Warning not raised?

This is probably a problem for the 2022 development team. But, it's on my mind now, so better bring it up before I forget.

I'm not sure what's up. So, hopefully :crossed_fingers: someone a little bit more QIIME CLI savy can help me.

I have a warning that gets raised (and tested) via the nomral python warn module

User experience says it doesn't get raised in the CLI interface without the --verbose flag.

I see that the scikit-learn throws a classifier warning. It's been a while since i trained a classifier, but i'm assuming that prints on the CLI. So, is there some brilliant witch craft I'm missing :woman_mage:?

Thanks!
Justine

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Hey there @jwdebelius! I don't think you're missing anything here - q2cli doesn't emit any stdout or stderr messages unless the --verbose flag is added (as you noted above). Personally I'm not a huge fan of this, for all the reasons you bring up here - sometimes its important to convey a message to folks. The challenge is how to do that in an interface-agnostic way. We probably have some super old GH issues about this somewhere, related to logging (for example, those messages might also be useful within an Artifact's provenance, too - we need to make sure the message is delivered to all of the right places!), but in the meantime, I think perhaps your best option is to strongly encourage q2cli users to run that command with the --verbose flag. Sorry I don't have a better answer for you!

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Thanks @thermokarst! Thats very helpful. I'll add that to the docs, then, or maybe shift to an error which can be ignored.

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