[BioPython] Patch to fix testing failures in biopython-1.30

[Bill Barnard]

I installed the release version of biopython, v1.30, a couple days ago.
I was familiarizing myself with the code by running the test suites and
noted a few small difficulties. I am attaching a patch which fixes one
problem, and permits the test suite to run to completion without errors
by stubbing out the implementation for one new feature, and moving a
broken test to a Tests/broken directory.

The fixed problem is in Bio/dbdefs/pdb.py - the location of the cgi has
changed, and there appears to be an extraneous newline in the returned
text.

The stubbed implementation is in Bio/EUtils/parse.py - a new
<OP>GROUP<OP/> element has appeared in the retrieved output that breaks
the test. I did not attempt to fix this, but added code as per
http://portal.open-bio.org/pipermail/biopython/2004-November/002473.html
to "cover it up" leaving a placeholder comment.

Finally, the Tests/test_SVDSuperimposer.py test does not appear to run
correctly. The function itself appears to be broken, as it runs for
upwards of two hours on my machine (1.8 GHz Athlon XP 2500+) with no
output. I moved the test to a new Tests/broken directory.

The patch is meant to be applied to a complete untarred biopython
directory. If you've untarred it to /usr/local/src/biopython-1.30 you
can run the patch from /usr/local/src by:

patch -p0 < biopython-1.30-test_Registry-fix.patch

I've attached the patch to this email. Use as you see fit. I'll be happy
to upload it to Bugzilla if this would be the appropriate way for me to
help out. It would also be simple to break the patch into pieces if that
is more appropriate.

Cheers,

Bill
-- 
Bill Barnard <bill at barnard-engineering.com>
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