pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print

[RalfG]

Description

Revisit of #6979. Replacing print statements in pyopenms/__init__.py with warnings.warn for info regarding the OPENMS_DATA_PATH environment variable.

If I understand correctly, #6979 was closed because it proposed to use the logging module, leading to multiple ways of logging implemented in pyOpenMS. I here propose to use warnings.warn instead in the pure Python code. Especially in the case of the OPENMS_DATA_PATH warnings, this makes sense.

Currently, using pyOpenMS with multiprocessing leads to a wall of warnings that cannot be disabled due to the use of print. With the proposed changes, developers of tools using pyOpenMS can choose to ignore these warnings when desired with

from warnings import filterwarnings

filterwarnings(
    "ignore",
    message="OPENMS_DATA_PATH environment variable already exists",
    category=UserWarning,
    module="pyopenms",
)

Checklist

• Make sure that you are listed in the AUTHORS file
• Add relevant changes and new features to the CHANGELOG file
• I have commented my code, particularly in hard-to-understand areas
• New and existing unit tests pass locally with my changes
• Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

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Advanced commands (admins / reviewer only)

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[jpfeuffer]

Yes, the referenced PR was only closed because they were looking for a way to control all logs and the logs and the ones coming from C++ require more work.
I'm fine with at least doing the python logs a bit nicer.

[timosachsenberg]

Thanks!

[radusuciu]

Thank you!!!