how to install python packages, again

[Anil F Duggirala <anilduggirala@fastmail.fm>]

hello,
Im having an issue while installing a piece of software with pip3:
pip3 install --user -r contrib/requirements/requirements-binaries.txt

Command "python setup.py egg_info" failed with error code 1 in
/tmp/pip-install-48wlqr39/PyQt5/

I had previously installed: apt install python3-pyqt5. Now, pyqt5 is
listed in the requirements-binaries.txt list, however, it requires a
newer version than the one installed by apt. 

Online I find many people getting a similar error and suggesting using
pip3 upgrade to upgrade the "pip" and the "setuptools" modules. And
this brings me to my question. What happens if I use pip3 to upgrade a
module that was installed via apt?

Now pip3 list is listing both the pip and setuptools modules (which
were installed using apt). It even tells me about a newer version
available (via pip). However pip3 list is not listing the pyqt5 module
as installed, why is it not showing this module, which is installed?
Does this have to do with the fact that my pip or setuptools modules
are outdated? (both have much newer versions available via pip)

thank you,

Anil