port q2-phylogeny actions to q2-iqtree2

[gregcaporaso]

I'm thinking a good start for this plugin would be to move iqtree action(s) from q2-phylogeny to q2-iqtree2, and deprecate those in q2-phylogeny. We can then target an initial release of this plugin with the 2020.11 release, and remove the deprecated iqtree functionality from q2-phylogeny in the 2021.2 release.

Does that strategy make sense?

[mikerobeson]

That makes sense to me. :-)

[mikerobeson]

The IQ-TREE 2 actions have been ported over to q2-iqtree2 along with associated tests, including the align-to-tree-mafft-iqtree pipeline.

Questions / Comments:
Can anyone help me set this up to be conda installable? (should we worry about this now?)
I'm not sure how to set up lint-build-test / code coverage, any pointers?

[mikerobeson]

Deprecation notice was applied to iqtree related actions in this PR.

[gregcaporaso]

Sounds good @mikerobeson! I'm meeting with the engineers on my team this week - we'll follow up with you about conda and the tests then (it might make sense to do this using new functionality that we're testing for the QIIME 2 Library).