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.

For local development, I recommend using the auto-reloading sphinx-autobuild package. This will not only build the book and create a local server for you to preview the book, it will also rebuild and reload the browser whenever you make a change. Neat! Use make develop to get that going.

To build a version ready to be deployed:

1. jupyter-book build docs --all for a full rebuild
2. python strip_js.py to remove thebe.js includes, which would otherwise cause a 500KB javascript file to be loaded

These two can be run via make build.

I use the netlify deploy -d _build/html --prod or make deploy to manually deploy the book to goodreseach.dev. This command won't work for you unless you have my netlify credentials.

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

The PDF of this book is built using LaTeX via CurveNote's MyST to tex conversion. As this feature is in alpha stage, there's an elaborate translation stage in assemble_one_pager.py. Because the CurveNote CLI is subject to change, make sure to use the exact version of the curvenote cli, v0.8.2, to build this.

Run git clone https://github.com/patrickmineault/plain_latex_book_chapter.git to fetch a plain tex template. Then place this under ../templates/plain_latex_book_chapter.

Build using make pdf. This will create a number of temporary files and the final pdf will live in tmp/exports/book-complete.pdf.

Citing this book

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