Not entirely sure what you mean by "multi-module", but I can do all sorts of stuff with PyCharm.

Multiple "sources-roots", multiple-projects in the same workspace. Also, you can install pip install external libs in source development mode and debug them, etc. Short of "project imports" that I miss from Eclipse, I'm not sure what you may be referring to.

Like multi-language projects where you're working with both Java and Python code in the same source tree (actually you can include arbitrary folders from anywhere), or using multiple Python versions (and virtualenvs) in for different modules/packages in the same project.