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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2754





------- Comment #6 from eric.talevich at gmail.com  2009-02-12 13:08 EST -------
Created an attachment (id=1239)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1239&action=view)
Use the warnings module for printing warnings

I grepped Bio/PDB for stderr and replaced what looked like warning messages
with calls to warnings.warn(). A couple of files need further attention:

StructureBuilder.py:
    Every warning is protected by "if __debug__:", which seems like something
    the warning module itself should cover.

PDBParser.py:
    Parsing exceptions are caught and passed to _handle_PDB_exception, which
    then decides whether to re-raise the exception or just issue a warning. The
    warnings module should be able to cover some of this functionality.

    There's also a feature to only show the first instance of the same warnings
    triggered by the same lines, which would make the output from parsing
    semi-malformed PDB files less annoying in permissive mode.


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