author int64 658 755k | date stringlengths 19 19 | timezone int64 -46,800 43.2k | hash stringlengths 40 40 | message stringlengths 5 490 | mods list | language stringclasses 20 values | license stringclasses 3 values | repo stringlengths 5 68 | original_message stringlengths 12 491 |
|---|---|---|---|---|---|---|---|---|---|
87,724 | 26.12.2021 14:33:21 | -7,200 | 40dfeb0dbafeafea22d7ed33d0b0686d089b8029 | add a test for A3TGCN2 that supports batches | [
{
"change_type": "MODIFY",
"old_path": "test/recurrent_test.py",
"new_path": "test/recurrent_test.py",
"diff": "@@ -37,9 +37,10 @@ def create_mock_attention_data(number_of_nodes, edge_per_node, in_channels, peri\nreturn X, edge_index\n+\ndef create_mock_attention_batch_data(number_of_nodes, edge_per... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | add a test for A3TGCN2 that supports batches |
87,724 | 02.01.2022 14:44:21 | -7,200 | ec9884600e0a10decd28604207468f07c3050543 | add comments to the TEMPORAL and SPATIAL attention modules of the ASTGCN architecture that explains the shapes of data and transformations applied | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/attention/astgcn.py",
"new_path": "torch_geometric_temporal/nn/attention/astgcn.py",
"diff": "@@ -196,9 +196,8 @@ class ChebConvAttention(MessagePassing):\nself._normalization,\n)\n-\nclass SpatialAttention(nn.Module):\n- r\"\"\"An ... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | add comments to the TEMPORAL and SPATIAL attention modules of the ASTGCN architecture that explains the shapes of data and transformations applied |
87,724 | 02.01.2022 20:22:06 | -7,200 | 4c9482458ac69500b197221ec2bb376218bd380c | add comments to the ASTGCN Block and model architecture that explains the shapes of data and transformations applied also giving examples from the shape of the los anglos traffic dataset used in the paper to make it easy for the reader to quickly grasp it | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/attention/astgcn.py",
"new_path": "torch_geometric_temporal/nn/attention/astgcn.py",
"diff": "@@ -46,6 +46,7 @@ class ChebConvAttention(MessagePassing):\n:class:`torch_geometric.nn.conv.MessagePassing`.\n\"\"\"\n+\ndef __init__(\nse... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | add comments to the ASTGCN Block and model architecture that explains the shapes of data and transformations applied also giving examples from the shape of the los anglos traffic dataset used in the paper to make it easy for the reader to quickly grasp it |
87,715 | 06.01.2022 13:23:00 | -3,600 | 4bd7c2e75383a5d1143de08b4705dd8b5170f221 | First commit for heterogeneous graph support
This includes:
a new data-structure 'StaticHeteroGraphTemporalSignal' that works like 'StaticGraphTemporalSignal' but with troch_geometric HeteroData objects as snapshots; instead of np arrays, dictionaries wirth key(node/edge types as strings)/value(indices/features as np arrays) are expected
code tests for the new data-structure
documentation for the new data-structure | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -19,6 +19,13 @@ Temporal Signal Iterators\n:members:\n:undoc-members:\n+Heterogeneous Temporal Signal Iterators\n+-------------------------\n+\n+.. automodule:: torch_ge... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | First commit for heterogeneous graph support
This includes:
- a new data-structure 'StaticHeteroGraphTemporalSignal' that works like 'StaticGraphTemporalSignal' but with troch_geometric HeteroData objects as snapshots; instead of np arrays, dictionaries wirth key(node/edge types as strings)/value(indices/features as np arrays) are expected
- code tests for the new data-structure
- documentation for the new data-structure |
87,715 | 20.01.2022 14:09:16 | -3,600 | 62a86b46bbb3a3cf19e246bbd88c5906588212aa | Static hetero graph temporla signal batch
This includes:
a new data structure, that represents PyG HeteroDataBatch snapshots for static heterogeneous graphs with temporal signals
documentation
tests | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -41,6 +41,13 @@ Temporal Signal Batch Iterators\n:members:\n:undoc-members:\n+Heterogeneous Temporal Signal Batch Iterators\n+-------------------------------\n+\n+.. aut... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Static hetero graph temporla signal batch
This includes:
- a new data structure, that represents PyG HeteroDataBatch snapshots for static heterogeneous graphs with temporal signals
- documentation
- tests |
87,718 | 22.01.2022 18:59:40 | -3,600 | 7f98426d5ced1200b7864214a84937a41217af73 | made temporal_signal_split copy additional features | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/signal/train_test_split.py",
"new_path": "torch_geometric_temporal/signal/train_test_split.py",
"diff": "@@ -40,6 +40,7 @@ def temporal_signal_split(\ndata_iterator.edge_weight,\ndata_iterator.features[0:train_snapshots],\ndata_iterato... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | made temporal_signal_split copy additional features |
87,718 | 22.01.2022 21:19:52 | -3,600 | a52e9b63315a13c8d0d8fde7c8bf5b9ab926abc4 | renamed test, there were two tests of the same name | [
{
"change_type": "MODIFY",
"old_path": "test/dataset_test.py",
"new_path": "test/dataset_test.py",
"diff": "@@ -653,7 +653,7 @@ def test_train_test_split_dynamic_graph_static_signal():\nassert getattr(snapshot, \"optional2\").shape == (100, 32)\n-def test_discrete_train_test_split_dynamic():\n+def t... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | renamed test, there were two tests of the same name |
87,715 | 26.01.2022 10:00:52 | -3,600 | 947d0fe33fda74397cc7b607a297eadcb1787c19 | Additional dataset tests for coverage
edge tests
edge index tests
additional attributes None test | [
{
"change_type": "MODIFY",
"old_path": "test/dataset_test.py",
"new_path": "test/dataset_test.py",
"diff": "@@ -169,11 +169,27 @@ def test_static_hetero_graph_temporal_signal_typing():\ndef test_static_hetero_graph_temporal_signal_additional_attrs():\ndataset = StaticHeteroGraphTemporalSignal(None, ... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Additional dataset tests for coverage
edge tests
edge index tests
additional attributes None test |
87,715 | 26.01.2022 10:10:58 | -3,600 | 74b18d076e4114412b04a1427b4916e2065b067c | Added batch tests for coverage
edge test
edge weights test
additional attributes None test
batch assigned test | [
{
"change_type": "MODIFY",
"old_path": "test/batch_test.py",
"new_path": "test/batch_test.py",
