MAINT: adding deprecation warnings to several actions

[mikerobeson]

Addresses #242.

Set deprecated=True for the following actions:

• Actions that depend on either the q2-feature-classifier or q2-alignment plugins (Amplicon distro). As far as I can tell these actions are the only ones that depend on these plugins.
  • evaluate-cross-validate
  • evaluate-fit-classifier
  • trim-alignment
• Metagenome (MOSHPIT distro) leaning plugins:
  • get-bv-brc-genome-features
  • get-bv-brc-genomes
  • get-bv-brc-metadata
  • get-ncbi-genomes

Eventually, these actions will either be migrated over to other QIIME 2 plugins, or migrated into relevant RESCRIPt variants for the various QIIME 2 distributions.

[nbokulich]

Thanks @mikerobeson ! I think we also discussed that get-ncbi-genomes should be split off into a separate plugin as well — @misialq @lizgehret is that right?

Also @lizgehret do you think it's enough to just add deprecated=True or do you think that we should use a custom warning message with these actions (as they will be moved to separate plugins in the future)?

[mikerobeson]

Hi @nbokulich, I do remember discussing moving get-ncbi-genomes too. PR has been updated.

[lizgehret]

Hey @nbokulich @mikerobeson I actually think it would be more clear if we add a migrated warning (instead of deprecated) as this may be confusing for folks.

deprecated is just an attr on the Action class:
https://github.com/qiime2/qiime2/blob/deba9d1b866ff6ea57056f5df76878cfef67721b/qiime2/sdk/action.py#L205

I think it should be pretty straightforward to add a similar attr for migrated. I'll aim to work on that next week; once that's finished we can get this PR updated with the new flag - I'm thinking it will look something like:

migrated=True
migrated_plugin=`q2-alignment`

And then the warning message will look something like:

This action has been migrated to q2-alignment.

[mikerobeson]

Thanks @lizgehret! Should we have an option that will differentiate "migrated in this current release" and "plans to be migrated in a future release"? Also, a note on which QIIME 2 distribution? As we won't be moving anything this cycle, and we are also considering which distributions some actions or entire plugins make sense for certain distributions? I think we'd want something like these?:

• This action will be migrated to q2-alignment of the amplicon distribution in a future release.
• This action will be migrated from the RESCRIPt plugin of the amplicon distribution to the RESCRIPt plugin of the MOSPHIT distribution in a future release.

[lizgehret]

Oh yeah I like that! I'll play around with formatting and see if we can include the distro/release epoch; that would make things very clear for users.