multi-echo-data-analysis

A Jupyter Book shamelessly copying off of https://github.com/naturalistic-data-analysis/naturalistic_data_analysis.

Building

This book uses Jupyter Book 1 (Sphinx, _config.yml / _toc.yml).

The Python environment is managed with uv and locked in uv.lock. The Makefile sets UV_PROJECT_ENVIRONMENT=meda, so the project environment is created in meda/ instead of the default .venv/.

To set up the environment:

make install

To check that the local environment still matches uv.lock:

make check-env

To build the Jupyter Book into _build/html/:

make book

Useful related targets:

• make clean removes generated site build files.
• make runall runs notebooks under content/ in place and saves outputs.
• make build is an alias-style HTML build target that also writes to _build/.
• make serve and make site use the repository's Ruby/Jekyll tooling and require those dependencies to be installed separately.

Publishing

The site is built locally; the HTML under docs/ on main is what GitHub Pages serves.

1. Install or update the locked environment with make install.
2. Build the book and copy _build/html/ into docs/ with make site-publish (or run make book followed by make sync-docs).
3. Commit the updated docs/ tree and push main.

In the GitHub repository settings, set Pages to Deploy from a branch, choose branch main, folder /docs. If the site was previously deployed with GitHub Actions, switch away from that source so Pages reads the committed docs/ folder.

Deployment no longer uses GitHub Actions; repository secrets such as CONFIG_EMAIL and CONFIG_NAME are not required for publishing.