pyg-nightly 2.7.0.dev20250920__tar.gz → 2.7.0.dev20250921__tar.gz

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/PKG-INFO

@@ -1,15 +1,14 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250920
+Version: 2.7.0.dev20250921
 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>
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-Expression: MIT
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -45,7 +44,6 @@ Requires-Dist: networkx ; extra == "full"
 Requires-Dist: numba<0.60.0 ; extra == "full"
 Requires-Dist: opt_einsum ; extra == "full"
 Requires-Dist: pandas ; extra == "full"
-Requires-Dist: pgmpy ; extra == "full"
 Requires-Dist: pynndescent ; extra == "full"
 Requires-Dist: pytorch-memlab ; extra == "full"
 Requires-Dist: rdflib ; extra == "full"
@@ -91,14 +89,21 @@ Provides-Extra: test
 
 ______________________________________________________________________
 
+<div align="center">
+
 [![PyPI Version][pypi-image]][pypi-url]
-[![Testing Status][testing-image]][testing-url]
-[![Linting Status][linting-image]][linting-url]
-[![Docs Status][docs-image]][docs-url]
-[![Contributing][contributing-image]][contributing-url]
+[![PyPI Download][pypi-download-image]][pypi-download-url]
 [![Slack][slack-image]][slack-url]
+[![Contributing][contributing-image]][contributing-url]
+
+**[Documentation](https://pytorch-geometric.readthedocs.io)** |
+**[PyG 1.0 Paper](https://arxiv.org/abs/1903.02428)** |
+**[PyG 2.0 Paper](https://arxiv.org/abs/2507.16991)** |
+**[Colab Notebooks](https://pytorch-geometric.readthedocs.io/en/latest/get_started/colabs.html)** |
+**[External Resources](https://pytorch-geometric.readthedocs.io/en/latest/external/resources.html)** |
+**[OGB Examples](https://github.com/snap-stanford/ogb/tree/master/examples)**
 
-**[Documentation](https://pytorch-geometric.readthedocs.io)** | **[PyG 1.0 Paper](https://arxiv.org/abs/1903.02428)** | **[PyG 2.0 Paper](https://arxiv.org/abs/2507.16991)** | **[Colab Notebooks](https://pytorch-geometric.readthedocs.io/en/latest/get_started/colabs.html)** | **[External Resources](https://pytorch-geometric.readthedocs.io/en/latest/external/resources.html)** | **[OGB Examples](https://github.com/snap-stanford/ogb/tree/master/examples)**
+</div>
 
 **PyG** *(PyTorch Geometric)* is a library built upon [PyTorch](https://pytorch.org/) to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
 
@@ -421,7 +426,7 @@ These approaches have been implemented in PyG, and can benefit from the above GN
 
 ## Installation
 
-PyG is available for Python 3.9 to Python 3.13.
+PyG is available for Python 3.10 to Python 3.13.
 
 From **PyG 2.3** onwards, you can install and use PyG **without any external library** required except for PyTorch.
 For this, simply run
@@ -546,16 +551,12 @@ If you notice anything unexpected, please open an [issue](https://github.com/pyg
 If you have any questions or are missing a specific feature, feel free [to discuss them with us](https://github.com/pyg-team/pytorch_geometric/discussions).
 We are motivated to constantly make PyG even better.
 
-[contributing-image]: https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat
+[contributing-image]: https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat&color=4B26A4
 [contributing-url]: https://github.com/pyg-team/pytorch_geometric/blob/master/.github/CONTRIBUTING.md
-[docs-image]: https://readthedocs.org/projects/pytorch-geometric/badge/?version=latest
-[docs-url]: https://pytorch-geometric.readthedocs.io/en/latest
-[linting-image]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/linting.yml/badge.svg
-[linting-url]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/linting.yml
-[pypi-image]: https://badge.fury.io/py/torch-geometric.svg
+[pypi-download-image]: https://img.shields.io/pypi/dm/torch_geometric?color=4B26A4
+[pypi-download-url]: https://pepy.tech/projects/torch_geometric
+[pypi-image]: https://img.shields.io/pypi/pyversions/torch-geometric?color=4B26A4
 [pypi-url]: https://pypi.python.org/pypi/torch-geometric
-[slack-image]: https://img.shields.io/badge/slack-pyg-brightgreen
+[slack-image]: https://img.shields.io/badge/slack-join-white.svg?logo=slack&color=4B26A4
 [slack-url]: https://data.pyg.org/slack.html
-[testing-image]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/testing.yml/badge.svg
-[testing-url]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/testing.yml
 

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/README.md

@@ -4,14 +4,21 @@
 
 ______________________________________________________________________
 
+<div align="center">
+
 [![PyPI Version][pypi-image]][pypi-url]
-[![Testing Status][testing-image]][testing-url]
-[![Linting Status][linting-image]][linting-url]
-[![Docs Status][docs-image]][docs-url]
-[![Contributing][contributing-image]][contributing-url]
+[![PyPI Download][pypi-download-image]][pypi-download-url]
 [![Slack][slack-image]][slack-url]
+[![Contributing][contributing-image]][contributing-url]
+
+**[Documentation](https://pytorch-geometric.readthedocs.io)** |
+**[PyG 1.0 Paper](https://arxiv.org/abs/1903.02428)** |
+**[PyG 2.0 Paper](https://arxiv.org/abs/2507.16991)** |
+**[Colab Notebooks](https://pytorch-geometric.readthedocs.io/en/latest/get_started/colabs.html)** |
+**[External Resources](https://pytorch-geometric.readthedocs.io/en/latest/external/resources.html)** |
+**[OGB Examples](https://github.com/snap-stanford/ogb/tree/master/examples)**
 
-**[Documentation](https://pytorch-geometric.readthedocs.io)** | **[PyG 1.0 Paper](https://arxiv.org/abs/1903.02428)** | **[PyG 2.0 Paper](https://arxiv.org/abs/2507.16991)** | **[Colab Notebooks](https://pytorch-geometric.readthedocs.io/en/latest/get_started/colabs.html)** | **[External Resources](https://pytorch-geometric.readthedocs.io/en/latest/external/resources.html)** | **[OGB Examples](https://github.com/snap-stanford/ogb/tree/master/examples)**
+</div>
 
 **PyG** *(PyTorch Geometric)* is a library built upon [PyTorch](https://pytorch.org/) to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
 
@@ -334,7 +341,7 @@ These approaches have been implemented in PyG, and can benefit from the above GN
 
 ## Installation
 
-PyG is available for Python 3.9 to Python 3.13.
+PyG is available for Python 3.10 to Python 3.13.
 
 From **PyG 2.3** onwards, you can install and use PyG **without any external library** required except for PyTorch.
 For this, simply run
@@ -459,15 +466,11 @@ If you notice anything unexpected, please open an [issue](https://github.com/pyg
 If you have any questions or are missing a specific feature, feel free [to discuss them with us](https://github.com/pyg-team/pytorch_geometric/discussions).
 We are motivated to constantly make PyG even better.
 
-[contributing-image]: https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat
+[contributing-image]: https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat&color=4B26A4
 [contributing-url]: https://github.com/pyg-team/pytorch_geometric/blob/master/.github/CONTRIBUTING.md
-[docs-image]: https://readthedocs.org/projects/pytorch-geometric/badge/?version=latest
-[docs-url]: https://pytorch-geometric.readthedocs.io/en/latest
-[linting-image]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/linting.yml/badge.svg
-[linting-url]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/linting.yml
-[pypi-image]: https://badge.fury.io/py/torch-geometric.svg
+[pypi-download-image]: https://img.shields.io/pypi/dm/torch_geometric?color=4B26A4
+[pypi-download-url]: https://pepy.tech/projects/torch_geometric
+[pypi-image]: https://img.shields.io/pypi/pyversions/torch-geometric?color=4B26A4
 [pypi-url]: https://pypi.python.org/pypi/torch-geometric
-[slack-image]: https://img.shields.io/badge/slack-pyg-brightgreen
+[slack-image]: https://img.shields.io/badge/slack-join-white.svg?logo=slack&color=4B26A4
 [slack-url]: https://data.pyg.org/slack.html
-[testing-image]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/testing.yml/badge.svg
-[testing-url]: https://github.com/pyg-team/pytorch_geometric/actions/workflows/testing.yml

