Merge branch 'master' into models/polynormer

xnuohz · web-flow · commit 8ba28f43cd1c · 2025-04-07T22:57:10.000+08:00
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: '2.5.0'
+    default: '2.6.0'
   cuda-version:
     required: false
     default: cpu
   torchvision-version:
     required: false
-    default: '0.20.0'
+    default: '0.21.0'
   full_install:
     required: false
     default: true
diff --git a/.github/workflows/building_nightly.yml b/.github/workflows/building_nightly.yml
diff --git a/.github/workflows/testing_dist.yml b/.github/workflows/testing_dist.yml
diff --git a/.github/workflows/testing_full.yml b/.github/workflows/testing_full.yml
@@ -16,8 +16,8 @@ jobs:
       fail-fast: false
       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, 2.5.0, nightly]
+        python-version: ['3.9']
+        torch-version: [1.13.0, 2.0.0, 2.1.0, 2.2.0, 2.3.0, 2.4.0, 2.5.0, 2.6.0, nightly]
         include:
           - torch-version: 1.13.0
             torchvision-version: 0.14.0
@@ -33,6 +33,8 @@ jobs:
             torchvision-version: 0.19.0
           - torch-version: 2.5.0
             torchvision-version: 0.20.0
+          - torch-version: 2.6.0
+            torchvision-version: 0.21.0
           - torch-version: nightly
             torchvision-version: nightly
         exclude:
@@ -44,10 +46,6 @@ jobs:
             torch-version: 2.1.0
           - os: macos-14
             torch-version: 2.2.0
-          # TODO Some dependency version conflict lets pytest crash on Windows/3.10/2.4.0
-          - os: windows-latest
-            python-version: '3.10'
-            torch-version: 2.4.0
 
     steps:
       - name: Checkout repository
diff --git a/.github/workflows/testing_full_gpu.yml b/.github/workflows/testing_full_gpu.yml
diff --git a/.github/workflows/testing_latest.yml b/.github/workflows/testing_latest.yml
@@ -1,4 +1,4 @@
-name: Testing PyTorch 2.5
+name: Testing latest PyTorch
 
 on:  # yamllint disable-line rule:truthy
   push:
@@ -67,7 +67,7 @@ jobs:
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
-        timeout-minutes: 10
+        timeout-minutes: 15
         run: |
           pytest --cov --cov-report=xml --durations 10
 
diff --git a/.github/workflows/testing_minimal.yml b/.github/workflows/testing_minimal.yml
@@ -1,4 +1,4 @@
-name: Testing minimal PyTorch 2.5
+name: Testing minimal PyTorch
 
 on:  # yamllint disable-line rule:truthy
   push:
diff --git a/.github/workflows/testing_nightly.yml b/.github/workflows/testing_nightly.yml
@@ -1,4 +1,4 @@
-name: Testing PyTorch nightly
+name: Testing nightly PyTorch
 
 on:  # yamllint disable-line rule:truthy
   push:
@@ -13,7 +13,7 @@ concurrency:
 
 jobs:
 
-  latest_pytest:
+  nightly_pytest:
     runs-on: ubuntu-latest
 
     steps:
diff --git a/.github/workflows/testing_prev.yml b/.github/workflows/testing_prev.yml
@@ -1,4 +1,4 @@
-name: Testing previous PyTorch versions
+name: Testing previous PyTorch
 
 on:  # yamllint disable-line rule:truthy
   push:
@@ -19,14 +19,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        torch-version: [1.13.0, 2.1.0, 2.4.0]
+        torch-version: [1.13.0, 2.1.0, 2.5.0]
         include:
           - torch-version: 1.13.0
             torchvision-version: 0.14.0
           - torch-version: 2.1.0
             torchvision-version: 0.16.0
-          - torch-version: 2.4.0
-            torchvision-version: 0.19.0
+          - torch-version: 2.5.0
+            torchvision-version: 0.21.0
 
     steps:
       - name: Checkout repository
@@ -64,6 +64,6 @@ jobs:
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
-        timeout-minutes: 10
+        timeout-minutes: 15
         run: |
           pytest
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 ### Added
 
 - Added `Polynormer` model and example ([#9908](https://github.com/pyg-team/pytorch_geometric/pull/9908))
+- Added PyTorch 2.6 support ([#10170](https://github.com/pyg-team/pytorch_geometric/pull/10170))
 - Added support for heterogenous graphs in `GNNExplainer` ([#10158](https://github.com/pyg-team/pytorch_geometric/pull/10158))
 - Added Graph Positional and Structural Encoder (GPSE) ([#9018](https://github.com/pyg-team/pytorch_geometric/pull/9018))
 - Added attract-repel link prediction example ([#10107](https://github.com/pyg-team/pytorch_geometric/pull/10107))
diff --git a/torch_geometric/metrics/link_pred.py b/torch_geometric/metrics/link_pred.py
@@ -670,6 +670,9 @@ class LinkPredDiversity(_LinkPredMetric):
     def __init__(self, k: int, category: Tensor) -> None:
         super().__init__(k)
 
+        self.accum: Tensor
+        self.total: Tensor
+
         if WITH_TORCHMETRICS:
             self.add_state('accum', torch.tensor(0.), dist_reduce_fx='sum')
             self.add_state('total', torch.tensor(0), dist_reduce_fx='sum')
@@ -736,11 +739,14 @@ def __init__(
         self.max_src_nodes = max_src_nodes
         self.batch_size = batch_size
 
+        self.preds: List[Tensor]
+        self.total: Tensor
+
         if WITH_TORCHMETRICS:
             self.add_state('preds', default=[], dist_reduce_fx='cat')
             self.add_state('total', torch.tensor(0), dist_reduce_fx='sum')
         else:
-            self.preds: List[Tensor] = []
+            self.preds = []
             self.register_buffer('total', torch.tensor(0), persistent=False)
 
     def update(
@@ -826,6 +832,9 @@ class LinkPredAveragePopularity(_LinkPredMetric):
     def __init__(self, k: int, popularity: Tensor) -> None:
         super().__init__(k)
 
+        self.accum: Tensor
+        self.total: Tensor
+
         if WITH_TORCHMETRICS:
             self.add_state('accum', torch.tensor(0.), dist_reduce_fx='sum')
             self.add_state('total', torch.tensor(0), dist_reduce_fx='sum')
diff --git a/torch_geometric/transforms/rooted_subgraph.py b/torch_geometric/transforms/rooted_subgraph.py
@@ -94,7 +94,7 @@ def map(
         arange = torch.arange(n_id.size(0), device=data.edge_index.device)
         node_map = data.edge_index.new_ones(num_nodes, num_nodes)
         node_map[n_sub_batch, n_id] = arange
-        sub_edge_index += (arange * data.num_nodes)[e_sub_batch]
+        sub_edge_index += (arange * num_nodes)[e_sub_batch]
         sub_edge_index = node_map.view(-1)[sub_edge_index]
 
         return sub_edge_index, n_id, e_id, n_sub_batch, e_sub_batch
diff --git a/torch_geometric/utils/_negative_sampling.py b/torch_geometric/utils/_negative_sampling.py
@@ -109,10 +109,9 @@ def negative_sampling(
         idx = idx.to('cpu')
         for _ in range(3):  # Number of tries to sample negative indices.
             rnd = sample(population, sample_size, device='cpu')
-            mask = np.isin(rnd.numpy(), idx.numpy())  # type: ignore
+            mask = torch.from_numpy(np.isin(rnd.numpy(), idx.numpy())).bool()
             if neg_idx is not None:
-                mask |= np.isin(rnd, neg_idx.to('cpu'))
-            mask = torch.from_numpy(mask).to(torch.bool)
+                mask |= torch.from_numpy(np.isin(rnd, neg_idx.cpu())).bool()
             rnd = rnd[~mask].to(edge_index.device)
             neg_idx = rnd if neg_idx is None else torch.cat([neg_idx, rnd])
             if neg_idx.numel() >= num_neg_samples:

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-name: Testing minimal PyTorch 2.5`
	`1`	`+name: Testing minimal PyTorch`
`2`	`2`
`3`	`3`	`on: # yamllint disable-line rule:truthy`
`4`	`4`	`push:`