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CONTRIBUTING

1. TL;DR

Install uv. Clone this repository, then from the root directory:

uv run python -m saev --help

You also need yek and lychee for generating docs.

If you want to do any of the web interface work, you need elm, elm-format, tailwindcss and bun.

2. Repo Layout

benchmark.py  <- Launch script for benchmarking models on tasks.
report.py     <- Launch script for producing the report.json file.
biobench/     <- Source code for benchmarking.
  beluga/
    __init__.py
    download.py
  fishnet/
    __init__.py
    download.py
  ...
  config.py
  registry.py
  reporting.py
  schema.sql
  third_party_models.py
docs/
  api/
  assets/
  data/
  research/
  todo/
  index.html
web/
  src/
    Leaderboard.elm
  index.html
  main.css

3. Coding Style & Conventions

See AGENTS.md.

4. Testing & Linting

  1. Run just test.
  2. Check that there are no regressions. Unless you are certain tests are not needed, the coverage % should either stay the same or increase.
  3. Run just docs.
  4. Fix any missing doc links.

5. Code of Conduct

Be polite, kind and assume good intent.