python improvements

[keiranmraine]

Initially forked to make it possible to install python under virtualenv.

• Converted scripts to python3 (python2 is at complete end of support Jan 2020).
• Added #! to py scripts so they can be installed
• Created a setup.py script to install python scripts and dependencies
  • Once installed under a virtual env you can add bin to PATH
  • ./setup.py develop - can edit scripts and changes picked up automatically
  • ./setup.py install - reinstall required to pick up changes.
• Added .gitignore to prevent accidental inclusion of env install.

Other improvements to consider:

• Add argparse to the scripts to pass input/output options
• If the C/C++ binaries are "relocatable", setup.py can install the binaries into the same bin path location (provided pre-built)
• Looks to be some items in committed tree that should only exist in users local workspace
  • packages, output
  • once these are cleaned up, add to .gitignore to prevent accidental re-addition

I'm happy to help you work through these items.

[rwtourdot]

I merged your python improvements, thanks for the help!. I do need to update some of the bash, python, and R scripts for v0.42. But if you have some improvements like those mentioned feel free.