[Preview] QIIME 2 2018.2 development changelog

Developer Discussion
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QIIME 2 2018.2 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 2018.2 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: 02/08
  • PRs must be merged by: 02/13
  • Release Day: 02/15

Here’s the highlights of the release:

  • QIIME 2 Framework
    • There are large changes to Metadata in QIIME 2, including a new file format and Metadata API. See this forum announcement for details on what changed, as well as the updated Metadata tutorial.
    • Improved the error reporting for all methods that support filtering with a SQL where clause.
  • docs
  • Keemei
  • q2cli
    • Some CLI option names related to Metadata have changed in a backwards-incompatible way. Previously, any QIIME 2 action accepting a metadata column as input would have an option name ending with -category. The new option names end with -column, so previous commands will not work with the new naming scheme. For example, if a command previously used an option called --m-metadata-category, the new option name will be --m-metadata-column. If the CLI detects usage of the older option names, it will error and describe how to update your command to use the new option names. See this forum announcement for details on other Metadata-related changes in this release.
    • Added a new subcommand: qiime tools inspect-metadata! This will let you interrogate metadata, allowing you to learn about the available columns, their declared or inferred type, and the dimensions of the metadata. :cool:!
  • q2-metadata
    • Metadata column types (e.g. numeric or categorical) are now displayed in the tabulate visualization. The column types are included in the exported TSV/CSV files using the #q2:types comment directive. See this forum announcement for details on the new Metadata column typing support in this release.
    • Fixed a bug when tabulating metadata with single quotes (') in metadata values.
    • Added more robust error handling when qiime metadata tabulate can’t display metadata in the interactive table. If the metadata can’t be displayed interactively, users still have an option to download the metadata as a TSV file (e.g. to load in Excel/Google Sheets, or for further use with QIIME 2).
    • qiime metadata tabulate now has a simple progress indicator while loading the interactive table. Note: there isn’t any meaningful representation of loading progress at this point, just a binary “loading” / “not loading” type of indicator.
  • q2-feature-table
    • Changed the behind-the-scenes mechanism responsible for merging feature tables — this should reduce the amount of time required to merge large feature tables.
  • q2-demux
    • @mahermassoud added the ability to download the backing quality score stats from the summarize visualization. Thanks @mahermassoud! :tada: :balloon:
  • q2-cutadapt
    • Updated the adapter parameter descriptions to hint at cutadapt's ability to handle linked primers.
  • q2-gneiss
    • The boxplots produced by qiime gneiss balance-taxonomy are now displayed regardless of the number of the groups within the categorical metadata column.
  • q2-diversity
    • Fixed a bug (:bug:) in alpha-rarefaction that caused visualizations to break when using metadata with column names that contained spaces (' ').
    • Upgraded the scatterplot symbols in the alpha-rarefaction plot to display boxplots instead of dots. The boxplots help convey the distribution of a particular metric at a given depth, which is useful for understanding these data with more context than just the dots on their own.
  • q2-quality-filter
    • Fixed a bug (:butterfly:) that caused a confusing error message when providing incompatible metadata to evaluate-composition.
  • q2-emperor
    • --p-custom-axis has been renamed to --p-custom-axes and is now a List[Str] type, meaning it can be provided multiple times.
  • q2-dada2
    • Fixed a bug that caused denoise-single and denoise-paired to fail when specifying 'none' as the chimera removal method.

Happy QIIME-ing! :sun_with_face:

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