When this runs, it seems to not let my code progress and it just ends up finishing when it is a continuous running application.

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I tried putting this in a file other than my main first, it failed with an error in the "on-the-fly" function of pypreprocessor. To test I put it in my main file just to put in a define and see if it would work. It does work, I was able to setup a small test similar to the examples you have as seen here:

pypreprocessor.parse()
#define yes
#ifdef yes
print('yes!')
#else
print('no!')
#endifall

That worked, but as it for to my main function which calls another class to start to run the main part of my application, it just exits. I am not sure exactly what is going on. Does this need to be present in all files of my project?