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FEAT: qiime tools show-types and qiime tools show-formats commands #291

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merged 22 commits into from
May 10, 2023

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colinvwood
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Added two commands to show the available semantic types and importable and exportable formats for a qiime deployment.

Will replace the functionality of the qiime tools import --show-importable-types and qiime tools import --show-importable-formats commands.

Additionally:

  • descriptions are given of each semantic type or format when available
  • semantic types or formats can be subsetted to only those of interest
  • a --tsv flag is available

Motivated by #289.

@gregcaporaso
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Hey @colinvwood, I haven't reviewed this in any detail, but I think it's worth removing the --show-importable-* functionality from qiime tools import ... in this PR too. I think the best way to do this is, if the user provides one of those flags, print a note saying that that functionality is now accessible instead through the new command and then exit (without printing the types/formats).

@gregcaporaso gregcaporaso self-requested a review March 11, 2023 14:06
@gregcaporaso gregcaporaso self-assigned this Mar 11, 2023
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Hey @colinvwood, I have some requests for changes on this PR. It might look like a lot, but they're all pretty minor so I think this should be relatively quick to address. Let me know if you have any questions.

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@colinvwood
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Not sure why the cache test is failing, maybe @Oddant1 can weigh in?

@colinvwood colinvwood marked this pull request as ready for review May 9, 2023 20:36
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Looks good to me, thanks for the updates @colinvwood!

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lgtm

@Oddant1 Oddant1 merged commit c7871c0 into qiime2:master May 10, 2023
@colinvwood colinvwood deleted the qiime-tools-show-importable branch May 10, 2023 20:58
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3 participants