[Preview] QIIME 2 2017.11 development changelog

Developer Discussion
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QIIME 2 2017.11 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 2017.11 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 Dates:

  • PRs must be submitted by: 11/20
  • PRs must be merged by: 11/27
  • Release Day: 11/29

Here’s the highlights of the release (so far):

  • QIIME 2 Framework
    • The Choices predicate used on Str primitive types will now raise an error if it is given an empty set. Thanks @patthehat033!
  • docs
    • Added help text on how to identify valid metric values in the longitudinal tutorial.
    • Clarified how to receive support and report bugs in the “Community” section of the docs.
    • Removed link to old “Planned Plugins” spreadsheet. The best place to learn about new plugins is here, on the QIIME 2 Forum!
    • Fixed a bug in the feature-classifier tutorial: an incorrect value was suggested for the trunc-len parameter in one of the commands.
    • Trained new classifiers with sklearn 0.19.1.
    • Added tutorials for the new evaluate-composition and evaluate-seqs actions in the q2-quality-control tutorials page.
    • Added tutorials describing new features in q2-longitudinal, including spaghetti plots and measuring baseline differences/distances.
    • q2-longitudinal tutorial: provided more information on using q2-metadata to view valid metric values in artifact inputs, on interpreting linear-mixed-effects results, and fixed an inaccurate description of the z-scores provided in LME results.
  • q2-vsearch
    • A new method join-pairs has been added to join paired end sequence reads using vsearch's merge_pairs command. See the paired end reads community tutorial for more details.
    • Perform open-reference OTU picking using cluster-features-open-reference.
    • dereplicate-sequences now supports using joined sequences (SampleData[JoinedSequencesWithQuality]) and SampleData[SequencesWithQuality].
  • q2-demux
    • Support SampleData[JoinedSequencesWithQuality] as input data for the summarize visualizer. See the paired end reads community tutorial for more details.
    • Added a new transformer: EMPPairedEndDirFmt -> BarcodeSequenceFastqIterator.
  • q2-quality-filter
  • q2-deblur
  • q2-quality-control
    • Added new actions: evaluate-seqs and evaluate-composition! These actions are described in the tutorials.
  • q2-longitudinal
    • linear-mixed-effects now shows the table at the top of the visualization.
    • Exposed random slope and intercept values in linear-mixed-effects.
    • first-differences and first-distances now accept a baseline parameter which allows comparison against a value in the provided state-column instead of the previous state.
    • The volatility method can now overlay spaghetti plots in its visualization with a new spaghetti parameter.
  • q2-types
    • Added new importable type SampleData[JoinedSequencesWithQuality] for representing demultiplexed paired end sequence data that has already been joined. See the paired end reads community tutorial for more details.
    • QIIME1DemuxFormat now supports empty files.
    • Added a new transformer: SingleLanePerSampleSingleEndFastqDirFmt -> QIIME1DemuxDirFmt.
  • q2cli
    • Updated file path validation, resulting in clearer error messages of file path-related errors for users of q2cli!
  • q2studio
    • Now displays a prominent warning that it is a prototype and that some features may not work as well as its CLI counterpart (q2cli).
  • q2-gneiss
    • Fixed a bug related to recent versions of pandas.
  • q2-feature-classifier
    • Bumped the minimum version of sklearn to 0.19.1.

Happy QIIME-ing! :sun_with_face:

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