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.
