OpenGenes MCP Server

name: CI on: push: branches: [ main ] pull_request: branches: [ main ] jobs: test: runs-on: ubuntu-latest strategy: matrix: python-version: ["3.12"] steps: - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v4 - name: Set up Python ${{ matrix.python-version }} run: uv python install ${{ matrix.python-version }} - name: Install dependencies run: uv sync --dev - name: Run tests run: uv run pytest -vvv -s - name: Test MCP server functionality run: | # Test that the server can be imported and instantiated uv run python -c " from opengenes_mcp.server import OpenGenesMCP print('✓ Server can be imported') try: # Test basic instantiation (will download DB from HuggingFace) server = OpenGenesMCP() print('✓ Server can be instantiated') print(f'✓ Database path: {server.db_manager.db_path}') # Test that database is accessible result = server.db_manager.execute_query('SELECT COUNT(*) as count FROM sqlite_master WHERE type=\"table\"') print(f'✓ Database has {result.rows[0][\"count\"]} tables') except Exception as e: print(f'✗ Server instantiation failed: {e}') sys.exit(1) " # Test server script help (should exit cleanly) uv run server --help test-windows: runs-on: windows-latest strategy: matrix: python-version: ["3.12"] steps: - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v4 - name: Set up Python ${{ matrix.python-version }} run: uv python install ${{ matrix.python-version }} - name: Install dependencies run: uv sync --dev - name: Run tests run: uv run pytest -vvv -s - name: Test MCP server functionality shell: pwsh run: | # Test that the server can be imported and instantiated uv run python -c " from opengenes_mcp.server import OpenGenesMCP print('✓ Server can be imported') try: # Test basic instantiation (will download DB from HuggingFace) server = OpenGenesMCP() print('✓ Server can be instantiated') print(f'✓ Database path: {server.db_manager.db_path}') # Test that database is accessible result = server.db_manager.execute_query('SELECT COUNT(*) as count FROM sqlite_master WHERE type=\"table\"') print(f'✓ Database has {result.rows[0][\"count\"]} tables') except Exception as e: print(f'✗ Server instantiation failed: {e}') sys.exit(1) " # Test server script uv run server --help lint: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v4 - name: Set up Python run: uv python install 3.11 - name: Install dependencies run: uv sync --dev - name: Check code formatting run: | uv run ruff check . uv run ruff format --check . continue-on-error: true lint-windows: runs-on: windows-latest steps: - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v4 - name: Set up Python run: uv python install 3.11 - name: Install dependencies run: uv sync --dev - name: Check code formatting run: | uv run ruff check . uv run ruff format --check . continue-on-error: true