[Preview] QIIME 2 2019.1 development changelog

Developer Discussion
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QIIME 2 2019.1 has been released!
Please see the official changelog for more details.

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:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2019.1 This post is a live-document which will be updated throughout our development cycle. Any links will in this topic will be broken until the release is officially published. When we are ready for release, we’ll copy this changelog and create a new post in the Announcements category.

Important Developer Dates (please keep an :eye: on this post, these :calendar: might change, also, times are approximate):

  • PRs must be submitted by: 2019-01-24T19:59:00Z
  • PRs must be merged by: 2019-01-28T19:59:00Z
  • Repo Freeze and Package Building: 2019-01-29T15:00:00Z
  • Release Day: 2019-01-31T19:00:00Z

Here’s the highlights of the release:

  • QIIME 2 Framework
    • @turanoo fixed a bug in Metadata.__repr__ that cause minor explosions in some edge cases. :balloon:
    • QIIME 2 now requires a minimum version of Python 3.6 to run — this is handled for you automatically when installing via one of our “official” methods, so no need to worry! Check out this post to learn more about the motivation and rationale for this change.
    • QIIME 2 environments now run on the latest versions of scipy, numpy, pandas, and matplotlib! :lemon: Now that’s what I call fresh!
  • docs
    • @gregcaporaso updated the Atacama tutorial’s paper reference. :open_book:
  • Library
    • @raptorace27, @J1411, tanman987, and jbell-97 teamed up to fix a bug when adding or editing plugins that didn’t check to see if the current editor was also listed as a plugin author. This was important because plugin permissions (in terms of being able to edit the plugin listing) are tied directly to “authorship,” so it was possible for a user to “lock themselves out” of their own plugin! Yikes! :lock: :lock_with_ink_pen:
  • q2cli
    • Corrected cross-device link error when using qiime tools export to convert an artifact to a single file. (This most commonly occurred when /tmp was on a different file system than where the exported file’s destination was.)
  • q2-longitudinal
    • Updated the plugin citation to reflect the final publication status.
  • q2-types
    • FeatureTables can now be used as metadata in QIIME 2 actions that consume metadata objects. Make sure you are inputting a table that is in the correct orientation! The default orientation of FeatureTables enable their use as sample metadata. Use the new transpose action (see below) to use feature tables as feature metadata. Thanks @Nicholas_Bokulich! :ice_cream:
    • @thermokarst updated the validator used for ensuring AlphaDiversityFormat files are well-behaved. This format now returns a clear error message when it runs into trouble (rather than just throwing its hands up in frustration :raised_hands:).
  • q2-feature-classifier
    • Both classify-consensus-* methods now have a query_cov parameter to optionally filter alignment results by query coverage.
  • q2-feature-table
    • @turanoo added a new method (transpose), which allows you to transpose the rows and columns of a FeatureTable[Frequency]! :cake:
  • q2-gneiss
    • @mortonjt fixed a bug in ilr-phylogenetic where mismatched tables and trees would raise an error.
  • q2-diversity
    • @thermokarst fixed a bug that caused the number of available cores to be incorrectly detected in certain environments, which caused a spurious error in a few methods.
    • @Nicholas_Bokulich added a new visualizer, adonis, that wraps the adonis function from the Vegan R package. This visualizer performs adonis (a.k.a. PERMANOVA) tests. Unlike the beta-group-significance action, adonis can perform multi-way PERMANOVA tests, and can operate on numeric variables. It does not generate plots or perform pairwise tests, so the beta-group-significance action is still the best method for one-way PERMANOVA tests.
  • q2-metadata
    • @Claudia_Coronel fixed a UI bug in tabulate, the rendered table now more clearly indicates which column sort widget belongs to which column label. :circus_tent:
  • Related Projects
    • iTOL
      • Added support for QZAs of FeatureData[AlignedSequence]. When dropped onto iTOL trees, these will automatically create a multiple sequence alignment dataset. Note that the display of alignments in iTOL is not supported in circular or unrooted modes.

Happy QIIME-ing! :sun_with_face:

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Just a quick reminder, PRs to QIIME 2 projects and plugins must be submitted tomorrow (2019-01-25T06:59:00Z) in order to be considered for the upcoming 2019.1 release. Please let us know if you have any questions, comments, or concerns! Thanks! :t_rex:

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A quick update from the trenches - we had to retrain the feature classifiers for this release. We are still waiting on those to finish up, so we are going to postpone the release until tomorrow. Thanks for your patience! :t_rex:

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