Update version of pyupgrade

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: pyupgrade
         args:
-          - --py36-plus
+          - --py39-plus
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0

ome_zarr/axes.py

@@ -1,7 +1,7 @@
 """Axes class for validating and transforming axes
 """
 
-from typing import Any, Dict, List, Union
+from typing import Any, Union
 
 from .format import CurrentFormat, Format
 
@@ -11,7 +11,7 @@
 class Axes:
     def __init__(
         self,
-        axes: Union[List[str], List[Dict[str, str]]],
+        axes: Union[list[str], list[dict[str, str]]],
         fmt: Format = CurrentFormat(),
     ) -> None:
         """
@@ -41,15 +41,15 @@ def validate(self) -> None:
 
     def to_list(
         self, fmt: Format = CurrentFormat()
-    ) -> Union[List[str], List[Dict[str, str]]]:
+    ) -> Union[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]]:
+        axes: Union[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:
@@ -74,7 +74,7 @@ def _validate_axes_types(self) -> None:
                 "Too many unknown axes types. 1 allowed, found: %s" % unknown_types
             )
 
-        def _last_index(item: str, item_list: List[Any]) -> int:
+        def _last_index(item: str, item_list: list[Any]) -> int:
             return max(loc for loc, val in enumerate(item_list) if val == item)
 
         if "time" in axes_types and _last_index("time", axes_types) > 0:
@@ -88,7 +88,7 @@ def _last_index(item: str, item_list: List[Any]) -> int:
         ) > axes_types.index("space"):
             raise ValueError("'space' axes must come after 'channel'")
 
-    def _get_names(self) -> List[str]:
+    def _get_names(self) -> list[str]:
         """Returns a list of axis names"""
         axes_names = []
         for axis in self.axes:

ome_zarr/cli.py

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

ome_zarr/conversions.py

@@ -1,9 +1,7 @@
 """Simple conversion helpers."""
 
-from typing import List
 
-
-def int_to_rgba(v: int) -> List[float]:
+def int_to_rgba(v: int) -> list[float]:
     """Get rgba (0-1) e.g. (1, 0.5, 0, 1) from integer.
     >>> print(int_to_rgba(0))
     [0.0, 0.0, 0.0, 0.0]
@@ -13,7 +11,7 @@ def int_to_rgba(v: int) -> List[float]:
     return [x / 255 for x in v.to_bytes(4, signed=True, byteorder="big")]
 
 
-def int_to_rgba_255(v: int) -> List[int]:
+def int_to_rgba_255(v: int) -> list[int]:
     """Get rgba (0-255) from integer.
     >>> print(int_to_rgba_255(0))
     [0, 0, 0, 0]

ome_zarr/csv.py

@@ -1,6 +1,6 @@
 import csv
 import os
-from typing import Dict, Union
+from typing import Union
 
 from zarr.convenience import open as zarr_open
 
@@ -50,7 +50,7 @@ def csv_to_zarr(
 
     # Use #d to denote double etc.
     # e.g. "area (pixels)#d,well_label#s,Width#l,Height#l"
-    cols_types_by_name: Dict[str, str] = {}
+    cols_types_by_name: dict[str, str] = {}
     for col_name_type in csv_keys.split(","):
         if "#" in col_name_type:
             col_name, col_type = col_name_type.rsplit("#", 1)
@@ -62,7 +62,7 @@ def csv_to_zarr(
     csv_columns = None
     id_column = None
 
-    props_by_id: Dict[Union[str, int], Dict] = {}
+    props_by_id: dict[Union[str, int], dict] = {}
 
     with open(csv_path, newline="") as csvfile:
         row_reader = csv.reader(csvfile, delimiter=",")
@@ -90,7 +90,7 @@ 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[Union[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/dask_utils.py

@@ -1,4 +1,4 @@
-from typing import Any, Tuple
+from typing import Any
 
 import numpy as np
 import skimage.transform
@@ -9,7 +9,7 @@
 
 
 def resize(
-    image: da.Array, output_shape: Tuple[int, ...], *args: Any, **kwargs: Any
+    image: da.Array, output_shape: tuple[int, ...], *args: Any, **kwargs: Any
 ) -> da.Array:
     r"""
     Wrapped copy of "skimage.transform.resize"
@@ -62,7 +62,7 @@ def resize_block(image_block: da.Array, block_info: dict) -> da.Array:
     return output.rechunk(image.chunksize).astype(image.dtype)
 
 
-def downscale_nearest(image: da.Array, factors: Tuple[int, ...]) -> da.Array:
+def downscale_nearest(image: da.Array, factors: tuple[int, ...]) -> da.Array:
     """
     Primitive downscaling by integer factors using stepped slicing.
     :type image: :class:`dask.array`

ome_zarr/data.py

@@ -1,7 +1,7 @@
 """Functions for generating synthetic data."""
 
 from random import randrange
-from typing import Callable, List, Optional, Tuple, Union
+from typing import Callable, Optional, Union
 
 import numpy as np
 import zarr
@@ -20,7 +20,7 @@
 CHANNEL_DIMENSION = 1
 
 
-def coins() -> Tuple[List, List]:
+def coins() -> tuple[list, list]:
     """Sample data from skimage."""
     # Thanks to Juan
     # https://gist.github.com/jni/62e07ddd135dbb107278bc04c0f9a8e7
@@ -36,7 +36,7 @@ def coins() -> Tuple[List, List]:
     return pyramid, labels
 
 
-def astronaut() -> Tuple[List, List]:
+def astronaut() -> tuple[list, list]:
     """Sample data from skimage."""
     scaler = Scaler()
 
@@ -85,7 +85,7 @@ def make_circle(h: int, w: int, value: int, target: np.ndarray) -> None:
     target[mask] = value
 
 
-def rgb_to_5d(pixels: np.ndarray) -> List:
+def rgb_to_5d(pixels: np.ndarray) -> list:
     """Convert an RGB image into 5D image (t, c, z, y, x)."""
     if len(pixels.shape) == 2:
         stack = np.array([pixels])
@@ -101,10 +101,10 @@ def rgb_to_5d(pixels: np.ndarray) -> List:
 
 def create_zarr(
     zarr_directory: str,
-    method: Callable[..., Tuple[List, List]] = coins,
+    method: Callable[..., tuple[list, list]] = coins,
     label_name: str = "coins",
     fmt: Format = CurrentFormat(),
-    chunks: Optional[Union[Tuple, List]] = None,
+    chunks: Optional[Union[tuple, list]] = None,
 ) -> zarr.Group:
     """Generate a synthetic image pyramid with labels."""
     pyramid, labels = method()

ome_zarr/format.py

@@ -2,7 +2,8 @@
 
 import logging
 from abc import ABC, abstractmethod
-from typing import Any, Dict, Iterator, List, Optional
+from collections.abc import Iterator
+from typing import Any, Optional
 
 from zarr.storage import FSStore
 
@@ -91,29 +92,29 @@ def __eq__(self, other: object) -> bool:
 
     @abstractmethod
     def generate_well_dict(
-        self, well: str, rows: List[str], columns: List[str]
+        self, well: str, rows: list[str], columns: list[str]
     ) -> dict:  # pragma: no cover
         raise NotImplementedError()
 
     @abstractmethod
     def validate_well_dict(
-        self, well: dict, rows: List[str], columns: List[str]
+        self, well: dict, rows: list[str], columns: list[str]
     ) -> None:  # pragma: no cover
         raise NotImplementedError()
 
     @abstractmethod
     def generate_coordinate_transformations(
-        self, shapes: List[tuple]
-    ) -> Optional[List[List[Dict[str, Any]]]]:  # pragma: no cover
+        self, shapes: list[tuple]
+    ) -> Optional[list[list[dict[str, Any]]]]:  # 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: Optional[list[list[dict[str, Any]]]] = None,
+    ) -> Optional[list[list[dict[str, Any]]]]:  # pragma: no cover
         raise NotImplementedError()
 
