Generators no longer return self, so the instantiation of network object, and the actual generation must be done separately.
- I only do this for consistency with the other objects (geom,phys,fluids,algs)
- Readded _geometries tracking list to network
- Renamed _reset_network to a more useful reset_graphs (as in graph theory)
- Removed explicit adj and inc matrix construction from init and now just call reset_graphs
I decided that add_method in phys,geom,fluids was to technical so renamed them to add_property, which might be confusing for true python programmers, but is more clear now linguistically.
- the add_method 'method' is still there, but labeled as deprecated.
Minor adjustments to Geometry naming
- makes sure that geometry label doesn't conflict with an existing label, geometry or not
- before it only check against other geometries
Minor tweaks to find_clusters
Major changes to the geom/fluid/phys regeneration steps
- Geometry must be generated with pores first, then throats, or else many methods fail
- Now, calling the Network's regeneration method takes care of this.
- Geometry still has it's own regenerate method, but these should only be called by experts since order matters
- It's not as important for fluid and physics
Cleaned up main init
House keeping
- moved arguments around to improve convenience of position defaults
- updated doc strings
Add site clustering option to find_clusters.