I’m afraid by using raw .py files you’re going against what PyInstaller 
does. It compiles you .pys to .pycs then bundles those into a PYZ archive 
so that there is a) no folder containing your scripts and b) even if there 
was, the scripts would be pre-compiled. 

That being said, it should be possible (although not really recommended) to 
do this. You can tell PyInstaller to add your encrypted Python scripts as 
data files by adding them to the datas=[] in the spec file (please do not 
debug in onefile mode). Exactly what you put in there depends on how you’re 
importing your encrypted code - whether files are loaded using Python’s 
import mechanisms or read from file, and where these scripts are located 
relative to main.py.

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