TreeNode.prune does not collapse single descendants from root properly

[wasade]

I noticed this while working on a collapse method (i.e., prune) for the tree arrays. The expectation is that ((a,b)c)extra; should become (a,b)c as extra only contains a single child. Interestingly, the collapse happens partially if there are multiple extras where (((a,b)c)extra1)extra2; becomes ((a,b)c)extra2;.

09:25:16 (daniel@sandbar):repicking> t = TreeNode.read(["((a,b)c)extra;"])

09:26:00 (daniel@sandbar):repicking> print(t.ascii_art())
                    /-a
-extra--- /c-------|
                    \-b

09:26:03 (daniel@sandbar):repicking> t.prune()

09:26:05 (daniel@sandbar):repicking> print(t.ascii_art())
                    /-a
-extra--- /c-------|
                    \-b

[jairideout]

@wasade, any bandwidth to work on this for the release? Ideally this could be fixed proper, but raising a NotImplementedError is also a big improvement over a silent bug.

[wasade]

Sure. Just for reference, I believe the only change necessary is to make include_self=True...

[jairideout]

Awesome, thanks @wasade!