pyg-nightly 2.7.0.dev20250606__py3-none-any.whl → 2.7.0.dev20250608__py3-none-any.whl

torch_geometric/transforms/base_transform.py

@@ -1,5 +1,5 @@
 import copy
-from abc import ABC
+from abc import ABC, abstractmethod
 from typing import Any
 
 
@@ -31,6 +31,7 @@ class BaseTransform(ABC):
         # Shallow-copy the data so that we prevent in-place data modification.
         return self.forward(copy.copy(data))
 
+    @abstractmethod
     def forward(self, data: Any) -> Any:
         pass
 

torch_geometric/transforms/gdc.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, Tuple
+from typing import Any, Dict, Optional, Tuple
 
 import numpy as np
 import torch
@@ -78,18 +78,17 @@ class GDC(BaseTransform):
         self_loop_weight: float = 1.,
         normalization_in: str = 'sym',
         normalization_out: str = 'col',
-        diffusion_kwargs: Dict[str, Any] = dict(method='ppr', alpha=0.15),
-        sparsification_kwargs: Dict[str, Any] = dict(
-            method='threshold',
-            avg_degree=64,
-        ),
+        diffusion_kwargs: Optional[Dict[str, Any]] = None,
+        sparsification_kwargs: Optional[Dict[str, Any]] = None,
         exact: bool = True,
     ) -> None:
         self.self_loop_weight = self_loop_weight
         self.normalization_in = normalization_in
         self.normalization_out = normalization_out
-        self.diffusion_kwargs = diffusion_kwargs
-        self.sparsification_kwargs = sparsification_kwargs
+        self.diffusion_kwargs = diffusion_kwargs or dict(
+            method='ppr', alpha=0.15)
+        self.sparsification_kwargs = sparsification_kwargs or dict(
+            method='threshold', avg_degree=64)
         self.exact = exact
 
         if self_loop_weight:

torch_geometric/transforms/largest_connected_components.py

@@ -47,7 +47,7 @@ class LargestConnectedComponents(BaseTransform):
             return data
 
         _, count = np.unique(component, return_counts=True)
-        subset_np = np.in1d(component, count.argsort()[-self.num_components:])
+        subset_np = np.isin(component, count.argsort()[-self.num_components:])
         subset = torch.from_numpy(subset_np)
         subset = subset.to(data.edge_index.device, torch.bool)
 

torch_geometric/transforms/normalize_features.py

@@ -1,4 +1,4 @@
-from typing import List, Union
+from typing import List, Optional, Union
 
 from torch_geometric.data import Data, HeteroData
 from torch_geometric.data.datapipes import functional_transform
@@ -14,8 +14,8 @@ class NormalizeFeatures(BaseTransform):
         attrs (List[str]): The names of attributes to normalize.
             (default: :obj:`["x"]`)
     """
-    def __init__(self, attrs: List[str] = ["x"]):
-        self.attrs = attrs
+    def __init__(self, attrs: Optional[List[str]] = None) -> None:
+        self.attrs = attrs or ["x"]
 
     def forward(
         self,

torch_geometric/transforms/random_link_split.py

@@ -245,7 +245,7 @@ class RandomLinkSplit(BaseTransform):
                 warnings.warn(
                     f"There are not enough negative edges to satisfy "
                     "the provided sampling ratio. The ratio will be "
-                    f"adjusted to {ratio:.2f}.")
+                    f"adjusted to {ratio:.2f}.", stacklevel=2)
                 num_neg_train = int((num_neg_train / num_neg) * num_neg_found)
                 num_neg_val = int((num_neg_val / num_neg) * num_neg_found)
                 num_neg_test = num_neg_found - num_neg_train - num_neg_val

torch_geometric/transforms/remove_duplicated_edges.py

@@ -1,4 +1,4 @@
-from typing import List, Union
+from typing import List, Optional, Union
 
 from torch_geometric.data import Data, HeteroData
 from torch_geometric.data.datapipes import functional_transform
@@ -22,9 +22,11 @@ class RemoveDuplicatedEdges(BaseTransform):
     """
     def __init__(
         self,
-        key: Union[str, List[str]] = ['edge_attr', 'edge_weight'],
+        key: Optional[Union[str, List[str]]] = None,
         reduce: str = "add",
     ) -> None:
+        key = key or ['edge_attr', 'edge_weight']
+
         if isinstance(key, str):
             key = [key]
 

