Msprime: Make API more Pythonic by removing lots of 'get_'s

[jeromekelleher]

Several aspects of the API are a little non-Pythonic. Mainly, this involves using methods like obj.get_x() rather than obj.x.

For example, we should change:

• SparseTree.get_root() -> SparseTree.root
• SparseTree.get_index() -> SparseTree.index
• SparseTree.get_interval() -> SparseTree.interval
• TreeSequence.get_sample_size() -> TreeSequence.sample_size
• TreeSequence.get_num_mutations() -> TreeSequence.num_mutations

Also, we should change things like

• SparseTree.get_branch_length(u) -> SparseTree.branch_length(u)
• SparseTree.get_mrca(u, v) -> SparseTree.mrca(u, v)

Existing methods should all be marked as deprecated, removed from the documentation, and (eventually) removed entirely.

[ashander]

I could help out as I familiarize myself with the API. I opened a PR with a list of candidate functions

[ashander]

A question: should the above be eg SparseTree.root()? (you don't intend to change them from instance methods, right?)

[jeromekelleher]

This is great @ashander, thanks! I think we do want to make them properties; I'll go into more detail on how your PR.

[shajoezhu]

sometimes I think github should have a 'like' buttom for things like this

[jeromekelleher]

Finally finished this up in #384.