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As a general observation, using the overlays to install Python-based packages is preferred as they will tend to resolve dependencies correctly.
If you want to install your own modules, do so using venv or virtualenv to keep them separate from the system python modules. Not only will this avoid your modules corrupting the system install, it also means that system updates won't corrupt anything you install.
Alternatively, use pipx.
Applications using matplotlib to generate graphs will only show the graphical output if tkinter is installed. To do this:
zap install-overlay tcl-tk zap install tkinter
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