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While working on #815 and #817, I remembered a suggestion for this. I think it would make them more obvious.
pip does this, with a custom logging.StreamHandler.
There are also a couple packages that hook into logging and use colorama (which Twine already uses for the red errors):
I think part of implementing this should be normalizing the way Twine reports warnings; it currently uses logger.warning and warnings.warn. It seems like the former is preferable for this purpose, although logging.captureWarnings could be a fallback.
Similarly, we might want to rework the red error implementation from #649 to use logger.error.