[Preview] QIIME 2 2019.7 development changelog

:exclamation: Important :exclamation:

The following is an early developer preview of the changes expected in 2019.7 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 Dates (please keep an :eye: on this post, these :calendar: might change):

  • PRs must be submitted by: July 22, 2019
  • PRs must be merged by: July 26, 2019
  • Repo Freeze and Package Building: July 29, 2019
  • Release Day: July 30, 2019

Here’s the highlights of the release:

  • QIIME 2 Framework

    • GH user @asoback updated the framework source code’s README file to provide a bit more context for the casual reader.

    • @Oddant1 made it so artifacts now validate the entire file on import, which should hopefully help prevent down-stream data issues. This will add a little bit of additional time to importing, but, we think it is worth the wait! :timer_clock:

  • docs

    • @thermokarst updated many of the metadata column names in a handful of tutorials, to use a new naming convention (e.g. BarcodeSequence is now barcode-sequence). :barber:

    • @thermokarst updated the SQL-where clause quoting convention in the tutorials to use the [column-name] syntax, which we think is a little easier to read! :eyeglasses:

    • @jwdebelius wrote a tutorial introducing a new dataset based on a mice study of Parkinson’s disease. :mouse2:

    • @thermokarst added the ability to capture command streams, which is useful for tutorial writing efforts. Neat! :meat_on_bone:

    • @thermokarst finally got around to adding the workshop deployment script to the main code base in this project, a feature useful for workshop instructors. :woman_teacher:

    • New pre-trained feature classifiers are available now. These pretrained feature classifiers reflect the recent update to scikit-learn 0.21.2. :ledger:

  • library

    • @Davrod29 Updated copyright in page to reflect current year.
  • q2cli

    • @Oddant1 added proper reporting of “out of space on drive” and “file path does not exist” errors.

    • @Davrod29 Made changes to the help text for qiime tools view. The change should now show users a valid command suggestion for extracting a Visualization.

    • @Oddant1 added the ability to customize command line text formatting.

  • q2templates

    • @Davrod29 Resized tables, adjusted text alignment, and centered table in browser window.
  • q2view

    • @Davrod29 Renamed Peek tab to Details and moved the provenance-recorded citations panel from the Provenance tab to the newly renamed Details tab.

    • @Davrod29 Refactored React code in Gallery file to help keep things clean for future developers! :spider_web:

  • q2-feature-classifier

    • Updated to the latest scikit-learn (v0.21.2)! :classical_building:
  • q2-cutadapt

    • @Oddant1 added a minimum_length parameter to the two demux methods in this plugin! :straight_ruler:
  • q2-demux

    • @Oddant1 added a filter-samples method for separating data from a single demux run using sample metadata.
  • q2-dada2

    • GH user @angrybee exposed individual forward and reverse maxEE parameters for denoise-paired. :honeybee:
  • q2-deblur

    • @Oddant1 added the ability for q2-deblur to parse sequence identifiers that include semicolons.
  • q2-taxa

    • @fedarko added a slider to adjust the bar widths in the barplot visualization! :bar_chart: :left_right_arrow:

    • @Oddant1 added a new error message for when the metadata is missing any Sample IDs that are present in the FeatureTable[Frequency].

  • q2-sample-classifier

    • @cduvallet & @Oddant1 collaborated to allow split_tables to work with all kinds of FeatureTables! :potable_water:

    • @Davrod29 Removed styling rule for tables generated by templates.

    • @Nicholas_Bokulich fixed the heatmap metadata descriptions in the help documentation.

  • q2-composition

    • GH user @Jiung-Wen fixed a bug in the ANCOM visualizer that prevented users from getting their hands on the backing data from the volcano plot. Thanks! :bug: :handshake:
  • q2-gneiss

    • @Oddant1 improved the error message produced when attempting to use categorical metadata columns where all values are numerical when running the balance_taxonomy visualizer. :sunglasses:
  • q2-longitudinal

    • @Nicholas_Bokulich updated the test data to accommodate changes to statsmodels=0.10.0 that resulted in very slight changes to MixedLM results when multiple random effects are used. Linear mixed effects models that used < 2 random effects were not impacted.
  • q2-types

    • @Oddant1 Made validation of FASTA files more robust.

Happy QIIME-ing! :sun_with_face:


A friendly reminder that PRs for the upcoming 2019.7 release must be submitted by: July 22, 2019. If you have something cooking right now please let us know, that way we can get it on our radar. Thanks!

@thermokarst I’ve been slammed recently (as I’m sure you all have been as well :slight_smile: ) but I will try to find some time over the weekend to polish up the q2-taxa barplot a little bit (e.g. making bar widths persist even when the chart is re-rendered due to something like the taxonomic level change).

I’ll try to have it in by the end of the weekend (and of course this isn’t a super high priority fix, so I completely understand if it won’t fit in before the next release – don’t want to stress you all out with more work right now).