run_script for new feature/Stitch branch
Added DG Script
Revert "Added DG Script"

This reverts commit aac580fdf6704fd4c2833c6d98f92b4d115ced42.
DGScript Real Version.
Adding a function that generates a set of boundaries that are 1 layer thin
Add code to segment each layer into the boundary layers.
Merge branch 'develop' of https://github.com/PMEAL/OpenPNM into feature/DG_StitchV2

# By jhinebau (15) and others
# Via jhinebau (3) and jgostick (2)
* 'develop' of https://github.com/PMEAL/OpenPNM: (24 commits)
  Changed James' run script renamed algorithms
  Removal of reference to IMG in the main init file
  Added a physics file to the documentation
  Remoing IMG folder which seemed to be pet project file (of Andreas?).  I have saved the script that was in there and will recommit as a feature once I know what it did.
  getting rid of accidentally commited merge files
  All working now
  Import almost working, debugging now.
  working on adding the import generator to the gui. need to merge first though
  tested with IP and VTP generator. seems to work. Merging now
  some bug fixes
  Code written, just debugging now.
  Tiny update to call of OrdinaryPercolation
  Committing __Import__ file early on, so that I don't make the same stupid mistake again of not selecting it
  added file poreproperty.py which gives the user an opportunity to add inlets and outlets (currenly only used by IP) to the network.
  Setup of algorithms.rst file for other's to added their documentation
  Added IP algorithm to the GUI.
  I think I fixed that issue Harold had.
  I have attempted to apply the folder/file name changes from develop onto the GUI branch. I have messed something up.  The gui runs but it ony allows for a generic network, so something is not import correctly.
  removing more pyc files
  deleting pyc files
  ...
Added generate_boundary_pores definition in cubic. Made necessary modifications otherwise. Added GUI files as well
Added numbering to append to the dictionary for the outer pores.
Added a feature which reduces the dimensions on each side of the input by 2 units. This is then compensated by adding the boundary layer, which will be stitched to the outer edge of the surface after being translated. Stitching and translating have not been developed yet at this point.
Edit Networks to append sizes
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
Modified to new code structure
Adding functionality to stitch code to concatenate dictionary properties - DG
Modifications to include all appends to properties of throat and pores except for connections.
Added connections script to throat properties to recalculate. Not sure if correct.
Modification in translate coordinates script to account for Lc in translation.
Minor Bug fix in coordinate translation
Major changes to script. Could be precursor to new objects and classes to stitch boundaries
Still need to implement subnetwork extraction + proper connections method.