Merge branch 'master' into affinity_docs

pyg-team · Mar 20, 2023 · c3e725f · c3e725f
2 parents 092a505 + 06ac5a4
commit c3e725f
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diff --git a/.github/actions/setup/action.yml b/.github/actions/setup/action.yml
@@ -3,16 +3,19 @@ name: Setup
 inputs:
   python-version:
     required: false
-    default: '3.7'
+    default: '3.8'
   torch-version:
     required: false
-    default: '1.13.0'
+    default: '2.0.0'
   cuda-version:
     required: false
     default: cpu
   torchvision-version:
     required: false
-    default: '0.14.0'
+    default: '0.15.0'
+  full_install:
+    required: false
+    default: true
 
 runs:
   using: composite
@@ -29,18 +32,20 @@ runs:
 
     - name: Install PyTorch ${{ inputs.torch-version }}+${{ inputs.cuda-version }}
       run: |
-        pip install torch==${{ inputs.torch-version }} torchvision==${{ inputs.torchvision-version }} --extra-index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
+        pip install torch==${{ inputs.torch-version }} --extra-index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
         python -c "import torch; print('PyTorch:', torch.__version__)"
         python -c "import torch; print('CUDA:', torch.version.cuda)"
       shell: bash
 
     - name: Install extension packages
+      if: ${{ inputs.full_install == 'true' }}
       run: |
+        pip install torchvision==${{ inputs.torchvision-version }} --extra-index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
         pip install torch-scatter torch-sparse torch-cluster torch-spline-conv -f https://data.pyg.org/whl/torch-${{ inputs.torch-version }}+${{ inputs.cuda-version }}.html
       shell: bash
 
-    - name: Install pyg-lib
-      if: ${{ runner.os == 'Linux' }}  # pyg-lib is currently only available on Linux.
+    - name: Install pyg-lib  # pyg-lib is currently only available on Linux.
+      if: ${{ inputs.full_install == 'true' && runner.os == 'Linux' }}
       run: |
         pip install pyg-lib -f https://data.pyg.org/whl/nightly/torch-${{ inputs.torch-version }}+${{ inputs.cuda-version }}.html
       shell: bash
diff --git a/.github/workflows/building_pyg_conda.yml b/.github/workflows/building_pyg_conda.yml
@@ -12,16 +12,34 @@ jobs:
       matrix:
         # We have trouble building for Windows - drop for now.
         os: [ubuntu-18.04, macos-10.15]  # windows-2019
-        python-version: ['3.7', '3.8', '3.9', '3.10']
-        torch-version: [1.12.0, 1.13.0]
-        cuda-version: ['cpu', 'cu102', 'cu113', 'cu116', 'cu117']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        torch-version: [1.12.0, 1.13.0, 2.0.0]
+        cuda-version: ['cpu', 'cu102', 'cu113', 'cu116', 'cu117', 'cu118']
         exclude:
+          - torch-version: 1.12.0
+            python-version: '3.11'
           - torch-version: 1.12.0
             cuda-version: 'cu117'
+          - torch-version: 1.12.0
+            cuda-version: 'cu118'
+          - torch-version: 1.13.0
+            python-version: '3.11'
           - torch-version: 1.13.0
             cuda-version: 'cu102'
           - torch-version: 1.13.0
             cuda-version: 'cu113'
+          - torch-version: 1.13.0
+            cuda-version: 'cu118'
+          - torch-version: 2.0.0
+            python-version: '3.7'
+          - torch-version: 2.0.0
+            cuda-version: 'cu102'
+          - torch-version: 2.0.0
+            cuda-version: 'cu113'
+          - torch-version: 2.0.0
+            cuda-version: 'cu115'
+          - torch-version: 2.0.0
+            cuda-version: 'cu116'
           - os: macos-10.15
             cuda-version: 'cu102'
           - os: macos-10.15
@@ -30,8 +48,8 @@ jobs:
             cuda-version: 'cu116'
           - os: macos-10.15
             cuda-version: 'cu117'
-          - os: windows-2019
-            cuda-version: 'cu102'
+          - os: macos-10.15
+            cuda-version: 'cu118'
 
     steps:
       - name: Checkout repository

diff --git a/.github/workflows/building_rusty1s_conda.yml b/.github/workflows/building_rusty1s_conda.yml
@@ -12,16 +12,34 @@ jobs:
       matrix:
         # We have trouble building for Windows - drop for now.
         os: [ubuntu-18.04, macos-10.15]  # windows-2019
-        python-version: ['3.7', '3.8', '3.9', '3.10']
-        torch-version: [1.12.0, 1.13.0]
-        cuda-version: ['cpu', 'cu102', 'cu113', 'cu116', 'cu117']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        torch-version: [1.12.0, 1.13.0, 2.0.0]
+        cuda-version: ['cpu', 'cu102', 'cu113', 'cu116', 'cu117', 'cu118']
         exclude:
+          - torch-version: 1.12.0
+            python-version: '3.11'
           - torch-version: 1.12.0
             cuda-version: 'cu117'
+          - torch-version: 1.12.0
+            cuda-version: 'cu118'
+          - torch-version: 1.13.0
+            python-version: '3.11'
           - torch-version: 1.13.0
             cuda-version: 'cu102'
           - torch-version: 1.13.0
             cuda-version: 'cu113'
+          - torch-version: 1.13.0
+            cuda-version: 'cu118'
+          - torch-version: 2.0.0
+            python-version: '3.7'
+          - torch-version: 2.0.0
+            cuda-version: 'cu102'
+          - torch-version: 2.0.0
+            cuda-version: 'cu113'
+          - torch-version: 2.0.0
+            cuda-version: 'cu115'
+          - torch-version: 2.0.0
+            cuda-version: 'cu116'
           - os: macos-10.15
             cuda-version: 'cu102'
           - os: macos-10.15
@@ -30,8 +48,8 @@ jobs:
             cuda-version: 'cu116'
           - os: macos-10.15
             cuda-version: 'cu117'
-          - os: windows-2019
-            cuda-version: 'cu102'
+          - os: macos-10.15
+            cuda-version: 'cu118'
 
     steps:
       - name: Checkout repository

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -34,10 +34,7 @@ jobs:
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         uses: ./.github/actions/setup
         with:
-          python-version: 3.8
-          cache: pip
-          cache-dependency-path: |
-            setup.py
+          full_install: false
 
       - name: Install main package
         if: steps.changed-files-specific.outputs.only_changed != 'true'

diff --git a/.github/workflows/full_testing.yml b/.github/workflows/full_testing.yml
@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
       - name: Checkout repository

diff --git a/.github/workflows/install.yml b/.github/workflows/install.yml
@@ -34,21 +34,17 @@ jobs:
       - name: Setup packages
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         uses: ./.github/actions/setup
+        with:
+          full_install: false
 
       - name: Install main package
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          pip install -e .[test]
+          pip install -e .
 
       - name: Test imports
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
           python -c "import torch_geometric"
-          python -c "import torch_geometric.datasets"
-          python -c "import torch_geometric.nn"
+          python -c "import torch_geometric.contrib"
           python -c "import torch_geometric.graphgym"
-
-      - name: Run tests
-        if: steps.changed-files-specific.outputs.only_changed != 'true'
-        run: |
-          pytest
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -17,6 +17,8 @@ jobs:
 
       - name: Setup packages
         uses: ./.github/actions/setup
+        with:
+          full_install: false
 
       - name: Install pyright
         run: |
@@ -37,7 +39,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4.3.0
         with:
-          python-version: 3.7
+          python-version: 3.8
           check-latest: true
           cache: pip
           cache-dependency-path: |
@@ -60,7 +62,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4.3.0
         with:
-          python-version: 3.7
+          python-version: 3.8
           check-latest: true
           cache: pip
           cache-dependency-path: |

diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4.3.0
         with:
-          python-version: 3.7
+          python-version: 3.8
           check-latest: true
           cache: pip
           cache-dependency-path: |

diff --git a/.github/workflows/prev_testing.yml b/.github/workflows/prev_testing.yml
@@ -0,0 +1,49 @@
+name: Testing PyTorch 1.13
+
+on:  # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+
+  prev_pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 40
+
+      # Skip workflow if only certain files have been changed.
+      - name: Get changed files
+        id: changed-files-specific
+        uses: tj-actions/changed-files@v34
+        with:
+          files: |
+            benchmark/**
+            conda/**
+            docker/**
+            docs/**
+            examples/**
+            graphgym/**
+            CHANGELOG.md
+
+      - name: Setup packages
+        if: steps.changed-files-specific.outputs.only_changed != 'true'
+        uses: ./.github/actions/setup
+        with:
+          torch-version: 1.13.0
+          torchvision-version: 0.14.0
+
+      - name: Install main package
+        if: steps.changed-files-specific.outputs.only_changed != 'true'
+        run: |
+          pip install -e .[full,test]
+
+      - name: Run tests
+        if: steps.changed-files-specific.outputs.only_changed != 'true'
+        run: |
+          pytest
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -1,4 +1,4 @@
-name: Testing
+name: Testing PyTorch 2.0
 
 on:  # yamllint disable-line rule:truthy
   push:

diff --git a/.gitignore b/.gitignore
@@ -24,8 +24,8 @@ coverage.xml
 *.out
 *.pt
 *.onnx
-examples/*.png
-examples/*.pdf
+examples/**/*.png
+examples/**/*.pdf
 benchmark/results/
 
 !torch_geometric/data/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,11 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- Added the `DistMult` KGE model ([#6958](https://github.com/pyg-team/pytorch_geometric/pull/6958))
+- Added `HeteroData.set_value_dict` functionality ([#6961](https://github.com/pyg-team/pytorch_geometric/pull/6961), [#6974](https://github.com/pyg-team/pytorch_geometric/pull/6974))
+- Added PyTorch >= 2.0 support ([#6934](https://github.com/pyg-team/pytorch_geometric/pull/6934))
+- Added PyTorch Lightning >= 2.0 support ([#6929](https://github.com/pyg-team/pytorch_geometric/pull/6929))
+- Added the `ComplEx` KGE model ([#6898](https://github.com/pyg-team/pytorch_geometric/pull/6898))
 - Added option to write benchmark results to csv ([#6888](https://github.com/pyg-team/pytorch_geometric/pull/6888))
 - Added `HeteroLayerNorm` and `HeteroBatchNorm` layers ([#6838](https://github.com/pyg-team/pytorch_geometric/pull/6838))
 - Added the `HeterophilousGraphDataset` suite ([#6846](https://github.com/pyg-team/pytorch_geometric/pull/6846))
@@ -29,7 +34,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `Pad` transform ([#5940](https://github.com/pyg-team/pytorch_geometric/pull/5940), [#6697](https://github.com/pyg-team/pytorch_geometric/pull/6697), [#6731](https://github.com/pyg-team/pytorch_geometric/pull/6731), [#6758](https://github.com/pyg-team/pytorch_geometric/pull/6758))
 - Added full batch mode to the inference benchmark ([#6631](https://github.com/pyg-team/pytorch_geometric/pull/6631))
 - Added `cat` aggregation type to the `HeteroConv` class so that features can be concatenated during grouping ([#6634](https://github.com/pyg-team/pytorch_geometric/pull/6634))
-- Added `torch.compile` support and benchmark study ([#6610](https://github.com/pyg-team/pytorch_geometric/pull/6610))
+- Added `torch.compile` support and benchmark study ([#6610](https://github.com/pyg-team/pytorch_geometric/pull/6610), [#6952](https://github.com/pyg-team/pytorch_geometric/pull/6952), [#6953](https://github.com/pyg-team/pytorch_geometric/pull/6953))
 - Added the `AntiSymmetricConv` layer ([#6577](https://github.com/pyg-team/pytorch_geometric/pull/6577))
 - Added a mixin for Huggingface model hub integration ([#5930](https://github.com/pyg-team/pytorch_geometric/pull/5930), [#6591](https://github.com/pyg-team/pytorch_geometric/pull/6591))
 - Added support for accelerated GNN layers in `nn.conv.cugraph` via `cugraph-ops` ([#6278](https://github.com/pyg-team/pytorch_geometric/pull/6278), [#6388](https://github.com/pyg-team/pytorch_geometric/pull/6388), [#6412](https://github.com/pyg-team/pytorch_geometric/pull/6412))
@@ -55,7 +60,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Warn on using latest documentation ([#6418](https://github.com/pyg-team/pytorch_geometric/pull/6418))
 - Added basic `pyright` type checker support ([#6415](https://github.com/pyg-team/pytorch_geometric/pull/6415))
 - Added a new external resource for link prediction ([#6396](https://github.com/pyg-team/pytorch_geometric/pull/6396))
-- Added `CaptumExplainer` ([#6383](https://github.com/pyg-team/pytorch_geometric/pull/6383), [#6387](https://github.com/pyg-team/pytorch_geometric/pull/6387), [#6433](https://github.com/pyg-team/pytorch_geometric/pull/6433), [#6487](https://github.com/pyg-team/pytorch_geometric/pull/6487))
+- Added `CaptumExplainer` ([#6383](https://github.com/pyg-team/pytorch_geometric/pull/6383), [#6387](https://github.com/pyg-team/pytorch_geometric/pull/6387), [#6433](https://github.com/pyg-team/pytorch_geometric/pull/6433), [#6487](https://github.com/pyg-team/pytorch_geometric/pull/6487), [#6966](https://github.com/pyg-team/pytorch_geometric/pull/6966))
 - Added support for custom `HeteroData` mini-batch class in remote backends ([#6377](https://github.com/pyg-team/pytorch_geometric/pull/6377))
 - Added the `GNNFF` model ([#5866](https://github.com/pyg-team/pytorch_geometric/pull/5866))
 - Added `MLPAggregation`, `SetTransformerAggregation`, `GRUAggregation`, and `DeepSetsAggregation` as adaptive readout functions ([#6301](https://github.com/pyg-team/pytorch_geometric/pull/6301), [#6336](https://github.com/pyg-team/pytorch_geometric/pull/6336), [#6338](https://github.com/pyg-team/pytorch_geometric/pull/6338))
@@ -92,7 +97,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `Data.edge_subgraph` and `HeteroData.edge_subgraph` functionalities ([#6193](https://github.com/pyg-team/pytorch_geometric/pull/6193))
 - Added `input_time` option to `LightningNodeData` and `transform_sampler_output` to `NodeLoader` and `LinkLoader` ([#6187](https://github.com/pyg-team/pytorch_geometric/pull/6187))
 - Added `summary` for PyG/PyTorch models ([#5859](https://github.com/pyg-team/pytorch_geometric/pull/5859), [#6161](https://github.com/pyg-team/pytorch_geometric/pull/6161))
-- Started adding `torch.sparse` support to PyG ([#5906](https://github.com/pyg-team/pytorch_geometric/pull/5906), [#5944](https://github.com/pyg-team/pytorch_geometric/pull/5944), [#6003](https://github.com/pyg-team/pytorch_geometric/pull/6003), [#6033](https://github.com/pyg-team/pytorch_geometric/pull/6033), [#6514](https://github.com/pyg-team/pytorch_geometric/pull/6514), [#6532](https://github.com/pyg-team/pytorch_geometric/pull/6532), [#6748](https://github.com/pyg-team/pytorch_geometric/pull/6748), [#6847](https://github.com/pyg-team/pytorch_geometric/pull/6847), [#6868](https://github.com/pyg-team/pytorch_geometric/pull/6868), [#6874](https://github.com/pyg-team/pytorch_geometric/pull/6874))
+- Started adding `torch.sparse` support to PyG ([#5906](https://github.com/pyg-team/pytorch_geometric/pull/5906), [#5944](https://github.com/pyg-team/pytorch_geometric/pull/5944), [#6003](https://github.com/pyg-team/pytorch_geometric/pull/6003), [#6033](https://github.com/pyg-team/pytorch_geometric/pull/6033), [#6514](https://github.com/pyg-team/pytorch_geometric/pull/6514), [#6532](https://github.com/pyg-team/pytorch_geometric/pull/6532), [#6748](https://github.com/pyg-team/pytorch_geometric/pull/6748), [#6847](https://github.com/pyg-team/pytorch_geometric/pull/6847), [#6868](https://github.com/pyg-team/pytorch_geometric/pull/6868), [#6874](https://github.com/pyg-team/pytorch_geometric/pull/6874), [#6897](https://github.com/pyg-team/pytorch_geometric/pull/6897), [#6930](https://github.com/pyg-team/pytorch_geometric/pull/6930), [#6932](https://github.com/pyg-team/pytorch_geometric/pull/6932), [#6936](https://github.com/pyg-team/pytorch_geometric/pull/6936), [#6937](https://github.com/pyg-team/pytorch_geometric/pull/6937), [#6939](https://github.com/pyg-team/pytorch_geometric/pull/6939), [#6947](https://github.com/pyg-team/pytorch_geometric/pull/6947), [#6950](https://github.com/pyg-team/pytorch_geometric/pull/6950), [#6951](https://github.com/pyg-team/pytorch_geometric/pull/6951), [#6957](https://github.com/pyg-team/pytorch_geometric/pull/6957))
 - Add `inputs_channels` back in training benchmark ([#6154](https://github.com/pyg-team/pytorch_geometric/pull/6154))
 - Added support for dropping nodes in `utils.to_dense_batch` in case `max_num_nodes` is smaller than the number of nodes ([#6124](https://github.com/pyg-team/pytorch_geometric/pull/6124))
 - Added the RandLA-Net architecture as an example ([#5117](https://github.com/pyg-team/pytorch_geometric/pull/5117))

diff --git a/README.md b/README.md
@@ -300,7 +300,9 @@ Unlike simple stacking of GNN layers, these models could involve pre-processing,
 * **[LINKX](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.models.LINKX.html)** from Lim *et al.*: [Large Scale Learning on Non-Homophilous Graphs:
 New Benchmarks and Strong Simple Methods](https://arxiv.org/abs/2110.14446) (NeurIPS 2021) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/linkx.py)]
 * **[RevGNN](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.models.GroupAddRev.html)** from Li *et al.*: [Training Graph Neural with 1000 Layers](https://arxiv.org/abs/2106.07476) (ICML 2021) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/rev_gnn.py)]
-* **[TransE](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.kge.TransE.html)** from Bordes *et al.*: [Translating Embeddings for Modeling Multi-Relational Data](https://proceedings.neurips.cc/paper/2013/file/1cecc7a77928ca8133fa24680a88d2f9-Paper.pdf) (NIPS 2013) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/transe_fb15k_237.py)]
+* **[TransE](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.kge.TransE.html)** from Bordes *et al.*: [Translating Embeddings for Modeling Multi-Relational Data](https://proceedings.neurips.cc/paper/2013/file/1cecc7a77928ca8133fa24680a88d2f9-Paper.pdf) (NIPS 2013) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/kge_fb15k_237.py)]
+* **[ComplEx](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.kge.ComplEx.html)** from Trouillon *et al.*: [Complex Embeddings for Simple Link Prediction](https://arxiv.org/abs/1606.06357) (ICML 2016) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/kge_fb15k_237.py)]
+* **[DistMult](https://pytorch-geometric.readthedocs.io/en/latest/generated/torch_geometric.nn.kge.DistMult.html)** from Yang *et al.*: [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://arxiv.org/abs/1412.6575) (ICLR 2015) [[**Example**](https://github.com/pyg-team/pytorch_geometric/blob/master/examples/kge_fb15k_237.py)]
 </details>
 
 **GNN operators and utilities:**