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


Former-commit-id: a44b14e9d5dbae31afbfcdfd1aee73c57e78270d
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


Former-commit-id: 3aeecfd50445387bfa6a50ecc3f11b14393f14ca
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.


Former-commit-id: e773733546a25c1ca2c86eb6e8e40e9a6416a96a
Updated documentation:
- changed a few autodoc calls to match new class names


Former-commit-id: 756985f0f91bc4ffd4b406b6fae33c615e08bb8e
Updated ExceptionError checking and messages:
- this ensures that all necessary information is supplied


Former-commit-id: 4dbc3627719691fec8dcf9db08d02117e1cdac48
Added documentation and logger to the __VTK__ file


Former-commit-id: 417a84ebe414ce7aa13456da0a064ac013633792
Forced 2D templates to create a Z-coordinate of 0


Former-commit-id: 6cf57303d551ed45d36a64efc670c9c5181240a3
Push of __Plots__.py file which was missed during updates to the Visualization module


Former-commit-id: 11447c9683b8941e172027d85a0183f446b311ba
Make sure we are working on the latest develop.


Former-commit-id: 5a72bb0d63dace1a47785244a30267d3f06ce4c4
More updates to the Visualization module
- Each class now inherits the GenericVisualization
- Add plotting for Pc Curves to Plots()


Former-commit-id: 16c6e4ae8184e2ec3c57f06d43d585b1ee60a78b
Latest changes with Jeff


Former-commit-id: f6d1de328301426ad09708307685072fa25efe2d
Full branch output


Former-commit-id: 0a76232c873e4ef27d427ba77a60f91b4eb1f28c
Reactivated Boundary Pore generation
- does not add coords yet


Former-commit-id: de6bc69b76da485f695878c9fd474741e3a1bc8e
Merge branch 'feature/gui' into develop


Former-commit-id: 507d67045da3a375a3a954449134a86afabb15fc
Merge branch 'feature/PhysicsClassToModule' into develop
- This changes all physics classes to collections of methods in a file


Former-commit-id: 34b6fc4d012866820ea7148bce8bb31dc3c83450
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

Former-commit-id: d12add80bfbcfff69905971d784c088da47e9371
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


Former-commit-id: 4cab979c9822b0de0d0f5e5606ebd0113311980b
Added default values to stats_pores and stats_throats, so that test networks can be generated on the fly


Former-commit-id: 2bf36846b262b663a14b6211fd33cbd1cc5e88db
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


Former-commit-id: 9fb08863e68fbf0ab87f0c82ec3908290576ea82
Unbroke IP


Former-commit-id: 40c407c5efe4913552e934e29f852da1bc1d7d5f