Python has a concept of a "virtual environment" for pulling together all the requirements needed for running a nontrivial program. This is roughly similar to a java jar file being used to hold all the libraries needed for a nontrivial Java program. Explaining how to set up a Python virtual environment is beyond what can be explained here so please search for "Python virtual environment", "virtualenv", and "Python activate" for that information.
Once the virtual environment is set up and tested, Java will probably need to use a shell script to invoke it. The script will probably have components that will change directories to the base of the Python project, run the virtual environment's activate command, then run your program with the "python <program.py>" command. The shell script will also make it easier to pass parameters.
BTW, Python 2 was EOL'ed as of the end of last year. For reasons known only to Apple, Catalina still uses Python 2. Thus /usr/bin/python is still version 2.7. Using Homebrew to install a modern version of python is definitely a good way to get it. It can install a modern version of (QT5) as well as the Python bindings (pyqt), although since I have not used QT, there may be more needed.
Since this project is targeted to go on a Rasberry PI, it might be a good idea to use Homebrew to install a copy of micropython to use for this project. That may reveal any code that may have trouble running in the Pi environment.
Apparently Java can be installed on a PI. However, Python is native on the Pi. Perhaps it would be worthwhile to take another look at recasting all of the Java code to Python. It may be much easier than it first looks even preparing the GUI.
There are Python IDE's that will make all this a bit easier, such as Pycharm
. Both have "community" or "personal" editions that are free.
This may have become a bigger project than you suspected at the beginning, but I hope you will continue this to completion.