[Biopython-dev] biopython-1.51 test log, sage inclusion

[Marshall Hampton]

Hi,

I am preparing biopython-1.51 for inclusion as an optional package for 
Sage (www.sagemath.org).  I ran the test suite and got 8 errors; I am not 
sure if these are all expected.  The KDTree ones I have seen before, but 
some look new.  My test log is available at:

http://sage.math.washington.edu/home/mhampton/biopython-1.51-testlog.txt

in case anyone wants to take a look.

Biopython has been available in Sage for several years as an optional 
package, but I would like to make it a standard component.  This has 
become much more likely since the clean-up of Numeric and mx-texttools 
dependencies.  I think the only real issue is setting up some testing 
during the Sage package installation, which is my motivation for really 
understanding the test failures.

Cheers,
Marshall Hampton
Department of Mathematics and Statistics
University of Minnesota, Duluth