group("labels")
         labels_grp.attrs["labels"] = [label_name]
 

ome_zarr/format.py

@@ -10,9 +10,7 @@
 
 
 def format_from_version(version: str) -> "Format":
-
     for fmt in format_implementations():
-
         # Support floating-point versions like `0.2`
         if isinstance(version, float):
             version = str(version)
@@ -110,7 +108,7 @@ def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: List[List[Dict[str, Any]]] = None,
+        coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
     ) -> Optional[List[List[Dict[str, Any]]]]:  # pragma: no cover
         raise NotImplementedError()
 
@@ -163,7 +161,7 @@ def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: List[List[Dict[str, Any]]] = None,
+        coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
     ) -> None:
         return None
 
@@ -258,7 +256,6 @@ def validate_well_dict(
     def generate_coordinate_transformations(
         self, shapes: List[tuple]
     ) -> Optional[List[List[Dict[str, Any]]]]:
-
         data_shape = shapes[0]
         coordinate_transformations: List[List[Dict[str, Any]]] = []
         # calculate minimal 'scale' transform based on pyramid dims
@@ -273,7 +270,7 @@ def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: List[List[Dict[str, Any]]] = None,
+        coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
     ) -> None:
         """
         Validates that a list of dicts contains a 'scale' transformation

ome_zarr/io.py

@@ -30,7 +30,6 @@ class ZarrLocation:
     def __init__(
         self, path: Union[Path, str], mode: str = "r", fmt: Format = CurrentFormat()
     ) -> None:
-
         LOGGER.debug("ZarrLocation.__init__ path: %s, fmt: %s", path, fmt.version)
         self.__fmt = fmt
         self.__mode = mode

ome_zarr/reader.py

@@ -624,7 +624,6 @@ def __init__(self, zarr: ZarrLocation) -> None:
     def __call__(self) -> Iterator[Node]:
         node = Node(self.zarr, self)
         if node.specs:  # Something has matched
-
             LOGGER.debug("treating %s as ome-zarr", self.zarr)
             yield from self.descend(node)
 
@@ -642,7 +641,6 @@ def __call__(self) -> Iterator[Node]:
             # yield nothing
 
     def descend(self, node: Node, depth: int = 0) -> Iterator[Node]:
-
         for pre_node in node.pre_nodes:
             yield from self.descend(pre_node, depth + 1)
 

ome_zarr/utils.py

@@ -27,7 +27,6 @@ def info(path: str, stats: bool = False) -> Iterator[Node]:
     assert zarr, f"not a zarr: {zarr}"
     reader = Reader(zarr)
     for node in reader():
-
         if not node.specs:
             print(f"not an ome-zarr node: {node}")
             continue
@@ -73,7 +72,6 @@ def download(input_path: str, output_dir: str = ".") -> None:
     print(f"to {output_dir}")
 
     for path, node in sorted(zip(paths, nodes)):
-
         target_path = output_path / Path(*path)
         target_path.mkdir(parents=True)
 

