Fixed dtype bug in cubic generate (2 ints were being divided, truncating to 0)
Changes to Visualization Class:
- removed __2D__.py
- created __Plots__.py, contains histogram overview of network formerly in __2D__
- cleaned up the Generic inheritance structure
- add logger to all classes
Removed my personal run_script, and replaced it with a general run_script.  I will make changes to a local untracked version and update the general one periodically.
Updated documentation:
- changed a few autodoc calls to match new class names
Updated ExceptionError checking and messages:
- this ensures that all necessary information is supplied