[hoosieree]

Notebooks aren't very git-friendly, so in practice you rarely know which version produced the paper.

The fact you can run notebook cells out-of-order exacerbates this problem. Not only do you not know what version the entire file was, you also don't know in what order or how many times each cell within the file executed in order to produce the plots you see in the paper.

This isn't to discount the improvement in UX that you get from notebooks compared to my preferred alternative (emacs with org-mode). Maybe I'm just bitter that the ipynb format exists at all. If notebooks were just a UX layered on top of emacs+org-mode, that would fix most of the core issues.