pyg-nightly 2.7.0.dev20250607__tar.gz → 2.7.0.dev20250609__tar.gz

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250607
+Version: 2.7.0.dev20250609
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>
@@ -58,7 +58,7 @@ Requires-Dist: torch_geometric[graphgym, modelhub] ; extra == "full"
 Requires-Dist: torchmetrics ; extra == "full"
 Requires-Dist: trimesh ; extra == "full"
 Requires-Dist: protobuf<4.21 ; extra == "graphgym"
-Requires-Dist: pytorch-lightning<2.3.0 ; extra == "graphgym"
+Requires-Dist: pytorch-lightning ; extra == "graphgym"
 Requires-Dist: yacs ; extra == "graphgym"
 Requires-Dist: huggingface_hub ; extra == "modelhub"
 Requires-Dist: pcst_fast ; extra == "rag"
@@ -69,6 +69,7 @@ Requires-Dist: sentencepiece ; extra == "rag"
 Requires-Dist: accelerate ; extra == "rag"
 Requires-Dist: onnx ; extra == "test"
 Requires-Dist: onnxruntime ; extra == "test"
+Requires-Dist: onnxscript ; extra == "test"
 Requires-Dist: pytest ; extra == "test"
 Requires-Dist: pytest-cov ; extra == "test"
 Project-URL: changelog, https://github.com/pyg-team/pytorch_geometric/blob/master/CHANGELOG.md

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250607"
+version="2.7.0.dev20250609"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]
@@ -45,7 +45,7 @@ dependencies=[
 [project.optional-dependencies]
 graphgym=[
     "protobuf<4.21",
-    "pytorch-lightning<2.3.0",
+    "pytorch-lightning",
     "yacs",
 ]
 modelhub=[
@@ -69,6 +69,7 @@ rag=[
 test=[
     "onnx",
     "onnxruntime",
+    "onnxscript",
     "pytest",
     "pytest-cov",
 ]
@@ -161,13 +162,6 @@ select = [
     "D",  # pydocstyle
 ]
 ignore = [
-    "B007",  # TODO Don't ignore "Loop control variable `{name}` not used within loop body"
-    "B008",  # TODO Don't ignore "Do not perform function call `{name}` in argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable"
-    "B020",  # TODO Don't ignore "Loop control variable `{name}` overrides iterable it iterates"
-    "B024",  # TODO Don't ignore "`{name}` is an abstract base class, but it has no abstract methods or properties"
-    "B026",  # TODO Don't ignore "Star-arg unpacking after a keyword argument is strongly discouraged"
-    "B027",  # TODO Don't ignore "`{name}` is an empty method in an abstract base class, but has no abstract decorator"
-    "B028",  # TODO Don't ignore "No explicit `stacklevel` keyword argument found"
     "D100",  # TODO Don't ignore "Missing docstring in public module"
     "D101",  # TODO Don't ignore "Missing docstring in public class"
     "D102",  # TODO Don't ignore "Missing docstring in public method"
@@ -207,6 +201,7 @@ filterwarnings = [
     "ignore:.*did not already require gradients, required_grads has been set automatically:UserWarning",
     # Filter `pytorch_lightning` warnings:
     "ignore:GPU available but not used:UserWarning",
+    "error::DeprecationWarning",
 ]
 markers = [
     "rag: mark test as RAG test",

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/__init__.py

@@ -31,7 +31,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250607'
+__version__ = '2.7.0.dev20250609'
 
 __all__ = [
     'Index',
@@ -60,9 +60,10 @@ __all__ = [
 if not torch_geometric.typing.WITH_PT113:
     import warnings as std_warnings
 
-    std_warnings.warn("PyG 2.7 removed support for PyTorch < 1.13. Consider "
-                      "Consider upgrading to PyTorch >= 1.13 or downgrading "
-                      "to PyG <= 2.6. ")
+    std_warnings.warn(
+        "PyG 2.7 removed support for PyTorch < 1.13. Consider "
+        "Consider upgrading to PyTorch >= 1.13 or downgrading "
+        "to PyG <= 2.6. ", stacklevel=2)
 
 # Serialization ###############################################################
 

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/_compile.py

@@ -36,6 +36,7 @@ def compile(
         :meth:`torch_geometric.compile` is deprecated in favor of
         :meth:`torch.compile`.
     """
-    warnings.warn("'torch_geometric.compile' is deprecated in favor of "
-                  "'torch.compile'")
+    warnings.warn(
+        "'torch_geometric.compile' is deprecated in favor of "
+        "'torch.compile'", stacklevel=2)
     return torch.compile(model, *args, **kwargs)  # type: ignore

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/contrib/__init__.py

@@ -7,6 +7,6 @@ import torch_geometric.contrib.explain  # noqa
 
 warnings.warn(
     "'torch_geometric.contrib' contains experimental code and is subject to "
-    "change. Please use with caution.")
+    "change. Please use with caution.", stacklevel=2)
 
 __all__ = []

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/data.py

@@ -850,14 +850,14 @@ class Data(BaseData, FeatureStore, GraphStore):
         # that maps global node indices to local ones in the final
         # heterogeneous graph:
         node_ids, index_map = {}, torch.empty_like(node_type)
-        for i, key in enumerate(node_type_names):
+        for i in range(len(node_type_names)):
             node_ids[i] = (node_type == i).nonzero(as_tuple=False).view(-1)
             index_map[node_ids[i]] = torch.arange(len(node_ids[i]),
                                                   device=index_map.device)
 
         # We iterate over edge types to find the local edge indices:
         edge_ids = {}
-        for i, key in enumerate(edge_type_names):
+        for i in range(len(edge_type_names)):
             edge_ids[i] = (edge_type == i).nonzero(as_tuple=False).view(-1)
 
         data = HeteroData()
@@ -1193,4 +1193,4 @@ def warn_or_raise(msg: str, raise_on_error: bool = True):
     if raise_on_error:
         raise ValueError(msg)
     else:
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=2)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/database.py

@@ -111,13 +111,17 @@ class Database(ABC):
             for key, value in schema_dict.items()
         }
 
+    @abstractmethod
     def connect(self) -> None:
         r"""Connects to the database.
         Databases will automatically connect on instantiation.
         """
+        raise NotImplementedError
 
+    @abstractmethod
     def close(self) -> None:
         r"""Closes the connection to the database."""
+        raise NotImplementedError
 
     @abstractmethod
     def insert(self, index: int, data: Any) -> None:

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/dataset.py

@@ -166,10 +166,11 @@ class Dataset(torch.utils.data.Dataset):
         elif y.numel() == y.size(0) and torch.is_floating_point(y):
             num_classes = torch.unique(y).numel()
             if num_classes > 2:
-                warnings.warn("Found floating-point labels while calling "
-                              "`dataset.num_classes`. Returning the number of "
-                              "unique elements. Please make sure that this "
-                              "is expected before proceeding.")
+                warnings.warn(
+                    "Found floating-point labels while calling "
+                    "`dataset.num_classes`. Returning the number of "
+                    "unique elements. Please make sure that this "
+                    "is expected before proceeding.", stacklevel=2)
             return num_classes
         else:
             return y.size(-1)
@@ -241,7 +242,8 @@ class Dataset(torch.utils.data.Dataset):
                 "The `pre_transform` argument differs from the one used in "
                 "the pre-processed version of this dataset. If you want to "
                 "make use of another pre-processing technique, pass "
-                "`force_reload=True` explicitly to reload the dataset.")
+                "`force_reload=True` explicitly to reload the dataset.",
+                stacklevel=2)
 
         f = osp.join(self.processed_dir, 'pre_filter.pt')
         if osp.exists(f) and torch.load(f, weights_only=False) != _repr(
@@ -250,7 +252,8 @@ class Dataset(torch.utils.data.Dataset):
                 "The `pre_filter` argument differs from the one used in "
                 "the pre-processed version of this dataset. If you want to "
                 "make use of another pre-fitering technique, pass "
-                "`force_reload=True` explicitly to reload the dataset.")
+                "`force_reload=True` explicitly to reload the dataset.",
+                stacklevel=2)
 
         if not self.force_reload and files_exist(self.processed_paths):
             return

