My solution for this problem is apk's virtual packages. I'll do something like this:

    apk add -t .myproject-deps py3-foobar py3-foobaz

This creates a fake ".myproject-deps" package which depends on py3-foobar and py3-foobaz, then I can just uninstall ".myproject-deps" later and it nukes the rest. `head /etc/apk/world` is generally sufficient to get a list of projects I've forgotten about whenever I feel like some spring cleaning.