BioMCP

name: CI on: push: branches: [main, develop] pull_request: branches: [main] workflow_dispatch: env: PYTHON_VERSION: "3.12" UV_VERSION: "0.4.29" jobs: # Quality check from main.yml - uses make check quality: runs-on: ubuntu-latest name: Quality steps: - name: Check out uses: actions/checkout@v5 - uses: actions/cache@v4 with: path: ~/.cache/pre-commit key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} - name: Set up Python uses: actions/setup-python@v6 with: python-version: ${{ env.PYTHON_VERSION }} - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Install dependencies run: | uv sync --group dev - name: Run checks run: make check # Tests and type check specifically on Python 3.11 tests-and-type-check: runs-on: ubuntu-latest name: Tests and Type Check (Python 3.11) steps: - name: Check out uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v6 with: python-version: "3.11" - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Install dependencies run: | uv sync --group dev - name: Run tests run: uv run python -m pytest tests -m "not integration" --cov --cov-config=pyproject.toml --cov-report=xml - name: Check typing run: uv run mypy - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11 uses: codecov/codecov-action@v5 # Documentation check from main.yml check-docs: runs-on: ubuntu-latest name: Check Docs steps: - name: Check out uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v6 with: python-version: ${{ env.PYTHON_VERSION }} - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Install dependencies run: | uv sync --group dev - name: Check if documentation can be built run: uv run mkdocs build -s # Build package check build-package: runs-on: ubuntu-latest name: Build Package steps: - uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v6 with: python-version: ${{ env.PYTHON_VERSION }} - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Build package run: | uvx --from build pyproject-build --installer uv - name: Check package run: | uvx twine check dist/* - name: Upload artifacts uses: actions/upload-artifact@v4 with: name: dist path: dist/ # MCP integration test - quick check test-mcp: runs-on: ubuntu-latest name: Test MCP Integration steps: - uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v6 with: python-version: ${{ env.PYTHON_VERSION }} - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Install dependencies run: | uv sync --group dev - name: Test MCP server startup run: | timeout 10s uv run biomcp run || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi - name: Run MCP integration tests run: | uv run python -m pytest tests/tdd/test_mcp_integration.py -v # Run integration tests separately - allowed to fail integration-tests: runs-on: ubuntu-latest name: Integration Tests (Optional) continue-on-error: true steps: - name: Check out uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v6 with: python-version: "3.11" - name: Install uv uses: astral-sh/setup-uv@v7 with: version: ${{ env.UV_VERSION }} - name: Install dependencies run: | uv sync --group dev - name: Run integration tests run: | uv run python -m pytest tests -m "integration" -v --tb=short continue-on-error: true