src/README.md

# ENCODE application source

The current architecture, model conventions, data layout, and deployment steps
are documented once in the repository [README](../README.md).

## Layout

- `backend/` — FastAPI routes, BGE-FT-VA query encoding, FAISS code search,
  two-surface phenotype retrieval, mappings, and graph responses.
- `frontend/` — static HTML, CSS, and JavaScript served by the backend and reused
  by the Netlify package.
- `requirements.txt` — pinned CPU runtime dependencies used by the Docker image.

For a local source-mode server with dependencies already installed:

```bash
uvicorn src.backend.app:app --host 127.0.0.1 --port 8000
```

The required model, indexes, embeddings, and runtime sidecars must exist under
`outputs/` or be redirected through the `ENCODE_*` environment variables defined
in `backend/paths.py`.