pyg-nightly 2.7.0.dev20250825__py3-none-any.whl → 2.7.0.dev20250827__py3-none-any.whl

{pyg_nightly-2.7.0.dev20250825.dist-info → pyg_nightly-2.7.0.dev20250827.dist-info}/METADATA

@@ -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.dist-info → pyg_nightly-2.7.0.dev20250827.dist-info}/RECORD

@@ -1,6 +1,6 @@
-torch_geometric/__init__.py,sha256=gW8Oh8YbJkaHeP3GCMHrya4iUQRSM5J_66CaZtNpvKQ,2250
+torch_geometric/__init__.py,sha256=zrScFs8nlSfWgDBBpXpfkFiUoXxIN10YeQdNHNX4kIw,2292
 torch_geometric/_compile.py,sha256=9yqMTBKatZPr40WavJz9FjNi7pQj8YZAZOyZmmRGXgc,1351
-torch_geometric/_onnx.py,sha256=V9ffrIKSqhDw6xUZ12lkuSfNs48cQp2EeJ6Z19GfnVw,349
+torch_geometric/_onnx.py,sha256=ODB_8cwFUiwBUjngXn6-K5HHb7IDul7DDXuuGX7vj_0,8178
 torch_geometric/backend.py,sha256=lVaf7aLoVaB3M-UcByUJ1G4T4FOK6LXAg0CF4W3E8jo,1575
 torch_geometric/config_mixin.py,sha256=hOTJu5LLVrEAZ6Pjt4ScLDLKv9aHbfAzF_3ufwKgO4I,4301
 torch_geometric/config_store.py,sha256=zdMzlgBpUmBkPovpYQh5fMNwTZLDq2OneqX47QEx7zk,16818
@@ -281,7 +281,7 @@ torch_geometric/loader/hgt_loader.py,sha256=1gjYFzn3rU4BlAozRWI0eefUfmi5XC5y6YXq
 torch_geometric/loader/ibmb_loader.py,sha256=6OAP_R1tK1Le5MCBYqtZPD0RFsDhfIXDnhgjmlXTAzw,31444
 torch_geometric/loader/imbalanced_sampler.py,sha256=clPERglHRk5SyeFevDrgezYFl7ir975OVFMyJwOV090,3754
 torch_geometric/loader/link_loader.py,sha256=XIYgwo5do_70r-wKQLTKTpET85DMCrEeC3fuKH5xOVQ,16208
-torch_geometric/loader/link_neighbor_loader.py,sha256=HdZifaJI3b0M11Og8m7ztY9YobkE_7fz8aY-dc4QyaM,14384
+torch_geometric/loader/link_neighbor_loader.py,sha256=0KjvWNYeGyrLOrpqITat6WF925zw6BO08T6CAkJhw58,14464
 torch_geometric/loader/mixin.py,sha256=_2sHZt3rkuWR2iqFMxnz4G9oscR2bt5q7y1hZahlOqY,10976
 torch_geometric/loader/neighbor_loader.py,sha256=vnLn_RhBKTux5h8pi0vzj0d7JPoOpLA3n3vjyIWv9lo,12452
 torch_geometric/loader/neighbor_sampler.py,sha256=mraVFXIIGctYot4Xr2VOAhCKAOQyW2gP9KROf7g6tcc,8497
@@ -432,7 +432,7 @@ torch_geometric/nn/kge/distmult.py,sha256=dGQ0bVzjreZgFN1lXE23_IIidsiOq7ehPrMb-N
 torch_geometric/nn/kge/loader.py,sha256=5Uc1j3OUMQnBYSHDqL7pLCty1siFLzoPkztigYO2zP8,771
 torch_geometric/nn/kge/rotate.py,sha256=XLuO1AbyTt5cJxr97ZzoyAyIEsHKesgW5TvDmnGJAao,3208
 torch_geometric/nn/kge/transe.py,sha256=jlejq5BLMm-sb1wWcLDp7pZqCdelWBgjDIC8ctbjSdU,3088
-torch_geometric/nn/models/__init__.py,sha256=71Hqc-ZMfCKn9lelFYDjpHXapbEa0wqVAd2OXCb1y5o,2448
+torch_geometric/nn/models/__init__.py,sha256=2INurndMehxviZcdD7REV7qnIaLJ9AXdnNvcwqa00HM,2496
 torch_geometric/nn/models/attentive_fp.py,sha256=1z3iTV2O5W9tqHFAdno8FeBFeXmuG-TDZk4lwwVh3Ac,6634
 torch_geometric/nn/models/attract_repel.py,sha256=h9OyogT0NY0xiT0DkpJHMxH6ZUmo8R-CmwZdKEwq8Ek,5277
 torch_geometric/nn/models/autoencoder.py,sha256=nGje-zty78Y3hxOJ9o0_6QziJjOvBlknk6z0_fDQwQU,10770
@@ -454,6 +454,7 @@ torch_geometric/nn/models/jumping_knowledge.py,sha256=9JR2EoViXKjcDSLb8tjJm-UHfv
 torch_geometric/nn/models/label_prop.py,sha256=6XYBKp7OLmUgcn-73jXXpYZpef9Za1m0gI9QLv2bMEw,3908
 torch_geometric/nn/models/lightgcn.py,sha256=dXKiBvM96jGKLtYp4l90Fko4he0kKdR9fRw-0ZCqSrA,12466
 torch_geometric/nn/models/linkx.py,sha256=BOWGdJ7rJxk4P0XrIy316vyw8PZabbUAK2XKbwYPMQw,5812
+torch_geometric/nn/models/lpformer.py,sha256=XjXr-w-QlMl_2ioBGWA1ph2tgt4xrl3umT4zXNpB-Ks,29706
