UPGMA Trees are None-rooted about dendropy

[jeetsukumaran]

No problem.

Thanks for taking the time to report this and other issues and thereby improve the library!

But I'm re-opening this to keep it open till I actually get around to updating the code to set the rooting.

[jeetsukumaran]

No, this is a bug. I overlooked setting the rooting state. Will do so. Thanks for pointing it out!

[yasuiniko]

Ok, glad to help. Two more things:

1. Is this correct practice for rooting/unrooting trees?

root_status = True # False
my_tree.is_rooted = root_status
my_tree.update_bipartitions()

2. The "nj_tree" method also appears to create None-rooted trees.

[jeetsukumaran]

Yep! There's more to it under the hood (is_rooted is actually a managed property as is is_unrooted; both is_rooted=True and is_unrooted=False, and vice versa, update the underlying hidden attribute correctly), but for client code that's all there is to it!

[yasuiniko]

Perfect, I'll mark this as closed then.

Thanks for developing this extremely useful library!

[jeetsukumaran]

Fixed in 285d33b .