em-template-lite

A self-hosted, in-browser-compute version of the Elemental Microscopy article template.

This is a fork of msa-em/em-template with the Curvenote / Binder dependency replaced by:

• JupyterLite running in the reader's browser (Pyodide kernel)
• GitHub Pages for static hosting
• GitHub Actions for build + deploy

No external compute service is required to view, build, or interact with the article.

What's the same

• Author workflow: write MyST markdown + Jupyter notebooks
• Article layout: MyST book-theme, same typography, same figure widgets
• Content: image / movie / 3D / FFT interactives

What's different

• No Curvenote, no Binder server, no CURVENOTE_TOKEN
• Interactive cells run via Thebe → JupyterLite (in-browser Pyodide)
• Movie data is pre-decoded from .mp4 to .npz in CI (Pyodide doesn't ship pyav)
• Deploys to https://msa-em.github.io/em-template-lite/

Local development

conda env create -f environment.yml
conda activate em-template-lite

# preview the article (no kernel needed for static content)
myst start

To work on interactive cells, run a local Jupyter server in parallel:

jupyter lab --IdentityProvider.token=devtoken --ServerApp.allow_origin='http://localhost:3000' --port=8888

…and uncomment the jupyter.server block in myst.yml.

Deploy

Pushing to main triggers .github/workflows/deploy.yml, which:

1. Pre-decodes mp4 → npz so notebooks can run in Pyodide
2. Builds JupyterLite (jupyter lite build)
3. Builds the MyST static site (myst build --html)
4. Combines them and publishes to GitHub Pages