hyphaeon-app

PrimAeon, the application for HyphAeon, live at https://veg.github.io/primaeon/ (a single-threaded preview deployment; see deploy/), a neural surrogate for HyPhy's MEME and BUSTED with co-selection networks, a digital deep mutational scan and phenotype association on top. This repository holds everything that runs:

Every result carries is_surrogate and a path to run the real analysis on Datamonkey. No Python and no HyPhy run anywhere in the product (PLAN.md D16, D22): a tree with branch lengths is used as given; without one, pairwise TN93 distances feed the model, the reference's own --use-tn93.

The two-repository rule

HyphAeon is two repositories split by what they are, and the line between them is not negotiable (PLAN.md D9, §5.5):

• veg/HyphAeon holds the methods: the Python reference (hyphaeon/*.py), the JavaScript library that mirrors it function for function (js/, published as @veg/hyphaeon-js), the fixtures generated from the Python and replayed by the JavaScript in the same CI run, the exported ONNX graphs and their manifest (models/), and the end-to-end parity harness (scripts/parity.py, PARITY.md). One tag publishes the Python to PyPI and the library to npm from one commit. The library is pure functions: no onnxruntime, no I/O, no workers, no server, no UI.

• This repository holds everything that runs the methods, and pins the library. If two different apps (a browser, an MCP, a batch CLI) would want a piece of code unchanged, it belongs in the library; if it knows about a URL, a file, a session, a thread count or a warning to show, it belongs here.

A method is ported from the reference source and never "improved" during the port. A Python bug is replicated, flagged, fixed upstream, the fixtures regenerated, then fixed in the JavaScript.

Related MCP server: mcp-server-proxy

Running locally

The library is consumed by a file: link (runtime/package.json: "@veg/hyphaeon-js": "file:../../HyphAeon/js"), and the runtime tests, the web build and the e2e read the engine's models/ and fixtures/ from the same place, so the engine must be checked out as a sibling of this repository, at the ref this repository is developed against (ENGINE_REF in .github/workflows/ci.yml; phase-3a today):

parent/
├── HyphAeon/        git clone git@github.com:veg/HyphAeon.git && git checkout phase-3a
└── hyphaeon-app/    this repository

Node 22 (.nvmrc; nvm use). Then, from this repository's root:

npm ci                                   # every workspace; links @veg/hyphaeon-js from ../HyphAeon/js
npm test                                 # vitest in runtime/, web/, mcp/, server/ (~1.5 min; scores the examples through the real graphs)
cd web && npm run check && npm run build # svelte-check, then the static build into web/build/
cd ../e2e && npx playwright install chromium && npx playwright test   # Playwright against `vite preview` of that build
cd ../web && npm run dev                 # the dev server (copies the ORT WASM and the graphs into static/ first)

The build's prebuild copies ONNX Runtime's WASM and the engine's graphs and manifest into web/static/, writes web/static/_headers, prebakes the five gallery reports under onnxruntime-node (stamp-cached; a full rebake is about three minutes) and validates web/caveats.json against the manifest. Nothing served by the site comes from another origin.

Environment variables you may need:

onnxruntime-node is pinned exactly to 1.23.2 (the last release with darwin/x64 bindings; see CLAUDE.md). On an Apple-silicon Mac running an x64 Node under Rosetta it is the version that loads; production is linux/x64 where the pin costs nothing.

The MCP server

Local, over stdio (private; nothing leaves your machine):

claude mcp add hyphaeon -- npx @veg/hyphaeon-mcp

Or from this checkout, after npm ci at the root:

claude mcp add hyphaeon -- node /path/to/hyphaeon-app/mcp/bin/hyphaeon-mcp.js

Set HYPHAEON_MODELS_DIR if the graphs are not where the search order in mcp/README.md expects them. Remote, over streamable HTTP: the server (server/) mounts the same package at /mcp behind its OAuth ceremony; add it as a connector the way the Datamonkey connector is added.

The server

cd server && HYPHAEON_MODELS_DIR=../web/static/models npm start   # listens on HYPHAEON_SERVER_PORT (7040)
curl -s localhost:7040/api/v1/health

deploy/README.md is the runbook: what the host needs (Node and the model files, nothing else), the Apache vhost, pm2 or Docker, and the smoke checks.

Parity against the Python reference

node runtime/scripts/parity-node.mjs --examples all --analyses meme,busted,epistasis,dms,phenotype --busted-examples all
cd ../HyphAeon && HYPHAEON_WEIGHTS=$PWD/model.safetensors HF_HUB_OFFLINE=1 \
  python scripts/parity.py --examples all --surfaces python,node,node-tn93

The runner writes the node surface (and node-tn93 for the runs that went tree-free) into the engine's parity/; parity.py runs the reference CLI on the same examples and compares at the classes of PLAN.md §5.4 (../HyphAeon/PARITY.md is the contract). The e2e writes the browser surface the same way. CI runs both on every push (.github/workflows/ci.yml; the parity job).

Continuous integration

.github/workflows/ci.yml runs two jobs on every push to main and every pull request: app (install, every workspace's tests, svelte-check, the full build, Playwright) and parity (the node surfaces, then the Python reference and the comparison). Both check out veg/HyphAeon at ENGINE_REF beside this repository with the ENGINE_DEPLOY_KEY secret (a read-only deploy key), because the engine is private; the section "CI" in CLAUDE.md says what to set and how to bump the ref.

Documents

• PLAN.md: the plan of record — architecture, the port, parity classes, phases and every decision (D1–D22).

• CLAUDE.md: the project notebook — commands, why each non-obvious configuration is the way it is, working rules, release notes per phase.

• Phase reports, each with the checks that were run and what they printed, the parity table and the gaps carried forward: PHASE0.md, PHASE1.md, PHASE2.md, PHASE3.md.

• In the engine: PHASE0.md, PHASE1A.md, PHASE2A.md, PHASE3A.md (the library side of each phase), PARITY.md (the parity contract) and MDS_SIGN.md (the eigenvector sign convention, D20).

• mcp/README.md, server/README.md, deploy/README.md.

License

MIT.