update faq #3
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| - dev | |
| - flake8 | |
| pull_request: | |
| branches: [ main, master, dev, flake8 ] | |
| permissions: | |
| contents: write | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12', '3.13'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Free disk space | |
| run: | | |
| sudo rm -rf /usr/local/lib/android | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf /usr/local/share/powershell | |
| sudo rm -rf /usr/local/share/chromium | |
| sudo rm -rf /usr/local/.ghcup | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install uv | |
| run: curl -LsSf https://astral.sh/uv/install.sh | sh | |
| - name: Cache uv dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/uv | |
| key: ${{ runner.os }}-uv-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-uv- | |
| - name: Create virtual environment and install dependencies | |
| env: | |
| UV_HTTP_TIMEOUT: 300 | |
| UV_CONCURRENT_DOWNLOADS: 4 | |
| run: | | |
| uv venv | |
| uv pip install -e ".[test,dev]" | |
| - name: Run linting and code quality checks with Ruff | |
| run: | | |
| source .venv/bin/activate | |
| # Check formatting | |
| ruff format --check . | |
| # Check linting | |
| ruff check . --statistics | |
| - name: Run flake8 checks for MCP module | |
| run: | | |
| source .venv/bin/activate | |
| # Install flake8 for MCP module compatibility check | |
| uv pip install flake8>=7.1.2 | |
| # Run flake8 on MCP module | |
| flake8 dnallm/mcp/ --max-line-length=79 --extend-ignore=E203,W503,C901,E402 | |
| # Run flake8 on other modules excluding metrics | |
| flake8 dnallm/ --max-line-length=79 --extend-ignore=E203,W503,C901,E402 --exclude=dnallm/tasks/metrics/ | |
| - name: Run type checking | |
| run: | | |
| source .venv/bin/activate | |
| mypy dnallm/ --ignore-missing-imports --no-strict-optional --disable-error-code=var-annotated --disable-error-code=assignment --disable-error-code=return-value --disable-error-code=arg-type --disable-error-code=index --disable-error-code=attr-defined --disable-error-code=operator --disable-error-code=call-overload --disable-error-code=valid-type --disable-error-code=no-redef --disable-error-code=dict-item --disable-error-code=return --disable-error-code=unreachable --disable-error-code=misc --disable-error-code=import-untyped --exclude=dnallm/tasks/metrics/ | |
| # - name: Run tests with coverage | |
| # run: | | |
| # source .venv/bin/activate | |
| # pytest tests/ -v --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short | |
| # - name: Upload coverage to Codecov | |
| # uses: codecov/codecov-action@v3 | |
| # with: | |
| # file: ./coverage.xml | |
| # fail_ci_if_error: false | |
| test-cuda: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| cuda-version: ['12.1', '12.4'] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Free disk space | |
| run: | | |
| sudo rm -rf /usr/local/lib/android | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf /usr/local/share/powershell | |
| sudo rm -rf /usr/local/share/chromium | |
| sudo rm -rf /usr/local/.ghcup | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install CUDA dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y nvidia-cuda-toolkit | |
| - name: Install uv | |
| run: curl -LsSf https://astral.sh/uv/install.sh | sh | |
| - name: Cache uv dependencies | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/uv | |
| key: ${{ runner.os }}-uv-cuda-${{ matrix.cuda-version }}-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-uv-cuda-${{ matrix.cuda-version }}- | |
| ${{ runner.os }}-uv- | |
| - name: Create virtual environment and install CUDA dependencies | |
| env: | |
| UV_HTTP_TIMEOUT: 300 | |
| UV_CONCURRENT_DOWNLOADS: 4 | |
| run: | | |
| uv venv | |
| if [ "${{ matrix.cuda-version }}" = "12.1" ]; then | |
| uv pip install -e ".[test,dev,cuda121]" | |
| elif [ "${{ matrix.cuda-version }}" = "12.4" ]; then | |
| uv pip install -e ".[test,dev,cuda124]" | |
| fi | |
| # - name: Run GPU-enabled tests | |
| # run: | | |
| # source .venv/bin/activate | |
| # pytest tests/ -v -m "not slow" --tb=short | |
| # test-mamba: | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # python-version: ['3.11'] | |
| # steps: | |
| # - name: Checkout code | |
| # uses: actions/checkout@v4 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Install uv | |
| # run: curl -LsSf https://astral.sh/uv/install.sh | sh | |
| # - name: Create virtual environment and install mamba dependencies | |
| # run: | | |
| # uv venv | |
| # uv pip install -e ".[test,dev]" | |
| # uv pip install -e ".[mamba]" --no-cache-dir --no-build-isolation | |
| # - name: Run mamba-specific tests | |
| # run: | | |
| # source .venv/bin/activate | |
| # pytest tests/ -v -m "not slow" --tb=short | |
| deploy: | |
| needs: [test, test-cuda] | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Configure Git credentials | |
| run: | | |
| git config user.name github-actions[bot] | |
| git config user.email 41898282+github-actions[bot]@users.noreply.github.com | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.11 | |
| - name: Cache mkdocs dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| key: mkdocs-material-${{ github.run_number }} | |
| path: .cache | |
| restore-keys: | | |
| mkdocs-material- | |
| - name: Install uv | |
| run: curl -LsSf https://astral.sh/uv/install.sh | sh | |
| - name: Create virtual environment and install documentation dependencies | |
| env: | |
| UV_HTTP_TIMEOUT: 120 | |
| UV_CONCURRENT_DOWNLOADS: 1 | |
| run: | | |
| uv venv | |
| uv pip install -e ".[base,docs]" | |
| - name: Deploy documentation to GitHub Pages | |
| run: | | |
| source .venv/bin/activate | |
| mkdocs gh-deploy --force |