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/pyproject.toml

@@ -4,13 +4,13 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250920"
+version="2.7.0.dev20250921"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]
 description="Graph Neural Network Library for PyTorch"
 readme="README.md"
-requires-python=">=3.9"
+requires-python=">=3.10"
 keywords=[
     "deep-learning",
     "pytorch",
@@ -23,7 +23,6 @@ license-files = ["LICENSE"]
 classifiers=[
     "Development Status :: 5 - Production/Stable",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -92,7 +91,8 @@ full = [
     "numba<0.60.0",
     "opt_einsum",
     "pandas",
-    "pgmpy",
+    # See https://github.com/pgmpy/pgmpy/issues/2360.
+    # "pgmpy",
     "pynndescent",
     "pytorch-memlab",
     "rdflib",
@@ -156,7 +156,7 @@ skip = [".gitignore", "__init__.py"]
 src = ["torch_geometric"]
 line-length = 80
 indent-width = 4
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = [
@@ -164,6 +164,7 @@ select = [
     "D",  # pydocstyle
 ]
 ignore = [
+    "B905",  # TODO Don't ignore "zip with strict=False"
     "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"
@@ -204,6 +205,8 @@ filterwarnings = [
     # Filter `pytorch_lightning` warnings:
     "ignore:GPU available but not used:UserWarning",
     "error::DeprecationWarning",
+    # TODO(rishipuri98): Remove usage of `torch_geometric.distributed` from `torch_geometric.llm`
+    "ignore:.*torch_geometric.distributed.*:DeprecationWarning",
 ]
 markers = [
     "rag: mark test as RAG test",

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/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.dev20250920'
+__version__ = '2.7.0.dev20250921'
 
 __all__ = [
     'Index',

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/config_store.py

@@ -168,7 +168,7 @@ def map_annotation(
         assert origin is not None
         args = tuple(map_annotation(a, mapping) for a in args)
         if type(annotation).__name__ == 'GenericAlias':
-            # If annotated with `list[...]` or `dict[...]` (>= Python 3.10):
+            # If annotated with `list[...]` or `dict[...]`:
             annotation = origin[args]
         else:
             # If annotated with `typing.List[...]` or `typing.Dict[...]`:

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/data/dataset.py

@@ -236,8 +236,8 @@ class Dataset(torch.utils.data.Dataset):
 
     def _process(self):
         f = osp.join(self.processed_dir, 'pre_transform.pt')
-        if osp.exists(f) and torch.load(f, weights_only=False) != _repr(
-                self.pre_transform):
+        if not self.force_reload and osp.exists(f) and torch.load(
+                f, weights_only=False) != _repr(self.pre_transform):
             warnings.warn(
                 "The `pre_transform` argument differs from the one used in "
                 "the pre-processed version of this dataset. If you want to "
@@ -246,8 +246,8 @@ class Dataset(torch.utils.data.Dataset):
                 stacklevel=2)
 
         f = osp.join(self.processed_dir, 'pre_filter.pt')
-        if osp.exists(f) and torch.load(f, weights_only=False) != _repr(
-                self.pre_filter):
+        if not self.force_reload and osp.exists(f) and torch.load(
+                f, weights_only=False) != _repr(self.pre_filter):
             warnings.warn(
                 "The `pre_filter` argument differs from the one used in "
                 "the pre-processed version of this dataset. If you want to "

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/datasets/molecule_gpt_dataset.py

@@ -174,7 +174,7 @@ def extract_name(
 class MoleculeGPTDataset(InMemoryDataset):
     r"""The dataset from the `"MoleculeGPT: Instruction Following Large
     Language Models for Molecular Property Prediction"
-    <https://ai4d3.github.io/papers/34.pdf>`_ paper.
+    <https://ai4d3.github.io/2023/papers/34.pdf>`_ paper.
 
