setup.sh

#!/bin/bash

# Exit on error
set -e

echo "Setting up BioContext environment..."

# Initialize and update submodules
git submodule update --init --recursive

# Setup each submodule
for module in modules/*; do
    if [ -d "$module" ]; then
        echo "Setting up $module..."
        (
            cd "$module"
            # Create virtual environment if it doesn't exist
            if [ ! -d ".venv" ]; then
                python -m venv .venv
            fi
            
            # Activate virtual environment and install dependencies
            source .venv/bin/activate
            if [ -f "requirements.txt" ]; then
                pip install -r requirements.txt
            elif [ -f "pyproject.toml" ]; then
                pip install -e .
            fi
            deactivate
        )
    fi
done

# Create necessary directories
mkdir -p data
mkdir -p logs

echo "Setup complete! You can now use the individual MCP servers or docker-compose to run all services."