pyg-nightly 2.7.0.dev20250825__tar.gz → 2.7.0.dev20250827__tar.gz

{pyg_nightly-2.7.0.dev20250825 → pyg_nightly-2.7.0.dev20250827}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250825
+Version: 2.7.0.dev20250827
 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>

{pyg_nightly-2.7.0.dev20250825 → pyg_nightly-2.7.0.dev20250827}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250825"
+version="2.7.0.dev20250827"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]

{pyg_nightly-2.7.0.dev20250825 → pyg_nightly-2.7.0.dev20250827}/torch_geometric/__init__.py

@@ -4,7 +4,7 @@ import torch
 import torch_geometric.typing
 
 from ._compile import compile, is_compiling
-from ._onnx import is_in_onnx_export
+from ._onnx import is_in_onnx_export, safe_onnx_export
 from .index import Index
 from .edge_index import EdgeIndex
 from .hash_tensor import HashTensor
@@ -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.dev20250825'
+__version__ = '2.7.0.dev20250827'
 
 __all__ = [
     'Index',
@@ -43,6 +43,7 @@ __all__ = [
     'compile',
     'is_compiling',
     'is_in_onnx_export',
+    'safe_onnx_export',
     'is_mps_available',
     'is_xpu_available',
     'device',

pyg_nightly-2.7.0.dev20250827/torch_geometric/_onnx.py

@@ -0,0 +1,228 @@
+import warnings
+from os import PathLike
+from typing import Any, Union
+
+import torch
+
+from torch_geometric import is_compiling
+
+
+def is_in_onnx_export() -> bool:
+    r"""Returns :obj:`True` in case :pytorch:`PyTorch` is exporting to ONNX via
+    :meth:`torch.onnx.export`.
+    """
+    if is_compiling():
+        return False
+    if torch.jit.is_scripting():
+        return False
+    return torch.onnx.is_in_onnx_export()
+
+
+def safe_onnx_export(
+    model: torch.nn.Module,
+    args: Union[torch.Tensor, tuple[Any, ...]],
+    f: Union[str, PathLike[Any], None],
+    skip_on_error: bool = False,
+    **kwargs: Any,
+) -> bool:
+    r"""A safe wrapper around :meth:`torch.onnx.export` that handles known
+    ONNX serialization issues in PyTorch Geometric.
+
+    This function provides workarounds for the ``onnx_ir.serde.SerdeError``
+    with boolean ``allowzero`` attributes that occurs in certain environments.
+
+    Args:
+        model (torch.nn.Module): The model to export.
+        args (torch.Tensor or tuple): The input arguments for the model.
+        f (str or PathLike): The file path to save the model.
+        skip_on_error (bool): If True, return False instead of raising when
+            workarounds fail. Useful for CI environments.
+        **kwargs: Additional arguments passed to :meth:`torch.onnx.export`.
+
+    Returns:
+        bool: True if export succeeded, False if skipped due to known issues
+              (only when skip_on_error=True).
+
+    Example:
+        >>> from torch_geometric.nn import SAGEConv
+        >>> from torch_geometric import safe_onnx_export
+        >>>
+        >>> class MyModel(torch.nn.Module):
+        ...     def __init__(self):
+        ...         super().__init__()
+        ...         self.conv = SAGEConv(8, 16)
+        ...     def forward(self, x, edge_index):
+        ...         return self.conv(x, edge_index)
+        >>>
+        >>> model = MyModel()
+        >>> x = torch.randn(3, 8)
+        >>> edge_index = torch.tensor([[0, 1, 2], [1, 0, 2]])
+        >>> success = safe_onnx_export(model, (x, edge_index), 'model.onnx')
+        >>>
+        >>> # For CI environments:
+        >>> success = safe_onnx_export(model, (x, edge_index), 'model.onnx',
+        ...                             skip_on_error=True)
+        >>> if not success:
+        ...     print("ONNX export skipped due to known upstream issue")
+    """
+    # Convert single tensor to tuple for torch.onnx.export compatibility
+    if isinstance(args, torch.Tensor):
+        args = (args, )
+
+    try:
+        # First attempt: standard ONNX export
+        torch.onnx.export(model, args, f, **kwargs)
+        return True
+
+    except Exception as e:
+        error_str = str(e)
+        error_type = type(e).__name__
+
+        # Check for the specific onnx_ir.serde.SerdeError patterns
+        is_allowzero_error = (('onnx_ir.serde.SerdeError' in error_str
+                               and 'allowzero' in error_str) or
+                              'ValueError: Value out of range: 1' in error_str
+                              or 'serialize_model_into' in error_str
+                              or 'serialize_attribute_into' in error_str)
+
+        if is_allowzero_error:
+            warnings.warn(
+                f"Encountered known ONNX serialization issue ({error_type}). "
+                "This is likely the allowzero boolean attribute bug. "
+                "Attempting workaround...", UserWarning, stacklevel=2)
+
+            # Apply workaround strategies
+            return _apply_onnx_allowzero_workaround(model, args, f,
+                                                    skip_on_error, **kwargs)
+
+        else:
+            # Re-raise other errors
+            raise
+
+
+def _apply_onnx_allowzero_workaround(
+    model: torch.nn.Module,
+    args: tuple[Any, ...],
+    f: Union[str, PathLike[Any], None],
+    skip_on_error: bool = False,
+    **kwargs: Any,
+) -> bool:
+    r"""Apply workaround strategies for onnx_ir.serde.SerdeError with allowzero
+    attributes.
+
+    Returns:
+        bool: True if export succeeded, False if skipped (when
+              skip_on_error=True).
+    """
+    # Strategy 1: Try without dynamo if it was enabled
+    if kwargs.get('dynamo', False):
+        try:
+            kwargs_no_dynamo = kwargs.copy()
+            kwargs_no_dynamo['dynamo'] = False
+
+            warnings.warn(
+                "Retrying ONNX export with dynamo=False as workaround",
+                UserWarning, stacklevel=3)
+
+            torch.onnx.export(model, args, f, **kwargs_no_dynamo)
+            return True
+
+        except Exception:
+            pass
+
+    # Strategy 2: Try with different opset versions
+    original_opset = kwargs.get('opset_version', 18)
+    for opset_version in [17, 16, 15, 14, 13, 11]:
+        if opset_version != original_opset:
+            try:
+                kwargs_opset = kwargs.copy()
+                kwargs_opset['opset_version'] = opset_version
+
+                warnings.warn(
+                    f"Retrying ONNX export with opset_version={opset_version}",
+                    UserWarning, stacklevel=3)
+
+                torch.onnx.export(model, args, f, **kwargs_opset)
+                return True
+
+            except Exception:
+                continue
+
+    # Strategy 3: Try legacy export (non-dynamo with older opset)
+    try:
+        kwargs_legacy = kwargs.copy()
+        kwargs_legacy['dynamo'] = False
+        kwargs_legacy['opset_version'] = 11
+
+        warnings.warn(
+            "Retrying ONNX export with legacy settings "
+            "(dynamo=False, opset_version=11)", UserWarning, stacklevel=3)
+
+        torch.onnx.export(model, args, f, **kwargs_legacy)
+        return True
+
+    except Exception:
+        pass
+
+    # Strategy 4: Try with minimal settings
+    try:
+        minimal_kwargs: dict[str, Any] = {
+            'opset_version': 11,
+            'dynamo': False,
+        }
+        # Add optional parameters if they exist
+        if kwargs.get('input_names') is not None:
+            minimal_kwargs['input_names'] = kwargs.get('input_names')
+        if kwargs.get('output_names') is not None:
+            minimal_kwargs['output_names'] = kwargs.get('output_names')
+
+        warnings.warn(
+            "Retrying ONNX export with minimal settings as last resort",
+            UserWarning, stacklevel=3)
+
+        torch.onnx.export(model, args, f, **minimal_kwargs)
+        return True
+
+    except Exception:
+        pass
+
+    # If all strategies fail, handle based on skip_on_error flag
+    import os
+    pytest_detected = 'PYTEST_CURRENT_TEST' in os.environ or 'pytest' in str(f)
+
+    if skip_on_error:
+        # For CI environments: skip gracefully instead of failing
+        warnings.warn(
+            "ONNX export skipped due to known upstream issue "
+            "(onnx_ir.serde.SerdeError). "
+            "This is caused by a bug in the onnx_ir package where boolean "
+            "allowzero attributes cannot be serialized. All workarounds "
+            "failed. Consider updating packages: pip install --upgrade onnx "
+            "onnxscript "
+            "onnx_ir", UserWarning, stacklevel=3)
+        return False
+
+    # For regular usage: provide detailed error message
+    error_msg = (
+        "Failed to export model to ONNX due to known serialization issue. "
+        "This is caused by a bug in the onnx_ir package where boolean "
+        "allowzero attributes cannot be serialized. "
+        "Workarounds attempted: dynamo=False, multiple opset versions, "
+        "and legacy export. ")
+
+    if pytest_detected:
+        error_msg += (
+            "\n\nThis error commonly occurs in pytest environments. "
+            "Try one of these solutions:\n"
+            "1. Run the export outside of pytest (in a regular Python "
+            "script)\n"
+            "2. Update packages: pip install --upgrade onnx onnxscript "
+            "onnx_ir\n"
+            "3. Use torch.jit.script() instead of ONNX export for testing\n"
+            "4. Use safe_onnx_export(..., skip_on_error=True) to skip "
+            "gracefully in CI")
+    else:
+        error_msg += ("\n\nTry updating packages: pip install --upgrade onnx "
+                      "onnxscript onnx_ir")
+
+    raise RuntimeError(error_msg)

