monai-weekly 1.5.dev2446__py3-none-any.whl → 1.5.dev2448__py3-none-any.whl

monai/networks/nets/swin_unetr.py

@@ -13,7 +13,6 @@ from __future__ import annotations
 
 import itertools
 from collections.abc import Sequence
-from typing import Final
 
 import numpy as np
 import torch
@@ -51,8 +50,6 @@ class SwinUNETR(nn.Module):
     <https://arxiv.org/abs/2201.01266>"
     """
 
-    patch_size: Final[int] = 2
-
     @deprecated_arg(
         name="img_size",
         since="1.3",
@@ -65,18 +62,24 @@ class SwinUNETR(nn.Module):
         img_size: Sequence[int] | int,
         in_channels: int,
         out_channels: int,
+        patch_size: int = 2,
         depths: Sequence[int] = (2, 2, 2, 2),
         num_heads: Sequence[int] = (3, 6, 12, 24),
+        window_size: Sequence[int] | int = 7,
+        qkv_bias: bool = True,
+        mlp_ratio: float = 4.0,
         feature_size: int = 24,
         norm_name: tuple | str = "instance",
         drop_rate: float = 0.0,
         attn_drop_rate: float = 0.0,
         dropout_path_rate: float = 0.0,
         normalize: bool = True,
+        norm_layer: type[LayerNorm] = nn.LayerNorm,
+        patch_norm: bool = True,
         use_checkpoint: bool = False,
         spatial_dims: int = 3,
-        downsample="merging",
-        use_v2=False,
+        downsample: str | nn.Module = "merging",
+        use_v2: bool = False,
     ) -> None:
         """
         Args:
@@ -86,14 +89,20 @@ class SwinUNETR(nn.Module):
                 It will be removed in an upcoming version.
             in_channels: dimension of input channels.
             out_channels: dimension of output channels.
+            patch_size: size of the patch token.
             feature_size: dimension of network feature size.
             depths: number of layers in each stage.
             num_heads: number of attention heads.
+            window_size: local window size.
+            qkv_bias: add a learnable bias to query, key, value.
+            mlp_ratio: ratio of mlp hidden dim to embedding dim.
             norm_name: feature normalization type and arguments.
             drop_rate: dropout rate.
             attn_drop_rate: attention dropout rate.
             dropout_path_rate: drop path rate.
             normalize: normalize output intermediate features in each stage.
+            norm_layer: normalization layer.
+            patch_norm: whether to apply normalization to the patch embedding.
             use_checkpoint: use gradient checkpointing for reduced memory usage.
             spatial_dims: number of spatial dims.
             downsample: module used for downsampling, available options are `"mergingv2"`, `"merging"` and a
@@ -116,13 +125,15 @@ class SwinUNETR(nn.Module):
 
         super().__init__()
 
-        img_size = ensure_tuple_rep(img_size, spatial_dims)
-        patch_sizes = ensure_tuple_rep(self.patch_size, spatial_dims)
-        window_size = ensure_tuple_rep(7, spatial_dims)
-
         if spatial_dims not in (2, 3):
             raise ValueError("spatial dimension should be 2 or 3.")
 
+        self.patch_size = patch_size
+
+        img_size = ensure_tuple_rep(img_size, spatial_dims)
+        patch_sizes = ensure_tuple_rep(self.patch_size, spatial_dims)
+        window_size = ensure_tuple_rep(window_size, spatial_dims)
+
         self._check_input_size(img_size)
 
         if not (0 <= drop_rate <= 1):
@@ -146,12 +157,13 @@ class SwinUNETR(nn.Module):
             patch_size=patch_sizes,
             depths=depths,
             num_heads=num_heads,
-            mlp_ratio=4.0,
-            qkv_bias=True,
+            mlp_ratio=mlp_ratio,
+            qkv_bias=qkv_bias,
             drop_rate=drop_rate,
             attn_drop_rate=attn_drop_rate,
             drop_path_rate=dropout_path_rate,
-            norm_layer=nn.LayerNorm,
+            norm_layer=norm_layer,
+            patch_norm=patch_norm,
             use_checkpoint=use_checkpoint,
             spatial_dims=spatial_dims,
             downsample=look_up_option(downsample, MERGING_MODE) if isinstance(downsample, str) else downsample,

monai/transforms/__init__.py

@@ -531,6 +531,8 @@ from .utility.array import (
     RandIdentity,
     RandImageFilter,
     RandLambda,
+    RandTorchIO,
+    RandTorchVision,
     RemoveRepeatedChannel,
     RepeatChannel,
     SimulateDelay,
@@ -540,6 +542,7 @@ from .utility.array import (
     ToDevice,
     ToNumpy,
     ToPIL,
+    TorchIO,
     TorchVision,
     ToTensor,
     Transpose,
@@ -620,6 +623,9 @@ from .utility.dictionary import (
     RandLambdad,
     RandLambdaD,
     RandLambdaDict,
+    RandTorchIOd,
+    RandTorchIOD,
+    RandTorchIODict,
     RandTorchVisiond,
     RandTorchVisionD,
     RandTorchVisionDict,
@@ -653,6 +659,9 @@ from .utility.dictionary import (
     ToPILd,
     ToPILD,
     ToPILDict,
+    TorchIOd,
+    TorchIOD,
+    TorchIODict,
     TorchVisiond,
     TorchVisionD,
     TorchVisionDict,

monai/transforms/utility/array.py

@@ -18,10 +18,10 @@ import logging
 import sys
 import time
 import warnings
-from collections.abc import Mapping, Sequence
+from collections.abc import Hashable, Mapping, Sequence
 from copy import deepcopy
 from functools import partial
-from typing import Any, Callable
+from typing import Any, Callable, Union
 
 import numpy as np
 import torch
@@ -99,11 +99,14 @@ __all__ = [
     "ConvertToMultiChannelBasedOnBratsClasses",
     "AddExtremePointsChannel",
     "TorchVision",
+    "TorchIO",
     "MapLabelValue",
     "IntensityStats",
     "ToDevice",
     "CuCIM",
     "RandCuCIM",
+    "RandTorchIO",
+    "RandTorchVision",
     "ToCupy",
     "ImageFilter",
     "RandImageFilter",
@@ -1136,12 +1139,44 @@ class AddExtremePointsChannel(Randomizable, Transform):
         return concatenate((img, points_image), axis=0)
 
 
-class TorchVision:
+class TorchVision(Transform):
     """
-    This is a wrapper transform for PyTorch TorchVision transform based on the specified transform name and args.
-    As most of the TorchVision transforms only work for PIL image and PyTorch Tensor, this transform expects input
-    data to be PyTorch Tensor, users can easily call `ToTensor` transform to convert a Numpy array to Tensor.
+    This is a wrapper transform for PyTorch TorchVision non-randomized transform based on the specified transform name and args.
+    Data is converted to a torch.tensor before applying the transform and then converted back to the original data type.
+    """
+
+    backend = [TransformBackends.TORCH]
+
+    def __init__(self, name: str, *args, **kwargs) -> None:
+        """
+        Args:
+            name: The transform name in TorchVision package.
+            args: parameters for the TorchVision transform.
+            kwargs: parameters for the TorchVision transform.
+
+        """
+        super().__init__()
+        self.name = name
+        transform, _ = optional_import("torchvision.transforms", "0.8.0", min_version, name=name)
+        self.trans = transform(*args, **kwargs)
+
+    def __call__(self, img: NdarrayOrTensor):
+        """
+        Args:
+            img: PyTorch Tensor data for the TorchVision transform.
 
+        """
+        img_t, *_ = convert_data_type(img, torch.Tensor)
+
+        out = self.trans(img_t)
+        out, *_ = convert_to_dst_type(src=out, dst=img)
+        return out
+
+
+class RandTorchVision(Transform, RandomizableTrait):
+    """
+    This is a wrapper transform for PyTorch TorchVision randomized transform based on the specified transform name and args.
+    Data is converted to a torch.tensor before applying the transform and then converted back to the original data type.
     """
 
     backend = [TransformBackends.TORCH]
@@ -1172,6 +1207,68 @@ class TorchVision:
         return out
 