 
@@ -122,7 +123,7 @@ class FormatV01(Format):
     Initial format. (2020)
     """
 
-    REQUIRED_PLATE_WELL_KEYS: Dict[str, type] = {"path": str}
+    REQUIRED_PLATE_WELL_KEYS: dict[str, type] = {"path": str}
 
     @property
     def version(self) -> str:
@@ -139,12 +140,12 @@ def init_store(self, path: str, mode: str = "r") -> FSStore:
         return store
 
     def generate_well_dict(
-        self, well: str, rows: List[str], columns: List[str]
+        self, well: str, rows: list[str], columns: list[str]
     ) -> dict:
         return {"path": str(well)}
 
     def validate_well_dict(
-        self, well: dict, rows: List[str], columns: List[str]
+        self, well: dict, rows: list[str], columns: list[str]
     ) -> None:
         if any(e not in self.REQUIRED_PLATE_WELL_KEYS for e in well.keys()):
             LOGGER.debug("%s contains unspecified keys", well)
@@ -157,15 +158,15 @@ def validate_well_dict(
                 raise ValueError("%s path must be of %s type", well, key_type)
 
     def generate_coordinate_transformations(
-        self, shapes: List[tuple]
-    ) -> Optional[List[List[Dict[str, Any]]]]:
+        self, shapes: list[tuple]
+    ) -> Optional[list[list[dict[str, Any]]]]:
         return None
 
     def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: Optional[List[List[Dict[str, Any]]]] = None,
+        coordinate_transformations: Optional[list[list[dict[str, Any]]]] = None,
     ) -> None:
         return None
 
@@ -230,7 +231,7 @@ def version(self) -> str:
         return "0.4"
 
     def generate_well_dict(
-        self, well: str, rows: List[str], columns: List[str]
+        self, well: str, rows: list[str], columns: list[str]
     ) -> dict:
         row, column = well.split("/")
         if row not in rows:
@@ -242,7 +243,7 @@ def generate_well_dict(
         return {"path": str(well), "rowIndex": rowIndex, "columnIndex": columnIndex}
 
     def validate_well_dict(
-        self, well: dict, rows: List[str], columns: List[str]
+        self, well: dict, rows: list[str], columns: list[str]
     ) -> None:
         super().validate_well_dict(well, rows, columns)
         if len(well["path"].split("/")) != 2:
@@ -258,10 +259,10 @@ def validate_well_dict(
             raise ValueError("Mismatching column index for %s", well)
 
     def generate_coordinate_transformations(
-        self, shapes: List[tuple]
-    ) -> Optional[List[List[Dict[str, Any]]]]:
+        self, shapes: list[tuple]
+    ) -> Optional[list[list[dict[str, Any]]]]:
         data_shape = shapes[0]
-        coordinate_transformations: List[List[Dict[str, Any]]] = []
+        coordinate_transformations: list[list[dict[str, Any]]] = []
         # calculate minimal 'scale' transform based on pyramid dims
         for shape in shapes:
             assert len(shape) == len(data_shape)
@@ -274,7 +275,7 @@ def validate_coordinate_transformations(
         self,
         ndim: int,
         nlevels: int,
-        coordinate_transformations: Optional[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

@@ -6,7 +6,7 @@
 import json
 import logging
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import Optional, Union
 from urllib.parse import urljoin
 
 import dask.array as da
@@ -165,7 +165,7 @@ def get_json(self, subpath: str) -> JSONDict:
             LOGGER.exception("Error while loading JSON")
             return {}
 
-    def parts(self) -> List[str]:
+    def parts(self) -> list[str]:
         if self._isfile():
             return list(Path(self.__path).parts)
         else: