[Preview] QIIME 2 2021.8 development changelog

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2021.8

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, weโ€™ll copy this changelog and create a new post in the Announcements category.


Important Developer Information

Dates (please keep an :eye: on this post, these :calendar: might change):

  • PRs must be submitted by: 2021-08-09T07:00:00Z
  • PRs must be merged by: 2021-08-23T07:00:00Z
  • Repo Freeze and Package Building: 2021-08-25T07:00:00Z - 2021-08-27T07:00:00Z
  • Release Day: 2021-08-30T07:00:00Z

Developer Project Board: 2021.8 ยท GitHub


:exclamation: BREAKING CHANGES

Please update scripts, workflows, etc. as appropriate. Stuck? Reach out here on the forum for help. Want to test this prior to the next release of QIIME 2? Check out the "development environment" instructions here:

https://dev.qiime2.org/latest/quickstart/


Hereโ€™s the highlights of the release:

  • QIIME 2 Framework

    • @lizgehret updated the .save() method on the Artifact, Visualization and Metadata classes, that now contains the ext argument, which takes string values as input. Default values (if left blank) for each class are as follows:

      Metadata: blank
      Artifact: .qza
      Visualization: .qzv

      Additionally, Metadata.save() will now return the filepath (including optional extension), just as Artifact and Visualization classes currently do.

  • q2-diversity-lib

    • @lizgehret updated the Conda recipe with Python under the run requirements, to ensure compatibility when installing directly through conda install
  • q2-phylogeny

    • @lizgehret fixed a :bug: within the align_to_tree_mafft_fasttree method. Previously, when the n_threads argument was set to 'auto', the OMP_NUM_THREADS environment variable would be set to 1 (rather than the max number of threads available on a user's machine). This has been resolved, and now when n_threads is set to 'auto', the max number of threads are used.
  • docs

    • @lizgehret updated the OTU Clustering tutorial segment regarding 'Closed Reference Clustering' to accurately reflect the file outputs (one artifact of data type: FeatureTable[Frequency] and two artifacts of data type: FeatureData[Sequence] ).

    • @lizgehret updated the q2studio installation guide to resolve an npm install package dependency issue that was reported on the QIIME 2 forum.

    • @Nicholas_Bokulich updated the Data References page to include the RESCRIPt pre-print citation, slightly adjusted the description and references for the weighted classifiers, and cited the references listed for the unweighted classifiers.

  • q2cli

    • placeholder
  • q2-plugin

    • placeholder
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