Fixed #180

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Cubic default 0.5 shift

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Some more fixes

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Fixed up cubic add_boundaries...did some basic checking seems to work

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Some updates to get the code 'release ready'
- All the 'topology' altering methods now have a check to prevent their us after Geom/Phys/Phase objects have been created
- Removed stitch and join
- Cleaned up the check_data_health to print better warnings, while still returning the True/False flag

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Added a flag for hydraulic and diffusive conductance calculators to do their own pore length calculations.

I need this because I don't have symmetrical pores in my extracted networks. Pore radii often exceed the pore-to-throat distance, grossly increasing the accumulated path length for diffusion.

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Temporarily replaced area calculator. I'm feeding in 1mm x 1mm samples and it was calculating areas of 5e-7 m (0.5 mm2).

Tried to spot check with cubic, but seems to still give bad coordinates.

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Fixed bugs in Cubic.add_boundaries

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Moved domain_size methods to cubic, and made the methods in GenericNetwork raise a NotImplemented area

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Caught bug in new Cubic, it was generating 'bidirectional' throats, so each pore was effectively connected twice
- Also added block to check_network_health to look for this.

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Fixed find_connecting_throat to now accept vector inputs, and return the corresponding throat, or [] for each element in the vector

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Moved amalgamate data to misc

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- renamed Load to IO to be more general
- moved save_model to Utilities / IO

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removed an import from misc

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My kid was sick tonight, so i sat beside him coding.   The result is a new save format that write directly to a numpy zip file, converts the extension to .pnm, and can read the whole shebang back in as well, with the exception of models, and I'm also struggling with sub-phases.

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Save and Load now include the phase and subphase hierarchy....only _models is left to tackle

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A first attempt at getting models to save...it kinda works, but fails for some of the models but not all

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Update the object retrieval methods to accept a list of names, and return a list of objects.  The returned value is now always a list, even if only one name is given.
- I needed this functionality for the Save/Load classes

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Load/Save now work COMPLETELY!  They save the object heirarchy, the models, the data, EVERYTHING. Whew...

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Reintroduced the save and load methods on base...these are meant to save the individual objects for retrieval later, not saving simulations.  This is denoted by the fact that they are left as .npz files, rather than .pnm files.

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