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/hetero_data.py

@@ -585,12 +585,13 @@ class HeteroData(BaseData, FeatureStore, GraphStore):
         global _DISPLAYED_TYPE_NAME_WARNING
         if not _DISPLAYED_TYPE_NAME_WARNING and '__' in name:
             _DISPLAYED_TYPE_NAME_WARNING = True
-            warnings.warn(f"There exist type names in the "
-                          f"'{self.__class__.__name__}' object that contain "
-                          f"double underscores '__' (e.g., '{name}'). This "
-                          f"may lead to unexpected behavior. To avoid any "
-                          f"issues, ensure that your type names only contain "
-                          f"single underscores.")
+            warnings.warn(
+                f"There exist type names in the "
+                f"'{self.__class__.__name__}' object that contain "
+                f"double underscores '__' (e.g., '{name}'). This "
+                f"may lead to unexpected behavior. To avoid any "
+                f"issues, ensure that your type names only contain "
+                f"single underscores.", stacklevel=2)
 
     def get_node_store(self, key: NodeType) -> NodeStorage:
         r"""Gets the :class:`~torch_geometric.data.storage.NodeStorage` object

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/hypergraph_data.py

@@ -223,4 +223,4 @@ def warn_or_raise(msg: str, raise_on_error: bool = True) -> None:
     if raise_on_error:
         raise ValueError(msg)
     else:
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=2)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/in_memory_dataset.py

@@ -297,7 +297,7 @@ class InMemoryDataset(Dataset):
             self._data_list = None
         msg += f' {msg4}'
 
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=2)
 
         return self._data
 
@@ -346,7 +346,7 @@ class InMemoryDataset(Dataset):
 
 def nested_iter(node: Union[Mapping, Sequence]) -> Iterable:
     if isinstance(node, Mapping):
-        for key, value in node.items():
+        for value in node.values():
             yield from nested_iter(value)
     elif isinstance(node, Sequence):
         yield from enumerate(node)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/large_graph_indexer.py

@@ -141,7 +141,7 @@ class LargeGraphIndexer:
                 self.edge_attr[default_key] = list()
             self.edge_attr[EDGE_PID] = edges
 
-            for i, tup in enumerate(edges):
+            for tup in edges:
                 h, r, t = tup
                 self.edge_attr[EDGE_HEAD].append(h)
                 self.edge_attr[EDGE_RELATION].append(r)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/lightning/datamodule.py

@@ -40,9 +40,11 @@ class LightningDataModule(PLLightningDataModule):
                           kwargs.get('num_workers', 0) > 0)
 
         if 'shuffle' in kwargs:
-            warnings.warn(f"The 'shuffle={kwargs['shuffle']}' option is "
-                          f"ignored in '{self.__class__.__name__}'. Remove it "
-                          f"from the argument list to disable this warning")
+            warnings.warn(
+                f"The 'shuffle={kwargs['shuffle']}' option is "
+                f"ignored in '{self.__class__.__name__}'. Remove it "
+                f"from the argument list to disable this warning",
+                stacklevel=2)
             del kwargs['shuffle']
 
         self.kwargs = kwargs
@@ -74,34 +76,39 @@ class LightningData(LightningDataModule):
             raise ValueError(f"Undefined 'loader' option (got '{loader}')")
 
