[Preview] QIIME 2 2019.10 development changelog

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2019.10 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: October 18, 2019
  • PRs must be merged by: October 25, 2019
  • Repo Freeze and Package Building: October 29, 2019
  • Release Day: October 30, 2019

Developer Project Board: https://github.com/orgs/qiime2/projects/17


Here’s the highlights of the release:

  • QIIME 2 Framework

    • @Oddant1 Added a .view method to the _FileFormat class allowing for easier type conversion of _FileFormat objects.
    • @Nicholas_Bokulich updated the citation info for the canonical QIIME 2 citation (Bolyen et al., 2019 Nature Biotechnol)
  • docs

    • @Nicholas_Bokulich updated the tutorials to reflect changes to the feature-table heatmap API (metadata -> sample-metadata).
  • q2cli

    • @David-Rod Reduced time to build docs by adding deprecated field to plugin action state in the cache.
  • q2-plugin

    • placeholder
  • q2-feature-classifier

    • @Oddant1 Exposed new n_jobs and batch_size parameters in the extract_reads method allowing for parallelization of the method.

    • @Oddant1 Changed extract-reads so it will now ensure that min-len is greater than trunc-len minus trim-left before executing.

  • q2-sample-classifier

    • @Oddant1 Added a heatmap to the output from the classify-samples pipeline.
    • @Nicholas_Bokulich fixed a bug in confusion-matrix that caused ROC plots to fail on unstratified, imbalanced data.
    • @Nicholas_Bokulich added cividis to the list of available colormaps.
    • @Oddant1 added ability to adjust color scale of heatmaps derived from confusion matrices
  • q2-feature-table

    • @Nicholas_Bokulich added cividis to the list of available colormaps for heatmap.
    • @Nicholas_Bokulich updated heatmap to accept both sample-metadata and feature-metadata, enabling sample/feature labeling along each axis.
  • q2-longitudinal

  • q2-gneiss

    • @Oddant1 Exposed new ignore_missing_samples parameter in the gradient_clustering method that defaults to False and determines whether the method should continue as normal or raise an exception when samples not present in the metadata are present in the table.
  • q2-types

    • @David-rod Removed white space and comments from taxonomic data files
    • @Oddant1 Made it so DNAFASTAFormat disallows duplicate records
  • q2-deblur

    • @Oddant1 Made it so an exception is raised when underscores are found in sample ids

Happy QIIME-ing! :sun_with_face: