[spiralk]

> someone who doesn't appear to respect the organizational capabilities of academic labs, you are condemning them to far more poorly organized outputs.

This is not a great way to make your argument, though you are not the not only one here making a personal judgement without even knowing about my background. These are all issues I have seen first hard. With most academic labs being funding limited, the "organizational capabilities of academic labs" seems irrelevant to me. In our field, no one is getting grants to manage code of any kind .py or .ipynb and I suspect its the same at most university labs. It's effort wasted that ultimately does take time away from the actual research that's fundable and publishable. As someone who has been responsible for wrangling people's notebooks in the past, it's enough of a problem that I would encourage to remove all .ipynb.

> That doesn't have anything to do with notebooks. It's as silly as saying that a Python package is a poor idea because you say somebody repeat code across multiple places.

Human factors make jupyter notebooks lead to the problems I have listed. The issues are most apparent with large groups and over long periods of time. Python and other programming languages already solved most of these problems with git. There isn't a tool that is as elegant and scales from individuals to massive organizations.

> There are roughly two modes for notebooks: exploration with a REPL, and well-documented reports. The best scientific reports I have ever seen are notebooks (or R Markdown output) that are the full report text plus code plus figures.

The REPL functionality is handled by .py cell execution, as I’ve mentioned in other comments. It baffles me how the minimal effort saved by not using separate tools -- one for code, one for documentation -- justifies the issues it introduces.