[FIX] Better warnings & end of Python 2 support

PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

http://www.openswath.org

BSD 3-Clause "New" or "Revised" License

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Closed grosenberger closed 5 years ago

grosenberger commented 5 years ago

This PR warns that transition-level scoring can only be conducted if MS1/MS2 scoring was conducted beforehand.

We should further consider removing support for Python 2, because many dependencies require workarounds which don't support Python 2 anymore.