Apply pyupgrade for Python 3.9+ syntax

This should have been included in 14b086b when Python 3.8 support was dropped.

Changes were automatically applied by running:
pre_commit run --all-files

Signed-off-by: James Butler <[email protected]>

Author: jamesobutler

.pre-commit-config.yaml

@@ -37,7 +37,7 @@ repos:
     rev: v3.18.0
     hooks:
       - id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
         name: Upgrade code excluding monai networks
         exclude: |
           (?x)(
@@ -49,7 +49,7 @@ repos:
               ^monai/data/grid_dataset.py
           )
       - id: pyupgrade
-        args: [--py38-plus, --keep-runtime-typing]
+        args: [--py39-plus, --keep-runtime-typing]
         name: Upgrade monai networks
         files: (?x)(
                    ^monai/networks/|

monai/apps/detection/networks/retinanet_network.py

@@ -42,7 +42,7 @@
 import math
 import warnings
 from collections.abc import Callable, Sequence
-from typing import Any, Dict
+from typing import Any
 
 import torch
 from torch import Tensor, nn
@@ -330,7 +330,7 @@ def forward(self, images: Tensor) -> Any:
         features = self.feature_extractor(images)
         if isinstance(features, Tensor):
             feature_maps = [features]
-        elif torch.jit.isinstance(features, Dict[str, Tensor]):
+        elif torch.jit.isinstance(features, dict[str, Tensor]):
             feature_maps = list(features.values())
         else:
             feature_maps = list(features)

monai/apps/detection/transforms/array.py

@@ -15,7 +15,9 @@
 
 from __future__ import annotations
 
-from typing import Any, Sequence
+from typing import Any
+
+from collections.abc import Sequence
 
 import numpy as np
 import torch

monai/apps/detection/utils/anchor_utils.py

@@ -39,7 +39,8 @@
 
 from __future__ import annotations
 
-from typing import List, Sequence
+
+from collections.abc import Sequence
 
 import torch
 from torch import Tensor, nn
@@ -106,7 +107,7 @@ class AnchorGenerator(nn.Module):
             anchor_generator = AnchorGenerator(sizes, aspect_ratios)
     """
 
-    __annotations__ = {"cell_anchors": List[torch.Tensor]}
+    __annotations__ = {"cell_anchors": list[torch.Tensor]}
 
     def __init__(
         self,
@@ -364,7 +365,7 @@ class AnchorGeneratorWithAnchorShape(AnchorGenerator):
             anchor_generator = AnchorGeneratorWithAnchorShape(feature_map_scales, base_anchor_shapes)
     """
 
-    __annotations__ = {"cell_anchors": List[torch.Tensor]}
+    __annotations__ = {"cell_anchors": list[torch.Tensor]}
 
     def __init__(
         self,

monai/apps/generation/maisi/networks/autoencoderkl_maisi.py

@@ -13,7 +13,7 @@
 
 import gc
 import logging
-from typing import Sequence
+from collections.abc import Sequence
 
 import torch
 import torch.nn as nn

monai/apps/generation/maisi/networks/controlnet_maisi.py

@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Sequence
+from collections.abc import Sequence
 
 import torch
 

monai/apps/pathology/engines/utils.py

@@ -11,7 +11,9 @@
 
 from __future__ import annotations
 
-from typing import Any, Sequence
+from typing import Any
+
+from collections.abc import Sequence
 
 import torch
 

monai/apps/pathology/inferers/inferer.py

@@ -11,7 +11,9 @@
 
 from __future__ import annotations
 
-from typing import Any, Callable, Sequence
+from typing import Any, Callable
+
+from collections.abc import Sequence
 
 import numpy as np
 import torch

monai/apps/pathology/metrics/lesion_froc.py

@@ -11,7 +11,9 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Iterable
+from typing import TYPE_CHECKING, Any
+
+from collections.abc import Iterable
 
 import numpy as np
 

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

@@ -12,7 +12,9 @@
 from __future__ import annotations
 
 import warnings
-from typing import Callable, Sequence
+from typing import Callable
+
+from collections.abc import Sequence
 
 import numpy as np
 import torch

monai/apps/tcia/utils.py

@@ -12,7 +12,7 @@
 from __future__ import annotations
 
 import os
-from typing import Iterable
+from collections.abc import Iterable
 
 import monai
 from monai.config.type_definitions import PathLike

monai/apps/utils.py

@@ -136,10 +136,7 @@ def check_hash(filepath: PathLike, val: str | None = None, hash_type: str = "md5
         return True
     actual_hash_func = look_up_option(hash_type.lower(), SUPPORTED_HASH_TYPES)
 
-    if sys.version_info >= (3, 9):
-        actual_hash = actual_hash_func(usedforsecurity=False)  # allows checks on FIPS enabled machines
-    else:
-        actual_hash = actual_hash_func()
+    actual_hash = actual_hash_func(usedforsecurity=False)  # allows checks on FIPS enabled machines
 
     try:
         with open(filepath, "rb") as f:

monai/apps/vista3d/transforms.py

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

monai/bundle/reference_resolver.py

@@ -14,7 +14,9 @@
 import re
 import warnings
 from collections.abc import Sequence
-from typing import Any, Iterator
+from typing import Any
+
+from collections.abc import Iterator
 
 from monai.bundle.config_item import ConfigComponent, ConfigExpression, ConfigItem
 from monai.bundle.utils import DEPRECATED_ID_MAPPING, ID_REF_KEY, ID_SEP_KEY

monai/bundle/workflows.py

@@ -19,7 +19,9 @@
 from copy import copy
 from logging.config import fileConfig
 from pathlib import Path
-from typing import Any, Sequence
+from typing import Any
+
+from collections.abc import Sequence
 
 from monai.apps.utils import get_logger
 from monai.bundle.config_parser import ConfigParser

monai/config/type_definitions.py

@@ -12,7 +12,9 @@
 from __future__ import annotations
 
 import os
-from typing import Collection, Hashable, Iterable, Sequence, TypeVar, Union
+from typing import TypeVar, Union
+
+from collections.abc import Collection, Hashable, Iterable, Sequence
 
 import numpy as np
 import torch

monai/data/meta_obj.py

@@ -14,7 +14,9 @@
 import itertools
 import pprint
 from copy import deepcopy
-from typing import Any, Iterable
+from typing import Any
+
+from collections.abc import Iterable
 
 import numpy as np
 import torch

monai/data/meta_tensor.py

@@ -14,7 +14,9 @@
 import functools
 import warnings
 from copy import deepcopy
-from typing import Any, Sequence
+from typing import Any
+
+from collections.abc import Sequence
 
 import numpy as np
 import torch

monai/engines/evaluator.py

@@ -12,7 +12,9 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence
+from typing import TYPE_CHECKING, Any, Callable
+
+from collections.abc import Iterable, Sequence
 
 import torch
 from torch.utils.data import DataLoader

monai/engines/trainer.py

@@ -12,7 +12,9 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, Any, Callable, Iterable, Sequence
+from typing import TYPE_CHECKING, Any, Callable
+
+from collections.abc import Iterable, Sequence
 
 import torch
 from torch.optim.optimizer import Optimizer

monai/engines/utils.py

@@ -13,7 +13,9 @@
 
 from abc import ABC, abstractmethod
 from collections.abc import Callable, Sequence
-from typing import TYPE_CHECKING, Any, Mapping, cast
+from typing import TYPE_CHECKING, Any, cast
+
+from collections.abc import Mapping
 
 import torch
 import torch.nn as nn

monai/handlers/clearml_handlers.py

@@ -11,7 +11,9 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Mapping, Sequence
+from typing import TYPE_CHECKING, Any
+
+from collections.abc import Mapping, Sequence
 
 from monai.utils import optional_import
 

monai/inferers/utils.py

@@ -13,7 +13,9 @@
 
 import itertools
 from collections.abc import Callable, Mapping, Sequence
-from typing import Any, Iterable
+from typing import Any
+
+from collections.abc import Iterable
 
