repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
mtenv | mtenv-main/mtenv/utils/types.py | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
from typing import Any, Dict, Tuple, Union
import numpy as np
TaskObsType = Union[str, int, float, np.ndarray]
ActionType = Union[str, int, float, np.ndarray]
EnvObsType = Union[np.ndarray]
ObsType = Dict[str, Union[EnvObsType, TaskObsType]]
Rewar... | 530 | 32.1875 | 70 | py |
mtenv | mtenv-main/mtenv/utils/seeding.py | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
from typing import Optional, Tuple
from gym.utils import seeding
from numpy.random import RandomState
def np_random(seed: Optional[int]) -> Tuple[RandomState, int]:
"""Set the seed for numpy's random generator.
Args:
seed (Option... | 521 | 25.1 | 74 | py |
mtenv | mtenv-main/mtenv/utils/__init__.py | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
| 71 | 35 | 70 | py |
mtenv | mtenv-main/local_dm_control_suite/base.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,139 | 35.637168 | 84 | py |
mtenv | mtenv-main/local_dm_control_suite/explore.py | # Copyright 2018 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,023 | 30.5 | 84 | py |
mtenv | mtenv-main/local_dm_control_suite/cartpole.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 9,502 | 36.561265 | 85 | py |
mtenv | mtenv-main/local_dm_control_suite/humanoid.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 8,547 | 34.915966 | 85 | py |
mtenv | mtenv-main/local_dm_control_suite/lqr.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 10,082 | 36.069853 | 87 | py |
mtenv | mtenv-main/local_dm_control_suite/fish.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 6,657 | 34.227513 | 84 | py |
mtenv | mtenv-main/local_dm_control_suite/walker.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 6,162 | 31.267016 | 83 | py |
mtenv | mtenv-main/local_dm_control_suite/ball_in_cup.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,550 | 32.819048 | 80 | py |
mtenv | mtenv-main/local_dm_control_suite/finger.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 8,498 | 33.975309 | 86 | py |
mtenv | mtenv-main/local_dm_control_suite/point_mass.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 5,007 | 36.096296 | 88 | py |
mtenv | mtenv-main/local_dm_control_suite/quadruped.py | # Copyright 2019 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 19,110 | 36.108738 | 87 | py |
mtenv | mtenv-main/local_dm_control_suite/swimmer.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 8,432 | 36.314159 | 88 | py |
mtenv | mtenv-main/local_dm_control_suite/reacher.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,543 | 36.553719 | 83 | py |
mtenv | mtenv-main/local_dm_control_suite/pendulum.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,748 | 31.6 | 83 | py |
mtenv | mtenv-main/local_dm_control_suite/lqr_solver.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,910 | 32.408163 | 94 | py |
mtenv | mtenv-main/local_dm_control_suite/stacker.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 8,131 | 35.142222 | 87 | py |
mtenv | mtenv-main/local_dm_control_suite/cheetah.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,505 | 32.075472 | 80 | py |
mtenv | mtenv-main/local_dm_control_suite/__init__.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,853 | 27.892857 | 86 | py |
mtenv | mtenv-main/local_dm_control_suite/manipulator.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 12,051 | 35.521212 | 88 | py |
mtenv | mtenv-main/local_dm_control_suite/acrobot.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,670 | 34.386364 | 85 | py |
mtenv | mtenv-main/local_dm_control_suite/humanoid_CMU.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 7,074 | 35.096939 | 85 | py |
mtenv | mtenv-main/local_dm_control_suite/hopper.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 5,194 | 34.101351 | 87 | py |
mtenv | mtenv-main/local_dm_control_suite/common/__init__.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 1,387 | 32.047619 | 78 | py |
