Skeleton repair

[nicholasturner1]

This PR implements a couple of tools that can be useful for skeleton analysis:

• Masking functionality to keep a set of vertices fixed within skeletonize.smooth_graph. [c8d011d]
• A wrapper around skeletonize.smooth_graph that can fix the root, branch_points, and/or end_points with a boolean switch (skeleton_repair.smooth_skeleton). [078c685]
• A function to remove duplicate skeleton vertices (skeleton_repair.remove_duplicates). These duplicates may cause subtle bugs with computing distances or connected components on the skeleton graph. [078c685]

Other changes:

• Refactors graph edge weight computation into its own function for general use (e.g. within skeleton_repair.remove_duplicates) [bb32b2a]
• Updates some documentation for skeletonize.smooth_graph [c8d011d]

The Travis tests currently fail, but this seems like an upstream problem. The failure point is the same as commits on the master branch, and the module tested seems unrelated to the functionality changed here.

[nicholasturner1]

Cleaning this from my PR window.