QIIME 2 Weekly Developer Meeting: 2017.03.10

This is the thread for the weekly developer discussion meeting on 2017.03.10.

Meeting date/time: 2017.03.10, 12pm-1pm MST (-0700 UTC)

Planned Agenda

Status Updates (1-2 min per person)

  • Caporaso Lab
  • Other attendees

Guided discussion (remainder of scheduled meeting time)

Discussion points:

  • pre-beta release of gneiss (@mortonjt)
  • microrelease of q2-deblur (@wasade)
  • DataFrame to HTML with tooltips (@wasade)
  • optional outputs from QIIME 2 methods (@wasade)
  • user docs are scattered / script index / usage examples (@yoshiki)
  • drop support for cookiecutter/q2-dummy-plugin (@jairideout)

To help us make the best use of everyone’s time please post any discussion topics to this thread before the developer meeting. This will help us identify and prepare for any questions/topics ahead of the call. Topics or questions of discussion are open to anyone, developers or users, but we ask that these discussion points be limited to thematic QIIME 2 questions (e.g. feature proposal, plugin idea, etc.) — we will not be able to provide technical support during these calls.

The developer meeting will be recorded and posted to YouTube, we will update this post with the streaming video link shortly before the meeting.

YouTube Link: https://www.youtube.com/watch?v=yjynendgnb0

If there are no discussion topics posted by 2017.03.09, 4pm MST (-0700 UTC), we will announce a meeting cancellation and share our status updates on this thread.

We have a pre-beta release of gneiss coming out in the next day or so.

This release has a direct dependency on qiime2, which proved to really simplify the user interface.
In addition to the q2 interface, we have support for interactive tree visualizations, adopting a similar to strategy to seaborn plots.

The documentation can be found here and an example of one of these tutorials can be found here.


Deblur came out in mSystems today, and we just pushed out a microrelease for q2-deblur to bump its minimum requirement to Deblur==1.0.1. The microrelease also includes revised citation information, and a mechanism to obtain per-sample stats (example .qzv).

On the per-sample stats, two items came up which may be useful to discuss:

  • A centralized helper method to generate an HTML table with tooltips automatically from a Pandas DataFrame. Tabular output seems to be relatively common in the ecosystem and centralizing this pattern may be useful (including column sorts, download links, etc).
  • The per-sample stats are currently optional in q2-deblur as they require a modest amount of filesystem trolling to produce. However, there currently is not a means that I’m aware of to have optional outputs from QIIME2 methods.
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The user-facing documentation seems a bit scattered right now. It would be good if we could come up with something similar to what http://scripts.qiime.org used to do. Also, usage examples would be fantastic, those were always a strong point of the documentation!

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Agenda item:

We’re thinking about killing the cookiecutter-based plugin templating functionality (as well as q2-dummy-plugin) as it’s hard to keep up-to-date, hasn’t been super useful (in my opinion), and we’ve noticed plugin devs have forgotten to remove unnecessary dependencies (e.g. q2-dummy-plugin) and commented out code from the templated package. Maintaining cookiecutter/q2-dummy-plugin is also a duplication of effort because we are effectively maintaining two sources of info for plugin developers via the plugin dev docs and the code generated by cookiecutter. We would instead like to focus our efforts on improving the plugin developer documentation and making that the single source of truth.

(Responding on the forum instead of the dev-call so other’s can see the link.)

We have the start of that here: https://docs.qiime2.org/2017.2/plugins/available/

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