You probably better invest the time in the preparation of a couple of beautiful Jupyter notebooks. That's where people expect interactivity and code to happen, not in PDFs. In my scientific community, virtually nobody uses Adobe Reader (people on Mac use Preview.App, people on Linux use poppler/xpdf/evince, browsers have their own internal readers).

Edit/Appendum: Crafting an interactive website (i.e. without the dependency on jupyter) might be more future proof.

Idyll (https://idyll-lang.org/) is a very promising tool in this field.

Thanks for the link! I think this is tightly connected to Donald Knuth's Literate programming paradigm, i.e. there are also platforms which generate beautiful reports out of the embedded comments in your traditional source codes. However, you won't get the interactivity for free.

I personally prefer Jupyter because it seperates the programming language (Python, R, C++, etc.) from the representation (for instance Web) and still allows interactivity for a certain degree (given a backend running the source code).

This is an interesting project, thank you!

He didn't say anything about interactivity though. But even a lower bar than this : just animation, is not currently cleared by the available document formats.

(And a website doesn't fit the requirements as it's not contained in a single file, so its archival is a lot more complicated.)

Unfortunately my school expects a PDF thesis. But you make a good point about popular alternate readers not supporting animations - maybe this is a wasted effort. Thank you! Probably better to link to notebooks or videos of the animations on vimeo/youtube.

Yes, PDF is the standard. Some people get it managed to generate HTML out of their PDFLatex code. This could be a nice starting point for an enriched reading experience in the web browser. However, with standard print-first latex, I never could generate HTML for any nontrivial documents (especially large documents with many hundred pages).

Putting your animations in traditional video formats (mp4, ogg) or on vimeo/youtube is probably the best way to make them accessible for most people. Many scientific labs have their own youtube channels.

Many 3D authoring program like Blender, Meshmixer can output U3D or RPC that you can use to embed into 3D PDF files. There are just many tools that can read the format. But beware that only Adobe Reader can show the 3D object

Thank you! Yes, I wasn't thinking about the read-time support.

Note that PDF 3D models have a static image (a bitmap) which readers that don't support 3D (most of them) will show instead. Actually Adobe Reader shows the static image too, until you click on it to activate the 3D rendered version.

I had a similar issue recently (for a much smaller project though). The sad reality is that it looks like that we currently don't have an actual, working, properly supported standard for electronic documents, which would include something as (relatively) basic as animation support : https://news.ycombinator.com/item?id=25612066