As someone who does Python software development on Debian constantly
for their $dayjob, my best advice is to just install things from
PyPI into and run them from venvs/virtualenvs. The default "--user"
install mode pip offers is fragile and leaves you with potential
conflicts anyway if you need different versions of dependencies for
different things.
To your original question, if you really want to use some
Debian-packaged libraries mixed with things installed from source or
from PyPI, make your venv with the --system-site-packages option.
--
Jeremy Stanley