Modify `tools` scripts for easier testing

[StokesMIDE]

Right now, test_tools.py uses subprocess, which takes things out of the test environment. It might make sense to modify each tool something like this:

import sys
...

def main(argv):
    ...
    args = argparser.parse_args(argv)
    ...

if __name__ == "__main__":
    main(sys.argv)

This way, tests could be done by calling main(test_args), and pytest could handle any errors/failures more directly.