Treating warnings as errors #262
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@anushka255 - I'm seeing a lot of warnings on running the snakemake pipeline, primarily from
pandas. While these are not critical now, they will turn into hard-to-debug errors in the future (e.g.SettingWithCopyWarning) whenpandaschanges its behavior in some future version. The Aspire project, for example, decided to totally get rid ofpandasbecause they couldn't handle the regular API behavior changes from them.This PR treats all warnings as errors when running the tests, and should serve as a base PR to ensure we've weeded out all warnings. We can handle these gradually of course.
Trying to catch all warnings instead of only the ones from
pandasmight seem like an overkill, but I think the warnings originate from a handful of lines (unclosed files in tests, other changes likenp.random.shuffle(<series>) -> <series>.sample(frac=1)), so it should be manageable. If this turns into a never ending exercise then we can restrict ourselves topandas.