Still need to continue using PDFs instead of epubs

Many electronic books are available as both epub and PDF. I’d much rather use epub on the tablet, where the fantastic Moon+ Reader (https://play.google.com/store/apps/details?id=com.flyersoft.moonreader) is available. You can resize fonts, highlight continuously without worrying about page breaks, links to formulas are awesome, the whole UI is just great and extremely configurable, etc (see my review from November 2018; fixed a typo recently: https://play.google.com/store/apps/details?id=com.flyersoft.moonreader&reviewId=gp%3AAOqpTOGgUr__eyaEXn2y5EjduVMtnggjOWjFgi8yG6J-HQ2FB1LbKw-aLzN09p0kVBexaL_lkhsjV9TCcWW3BzA )

But I want:

• To have annotations accessible in the tablet and computers. (This is a piece of cake with any decent PDF editor, as the annotations and highlights are placed in the PDF itself).
• Be able to easily extract all annotations from a document to a file. Much better if I can use batch processing for a whole bunch of documents. This is also a piece of cake with Zotero (https://www.zotero.org/) and Zotfile (http://zotfile.com/).
• And reading and annotation must be doable offline.

So from time to time I search around for options (the contrast between usine Moon+ Reader and any PDF reader is just painful). A few years ago there was a proposal to include annotations in the epub standard (http://www.idpf.org/epub/oa/); but that is not yet a reality.

These are my key notes from my last search (2019-01-28):

• No way to extract annotations via Zotero: https://forums.zotero.org/discussion/70860/epub-annotation-extraction
• There still insn’t (and probably never will) a web or desktop version of Moon+ Reader (neither Linux nor Windows —I’d be willing to fire up a Windoze virtual machine just for this). A desktop/web version would make the “annotations and highlights not in the epub” less of an issue if we can continue using the very same app, as it syncs its annotations and highlights. About a year ago I tried installing several Android emulators to run Moon+ Reader on the laptop, but it was a mess an never worked well.
• Polar (https://getpolarized.io/) does not do epubs (at least not yet).
• hypothes.is (e.g., https://web.hypothes.is/demos/epubjs/) does not work on Android yet for me:
  • it requires being online;
  • it is not clear to me if annotations can be made private;
  • there is no easy way so far to download all annotations, though this is often requested and there is work being done: https://github.com/hypothesis/product-backlog/issues/566,https://github.com/hypothesis/product-backlog/issues/566#issuecomment-435714949
    

There are, of course, many other entries on the internet about how to deal with epub annotations. But for all practical purposes, given what is available, the working summary for me is still that, so far, I need to continue with my PDF-based workflow where I annotate in the PDF itself in the tablet and the computer, and I extract annotations with Zotero + Zotfile.