torch_geometric/typing.py

@@ -81,8 +81,9 @@ try:
         WITH_CUDA_HASH_MAP = False
 except Exception as e:
     if not isinstance(e, ImportError):  # pragma: no cover
-        warnings.warn(f"An issue occurred while importing 'pyg-lib'. "
-                      f"Disabling its usage. Stacktrace: {e}")
+        warnings.warn(
+            f"An issue occurred while importing 'pyg-lib'. "
+            f"Disabling its usage. Stacktrace: {e}", stacklevel=2)
     pyg_lib = object
     WITH_PYG_LIB = False
     WITH_GMM = False
@@ -125,8 +126,9 @@ try:
     WITH_TORCH_SCATTER = True
 except Exception as e:
     if not isinstance(e, ImportError):  # pragma: no cover
-        warnings.warn(f"An issue occurred while importing 'torch-scatter'. "
-                      f"Disabling its usage. Stacktrace: {e}")
+        warnings.warn(
+            f"An issue occurred while importing 'torch-scatter'. "
+            f"Disabling its usage. Stacktrace: {e}", stacklevel=2)
     torch_scatter = object
     WITH_TORCH_SCATTER = False
 
@@ -136,8 +138,9 @@ try:
     WITH_TORCH_CLUSTER_BATCH_SIZE = 'batch_size' in torch_cluster.knn.__doc__
 except Exception as e:
     if not isinstance(e, ImportError):  # pragma: no cover
-        warnings.warn(f"An issue occurred while importing 'torch-cluster'. "
-                      f"Disabling its usage. Stacktrace: {e}")
+        warnings.warn(
+            f"An issue occurred while importing 'torch-cluster'. "
+            f"Disabling its usage. Stacktrace: {e}", stacklevel=2)
     WITH_TORCH_CLUSTER = False
     WITH_TORCH_CLUSTER_BATCH_SIZE = False
 
@@ -154,7 +157,7 @@ except Exception as e:
     if not isinstance(e, ImportError):  # pragma: no cover
         warnings.warn(
             f"An issue occurred while importing 'torch-spline-conv'. "
-            f"Disabling its usage. Stacktrace: {e}")
+            f"Disabling its usage. Stacktrace: {e}", stacklevel=2)
     WITH_TORCH_SPLINE_CONV = False
 
 try:
@@ -163,8 +166,9 @@ try:
     WITH_TORCH_SPARSE = True
 except Exception as e:
     if not isinstance(e, ImportError):  # pragma: no cover
-        warnings.warn(f"An issue occurred while importing 'torch-sparse'. "
-                      f"Disabling its usage. Stacktrace: {e}")
+        warnings.warn(
+            f"An issue occurred while importing 'torch-sparse'. "
+            f"Disabling its usage. Stacktrace: {e}", stacklevel=2)
     WITH_TORCH_SPARSE = False
 
     class SparseStorage:  # type: ignore

torch_geometric/utils/_scatter.py

@@ -88,9 +88,10 @@ def scatter(
 
             if (src.is_cuda and src.requires_grad and not is_compiling()
                     and not is_in_onnx_export()):
-                warnings.warn(f"The usage of `scatter(reduce='{reduce}')` "
-                              f"can be accelerated via the 'torch-scatter'"
-                              f" package, but it was not found")
+                warnings.warn(
+                    f"The usage of `scatter(reduce='{reduce}')` "
+                    f"can be accelerated via the 'torch-scatter'"
+                    f" package, but it was not found", stacklevel=2)
 
             index = broadcast(index, src, dim)
             if not is_in_onnx_export():
@@ -120,9 +121,10 @@ def scatter(
                 or not src.is_cuda):
 
             if src.is_cuda and not is_compiling():
-                warnings.warn(f"The usage of `scatter(reduce='{reduce}')` "
-                              f"can be accelerated via the 'torch-scatter'"
-                              f" package, but it was not found")
+                warnings.warn(
+                    f"The usage of `scatter(reduce='{reduce}')` "
+                    f"can be accelerated via the 'torch-scatter'"
+                    f" package, but it was not found", stacklevel=2)
 
             index = broadcast(index, src, dim)
             # We initialize with `one` here to match `scatter_mul` output:

torch_geometric/utils/_spmm.py

@@ -63,18 +63,20 @@ def spmm(
 
         # Always convert COO to CSR for more efficient processing:
         if src.layout == torch.sparse_coo:
-            warnings.warn(f"Converting sparse tensor to CSR format for more "
-                          f"efficient processing. Consider converting your "
-                          f"sparse tensor to CSR format beforehand to avoid "
-                          f"repeated conversion (got '{src.layout}')")
+            warnings.warn(
+                f"Converting sparse tensor to CSR format for more "
+                f"efficient processing. Consider converting your "
+                f"sparse tensor to CSR format beforehand to avoid "
+                f"repeated conversion (got '{src.layout}')", stacklevel=2)
             src = src.to_sparse_csr()
 
         # Warn in case of CSC format without gradient computation:
         if src.layout == torch.sparse_csc and not other.requires_grad:
-            warnings.warn(f"Converting sparse tensor to CSR format for more "
-                          f"efficient processing. Consider converting your "
-                          f"sparse tensor to CSR format beforehand to avoid "
-                          f"repeated conversion (got '{src.layout}')")
+            warnings.warn(
+                f"Converting sparse tensor to CSR format for more "
+                f"efficient processing. Consider converting your "
+                f"sparse tensor to CSR format beforehand to avoid "
+                f"repeated conversion (got '{src.layout}')", stacklevel=2)
 
         # Use the default code path for `sum` reduction (works on CPU/GPU):
         if reduce == 'sum':
@@ -99,10 +101,11 @@ def spmm(
         # TODO The `torch.sparse.mm` code path with the `reduce` argument does
         # not yet support CSC :(
         if src.layout == torch.sparse_csc:
-            warnings.warn(f"Converting sparse tensor to CSR format for more "
-                          f"efficient processing. Consider converting your "
-                          f"sparse tensor to CSR format beforehand to avoid "
-                          f"repeated conversion (got '{src.layout}')")
+            warnings.warn(
+                f"Converting sparse tensor to CSR format for more "
+                f"efficient processing. Consider converting your "
+                f"sparse tensor to CSR format beforehand to avoid "
+                f"repeated conversion (got '{src.layout}')", stacklevel=2)
             src = src.to_sparse_csr()
 
         return torch.sparse.mm(src, other, reduce)

torch_geometric/utils/convert.py

@@ -251,13 +251,13 @@ def from_networkx(
     if group_edge_attrs is not None and not isinstance(group_edge_attrs, list):
         group_edge_attrs = edge_attrs
 
-    for i, (_, feat_dict) in enumerate(G.nodes(data=True)):
+    for _, feat_dict in G.nodes(data=True):
         if set(feat_dict.keys()) != set(node_attrs):
             raise ValueError('Not all nodes contain the same attributes')
         for key, value in feat_dict.items():
             data_dict[str(key)].append(value)
 
-    for i, (_, _, feat_dict) in enumerate(G.edges(data=True)):
+    for _, _, feat_dict in G.edges(data=True):
         if set(feat_dict.keys()) != set(edge_attrs):
             raise ValueError('Not all edges contain the same attributes')
         for key, value in feat_dict.items():

torch_geometric/utils/embedding.py

@@ -42,7 +42,8 @@ def get_embeddings(
             hook_handles.append(module.register_forward_hook(hook))
 
     if len(hook_handles) == 0:
-        warnings.warn("The 'model' does not have any 'MessagePassing' layers")
+        warnings.warn("The 'model' does not have any 'MessagePassing' layers",
+                      stacklevel=2)
 
     training = model.training
     model.eval()
@@ -123,8 +124,9 @@ def get_embeddings_hetero(
                 hook_handles.append(module.register_forward_hook(hook))
 
     if len(hook_handles) == 0:
-        warnings.warn("The 'model' does not have any heterogenous "
-                      "'MessagePassing' layers")
+        warnings.warn(
+            "The 'model' does not have any heterogenous "
+            "'MessagePassing' layers", stacklevel=2)
 
     # Run the model forward pass
     training = model.training

torch_geometric/utils/geodesic.py

@@ -66,9 +66,10 @@ def geodesic_distance(  # noqa: D417
 
     if 'dest' in kwargs:
         dst = kwargs['dest']
-        warnings.warn("'dest' attribute in 'geodesic_distance' is deprecated "
-                      "and will be removed in a future release. Use the 'dst' "
-                      "argument instead.")
+        warnings.warn(
+            "'dest' attribute in 'geodesic_distance' is deprecated "
+            "and will be removed in a future release. Use the 'dst' "
+            "argument instead.", stacklevel=2)
 
     max_distance = float('inf') if max_distance is None else max_distance
 

torch_geometric/utils/sparse.py

@@ -70,8 +70,9 @@ def dense_to_sparse(
                          f"three-dimensional (got {adj.dim()} dimensions)")
 
     if mask is not None and adj.dim() == 2:
-        warnings.warn("Mask should not be provided in case the dense "
-                      "adjacency matrix is two-dimensional")
+        warnings.warn(
+            "Mask should not be provided in case the dense "
+            "adjacency matrix is two-dimensional", stacklevel=2)
         mask = None
 
     if mask is not None and mask.dim() != 2: