raise-visible-warning.md

(howto-raise-visible-warning)=

Raising a Visible Warning

Warnings raised by the Python warning library are suppressed by the QIIME2 framework by defualt. In order to make sure the warnings raised by your plugin are visible on the command line you must use the RachisWarning subclass. This class can be imported from the QIIME2 framework, specifically from qiime2.core.exceptions. Below is an excerpt from a QIIME2 plugin registered in q2-feature-table importing and raising a RachisWarning.

from qiime2.core.excpetions import RachisWarnings

def merge_taxa(data: pd.DataFrame) -> pd.DataFrame:
    if len(data) > 1:
        depths = []
        for taxonomy in data:
            max = 0
            for _, row in taxonomy.iterrows():
                depth = row['Taxon'].count(';')
                if depth > max:
                    max = depth

            depths.append(max)
        if len(set(depths)) != 1:
            warnings.warn(
                "You are merging taxonomies with different depths.",
                RachisWarning
            )

This plugin has a RachisWarning raised when the taxonomies have different depths. Since the RachisWarning is a subclass of UserWarning from the built in Python warnings library, on which you can find more in depth documentation here, they behave completely the same outside of command line visibility.