[Biopython-dev] [Bug 2754] Bio.PDB: Parse warnings should print to stderr, not stdout

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Feb 12 17:00:53 UTC 2009


------- Comment #5 from eric.talevich at gmail.com  2009-02-12 12:00 EST -------
(In reply to comment #3-4)

Using warnings.warn() sounds right. That module is used in other places in
Biopython, but not in Bio.PDB yet.

> And what about the logging module?
> It allows configuration, personalization of the output, etc..

The logging module is probably overkill for a library, I think. It's very
flexible, but the setup is kind of tedious, and generally an application using
both Biopython and the logging module would figure out how to raise the
warnings as exceptions, re-capture then, and log them in whatever customized
way is needed.

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