Implement Sum RF Distances

[willdumm]

This is looking great, Claris! The test still isn't passing, but I rewrote it a bit to make it more clear what's supposed to happen, and I fixed a couple of minor things.

I'm not quite sure what's going on here, but it's possible that either some math is incorrect (for example in the issue #39 ), or there's something wrong with count_nodes, etc.

A couple of comments:

• We don't need the rooted keyword argument for the sum RF distance stuff, because we're going to just compute rooted RF distance. But the existing RF distance code is unrooted by default, so we have to specify that when computing expected values in the tests.
• We should probably rename HistoryDag.sum_rf_distance to HistoryDag.optimal_sum_rf_distance because that's what it's doing: finding the optimal sum RF distance for any tree in self to trees in reference_dag. We should therefore also include the argument optimal_func to specify whether we want min or max sum RF distance, similar to in HistoryDag.optimal_rf_distance.

[willdumm]

^^ I figured out where the math was wrong, and pushed the changes needed to make the test run.

Here's a list of to-do's, just so we can keep track (I know we've talked about some of these already):

• use IntState to shift by a constant automatically. Notice that I had to change the constant computation slightly in sum_rf_distance.
• rename sum_rf_distance to optimal_sum_rf_distance for consistency with optimal_rf_distance, and add the optimal_func keyword argument (just like in optimal_rf_distance to allow the user to specify whether optimal means max or min, or something else.
• add a trim_optimal_sum_rf_distance method, analogous to trim_optimal_rf_distance, and make sure the docstring mentions that trimming to minimum sum rf distance is finding 'median' topologies, and trimming to maximum sum rf distance is finding topological outliers.
• Add informative docstrings to all new methods, emphasizing that they compute rooted RF distance

[willdumm]

This looks great, Claris! Feel free to merge it whenever you're ready.

[willdumm]

^ I just rebased, to make things easier!