{
  "mcpServers": {
    "ncbi-datasets": {
      "command": "uvx",
      "args": ["ncbi-datasets-mcp"],
      "env": {
        "NCBI_API_KEY": "your_key_here",
        "NCBI_DOWNLOAD_DIR": "/path/to/downloads",
        "NCBI_AUTO_INSTALL": "true"
      }
    }
  }
}

# Install with dev extras
pip install -e ".[dev]"

# Run unit tests
pytest

# Run all tests including live network calls
pytest -m integration

# Regenerate enums from the current NCBI OpenAPI spec
python scripts/gen_enums.py

# Run the server locally (stdio transport)
ncbi-datasets-mcp

src/ncbi_datasets_mcp/
  server.py           FastMCP app — tool registrations only
  config.py           Pydantic-settings env config
  cli/
    locator.py        Find datasets/dataformat (config → PATH → cache)
    installer.py      Download binaries from NCBI FTP
    runner.py         Async subprocess wrapper
  rest/
    client.py         httpx client for metadata/summary endpoints
  domains/
    _generated_enums.py  Vendored enums from OpenAPI spec
    common.py         Shared utilities (output dir, filename sanitising)
    genome.py         Genome CLI arg builders + response shaping
    taxonomy.py       Taxonomy CLI arg builders
  models/
    responses.py      Shared DownloadResult dataclass