Currently finishing up my own PhD thesis. My approach to the same problem is quite different. I write my thesis in Org mode. Exporting to HTML is pretty painless. Been doing the same for years for my notes. PDF export via LaTeX & HTML export. LaTeX and PDFs fail pretty hard when including source code (some literate programming in Org). That was my initial motivation behind also producing HTML.
The final thesis that I will hand in is of course a regular PDF (well, a print based on that). But the HTML version can contain lots more stuff that doesn't fit (and belong) into the actual paper thesis, e.g. code snippets to generate plots etc. (optional export of Org subsections). By publishing the git repository of the thesis, linking all code and data + a bit of work -> full reproducible thesis.
Heh, I also write papers in org and am currently writing my dissertation in org.
Source code is always a pain to export for PDF, especially when switching from 1 to 2 column layout depending on the publication.
My blog is written in org too, but I post-process to make it fit in with the rest of my static site. At some point maybe I'll get enough free time to swap out my makefile setup for org-publish, but if it ain't broke...
To anyone who'll listen I advocate for org-mode as a better alternative to Jupyter notebooks, Markdown, and LaTeX. It's in some ways the antithesis to "do one thing well". If you try to do N things well while adhering to the unix philosophy you end up learning N different tools. But org-mode is one tool that does N things well, and some of the things you learn doing thing N transfer to thing N+1, so you get economies of scale.
How do you plot graphs with org? I've been trying to use it for that purpose but I can't wrap my head around how to do it without some tikz incantation I don't really understand. I've seen gnuplot mentioned here and there but the setup seems pretty involved.
I'm looking for a way to plot simple numeric data signals in time series, which are pretty trivial in jupyter notebooks.
If I had more time and wanted something more convenient and magical, I would probably write a elisp function that takes X Y (Z) columns and generates a plot from those using a simple Nim program in the back that receives the data, generates the plot and returns it somehow. Haven't given this much thought though.