[Preview] QIIME 2 2019.4 development changelog

(Matthew Ryan Dillon) #1

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2019.4 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):

  • PRs must be submitted by: April 24, 2019
  • PRs must be merged by: April 26, 2019
  • Repo Freeze and Package Building: April 29, 2019
  • Release Day: April 30, 2019

Here’s the highlights of the release:

  • QIIME 2 Framework

    • @ChrisKeefe fixed a bug caused by invalid primitive arguments :three::no_good_man:. Expanded type mismatch error messages to better describe various invalid-input situations. :speaking_head:
    • @ChrisKeefe fixed some pretty confusing language in the SemanticType docstring.
  • Library

    • @thermokarst fixed a bug that prevented admins from editing plugins (due to an over-specified database rule).
  • docs

  • dev-docs

    • @ChrisKeefe busted out his editor’s red pencil on the dev docs.
  • q2cli

    • @epruesse cleaned up the --version output when looking at a plugin’s details! :cherry_blossom:
  • q2-diversity

    • @thermokarst fixed a bug :bug: in the adonis visualizer that prevented some metadata headers from working as expected.
    • @Nicholas_Bokulich fixed a bug in the adonis visualizer that caused an error if metadata values contained single quotes (e.g., apostrophes). :butterfly:
    • @Nicholas_Bokulich fixed a typo in the adonis visualizer help text. :alembic:
  • q2-longitudinal

  • q2-deblur

    • @thermokarst added a new left_trim_len parameter to the denoising methods of this plugin! :mountain_biking_man:
  • q2-demux

    • Fixed the per-sample sequence count table layout (that thing sure was bothering @ChrisKeefe!) :fish_cake:
    • @wasade brought Golay barcode correction to emp-single and emp-paired - the future is now! :baseball:
  • q2-cutadapt

    • @thermokarst added a new minimum_length parameter to trim_single and trim_paired! :scissors:

    • The ability to discard_untrimmed reads has been added to trim_single and trim_paired by @thermokarst. :grapes:

    • @thermokarst fixed a bug related to too many files being opened when demuxing datasets with many samples in it. Check out the new batch_size parameter on demux-paired and demux-single to control how many samples are demultiplexed at a time! :broccoli:

  • q2-feature-classifier

  • q2-sample-classifier

    • @Nicholas_Bokulich updated the citation information to include the report describing this plugin in the Journal of Open Source Software.
  • q2-feature-table

    • @gwarmstrong (GH) added a feature to allow disabling of clustering on both the sample and feature axes when creating a heatmap! :fire:
  • q2-quality-control

    • @Nicholas_Bokulich fixed a bug in evaluate-composition that caused linear regression R values of zero to be reported when observed and expected feature tables contain only a single observation at any taxonomic level. (the correct answer is no R value should be reported). :bug:

Happy QIIME-ing! :sun_with_face:


(Devon O'rourke) #2

Still time to throw in a --discard-untrimmed parameter with this update @thermokarst? One of the things I realized was invaluable in my workflow was using the linked adapters feature in Cutadapt; however, I only wanted to keep the reads that were framed by those 5’ and 3’ primers, and that required passing that flag (I think/hope!?).

Perhaps a future request for 2019.8?

Thanks for the improvements everyone!


(Matthew Ryan Dillon) #3


Ask, and you shall receive.


(Matthew Ryan Dillon) #4

Just a friendly reminder, PRs must be submitted by April 19, 2019 in order to be considered for the 2019.4 release. Keep us posted if you have incoming work that might not be on our radar - thanks! :qiime2:


(Matthew Ryan Dillon) #5

Scratch that, we are going to postpone the release by a few days so that we have time here to wrap up a few bigger projects:

  • PRs must be submitted by: April 24, 2019
  • PRs must be merged by: April 26, 2019
  • Repo Freeze and Package Building: April 29, 2019
  • Release Day: April 30, 2019