I really wish there was a practical alternative to Calibre for general ebook organization purposes. It's extra-painful that Books.app on Mac could almost fit that role, except that it doesn't let you edit enough metadata for your own imported files to properly manage series/publisher stuff.
Sorry for the snarkiness in my previous comment, if you get the chance perhaps you can look into helping with this issue. Contributing to the distributions I use has taught me a lot about the tools I use every day.
$ calibre
Fatal Python error: PyQt5.QtCore: Unable to embed qt.conf
[1] 13321 abort (core dumped) calibre
At that moment, I didn't have time to workaround on it :(