 torch_geometric/nn/models/mask_label.py,sha256=B2HcL6ZkaUEo3a8nebZoUqEIfDEfcIGOV56sEmNgOxQ,2580
 torch_geometric/nn/models/meta.py,sha256=lQWovjdQgTGT_rDAm6L186ObINeQCD9tLBz8xenmrF0,6540
 torch_geometric/nn/models/metapath2vec.py,sha256=jwpEwVUnt9uWcriVfyX1BVCzXOqKpnDVsPQSxJAGoBQ,10788
@@ -518,11 +519,11 @@ torch_geometric/profile/nvtx.py,sha256=AKBr-rqlHDnls_UM02Dfq5BZmyFTHS5Li5gaeKmsA
 torch_geometric/profile/profile.py,sha256=cHCY4U0XtyqyKC5u380q6TspsOZ5tGHNXaZsKuzYi1A,11793
 torch_geometric/profile/profiler.py,sha256=rfNciRzWDka_BgO6aPFi3cy8mcT4lSgFWy-WfPgI2SI,16891
 torch_geometric/profile/utils.py,sha256=ynlUVemNJZ6XjJKIkPJNwFPoUyBgVAnchfHBpKOp_HE,5903
-torch_geometric/sampler/__init__.py,sha256=0h_xJ7CQnlTxF5hUpc81WPQ0QaBtouG8eKK1RzPGA-s,512
-torch_geometric/sampler/base.py,sha256=0z5e6DYqUGa1-eyJKUGCyUJe6T-DoKBVpOdNxD-dOzM,29225
+torch_geometric/sampler/__init__.py,sha256=NsAvP6S9wfR0Dsc1d5tR7fj5owRlARRUj3RuUeh8ydg,578
+torch_geometric/sampler/base.py,sha256=GifHECotqBrD82yeqFHuW67MyTB7djN3ejHEkqR3GNI,41187
 torch_geometric/sampler/hgt_sampler.py,sha256=jizRJyEoz4WBOEELuqdytG2hB3UpVQX7yVPM83kvpfE,2991
-torch_geometric/sampler/neighbor_sampler.py,sha256=GBnIwPF5pf85wDo_FaMKtMgBlQhzRx5ysiAomMNhCrQ,34092
-torch_geometric/sampler/utils.py,sha256=U4XGCEBX6rhmKHpCwYjskNvKNnRTXb9GeVKR1vSWuvA,7250
+torch_geometric/sampler/neighbor_sampler.py,sha256=hH8mSbdlq5J9ijFrO_qlkY-1hodhUzaxyFnx_BsEkGQ,45450
+torch_geometric/sampler/utils.py,sha256=vZU--z8OELmV1pqnUA2Xn56HmAt4eUD8R4m8izJGfxk,8571
 torch_geometric/testing/__init__.py,sha256=m3yp_5UnCAxVgzTFofpiVt0vdbl5GwVAve8WTrAaNxo,1319
 torch_geometric/testing/asserts.py,sha256=DLC9HnBgFWuTIiQs2OalsQcXGhOVG-e6R99IWhkO32c,4606
 torch_geometric/testing/data.py,sha256=O1qo8FyNxt6RGf63Ys3eXBfa5RvYydeZLk74szrez3c,2604
@@ -645,7 +646,7 @@ torch_geometric/utils/undirected.py,sha256=H_nfpI0_WluOG6VfjPyldvcjL4w5USAKWu2x5
 torch_geometric/visualization/__init__.py,sha256=b-HnVesXjyJ_L1N-DnjiRiRVf7lhwKaBQF_2i5YMVSU,208
 torch_geometric/visualization/graph.py,sha256=mfZHXYfiU-CWMtfawYc80IxVwVmtK9hbIkSKhM_j7oI,14311
 torch_geometric/visualization/influence.py,sha256=CWMvuNA_Nf1sfbJmQgn58yS4OFpeKXeZPe7kEuvkUBw,477
-pyg_nightly-2.7.0.dev20250825.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
-pyg_nightly-2.7.0.dev20250825.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-pyg_nightly-2.7.0.dev20250825.dist-info/METADATA,sha256=8Gvqce4-VL_jOaNBwDxOxfD05-94P4j90fLWbCV4IgA,64100
-pyg_nightly-2.7.0.dev20250825.dist-info/RECORD,,
+pyg_nightly-2.7.0.dev20250827.dist-info/licenses/LICENSE,sha256=ic-27cMJc1kWoMEYncz3Ya3Ur2Bi3bNLWib2DT763-o,1067
+pyg_nightly-2.7.0.dev20250827.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+pyg_nightly-2.7.0.dev20250827.dist-info/METADATA,sha256=v9ks0RFVcvThZaDFy2GCqnuXZGHqkd3DJD2w4UQpCFU,64100
+pyg_nightly-2.7.0.dev20250827.dist-info/RECORD,,

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',

torch_geometric/_onnx.py

@@ -1,3 +1,7 @@
+import warnings
+from os import PathLike
+from typing import Any, Union
+
 import torch
 
 from torch_geometric import is_compiling
@@ -12,3 +16,213 @@ def is_in_onnx_export() -> bool:
     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)

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.

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',