Dear Andreas, I send a PR for the autopkgtest boilerplate for hyphy. You can review it here: https://salsa.debian.org/med-team/hyphy/merge_requests/1
It's a WIP (sorry for being late but it was my last essay for the semester, phew!). If you are happy to include my contribution I'll be allowed to send an application to be considered for Outreachy and I am going to implement the tests (as I comment on my PR that would be for a started the existing tests on run_tests.sh on the root folder)! Actually, if you give me some extra help, I can also finish it today; let me know if you have the time for that though. I would like to find out what's the best way to test the autopkgtests myself? Do you usually do this via chroot? Also let's say that I want to include the tests on the /usr/share/doc directory, do I need to copy the whole dir with the Examples there as well? Best ioannis