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biocore / qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
https://biocore.github.io/qurro
BSD 3-Clause "New" or "Revised" License
31 stars 10 forks source link

Remove reliance on songbird for the differentials type in the future #154

Closed fedarko closed 5 years ago

fedarko commented 5 years ago

When https://github.com/qiime2/q2-types/pull/212 is merged into a release of QIIME 2 (probs the next one, i.e. 2019.7), we can just require that at least that version of QIIME 2 is used with Qurro and remove our reliance on Songbird to define the Q2 FeatureData[Differential] type.

Along with letting us clean up some complex/ugly code in plugin_setup.py, this will impact the example jupyter notebook(s?), .travis.yml (no need to install songbird during the testing process), and some documentation I think. All in all this will make using Qurro easier.

thermokarst commented 5 years ago

BTW, one thing you can do in your .travis config is update this to use a "dev env" version of QIIME 2 - then you will be able to test changes like the ones in qiime2/q2-types#212 right after the PR is merged (and busywork spits out a new dev env).

thermokarst commented 5 years ago

Sorry, forgot the dev env link: https://dev.qiime2.org/latest/quickstart/

fedarko commented 5 years ago

I had no idea that existed—this is really useful for immediately testing with the latest Q2 version. Thanks Matt!

(I'm working on a dev branch of Qurro r/n but these changes should be merged back into master within a week or so)