Installation

Quick install (PyPI)

alphafold-sovereign-mcp is published on PyPI:

pip install alphafold-sovereign-mcp

Or run without installing using uvx:

uvx alphafold-sovereign-mcp

A signed wheel and sdist are attached to every GitHub Release with SLSA L3 build provenance and Sigstore (cosign) signatures. Verify the supply chain with scripts/replicate.sh.

Install from source

git clone https://github.com/smaniches/alphafold-sovereign-mcp
cd alphafold-sovereign-mcp
uv pip install -e .

With persistent-homology TDA (requires gudhi):

uv pip install -e ".[tda]"

Verify the install

alphafold-sovereign --version       # → 1.1.7
alphafold-sovereign --self-test     # → SELF-TEST PASS

--self-test boots the server in offline mode and exercises the deterministic logic of the ACMG helpers against a built-in BRCA1 c.5266dupC fixture. It does not make any network calls. Returns exit code 0 on PASS, non-zero on FAIL.

Configure Claude Desktop

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "alphafold-sovereign": {
      "command": "alphafold-sovereign-mcp",
      "args": []
    }
  }
}

Restart Claude Desktop and the tools become available in conversations. See Examples for what a session looks like.

Offline / air-gap mode

Set ALPHAFOLD_OFFLINE=1 to refuse all outbound HTTP and serve only from the local SQLite cache:

ALPHAFOLD_OFFLINE=1 alphafold-sovereign-mcp