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Contributing to GA4GH-RegBot

Environment

  • Use Python 3.10–3.13 (the range pyproject.toml accepts; 3.11 matches CI). Avoid 3.14 for the full ML/Chroma stack until wheels catch up.
  • Working on frontend/ also needs Node 20.9+ (CI uses 22).
  • Create a venv and install runtime deps:
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
pip install -r requirements.txt
  • Optional dev tools (lint + pre-commit):
pip install -r requirements-dev.txt
pre-commit install

Run pre-commit run --all-files before pushing if you use the hook.

Unit tests do not require Ollama or OPENAI_API_KEY; the pipeline test forces the offline path.

Tests

python -m pytest -q

Lint

ruff check src tests tools
ruff format --check src tests tools

Auto-format:

ruff format src tests tools

Type check (optional)

pip install -r requirements-dev.txt
python -m mypy -p src.regbot

This type-checks the src.regbot package (same as CI).

Frontend (frontend/)

Run all three before pushing a change to the Next.js UI — CI runs the same set on any PR that touches frontend/:

npm --prefix frontend run lint
npx --prefix frontend tsc -p frontend/tsconfig.json --noEmit
npm --prefix frontend run build

npm run lint enforces the React hook rules, including set-state-in-effect: an effect body may not update state synchronously. Mirroring a prop into state, or starting a fetch with setLoading(true), will fail here — derive from the prop instead, or raise the flag in the event handler that starts the fetch.

Secrets and local data

  • Do not commit .env, API keys, or your local vector store under data/regbot_store/.
  • Keep PRs focused: one logical change per PR, update tests when behavior changes.

Where to start

  • See docs/eval_results.md for measured limitations and docs/RELEASE_CHECKLIST.md for the remaining release blocker: independent review of the contributor-labelled gold set.