         if loader == 'full' and kwargs['batch_size'] != 1:
-            warnings.warn(f"Re-setting 'batch_size' to 1 in "
-                          f"'{self.__class__.__name__}' for loader='full' "
-                          f"(got '{kwargs['batch_size']}')")
+            warnings.warn(
+                f"Re-setting 'batch_size' to 1 in "
+                f"'{self.__class__.__name__}' for loader='full' "
+                f"(got '{kwargs['batch_size']}')", stacklevel=2)
             kwargs['batch_size'] = 1
 
         if loader == 'full' and kwargs['num_workers'] != 0:
-            warnings.warn(f"Re-setting 'num_workers' to 0 in "
-                          f"'{self.__class__.__name__}' for loader='full' "
-                          f"(got '{kwargs['num_workers']}')")
+            warnings.warn(
+                f"Re-setting 'num_workers' to 0 in "
+                f"'{self.__class__.__name__}' for loader='full' "
+                f"(got '{kwargs['num_workers']}')", stacklevel=2)
             kwargs['num_workers'] = 0
 
         if loader == 'full' and kwargs.get('sampler') is not None:
-            warnings.warn("'sampler' option is not supported for "
-                          "loader='full'")
+            warnings.warn(
+                "'sampler' option is not supported for "
+                "loader='full'", stacklevel=2)
             kwargs.pop('sampler', None)
 
         if loader == 'full' and kwargs.get('batch_sampler') is not None:
-            warnings.warn("'batch_sampler' option is not supported for "
-                          "loader='full'")
+            warnings.warn(
+                "'batch_sampler' option is not supported for "
+                "loader='full'", stacklevel=2)
             kwargs.pop('batch_sampler', None)
 
         super().__init__(has_val, has_test, **kwargs)
 
         if loader == 'full':
             if kwargs.get('pin_memory', False):
-                warnings.warn(f"Re-setting 'pin_memory' to 'False' in "
-                              f"'{self.__class__.__name__}' for loader='full' "
-                              f"(got 'True')")
+                warnings.warn(
+                    f"Re-setting 'pin_memory' to 'False' in "
+                    f"'{self.__class__.__name__}' for loader='full' "
+                    f"(got 'True')", stacklevel=2)
             self.kwargs['pin_memory'] = False
 
         self.data = data
@@ -127,10 +134,11 @@ class LightningData(LightningDataModule):
                 graph_sampler.__class__,
             )
             if len(sampler_kwargs) > 0:
-                warnings.warn(f"Ignoring the arguments "
-                              f"{list(sampler_kwargs.keys())} in "
-                              f"'{self.__class__.__name__}' since a custom "
-                              f"'graph_sampler' was passed")
+                warnings.warn(
+                    f"Ignoring the arguments "
+                    f"{list(sampler_kwargs.keys())} in "
+                    f"'{self.__class__.__name__}' since a custom "
+                    f"'graph_sampler' was passed", stacklevel=2)
             self.graph_sampler = graph_sampler
 
         else:

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/data/storage.py

@@ -454,7 +454,7 @@ class NodeStorage(BaseStorage):
             f"'{set(self.keys())}'. Please explicitly set 'num_nodes' as an "
             f"attribute of " +
             ("'data'" if self._key is None else f"'data[{self._key}]'") +
-            " to suppress this warning")
+            " to suppress this warning", stacklevel=2)
         if 'edge_index' in self and isinstance(self.edge_index, Tensor):
             if self.edge_index.numel() > 0:
                 return int(self.edge_index.max()) + 1

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/datasets/dbp15k.py

@@ -73,7 +73,7 @@ class DBP15K(InMemoryDataset):
     def process(self) -> None:
         embs = {}
         with open(osp.join(self.raw_dir, 'sub.glove.300d')) as f:
-            for i, line in enumerate(f):
+            for line in f:
                 info = line.strip().split(' ')
                 if len(info) > 300:
                     embs[info[0]] = torch.tensor([float(x) for x in info[1:]])

