Adapt Pasta to the current version of DendroPy

[simeonborko]

Pasta is compatible with Dendropy <= 4.5.2. I observed these incompatibilities:

• _convert_node_to_root_polytomy became a method of the Node class. In the newest release it's still a protected method, in the master branch is should be public: Provide public interface for _convert_node_to_root_polytomy jeetsukumaran/DendroPy#169
• Dataset.read now requires keyword argument instead of positional.

This is what I just observed, there may be more work. But wait for the next release of DendroPy, because the last release v4.6.1 is from June 9, 2023, but the master branch has new changes (for example fixes missing @classmethod annotation).

[smirarab]

1fa5fa82db6ee97e8a681a8d32e5c3b5c1a1116 should fix the first issue for now (version 1.9.1) and it worked just fine for me. Will see what other challenges arise. Keeping this open to document new changes needed.