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Pluto solves¹ many of these problems, but it’s Julia only. Most importantly:

- cells are linked through a dependency graph, so the output you see is independent of the order in which the cells appear;

- each notebook is backed by a plain Julia module, so you can use version control, edit in a real editor instead of only in the browser, and import other notebooks;

- You can create interaction² using HTML inputs, Julia wrappers over those, or go crazy with your own custom JavaScript controls;

- It’s easy to embed LaTeX into the MarkDown, and you can use HTML, so any hyperlinking works.

    1 ‘An introduction to pluto’. LWN. Available from: https://lwn.net/Articles/835930/

    2 ‘PlutoUI demonstration’. Available from: https://pluton.lee-phillips.org/sliders/uiDemo.html



But unfortunately it doesn't have option to turn off reactivity which makes it not appropriate for intensive computation.

I wish it had a sequential mode.




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