Merge branch 'pprgo' of https://github.com/ryspark/pytorch_geometric …

…into pprgo
pyg-team · Dec 11, 2024 · 0eb2673 · 0eb2673
2 parents 4741efb + fba95c9
commit 0eb2673
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diff --git a/.github/actions/setup/action.yml b/.github/actions/setup/action.yml
@@ -6,13 +6,13 @@ inputs:
     default: '3.9'
   torch-version:
     required: false
-    default: '2.4.0'
+    default: '2.5.0'
   cuda-version:
     required: false
     default: cpu
   torchvision-version:
     required: false
-    default: '0.19.0'
+    default: '0.20.0'
   full_install:
     required: false
     default: true
@@ -31,7 +31,6 @@ runs:
           pyproject.toml
 
     - name: Install numpy
-      if: ${{ runner.os == 'Windows' }}
       run: |
         pip install "numpy<2"
       shell: bash

diff --git a/.github/workflows/building_pyg_conda.yml b/.github/workflows/building_pyg_conda.yml
@@ -12,7 +12,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04, macos-14, windows-2019]
         python-version: ['3.9', '3.10', '3.11', '3.12']
-        torch-version: [2.3.0, 2.4.0]
+        torch-version: [2.4.0, 2.5.0]
         cuda-version: ['cpu', 'cu118', 'cu121', 'cu124']
         exclude:
           - torch-version: 2.3.0

diff --git a/.github/workflows/building_rusty1s_conda.yml b/.github/workflows/building_rusty1s_conda.yml
@@ -12,7 +12,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04, macos-14, windows-2019]
         python-version: ['3.9', '3.10', '3.11', '3.12']
-        torch-version: [2.3.0, 2.4.0]
+        torch-version: [2.4.0, 2.5.0]
         cuda-version: ['cpu', 'cu118', 'cu121', 'cu124']
         exclude:
           - torch-version: 2.3.0

diff --git a/.github/workflows/dist_testing.yml b/.github/workflows/dist_testing.yml
@@ -6,6 +6,11 @@ on:  # yamllint disable-line rule:truthy
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   dist_pytest:

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -6,6 +6,11 @@ on:  # yamllint disable-line rule:truthy
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   make_html:

diff --git a/.github/workflows/full_testing.yml b/.github/workflows/full_testing.yml
@@ -16,7 +16,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-14]
         python-version: ['3.9', '3.10']
-        torch-version: [1.13.0, 2.0.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0, nightly]
+        torch-version: [1.13.0, 2.0.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0, 2.5.0, nightly]
         include:
           - torch-version: 1.13.0
             torchvision-version: 0.14.0
@@ -30,6 +30,8 @@ jobs:
             torchvision-version: 0.18.0
           - torch-version: 2.4.0
             torchvision-version: 0.19.0
+          - torch-version: 2.5.0
+            torchvision-version: 0.20.0
           - torch-version: nightly
             torchvision-version: nightly
         exclude:

diff --git a/.github/workflows/latest_testing.yml b/.github/workflows/latest_testing.yml
@@ -6,6 +6,11 @@ on:  # yamllint disable-line rule:truthy
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   latest_pytest:

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -6,6 +6,11 @@ on:  # yamllint disable-line rule:truthy
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   mypy:

diff --git a/.github/workflows/minimal_testing.yml b/.github/workflows/minimal_testing.yml
@@ -1,11 +1,16 @@
-name: Testing minimal PyTorch 2.4
+name: Testing minimal PyTorch 2.5
 
 on:  # yamllint disable-line rule:truthy
   push:
     branches:
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   minimal_pytest:

diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -5,6 +5,11 @@ on:  # yamllint disable-line rule:truthy
   schedule:
     - cron: "0 6 * * *"  # Everyday at 6:00am UTC/10:00pm PST
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   build:

diff --git a/.github/workflows/prev_testing.yml b/.github/workflows/prev_testing.yml
@@ -6,6 +6,11 @@ on:  # yamllint disable-line rule:truthy
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   prev_pytest:
@@ -14,14 +19,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        torch-version: [1.13.0, 2.1.0, 2.3.0]
+        torch-version: [1.13.0, 2.1.0, 2.4.0]
         include:
           - torch-version: 1.13.0
             torchvision-version: 0.14.0
           - torch-version: 2.1.0
             torchvision-version: 0.16.0
-          - torch-version: 2.3.0
-            torchvision-version: 0.18.0
+          - torch-version: 2.4.0
+            torchvision-version: 0.19.0
 
     steps:
       - name: Checkout repository
@@ -54,7 +59,7 @@ jobs:
       - name: Install main package
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          pip install -e .[full,test]
+          pip install -e .[test]
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -1,11 +1,16 @@
-name: Testing PyTorch 2.4
+name: Testing PyTorch 2.5
 
 on:  # yamllint disable-line rule:truthy
   push:
     branches:
       - master
   pull_request:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}-${{ startsWith(github.ref, 'refs/pull/') || github.run_number }}  # yamllint disable-line
+  # Only cancel intermediate builds if on a PR:
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
 
   pytest:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,18 +7,34 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Added
 
+- Update Dockerfile to use latest from NVIDIA ([#9794](https://github.com/pyg-team/pytorch_geometric/pull/9794))
+- Added various GRetriever Architecture Benchmarking examples ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `profiler.nvtxit` with some examples ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `loader.RagQueryLoader` with Remote Backend Example ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `data.LargeGraphIndexer` ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `GIT-Mol` ([#9730](https://github.com/pyg-team/pytorch_geometric/pull/9730))
+- Added comment in `g_retriever.py` pointing to `Neo4j` Graph DB integration demo ([#9748](https://github.com/pyg-team/pytorch_geometric/pull/9797))
+- Added `MoleculeGPT` example ([#9710](https://github.com/pyg-team/pytorch_geometric/pull/9710))
+- Added `nn.models.GLEM` ([#9662](https://github.com/pyg-team/pytorch_geometric/pull/9662))
+- Added `TAGDataset` ([#9662](https://github.com/pyg-team/pytorch_geometric/pull/9662))
+- Added support for fast `Delaunay()` triangulation via the `torch_delaunay` package ([#9748](https://github.com/pyg-team/pytorch_geometric/pull/9748))
+- Added PyTorch 2.5 support ([#9779](https://github.com/pyg-team/pytorch_geometric/pull/9779), [#9779](https://github.com/pyg-team/pytorch_geometric/pull/9780))
+- Support 3D tetrahedral mesh elements of shape `[4, num_faces]` in the `FaceToEdge` transformation ([#9776](https://github.com/pyg-team/pytorch_geometric/pull/9776))
 - Added the `use_pcst` option to `WebQSPDataset` ([#9722](https://github.com/pyg-team/pytorch_geometric/pull/9722))
 - Allowed users to pass `edge_weight` to `GraphUNet` models ([#9737](https://github.com/pyg-team/pytorch_geometric/pull/9737))
 - Consolidated `examples/ogbn_{papers_100m,products_gat,products_sage}.py` into `examples/ogbn_train.py` ([#9467](https://github.com/pyg-team/pytorch_geometric/pull/9467))
 
 ### Changed
 
 - Dropped Python 3.8 support ([#9696](https://github.com/pyg-team/pytorch_geometric/pull/9606))
+- Added a check that confirms that custom edge types of `NumNeighbors` actually exist in the graph ([#9807](https://github.com/pyg-team/pytorch_geometric/pull/9807))
 
 ### Deprecated
 
 ### Fixed
 
+- Fixed the `k_hop_subgraph()` method for directed graphs ([#9756](https://github.com/pyg-team/pytorch_geometric/pull/9756))
+- Fixed `utils.group_cat` concatenating dimension ([#9766](https://github.com/pyg-team/pytorch_geometric/pull/9766))
 - Fixed `WebQSDataset.process` raising exceptions ([#9665](https://github.com/pyg-team/pytorch_geometric/pull/9665))
 
 ### Removed

diff --git a/README.md b/README.md
@@ -371,12 +371,12 @@ We recommend to start with a minimal installation, and install additional depend
 
 For ease of installation of these extensions, we provide `pip` wheels for all major OS/PyTorch/CUDA combinations, see [here](https://data.pyg.org/whl).
 
-#### PyTorch 2.4
+#### PyTorch 2.5
 
-To install the binaries for PyTorch 2.4.0, simply run
+To install the binaries for PyTorch 2.5.0, simply run
 
 ```
-pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+${CUDA}.html
+pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.5.0+${CUDA}.html
 ```
 
 where `${CUDA}` should be replaced by either `cpu`, `cu118`, `cu121`, or `cu124` depending on your PyTorch installation.
@@ -387,23 +387,23 @@ where `${CUDA}` should be replaced by either `cpu`, `cu118`, `cu121`, or `cu124`
 | **Windows** | ✅    | ✅      | ✅      | ✅      |
 | **macOS**   | ✅    |         |         |         |
 
-#### PyTorch 2.3
+#### PyTorch 2.4
 
-To install the binaries for PyTorch 2.3.0, simply run
+To install the binaries for PyTorch 2.4.0, simply run
 
 ```
-pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.3.0+${CUDA}.html
+pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+${CUDA}.html
 ```
 
-where `${CUDA}` should be replaced by either `cpu`, `cu118`, or `cu121` depending on your PyTorch installation.
+where `${CUDA}` should be replaced by either `cpu`, `cu118`, `cu121`, or `cu124` depending on your PyTorch installation.
 
-|             | `cpu` | `cu118` | `cu121` |
-| ----------- | ----- | ------- | ------- |
-| **Linux**   | ✅    | ✅      | ✅      |
-| **Windows** | ✅    | ✅      | ✅      |
-| **macOS**   | ✅    |         |         |
+|             | `cpu` | `cu118` | `cu121` | `cu124` |
+| ----------- | ----- | ------- | ------- | ------- |
+| **Linux**   | ✅    | ✅      | ✅      | ✅      |
+| **Windows** | ✅    | ✅      | ✅      | ✅      |
+| **macOS**   | ✅    |         |         |         |
 
-**Note:** Binaries of older versions are also provided for PyTorch 1.4.0, PyTorch 1.5.0, PyTorch 1.6.0, PyTorch 1.7.0/1.7.1, PyTorch 1.8.0/1.8.1, PyTorch 1.9.0, PyTorch 1.10.0/1.10.1/1.10.2, PyTorch 1.11.0, PyTorch 1.12.0/1.12.1, PyTorch 1.13.0/1.13.1, PyTorch 2.0.0/2.0.1, PyTorch 2.1.0/2.1.1/2.1.2, and PyTorch 2.2.0/2.2.1/2.2.2 (following the same procedure).
+**Note:** Binaries of older versions are also provided for PyTorch 1.4.0, PyTorch 1.5.0, PyTorch 1.6.0, PyTorch 1.7.0/1.7.1, PyTorch 1.8.0/1.8.1, PyTorch 1.9.0, PyTorch 1.10.0/1.10.1/1.10.2, PyTorch 1.11.0, PyTorch 1.12.0/1.12.1, PyTorch 1.13.0/1.13.1, PyTorch 2.0.0/2.0.1, PyTorch 2.1.0/2.1.1/2.1.2, PyTorch 2.2.0/2.2.1/2.2.2, and PyTorch 2.3.0/2.3.1 (following the same procedure).
 **For older versions, you might need to explicitly specify the latest supported version number** or install via `pip install --no-index` in order to prevent a manual installation from source.
 You can look up the latest supported version number [here](https://data.pyg.org/whl).