[Preview] QIIME 2 2022.2 development changelog

QIIME 2 2022.2 has been released!
Please see the official changelog for more details.

Original content of post

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2022.2

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 Information

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

  • PRs must be submitted by: 2/4/22
  • PRs must be merged by: 2/11/22
  • Repo Freeze and Package Building: 2/18/22
  • Release Day: 2/21/22

Developer Project Board:

QIIME 2 2022.2 Project on Github

Here are the highlights of the release:

  • QIIME 2 Framework

    • @ChrisKeefe made a handful of improvements/tweaks to Usage :hammer_and_wrench:
    • @ebolyen fixed an inconsistency in the view_type parameter of Usage.import_from_format, both string and classes are accepted as arguments now :2nd_place_medal:
    • Artifact API has now been renamed to the Python3 API :amphora::arrow_right::snake:
  • q2cli

    • @ebolyen fixed a bug in the Usage driver which resulted in a namespace collision :lady_beetle:
    • @ebolyen fixed an issue where the incorrect usage variable was returned for Usage.view_as_metadata :cockroach:
  • q2galaxy

    • When installing q2galaxy via the pre-built docker image, the conda environment is now already included. This results in a larger base image, but makes it far less likely that installation will fail. As a result, the first job will no longer take in excess of 40 minutes to complete :champagne::tada::confetti_ball::bento:
    • @ebolyen added a new Usage driver to automatically generate RST instructions for use within Galaxy tools and documentation :capital_abcd:
    • @ebolyen fixed an issue with string sanitization in the generated tools. (Unusual characters like ; would be silently converted, breaking functionality.) :cry::smiley:
    • @ebolyen added a new template function to provide an automatically nested and alphabetized tool_conf.xml file. See q2galaxy template tool-conf --help :nesting_dolls:
  • q2-sample-classifier

    • @misialq added cross-validation to KNN sample classification based on distance matrices :motorway:
  • q2-dada2

  • q2-longitudinal

    • @ebolyen added support for automatically quoting formula terms in linear-mixed-effects. Now column names like my-category will be quoted as Q('my-category') instead of raising an error. :crossed_swords:
  • q2-mystery-stew

    • @ebolyen added more sophisticated metadata interactions. Now tests include Usage.view_as_metadata and Usage.merge_metadata :stew:


This release is timed with the release of several QIIME 2 documentation projects that provide new ways to learn QIIME 2 now, and a glimpse into where we're headed with QIIME 2 documentation in the future.