Update ordination class to support new scikit-bio pcoa API

qiime2 / q2-diversity

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Update ordination class to support new scikit-bio pcoa API #217

Closed HannesHolste closed 6 years ago

HannesHolste commented 6 years ago

Update ordination class to support new scikit-bio's fast heuristic pcoa method https://github.com/biocore/scikit-bio/pull/1569

Changes are fully backwards-compatible.

TO-DO:

[x] 1. Wait until scikit-bio 0.5.4 is released (I am working on this with Yoshiki).
[x] 2. Wait until this q2-types PR is merged, which updates q2's skbio dependency to 0.5.4: https://github.com/qiime2/q2-types/pull/192
[x] 3. Wait for CI to pass and review/merge this PR

HannesHolste commented 6 years ago

I anticipate all the TODOs to be complete today. Currently preparing skbio for a new release with Yoshiki.

HannesHolste commented 6 years ago

@thermokarst just wanted to put this on your radar to mark for review the QIIME2 release.

HannesHolste commented 6 years ago

@thermokarst How to trigger q2d2 to generate a new dev/staging environment file based on the latest package dependencies in q2-types (which contains skbio 0.5.4, which is needed by this PR)? https://github.com/qiime2/environment-files/tree/master/latest/staging

ebolyen commented 6 years ago

It's in progress already, https://busywork.qiime2.org. In a few hours there will be a new environment file for travis.

HannesHolste commented 6 years ago

@ElDeveloper thanks, implemented! @ebolyen travis is passing!

ElDeveloper commented 6 years ago

Great, thanks!

On (Aug-28-18|19:29), Hannes Holste wrote:

@ElDeveloper thanks, implemented! @ebolyen travis is passing!

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