     Args:
         root (str): Root directory where the dataset should be saved.

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/distributed/__init__.py

@@ -1,3 +1,5 @@
+from warnings import warn
+
 from .dist_context import DistContext
 from .local_feature_store import LocalFeatureStore
 from .local_graph_store import LocalGraphStore
@@ -7,6 +9,17 @@ from .dist_loader import DistLoader
 from .dist_neighbor_loader import DistNeighborLoader
 from .dist_link_neighbor_loader import DistLinkNeighborLoader
 
+warn(
+    "`torch_geometric.distributed` has been deprecated since 2.7.0 and will "
+    "no longer be maintained. For distributed training, refer to our "
+    "tutorials on distributed training at "
+    "https://pytorch-geometric.readthedocs.io/en/latest/tutorial/distributed.html "  # noqa: E501
+    "or cuGraph examples at "
+    "https://github.com/rapidsai/cugraph-gnn/tree/main/python/cugraph-pyg/cugraph_pyg/examples",  # noqa: E501
+    stacklevel=2,
+    category=DeprecationWarning,
+)
+
 __all__ = classes = [
     'DistContext',
     'LocalFeatureStore',

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/nn/models/basic_gnn.py

@@ -415,7 +415,8 @@ class GCN(BasicGNN):
             (default: :obj:`None`)
         jk (str, optional): The Jumping Knowledge mode. If specified, the model
             will additionally apply a final linear transformation to transform
-            node embeddings to the expected output feature dimensionality.
+            node embeddings to the expected output feature dimensionality,
+            while default will not.
             (:obj:`None`, :obj:`"last"`, :obj:`"cat"`, :obj:`"max"`,
             :obj:`"lstm"`). (default: :obj:`None`)
         **kwargs (optional): Additional arguments of

{pyg_nightly-2.7.0.dev20250920 → pyg_nightly-2.7.0.dev20250921}/torch_geometric/typing.py

@@ -3,17 +3,12 @@ import os
 import sys
 import typing
 import warnings
-from typing import Any, Dict, List, Optional, Set, Tuple, Union
+from typing import Any, Dict, List, Optional, Set, Tuple, TypeAlias, Union
 
 import numpy as np
 import torch
 from torch import Tensor
 
-try:
-    from typing import TypeAlias  # type: ignore
-except ImportError:
-    from typing_extensions import TypeAlias
-
 WITH_PT20 = int(torch.__version__.split('.')[0]) >= 2
 WITH_PT21 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 1
 WITH_PT22 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 2
@@ -98,7 +93,7 @@ except Exception as e:
     WITH_CUDA_HASH_MAP = False
 
 if WITH_CPU_HASH_MAP:
-    CPUHashMap: TypeAlias = torch.classes.pyg.CPUHashMap
+    CPUHashMap: TypeAlias = torch.classes.pyg.CPUHashMap  # type: ignore[name-defined]  # noqa: E501
 else:
 
     class CPUHashMap:  # type: ignore
@@ -110,7 +105,7 @@ else:
 
 
 if WITH_CUDA_HASH_MAP:
-    CUDAHashMap: TypeAlias = torch.classes.pyg.CUDAHashMap
+    CUDAHashMap: TypeAlias = torch.classes.pyg.CUDAHashMap  # type: ignore[name-defined]  # noqa: E501
 else:
 
     class CUDAHashMap:  # type: ignore