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

[Michiel Jan Laurens de Hoon]

Thanks for your patch, Bill. The failed test_SVDSuperimposer may be due 
to an incorrect compilation of the Lapack libraries on your computer. 
For example, the default compilation of numerical python on Cygwin and 
possibly Linux results in a broken Lapack, in which some linear algebra 
functions hang forever. The SVD code in Biopython uses these functions, 
so that may be the reason that the test didn't finish. You can try this 
with:

 >>> from Numeric import *
 >>> from LinearAlgebra import eigenvalues
 >>> x = array([[1,2],[3,4]])
 >>> eigenvalues(x)

If eigenvalues doesn't return, Lapack is broken. I submitted a patch for 
this bug to Numerical Python and numarray a while ago, but they have not 
(yet) been included.

--Michiel.

Bill Barnard wrote:
> 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.
>