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The documentation for PyRun suggests that adding modules is just
The easiest way to have modules or whole packages added to PyRun is to
modify PyRun/Runtime/pyrun_extras.py and import them in that file.
However it's not clear where those Python modules need to be located? I edited makepyrun to print the LIBDIR directory and it looks like it's searching something like build/3.9-ucs4/python-installation/lib/python3.9/, but that directory isn't there pre-build and is cleared out during clean anyway?
I made it work by making clean, then interpreter, then copying the modules into the above directory before making runtime, but that took a lot of effort to figure out if that's the intended method.