MCP server evaluation

Setup

The setup requires uv, please install it, if it's not available on your machine.

You also need to create a .env file in this directory with the following variables:

OPENAI_API_KEY=your_openai_api_key
MCP_SERVER_URL=your_mcp_server_url

You can create the virtual environment and install all dependencies with the setup script:

bash ./setup.sh

Running the BioContextAI server locally

If you want to run the MCP server as the BioContextAI server locally, first install it, then start the server with:

export MCP_ENVIRONMENT=PRODUCTION
export MCP_INCLUDE_KEGG=true
uv run biocontext_server

Running the tests

bash ./run.sh