IMP: migrate types/formats/transformers from types-genomics

[Oddant1]

Closes #308 by moving all the types_genomics` stuff over to types

The feature_data from types_genomics was renamed to feature_data_mag to avoid circular imports that came up when trying to integrate the two modules.

Blocking:
bokulich-lab/q2-assembly#71
bokulich-lab/q2-annotate#133
bokulich-lab/RESCRIPt#176

If more repos need changed let me know, these were the three things that were dependent on q2-types-genomics when I removed it from my test env.

[Oddant1]

@lizgehret merging the two feature-data folders proved a bit painful, so I renamed the feature-data from types-genomics to feature-data-mag for now. I'll take a crack at merging per-sample-sequences and maybe another at feature-data tomorrow.

[lizgehret]

Sounds good, thanks @Oddant1!

[Oddant1]

@lizgehret merging the two feature-data folders is not going to be feasible without some other shenanigans.

feature-data-mag imports from genome-data here.

genome-data imports from feature-data here.

Merging feature-data-mag into feature-data creates a circular import. The only feasible way to resolve this seems to be cutting the ortholog related bits of genome-data, and OrthologAnnotationDirFmt which is in feature-data-mag for some reason into their own module. I'm inclined to just let feature-data-mag be.

[lizgehret]

okay generally this all looks like it was ported over successfully and in a consistent structure. i think the feature_data_mag dir is reasonable, and probably our best bet (to my knowledge) to keep ourselves out of a nest of circular imports. going to pull down locally to test in conjunction with the other bok lab PRs you have open to make sure everything plays nicely together.

[lizgehret]

If more repos need changed let me know, these were the three things that were dependent on q2-types-genomics when I removed it from my test env.

So in terms of the shotgun distro, those are the only three we need to worry about for tomorrow's release. In the context of Bokulich lab plugins as a whole, it looks like q2-amr and q2-checkm both have types_genomics imports that will need to be updated. @nbokulich do you want us to get those updated as well? Or hold off until you're ready to fully deprecate types_genomics wholesale?

[nbokulich]

thanks @lizgehret ! neither of those plugins are in the distro I think, so we have a little more flexibility. You can move ahead and not worry about these right now, we will take care of those two.

@VinzentRisch could you please update q2-amr and q2-checkm to import from q2-types instead of q2-types-genomics? @misialq can check full deprecation of q2-types-genomics when he gets back. Thanks!

[VinzentRisch]

Hi @nbokulich, yes I will do that today.

[lizgehret]

Okay local tests all pass for assembly, moshpit, and RESCRIPt! I'm going to go ahead and merge this, after which I'll run a prepare to percolate the latest changes here into CI and then we can re-run tests for the other three repos before merging those PRs. Thanks @Oddant1!