Use the RachisWarning Class: An Always-Visible Warning

Warnings issued by the Python warning library are suppressed by defualt when using the command line interface (CLI). In order to make sure the warnings issued by your plugin are visible in the CLI you must use the RachisWarning class. This class can be imported from the QIIME2 framework, specifically from qiime2.core.exceptions. Below is an excerpt from the q2-feature-table plugin that may issue such a warning.

from qiime2.core.exceptions import RachisWarning

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 action issues a RachisWarning when the taxonomies have different depths. Since the RachisWarning class is an empty subclass of UserWarning from the Python warnings library, the only difference in behavior is command line visibility.