error if feature table samples aren't found in metadata about q2-gneiss HOT 12 CLOSED

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yes we are getting close to having ALDEx2 up and running inside QIIME2. https://github.com/dgiguer is just putting the finishing touches on this

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Is this still a relevant issue? The error definitely isn't being raised, but it looks like all of the methods that even use metadata in gneiss are deprecated.

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It might still be relevant:

• https://docs.qiime2.org/2019.7/plugins/available/gneiss/gradient-clustering/

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Thanks @thermokarst - yes this is still an outstanding issue

It'll boil down to something as follows here: https://github.com/qiime2/q2-gneiss/blob/master/q2_gneiss/cluster/_cluster.py#L93

difference = set(table.index) - set(gradient.index)
if difference and not ignore_missing_samples:
            raise KeyError("There are samples not included in the mapping "
                           "file. Override this error by using the "
                           "`ignore_missing_samples` argument. Offending "
                           "samples: %s"
                           % ', '.join(sorted([str(i) for i in difference])))

Concerning deprecation - the stats methods are being deprecated in favor of other differential abundance methods such as songbird and hopefully aldex2. CC @ggloor

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And this should be a thing in all q2-gneiss methods taking a Metadata or MetadataColumn as input?

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😆 those poor lonely deprecated methods

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I'm not finding any relevant methods other than gradient_clustering

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Also, do we want ignore_missing_samples arguments to be included in any relevant methods?

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Yeah I realized that after looking at it a bit more closely

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