I love jupyter notebooks. Without them, I wouldn’t have been half as productive as I was during my PhD.

Here’s a post I wrote just a few weeks ago describing some of the conventions that I established for myself over the course of 5 years:

https://jessimekirk.com/blog/notebook_rules/

I suspect that a lot of the conventions I describe help mitigate problems described here, some of which should be strictly or optionally enforced by the notebook instead of the user.

(The site’s very much a work in progress, so expect to see odd and broken things if you go poking around.)