I'm working on my data science degree (previously a senior sysadmin), and this is also the workflow I have settled on. Along with versioning/diffs so you can walk back in time to see your changes in a script, I think it's one of the more robust and reproduceable systems around.

So my scripts focus on the data, but around the code block are comments and notes about what is being done, etc.

I've recently been looking at how to integrate makefile into this since watching the following video: https://www.youtube.com/watch?v=sd0HhW8vkSQ

All that said, kudos to the author for this, reading through it I see a few things I hadn't even though of yet, and I live on the command line in general. If it werent for browsing the internet (eww in emacs is nice though) and gaming, I don't think I'd even need a desktop environment.