[Preview] QIIME 2 2023.9 development changelog

Developer Discussion
1

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2023.9

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):

  • Repo Freeze and Package Building:
  • Release Day:

Developer Project Board:

QIIME 2 2023.9 Project on Github

:bangbang: Important Announcements :bangbang:

  • q2-gneiss - DEPRECATION NOTICE
    • gneiss is no longer actively maintained, and thus we will be fully removing q2-gneiss from the QIIME 2 core distribution in our upcoming release (2023.9).

Here are the highlights of the release:

  • qiime2

    • @Oddant1 Added support for kebab-case-keys to the artifact cache :oden:

  • q2-types

    • @lizgehret Added FeatureMap from q2-types-genomics to q2-types :heavy_plus_sign:

  • q2-demux

    • @Oddant1 Added actions to partition demultiplexed sequences into collections of smaller artifacts :heavy_division_sign:
    • @crusher083 Fixed some deprecation warnings :warning:
    • @gregcaporaso added the tabulate-read-counts action, which generates an ImmutableMetadata artifact from various demultiplexed sequence type that describes the number of reads observed per sample. This information was previously only available in the summarize visualization, making it hard to integrate this information in downstream analyses (e.g., to color points in a PCoA plot based on how many sequences were obtained for them).

  • q2-feature-classifier

    • @Nicholas_Bokulich Enabled optional use of pre-indexed databases with blast :boom:
    • @isaiahraspet added optional Metadata and Collection[FeatureData[Taxonomy]] to the tabulate-seqs visualization. This simplifies comparing the results of multiple taxonomy assignment approaches (such as different databases), and putting that information along side the sequence for easy BLASTing, to see what NCBI thinks. More feature information is coming soon to this visualization. Happy feature exploring! :1234::microbe:

  • q2-feature-table

    • @gregcaporaso Added the ability to merge FeatureTable[PresenceAbsence] :face_in_clouds: