Bng sim for data model - Githubissues

DONE: Code restructuring, various bugfixes, some testing.

TODO

Potentially improve command line argumentation via argparse
Further testing, I tested various compartmental models but I should do so with workshop models
Cellblender imports haven't been tested yet. The data model should be correct but I have no validation for it as of yet. I expect some slight differences due to XML parsing so I can't do a simple diff for validation
Even more code restructuring. This script can benefit from a fully structured data model class. Currently I'm using a data model class but it's more of a code centralization trick than a properly thought out class.
Also another good idea is to bake all of the helper functions into the data model class and allow no external modifications to the internal data model dictionary, move the class to another file and have a separate parsing script for the command line tool that uses the class
Consistent indentation, currently there are some 2 space and 4 space indentations. Let me know if you specifically want 2 spaces, I tend to use 4 (PEP8 recommendation).

mcellteam / cellblender