Enable Python 3.10+ in pre-commit hooks

.pre-commit-config.yaml

@@ -15,14 +15,13 @@ repos:
     rev: 24.10.0
     hooks:
       - id: black
-        args: [--target-version=py36]
 
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.19.0
     hooks:
       - id: pyupgrade
         args:
-          - --py39-plus
+          - --py310-plus
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0

ome_zarr/axes.py

@@ -1,7 +1,7 @@
 """Axes class for validating and transforming axes
 """
 
-from typing import Any, Union
+from typing import Any
 
 from .format import CurrentFormat, Format
 
@@ -11,7 +11,7 @@
 class Axes:
     def __init__(
         self,
-        axes: Union[list[str], list[dict[str, str]]],
+        axes: list[str] | list[dict[str, str]],
         fmt: Format = CurrentFormat(),
     ) -> None:
         """
@@ -41,15 +41,13 @@ def validate(self) -> None:
 
     def to_list(
         self, fmt: Format = CurrentFormat()
-    ) -> Union[list[str], list[dict[str, str]]]:
+    ) -> list[str] | list[dict[str, str]]:
         if fmt.version == "0.3":
             return self._get_names()
         return self.axes
 
     @staticmethod
-    def _axes_to_dicts(
-        axes: Union[list[str], list[dict[str, str]]]
-    ) -> list[dict[str, str]]:
+    def _axes_to_dicts(axes: list[str] | list[dict[str, str]]) -> list[dict[str, str]]:
         """Returns a list of axis dicts with name and type"""
         axes_dicts = []
         for axis in axes:

ome_zarr/cli.py

@@ -3,7 +3,6 @@
 import argparse
 import logging
 import sys
-from typing import Union
 
 from .csv import csv_to_zarr
 from .data import astronaut, coins, create_zarr
@@ -81,7 +80,7 @@ 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: Union[list[str], None] = None) -> None:
+def main(args: list[str] | None = None) -> None:
     """Run appropriate function with argparse arguments, handling errors."""
     parser = argparse.ArgumentParser()
     parser.add_argument(

ome_zarr/csv.py

@@ -1,6 +1,5 @@
 import csv
 import os
-from typing import Union
 
 from zarr.convenience import open as zarr_open
 
@@ -13,9 +12,9 @@
 COLUMN_TYPES = ["d", "l", "s", "b"]
 
 
-def parse_csv_value(value: str, col_type: str) -> Union[str, float, int, bool]:
+def parse_csv_value(value: str, col_type: str) -> str | float | int | bool:
     """Parse string value from csv, according to COLUMN_TYPES"""
-    rv: Union[str, float, int, bool] = value
+    rv: str | float | int | bool = value
     try:
         if col_type == "d":
             rv = float(value)
@@ -62,7 +61,7 @@ def csv_to_zarr(
     csv_columns = None
     id_column = None
 
-    props_by_id: dict[Union[str, int], dict] = {}
+    props_by_id: dict[str | int, dict] = {}
 
     with open(csv_path, newline="") as csvfile:
         row_reader = csv.reader(csvfile, delimiter=",")
@@ -90,7 +89,7 @@ def csv_to_zarr(
 
 
 def dict_to_zarr(
-    props_to_add: dict[Union[str, int], dict], zarr_path: str, zarr_id: str
+    props_to_add: dict[str | int, dict], zarr_path: str, zarr_id: str
 ) -> None:
     """
     Add keys:values to the label properties of a ome-zarr Plate or Image.

ome_zarr/data.py

@@ -1,7 +1,7 @@
 """Functions for generating synthetic data."""
 
+from collections.abc import Callable
 from random import randrange
-from typing import Callable, Optional, Union
 
 import numpy as np
 import zarr
@@ -122,7 +122,7 @@ def create_zarr(
     method: Callable[..., tuple[list, list]] = coins,
     label_name: str = "coins",
     fmt: Format = CurrentFormat(),
-    chunks: Optional[Union[tuple, list]] = None,
+    chunks: tuple | list | None = None,
 ) -> zarr.Group:
     """Generate a synthetic image pyramid with labels."""
     pyramid, labels = method()

ome_zarr/format.py

@@ -3,7 +3,7 @@
 import logging
 from abc import ABC, abstractmethod
 from collections.abc import Iterator
-from typing import Any, Optional
+from typing import Any
 
 from zarr.storage import FSStore
 
@@ -67,7 +67,7 @@ def init_store(self, path: str, mode: str = "r") -> FSStore:
     def init_channels(self) -> None:  # pragma: no cover
         raise NotImplementedError()
 
-    def _get_metadata_version(self, metadata: dict) -> Optional[str]:
+    def _get_metadata_version(self, metadata: dict) -> str | None:
         """
         Checks the metadata dict for a version
 
@@ -105,16 +105,16 @@ def validate_well_dict(
     @abstractmethod
     def generate_coordinate_transformations(
         self, shapes: list[tuple]
-    ) -> Optional[list[list[dict[str, Any]]]]:  # pragma: no cover
+    ) -> list[list[dict[str, Any]]] | None:  # pragma: no cover
         raise NotImplementedError()
 
     @abstractmethod
     def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: Optional[list[list[dict[str, Any]]]] = None,
-    ) -> Optional[list[list[dict[str, Any]]]]:  # pragma: no cover
+        coordinate_transformations: list[list[dict[str, Any]]] | None = None,
+    ) -> list[list[dict[str, Any]]] | None:  # pragma: no cover
         raise NotImplementedError()
 
 
@@ -159,14 +159,14 @@ def validate_well_dict(
 
     def generate_coordinate_transformations(
         self, shapes: list[tuple]
-    ) -> Optional[list[list[dict[str, Any]]]]:
+    ) -> list[list[dict[str, Any]]] | None:
         return None
 
     def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: Optional[list[list[dict[str, Any]]]] = None,
+        coordinate_transformations: list[list[dict[str, Any]]] | None = None,
     ) -> None:
         return None
 
@@ -260,7 +260,7 @@ def validate_well_dict(
 
     def generate_coordinate_transformations(
         self, shapes: list[tuple]
-    ) -> Optional[list[list[dict[str, Any]]]]:
+    ) -> list[list[dict[str, Any]]] | None:
         data_shape = shapes[0]
         coordinate_transformations: list[list[dict[str, Any]]] = []
         # calculate minimal 'scale' transform based on pyramid dims
@@ -275,7 +275,7 @@ def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: Optional[list[list[dict[str, Any]]]] = None,
+        coordinate_transformations: list[list[dict[str, Any]]] | None = None,
     ) -> None:
         """
         Validates that a list of dicts contains a 'scale' transformation

ome_zarr/io.py

@@ -6,7 +6,6 @@
 import json
 import logging
 from pathlib import Path
-from typing import Optional, Union
 from urllib.parse import urljoin
 
 import dask.array as da
@@ -29,7 +28,7 @@ class ZarrLocation:
 
     def __init__(
         self,
-        path: Union[Path, str, FSStore],
+        path: Path | str | FSStore,
         mode: str = "r",
         fmt: Format = CurrentFormat(),
     ) -> None:
@@ -207,8 +206,8 @@ def _ishttp(self) -> bool:
 
 
 def parse_url(
-    path: Union[Path, str], mode: str = "r", fmt: Format = CurrentFormat()
-) -> Optional[ZarrLocation]:
+    path: Path | str, mode: str = "r", fmt: Format = CurrentFormat()
+) -> ZarrLocation | None:
     """Convert a path string or URL to a ZarrLocation subclass.
 
     :param path: Path to parse.

ome_zarr/reader.py

@@ -112,7 +112,7 @@ def add(
         self,
         zarr: ZarrLocation,
         prepend: bool = False,
-        visibility: Optional[bool] = None,
+        visibility: bool | None = None,
         plate_labels: bool = False,
     ) -> "Optional[Node]":
         """Create a child node if this location has not yet been seen.
@@ -227,7 +227,7 @@ def __init__(self, node: Node) -> None:
             LOGGER.warning("no parent found for %s: %s", self, image)
 
         # Metadata: TODO move to a class
-        colors: dict[Union[int, bool], list[float]] = {}
+        colors: dict[int | bool, list[float]] = {}
         color_list = image_label.get("colors", [])
         if color_list:
             for color in color_list:
@@ -352,7 +352,7 @@ def __init__(self, node: Node) -> None:
                 return  # EARLY EXIT
 
             colormaps = []
-            contrast_limits: Optional[list[Optional[Any]]] = [None for x in channels]
+            contrast_limits: list[Any | None] | None = [None for x in channels]
             names: list[str] = [("channel_%d" % idx) for idx, ch in enumerate(channels)]
             visibles: list[bool] = [True for x in channels]
 
@@ -496,7 +496,7 @@ def get_pyramid_lazy(self, node: Node) -> None:
         # Get the first well...
         well_zarr = self.zarr.create(self.well_paths[0])
         well_node = Node(well_zarr, node)
-        well_spec: Optional[Well] = well_node.first(Well)
+        well_spec: Well | None = well_node.first(Well)
         if well_spec is None:
             raise Exception("Could not find first well")
         self.first_field_path = well_spec.well_data["images"][0]["path"]

ome_zarr/scale.py

@@ -6,9 +6,9 @@
 import inspect
 import logging
 import os
-from collections.abc import Iterator, MutableMapping
+from collections.abc import Callable, Iterator, MutableMapping
 from dataclasses import dataclass
-from typing import Any, Callable, Union
+from typing import Any, Union
 
 import dask.array as da
 import numpy as np

ome_zarr/types.py

@@ -1,6 +1,7 @@
 """Definition of complex types for use elsewhere."""
 
-from typing import Any, Callable, Union
+from collections.abc import Callable
+from typing import Any, Union
 
 LayerData = Union[tuple[Any], tuple[Any, dict], tuple[Any, dict, str]]