Single line commit. Sorry!
Merge branch 'develop' into feature/gui
Fix to issue 36 (compliments of Harold).
Documentation changes
Removed issue36.py script.  Added a general template called issue0000.py that should be used to create new tests.
Deleting issue37.py since Issue 37 is resolved
Removing script files for the customGenerator and PhysicsModule branches since they're merged and done.
Changed all Physics classes to modules, with no inits and no inheritance.  This is better for the GUI apparently, but also makes more sense to the program.  The concept of generic physics didn't really make sense.
- Note: Physics was like this previously, but I changed them all to classes and created the GenericPhysics class just to be consistent with the rest of the code.
Converted the Geometry manipulation methods (translate, scale) to staticmethods.  This means they no longer require a self in the definition
Changed name of pore and throat size distribution keys in the params dictionary to work better for Harold's GUI.
Updated physics.rst to use automodule rather than autoclass to pull docstrings from physics modules.
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
Added documentation and logger to the __VTK__ file
Forced 2D templates to create a Z-coordinate of 0
Push of __Plots__.py file which was missed during updates to the Visualization module
Make sure we are working on the latest develop.