BioMCP

.PHONY: install install: ## Install the virtual environment and install the pre-commit hooks @echo "🚀 Creating virtual environment using uv" @uv sync --all-extras @uv run pre-commit install .PHONY: check check: ## Run code quality tools. @echo "🚀 Checking lock file consistency with 'pyproject.toml'" @uv lock --locked @echo "🚀 Checking for critical linting issues: Running ruff check" @uv run ruff check src tests @echo "🚀 Linting code: Running pre-commit" @uv run pre-commit run --all-files @echo "🚀 Static type checking: Running mypy" @uv run mypy @echo "🚀 Checking for obsolete dependencies: Running deptry" @uv run deptry . .PHONY: test test: ## Test the code with pytest and JavaScript tests @echo "🚀 Testing code: Running pytest with parallel execution" @uv run python -m pytest -x --ff -n auto --dist loadscope @echo "🚀 Testing JavaScript: Running worker sanitization tests" @node --test tests/tdd/workers/test_worker_sanitization.js .PHONY: test-js test-js: ## Test JavaScript code only @echo "🚀 Testing JavaScript: Running worker sanitization tests" @node --test tests/tdd/workers/test_worker_sanitization.js .PHONY: cov cov: ## Generate HTML coverage report @echo "🚀 Generating HTML coverage report" @uv run python -m pytest --cov --cov-config=pyproject.toml --cov-report=html .PHONY: build build: clean-build ## Build wheel file @echo "🚀 Creating wheel file" @uvx --from build pyproject-build --installer uv .PHONY: clean-build clean-build: ## Clean build artifacts @echo "🚀 Removing build artifacts" @uv run python -c "import shutil; import os; shutil.rmtree('dist') if os.path.exists('dist') else None" .PHONY: publish publish: build ## Publish a release to PyPI. @echo "🚀 Publishing." @uvx twine upload -r pypi dist/* .PHONY: docs-test docs-test: check-docs ## Test if documentation can be built without warnings or errors @uv run mkdocs build -s .PHONY: check-docs check-docs: ## Check that all docs are in mkdocs.yml @uv run python scripts/check_docs_in_mkdocs.py .PHONY: docs docs: update-endpoints ## Build and serve the documentation @uv run mkdocs serve .PHONY: update-endpoints update-endpoints: ## Update third-party endpoints documentation @echo "🚀 Updating third-party endpoints documentation" @uv run python scripts/generate_endpoints_doc.py @uv run python docs/developer-guides/generate_endpoints.py .PHONY: help help: @uv run python -c "import re; \ [[print(f'\033[36m{m[0]:<20}\033[0m {m[1]}') for m in re.findall(r'^([a-zA-Z_-]+):.*?## (.*)$$', open(makefile).read(), re.M)] for makefile in ('$(MAKEFILE_LIST)').strip().split()]" .DEFAULT_GOAL := help .PHONY: inspector inspector: @echo "🚀 Starting MCP Inspector" npx @modelcontextprotocol/inspector uv run --with . biomcp run .PHONY: pbdiff pbdiff: ## Copy git diff to clipboard @git diff -- . ':(exclude)uv.lock' | pbcopy