 
+class TorchIO(Transform):
+    """
+    This is a wrapper for TorchIO non-randomized transforms based on the specified transform name and args.
+    See https://torchio.readthedocs.io/transforms/transforms.html for more details.
+    """
+
+    backend = [TransformBackends.TORCH]
+
+    def __init__(self, name: str, *args, **kwargs) -> None:
+        """
+        Args:
+            name: The transform name in TorchIO package.
+            args: parameters for the TorchIO transform.
+            kwargs: parameters for the TorchIO transform.
+        """
+        super().__init__()
+        self.name = name
+        transform, _ = optional_import("torchio.transforms", "0.18.0", min_version, name=name)
+        self.trans = transform(*args, **kwargs)
+
+    def __call__(self, img: Union[NdarrayOrTensor, Mapping[Hashable, NdarrayOrTensor]]):
+        """
+        Args:
+            img: an instance of torchio.Subject, torchio.Image, numpy.ndarray, torch.Tensor, SimpleITK.Image,
+                 or dict containing 4D tensors as values
+
+        """
+        return self.trans(img)
+
+
+class RandTorchIO(Transform, RandomizableTrait):
+    """
+    This is a wrapper for TorchIO randomized transforms based on the specified transform name and args.
+    See https://torchio.readthedocs.io/transforms/transforms.html for more details.
+    Use this wrapper for all TorchIO transform inheriting from RandomTransform:
+    https://torchio.readthedocs.io/transforms/augmentation.html#randomtransform
+    """
+
+    backend = [TransformBackends.TORCH]
+
+    def __init__(self, name: str, *args, **kwargs) -> None:
+        """
+        Args:
+            name: The transform name in TorchIO package.
+            args: parameters for the TorchIO transform.
+            kwargs: parameters for the TorchIO transform.
+        """
+        super().__init__()
+        self.name = name
+        transform, _ = optional_import("torchio.transforms", "0.18.0", min_version, name=name)
+        self.trans = transform(*args, **kwargs)
+
+    def __call__(self, img: Union[NdarrayOrTensor, Mapping[Hashable, NdarrayOrTensor]]):
+        """
+        Args:
+            img: an instance of torchio.Subject, torchio.Image, numpy.ndarray, torch.Tensor, SimpleITK.Image,
+                 or dict containing 4D tensors as values
+
+        """
+        return self.trans(img)
+
+
 class MapLabelValue:
     """
     Utility to map label values to another set of values.

monai/transforms/utility/dictionary.py

@@ -60,6 +60,7 @@ from monai.transforms.utility.array import (
     ToDevice,
     ToNumpy,
     ToPIL,
+    TorchIO,
     TorchVision,
     ToTensor,
     Transpose,
@@ -136,6 +137,9 @@ __all__ = [
     "RandLambdaD",
     "RandLambdaDict",
     "RandLambdad",
+    "RandTorchIOd",
+    "RandTorchIOD",
+    "RandTorchIODict",
     "RandTorchVisionD",
     "RandTorchVisionDict",
     "RandTorchVisiond",
@@ -172,6 +176,9 @@ __all__ = [
     "ToTensorD",
     "ToTensorDict",
     "ToTensord",
+    "TorchIOD",
+    "TorchIODict",
+    "TorchIOd",
     "TorchVisionD",
     "TorchVisionDict",
     "TorchVisiond",
@@ -1445,6 +1452,64 @@ class RandTorchVisiond(MapTransform, RandomizableTrait):
         return d
 
 
+class TorchIOd(MapTransform):
+    """
+    Dictionary-based wrapper of :py:class:`monai.transforms.TorchIO` for non-randomized transforms.
+    For randomized transforms of TorchIO use :py:class:`monai.transforms.RandTorchIOd`.
+    """
+
+    backend = TorchIO.backend
+
+    def __init__(self, keys: KeysCollection, name: str, allow_missing_keys: bool = False, *args, **kwargs) -> None:
+        """
+        Args:
+            keys: keys of the corresponding items to be transformed.
+                See also: :py:class:`monai.transforms.compose.MapTransform`
+            name: The transform name in TorchIO package.
+            allow_missing_keys: don't raise exception if key is missing.
+            args: parameters for the TorchIO transform.
+            kwargs: parameters for the TorchIO transform.
+
+        """
+        super().__init__(keys, allow_missing_keys)
+        self.name = name
+        kwargs["include"] = self.keys
+
+        self.trans = TorchIO(name, *args, **kwargs)
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Mapping[Hashable, NdarrayOrTensor]:
+        return dict(self.trans(data))
+
+
+class RandTorchIOd(MapTransform, RandomizableTrait):
+    """
+    Dictionary-based wrapper of :py:class:`monai.transforms.TorchIO` for randomized transforms.
+    For non-randomized transforms of TorchIO use :py:class:`monai.transforms.TorchIOd`.
+    """
+
+    backend = TorchIO.backend
+
+    def __init__(self, keys: KeysCollection, name: str, allow_missing_keys: bool = False, *args, **kwargs) -> None:
+        """
+        Args:
+            keys: keys of the corresponding items to be transformed.
+                See also: :py:class:`monai.transforms.compose.MapTransform`
+            name: The transform name in TorchIO package.
+            allow_missing_keys: don't raise exception if key is missing.
+            args: parameters for the TorchIO transform.
+            kwargs: parameters for the TorchIO transform.
+
+        """
+        super().__init__(keys, allow_missing_keys)
+        self.name = name
+        kwargs["include"] = self.keys
+
+        self.trans = TorchIO(name, *args, **kwargs)
+
+    def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> Mapping[Hashable, NdarrayOrTensor]:
+        return dict(self.trans(data))
+
+
 class MapLabelValued(MapTransform):
     """
     Dictionary-based wrapper of :py:class:`monai.transforms.MapLabelValue`.
@@ -1871,8 +1936,10 @@ ConvertToMultiChannelBasedOnBratsClassesD = ConvertToMultiChannelBasedOnBratsCla
     ConvertToMultiChannelBasedOnBratsClassesd
 )
 AddExtremePointsChannelD = AddExtremePointsChannelDict = AddExtremePointsChanneld
+TorchIOD = TorchIODict = TorchIOd
 TorchVisionD = TorchVisionDict = TorchVisiond
 RandTorchVisionD = RandTorchVisionDict = RandTorchVisiond
+RandTorchIOD = RandTorchIODict = RandTorchIOd
 RandLambdaD = RandLambdaDict = RandLambdad
 MapLabelValueD = MapLabelValueDict = MapLabelValued
 IntensityStatsD = IntensityStatsDict = IntensityStatsd

monai/utils/module.py

@@ -649,7 +649,7 @@ def compute_capabilities_after(major: int, minor: int = 0, current_ver_string: s
         current_ver_string: if None, the current system GPU CUDA compute capability will be used.
 
     Returns:
-        True if the current system GPU CUDA compute capability is greater than the specified version.
+        True if the current system GPU CUDA compute capability is greater than or equal to the specified version.
     """
     if current_ver_string is None:
         cuda_available = torch.cuda.is_available()
@@ -667,11 +667,11 @@ def compute_capabilities_after(major: int, minor: int = 0, current_ver_string: s
 
     ver, has_ver = optional_import("packaging.version", name="parse")
     if has_ver:
-        return ver(".".join((f"{major}", f"{minor}"))) < ver(f"{current_ver_string}")  # type: ignore
+        return ver(".".join((f"{major}", f"{minor}"))) <= ver(f"{current_ver_string}")  # type: ignore
     parts = f"{current_ver_string}".split("+", 1)[0].split(".", 2)
     while len(parts) < 2:
         parts += ["0"]
     c_major, c_minor = parts[:2]
     c_mn = int(c_major), int(c_minor)
     mn = int(major), int(minor)
-    return c_mn >= mn
+    return c_mn > mn

