relocate the argument parser to end of file

[BenjaminRuston]

Description

relocate the argument parsing to the end of the file

Checklist

• [ ] I have performed a self-review of my own code

[BenjaminRuston]

@smaticka this just relocated the section of code dealing with the input arguments and places that at the bottom of the file

if you think it's alright, you can approve AND you can merge into your branch