 import numpy as np
 import torch

monai/metrics/utils.py

@@ -14,7 +14,9 @@
 import warnings
 from functools import lru_cache, partial
 from types import ModuleType
-from typing import Any, Iterable, Sequence
+from typing import Any
+
+from collections.abc import Iterable, Sequence
 
 import numpy as np
 import torch

monai/networks/blocks/attention_utils.py

@@ -9,7 +9,6 @@
 
 from __future__ import annotations
 
-from typing import Tuple
 
 import torch
 import torch.nn.functional as F
@@ -50,7 +49,7 @@ def get_rel_pos(q_size: int, k_size: int, rel_pos: torch.Tensor) -> torch.Tensor
 
 
 def add_decomposed_rel_pos(
-    attn: torch.Tensor, q: torch.Tensor, rel_pos_lst: nn.ParameterList, q_size: Tuple, k_size: Tuple
+    attn: torch.Tensor, q: torch.Tensor, rel_pos_lst: nn.ParameterList, q_size: tuple, k_size: tuple
 ) -> torch.Tensor:
     r"""
     Calculate decomposed Relative Positional Embeddings from mvitv2 implementation:

monai/networks/blocks/crossattention.py

@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Optional, Tuple
+from typing import Optional
 
 import torch
 import torch.nn as nn
@@ -42,7 +42,7 @@ def __init__(
         causal: bool = False,
         sequence_length: int | None = None,
         rel_pos_embedding: Optional[str] = None,
-        input_size: Optional[Tuple] = None,
+        input_size: Optional[tuple] = None,
         attention_dtype: Optional[torch.dtype] = None,
         use_flash_attention: bool = False,
     ) -> None:

monai/networks/blocks/denseblock.py

@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Sequence
+from collections.abc import Sequence
 
 import torch
 import torch.nn as nn

monai/networks/blocks/pos_embed_utils.py

@@ -13,7 +13,7 @@
 
 import collections.abc
 from itertools import repeat
-from typing import List, Union
+from typing import Union
 
 import torch
 import torch.nn as nn
@@ -33,7 +33,7 @@ def parse(x):
 
 
 def build_sincos_position_embedding(
-    grid_size: Union[int, List[int]], embed_dim: int, spatial_dims: int = 3, temperature: float = 10000.0
+    grid_size: Union[int, list[int]], embed_dim: int, spatial_dims: int = 3, temperature: float = 10000.0
 ) -> torch.nn.Parameter:
     """
     Builds a sin-cos position embedding based on the given grid size, embed dimension, spatial dimensions, and temperature.

monai/networks/blocks/rel_pos_embedding.py

@@ -9,7 +9,8 @@
 
 from __future__ import annotations
 
-from typing import Iterable, Tuple
+
+from collections.abc import Iterable
 
 import torch
 from torch import nn
@@ -19,7 +20,7 @@
 
 
 class DecomposedRelativePosEmbedding(nn.Module):
-    def __init__(self, s_input_dims: Tuple[int, int] | Tuple[int, int, int], c_dim: int, num_heads: int) -> None:
+    def __init__(self, s_input_dims: tuple[int, int] | tuple[int, int, int], c_dim: int, num_heads: int) -> None:
         """
         Args:
             s_input_dims (Tuple): input spatial dimension. (H, W) or (H, W, D)

monai/networks/blocks/selfattention.py

@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Tuple, Union
+from typing import Union
 
 import torch
 import torch.nn as nn
@@ -41,7 +41,7 @@ def __init__(
         causal: bool = False,
         sequence_length: int | None = None,
         rel_pos_embedding: str | None = None,
-        input_size: Tuple | None = None,
+        input_size: tuple | None = None,
         attention_dtype: torch.dtype | None = None,
         include_fc: bool = True,
         use_combined_linear: bool = True,

monai/networks/layers/simplelayers.py

@@ -13,7 +13,7 @@
 
 import math
 from copy import deepcopy
-from typing import Sequence
+from collections.abc import Sequence
 
 import torch
 import torch.nn.functional as F