xliu443 / codebook

The Good Research Code Handbook

The Good Research Code Handbook source

This is the source for the Good Research Code Handbook, by Patrick Mineault. The website lives at goodresearch.dev. This book uses jupyterbook to build, with a highly customized theme based off of tufte.css.

Reporting issues with the website

Please report any issues via the Issues tab.

Building the book

Recreate the conda environment with:

conda env create -n cb --file environment.yml

Then conda activate cb.

Run jupyter-book build . to build.

Use Run jupyter-book build . --all to force a full rebuild.

The book can be visualized locally using a development server. Typically, I use netlify dev for this purpose.

To remove thebe.js includes (which causes a 500KB javascript file to be loaded), run python strip_js.py (a hack).

Note: when you push a PR through Github, it will build a preview of your work through Netlify automatically. When I merge the PR, it will automatically deploy the built website to goodresearch.dev. See the badge above for build status.

Building the book to PDF

Manually change _config.yml so the author name appears correctly:

author: "Patrick Mineault"

Use jupyter-book build . --builder pdflatex to build to PDF. See here for the required environment.

Citing this book

Patrick J Mineault & The Good Research Code Handbook Community (2021). The Good Research Code Handbook. Zenodo. doi:10.5281/zenodo.5796873