Open a command window (start->run...-> cmd)
In the command window, go to the directory with setup, and run it with python:
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> cd \path\to\ply-x.y
> python setup.py install
You can do the same with nml, but it is not needed, as you need the terminal window also for running nmlc, and at that time, the directories are set up such that it also works without installing.
To run nml:
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> cd \path\to\nml-x.y
> python nmlc --help
Gives help, I think you need 'nmlc --grf myfile.grf myfile.nml' to convert 'myfile.nml' to .grf. You can also output .nfo files.
Edit: fixed some white spaces, and the \path\to\nml-x.y