mtenv | mtenv-main/local_dm_control_suite/tests/loader_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 1,640 | 30.557692 | 79 | py |
mtenv | mtenv-main/local_dm_control_suite/tests/domains_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 12,919 | 39.375 | 88 | py |
mtenv | mtenv-main/local_dm_control_suite/tests/lqr_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,097 | 34.204545 | 87 | py |
mtenv | mtenv-main/local_dm_control_suite/wrappers/action_noise_test.py | # Copyright 2018 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 5,875 | 39.805556 | 86 | py |
mtenv | mtenv-main/local_dm_control_suite/wrappers/pixels.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,704 | 36.943548 | 85 | py |
mtenv | mtenv-main/local_dm_control_suite/wrappers/__init__.py | # Copyright 2018 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 742 | 42.705882 | 78 | py |
mtenv | mtenv-main/local_dm_control_suite/wrappers/action_noise.py | # Copyright 2018 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 2,891 | 36.076923 | 84 | py |
mtenv | mtenv-main/local_dm_control_suite/wrappers/pixels_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 4,549 | 32.455882 | 84 | py |
mtenv | mtenv-main/local_dm_control_suite/utils/parse_amc.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 8,977 | 28.728477 | 83 | py |
mtenv | mtenv-main/local_dm_control_suite/utils/parse_amc_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 2,358 | 33.188406 | 79 | py |
mtenv | mtenv-main/local_dm_control_suite/utils/randomizers.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 3,330 | 35.604396 | 82 | py |
mtenv | mtenv-main/local_dm_control_suite/utils/__init__.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 718 | 41.294118 | 78 | py |
mtenv | mtenv-main/local_dm_control_suite/utils/randomizers_test.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 6,331 | 34.573034 | 83 | py |
mtenv | mtenv-main/local_dm_control_suite/demos/mocap_demo.py | # Copyright 2017 The dm_control Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | 2,633 | 28.266667 | 86 | py |
mtenv | mtenv-main/docs_src/source/conf.py | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup ... | 2,375 | 33.434783 | 88 | py |
libzmq | libzmq-master/perf/generate_graphs.py | #!/usr/bin/python3
#
# This script assumes that the set of CSV files produced by "generate_csv.sh" is provided as input
# and that locally there is the "results" folder.
#
# results for TCP:
INPUT_FILE_PUSHPULL_TCP_THROUGHPUT="results/pushpull_tcp_thr_results.csv"
INPUT_FILE_REQREP_TCP_LATENCY="results/reqrep_tcp_lat... | 2,542 | 33.364865 | 117 | py |
cwn | cwn-main/conftest.py | import pytest
def pytest_addoption(parser):
parser.addoption(
"--runslow", action="store_true", default=False, help="run slow tests",
)
parser.addoption(
"--rundata", action="store_true", default=False, help="run tests using datasets",
)
def pytest_configure(config):
config.addin... | 956 | 29.870968 | 89 | py |
cwn | cwn-main/definitions.py | import os
ROOT_DIR = os.path.dirname(os.path.abspath(__file__)) | 63 | 31 | 53 | py |
cwn | cwn-main/mp/cell_mp.py | """
Based on https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/nn/conv/message_passing.py
MIT License
Copyright (c) 2020 Matthias Fey <[email protected]>
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this so... | 26,998 | 48 | 110 | py |
cwn | cwn-main/mp/test_layers.py | import torch
import torch.optim as optim
from mp.layers import (
DummyCellularMessagePassing, CINConv, OrientedConv, InitReduceConv, EmbedVEWithReduce)
from data.dummy_complexes import get_house_complex, get_molecular_complex
from torch import nn
from data.datasets.flow import load_flow_dataset
def test_dummy_ce... | 6,243 | 34.276836 | 96 | py |
cwn | cwn-main/mp/cell_mp_inspector.py | """
Based on https://github.com/rusty1s/pytorch_geometric/blob/76d61eaa9fc8702aa25f29dfaa5134a169d0f1f6/torch_geometric/nn/conv/utils/inspector.py
MIT License
Copyright (c) 2020 Matthias Fey <[email protected]>
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any ... | 2,143 | 41.88 | 142 | py |
cwn | cwn-main/mp/ring_exp_models.py | import torch
from mp.layers import SparseCINConv
from mp.nn import get_nonlinearity, get_graph_norm
from data.complex import ComplexBatch
from torch.nn import Linear, Sequential
from torch_geometric.nn import GINConv
class RingSparseCIN(torch.nn.Module):
"""
A simple cellular version of GIN employed for Ring... | 4,771 | 35.151515 | 102 | py |
cwn | cwn-main/mp/test_permutation.py | import torch
from data.utils import compute_ring_2complex
from data.perm_utils import permute_graph, generate_permutation_matrices
from data.dummy_complexes import get_mol_testing_complex_list, convert_to_graph
from data.complex import ComplexBatch
from mp.models import SparseCIN
def test_sparse_cin0_perm_invariance_... | 1,983 | 52.621622 | 127 | py |
cwn | cwn-main/mp/molec_models.py | import torch
import torch.nn.functional as F
from torch.nn import Linear, Embedding, Sequential, BatchNorm1d as BN
from torch_geometric.nn import JumpingKnowledge, GINEConv
from mp.layers import InitReduceConv, EmbedVEWithReduce, OGBEmbedVEWithReduce, SparseCINConv, CINppConv
from ogb.graphproppred.mol_encoder import ... | 26,185 | 42.140033 | 106 | py |
cwn | cwn-main/mp/test_models.py | import torch
import pytest
import itertools
from data.complex import ComplexBatch
from data.dummy_complexes import get_testing_complex_list
from mp.models import CIN0, EdgeCIN0, SparseCIN
from data.data_loading import DataLoader, load_dataset
def test_cin_model_with_batching():
"""Check this runs without errors ... | 9,019 | 37.712446 | 99 | py |
cwn | cwn-main/mp/layers.py | import torch
from typing import Any, Callable, Optional
from torch import Tensor
from mp.cell_mp import CochainMessagePassing, CochainMessagePassingParams
from torch_geometric.nn.inits import reset
from torch.nn import Linear, Sequential, BatchNorm1d as BN, Identity
from data.complex import Cochain
from torch_scatter ... | 26,386 | 43.422559 | 130 | py |
cwn | cwn-main/mp/nn.py | import torch
import torch.nn.functional as F
from torch_geometric.nn import global_mean_pool, global_add_pool
from torch.nn import BatchNorm1d as BN, LayerNorm as LN, Identity
def get_nonlinearity(nonlinearity, return_module=True):
if nonlinearity == 'relu':
module = torch.nn.ReLU
function = F.rel... | 2,030 | 32.295082 | 101 | py |
cwn | cwn-main/mp/models.py | import torch
import torch.nn.functional as F
from torch.nn import Linear, Sequential, BatchNorm1d as BN
from torch_geometric.nn import JumpingKnowledge
from mp.layers import (
CINConv, EdgeCINConv, SparseCINConv, CINppConv,DummyCellularMessagePassing, OrientedConv)
from mp.nn import get_nonlinearity, get_pooling_f... | 27,151 | 40.015106 | 102 | py |
cwn | cwn-main/mp/__init__.py | 0 | 0 | 0 | py | |
cwn | cwn-main/mp/test_orientation.py | import torch
import numpy as np
from data.datasets.flow import load_flow_dataset
from mp.models import EdgeOrient, EdgeMPNN
from mp.layers import OrientedConv
from data.complex import CochainBatch
from data.data_loading import DataLoader
from data.datasets.flow_utils import build_cochain
def generate_oriented_flow_p... | 5,926 | 39.047297 | 107 | py |
cwn | cwn-main/mp/graph_models.py | """
Code based on https://github.com/rusty1s/pytorch_geometric/blob/master/benchmark/kernel/gin.py
Copyright (c) 2020 Matthias Fey <[email protected]>
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated docum... | 10,168 | 37.086142 | 96 | py |
cwn | cwn-main/mp/test_molec_models.py | import torch
import itertools
import pytest
from data.complex import ComplexBatch
from data.dummy_complexes import get_testing_complex_list
from mp.molec_models import EmbedSparseCIN, OGBEmbedSparseCIN, EmbedSparseCINNoRings, EmbedGIN
from data.data_loading import DataLoader, load_dataset
def test_zinc_sparse_cin0_m... | 11,149 | 38.122807 | 102 | py |
cwn | cwn-main/mp/test_cell_mp.py | import pytest
import torch
from data.helper_test import check_edge_index_are_the_same, check_edge_attr_are_the_same
from mp.cell_mp import CochainMessagePassing
from torch_geometric.nn.conv import MessagePassing
from data.dummy_complexes import (get_square_dot_complex, get_house_complex,
... | 13,576 | 49.285185 | 180 | py |
cwn | cwn-main/data/test_dataset.py | import pytest
import os
from data.data_loading import load_graph_dataset
from data.datasets import TUDataset, DummyMolecularDataset, DummyDataset
from data.utils import compute_clique_complex_with_gudhi, compute_ring_2complex
from data.helper_test import compare_complexes, compare_complexes_without_2feats
from definit... | 3,813 | 46.08642 | 109 | py |
cwn | cwn-main/data/perm_utils.py | import torch
import numpy as np
from scipy import sparse as sp
from torch_geometric.data import Data
def permute_graph(graph: Data, P: np.ndarray) -> Data:
# TODO: support edge features and their permutation
assert graph.edge_attr is None
# Check validity of permutation matrix
n = graph.x.size(0)
... | 2,177 | 29.25 | 110 | py |
cwn | cwn-main/data/test_data.py | import torch
from data.dummy_complexes import get_house_complex
def test_up_and_down_feature_extraction_on_house_complex():
house_complex = get_house_complex()
v_cochain_params = house_complex.get_cochain_params(dim=0)
v_up_attr = v_cochain_params.kwargs['up_attr']
expected_v_up_attr = torch.tensor(... | 2,318 | 41.163636 | 100 | py |
cwn | cwn-main/data/helper_test.py | import itertools
import torch
import networkx as nx
from torch_geometric.utils import convert
from torch_geometric.data import Data
def check_edge_index_are_the_same(upper_index, edge_index):
"""Checks that two edge/cell indexes are the same."""
# These two tensors should have the same content but in differe... | 8,463 | 41.532663 | 98 | py |
cwn | cwn-main/data/data_loading.py | """
Code is adapted from https://github.com/rusty1s/pytorch_geometric/blob/6442a6e287563b39dae9f5fcffc52cd780925f89/torch_geometric/data/dataloader.py
Copyright (c) 2020 Matthias Fey <[email protected]>
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any person ob... | 14,860 | 56.378378 | 146 | py |
cwn | cwn-main/data/tu_utils.py | """
Based on code from https://github.com/weihua916/powerful-gnns/blob/master/util.py
MIT License
Copyright (c) 2021 Weihua Hu
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), ... | 8,611 | 34.883333 | 119 | py |
cwn | cwn-main/data/utils.py | import graph_tool as gt
import graph_tool.topology as top
import numpy as np
import torch
import gudhi as gd
import itertools
import networkx as nx
from tqdm import tqdm
from data.complex import Cochain, Complex
from typing import List, Dict, Optional, Union
from torch import Tensor
from torch_geometric.typing import ... | 23,431 | 41.915751 | 120 | py |
cwn | cwn-main/data/complex.py | """
Copyright (c) 2020 Matthias Fey <[email protected]>
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without ... | 30,723 | 41.145405 | 110 | py |
cwn | cwn-main/data/test_parallel.py | import pytest
from data.dummy_complexes import get_mol_testing_complex_list, convert_to_graph
from data.utils import convert_graph_dataset_with_rings
from data.test_dataset import compare_complexes
@pytest.mark.slow
def test_parallel_conversion_returns_same_order():
complexes = get_mol_testing_complex_list(... | 686 | 35.157895 | 93 | py |
cwn | cwn-main/data/test_tu_utils.py | import pytest
import os
import numpy as np
import torch
import random
from data.tu_utils import get_fold_indices, load_data, S2V_to_PyG
from torch_geometric.utils import degree
from definitions import ROOT_DIR
@pytest.fixture
def imdbbinary_graphs():
data, num_classes = load_data(os.path.join(ROOT_DIR, 'datasets'... | 3,720 | 32.827273 | 111 | py |
cwn | cwn-main/data/test_batching.py | import torch
import pytest
import itertools
from data.dummy_complexes import (get_house_complex, get_square_complex, get_pyramid_complex,
get_square_dot_complex, get_kite_complex)
from data.complex import ComplexBatch
from data.dummy_complexes import get_testing_complex_list
from data.data_loading import DataLoad... | 46,797 | 43.065913 | 201 | py |
cwn | cwn-main/data/sr_utils.py | import networkx as nx
import torch
from torch_geometric.utils import to_undirected
def load_sr_dataset(path):
"""Load the Strongly Regular Graph Dataset from the supplied path."""
nx_graphs = nx.read_graph6(path)
graphs = list()
for nx_graph in nx_graphs:
n = nx_graph.number_of_nodes()
... | 485 | 29.375 | 105 | py |
cwn | cwn-main/data/__init__.py | 0 | 0 | 0 | py | |
cwn | cwn-main/data/dummy_complexes.py | import torch
from data.complex import Cochain, Complex
from torch_geometric.data import Data
# TODO: make the features for these dummy complexes disjoint to stress tests even more
def convert_to_graph(complex):
"""Extracts the underlying graph of a cochain complex."""
assert 0 in complex.cochains
assert ... | 23,206 | 39.220104 | 168 | py |
cwn | cwn-main/data/parallel.py | from tqdm.auto import tqdm
from joblib import Parallel
class ProgressParallel(Parallel):
"""A helper class for adding tqdm progressbar to the joblib library."""
def __init__(self, use_tqdm=True, total=None, *args, **kwargs):
self._use_tqdm = use_tqdm
self._total = total
super().__init_... | 714 | 33.047619 | 79 | py |
cwn | cwn-main/data/test_utils.py | import torch
from torch_geometric.data import Data
from data.utils import compute_clique_complex_with_gudhi, compute_ring_2complex
from data.utils import convert_graph_dataset_with_gudhi, convert_graph_dataset_with_rings
from data.complex import ComplexBatch
from data.dummy_complexes import convert_to_graph, get_testi... | 31,625 | 48.883281 | 148 | py |
cwn | cwn-main/data/datasets/test_flow.py | import numpy as np
import torch
from scipy.spatial import Delaunay
from data.datasets.flow_utils import load_flow_dataset, create_hole, is_inside_rectangle
def test_create_hole():
# This seed contains some edge cases.
np.random.seed(4)
points = np.random.uniform(size=(400, 2))
tri = Delaunay(points)
... | 2,416 | 36.184615 | 94 | py |
cwn | cwn-main/data/datasets/peptides_structural.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 2 21:37:42 2023
@author: renz
"""
import hashlib
import os.path as osp
import os
import pickle
import shutil
import pandas as pd
import torch
from ogb.utils import smiles2graph
from ogb.utils.torch_util import replace_numpy_with_torchtensor
from ... | 11,359 | 41.546816 | 134 | py |
cwn | cwn-main/data/datasets/peptides_functional.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 2 21:37:42 2023
@author: renz
"""
import hashlib
import os.path as osp
import os
import pickle
import shutil
import pandas as pd
import torch
from ogb.utils import smiles2graph
from ogb.utils.torch_util import replace_numpy_with_torchtensor
from ... | 10,424 | 39.564202 | 124 | py |
cwn | cwn-main/data/datasets/ocean.py | import pickle
import os.path as osp
from data.datasets import InMemoryComplexDataset
from data.datasets.ocean_utils import load_ocean_dataset
# TODO: Set up a cochain dataset structure or make complex dataset better support cochain-only data.
# TODO: Refactor the dataset to use the latest storage formatting.
class O... | 2,602 | 34.175676 | 100 | py |
cwn | cwn-main/data/datasets/plot_ringtree_dataset.py | import networkx as nx
import matplotlib.pyplot as plt
from data.datasets.ring_utils import generate_ring_transfer_graph_dataset
from torch_geometric.utils import convert
def visualise_ringtree_dataset():
dataset = generate_ring_transfer_graph_dataset(nodes=10, samples=100, classes=5)
data = dataset[0]
g... | 495 | 23.8 | 84 | py |
cwn | cwn-main/data/datasets/test_ringtransfer.py | import os.path as osp
from data.datasets.ring_utils import generate_ring_transfer_graph_dataset
from data.utils import convert_graph_dataset_with_rings
from data.datasets import RingTransferDataset
from definitions import ROOT_DIR
def test_ringtree_dataset_generation():
dataset = generate_ring_transfer_graph_dat... | 1,900 | 35.557692 | 95 | py |
cwn | cwn-main/data/datasets/cluster.py | import pickle
from data.datasets import InMemoryComplexDataset
from data.utils import convert_graph_dataset_with_gudhi
from torch_geometric.datasets import GNNBenchmarkDataset
class ClusterDataset(InMemoryComplexDataset):
"""This is the Cluster dataset from the Benchmarking GNNs paper.
The dataset contains ... | 3,283 | 41.102564 | 140 | py |
cwn | cwn-main/data/datasets/csl.py | import os.path as osp
import numpy as np
import torch
from data.datasets import InMemoryComplexDataset
from data.utils import convert_graph_dataset_with_rings
from torch_geometric.datasets import GNNBenchmarkDataset
from torch_geometric.utils import remove_self_loops
class CSLDataset(InMemoryComplexDataset):
"""... | 4,912 | 39.270492 | 127 | py |
cwn | cwn-main/data/datasets/flow.py | import pickle
import os.path as osp
from data.datasets import InMemoryComplexDataset
from data.datasets.flow_utils import load_flow_dataset
# TODO: Set up a cochain dataset structure or make complex dataset better support cochain-only data.
# TODO: Make this dataset use the new storage system.
class FlowDataset(InMe... | 2,666 | 34.56 | 100 | py |
cwn | cwn-main/data/datasets/flow_utils.py | import numpy as np
import random
import torch
import networkx as nx
import itertools
from scipy.spatial import Delaunay
from scipy import sparse
from data.complex import Cochain
from data.parallel import ProgressParallel
from joblib import delayed
def is_inside_rectangle(x, rect):
return rect[0, 0] <= x[0] <= re... | 10,807 | 30.976331 | 89 | py |
cwn | cwn-main/data/datasets/sr.py | import os
import torch
import pickle
from data.sr_utils import load_sr_dataset
from data.utils import compute_clique_complex_with_gudhi, compute_ring_2complex
from data.utils import convert_graph_dataset_with_rings, convert_graph_dataset_with_gudhi
from data.datasets import InMemoryComplexDataset
from definitions impo... | 4,522 | 39.747748 | 107 | py |
cwn | cwn-main/data/datasets/ring_utils.py | import numpy as np
import torch
import random
from torch_geometric.data import Data
from sklearn.preprocessing import LabelBinarizer
# TODO: Add a graph dataset for ring lookup.
def generate_ring_lookup_graph(nodes):
"""This generates a dictionary lookup ring. No longer being used for now."""
# Assign all th... | 3,276 | 30.509615 | 82 | py |
cwn | cwn-main/data/datasets/zinc.py | import torch
import os.path as osp
from data.utils import convert_graph_dataset_with_rings
from data.datasets import InMemoryComplexDataset
from torch_geometric.datasets import ZINC
class ZincDataset(InMemoryComplexDataset):
"""This is ZINC from the Benchmarking GNNs paper. This is a graph regression task."""
... | 5,282 | 36.468085 | 91 | py |
cwn | cwn-main/data/datasets/dataset.py | """
The code is based on https://github.com/rusty1s/pytorch_geometric/blob/76d61eaa9fc8702aa25f29dfaa5134a169d0f1f6/torch_geometric/data/dataset.py#L19
and https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/data/in_memory_dataset.py
Copyright (c) 2020 Matthias Fey <[email protected]>
Co... | 14,872 | 38.873995 | 147 | py |
cwn | cwn-main/data/datasets/test_zinc.py | import torch
import os.path as osp
import pytest
from data.data_loading import load_dataset
from data.helper_test import (check_edge_index_are_the_same,
check_edge_attr_are_the_same, get_rings,
get_complex_rings)
from torch_geometric.datasets import ZINC
... | 2,395 | 38.933333 | 107 | py |
cwn | cwn-main/data/datasets/ocean_utils.py | """
Based on
- https://github.com/nglaze00/SCoNe_GCN/blob/master/ocean_drifters_data/buoy_data.py
- https://github.com/nglaze00/SCoNe_GCN/blob/master/trajectory_analysis/synthetic_data_gen.py
MIT License
Copyright (c) 2021 Nicholas Glaze
Copyright (c) 2021 The CWN Project Authors
Permission is hereby granted, free o... | 9,466 | 34.193309 | 135 | py |
cwn | cwn-main/data/datasets/tu.py | import os
import torch
import pickle
import numpy as np
from definitions import ROOT_DIR
from data.tu_utils import load_data, S2V_to_PyG, get_fold_indices
from data.utils import convert_graph_dataset_with_gudhi, convert_graph_dataset_with_rings
from data.datasets import InMemoryComplexDataset
def load_tu_graph_datas... | 6,539 | 49.307692 | 110 | py |
cwn | cwn-main/data/datasets/plot_flow_dataset.py | import seaborn as sns
import matplotlib.pyplot as plt
import os
from data.datasets import FlowDataset
from definitions import ROOT_DIR
sns.set_style('white')
sns.color_palette("tab10")
def plot_arrow(p1, p2, color='red'):
plt.arrow(p1[0], p1[1], p2[0] - p1[0], p2[1] - p1[1], color=color,
shape='full', l... | 2,723 | 33.05 | 94 | py |
cwn | cwn-main/data/datasets/ogb.py | import torch
import os.path as osp
from data.utils import convert_graph_dataset_with_rings
from data.datasets import InMemoryComplexDataset
from ogb.graphproppred import PygGraphPropPredDataset
class OGBDataset(InMemoryComplexDataset):
"""This is OGB graph-property prediction. This are graph-wise classification ... | 4,176 | 42.061856 | 97 | py |
cwn | cwn-main/data/datasets/ringlookup.py | import torch
import os.path as osp
from data.datasets import InMemoryComplexDataset
from data.datasets.ring_utils import generate_ringlookup_graph_dataset
from data.utils import convert_graph_dataset_with_rings
class RingLookupDataset(InMemoryComplexDataset):
"""A dataset where the task is to perform dictionary ... | 3,214 | 32.842105 | 98 | py |
cwn | cwn-main/data/datasets/test_ocean.py | import torch
import pytest
from data.datasets.ocean_utils import load_ocean_dataset
@pytest.mark.data
def test_ocean_dataset_generation():
train, test, _ = load_ocean_dataset()
assert len(train) == 160
assert len(test) == 40
for cochain in train + test:
# checks the upper/lower orientation fe... | 1,247 | 43.571429 | 94 | py |
cwn | cwn-main/data/datasets/ringtransfer.py | import torch
import os.path as osp
from data.datasets import InMemoryComplexDataset
from data.datasets.ring_utils import generate_ring_transfer_graph_dataset
from data.utils import convert_graph_dataset_with_rings
class RingTransferDataset(InMemoryComplexDataset):
"""A dataset where the task is to transfer featu... | 3,322 | 32.908163 | 92 | py |
cwn | cwn-main/data/datasets/__init__.py | from data.datasets.dataset import ComplexDataset, InMemoryComplexDataset
from data.datasets.sr import SRDataset, load_sr_graph_dataset
from data.datasets.cluster import ClusterDataset
from data.datasets.tu import TUDataset, load_tu_graph_dataset
from data.datasets.flow import FlowDataset
from data.datasets.ocean import... | 941 | 57.875 | 97 | py |
cwn | cwn-main/data/datasets/dummy.py | import torch
from data.datasets import InMemoryComplexDataset
from data.dummy_complexes import get_testing_complex_list, get_mol_testing_complex_list
class DummyDataset(InMemoryComplexDataset):
"""A dummy dataset using a list of hand-crafted cell complexes with many edge cases."""
def __init__(self, root):
... | 3,221 | 34.021739 | 101 | py |
cwn | cwn-main/exp/parser.py | import os
import time
import argparse
from definitions import ROOT_DIR
def get_parser():
parser = argparse.ArgumentParser(description='CWN experiment.')
parser.add_argument('--seed', type=int, default=43,
help='random seed to set (default: 43, i.e. the non-meaning of life))')
pars... | 11,349 | 59.695187 | 126 | py |
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