minor changes to some geometry methods
Significant changes to query methods, please read:
- find_neighbor_pores/throrats NO LONGER accepts labels.  If the user wants to filter by label they can do it themselves aftwerwards.  I might add a new query method for this...
- num_neighbors not longer accepts flatten. This didn't make sense and had the ability to count things twice
- find_neighbor_pores now has an excl_self flag which removes input pore from output list