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I believe emacs org can be used for this kind of notebook developement, however it looked like a configuration nightmare so I still haven't dived into it.

It's actually pretty easy to set up for general use. I do know and use emacs lisp, but I've not really used any at all for org-mode.

It does support "sessions" which allow persistence across the code throughout the document (you could even have multiple sessions), but the wat it's done for Python is quite hacky. It uses an interactive Python shell so you have to write code as if you're using the shell (double returns etc.) There is a better way using ob-ipython, but after spending a long time getting it to work at all I found it not good enough. Using Jupyter kernels is the way to go, I think, but it would be a lot of work to get it working well with org-mode.

You should give it a go, it's not hard to configure, and it allows you to trivially use several languages in the same file, which is really practical in many cases. It also exports nicely to HTML and PDF (via LaTeX)

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