M4

[build-system] requires = ["pdm-backend"] build-backend = "pdm.backend" [project] name = "m4-mcp" dynamic = ["version"] description = "MIMIC-IV + MCP + Models: Local MIMIC-IV querying with LLMs via Model Context Protocol" requires-python = ">=3.10" authors = [ { name = "Rafi Al Attrach", email = "rafiaa@mit.edu" }, { name = "Pedro Moreira", email = "pedrojfm@mit.edu" }, { name = "Rajna Fani", email = "rajnaf@mit.edu" }, ] maintainers = [ { name = "Rafi Al Attrach", email = "rafiaa@mit.edu" }, { name = "Pedro Moreira", email = "pedrojfm@mit.edu" }, { name = "Rajna Fani", email = "rajnaf@mit.edu" }, ] readme = "README.md" license = "MIT" keywords = ["mimic-iv", "clinical-data", "mcp", "llm", "medical", "healthcare", "duckdb", "bigquery"] classifiers = [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "Intended Audience :: Healthcare Industry", "Topic :: Scientific/Engineering :: Medical Science Apps.", "Topic :: Database :: Database Engines/Servers", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Operating System :: OS Independent", ] dependencies = [ "typer>=0.9.0", # Typer as a core dependency for the CLI "rich>=13.0.0", # For Typer's rich output "requests>=2.30.0", "beautifulsoup4>=4.12.0", "polars[pyarrow]>=0.20.10", "appdirs>=1.4.0", "sqlalchemy>=2.0.0", "pandas>=2.0.0", "fastmcp>=0.1.0", # MCP server functionality "google-cloud-bigquery>=3.0.0", # BigQuery support "db-dtypes>=1.0.0", # BigQuery data types "sqlparse>=0.4.0", # SQL parsing for security validation "pyjwt[crypto]>=2.8.0", # JWT token handling with cryptography support "cryptography>=41.0.0", # Cryptographic operations for JWT "python-jose[cryptography]>=3.3.0", # Additional JWT support with crypto "httpx>=0.24.0", # Modern HTTP client for OAuth2 token validation "duckdb>=1.4.1", ] [dependency-groups] dev = [ "ruff>=0.4.0", "pre-commit>=3.0.0", "pytest>=8.0.0", "pytest-asyncio>=0.24.0", "pytest-mock>=3.10.0", "aiohttp>=3.8.0", # For MCP client testing ] [project.scripts] m4 = "m4.cli:app" m4-mcp = "m4.mcp_server:main" # Primary entry point for simplicity (enables `uvx m4-mcp`) m4-mcp-server = "m4.mcp_server:main" # Kept for backwards compatibility [project.urls] Homepage = "https://github.com/rafiattrach/m4" Repository = "https://github.com/rafiattrach/m4" Documentation = "https://github.com/rafiattrach/m4#readme" Issues = "https://github.com/rafiattrach/m4/issues" Changelog = "https://github.com/rafiattrach/m4/releases" [tool.pdm.version] source = "file" path = "src/m4/__init__.py" [tool.ruff] line-length = 88 target-version = "py310" src = ["src"] [tool.ruff.lint] select = [ "E", # pycodestyle errors "W", # pycodestyle warnings "F", # Pyflakes "I", # isort (import sorting) "UP", # pyupgrade (modernize syntax) "RUF",# Ruff-specific rules ] ignore = [ "E501", # Line too long (let ruff-format handle line length) ] [tool.ruff.format] # Ruff's default formatter will be used. [tool.ruff.lint.isort] known-first-party = ["m4"] [tool.pytest.ini_options] asyncio_mode = "auto" asyncio_default_fixture_loop_scope = "function" # Filter out Jupyter deprecation warning filterwarnings = [ "ignore::DeprecationWarning:jupyter_client.*", ]