Add uv as dependency manager and ruff as linter/formatter

.devcontainer/Dockerfile

@@ -1,22 +1,11 @@
-FROM pytorch/pytorch:2.4.1-cuda12.1-cudnn9-runtime
+FROM astral/uv:0.8.22-python3.10-bookworm-slim
 WORKDIR /workspaces/pathpyG
-RUN apt-get update
-RUN apt-get -y install git
 
-# For signed commits: https://code.visualstudio.com/remote/advancedcontainers/sharing-git-credentials#_sharing-gpg-keys
-RUN apt install gnupg2 -y
+# Install git (and gpg for signed commits: https://code.visualstudio.com/remote/advancedcontainers/sharing-git-credentials#_sharing-gpg-keys)
+RUN apt-get update && apt-get -y install git gnupg2
 
 # Install dependencies for .svg support in tikz
-RUN apt update && apt install -y ghostscript
+RUN apt-get update && apt-get -y install ghostscript
 
 # Install dependencies for manim
-RUN apt-get install -y build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg
-
-# Install torch
-RUN pip install torch==2.4.1+cu121 --index-url https://download.pytorch.org/whl/cu121
-# pip install torch==2.4.1+cpu --index-url https://download.pytorch.org/whl/cpu # CPU only
-
-# Install torch_geometric and dependencies
-RUN pip install torch_geometric>=2.5.0
-RUN pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+cu121.html
-# RUN pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+cpu.html # CPU only
+RUN apt-get update && apt-get -y install build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg

.devcontainer/devcontainer.json

@@ -2,32 +2,30 @@
 	"build": {
 		"dockerfile": "Dockerfile"
 	},
-	"name": "pathpyG-torch2.4.1-cuda12.1",
+	"name": "pathpyG-torch2.8.0-cuda12.9",
 	"customizations": {
 		"vscode": {
 			"extensions": [
 				"ms-python.python",
-				"ms-python.black-formatter",
-				"ms-python.isort",
-				"ms-python.pylint",
-				"ms-python.flake8",
-				"ms-python.mypy-type-checker",
-				"ms-toolsai.jupyter"
+				"ms-toolsai.jupyter",
+				"charliermarsh.ruff",
+				"ms-python.mypy-type-checker"
 			],
-			"python.defaultInterpreterPath": "/opt/conda/bin/python",
-			"python.linting.enabled": true,
-			"python.linting.pylintEnabled": true,
-			"python.analysis.typeCheckingMode": "basic"
+			"settings": {
+				"[python]": {
+					"analysis.languageServerMode": "light",
+					"editor.defaultFormatter": "charliermarsh.ruff",
+					"notebook.defaultFormatter": "charliermarsh.ruff",
+					"mypy-type-checker.importStrategy": "fromEnvironment"
+				}
+			}
 		},
 		// Add IDs of extensions you want to be installed when container is created.
 		"extensions": [
 			"ms-python.python",
-			"ms-python.black-formatter",
-			"ms-python.isort",
-			"ms-python.pylint",
-			"ms-python.flake8",
-			"ms-python.mypy-type-checker",
-			"ms-toolsai.jupyter"
+			"ms-toolsai.jupyter",
+			"charliermarsh.ruff",
+			"ms-python.mypy-type-checker"
 		]
 	},
 	// Use GPU for CUDA
@@ -37,7 +35,12 @@
 		"all"
 	],
 	// Install pathpyG as editable python package
-	"postCreateCommand": "pip install -e '.[dev,test,doc,vis]' && git config --global --add safe.directory /workspaces/pathpyG",
+	// Use optional dependencies 'vis' for visualization (manim) and 'cu129' for CUDA 12.9 support
+	// (change 'cu129' to 'cpu' if you want to use the CPU version of PyTorch and PyTorch Geometric)
+	"postCreateCommand": "uv sync --frozen --extra vis --extra cu129 && git config --global --add safe.directory /workspaces/pathpyG",
+	"remoteEnv": {
+		"PATH": "/workspaces/pathpyG/.venv/bin:${containerEnv:PATH}"
+	},
 	"features": {
 		"ghcr.io/prulloac/devcontainer-features/latex:1": {
 			"scheme": "minimal",

.github/actions/setup/action.yml

@@ -7,57 +7,40 @@ inputs: # defaults are set to the version used in the dev container
     required: false
     default: "3.10"
     description: "The Python version to use."
-  torch-version:
-    required: false
-    default: "2.4.0"
-    description: "The PyTorch version to use."
   cuda-version:
     required: false
     default: cpu # For GPU support a self-hosted runner is required.
     description: "If CUDA should be used or not."
   full_install:
     required: false
     default: true
-    description: "If all side packages of PyTorch Geometric should be installed."
+    description: "If optional dependencies like `manim` and `LaTeX` should be installed."
 
 runs:
   using: composite
 
   steps:
-    - name: Set up Python ${{ inputs.python-version }}
-      uses: actions/setup-python@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
         python-version: ${{ inputs.python-version }}
-        check-latest: true
-        cache: pip
-        cache-dependency-path: |
-          pyproject.toml
-
-    - name: Install manim dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg
-      shell: bash
+        activate-environment: true
 
-    - name: Install PyTorch ${{ inputs.torch-version }}+${{ inputs.cuda-version }}
+    - name: Install pathpyG
       run: |
-        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 available:', torch.cuda.is_available())"
-        python -c "import torch; print('CUDA:', torch.version.cuda)"
+        uv sync --frozen --extra ${{ inputs.cuda-version }}
       shell: bash
 
-    - name: Install pyg-lib # pyg-lib is currently only available on Linux.
-      if: ${{runner.os == 'Linux' }}
+    - name: Check installation
       run: |
-        pip uninstall -y pyg-lib
-        pip install --no-index pyg-lib -f https://data.pyg.org/whl/torch-${{ inputs.torch-version }}+${{ inputs.cuda-version }}.html
+        uv run python -c "import torch; print('PyTorch:', torch.__version__)"
+        uv run python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
+        uv run python -c "import torch; print('CUDA:', torch.version.cuda)"
       shell: bash
 
     - name: Install extension packages
       if: ${{ inputs.full_install == 'true' }}
-      run: | # scipy installation before torch-scatter is required to solve dependency conflicts
-        pip install torch_geometric
-        pip install scipy
-        pip install --no-index --upgrade torch-scatter torch-sparse torch-cluster torch-spline-conv -f https://data.pyg.org/whl/torch-${{ inputs.torch-version }}+${{ inputs.cuda-version }}.html
+      run: | # ToDo: Add LaTeX installation
+        sudo apt-get update && sudo apt-get install -y build-essential python3-dev libcairo2-dev libpango1.0-dev ffmpeg
+        uv sync --frozen --extra vis --extra ${{ inputs.cuda-version }}
       shell: bash

.github/workflows/docs-dev.yml

@@ -10,17 +10,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
       - name: Setup packages
         uses: ./.github/actions/setup
 
-      - name: Install dependencies
-        run: |
-          pip install -e .[doc]
-
       - name: Get variables
         run: |
           python -c 'import pathpyG; print(f"package_version={pathpyG.__version__}")' >> "$GITHUB_ENV"

.github/workflows/docs-stable.yml

@@ -8,17 +8,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
       - name: Setup packages
         uses: ./.github/actions/setup
 
-      - name: Install dependencies
-        run: |
-          pip install -e .[doc]
-
       - name: Get package version
         run: |
           python -c 'import pathpyG; print(f"package_version={pathpyG.__version__}")' >> "$GITHUB_ENV"

.github/workflows/full_testing.yml

@@ -18,18 +18,14 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup packages
         uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
           torch-version: ${{ matrix.torch-version }}
 
-      - name: Install main package
-        run: |
-          pip install -e .[test,vis]
-
       - name: Run tests
         run: |
           pytest

.github/workflows/linting.yml

@@ -1,66 +1,46 @@
 # Inspired by https://github.com/pyg-team/pytorch_geometric/blob/ee30973ed0957a7f29f345d4eeaf9cfd70805109/.github/workflows/linting.yml
 name: Linting
 
+description: Run ruff and mypy to check code quality and type hints.
+
 on:
   push:
     branches:
       - main
   pull_request:
 
 jobs:
-  pylint: # linter: tool that checks for errors in Python code, tries to enforce a coding standard and looks for bad code smells
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Setup packages
-        uses: ./.github/actions/setup
-        with:
-          full_install: false
-
-      - name: Install dependencies
-        run: pip install pylint
-
-      - name: Run linting
-        continue-on-error: true
-        run: pylint $(git ls-files '*.py')
-
-  flake8: # Another linter: Mostly checks if code is PEP8 conform but has some additional plugins.
+  ruff:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.10.13" # As in docker image (pytorch/pytorch:2.1.0-cuda12.1-cudnn8-runtime) used as dev container
+          python-version: "3.10.18" # As in docker image (pytorch/pytorch:2.1.0-cuda12.1-cudnn8-runtime) used as dev container
 
       - name: Install dependencies
-        run: pip install flake8 flake8-pyproject flake8-bugbear
+        run: pip install ruff
 
       - name: Run linting
         continue-on-error: true
-        run: flake8 $(git ls-files '*.py')
+        run: ruff check .
 
-  mypy: # stricter static type checker
+  mypy:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup packages
         uses: ./.github/actions/setup
         with:
           full_install: false
 
-      - name: Install dependencies
-        run: pip install mypy
-
       - name: Check type hints
         continue-on-error: true
         run: |

.github/workflows/testing.yml

@@ -14,7 +14,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       # Only run workflow if certain files have been changed.
       - name: Get changed files
@@ -31,11 +31,6 @@ jobs:
         if: steps.changed-files.outputs.any_changed == 'true'
         uses: ./.github/actions/setup
 
-      - name: Install main package
-        if: steps.changed-files.outputs.any_changed == 'true'
-        run: |
-          pip install -e .[test,vis]
-
       - name: Run tests
         if: steps.changed-files.outputs.any_changed == 'true'
         run: |

.vscode/settings.json

@@ -4,33 +4,9 @@
     "[jsonc]": {
         "editor.defaultFormatter": "vscode.json-language-features"
     },
-    "[python]": {
-        "editor.defaultFormatter": "ms-python.black-formatter",
-    },
-    "python.defaultInterpreterPath": "/opt/conda/bin/python",
-    "python.formatting.provider": "none", // disable for now. Will be deprecated in the future
+    "python.defaultInterpreterPath": "/workspaces/pathpyG/.venv/bin/python",
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
-    "black-formatter.importStrategy": "fromEnvironment",
-    "black-formatter.args": [
-        "--config=pyproject.toml"
-    ],
-    "pylint.importStrategy": "fromEnvironment",
-    "pylint.args": [
-        "--rcfile=pyproject.toml"
-    ],
-    "flake8.importStrategy": "fromEnvironment",
-    "flake8.args": [
-        "--toml-config=pyproject.toml"
-    ],
-    "isort.importStrategy": "fromEnvironment",
-    "isort.args": [
-        "--settings-path=pyproject.toml"
-    ],
-    "mypy-type-checker.importStrategy": "fromEnvironment",
-    "mypy-type-checker.args": [
-        "--config-file=pyproject.toml"
-    ],
     "python.testing.pytestArgs": [
         "tests"
     ],