Just thinking out loud about how python modules and packaging works. 

We have a troi.py and troi module. This is potentially confusing if we wanted to do import troi from within the source folder. I recommend that we either rename the py file, or add it as _init_.py of the module.

The setup.py file uses find_packages(), which means that it finds both the troi package as well as the package called patches, and installs it into the python packages directory. We should try and not pollute this namespace too much.

I'm not sure about the setup instructions to pip install -e the working directory - Is there a specific reason why this is required? 

If we want troi to be installable through pip, I think it makes sense to merge both the patches directory and the run script into the troi package.