Remove heavy dependencies

[ebolyen]

It looks like we may be able to drop some rather significant weight from the recipe:

    - q2-longitudinal {{ qiime2_epoch }}.* 
    - q2-feature-classifier {{ qiime2_epoch }}.*

I can't find an import of longitudinal, which is bringing along sample-classifier as well.
And for feature-classifier, the only imports are these which I don't think is actually worth the cost of pulling feature-classifier along (requiring quality-control as well).

[nbokulich]

Yeah the longitudinal dependency can definitely be dropped... I think that is historical.

dropping q2-feature-classifier would require dropping a couple actions in RESCRIPt — is that what you are proposing? Or add instructions that users who wish to run those actions will need to install q2-feature-classifier separately?

[ebolyen]

No, I would want to keep those actions, but I think we can just duplicate the parameter descriptions (and move the type over to q2-types) (from these imports here:

RESCRIPt/rescript/plugin_setup.py

Lines 40 to 42 in 11aedaa

	from q2_feature_classifier.classifier import (_parameter_descriptions,
	_classify_parameters)
	from q2_feature_classifier._taxonomic_classifier import TaxonomicClassifier

).

Is there a pipeline that uses feature-classifier directly that I am missing?

[nbokulich]

Is there a pipeline that uses feature-classifier directly that I am missing?

Yes, see e.g.:

RESCRIPt/rescript/cross_validate.py

Lines 38 to 39 in 11aedaa

	fit = ctx.get_action('feature_classifier', 'fit_classifier_naive_bayes')
	classify = ctx.get_action('feature_classifier', 'classify_sklearn')

I would be very tempted to deprecated these actions though. Maybe just port those pipelines over into the classifier training workflows to use them for our purposes. I was never very happy with those pipelines.

[lizgehret]

This seems like a good candidate to finish up in this upcoming release cycle since we are adding RESCRIPt to the amplicon distro. @nbokulich I can bring this up in this week's eng meeting - your preference would still be to deprecate these actions?

[nbokulich]

Hi @lizgehret thanks for the reminder! Yes let's discuss this week.

Which dependencies are priority to drop? It looks like q2-longitudinal is indeed used in a couple places, e.g., here:

RESCRIPt/rescript/evaluate.py

Line 51 in a19d106

volatility = ctx.get_action('longitudinal', 'volatility')

though it is just to get the line plots from the volatility plot. So I would favor waiting until we have similar functionality up and running in q2-visard before dropping this.

The actions depending on q2-feature-classifier could always be ported over to another plugin (a new one) to simplify RESCRIPt's dependencies and focus more on the core functionality. But as q2-feature-classifier is already in the amplicon distro anyway, is this needed?

[nbokulich]

q2-longitudinal is dropped as a dependency with #204

so we are halfway there. Should we discuss if/how to address the q2-feature-classifier dependency? This will require dropping or porting a couple actions. Porting to a new plugin could be an option, I think the classifier eval actions are probably not needed by most users.

[lizgehret]

q2-longitudinal is dropped as a dependency with #204

so we are halfway there. Should we discuss if/how to address the q2-feature-classifier dependency? This will require dropping or porting a couple actions. Porting to a new plugin could be an option, I think the classifier eval actions are probably not needed by most users.

Yeah! Maybe this would be a good thing to discuss in next month's meeting post-release? Once we have all of the grant objectives wrapped up, it'll be a good time to figure out what we can add to our plates for the next development cycle.