"diff": "@@ -163,11 +163,13 @@ def test_static_graph_temporal_signal_batch_additional_attrs():\ndef test_static_hetero_graph_temporal_signal_batch_additional_attrs():\ndataset = StaticHeteroGraphTemporalSi... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Added batch tests for coverage
edge test
edge weights test
additional attributes None test
batch assigned test |
87,729 | 01.02.2022 10:28:13 | 0 | 83830d9dcd1ebcb56b77643884b0fae129bae9b0 | Refactor __get_item__ into __getitem__ | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/signal/dynamic_graph_static_signal.py",
"new_path": "torch_geometric_temporal/signal/dynamic_graph_static_signal.py",
"diff": "@@ -105,7 +105,7 @@ class DynamicGraphStaticSignal(object):\ndef __len__(self):\nreturn len(self.targets)\n-... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Refactor __get_item__ into __getitem__ |
87,715 | 03.02.2022 09:42:57 | -3,600 | f7ae5d0a0e75ae622fdc2648f40efb6d8099eaee | refactor __getitem__ for hetero graphs | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/signal/static_hetero_graph_temporal_signal.py",
"new_path": "torch_geometric_temporal/signal/static_hetero_graph_temporal_signal.py",
"diff": "@@ -162,7 +162,7 @@ class StaticHeteroGraphTemporalSignal(object):\n}\nreturn additional_fea... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | refactor __getitem__ for hetero graphs |
87,715 | 03.02.2022 09:44:52 | -3,600 | 8e4ddd12e2f96a27743b98cba46ea9a092ef13ac | dynamic hetero graph static signal
new data structure that works like DynamicGraphStaticSignal but with PyG HeteroData objects
tests
documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -26,6 +26,10 @@ Heterogeneous Temporal Signal Iterators\n:members:\n:undoc-members:\n+.. automodule:: torch_geometric_temporal.signal.dynamic_hetero_graph_static_signal\... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | dynamic hetero graph static signal
- new data structure that works like DynamicGraphStaticSignal but with PyG HeteroData objects
- tests
- documentation |
87,715 | 03.02.2022 10:09:13 | -3,600 | 591ca3b7f4d7bef1433057c922b374edc9790309 | dynamic hetero graph static signal batch
data structure that works like DynamicGraphStaticSignal but with PyG HeteroData Batches
tests
documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -52,6 +52,10 @@ Heterogeneous Temporal Signal Batch Iterators\n:members:\n:undoc-members:\n+.. automodule:: torch_geometric_temporal.signal.dynamic_hetero_graph_static_s... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | dynamic hetero graph static signal batch
- data structure that works like DynamicGraphStaticSignal but with PyG HeteroData Batches
- tests
- documentation |
87,715 | 03.02.2022 10:31:16 | -3,600 | c354f9b25977f1398224481a7f56067d38ae5c54 | dynamic hetero graph temporal signal
new data structure that works like DynamicGraphTemporalSignal but with PyG HeteroData objects
tests
documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -26,6 +26,10 @@ Heterogeneous Temporal Signal Iterators\n:members:\n:undoc-members:\n+.. automodule:: torch_geometric_temporal.signal.dynamic_hetero_graph_temporal_signa... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | dynamic hetero graph temporal signal
- new data structure that works like DynamicGraphTemporalSignal but with PyG HeteroData objects
- tests
-documentation |
87,715 | 03.02.2022 10:51:42 | -3,600 | 0437310837b3826acc5152a77508377ba990c2f3 | dynamic hetero graph temporal signal batch
data structure that works like DynamicGraphTemporalSignalBatch but with PyG HeteroData Batches instead
tests
documentation | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/signal.rst",
"new_path": "docs/source/modules/signal.rst",
"diff": "@@ -56,6 +56,10 @@ Heterogeneous Temporal Signal Batch Iterators\n:members:\n:undoc-members:\n+.. automodule:: torch_geometric_temporal.signal.dynamic_hetero_graph_temporal... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | dynamic hetero graph temporal signal batch
- data structure that works like DynamicGraphTemporalSignalBatch but with PyG HeteroData Batches instead
- tests
-documentation |
87,717 | 10.02.2022 02:49:02 | -3,600 | 1924595741d8da2b71e21665888619bfd7a266c9 | Fix an error in documentation for TGCN cell.
It says that "improved" parameter is set on default to True, however it is set defaultly to False. | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"new_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"diff": "@@ -10,7 +10,7 @@ class TGCN(torch.nn.Module):\nArgs:\nin_channels (int): Number of input features.\nout_channels (int): Number ... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Fix an error in documentation for TGCN cell.
It says that "improved" parameter is set on default to True, however it is set defaultly to False. |
87,715 | 16.02.2022 13:10:37 | -3,600 | 87a1f7361c0dfc0fa079a016dbade6cee676b2d8 | adapt train/test split for heterogeneous data structures
adapted train/test split method to heterogeneous data structures
train/test split tests for hetero signals
train/test split tests for hetero batches | [
{
"change_type": "MODIFY",
"old_path": "test/batch_test.py",
"new_path": "test/batch_test.py",
"diff": "@@ -51,6 +51,52 @@ def generate_signal(snapshot_count, node_count, feature_count, graph_count):\nreturn edge_indices, edge_weights, features, targets, batches\n+def generate_heterogeneous_signal(s... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | adapt train/test split for heterogeneous data structures
- adapted train/test split method to heterogeneous data structures
- train/test split tests for hetero signals
- train/test split tests for hetero batches |
87,715 | 02.03.2022 11:26:27 | -3,600 | 437c1cff901549849fd280f4433e8f731c36b0b8 | layer similar to GCLSTM for heterogeneous graphs | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/__init__.py",
"new_path": "torch_geometric_temporal/nn/__init__.py",
"diff": "from .recurrent import *\nfrom .attention import *\n+from .hetero import *\n"
},
{
"change_type": "ADD",
"old_path": null,
"new_path": "to... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | layer similar to GCLSTM for heterogeneous graphs |
87,715 | 02.03.2022 11:26:39 | -3,600 | 90d54e891e170f976c1f71b00f4da37f7002a175 | Create heterogeneous_test.py
tests for new layer | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "test/heterogeneous_test.py",
"diff": "+import torch\n+import numpy as np\n+import networkx as nx\n+import torch_geometric.transforms as T\n+from torch_geometric.data import HeteroData\n+from torch_geometric_temporal.nn.hetero import HeteroGCLSTM... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Create heterogeneous_test.py
tests for new layer |
87,715 | 02.03.2022 11:26:49 | -3,600 | 7564301ad3d4ea092f20ef74f312abc2aacce413 | documentation for new layer | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/root.rst",
"new_path": "docs/source/modules/root.rst",
"diff": "@@ -124,3 +124,12 @@ Auxiliary Graph Convolutional Layers\n:members:\n:undoc-members:\n:exclude-members: bn_init, conv_init, conv_branch_init, GraphAAGCN, AAGCN\n+\n+\n+Heterog... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | documentation for new layer |
87,730 | 24.03.2022 11:14:22 | -3,600 | 0725f2fa7725f6e32acff89f9fec32a82214c5af | Fixed Montevideo Bus dataset
Map bus stop identifiers to node indices in edges | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/dataset/montevideo_bus.py",
"new_path": "torch_geometric_temporal/dataset/montevideo_bus.py",
"diff": "@@ -24,9 +24,14 @@ class MontevideoBusDatasetLoader(object):\nurl = \"https://raw.githubusercontent.com/benedekrozemberczki/pytorch_... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Fixed Montevideo Bus dataset
Map bus stop identifiers to node indices in edges |
87,715 | 29.03.2022 16:46:08 | -7,200 | ceee0c39b3de53f643cd27c6065e49977a367705 | Matrix multiplication bug fixed | [
{
"change_type": "MODIFY",
"old_path": "docs/source/modules/root.rst",
"new_path": "docs/source/modules/root.rst",
"diff": "@@ -132,4 +132,3 @@ Heterogeneous Graph Convolutional Layers\n.. automodule:: torch_geometric_temporal.nn.hetero.heterogclstm\n:members:\n:undoc-members:\n- :exclude-members: H... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Matrix multiplication bug fixed |
87,722 | 31.03.2022 17:04:47 | -7,200 | 1a8826f687ddb7490a33144e3cec999fb7c87a5c | fixed lambda_max error when normalization != sym | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/recurrent/gc_lstm.py",
"new_path": "torch_geometric_temporal/nn/recurrent/gc_lstm.py",
"diff": "@@ -133,31 +133,31 @@ class GCLSTM(torch.nn.Module):\nC = torch.zeros(X.shape[0], self.out_channels).to(X.device)\nreturn C\n- def _calc... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | fixed lambda_max error when normalization != sym |
87,709 | 05.04.2022 15:24:24 | 0 | 609148a5876463e11432c98511fb1be42d6902a5 | remove unused parameters and variables for MPNNLSTM | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/recurrent/mpnn_lstm.py",
"new_path": "torch_geometric_temporal/nn/recurrent/mpnn_lstm.py",
"diff": "@@ -11,7 +11,6 @@ class MPNNLSTM(nn.Module):\nArgs:\nin_channels (int): Number of input features.\nhidden_size (int): Dimension of h... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | remove unused parameters and variables for MPNNLSTM |
87,709 | 05.04.2022 15:31:12 | 0 | e0622fd0eb23ef5b9292255f75c91b0ae5d4a9c5 | update test for mpnnlstm | [
{
"change_type": "MODIFY",
"old_path": "test/recurrent_test.py",
"new_path": "test/recurrent_test.py",
"diff": "@@ -150,7 +150,6 @@ def test_mpnn_lstm_layer():\nedge_per_node = 10\nin_channels = 64\nhidden_size = 32\n- out_channels = 16\nwindow = 1\ndevice = torch.device(\"cuda\" if torch.cuda.is_av... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | update test for mpnnlstm |
87,726 | 21.04.2022 10:10:11 | -3,600 | d673730ab19dca0c10c555e7b6897a5c22a1fc4d | support for slicing signals | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/signal/dynamic_graph_static_signal.py",
"new_path": "torch_geometric_temporal/signal/dynamic_graph_static_signal.py",
"diff": "@@ -105,7 +105,16 @@ class DynamicGraphStaticSignal(object):\ndef __len__(self):\nreturn len(self.targets)\n... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | support for slicing signals |
87,725 | 10.07.2022 15:30:46 | 14,400 | 5aad6554f349390706daf2584e830203ebf1cb8a | Change dicts to nn.ParamaterDicts so setting the model device changes paramaters | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/hetero/heterogclstm.py",
"new_path": "torch_geometric_temporal/nn/hetero/heterogclstm.py",
"diff": "@@ -2,7 +2,7 @@ import torch\nfrom torch.nn import Parameter\nfrom torch_geometric.nn import HeteroConv, SAGEConv\nfrom torch_geomet... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Change dicts to nn.ParamaterDicts so setting the model device changes paramaters |
87,725 | 11.07.2022 13:09:24 | 14,400 | 89f8595ac5093b80373ed4de5a5fa0b731b2677e | optimize code to prevent repeated calls to convolution operator | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/hetero/heterogclstm.py",
"new_path": "torch_geometric_temporal/nn/hetero/heterogclstm.py",
"diff": "@@ -109,21 +109,24 @@ class HeteroGCLSTM(torch.nn.Module):\ndef _calculate_input_gate(self, x_dict, edge_index_dict, h_dict, c_dict)... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | optimize code to prevent repeated calls to convolution operator |
87,714 | 01.08.2022 11:28:40 | -3,600 | 26c4876f637f0b0a9ef26a335d8fa47ac48dd7ae | Remove redundant steps from CI workflow | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/main.yml",
"new_path": ".github/workflows/main.yml",
"diff": "@@ -28,22 +28,17 @@ jobs:\npython-version: 3.7\n- run: conda --version\n- run: which python\n- - name: Run installation.\n+ - name: Install main dependencies\nrun: |\nconda install... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Remove redundant steps from CI workflow |
87,714 | 01.08.2022 11:31:22 | -3,600 | 59bf787b48c00a921db587052e883ed387252329 | Use "python -m pytest"
This is more reliable | [
{
"change_type": "MODIFY",
"old_path": "README.md",
"new_path": "README.md",
"diff": "@@ -189,7 +189,7 @@ where `${CUDA}` should be replaced by either `cpu`, `cu102`, or `cu113` dependin\n**Running tests**\n```\n-$ pytest test\n+$ python -m pytest test\n```\n-----------------------------------------... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Use "python -m pytest"
This is more reliable |
87,714 | 01.08.2022 12:06:23 | -3,600 | 9c876342f85beae69b4b481b2d38880ef34594ed | Remove unittest from test requirements | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -14,7 +14,7 @@ install_requires = [\n\"six\",\n\"networkx\",\n]\n-tests_require = [\"pytest\", \"pytest-cov\", \"mock\", \"unittest\", \"networkx\"]\n+tests_require = [\"pytest\", \"pytest-cov\", \"mock\", \"netwo... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Remove unittest from test requirements |
87,720 | 29.08.2022 14:32:10 | -7,200 | c5a96b6025a274e41a549094d6aa0f67160e8f93 | change on _set_hidden_state()
Allows TGCN2 to work with batch from different sizes. Current implementation forces all batches to be the same size (defined by self.batch_size). | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"new_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"diff": "@@ -138,13 +138,13 @@ class TGCN2(torch.nn.Module):\nArgs:\nin_channels (int): Number of input features.\nout_channels (int): Nu... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | change on _set_hidden_state()
Allows TGCN2 to work with batch from different sizes. Current implementation forces all batches to be the same size (defined by self.batch_size). |
87,720 | 30.08.2022 10:25:18 | -7,200 | cbb8ba51c3f7485450f3e50858228e530da66ca0 | Must keep batch_size as parameter | [
{
"change_type": "MODIFY",
"old_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"new_path": "torch_geometric_temporal/nn/recurrent/temporalgcn.py",
"diff": "@@ -138,12 +138,14 @@ class TGCN2(torch.nn.Module):\nArgs:\nin_channels (int): Number of input features.\nout_channels (int): Nu... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Must keep batch_size as parameter |
87,714 | 30.08.2022 15:28:19 | -3,600 | 60a5428ef053d5f077d396b5b10e7dca176f5944 | Make tqdm an optional dependency | [
{
"change_type": "MODIFY",
"old_path": "examples/recurrent/a3tgcn_example.py",
"new_path": "examples/recurrent/a3tgcn_example.py",
"diff": "+try:\nfrom tqdm import tqdm\n+except ImportError:\n+ def tqdm(iterable):\n+ return iterable\nimport torch\nimport torch.nn.functional as F\n"
},
{
"cha... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Make tqdm an optional dependency |
87,714 | 30.08.2022 16:04:47 | -3,600 | 489ffc6a1fc3fed48b80ea0686dcade19ae0ef27 | Restore networkx as tests dependency
Not actually used in main code | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -13,7 +13,7 @@ install_requires = [\n\"six\",\n\"networkx\",\n]\n-tests_require = [\"pytest\", \"pytest-cov\", \"mock\", \"tqdm\"]\n+tests_require = [\"pytest\", \"pytest-cov\", \"mock\", \"networkx\", \"tqdm\"]\n... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Restore networkx as tests dependency
Not actually used in main code |
87,714 | 30.08.2022 16:45:09 | -3,600 | 2bd4e5db0233f77174e9a88dbb9dbe1e8aa706e6 | Update installation instructions for PyTorch 1.11.0 and PyG 2.x | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/main.yml",
"new_path": ".github/workflows/main.yml",
"diff": "name: CI\non:\n-\npush:\nbranches: [ master ]\npull_request:\nbranches: [ master ]\n-\nworkflow_dispatch:\njobs:\n@@ -30,11 +28,8 @@ jobs:\n- run: which python\n- name: Install mai... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Update installation instructions for PyTorch 1.11.0 and PyG 2.x |
87,714 | 30.08.2022 16:51:55 | -3,600 | 4c8f670561302744ad0a16e430f5ec03925673eb | Fix torch 1.11.0 installation | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/main.yml",
"new_path": ".github/workflows/main.yml",
"diff": "@@ -28,7 +28,7 @@ jobs:\n- run: which python\n- name: Install main dependencies\nrun: |\n- python -m pip install pytorch==1.11.0 torchvision==0.12.0 torchaudio==0.11.0\n+ python -m... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Fix torch 1.11.0 installation |
87,714 | 30.08.2022 16:00:10 | -3,600 | b7960f21299a2cf726332469053d15737f4b5bea | Remove unused import of eigs from scipy | [
{
"change_type": "MODIFY",
"old_path": "notebooks/astgcn_for_traffic_flow_forecasting.ipynb",
"new_path": "notebooks/astgcn_for_traffic_flow_forecasting.ipynb",
"diff": "\"import torch.nn as nn\\n\",\n\"import torch.optim as optim\\n\",\n\"import torch.nn.functional as F\\n\",\n- \"from scipy.sparse... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Remove unused import of eigs from scipy |
87,714 | 04.09.2022 21:36:15 | -3,600 | 0972adde44ca6fe24671fa24dbcbb0d5db7f287b | Remove dependency on six
Also remove unused "import io" | [
{
"change_type": "MODIFY",
"old_path": "docs/requirements.txt",
"new_path": "docs/requirements.txt",
"diff": "@@ -8,4 +8,3 @@ https://data.pyg.org/whl/torch-1.10.0%2Bcpu/torch_spline_conv-1.2.1-cp37-cp37m-l\ntorch_geometric\nsphinx==4.0.2\nsphinx_rtd_theme==0.5.2\n-six\n"
},
{
"change_type":... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Remove dependency on six
Also remove unused "import io" |
87,721 | 24.10.2022 15:42:59 | -7,200 | e248e1de8034cbb59675f4f2173b4e8b9e807490 | Update introduction.rst
fix typo in intro rst | [
{
"change_type": "MODIFY",
"old_path": "docs/source/notes/introduction.rst",
"new_path": "docs/source/notes/introduction.rst",
"diff": "@@ -11,7 +11,7 @@ If you find *PyTorch Geometric Temporal* useful in your research, please conside\n.. code-block:: latex\n>@inproceedings{rozemberczki2021pytorch,\... | Python | MIT License | benedekrozemberczki/pytorch_geometric_temporal | Update introduction.rst
fix typo in intro rst |
89,685 | 01.05.2017 22:13:25 | 25,200 | 7d3b30579ec42882ff63774e58a3605fe63d9fd9 | additions to support homolog service | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -36,12 +36,11 @@ object for the intermediate entity.\nTODO\n\"\"\"\n-import logging\n-\n-import pysolr\nimport json\nimport logging\n-import time\n+import pysolr\n+\n+from ontob... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | additions to support homolog service |
89,697 | 21.06.2017 13:26:29 | 25,200 | 4a7f2240fae136111785f829a31bb6746ed0b7c2 | named arguments must come before variable args | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -854,7 +854,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nstart = n_docs\nwhile n_docs >= self.rows:\nlogging.info(\"Iterating; start={}\".format(start))\n- next_results ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | named arguments must come before variable args |
89,697 | 22.06.2017 12:44:27 | 25,200 | a3c458bac73024791ffd3fc377607a0ecea3366a | Implemented query for association by a list of concept ID's.
Added 'concepts' parameter to GolrAssociationQuery constructor
which is a list of concept id's to be matched against either
the subject_closure or the object_closure. | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -433,6 +433,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nsubject_category=None,\nobject_category=None,\nrelation=None,\n+ concepts=None,\nsubject=None,\nsubjects=None,\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Implemented query for association by a list of concept ID's.
- Added 'concepts' parameter to GolrAssociationQuery constructor
which is a list of concept id's to be matched against either
the subject_closure or the object_closure. |
89,697 | 22.06.2017 13:46:12 | 25,200 | d6dc6c99c2a21d05c29bad706247414cbb8a43af | Changed 'concepts' to 'subject_or_object_ids' | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -433,7 +433,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nsubject_category=None,\nobject_category=None,\nrelation=None,\n- concepts=None,\n+ subject_or_object_ids=None,\n... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Changed 'concepts' to 'subject_or_object_ids' |
89,697 | 29.06.2017 17:23:33 | 25,200 | bbe3c01eeb4fb67d3621c395d3c00930b5b7f87b | Refactored subject_or_object searching, and added semantic category filter with subject_or_object_category | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -131,6 +131,9 @@ def flip(d, x, y):\ndef solr_quotify(v):\nif isinstance(v, list):\n+ if len(v) == 1:\n+ return solr_quotify(v[0])\n+ else:\nreturn '({})'.format(\" OR \".join([... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Refactored subject_or_object searching, and added semantic category filter with subject_or_object_category |
89,697 | 30.06.2017 12:19:35 | 25,200 | 4b32b28ac83fe2e8aad0366c799490e520b4b87a | Renamed vars for clarity | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -764,23 +764,23 @@ class GolrAssociationQuery(GolrAbstractQuery):\n# with an ID that is contained in subject_or_object_ids.\nif subject_or_object_ids is not None:\nquotified_ids... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Renamed vars for clarity |
89,683 | 03.07.2017 18:19:03 | 25,200 | 17d7face1a9d336cf4bc491e45aaeaf617cb18d2 | add check that install python 3 | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "import os\n+import sys\nimport re\nimport subprocess\nimport setuptools\n+if sys.version_info.major < 3:\n+ sys.exit(\"Error: Python 3 is required\")\n+\ndirectory = os.path.dirname(os.path.abspath(__file__))\n# vers... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add check that install python 3 |
89,697 | 07.07.2017 15:03:34 | 25,200 | a908d0579b8ae09cdccadffbd4037b7ea9f84224 | In subject_or_object_ids association search changed from subject and object to subject_closure and object_closure. | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -764,8 +764,8 @@ class GolrAssociationQuery(GolrAbstractQuery):\n# with an ID that is contained in subject_or_object_ids.\nif subject_or_object_ids is not None:\nquotified_ids =... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | In subject_or_object_ids association search changed from subject and object to subject_closure and object_closure. |
89,697 | 07.07.2017 16:37:54 | 25,200 | 5028d263f73583721786e147efbc7f33a22667f7 | Added non_null_fields to GolrAssociationQuery | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -476,6 +476,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nrows=10,\nstart=None,\nhomology_type=None,\n+ non_null_fields=[],\n**kwargs):\n\"\"\"Fetch a set of association ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Added non_null_fields to GolrAssociationQuery |
89,687 | 12.10.2017 09:08:30 | 25,200 | 250d6272fd743a0cf05e64d43f8e6679e11ca75f | Added WB : WormBase to prefix normalization | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -120,7 +120,8 @@ M=GolrFields()\n# normalize to what Monarch uses\nPREFIX_NORMALIZATION_MAP = {\n'MGI:MGI' : 'MGI',\n- 'FB' : 'FlyBase'\n+ 'FB' : 'FlyBase',\n+ 'WB' : 'WormBase'... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Added WB : WormBase to prefix normalization |
89,698 | 16.02.2018 11:47:54 | 28,800 | c0022ae82c560f7fd9f9d176f5bb72de2f9cf38a | Initial resolution for issue
Performs case sensitive search, which is a problem. Need to implement
case insensitive search for keywords at least. | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "ontobio/golr/beacon_query.py",
"diff": "+from ontobio.golr.golr_query import GolrAssociationQuery, M\n+\n+class BeaconAssociationQuery(GolrAssociationQuery):\n+ \"\"\"\n+ A query object for performing the beacon association search functionality.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Initial resolution for issue #143
- Performs case sensitive search, which is a problem. Need to implement
case insensitive search for keywords at least. |
89,685 | 02.03.2018 14:46:01 | 28,800 | 581be30ea8b7aa9ac2b776d0c9435e11bda3a1d8 | revert back notebook files | [
{
"change_type": "MODIFY",
"old_path": "notebooks/output/anxiety-disorder.png",
"new_path": "notebooks/output/anxiety-disorder.png",
"diff": "Binary files a/notebooks/output/anxiety-disorder.png and b/notebooks/output/anxiety-disorder.png differ\n"
}
] | Python | BSD 3-Clause New or Revised License | biolink/ontobio | revert back notebook files |
89,692 | 06.03.2018 14:39:23 | 28,800 | d7b5cba57a7a7849e8e292c4069711053258789a | if querying AmiGO golr instance then use AmiGO schema-specific evidence fields in Solr query | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -104,6 +104,20 @@ class GolrFields:\nRELATION='relation'\nRELATION_LABEL='relation_label'\n+ # This is a temporary fix until\n+ # https://github.com/biolink/ontobio/issues/126 i... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | if querying AmiGO golr instance then use AmiGO schema-specific evidence fields in Solr query |
89,685 | 06.03.2018 20:00:50 | 28,800 | ca818abfbbfdbbefd950e017a5b31b1391b5f973 | add autocomplete endpoint for layperson synonyms | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -39,7 +39,8 @@ TODO\nimport json\nimport logging\nimport pysolr\n-\n+import xml.etree.ElementTree as ET\n+from collections import OrderedDict\nfrom ontobio.vocabulary.relations ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add autocomplete endpoint for layperson synonyms |
89,692 | 08.03.2018 16:27:30 | 28,800 | 480e14739d9dffe8a33e2c20f7149596a5429851 | add 4 additional evidence fields | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -112,10 +112,14 @@ class GolrFields:\n'evidence',\n'evidence_label',\n'evidence_type',\n+ 'evidence_type_label',\n+ 'evidence_with',\n'evidence_closure',\n'evidence_closure_labe... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add 4 additional evidence fields |
89,692 | 26.03.2018 18:06:03 | 25,200 | 18c8ae88f1cc81dfb533432d947eafa64673ca97 | add 'reference', 'qualifier', 'is_redundant_for' and 'type' for GOlr query | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -107,8 +107,12 @@ class GolrFields:\n# This is a temporary fix until\n# https://github.com/biolink/ontobio/issues/126 is resolved.\n- # AmiGO specific evidence fields\n- AMIGO_E... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add 'reference', 'qualifier', 'is_redundant_for' and 'type' for GOlr query |
89,692 | 27.03.2018 14:45:42 | 25,200 | 7468558d959dd0d92c98f8b22e1f2967dccb6a29 | Fix condition for checking select_fields before adding GOlr specific fields | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -847,8 +847,7 @@ class GolrAssociationQuery(GolrAbstractQuery):\nfacet_fields = [ map_field(fn, self.field_mapping) for fn in facet_fields ]\nif self._use_amigo_schema:\n- if le... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix condition for checking select_fields before adding GOlr specific fields |
89,692 | 29.03.2018 15:35:06 | 25,200 | e8f5106f2c971fa9d2e9c84cfecca266293481a3 | Include result hits as 'numFound' in payload returned by GolrSearchQuery and GolrAssociationQuery | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -388,6 +388,7 @@ class GolrSearchQuery(GolrAbstractQuery):\npayload = {\n'facet_counts': translate_facet_field(fcs),\n'pagination': {},\n+ 'numFound': results.hits,\n'highlighti... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Include result hits as 'numFound' in payload returned by GolrSearchQuery and GolrAssociationQuery |
89,685 | 05.04.2018 17:55:17 | 25,200 | f9fecc2d552152d899723e72012625e456c01fd1 | add autocomplete, best hl to search | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -258,7 +258,9 @@ class GolrSearchQuery(GolrAbstractQuery):\nfacet_fields=None,\nsearch_fields=None,\nrows=100,\n- start=None):\n+ start=None,\n+ prefix=None,\n+ boost_fx=None):\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add autocomplete, best hl to search |
89,685 | 05.04.2018 18:47:39 | 25,200 | 4c351d9bb7716028f33fda0169b7f214e97a1629 | genotypes break xml parser | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -5,7 +5,7 @@ amigo_solr_assocs:\nurl: \"http://golr.berkeleybop.org\"\ntimeout: 4\nsolr_search:\n- url: \"https://solr.monarchinitiative.org/solr/search\"\n+ url: \"https://solr-dev.monarchin... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | genotypes break xml parser |
89,685 | 06.04.2018 15:31:54 | 25,200 | 23108991c6a0494d640f61a0f0f56e35d283ec4d | use first label when hl fails | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -414,8 +414,8 @@ class GolrSearchQuery(GolrAbstractQuery):\n}\nexcept ET.ParseError:\nhighlight = {\n- 'highlight': doc['label'],\n- 'match': doc['label']\n+ 'highlight': doc['l... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use first label when hl fails |
89,685 | 10.04.2018 20:03:41 | 25,200 | d22bc031e1f635603add660c38aa7d926f39e377 | add option for hl class | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -282,7 +282,8 @@ class GolrSearchQuery(GolrAbstractQuery):\nrows=100,\nstart=None,\nprefix=None,\n- boost_fx=None):\n+ boost_fx=None,\n+ highlight_class=None):\nself.term = term... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add option for hl class |
89,685 | 11.04.2018 15:52:47 | 25,200 | 9930ce2f1b66b912444c2553bd6c95794ef63df7 | update to match monarch qf weights | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -306,8 +306,14 @@ class GolrSearchQuery(GolrAbstractQuery):\nself.facet_fields = ['category', 'taxon_label']\nif self.search_fields is None:\n- self.search_fields = dict(iri=3, ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update to match monarch qf weights |
89,685 | 11.04.2018 16:28:02 | 25,200 | c59a70dbea8cc7393439ddf670fb2af2441fd935 | add solr boost query as option | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -283,6 +283,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nstart=None,\nprefix=None,\nboost_fx=None,\n+ boost_q=None,\nhighlight_class=None):\nself.term = term\nself.category =... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add solr boost query as option |
89,685 | 16.04.2018 21:54:09 | 25,200 | a3d860520ebefcb467587d1128f5a38958433075 | refactor, add support for taxon filter | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -39,9 +39,11 @@ TODO\nimport json\nimport logging\nimport pysolr\n+from typing import Dict, List\nimport xml.etree.ElementTree as ET\nfrom collections import OrderedDict\nfrom o... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | refactor, add support for taxon filter |
89,685 | 16.04.2018 22:04:47 | 25,200 | dad0b49a877edb8e7d5b879a2f81c891f0c6eb7a | return tuple as dict | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -455,7 +455,7 @@ class GolrSearchQuery(GolrAbstractQuery):\nif results.highlighting:\nfor doc in results.docs:\nhl = self._process_highlight(results, doc)\n- highlighting[doc['i... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | return tuple as dict |
89,685 | 17.04.2018 16:09:24 | 25,200 | 7c449e68d236ec813caa404b5dc50c1a6c3afb02 | add some functional tests | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -323,7 +323,6 @@ class GolrSearchQuery(GolrAbstractQuery):\nequivalent_curie=1)\ndef solr_params(self):\n- #facet_fields = [ map_field(fn, self.field_mapping) for fn in self.fac... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add some functional tests |
89,685 | 17.04.2018 17:16:36 | 25,200 | 8c27ab4b3315b3ebd5fd0807ee1b65d55e5060dc | default taxon and taxon_label to empty string | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -492,8 +492,8 @@ class GolrSearchQuery(GolrAbstractQuery):\nelse:\nhl = Highlight(None, None, None)\n- doc['taxon'] = doc['taxon'] if 'taxon' in doc else []\n- doc['taxon_label'... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | default taxon and taxon_label to empty string |
89,685 | 20.04.2018 17:26:35 | 25,200 | 4175402aab7d265d4cc89f534a06a27d339d83d5 | use MagicMock to test more functions | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -21,7 +21,7 @@ foo:\n# only run local tests\ntravis_test:\n- pytest tests/test_*local*.py tests/test_*parser*.py tests/test_qc.py\n+ pytest tests/test_*local*.py tests/test_*parser*.py tests/test_qc.py tests/unit/... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | use MagicMock to test more functions |
89,685 | 20.04.2018 17:32:46 | 25,200 | 3a2c1ea63e6478c61d4545c38646d8df8045309c | python -m pytest | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -8,7 +8,7 @@ PACKAGES = ontobio prefixcommons\nsubpackage_tests: $(patsubst %,test-%,$(PACKAGES))\ntest:\n- pytest tests/*.py\n+ python -m pytest tests/*.py tests/unit/\ndebug_test:\npytest -s -vvvv tests/*.py\n@@... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | python -m pytest |
89,685 | 20.04.2018 17:56:43 | 25,200 | cf52528e64a7691cb3266eafd4714b04190c14cb | out of curiosity... | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -11,7 +11,7 @@ install:\n- pip install --only-binary=numpy,scipy numpy scipy\n- python setup.py install\n- python setup.py sdist bdist_wheel\n-# - \"pip install -r requirements.txt\"\n+ - pip install -r requ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | out of curiosity... |
89,685 | 20.04.2018 17:59:27 | 25,200 | 294754d70386f56215c648909c92a3a800589f76 | is marshmallow version the issue? | [
{
"change_type": "MODIFY",
"old_path": ".travis.yml",
"new_path": ".travis.yml",
"diff": "@@ -11,7 +11,7 @@ install:\n- pip install --only-binary=numpy,scipy numpy scipy\n- python setup.py install\n- python setup.py sdist bdist_wheel\n- - pip install -r requirements.txt\n+# - \"pip install -r requir... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | is marshmallow version the issue? |
89,685 | 20.04.2018 18:01:58 | 25,200 | 67c3f9c81f9b5028aa774c73b1108fcb3f66ae97 | revert to pytest instead of python -m pytest | [
{
"change_type": "MODIFY",
"old_path": "Makefile",
"new_path": "Makefile",
"diff": "@@ -8,7 +8,7 @@ PACKAGES = ontobio prefixcommons\nsubpackage_tests: $(patsubst %,test-%,$(PACKAGES))\ntest:\n- python -m pytest tests/*.py tests/unit/\n+ pytest tests/*.py tests/unit/\ndebug_test:\npytest -s -vvvv te... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | revert to pytest instead of python -m pytest |
89,685 | 23.04.2018 13:41:08 | 25,200 | f04705029043b2a12636fbeef3fd5d28b552b1de | fix RO relation | [
{
"change_type": "MODIFY",
"old_path": "ontobio/vocabulary/relations.py",
"new_path": "ontobio/vocabulary/relations.py",
"diff": "@@ -23,7 +23,7 @@ class Evidence():\n_prefixmap = {\n'SEPIO': 'http://purl.obolibrary.org/obo/SEPIO_',\n'IAO': 'http://purl.obolibrary.org/obo/IAO_',\n- 'RO': 'RO://purl.... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix RO relation |
89,692 | 26.04.2018 13:33:19 | 25,200 | 8953b47770ecbe9cd43ae7737d4576c04ec68e4a | Fix the way results are parsed when 'invert_subject_object' is True | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -142,6 +142,25 @@ class GolrFields:\n# create an instance\nM=GolrFields()\n+# fields in the result docs that are to be inverted when 'invert_subject_object' is True\n+INVERT_FIE... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix the way results are parsed when 'invert_subject_object' is True |
89,692 | 26.04.2018 13:35:48 | 25,200 | 26fe50b3ea58972907e1135462301c7b4a7aa904 | add kwargs to golr_associations.get_homologs() | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_associations.py",
"new_path": "ontobio/golr/golr_associations.py",
"diff": "@@ -293,10 +293,10 @@ def calculate_information_content(**kwargs):\nfrom ontobio.vocabulary.relations import HomologyTypes\n-def get_homologs(gene, relation=HomologyT... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add kwargs to golr_associations.get_homologs() |
89,685 | 02.05.2018 10:59:29 | 25,200 | 8556bc20d9dfa067c9303cd4a1df99f9ff5e4e3f | Support a list of prefix filters (pos and neg) | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -415,10 +415,18 @@ class GolrSearchQuery(GolrAbstractQuery):\nparams['fq'] = []\nif self.prefix is not None:\n- if self.prefix.startswith('-'):\n- params['fq'].append('-prefix:\... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Support a list of prefix filters (pos and neg) |
89,685 | 06.06.2018 13:48:24 | 25,200 | 6bb2d66e48c63c201b4dcd2156146088443498d1 | handle solr docs without a category | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -519,13 +519,16 @@ class GolrSearchQuery(GolrAbstractQuery):\nelse:\nhl = Highlight(None, None, None)\n+ # In some cases a node does not have a category\n+ category = doc['categ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | handle solr docs without a category |
89,691 | 14.06.2018 11:16:52 | 25,200 | fbcfb0263fd914f3d98e6744f5c8a20e7ad0aeda | Potentially fixing issue for parent_index method | [
{
"change_type": "MODIFY",
"old_path": "ontobio/ontol.py",
"new_path": "ontobio/ontol.py",
"diff": "@@ -622,7 +622,7 @@ class Ontology():\ng = self.get_filtered_graph(relations)\nl = []\nfor n in g:\n- l.append([n] ++ g.predecessors(b))\n+ l.append([n] + g.predecessors(n))\nreturn l\ndef text_defini... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Potentially fixing issue #187 for parent_index method |
89,691 | 14.06.2018 12:03:25 | 25,200 | 9dffcef020038d0d8f1a3de7f37ffdc1ec7d505b | Adding parent_index test for issue | [
{
"change_type": "MODIFY",
"old_path": "tests/test_wd_ontol.py",
"new_path": "tests/test_wd_ontol.py",
"diff": "@@ -45,3 +45,7 @@ def test_factory():\nw.write(ont, query_ids=qids)\n+def test_parent_index():\n+ ont = OntologyFactory().create(\"go\")\n+ sub = ont.subontology(ont.ancestors('GO:0010971'... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Adding parent_index test for issue #187 |
89,692 | 26.06.2018 11:13:57 | 25,200 | 54b21c2df6145a56e20169cb2448dddabb74c490 | update AmiGO Solr URL | [
{
"change_type": "MODIFY",
"old_path": "conf/config.yaml",
"new_path": "conf/config.yaml",
"diff": "@@ -2,7 +2,7 @@ solr_assocs:\nurl: \"https://solr.monarchinitiative.org/solr/golr\"\ntimeout: 5\namigo_solr_assocs:\n- url: \"http://golr.berkeleybop.org\"\n+ url: \"http://golr-aux.geneontology.io/so... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update AmiGO Solr URL |
89,692 | 26.06.2018 13:23:39 | 25,200 | 8b37f6e7bebb97378fa5d36766df1b93f8697501 | update AmiGO Solr URLs for tests | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -2,7 +2,7 @@ solr_assocs:\nurl: \"https://solr.monarchinitiative.org/solr/golr\"\ntimeout: 5\namigo_solr_assocs:\n- url: \"http://golr.berkeleybop.org\"\n+ url: \"http://golr-aux.geneontology... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update AmiGO Solr URLs for tests |
89,692 | 13.07.2018 15:25:57 | 25,200 | d9bf8850062c9fe9870ceb1d5b30a722f5715ba2 | Tidy up the way Solr is instantiated in golr_query | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -281,8 +281,8 @@ class GolrAbstractQuery():\nself.config = get_config()\nreturn self.config\n- def _set_solr(self, endpoint):\n- self.solr = pysolr.Solr(endpoint.url, timeout=en... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Tidy up the way Solr is instantiated in golr_query |
89,692 | 16.07.2018 13:46:57 | 25,200 | 6dafbb4498865c284131cd9f60cbb99f64392bf5 | Use appropriate user-agent in requests | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -9,6 +9,7 @@ import re\nfrom functools import wraps\n+from ontobio.util.user_agent import get_user_agent\nfrom ontobio.ontol_factory import OntologyFactory\nfrom ontobio.io.gafparser import GafParser... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Use appropriate user-agent in requests |
89,692 | 17.07.2018 17:54:38 | 25,200 | 975c01a26266edabd35cdc3ea8f083409a43e1e0 | Update User-Agent format | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -79,7 +79,7 @@ def download_source_gafs(group_metadata, target_dir, exclusions=[]):\nif urllib.parse.urlparse(gaf_url)[0] in [\"ftp\", \"file\"]:\nurllib.request.urlretrieve(gaf_url, path)\nelse:\n- ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Update User-Agent format |
89,692 | 18.07.2018 13:40:10 | 25,200 | 1e39431bc8210487b348683e80f53d61187908ed | Expose User-Agent as an argument in golr_query with sensible default | [
{
"change_type": "MODIFY",
"old_path": "bin/validate.py",
"new_path": "bin/validate.py",
"diff": "@@ -79,7 +79,7 @@ def download_source_gafs(group_metadata, target_dir, exclusions=[]):\nif urllib.parse.urlparse(gaf_url)[0] in [\"ftp\", \"file\"]:\nurllib.request.urlretrieve(gaf_url, path)\nelse:\n- ... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Expose User-Agent as an argument in golr_query with sensible default |
89,692 | 30.07.2018 17:03:29 | 25,200 | 26197e51f6b38bc8409b61bed898ec8631d0a448 | Add relationship_type argument to GolrAssociationQuery | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -47,6 +47,13 @@ from ontobio.vocabulary.relations import HomologyTypes\nfrom ontobio.model.GolrResults import SearchResults, AutocompleteResult, Highlight\nfrom ontobio.util.use... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Add relationship_type argument to GolrAssociationQuery |
89,688 | 13.08.2018 10:27:40 | 25,200 | 316c4f89b2ced2e2b94801b1380f42cea9415849 | Adding some Enums and some JSON transform functions, as well as sparql_go.py with SPARQL queries | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "ontobio/sparql/sparql_go.py",
"diff": "+from ontobio.sparql.sparql_ontol_utils import SEPARATOR\n+\n+def correctGOID(self, goid):\n+ return goid.replace(\":\", \"_\")\n+\n+def correctGOCAM(self, gocam):\n+ if gocam.find('/') != -1:\n+ gocam = go... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Adding some Enums and some JSON transform functions, as well as sparql_go.py with SPARQL queries |
89,698 | 22.08.2018 14:30:13 | 25,200 | 891256480a50e2342971fbe9e9650cf0fd74e3e7 | create_from_file chooses parser by file suffixes if fmt is None
Added a test for this case | [
{
"change_type": "MODIFY",
"old_path": ".gitignore",
"new_path": ".gitignore",
"diff": "@@ -44,6 +44,7 @@ nosetests.xml\ncoverage.xml\n*,cover\n.hypothesis/\n+.pytest_cache/\n# Translations\n*.mo\n"
},
{
"change_type": "MODIFY",
"old_path": "ontobio/assoc_factory.py",
"new_path": "on... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | create_from_file chooses parser by file suffixes if fmt is None
- Added a test for this case |
89,698 | 23.08.2018 11:30:16 | 25,200 | a43d6deee8fbb9ba2c4ec71d6b5ee3eea8eb00dd | Added slim parameter to AssocationFactory.create | [
{
"change_type": "MODIFY",
"old_path": "ontobio/assoc_factory.py",
"new_path": "ontobio/assoc_factory.py",
"diff": "@@ -33,7 +33,7 @@ class AssociationSetFactory():\ninitializes based on an ontology name\n\"\"\"\n- def create(self, ontology=None,subject_category=None,object_category=None,evidence=No... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Added slim parameter to AssocationFactory.create |
89,698 | 23.08.2018 11:31:02 | 25,200 | 139fe232fd3d6ec71fb791f3cf906daced39e5fa | Created analysis module, moved jaccard_similarity into it | [
{
"change_type": "ADD",
"old_path": "ontobio/analysis/__init__.py",
"new_path": "ontobio/analysis/__init__.py",
"diff": ""
},
{
"change_type": "ADD",
"old_path": null,
"new_path": "ontobio/analysis/semsim.py",
"diff": "+from ontobio.assocmodel import AssociationSet\n+\n+def jacca... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Created analysis module, moved jaccard_similarity into it |
89,692 | 06.09.2018 14:17:01 | 25,200 | 002e53cecd49da06aefa26a90ff98ef4468b3823 | Fix bug introduced when adding relationship_type parameter to GolrAssociationQuery class | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -254,7 +254,7 @@ def goassoc_fieldmap(relationship_type=ACTS_UPSTREAM_OF_OR_WITHIN):\nM.SUBJECT_TAXON_CLOSURE: 'taxon_closure',\nM.RELATION: 'qualifier',\nM.OBJECT: 'annotation_... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Fix bug introduced when adding relationship_type parameter to GolrAssociationQuery class |
89,692 | 06.09.2018 14:17:37 | 25,200 | 7c0e240d48b24221ccee57d4a83a2f0c2b2757f7 | Avoid initializing GolrAssociationQuery for each document | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1434,7 +1434,6 @@ class GolrAssociationQuery(GolrAbstractQuery):\nlf = M.label_field(fname)\n- gq = GolrAssociationQuery(relationship_type=self.relationship_type) ## TODO - mak... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Avoid initializing GolrAssociationQuery for each document |
89,685 | 12.09.2018 11:44:57 | 25,200 | 4065c33d8974683149f86be1237bc2fa54cb392c | boost kw fields for curies | [
{
"change_type": "DELETE",
"old_path": "conf/config.yaml",
"new_path": null,
"diff": "-solr_assocs:\n- url: \"https://solr.monarchinitiative.org/solr/golr\"\n- timeout: 5\n-amigo_solr_assocs:\n- url: \"http://golr-aux.geneontology.io/solr\"\n- timeout: 4\n-solr_search:\n- url: \"https://solr.monarch... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | boost kw fields for curies |
89,685 | 12.09.2018 11:51:22 | 25,200 | fbbcedb40b286a6b5c1c78709cf5af60a5418fed | update lay hpo qf | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -669,7 +669,8 @@ class GolrLayPersonSearch(GolrSearchQuery):\ndef set_lay_params(self):\nparams = self.solr_params()\nsuffixes = ['std', 'kw', 'eng']\n- params['qf'] = self._get... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | update lay hpo qf |
89,688 | 13.09.2018 15:53:07 | 25,200 | 3e48b9638f0aba21cb46726d9a53551e19b029a2 | Required for new GO queries in BioLink - some GOlr queries will probably be later replaced | [
{
"change_type": "MODIFY",
"old_path": "ontobio/golr/golr_query.py",
"new_path": "ontobio/golr/golr_query.py",
"diff": "@@ -1610,3 +1610,76 @@ class GolrAssociationQuery(GolrAbstractQuery):\n# default to input\nreturn id\nreturn ids[0]\n+\n+\n+\n+\n+\n+### This may quite possibly be a temporary code... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Required for new GO queries in BioLink - some GOlr queries will probably be later replaced |
89,688 | 13.09.2018 18:23:43 | 25,200 | 4ae9994791c74024f9d3ce00547a0d9c7293dd73 | Adding taxon_restriction features (restrict the results based on provided taxons if any) | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.py",
"new_path": "ontobio/config.py",
"diff": "@@ -52,6 +52,7 @@ class ConfigSchema(Schema):\ndefault_solr_schema = fields.Str()\nontologies = fields.List(fields.Nested(OntologyConfigSchema))\ncategories = fields.List(fields.Nested(CategorySchem... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | Adding taxon_restriction features (restrict the results based on provided taxons if any) |
89,685 | 10.10.2018 17:02:35 | 25,200 | c2ec0a95d65e73626c3e9c76c4bdf88be4c09196 | implement annotation sufficiency | [
{
"change_type": "MODIFY",
"old_path": "ontobio/config.yaml",
"new_path": "ontobio/config.yaml",
"diff": "@@ -24,7 +24,7 @@ scigraph_data:\ntimeout: 2\nowlsim2:\nurl: \"https://monarchinitiative.org/owlsim/\"\n- timeout: 2\n+ timeout: 5\nuse_amigo_for:\n- function\nontologies:\n"
},
{
"chang... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | implement annotation sufficiency |
89,685 | 19.10.2018 18:00:51 | 25,200 | 50fbc814b9a0b23089670fd2d882d37949dcb4c2 | add owlsim2 api class | [
{
"change_type": "ADD",
"old_path": "ontobio/sim/api/__init__.py",
"new_path": "ontobio/sim/api/__init__.py",
"diff": ""
},
{
"change_type": "ADD",
"old_path": null,
"new_path": "ontobio/sim/api/owlsim2.py",
"diff": "+from ontobio.config import get_config\n+from typing import Lis... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | add owlsim2 api class |
89,685 | 24.10.2018 09:09:10 | 25,200 | 6fa18bd98c2c47f06e54dd0466598635dcf22046 | fix tests, implement compare | [
{
"change_type": "MODIFY",
"old_path": "ontobio/model/similarity.py",
"new_path": "ontobio/model/similarity.py",
"diff": "@@ -47,7 +47,7 @@ class SimMatch:\ndef __init__(self,\nid: str,\nlabel: str,\n- rank: int,\n+ rank: Union[int, str],\nscore: Union[float, int],\ntype: Optional[str]=None,\ntaxon:... | Python | BSD 3-Clause New or Revised License | biolink/ontobio | fix tests, implement compare |
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