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/datasets/molecule_net.py

@@ -210,8 +210,9 @@ class MoleculeNet(InMemoryDataset):
             data.y = y
 
             if data.num_nodes == 0:
-                warnings.warn(f"Skipping molecule '{smiles}' since it "
-                              f"resulted in zero atoms")
+                warnings.warn(
+                    f"Skipping molecule '{smiles}' since it "
+                    f"resulted in zero atoms", stacklevel=2)
                 continue
 
             if self.pre_filter is not None and not self.pre_filter(data):

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/datasets/tag_dataset.py

@@ -128,7 +128,7 @@ class TAGDataset(InMemoryDataset):
     @property
     def raw_file_names(self) -> List[str]:
         file_names = []
-        for root, _, files in os.walk(osp.join(self.root, 'raw')):
+        for _, _, files in os.walk(osp.join(self.root, 'raw')):
             for file in files:
                 file_names.append(file)
         return file_names

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/datasets/wikics.py

@@ -45,7 +45,8 @@ class WikiCS(InMemoryDataset):
             warnings.warn(
                 f"The {self.__class__.__name__} dataset now returns an "
                 f"undirected graph by default. Please explicitly specify "
-                f"'is_undirected=False' to restore the old behavior.")
+                f"'is_undirected=False' to restore the old behavior.",
+                stacklevel=2)
             is_undirected = True
         self.is_undirected = is_undirected
         super().__init__(root, transform, pre_transform,

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/deprecation.py

@@ -23,7 +23,7 @@ def deprecated(
             out = f"'{name}' is deprecated"
             if details is not None:
                 out += f", {details}"
-            warnings.warn(out)
+            warnings.warn(out, stacklevel=2)
             return func(*args, **kwargs)
 
         return wrapper

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/distributed/rpc.py

@@ -92,7 +92,7 @@ def shutdown_rpc(id: str = None, graceful: bool = True,
 class RPCRouter:
     r"""A router to get the worker based on the partition ID."""
     def __init__(self, partition_to_workers: List[List[str]]):
-        for pid, rpc_worker_list in enumerate(partition_to_workers):
+        for rpc_worker_list in partition_to_workers:
             if len(rpc_worker_list) == 0:
                 raise ValueError('No RPC worker is in worker list')
         self.partition_to_workers = partition_to_workers
@@ -120,7 +120,7 @@ def rpc_partition_to_workers(
     partition_to_workers = [[] for _ in range(num_partitions)]
     gathered_results = global_all_gather(
         (ctx.role, num_partitions, current_partition_idx))
-    for worker_name, (role, nparts, idx) in gathered_results.items():
+    for worker_name, (_, _, idx) in gathered_results.items():
         partition_to_workers[idx].append(worker_name)
     return partition_to_workers
 

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/explain/algorithm/captum_explainer.py

@@ -73,7 +73,8 @@ class CaptumExplainer(ExplainerAlgorithm):
                              f"{self.attribution_method_class.__name__}")
 
         if kwargs.get('internal_batch_size', 1) != 1:
-            warnings.warn("Overriding 'internal_batch_size' to 1")
+            warnings.warn("Overriding 'internal_batch_size' to 1",
+                          stacklevel=2)
 
         if 'internal_batch_size' in self._get_attribute_parameters():
             kwargs['internal_batch_size'] = 1

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/explain/algorithm/graphmask_explainer.py

@@ -202,25 +202,25 @@ class GraphMaskExplainer(ExplainerAlgorithm):
 
         baselines, self.gates, full_biases = [], torch.nn.ModuleList(), []
 
-        for v_dim, m_dim, h_dim in zip(i_dim, j_dim, h_dim):
+        for v_dim, m_dim, o_dim in zip(i_dim, j_dim, h_dim):
             self.transform, self.layer_norm = [], []
             input_dims = [v_dim, m_dim, v_dim]
             for _, input_dim in enumerate(input_dims):
                 self.transform.append(
-                    Linear(input_dim, h_dim, bias=False).to(device))
-                self.layer_norm.append(LayerNorm(h_dim).to(device))
+                    Linear(input_dim, o_dim, bias=False).to(device))
+                self.layer_norm.append(LayerNorm(o_dim).to(device))
 
             self.transforms = torch.nn.ModuleList(self.transform)
             self.layer_norms = torch.nn.ModuleList(self.layer_norm)
 
             self.full_bias = Parameter(
-                torch.tensor(h_dim, dtype=torch.float, device=device))
+                torch.tensor(o_dim, dtype=torch.float, device=device))
             full_biases.append(self.full_bias)
 
