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Notebooks may be suitable for scratching things, but not much else. The problems noted by the OP are very serious, specially in the scientific world, where many do not have proper software engineering skills. The real issue is that newcomers do not know better, and so they don't realize the damage they're inflicting upon themselves and others before it's too late (irreproducible code, hidden states, dep. management, etc). Even the fast.ai library, which is a wonder, has broken notebooks. For those who try to follow the course at home, trying to run the notebooks is frustrating, as things are out of order and so errors pop up all the time. Jeremy is a wonderful teacher, but compare following a Fast.ai course video, which uses notebooks, to following a python video from, e.g., Raymond Hettinger [2], which uses sphinx and a shell. While the documentation style and ugly shell don't look nearly as cool, they are so much clearer and better structured. Notebooks become popular because they fill one gap that was left uncovered. As the scientific community moves away from Matlab into Python and R, reading code - pushed, amongst others, by the popularity of Github - becomes a day-to-day activity. Matlab scripts were easily explorable because users would load them, set breakpoints here and there, and look at results interactively - exactly what notebooks aim to provide. The difference is that what used to be breakpoints now become cells, comments now turn into Markdown and figures are i