# NMDC MCP
A fastmcp-based tool for writing prompts against data in the NMDC database.
## Installation
You can install the package from source using uv:
```bash
uv sync
```
## Usage
You can use the CLI:
```bash
nmdc-mcp
```
Or import in your Python code:
```python
from nmdc_mcp.main import create_mcp
mcp = create_mcp()
mcp.run()
```
## Development
### Local Setup
```bash
# Clone the repository
git clone https://github.com/microbiomedata/nmdc-mcp.git
cd nmdc-mcp
# Install development dependencies
make dev
```
### Development Workflow
The project uses a comprehensive Makefile for development tasks:
```bash
# Run all development checks (tests, formatting, linting, type checking)
make all
# Individual commands
make dev # Install development dependencies
make test-coverage # Run tests with coverage
make format # Format code with black
make lint # Lint with ruff
make mypy # Type checking
make deptry # Check for unused dependencies
make build # Build package
```
### Testing
```bash
# Run all tests with coverage
make test-coverage
# Run specific test types
make test-unit # Unit tests only
make test-integration # Integration tests
make test-real-api # Tests against real NMDC API
make test-mcp # Test MCP protocol
```
### MCP Integration
#### Claude Desktop Setup
Add to `~/Library/Application Support/Claude/claude_desktop_config.json`:
```json
{
"mcpServers": {
"nmdc-mcp": {
"command": "uvx",
"args": ["nmdc-mcp"]
}
}
}
```
#### Claude Code MCP Setup
```bash
claude mcp add -s project nmdc-mcp uvx nmdc-mcp
```
#### Goose Setup
```bash
goose session --with-extension "uvx nmdc-mcp"
```
## License
MIT
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