{monai_weekly-1.5.dev2446.dist-info → monai_weekly-1.5.dev2448.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: monai-weekly
-Version: 1.5.dev2446
+Version: 1.5.dev2448
 Summary: AI Toolkit for Healthcare Imaging
 Home-page: https://monai.io/
 Author: MONAI Consortium
@@ -35,20 +35,24 @@ Provides-Extra: all
 Requires-Dist: nibabel; extra == "all"
 Requires-Dist: ninja; extra == "all"
 Requires-Dist: scikit-image>=0.14.2; extra == "all"
+Requires-Dist: scipy>=1.12.0; python_version >= "3.9" and extra == "all"
 Requires-Dist: pillow; extra == "all"
 Requires-Dist: tensorboard; extra == "all"
 Requires-Dist: gdown>=4.7.3; extra == "all"
 Requires-Dist: pytorch-ignite==0.4.11; extra == "all"
+Requires-Dist: torchio; extra == "all"
 Requires-Dist: torchvision; extra == "all"
 Requires-Dist: itk>=5.2; extra == "all"
 Requires-Dist: tqdm>=4.47.0; extra == "all"
 Requires-Dist: lmdb; extra == "all"
 Requires-Dist: psutil; extra == "all"
+Requires-Dist: cucim-cu12; (python_version >= "3.9" and python_version <= "3.10") and extra == "all"
 Requires-Dist: openslide-python; extra == "all"
 Requires-Dist: tifffile; extra == "all"
 Requires-Dist: imagecodecs; extra == "all"
 Requires-Dist: pandas; extra == "all"
 Requires-Dist: einops; extra == "all"
+Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "all"
 Requires-Dist: mlflow>=2.12.2; extra == "all"
 Requires-Dist: clearml>=1.10.0rc0; extra == "all"
 Requires-Dist: matplotlib>=3.6.3; extra == "all"
@@ -62,96 +66,95 @@ Requires-Dist: h5py; extra == "all"
 Requires-Dist: nni; extra == "all"
 Requires-Dist: optuna; extra == "all"
 Requires-Dist: onnx>=1.13.0; extra == "all"
+Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "all"
 Requires-Dist: zarr; extra == "all"
 Requires-Dist: lpips==0.1.4; extra == "all"
 Requires-Dist: nvidia-ml-py; extra == "all"
-Requires-Dist: huggingface-hub; extra == "all"
+Requires-Dist: huggingface_hub; extra == "all"
 Requires-Dist: pyamg>=5.0.0; extra == "all"
-Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "all"
-Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "all"
-Requires-Dist: scipy>=1.12.0; python_version >= "3.9" and extra == "all"
-Requires-Dist: cucim-cu12; (python_version >= "3.9" and python_version <= "3.10") and extra == "all"
-Provides-Extra: clearml
-Requires-Dist: clearml; extra == "clearml"
-Provides-Extra: cucim
-Requires-Dist: cucim-cu12; extra == "cucim"
-Provides-Extra: einops
-Requires-Dist: einops; extra == "einops"
-Provides-Extra: fire
-Requires-Dist: fire; extra == "fire"
+Provides-Extra: nibabel
+Requires-Dist: nibabel; extra == "nibabel"
+Provides-Extra: ninja
+Requires-Dist: ninja; extra == "ninja"
+Provides-Extra: skimage
+Requires-Dist: scikit-image>=0.14.2; extra == "skimage"
+Provides-Extra: scipy
+Requires-Dist: scipy>=1.12.0; python_version >= "3.9" and extra == "scipy"
+Provides-Extra: pillow
+Requires-Dist: pillow!=8.3.0; extra == "pillow"
+Provides-Extra: tensorboard
+Requires-Dist: tensorboard; extra == "tensorboard"
 Provides-Extra: gdown
 Requires-Dist: gdown>=4.7.3; extra == "gdown"
-Provides-Extra: h5py
-Requires-Dist: h5py; extra == "h5py"
-Provides-Extra: huggingface_hub
-Requires-Dist: huggingface-hub; extra == "huggingface-hub"
 Provides-Extra: ignite
 Requires-Dist: pytorch-ignite==0.4.11; extra == "ignite"
-Provides-Extra: imagecodecs
-Requires-Dist: imagecodecs; extra == "imagecodecs"
+Provides-Extra: torchio
+Requires-Dist: torchio; extra == "torchio"
