[Preview] QIIME 2 2023.2 development changelog

lizgehret · January 30, 2023, 7:05pm

QIIME 2 2023.2 has been released!
Please see the official changelog for more details.

Original content of post

Important

The following is an early developer preview of the changes expected in 2023.2

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 Information

Dates (please keep an on this post, these might change):

PRs must be merged by: February 20th, 2023
Repo Freeze and Package Building: February 27th, 2023
Release Day: February 28th, 2023

Developer Project Board:

QIIME 2 2023.2 Project on Github

Exciting Announcements!

BREAKING CHANGES

Here are the highlights of the release:

q2-composition
- @lizgehret fixed a in ANCOM-BC where a reference_level value was chosen that is a column within the metadata, but the associated IDs from that group are not found in the feature table No error would be raised, ANCOM-BC just defaulted back to alphabetical order for the intercept column
  This will now produce an error that includes the reference_level value, along with the IDs not found in the table
- @lizgehret added type enforcement for the reference_level parameter, which now only allows numerical metadata columns to be used
- @lizgehret added citations for ANCOM and ANCOM-BC methods
- @lizgehret made some improvements to the tabulate visualizer:
  - Each tab now contains the data slice name and short descriptions for LFC and W-Scores
  - Columns used to calculate the intercept are included at the top of each slice's table
- @gregcaporaso added a new visualizer called da_barplot that adds support for generating bar plots from ANCOM-BC data, inspired by Figure 6 in the ANCOM-BC paper
- @crusher083 added a new flag in ANCOM called --filter-missing that will filter samples with missing metadata when enabled, and will produce an error that includes the IDs with missing metadata if disabled
q2-feature-table
- ghubrakesh authored a change that makes the language used for the summarize output more clear, changing feature count to frequency.
q2-fmt
- @cherman2 added a Proportional Engraftment of Donor Strains(PEDS) method called sample_peds that tracks percentage of donor features that were transferred to the recipient after FMT intervention The method is further explained in Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes | Nature Microbiology.
- @cherman2 added a new visualizer called plot_heatmap that adds support for generating a heatmap to visualize PEDS for each subject over time
q2-stats
- @lizgehret fixed some and associated test failures caused by API changes to the frictionless dependency
q2-types
- @colinbrislawn made a small update within the per_sample_sequences formats that updates the call of .iteritems to .items, since pandas will be deprecating .iteritems in the near future
docs
- @wasade revised the Greengenes entries to now include 2022.10, which is the latest release of Greengenes2