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bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline
BSD 3-Clause "New" or "Revised" License
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Remove heavy dependencies #163

Open ebolyen opened 9 months ago

ebolyen commented 9 months ago

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 commented 9 months ago

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 commented 9 months ago

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: https://github.com/bokulich-lab/RESCRIPt/blob/11aedaa7dc46a3e4f0b9523b9ff4043f60e5a999/rescript/plugin_setup.py#L40-L42).

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

nbokulich commented 9 months ago

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

Yes, see e.g.: https://github.com/bokulich-lab/RESCRIPt/blob/11aedaa7dc46a3e4f0b9523b9ff4043f60e5a999/rescript/cross_validate.py#L38-L39

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 commented 4 months ago

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 commented 4 months ago

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: https://github.com/bokulich-lab/RESCRIPt/blob/a19d106d741c3e064f6d17f2b91bf131fd28903f/rescript/evaluate.py#L51

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?