fix encoder position learning #33
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| name: Build and Deploy Documentation | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued. | |
| concurrency: | |
| group: "pages" | |
| cancel-in-progress: false | |
| jobs: | |
| # Build job | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| - name: Cache pip dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt', '**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| # Install basic dependencies for documentation | |
| pip install sphinx sphinx-autodoc-typehints sphinx-rtd-theme | |
| pip install numpy pandas matplotlib tqdm h5py | |
| # Install torch and torch-geometric (CPU versions for docs) | |
| pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu | |
| pip install torch-geometric | |
| # Try to install project dependencies if they exist | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| if [ -f pyproject.toml ]; then pip install -e .; fi | |
| - name: Setup Sphinx documentation | |
| run: | | |
| # Create docs directory if it doesn't exist | |
| mkdir -p docs | |
| cd docs | |
| # Initialize Sphinx if not already done | |
| if [ ! -f conf.py ]; then | |
| sphinx-quickstart --quiet --sep --project "FoldTree2" \ | |
| --author "DessimozLab" --release "1.0" --language en \ | |
| --extensions sphinx.ext.autodoc,sphinx.ext.viewcode,sphinx.ext.napoleon \ | |
| --makefile --no-batchfile . | |
| fi | |
| - name: Configure Sphinx | |
| run: | | |
| cd docs | |
| # Create or update conf.py with proper configuration | |
| cat > conf.py << 'EOF' | |
| import os | |
| import sys | |
| sys.path.insert(0, os.path.abspath('..')) | |
| project = 'FoldTree2' | |
| copyright = '2025, DessimozLab' | |
| author = 'DessimozLab' | |
| release = '1.0' | |
| extensions = [ | |
| 'sphinx.ext.autodoc', | |
| 'sphinx.ext.viewcode', | |
| 'sphinx.ext.napoleon', | |
| 'sphinx.ext.githubpages', | |
| ] | |
| templates_path = ['_templates'] | |
| exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] | |
| html_theme = 'sphinx_rtd_theme' | |
| html_static_path = ['_static'] | |
| # Napoleon settings for Google/NumPy style docstrings | |
| napoleon_google_docstring = True | |
| napoleon_numpy_docstring = True | |
| napoleon_include_init_with_doc = False | |
| napoleon_include_private_with_doc = False | |
| # Autodoc settings | |
| autodoc_default_options = { | |
| 'members': True, | |
| 'undoc-members': True, | |
| 'show-inheritance': True, | |
| } | |
| EOF | |
| - name: Generate API documentation | |
| run: | | |
| cd docs | |
| # Create index.rst if it doesn't exist | |
| cat > index.rst << 'EOF' | |
| FoldTree2 Documentation | |
| ======================= | |
| FoldTree2 is a toolkit for protein structure phylogenetic analysis using neural network encoders. | |
| .. toctree:: | |
| :maxdepth: 2 | |
| :caption: Contents: | |
| modules | |
| Overview | |
| -------- | |
| FoldTree2 combines structural biology and phylogenetics by: | |
| * Encoding protein structures using trained neural networks | |
| * Generating structure-based substitution matrices | |
| * Performing phylogenetic inference with structural information | |
| API Reference | |
| ============= | |
| .. toctree:: | |
| :maxdepth: 4 | |
| foldtree2 | |
| Indices and tables | |
| ================== | |
| * :ref:`genindex` | |
| * :ref:`modindex` | |
| * :ref:`search` | |
| EOF | |
| # Generate module documentation | |
| sphinx-apidoc -f -o . ../foldtree2 --separate | |
| - name: Build documentation | |
| run: | | |
| cd docs | |
| make html | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v3 | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v2 | |
| with: | |
| path: './docs/_build/html' | |
| # Deployment job | |
| deploy: | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| needs: build | |
| if: github.ref == 'refs/heads/main' | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v2 |