[Preview] QIIME 2 2020.8 development changelog

Developer Discussion
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QIIME 2 2020.8 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 2020.8

This post is a live-document which will be updated throughout our development cycle. Any links 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 10, 2020
  • PRs must be merged by: August 17, 2020
  • Repo Freeze and Package Building: August 20, 2020
  • Release Day: August 24, 2020

Developer Project Board: https://github.com/orgs/qiime2/projects/20

:exclamation: BREAKING CHANGES

  • q2-diversity
    • beta-phylogenetic
      • The parameter threads has replaced n_jobs to reflect the parallelization behavior of unifrac.
    • alpha
      • The metric name observed_otus has been renamed to observed_features. “Observed features” better describes the different ways in which users work with non-taxonomic features in QIIME 2. (An OTU is a feature, but a feature isn’t necessarily an OTU.)
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-phylogenetic
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-rarefaction
      • The metric name observed_otus has been renamed to observed_features. “Observed features” better describes the different ways in which users work with non-taxonomic features in QIIME 2. (An OTU is a feature, but a feature isn’t necessarily an OTU.)
    • beta
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • beta-phylogenetic
      • This Method has been converted to a Pipeline to accommodate dispatch to q2_diversity_lib. Artifact API users might need to update their import paths. q2cli users are not impacted by this change.
    • alpha-phylogenetic-old
    • alpha-phylogenetic-alt
      • This deprecated Method has been removed, because this implementation is used in alpha-phylogenetic.
  • q2-quality-filter
    • q-score-joined
      • This deprecated method was removed. The q-score method can handle joined reads, so no need to for two methods.

Please update scripts, workflows, etc. as appropriate. Stuck? Reach out here on the forum for help. Want to test this prior to the next release of QIIME 2? Check on the “development environment” instructions here:

https://dev.qiime2.org/latest/quickstart/

Here’s the highlights of the release:

  • QIIME 2 Framework
    • @Oddant1 fixed a bug preventing the usage of TypeMatch on Actions with a List or Set type parameter. :balance_scale:
    • @Oddant1 changed an error message so it points out a common mistake seen when importing metadata. :t_rex:
    • @Oddant1 fixed the error message reporting duplicated transformers, which can happen when developing a QIIME 2 plugin. :balloon:
  • docs
    • @Oddant1 changed all references to the deprecated q-score-joined method to q-score. Please see BREAKING CHANGES, above. :bike:
    • @andrewsanchez provided some editorial services for a few tutorials! :unicorn:
  • q2-types
    • @Oddant1 implemented improved validation for AlignedDNAFASTAFormat. :safety_vest:
    • @Oddant1 added an extra check during the creation of MANIFEST files for CasavaOneEightSingleLanePerSampleDirFmt to better allow for reverse only reads. :lacrosse:
    • New types and formats were added for working with Bowtie2 index files. :bow_and_arrow:
    • @Leo-Simpson (GH) added a new FeatureTable variant, called Design. It represents transformed/coded data, as an alternative to composition which only positive values. :desert_island:
  • q2-phylogeny
    • @SoilRotifer updated the citation for IQ-TREE 2. :nail_care:
    • @SoilRotifer added a new n_cores_auto parameter to iqtree and iqtree-ultrafast-bootstrap, used when n_cores auto is set. That is, n_cores_max will limit how many cores auto is allowed to scale to. :oden:
  • q2-longitudinal
  • q2-sample-classifier
    • @Oddant1 cleaned up new linting errors introduced by the latest flake8. :city_sunset:
    • @Leo-Simpson (GH) added support for the new FeatureTable[Design] type in split-table. :non-potable_water:
  • q2-quality-filter
    • @Oddant1 removed the previously deprecated q_score_joined Method. Please see BREAKING CHANGES, above. :baby_chick:
  • q2-diversity
    • @Oddant1 fixed a bug in alpha_rarefaction that prevented metadata with a column named “depth” from working as expected. :bug:
    • @ChrisKeefe wired up alpha, alpha_phylogenetic, beta, beta_phylogenetic, and alpha_rarefaction to metrics implemented in q2_diversity_lib, for improved type flexibility, safety, and specificity in primary source citations. See BREAKING CHANGES above for related API changes. :electric_plug:
  • q2-diversity-lib
    • @ChrisKeefe added alpha_passthrough, beta_passthrough, and beta_phylogenetic_passthrough Methods, which provide access to unifrac and scikit-bio metrics that have not yet been implemented/constrained locally. Most users will prefer to access these Methods indirectly, using diversity.alpha, diversity.beta, or diversity.beta_phylogenetic :crystal_ball:
  • q2-demux
    • @Oddant1 modified demux summarize to better support reverse only reads. :previous_track_button:
  • q2-dada2
1 Like
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Hey all - the 2020.8 development cycle is quite a bit shorter than normal (since 2020.6 wound up running a bit long). Anyway, we are planning on shipping in the first half of August, so today(ish) is the cutoff for PR submissions. If you have something you’re working on, but it isn’t yet on our radar please ping us here so that we can discuss a plan for ensuring your work catches the 2020.8 train, so to speak.

Thanks! :t_rex:

4

Just a quick follow-up, we had a change in plans that has allowed us to push the release out a little bit, which is great news, it’ll allow us to get a few more features etc pushed in. Please see above for a revised schedule.

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