Fixed dtype bug in cubic generate (2 ints were being divided, truncating to 0)


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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


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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.


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Updated documentation:
- changed a few autodoc calls to match new class names


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Updated ExceptionError checking and messages:
- this ensures that all necessary information is supplied


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Added documentation and logger to the __VTK__ file


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Forced 2D templates to create a Z-coordinate of 0


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Push of __Plots__.py file which was missed during updates to the Visualization module


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Make sure we are working on the latest develop.


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More updates to the Visualization module
- Each class now inherits the GenericVisualization
- Add plotting for Pc Curves to Plots()


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Latest changes with Jeff


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Full branch output


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Reactivated Boundary Pore generation
- does not add coords yet


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Merge branch 'feature/gui' into develop


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Merge branch 'feature/PhysicsClassToModule' into develop
- This changes all physics classes to collections of methods in a file


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Merge branch 'develop' into feature/DG_StitchV2

# By jgostick (70) and jhinebau (2)
# Via jgostick (11) and jhinebau (1)
* develop: (72 commits)
  Add autoclass directives to Visualization/__init__.py.  This will enable Visualization module methods to appear in function reference.
  - Added loggers to the Physics Modules - Renamed Thermo to ThermoPhysical, and Multiphase to MultiPhase
  Updated Visualization, new usage: OpenPNM.Visualization.VTK().write(pn) - I couldn't find James' old vtk visualization/output code in the current repository, so I cut&pasted from an old version. - This VTK method only has the ability to write at the moment, but I imagine one day we could have this module call up Paraview automatically instead of writing, but that is a 'todo'
  Standardized the Visualization module with __GenericVisualization__ file containing the GenericVisualization class.
  On going documentation updates: added an example folder, included a cubic.rst example, and updated the naviation links in the html.
  Another big batch of documentation updates: cleaned up a bunch more of the autodoc directives, corrected naming and references in docstrings, and added some documentation to the geometry file.
  Made my run_script a bit more general to work with all Geometries
  Updated Template Geometry a bit, mostly to fix errors in the merge, updated documentation, cleaned up a few pieces of code
  Removed Sandbox_doc
  Updates to documentation
  Sifting through files to cleanup documentation, like fixed missed module name changes, adding automodule methods, enhancing docstrings, etc.
  Changed the definition of the _generate_setup() method to declare some default values, as this used to happen in __init__ before.
  Clean-up after a messy mergy of 'feature/Custom' back onto 'develop'.
  Changes to Template geometry: changed network shape referneces from image to template
  Minor changes to new Geometry generate scheme
  Made several changes to the way the Geometry class performs the 'generation'.  This will make it more consistent with the other functions this class will now do to the geometry in general.  generate() is now treated just like another geometric manipulation such as translate() or stitch(). - The network setup parameters (params) are now sent as a set of kwargs to the .generate() function rather than to the geometry class. - The geometry class still receives kwargs, but these will be limited to general things like loglevel - The network-size-type calculations that occurred in the geometry class's __init__ are now moved (since the network params are not sent to the geometry class directly anymore)...see next item. - A new step has been added to the generate() method called _generate_setup() which now does all the network-size-type calculations (instead of the __init__)...see above - All methods related to the generation steps have been made 'private' by prepending an underscore to their name.  This means only methods that actually manipulate geometry of existing networks are 'public' (no underscores).
  Trying out a different way send parameters to the generator
  Renamed 'custom' network to 'template' to avoid confusion with user's custom-made networks
  Documentation in progress
  Added a SaveNetwork class to __io__.
  ...

Conflicts:
	OpenPNM/Generators/__GenericGenerator__.py
	OpenPNM/Geometry/__Cubic__.py
	OpenPNM/__init__.pyc

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Fixed some data type issues with Cubic. Note: the '==' operator does not work with floating point values, as depending on the order of operations that generated the value, there can be tiny differences with values like '0.2'. Notice the change on lines 208-209.

OCD change on IP script.

Example in VTK doc


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Added default values to stats_pores and stats_throats, so that test networks can be generated on the fly


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Uncommented the Add 'coords' to boundaries code

Line 149 had to stay commented, as 'coords' was already appended with zeros.

It looks like it's working alright


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Unbroke IP


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