I've been using F-Droid to get my apps. I'm not happy with any of the PDF readers available.  I'm looking for the following:
* Read PDF
* Read from a home library, such as Calibre
* Make annotations, such as notes and highlighting.  Making diagrams/drawings would also be nice--like a real book.

I've used MuPDF and Document Viewer (from sufficientlysecure.org) already.  I know there are solutions for ePub, but I'm specifically asking about PDF.

The permissions are ridiculous, but for example, Moon+ Reader seems to have the options I desire:
https://play.google.com/store/apps/details?id=com.flyersoft.moonreader
and from the photos, it has a nice UI.  Alas, it is far and away from FOSS.