Development

The maintained surface is src/gpn, tests, documentation, and the two prepared-data training recipes. Historical analysis and dataset construction are preserved separately from main.

Setup and checks

uv sync --extra train --group dev --group docs
uv run pre-commit run --all-files
uv run pytest
python docs/prepare_notebooks.py
uv run sphinx-build -n -W --keep-going -b html docs docs/_build/html

Normal checks are offline. See the root CONTRIBUTING.md and AGENTS.md for dependency placement, scientific-fixture approval, jaxtyping conventions, and the off-main research lifecycle.

The release dependency group is intentionally separate from ordinary development and documentation. It contains only the locked build and distribution inspection tools used by the release workflow; see the release runbook.

Documentation policy

• Markdown under docs/ is the source for all published documentation.

• Three existing model demos and one lightweight precomputed-score workflow live under colabs/. All four retain committed outputs; Sphinx and Read the Docs never execute any notebook.

• Notebook output refreshes are deliberate scientific changes. Record package, Transformers, model revision, dtype, and device metadata and compare numerical results to fixtures.

• Do not commit local paths, secrets, downloaded models, whole-genome alignments, or transient build output.

Refresh all three outputs together on a dedicated compute node. The notebooks use only pinned model revisions and the tiny checked-in alignment fixture; the command must never be pointed at or made to download a whole-genome MSA.

# Submit this command through Slurm with at most 8 CPUs and 1 GPU.
uv run --no-sync --with seaborn --with scikit-learn \
  python -m docs.refresh_notebooks

The script refuses to run outside a Slurm allocation unless --allow-local is passed explicitly for another dedicated compute environment. Review every output diff and rerun the published-model audit before accepting a refresh.