ome_zarr/writer.py

@@ -22,8 +22,8 @@
 
 
 def _get_valid_axes(
-    ndim: int = None,
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
+    ndim: Optional[int] = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
     fmt: Format = CurrentFormat(),
 ) -> Union[None, List[str], List[Dict[str, str]]]:
     """Returns list of axes valid for fmt.version or raise exception if invalid"""
@@ -64,7 +64,6 @@ def _get_valid_axes(
 def _validate_well_images(
     images: List[Union[str, dict]], fmt: Format = CurrentFormat()
 ) -> List[dict]:
-
     VALID_KEYS = [
         "acquisition",
         "path",
@@ -91,7 +90,6 @@ def _validate_well_images(
 def _validate_plate_acquisitions(
     acquisitions: List[Dict], fmt: Format = CurrentFormat()
 ) -> List[Dict]:
-
     VALID_KEYS = [
         "id",
         "name",
@@ -117,7 +115,6 @@ def _validate_plate_rows_columns(
     rows_or_columns: List[str],
     fmt: Format = CurrentFormat(),
 ) -> List[dict]:
-
     if len(set(rows_or_columns)) != len(rows_or_columns):
         raise ValueError(f"{rows_or_columns} must contain unique elements")
     validated_list = []
@@ -131,7 +128,6 @@ def _validate_plate_rows_columns(
 def _validate_datasets(
     datasets: List[dict], dims: int, fmt: Format = CurrentFormat()
 ) -> List[Dict]:
-
     if datasets is None or len(datasets) == 0:
         raise ValueError("Empty datasets list")
     transformations = []
@@ -156,7 +152,6 @@ def _validate_plate_wells(
     columns: List[str],
     fmt: Format = CurrentFormat(),
 ) -> List[dict]:
-
     validated_wells = []
     if wells is None or len(wells) == 0:
         raise ValueError("Empty wells list")
@@ -176,12 +171,12 @@ def _validate_plate_wells(
 def write_multiscale(
     pyramid: ListOfArrayLike,
     group: zarr.Group,
-    chunks: Union[Tuple[Any, ...], int] = None,
+    chunks: Optional[Union[Tuple[Any, ...], int]] = None,
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    coordinate_transformations: List[List[Dict[str, Any]]] = None,
-    storage_options: Union[JSONDict, List[JSONDict]] = None,
-    name: str = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+    storage_options: Optional[Union[JSONDict, List[JSONDict]]] = None,
+    name: Optional[str] = None,
     **metadata: Union[str, JSONDict, List[JSONDict]],
 ) -> None:
     """
@@ -277,8 +272,8 @@ def write_multiscales_metadata(
     group: zarr.Group,
     datasets: List[dict],
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    name: str = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    name: Optional[str] = None,
     **metadata: Union[str, JSONDict, List[JSONDict]],
 ) -> None:
     """
@@ -334,9 +329,9 @@ def write_plate_metadata(
     columns: List[str],
     wells: List[Union[str, dict]],
     fmt: Format = CurrentFormat(),
-    acquisitions: List[dict] = None,
-    field_count: int = None,
-    name: str = None,
+    acquisitions: Optional[List[dict]] = None,
+    field_count: Optional[int] = None,
+    name: Optional[str] = None,
 ) -> None:
     """
     Write the plate metadata in the group.
@@ -405,11 +400,11 @@ def write_image(
     image: ArrayLike,
     group: zarr.Group,
     scaler: Scaler = Scaler(),
-    chunks: Union[Tuple[Any, ...], int] = None,
+    chunks: Optional[Union[Tuple[Any, ...], int]] = None,
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    coordinate_transformations: List[List[Dict[str, Any]]] = None,
-    storage_options: Union[JSONDict, List[JSONDict]] = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+    storage_options: Optional[Union[JSONDict, List[JSONDict]]] = None,
     **metadata: Union[str, JSONDict, List[JSONDict]],
 ) -> None:
     """Writes an image to the zarr store according to ome-zarr specification
@@ -497,15 +492,14 @@ def _write_dask_image(
     image: da.Array,
     group: zarr.Group,
     scaler: Scaler = Scaler(),
-    chunks: Union[Tuple[Any, ...], int] = None,
+    chunks: Optional[Union[Tuple[Any, ...], int]] = None,
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    coordinate_transformations: List[List[Dict[str, Any]]] = None,
-    storage_options: Union[JSONDict, List[JSONDict]] = None,
-    name: str = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+    storage_options: Optional[Union[JSONDict, List[JSONDict]]] = None,
+    name: Optional[str] = None,
     **metadata: Union[str, JSONDict, List[JSONDict]],
 ) -> None:
-
     if fmt.version in ("0.1", "0.2"):
         # v0.1 and v0.2 are strictly 5D
         shape_5d: Tuple[Any, ...] = (*(1,) * (5 - image.ndim), *image.shape)
@@ -584,8 +578,8 @@ def _write_dask_image(
 def write_label_metadata(
     group: zarr.Group,
     name: str,
-    colors: List[JSONDict] = None,
-    properties: List[JSONDict] = None,
+    colors: Optional[List[JSONDict]] = None,
+    properties: Optional[List[JSONDict]] = None,
     fmt: Format = CurrentFormat(),
     **metadata: Union[List[JSONDict], JSONDict, str],
 ) -> None:
@@ -633,12 +627,12 @@ def write_multiscale_labels(
     pyramid: List,
     group: zarr.Group,
     name: str,
-    chunks: Union[Tuple[Any, ...], int] = None,
+    chunks: Optional[Union[Tuple[Any, ...], int]] = None,
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    coordinate_transformations: List[List[Dict[str, Any]]] = None,
-    storage_options: Union[JSONDict, List[JSONDict]] = None,
-    label_metadata: JSONDict = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+    storage_options: Optional[Union[JSONDict, List[JSONDict]]] = None,
+    label_metadata: Optional[JSONDict] = None,
     **metadata: JSONDict,
 ) -> None:
     """
@@ -710,12 +704,12 @@ def write_labels(
     group: zarr.Group,
     name: str,
     scaler: Scaler = Scaler(),
-    chunks: Union[Tuple[Any, ...], int] = None,
+    chunks: Optional[Union[Tuple[Any, ...], int]] = None,
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str], List[Dict[str, str]]] = None,
-    coordinate_transformations: List[List[Dict[str, Any]]] = None,
-    storage_options: Union[JSONDict, List[JSONDict]] = None,
-    label_metadata: JSONDict = None,
+    axes: Optional[Union[str, List[str], List[Dict[str, str]]]] = None,
+    coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+    storage_options: Optional[Union[JSONDict, List[JSONDict]]] = None,
+    label_metadata: Optional[JSONDict] = None,
     **metadata: JSONDict,
 ) -> None:
     """