Tskit-based Demo Notebooks in JupyterLite

This is the source repository for notebooks hosted at

https://tskit.dev/explore/

These notebooks run JupyterLite as a static site, with compiled versions of the lastest versions of tskit and msprime. They therefore provide pyodide access to the most recent released versions of these libraries. Notebooks can be used in any modern browser:

• How-to Guides: https://jupyterlite.readthedocs.io/en/latest/howto/index.html
• Reference: https://jupyterlite.readthedocs.io/en/latest/reference/index.html

Generic information

This repo provides the Pyodide kernel (jupyterlite-pyodide-kernel), the JavaScript kernel (jupyterlite-javascript-kernel), and the p5 kernel (jupyterlite-p5-kernel), along with other optional utilities and extensions to make the JupyterLite experience more enjoyable.

Rebuilding Pyodide and packages from pyodide-recipes

To rebuild a full Pyodide runtime plus all packages from the latest pyodide-recipes:

1. Ensure you have conda and rustup (rustup must be on PATH).
2. From the repo root, run:

   pyodide/build_world_from_recipes.sh

   This will:
   • create or update a pyodide-env conda environment based on pyodide-recipes/environment.yml
   • clone or update pyodide-recipes (by default into _pyodide-recipes/)
   • use pyodide build-recipes to build all recipes and generate a pyodide-lock.json
   • copy the resulting runtime, lock file, and wheels into this repo’s pyodide/ directory
3. Rebuild the site:

   ./build.sh

Environment variables:

• PYODIDE_RECIPES_DIR – where to clone pyodide-recipes (default: _pyodide-recipes under the repo root).
• PYODIDE_ENV_NAME – conda env name (default: pyodide-env).
• PYODIDE_RECIPES_TARGETS – package selection string for pyodide build-recipes (default: "*" for all packages; e.g. *,!imgui-bundle to disable a problematic recipe).