+Provides-Extra: torchvision
+Requires-Dist: torchvision; extra == "torchvision"
 Provides-Extra: itk
 Requires-Dist: itk>=5.2; extra == "itk"
-Provides-Extra: jsonschema
-Requires-Dist: jsonschema; extra == "jsonschema"
+Provides-Extra: tqdm
+Requires-Dist: tqdm>=4.47.0; extra == "tqdm"
 Provides-Extra: lmdb
 Requires-Dist: lmdb; extra == "lmdb"
-Provides-Extra: lpips
-Requires-Dist: lpips==0.1.4; extra == "lpips"
-Provides-Extra: matplotlib
-Requires-Dist: matplotlib>=3.6.3; extra == "matplotlib"
+Provides-Extra: psutil
+Requires-Dist: psutil; extra == "psutil"
+Provides-Extra: cucim
+Requires-Dist: cucim-cu12; extra == "cucim"
+Provides-Extra: openslide
+Requires-Dist: openslide-python; extra == "openslide"
+Provides-Extra: tifffile
+Requires-Dist: tifffile; extra == "tifffile"
+Provides-Extra: imagecodecs
+Requires-Dist: imagecodecs; extra == "imagecodecs"
+Provides-Extra: pandas
+Requires-Dist: pandas; extra == "pandas"
+Provides-Extra: einops
+Requires-Dist: einops; extra == "einops"
+Provides-Extra: transformers
+Requires-Dist: transformers<4.41.0,>=4.36.0; python_version <= "3.10" and extra == "transformers"
 Provides-Extra: mlflow
 Requires-Dist: mlflow>=2.12.2; extra == "mlflow"
-Provides-Extra: nibabel
-Requires-Dist: nibabel; extra == "nibabel"
-Provides-Extra: ninja
-Requires-Dist: ninja; extra == "ninja"
+Provides-Extra: matplotlib
+Requires-Dist: matplotlib>=3.6.3; extra == "matplotlib"
+Provides-Extra: clearml
+Requires-Dist: clearml; extra == "clearml"
+Provides-Extra: tensorboardx
+Requires-Dist: tensorboardX; extra == "tensorboardx"
+Provides-Extra: pyyaml
+Requires-Dist: pyyaml; extra == "pyyaml"
+Provides-Extra: fire
+Requires-Dist: fire; extra == "fire"
+Provides-Extra: packaging
+Requires-Dist: packaging; extra == "packaging"
+Provides-Extra: jsonschema
+Requires-Dist: jsonschema; extra == "jsonschema"
+Provides-Extra: pynrrd
+Requires-Dist: pynrrd; extra == "pynrrd"
+Provides-Extra: pydicom
+Requires-Dist: pydicom; extra == "pydicom"
+Provides-Extra: h5py
+Requires-Dist: h5py; extra == "h5py"
 Provides-Extra: nni
 Requires-Dist: nni; extra == "nni"
+Provides-Extra: optuna
+Requires-Dist: optuna; extra == "optuna"
 Provides-Extra: onnx
 Requires-Dist: onnx>=1.13.0; extra == "onnx"
 Requires-Dist: onnxruntime; python_version <= "3.10" and extra == "onnx"
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-Provides-Extra: packaging
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-Provides-Extra: pandas
-Requires-Dist: pandas; extra == "pandas"
-Provides-Extra: pillow
-Requires-Dist: pillow!=8.3.0; extra == "pillow"
+Provides-Extra: zarr
+Requires-Dist: zarr; extra == "zarr"
+Provides-Extra: lpips
+Requires-Dist: lpips==0.1.4; extra == "lpips"
+Provides-Extra: pynvml
+Requires-Dist: nvidia-ml-py; extra == "pynvml"
 Provides-Extra: polygraphy
 Requires-Dist: polygraphy; extra == "polygraphy"
-Provides-Extra: psutil
-Requires-Dist: psutil; extra == "psutil"
+Provides-Extra: huggingface-hub
+Requires-Dist: huggingface_hub; extra == "huggingface-hub"
 Provides-Extra: pyamg
 Requires-Dist: pyamg>=5.0.0; extra == "pyamg"
-Provides-Extra: pydicom
-Requires-Dist: pydicom; extra == "pydicom"
-Provides-Extra: pynrrd
-Requires-Dist: pynrrd; extra == "pynrrd"
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-Requires-Dist: nvidia-ml-py; extra == "pynvml"
-Provides-Extra: pyyaml
-Requires-Dist: pyyaml; extra == "pyyaml"
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