LyX is great, and if only LyX could a) generate code from math, b) run that code and also any other embedded code, c) produce and embed graphs and other illustrations from the results of running that code, then LyX would be perfect.
If you asking this, you are the wrong audience. All academic journals accept submissions in Microsoft Word, this is a similar tool targeted at the WYSIWYG crowd.
TeXmacs can execute code too. Honestly, if it had 1/10 the community of Emacs, I would be using it for everything from running my window manager to driving my statistical simulations. It's already what Stallman keeps asking Emacs to become.
Basically we need to marry LyX and Jupyter.