{pyg_nightly-2.7.0.dev20250825 → pyg_nightly-2.7.0.dev20250827}/torch_geometric/loader/link_neighbor_loader.py

@@ -170,6 +170,7 @@ class LinkNeighborLoader(LinkLoader):
             negative sampling mode.
             If set to :obj:`None`, no negative sampling strategy is applied.
             (default: :obj:`None`)
+            For example use obj:`neg_sampling=dict(mode= 'binary', amount=0.5)`
         neg_sampling_ratio (int or float, optional): The ratio of sampled
             negative edges to the number of positive edges.
             Deprecated in favor of the :obj:`neg_sampling` argument.

{pyg_nightly-2.7.0.dev20250825 → pyg_nightly-2.7.0.dev20250827}/torch_geometric/nn/models/__init__.py

@@ -34,7 +34,9 @@ from .git_mol import GITMol
 from .molecule_gpt import MoleculeGPT
 from .protein_mpnn import ProteinMPNN
 from .glem import GLEM
+from .lpformer import LPFormer
 from .sgformer import SGFormer
+
 from .polynormer import Polynormer
 # Deprecated:
 from torch_geometric.explain.algorithm.captum import (to_captum_input,
@@ -90,6 +92,7 @@ __all__ = classes = [
     'MoleculeGPT',
     'ProteinMPNN',
     'GLEM',
+    'LPFormer',
     'SGFormer',
     'Polynormer',
     'ARLinkPredictor',