ENH: Route all alpha and beta diversity calculations through q2-diversity-lib

[ChrisKeefe]

Improvement Description The following Actions should be made into Pipelines, dependent on Actions from q2-diversity-lib:

• alpha
• alpha phylogenetic
• beta
• beta phylogenetic

q2-diversity-lib, in turn, will dispatch these calls to the best available implementation of the requested method. See https://github.com/qiime2/q2-diversity-lib/issues/22

Current Behavior core-metrics and core-metrics-phylogenetic call methods from q2-diversity-lib for alpha and beta diversity calculations. The alpha and beta Actions, however, are called directly from q2-diversity.

This proposal makes q2-diversity-lib uniquely responsible for determining what implementation of a given method should be used. This allows q2-diversity to stop caring about what methods have been implemented/constrained in q2-diversity-lib at any given moment, and which methods will simply be passed through to an appropriate dependency.

Proposed Behavior

• The four actions above are re-implemented as Pipelines
• https://github.com/qiime2/q2-diversity-lib/issues/22 has been closed, and dispatch functions are properly meeting the needs of this issue
• Any other impacted methods (e.g. alpha-rarefaction are cleaned up as needed)

Comments

1. This will likely require minor changes to other Actions that use these functions - e.g. alpha_phylogenetic

[thermokarst]

Please see https://github.com/qiime2/q2-diversity/pull/281#issuecomment-665974036 for some modifications to this plan.