Format fixes and script fixes

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Author: ericspod

.github/workflows/cicd_tests.yml

@@ -198,6 +198,7 @@ jobs:
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
         python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
+      shell: bash
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |

monai/_version.py

@@ -15,7 +15,8 @@
 import re
 import subprocess
 import sys
-from typing import Callable, Dict
+from typing import Dict
+from collections.abc import Callable
 import functools
 
 
@@ -54,8 +55,8 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY: Dict[str, str] = {}
-HANDLERS: Dict[str, Dict[str, Callable]] = {}
+LONG_VERSION_PY: dict[str, str] = {}
+HANDLERS: dict[str, dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs, method):  # decorator
@@ -145,7 +146,7 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs) as fobj:
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)

monai/apps/pathology/inferers/inferer.py

@@ -11,9 +11,8 @@
 
 from __future__ import annotations
 
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from typing import Any
-from collections.abc import Callable
 
 import numpy as np
 import torch

monai/apps/pathology/transforms/post/array.py

@@ -12,8 +12,7 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Sequence
-from collections.abc import Callable
+from collections.abc import Callable, Sequence
 
 import numpy as np
 import torch

monai/bundle/scripts.py

@@ -17,14 +17,13 @@
 import re
 import urllib
 import warnings
-from collections.abc import Mapping, Sequence
+from collections.abc import Callable, Mapping, Sequence
 from functools import partial
 from pathlib import Path
 from pydoc import locate
 from shutil import copyfile
 from textwrap import dedent
 from typing import Any
-from collections.abc import Callable
 
 import torch
 from torch.cuda import is_available

monai/config/type_definitions.py

@@ -53,21 +53,21 @@
 #        convenience to end-users.  All supplied values will be
 #        internally converted to a tuple of `Hashable`'s before
 #        use
-KeysCollection = Union[Collection[Hashable], Hashable]
+KeysCollection = Collection[Hashable] | Hashable
 
 #: IndexSelection
 #
 # The IndexSelection type is used to for defining variables
 # that store a subset of indices to select items from a List or Array like objects.
 # The indices must be integers, and if a container of indices is specified, the
 # container must be iterable.
-IndexSelection = Union[Iterable[int], int]
+IndexSelection = Iterable[int] | int
 
 #: Type of datatypes: Adapted from https://github.com/numpy/numpy/blob/v1.21.4/numpy/typing/_dtype_like.py#L121
-DtypeLike = Union[np.dtype, type, str, None]
+DtypeLike = np.dtype | type | str | None
 
 #: NdarrayOrTensor: Union of numpy.ndarray and torch.Tensor to be used for typing
-NdarrayOrTensor = Union[np.ndarray, torch.Tensor]
+NdarrayOrTensor = np.ndarray | torch.Tensor
 
 #: NdarrayTensor
 #
@@ -76,11 +76,11 @@
 NdarrayTensor = TypeVar("NdarrayTensor", bound=NdarrayOrTensor)
 
 #: TensorOrList: The TensorOrList type is used for defining `batch-first Tensor` or `list of channel-first Tensor`.
-TensorOrList = Union[torch.Tensor, Sequence[torch.Tensor]]
+TensorOrList = torch.Tensor | Sequence[torch.Tensor]
 
 #: PathLike: The PathLike type is used for defining a file path.
-PathLike = Union[str, os.PathLike]
+PathLike = str | os.PathLike
 
 #: SequenceStr
 # string or a sequence of strings for `mode` types.
-SequenceStr = Union[Sequence[str], str]
+SequenceStr = Sequence[str] | str

monai/data/image_reader.py

@@ -60,7 +60,7 @@
 if TYPE_CHECKING:
     import cupy
 
-    NdarrayOrCupy = Union[np.ndarray, cupy.ndarray]
+    NdarrayOrCupy = np.ndarray | cupy.ndarray
 else:
     NdarrayOrCupy = Any
 

monai/engines/evaluator.py

@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
 from typing import TYPE_CHECKING, Any
-from collections.abc import Callable
 
 import torch
 from torch.utils.data import DataLoader

monai/engines/trainer.py

@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
 from typing import TYPE_CHECKING, Any
-from collections.abc import Callable
 
 import torch
 from torch.optim.optimizer import Optimizer

monai/networks/nets/vista3d.py

@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import math
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from typing import Any
-from collections.abc import Callable
 
 import numpy as np
 import torch