[Preview] QIIME 2 2023.7 development changelog

Developer Discussion
1

QIIME 2 2023.7 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 2023.7

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: August 8th, 2023
  • Release Day: August 10th, 2023

Developer Project Board:

QIIME 2 2023.7 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    • gneiss is no longer actively maintained, and thus we will be fully removing q2-gneiss from the QIIME 2 core distribution in our next release (2023.9).

Here are the highlights of the release:

  • qiime2

    • @oddant1 made some small improvements and bug fixes to Output Collections :books:
    • @oddant1 improved the error message raised when an unregistered semantic type is used. Previously, this error message stated that there was no associated format with the given semantic type, and it now specifies that the semantic type used has not yet been registered :no_entry_sign:

  • q2galaxy

  • provenance-lib

  • q2-composition

    • @bvan-tassel improved da-barplot, enabling longer y-axis labels so they don't get cut off, and updating the y-axis title placement so that it no longer collides with the Feature ID names. :boom:

  • q2-cutadapt

    • vaamb Added support for demultiplexing reads of mixed orientation with dual indices :two:

  • q2-feature-table

    • @cherman2 fixed a :bug: in feature-table summarize, removing unneccesary placeholder :zero:s that were being added as headers to the downloadable CSVs from the frequency per sample and frequency per feature tables.
    • @gregcaporaso added a new action, split, which splits a single feature table into multiple feature tables based on values associated with the samples in a categorical metadata column :bar_chart:

  • q2-metadata

    • @gregcaporaso added the merge method, which adds support for merging multiple metadata files, either with overlapping IDs or overlapping columns, or tables with neither overlapping IDs or columns overlap :card_index:
    • @hagenjp added the new parameter --p-encode-sample-size to shuffle-groups, which (when enabled) will append the sample size of each metadata group to the shuffled metadata column values :abacus:

  • q2-types

    • @gregcaporaso updated GenomeData[BLAST6] -> SampleData[BLAST6] to support updates to eggnog-diamond-search outputs within q2-moshpit :dna:

Additional Updates :hammer_and_wrench:

  • @ebolyen has just completed a massive overhaul of our continuous integration/continuous deployment (CI/CD) system :exploding_head: This is a minor note on this release, as we are still in the process of smoothing out any remaining kinks in the system, and documenting everything that has changed. We will create a formal announcement on this in our next release, but the TL;DR is that this will end up creating a much easier process for community developers to add their plugins to a QIIME 2 distribution, and will allow for more targeted distributions to be created, depending on the specific needs of users' analysis (i.e. 16S, metagenomics, etc). We currently have three QIIME 2 distributions that will be available for use - the core distribution (which we'll be renaming the "amplicon distribution" soon), the community distribution, and our new 'tiny' distribution - which contains only the framework, q2-types, q2cli, provenance-lib, and q2-mystery-stew. The core distribution is currently available for install, and the latter two distributions will be available for use sometime next week!
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