About¶

Lab notebook for work in the Chiappe lab (Champalimaud) on circuits that estimate self-movement during visually guided locomotion.

Notebook chapters are marimo notebooks from jaehho/champalimaud, built with marimo-book. Each .py chapter is re-executed at build time against the local FlyWire data/ cache, then baked into static HTML.

The home page is generated from notebooks/ (book/gen_site.py): titles, blurbs, and thumbnails come from the rendered notebooks, so a new notebook appears on the next build without editing pages.

What is not here¶

The data/ cache (tens of gigabytes of parquet and skeletons). marimo-book copies a book-root data/ directory into the published site, so this book lives in book/ and the cache stays at the repo root. Notebook sources under book/content/notebooks/ are symlinks into notebooks/.
API tokens and anything in .env.
A live kernel. Re-running a notebook needs the repo, data/, and uv sync.

Build¶

make docs

Generates the home page, then runs marimo-book build -b book/book.yml --strict in the project venv. data/ must be present; the build re-executes every listed notebook. Deploy is make deploy (wrangler to champalimaud.jaehho.com).