pyenv needs to have its shims in place by running the pyenv init. You can run it when your shell starts but I find it kind of slow and for a while it used to be wonky in fish. But once I run the init, pyenv does work.

That's just for managing your python installation and virtualenv though. You still need to manage your packages and for that you have options like requirements.txt, pipenv (not pyenv lol), Poetry, and others.