Add GitHub CI/CD pipeline

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+Brief description of the changes in this PR.
+
+## Type of Change
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Performance improvement
+- [ ] Code refactoring
+
+## Testing
+- [ ] Tests pass locally
+- [ ] New tests added for new functionality
+- [ ] All existing tests pass
+- [ ] Manual testing completed
+
+## Checklist
+- [ ] Code follows the project's coding standards
+- [ ] Self-review of the code completed
+- [ ] Code is properly commented
+- [ ] Documentation updated (if applicable)
+- [ ] No new warnings or errors introduced
+
+## Related Issues
+Closes #(issue number)
+
+## Additional Notes
+Any additional information that reviewers should know.

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "09:00"
+    open-pull-requests-limit: 10
+    reviewers: []
+    assignees: []
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "09:00"
+    open-pull-requests-limit: 5
+    reviewers: []
+    assignees: []
+    commit-message:
+      prefix: "chore"
+      include: "scope"

.github/workflows/benchmark.yml

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+name: Performance Benchmarks
+
+on:
+  push:
+    branches: [ main ]
+  schedule:
+    - cron: '0 0 * * 0'  # Weekly on Sunday
+  workflow_dispatch:
+
+jobs:
+  benchmark:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest-benchmark memory-profiler
+
+    - name: Run benchmarks
+      run: |
+        pytest tests/benchmarks/ -v --benchmark-only --benchmark-save=benchmark
+        python scripts/run_benchmarks.py
+
+    - name: Upload benchmark results
+      uses: actions/upload-artifact@v3
+      with:
+        name: benchmark-results
+        path: |
+          .benchmarks/
+          benchmark_results/

.github/workflows/dependency-update.yml

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+name: Dependency Updates
+
+on:
+  schedule:
+    - cron: '0 0 * * 1'  # Weekly on Monday
+  workflow_dispatch:
+
+jobs:
+  update-dependencies:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pip-tools
+
+    - name: Update requirements
+      run: |
+        pip-compile requirements.in --upgrade
+        pip-compile requirements-dev.in --upgrade
+
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v5
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        commit-message: 'chore: update dependencies'
+        title: 'Automated dependency updates'
+        body: |
+          This PR contains automated dependency updates.
+
+          Please review the changes and test before merging.
+        branch: dependency-updates
+        delete-branch: true

.github/workflows/docs.yml

@@ -1,77 +1,41 @@
-name: Build and Deploy Documentation
+name: Documentation
 
 on:
   push:
-    branches: [ develop ]
+    branches: [ main, develop ]
   pull_request:
-    branches: [ develop ]
-  workflow_dispatch:
-
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Use a unique concurrency group to avoid conflicts
-concurrency:
-  group: "sphinx-docs-${{ github.workflow }}-${{ github.ref }}"
-  cancel-in-progress: true
+    branches: [ main, develop ]
 
 jobs:
-  build-docs:
-    name: Build Sphinx Documentation
+  docs:
     runs-on: ubuntu-latest
+
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-
+    - uses: actions/checkout@v4
+
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
-        
+        python-version: '3.10'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e .[docs]
-        # Also install the main package dependencies
-        pip install -e .
-
+        pip install -r requirements.txt
+        pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints
+
     - name: Build documentation
       run: |
-        echo "Starting documentation build..."
-        cd docs
-        echo "Current directory: $(pwd)"
-        echo "Contents of source directory:"
-        ls -la source/
-        make clean
-        echo "Building Sphinx documentation..."
-        sphinx-build -b html source build/html
-        echo "Creating .nojekyll file..."
-        touch build/html/.nojekyll
-        echo "Documentation build complete!"
-        echo "Contents of build directory:"
-        ls -la build/html/
-
-    - name: Setup Pages
-      if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
-      uses: actions/configure-pages@v5
-
-    - name: Upload artifact
-      if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
-      uses: actions/upload-pages-artifact@v3
+        cd docs/
+        sphinx-build -b html . _build/html
+
+    - name: Check for broken links
+      run: |
+        pip install linkchecker
+        linkchecker docs/_build/html/ --check-extern
+
+    - name: Upload documentation
+      uses: actions/upload-artifact@v3
       with:
-        path: './docs/build/html'
-
-  deploy-docs:
-    name: Deploy to GitHub Pages
-    if: github.event_name == 'push' && github.ref == 'refs/heads/develop'
-    runs-on: ubuntu-latest
-    needs: build-docs
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4 
+        name: documentation
+        path: docs/_build/html/

.github/workflows/gpu-test.yml

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+name: GPU Tests
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+  workflow_dispatch:
+
+jobs:
+  gpu-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install CUDA dependencies
+      run: |
+        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
+        sudo dpkg -i cuda-keyring_1.0-1_all.deb
+        sudo apt-get update
+        sudo apt-get -y install cuda-toolkit-12-0
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest pytest-cov
+
+    - name: Run GPU tests
+      run: |
+        python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"
+        pytest tests/test_gpu/ -v --tb=short
+      env:
+        CUDA_VISIBLE_DEVICES: 0

.github/workflows/lint.yml

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+name: Code Quality
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install black isort flake8 mypy pre-commit
+
+    - name: Run black (code formatting)
+      run: black --check --diff src/ tests/ scripts/
+
+    - name: Run isort (import sorting)
+      run: isort --check-only --diff src/ tests/ scripts/
+
+    - name: Run flake8 (linting)
+      run: flake8 src/ tests/ scripts/ --max-line-length=100 --ignore=E203,W503
+
+    - name: Run mypy (type checking)
+      run: mypy src/alignment/ --ignore-missing-imports --no-strict-optional
+
+    - name: Check for TODO/FIXME comments
+      run: |
+        if grep -r "TODO\|FIXME" src/ tests/; then
+          echo "Found TODO/FIXME comments. Please address them."
+          exit 1
+        fi

.github/workflows/pre-commit.yml

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+name: Pre-commit
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install pre-commit
+      run: |
+        python -m pip install --upgrade pip
+        pip install pre-commit
+
+    - name: Run pre-commit
+      uses: pre-commit/action@v3.0.0