[Preview] QIIME 2 2022.8 development changelog

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2022.8

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: August 11th, 2022
  • PRs must be merged by: August 18th, 2022
  • Repo Freeze and Package Building: August 23rd, 2022
  • Release Day: August 25th, 2022

Developer Project Board:

QIIME 2 2022.8 Project on Github


:exclamation: BREAKING CHANGES :exclamation:

  • Community Distribution!

    • TODO: add details on community distro and what this means for future developers
  • q2-FMT

    • TODO: New!
  • q2-stats

    • TODO: New!
  • q2studio

    • TODO: q2studio will be removed from our user documentation and will no longer be maintained - q2galaxy should be used for all GUI needs

Here are the highlights of the release:

  • QIIME 2 Framework

    • @ebolyen added support for all INSDC missing values to be processed as NULL within QIIME 2 Metadata :mag_right: :thinking:
    • @misialq added support for typing.Union in view types by selecting the first available transformer. This adds the ability for transformers to solve to a typing type like Union which will make paired-end visualizations simpler :robot: :microbe:
  • q2galaxy

    • TODO: now fully supported on Galaxy!
  • q2-dada2

    • @jordanrabasco submitted a huge refactor in q2-dada2 that combines all of the R scripts into one file for single, paired end, and ccs reads - for easier readability and reduced code duplication! :partying_face: :raised_hands:t3: :dna:
    • @leasi added the allowOneOff argument in the runBimeraDenovo() method, which enables users to allow for one mismatch or indel in bimera detection when set to True :space_invader: :dizzy:
  • q2-demux

    • @lizgehret added more concise error handling for metadata file handling when running qiime demux emp-single to include the specific column where any metadata.tsv (or sequences.qza) errors occur :page_with_curl: :interrobang:
  • q2-diversity

    • @yoshiki added support for sub-sampling with replacement in phylo-cm, which is useful for metagenomic studies where there's frequently over 1M counts per sample :100:
    • @ChrisKeefe updated the Halko citation and added a DOI field for a number of other citations :memo:
  • q2-diversity-lib

    • @ChrisKeefe added some Usage API examples on Faith's Phylogenetic Diversity, Observed Features, Pielou's Evenness, and Shannon's Entropy :mag: :chart_with_upwards_trend:
    • @wasade added new citations for inpress UniFrac and optimized Faith's PD papers :newspaper_roll: :bookmark:
  • q2-types

    • @Nicholas_Bokulich added a transformer that allows for BLAST6Format data to be transformed into QIIME 2 Metadata :boom: :firecracker:

Documentation:

  • @thermokarst published new developer tutorials on the following:

    • How to publish a plugin using Library :books: :open_book: :worm:
    • An overview of our packaging infrastructure :package: :spider_web:
  • @ChrisKeefe published a new developer tutorial on the usage API and how to write basic usage examples :nerd_face:

  • @ChrisKeefe published a new user tutorial on the Artifact API :gem: :sparkles:

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