-            self.reset_parameters(input_dims, h_dim)
+            self.reset_parameters(input_dims, o_dim)
 
             self.non_linear = ReLU()
-            self.output_layer = Linear(h_dim, 1).to(device)
+            self.output_layer = Linear(o_dim, 1).to(device)
 
             gate = [
                 self.transforms, self.layer_norms, self.non_linear,
@@ -385,7 +385,7 @@ class GraphMaskExplainer(ExplainerAlgorithm):
                         f'Train explainer for graph {index} with layer '
                         f'{layer}')
             self._enable_layer(layer)
-            for epoch in range(self.epochs):
+            for _ in range(self.epochs):
                 with torch.no_grad():
                     model(x, edge_index, **kwargs)
                 gates, total_penalty = [], 0

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/explain/explainer.py

@@ -192,7 +192,7 @@ class Explainer:
             if target is not None:
                 warnings.warn(
                     f"The 'target' should not be provided for the explanation "
-                    f"type '{self.explanation_type.value}'")
+                    f"type '{self.explanation_type.value}'", stacklevel=2)
             prediction = self.get_prediction(x, edge_index, **kwargs)
             target = self.get_target(prediction)
 

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/graphgym/config.py

@@ -16,8 +16,9 @@ try:  # Define global config object
     cfg = CN()
 except ImportError:
     cfg = None
-    warnings.warn("Could not define global config object. Please install "
-                  "'yacs' via 'pip install yacs' in order to use GraphGym")
+    warnings.warn(
+        "Could not define global config object. Please install "
+        "'yacs' via 'pip install yacs' in order to use GraphGym", stacklevel=2)
 
 
 def set_cfg(cfg):

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/graphgym/imports.py

@@ -11,5 +11,7 @@ except ImportError:
     LightningModule = torch.nn.Module
     Callback = object
 
-    warnings.warn("Please install 'pytorch_lightning' via  "
-                  "'pip install pytorch_lightning' in order to use GraphGym")
+    warnings.warn(
+        "Please install 'pytorch_lightning' via  "
+        "'pip install pytorch_lightning' in order to use GraphGym",
+        stacklevel=2)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/graphgym/logger.py

@@ -239,7 +239,7 @@ def create_logger():
     r"""Create logger for the experiment."""
     loggers = []
     names = ['train', 'val', 'test']
-    for i, dataset in enumerate(range(cfg.share.num_splits)):
+    for i, _ in enumerate(range(cfg.share.num_splits)):
         loggers.append(Logger(name=names[i], task_type=infer_task()))
     return loggers
 

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/graphgym/models/encoder.py

@@ -53,7 +53,7 @@ class AtomEncoder(torch.nn.Module):
 
         self.atom_embedding_list = torch.nn.ModuleList()
 
-        for i, dim in enumerate(get_atom_feature_dims()):
+        for dim in get_atom_feature_dims():
             emb = torch.nn.Embedding(dim, emb_dim)
             torch.nn.init.xavier_uniform_(emb.weight.data)
             self.atom_embedding_list.append(emb)
@@ -87,7 +87,7 @@ class BondEncoder(torch.nn.Module):
 
         self.bond_embedding_list = torch.nn.ModuleList()
 
-        for i, dim in enumerate(get_bond_feature_dims()):
+        for dim in get_bond_feature_dims():
             emb = torch.nn.Embedding(dim, emb_dim)
             torch.nn.init.xavier_uniform_(emb.weight.data)
             self.bond_embedding_list.append(emb)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/hash_tensor.py

@@ -69,10 +69,11 @@ def get_hash_map(key: Tensor) -> Union[CPUHashMap, CUDAHashMap]:
         return CUDAHashMap(key, 0.5)
 
     if key.is_cuda:
-        warnings.warn("Fallback to CPU-based mapping algorithm which may "
-                      "cause slowdowns and device synchronization. Please "
-                      "install 'pyg-lib' for an accelerated 'HashTensor' "
-                      "implementation.")
+        warnings.warn(
+            "Fallback to CPU-based mapping algorithm which may "
+            "cause slowdowns and device synchronization. Please "
+            "install 'pyg-lib' for an accelerated 'HashTensor' "
+            "implementation.", stacklevel=2)
 
     if torch_geometric.typing.WITH_CPU_HASH_MAP:
         return CPUHashMap(key.cpu(), -1)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/io/fs.py

@@ -226,11 +226,12 @@ def torch_load(path: str, map_location: Any = None) -> Any:
                             "compatible in your case.")
                 match = re.search(r'add_safe_globals\(.*?\)', error_msg)
                 if match is not None:
-                    warnings.warn(f"{warn_msg} Please use "
-                                  f"`torch.serialization.{match.group()}` to "
-                                  f"allowlist this global.")
+                    warnings.warn(
+                        f"{warn_msg} Please use "
+                        f"`torch.serialization.{match.group()}` to "
+                        f"allowlist this global.", stacklevel=2)
                 else:
-                    warnings.warn(warn_msg)
+                    warnings.warn(warn_msg, stacklevel=2)
 
                 with fsspec.open(path, 'rb') as f:
                     return torch.load(f, map_location, weights_only=False)

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/loader/ibmb_loader.py

@@ -148,7 +148,7 @@ def indices_complete_check(
         if isinstance(aux, Tensor):
             aux = aux.cpu().numpy()
 
-        assert np.all(np.in1d(out,
+        assert np.all(np.isin(out,
                               aux)), "Not all output nodes are in aux nodes!"
         outs.append(out)
 
@@ -236,7 +236,7 @@ def create_batchwise_out_aux_pairs(
             logits[tele_set, i] = 1. / len(tele_set)
 
         new_logits = logits.clone()
-        for i in range(num_iter):
+        for _ in range(num_iter):
             new_logits = adj @ new_logits * (1 - alpha) + alpha * logits
 
         inds = new_logits.argsort(0)
@@ -498,7 +498,7 @@ class IBMBBaseLoader(torch.utils.data.DataLoader):
             assert adj is not None
 
         for out, aux in pbar:
-            mask = torch.from_numpy(np.in1d(aux, out))
+            mask = torch.from_numpy(np.isin(aux, out))
             if isinstance(aux, np.ndarray):
                 aux = torch.from_numpy(aux)
             subg = get_subgraph(aux, graph, return_edge_index_type, adj,
@@ -541,7 +541,7 @@ class IBMBBaseLoader(torch.utils.data.DataLoader):
         out, aux = zip(*data_list)
         out = np.concatenate(out)
         aux = np.unique(np.concatenate(aux))
-        mask = torch.from_numpy(np.in1d(aux, out))
+        mask = torch.from_numpy(np.isin(aux, out))
         aux = torch.from_numpy(aux)
 
         subg = get_subgraph(aux, self.graph, self.return_edge_index_type,

{pyg_nightly-2.7.0.dev20250607 → pyg_nightly-2.7.0.dev20250609}/torch_geometric/loader/mixin.py

@@ -248,7 +248,8 @@ class AffinityMixin:
             warnings.warn(
                 "Due to conflicting parallelization methods it is not advised "
                 "to use affinitization with 'HeteroData' datasets. "
-                "Use `enable_multithreading` for better performance.")
+                "Use `enable_multithreading` for better performance.",
+                stacklevel=2)
 
         self.loader_cores = loader_cores[:] if loader_cores else None
         if self.loader_cores is None: