chore: Update uv usage

.github/actions/setup/action.yml

@@ -40,13 +40,13 @@ runs:
     - name: Install PyTorch ${{ inputs.torch-version }}+${{ inputs.cuda-version }}
       if: ${{ inputs.torch-version != 'nightly' }}
       run: |
-        uv pip install torch==${{ inputs.torch-version }} --extra-index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
+        uv pip install torch==${{ inputs.torch-version }} --index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
       shell: bash
 
     - name: Install PyTorch ${{ inputs.torch-version }}+${{ inputs.cuda-version }}
       if: ${{ inputs.torch-version == 'nightly' }}
       run: |
-        uv pip install --pre torch --extra-index-url https://download.pytorch.org/whl/nightly/${{ inputs.cuda-version }}
+        uv pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/${{ inputs.cuda-version }}
       shell: bash
 
     - name: Install compatible networkx
@@ -57,10 +57,11 @@ runs:
 
     - name: Check installation
       run: |
-        uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-        uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-        uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-      shell: bash
+        import torch
+        print('PyTorch:', torch.__version__)
+        print('CUDA available:', torch.cuda.is_available())
+        print('CUDA:', torch.version.cuda)
+      shell: python
 
     - name: Install pyg-lib
       if: ${{ inputs.torch-version != 'nightly' }}
@@ -83,7 +84,7 @@ runs:
     - name: Install torchvision
       if: ${{ inputs.full_install == 'true' && inputs.torch-version != 'nightly' }}
       run: |
-        uv pip install torchvision==${{ inputs.torchvision-version }} --extra-index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
+        uv pip install torchvision==${{ inputs.torchvision-version }} --index-url https://download.pytorch.org/whl/${{ inputs.cuda-version }}
       shell: bash
 
     - name: Install extension packages

.github/workflows/documentation.yml

@@ -45,12 +45,10 @@ jobs:
       - name: Install main package
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv pip install nbsphinx
-          uv pip install git+https://github.com/pyg-team/pyg_sphinx_theme.git
-          uv pip install -e .
+          uv pip install -e . nbsphinx git+https://github.com/pyg-team/pyg_sphinx_theme.git
 
       - name: Build documentation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         working-directory: ./docs
         run: |
-          uv run --no-project sphinx-build -M html "source" "build" -W  # Fail on warning.
+          sphinx-build -M html "source" "build" -W  # Fail on warning.

.github/workflows/examples.yml

@@ -24,22 +24,22 @@ jobs:
 
       - name: Run GCN on Cora
         run: |
-          uv run --no-project python examples/gcn.py --wandb
+          python examples/gcn.py --wandb
         env:
           WANDB_API_KEY: ${{ secrets.WANDB_API_KEY }}
 
       - name: Run GAT on Cora
         run: |
-          uv run --no-project python examples/gat.py --wandb
+          python examples/gat.py --wandb
         env:
           WANDB_API_KEY: ${{ secrets.WANDB_API_KEY }}
 
       - name: Run GIN on MUTAG
         run: |
-          uv run --no-project python examples/mutag_gin.py --wandb
+          python examples/mutag_gin.py --wandb
         env:
           WANDB_API_KEY: ${{ secrets.WANDB_API_KEY }}
 
       - name: Run GNNExplainer
         run: |
-          uv run --no-project python examples/explain/gnn_explainer.py
+          python examples/explain/gnn_explainer.py

.github/workflows/linting.yml

@@ -50,4 +50,5 @@ jobs:
       - name: Check type hints
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv run --no-project mypy --cache-dir=/dev/null
+          which mypy
+          mypy --cache-dir=/dev/null

.github/workflows/testing_dist.yml

@@ -43,14 +43,14 @@ jobs:
       - name: Check installation
         if: steps.changed-files-specific.outputs.any_changed == 'true'
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
+          python -c "import torch; print('PyTorch:', torch.__version__)"
+          python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
+          python -c "import torch; print('CUDA:', torch.version.cuda)"
         shell: bash
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.any_changed == 'true'
         timeout-minutes: 10
         run: |
-          DIST_TEST=1 uv run --no-project pytest test/distributed --durations 10
+          DIST_TEST=1 pytest test/distributed --durations 10
         shell: bash

.github/workflows/testing_full.yml

@@ -82,15 +82,16 @@ jobs:
 
       - name: Check installation
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         timeout-minutes: 20
         run: |
-          FULL_TEST=1 uv run --no-project pytest --cov --cov-report=xml --durations 10
+          FULL_TEST=1 pytest --cov --cov-report=xml --durations 10
         shell: bash
 
       - name: Upload coverage

.github/workflows/testing_full_gpu.yml

@@ -30,13 +30,14 @@ jobs:
 
       - name: Check installation
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         timeout-minutes: 20
         run: |
-          FULL_TEST=1 uv run --no-project pytest --durations 10
+          FULL_TEST=1 pytest --durations 10
         shell: bash

.github/workflows/testing_latest.yml

@@ -68,16 +68,17 @@ jobs:
       - name: Check installation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --cov --cov-report=xml --durations 10
+          pytest --cov --cov-report=xml --durations 10
 
       - name: Upload coverage
         if: ${{ steps.changed-files-specific.outputs.only_changed != 'true' && runner.os == 'Linux' }}

.github/workflows/testing_minimal.yml

@@ -51,13 +51,14 @@ jobs:
       - name: Check installation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          pytest --durations 10

.github/workflows/testing_nightly.yml

@@ -51,13 +51,14 @@ jobs:
       - name: Check installation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          pytest --durations 10

.github/workflows/testing_prev.yml

@@ -64,13 +64,14 @@ jobs:
       - name: Check installation
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         run: |
-          uv run --no-project python -c "import torch; print('PyTorch:', torch.__version__)"
-          uv run --no-project python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
-          uv run --no-project python -c "import torch; print('CUDA:', torch.version.cuda)"
-        shell: bash
+          import torch
+          print('PyTorch:', torch.__version__)
+          print('CUDA available:', torch.cuda.is_available())
+          print('CUDA:', torch.version.cuda)
+        shell: python
 
       - name: Run tests
         if: steps.changed-files-specific.outputs.only_changed != 'true'
         timeout-minutes: 15
         run: |
-          uv run --no-project pytest --durations 10
+          pytest --durations 10