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Requirements

  • Python 3.12 or newer
  • uv recommended (see the repo pyproject.toml for direct dependencies)

Install

git clone https://github.com/ckmah/polyplot.git
cd polyplot
uv sync

Sample data

The repository includes a small sample_data/liver_crop_sample.parquet (about 50 cells in one spatial patch) for demos and CI. To build a new subset from a local full liver_crop.parquet, use:

uv run python scripts/make_liver_subset.py

Larger local parquets in sample_data/ are not tracked by git (see sample_data/README.md in the repository).

Quick start (marimo)

The shortest path is quickstart.py at the repository root (marimo). From a clone of the repository:

uv run marimo edit quickstart.py

A “Open in molab” badge in the README links to a hosted run once the file is on the default branch.

Full demo

For a longer walkthrough, see notebook.py:

uv run marimo edit notebook.py

Build this documentation site locally

uvx zensical serve

Open the URL printed in the terminal (by default http://127.0.0.1:8000).

Publish

Documentation for this site is built with Zensical in CI and published to GitHub Pages at the site_url configured in zensical.toml.