nixpkgs/pkgs/development/python-modules/torch-geometric/default.nix

{
  lib,
  stdenv,
  buildPythonPackage,
  fetchFromGitHub,

  # build-system
  flit-core,

  # dependencies
  aiohttp,
  fsspec,
  jinja2,
  numpy,
  psutil,
  pyparsing,
  requests,
  torch,
  tqdm,

  # optional-dependencies
  matplotlib,
  networkx,
  pandas,
  protobuf,
  wandb,
  ipython,
  matplotlib-inline,
  pre-commit,
  torch-geometric,
  ase,
  # captum,
  graphviz,
  h5py,
  numba,
  opt-einsum,
  pgmpy,
  pynndescent,
  # pytorch-memlab,
  rdflib,
  rdkit,
  scikit-image,
  scikit-learn,
  scipy,
  statsmodels,
  sympy,
  tabulate,
  torchmetrics,
  trimesh,
  pytorch-lightning,
  yacs,
  huggingface-hub,
  onnx,
  onnxruntime,
  pytest,
  pytest-cov-stub,

  # tests
  pytestCheckHook,
  writableTmpDirAsHomeHook,
  pythonAtLeast,
}:

buildPythonPackage rec {
  pname = "torch-geometric";
  version = "2.6.1";
  pyproject = true;

  src = fetchFromGitHub {
    owner = "pyg-team";
    repo = "pytorch_geometric";
    tag = version;
    hash = "sha256-Zw9YqPQw2N0ZKn5i5Kl4Cjk9JDTmvZmyO/VvIVr6fTU=";
  };

  build-system = [
    flit-core
  ];

  dependencies = [
    aiohttp
    fsspec
    jinja2
    numpy
    psutil
    pyparsing
    requests
    torch
    tqdm
  ];

  optional-dependencies = {
    benchmark = [
      matplotlib
      networkx
      pandas
      protobuf
      wandb
    ];
    dev = [
      ipython
      matplotlib-inline
      pre-commit
      torch-geometric
    ];
    full = [
      ase
      # captum
      graphviz
      h5py
      matplotlib
      networkx
      numba
      opt-einsum
      pandas
      pgmpy
      pynndescent
      # pytorch-memlab
      rdflib
      rdkit
      scikit-image
      scikit-learn
      scipy
      statsmodels
      sympy
      tabulate
      torch-geometric
      torchmetrics
      trimesh
    ];
    graphgym = [
      protobuf
      pytorch-lightning
      yacs
    ];
    modelhub = [
      huggingface-hub
    ];
    test = [
      onnx
      onnxruntime
      pytest
      pytest-cov-stub
    ];
  };

  pythonImportsCheck = [
    "torch_geometric"
  ];

  nativeCheckInputs = [
    pytestCheckHook
    writableTmpDirAsHomeHook
  ];

  disabledTests = [
    # RuntimeError: addmm: computation on CPU is not implemented for SparseCsr + SparseCsr @ SparseCsr without MKL.
    # PyTorch built with MKL has better support for addmm with sparse CPU tensors.
    "test_asap"
    "test_graph_unet"

    # AttributeError: type object 'Any' has no attribute '_name'
    "test_type_repr"

    # AttributeError: module 'torch.fx._symbolic_trace' has no attribute 'List'
    "test_set_clear_mask"
    "test_sequential_to_hetero"
    "test_to_fixed_size"
    "test_to_hetero_basic"
    "test_to_hetero_with_gcn"
    "test_to_hetero_with_basic_model"
    "test_to_hetero_and_rgcn_equal_output"
    "test_graph_level_to_hetero"
    "test_hetero_transformer_self_loop_error"
    "test_to_hetero_validate"
    "test_to_hetero_on_static_graphs"
    "test_to_hetero_with_bases"
    "test_to_hetero_with_bases_and_rgcn_equal_output"
    "test_to_hetero_with_bases_validate"
    "test_to_hetero_with_bases_on_static_graphs"
    "test_to_hetero_with_bases_save"

    # Failed: DID NOT WARN.
    "test_to_hetero_validate"
    "test_to_hetero_with_bases_validate"

    # Failed: DID NOT RAISE
    "test_scatter_backward"
  ]
  ++ lib.optionals stdenv.hostPlatform.isDarwin [
    # This test uses `torch.jit` which might not be working on darwin:
    # RuntimeError: required keyword attribute 'value' has the wrong type
    "test_traceable_my_conv_with_self_loops"

    # RuntimeError: no response from torch_shm_manager
    "test_data_loader"
    "test_data_share_memory"
    "test_dataloader"
    "test_edge_index_dataloader"
    "test_heterogeneous_dataloader"
    "test_index_dataloader"
    "test_multiprocessing"
    "test_share_memory"
    "test_storage_tensor_methods"
  ]
  ++ lib.optionals (pythonAtLeast "3.13") [
    # RuntimeError: Dynamo is not supported on Python 3.13+
    "test_compile"

    # RuntimeError: Python 3.13+ not yet supported for torch.compile
    "test_compile_graph_breaks"
    "test_compile_multi_aggr_sage_conv"
    "test_compile_hetero_conv_graph_breaks"

    # AttributeError: module 'typing' has no attribute 'io'. Did you mean: 'IO'?
    "test_packaging"

    # RuntimeError: Boolean value of Tensor with more than one value is ambiguous
    "test_feature_store"
  ];

  meta = {
    description = "Graph Neural Network Library for PyTorch";
    homepage = "https://github.com/pyg-team/pytorch_geometric";
    changelog = "https://github.com/pyg-team/pytorch_geometric/blob/${src.rev}/CHANGELOG.md";
    license = lib.licenses.mit;
    maintainers = with lib.maintainers; [ GaetanLepage ];
  };
}