[Biopython-dev] [Bug 2589] Errors in running tests in 1.48

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2589





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-09-18 18:33 EST -------
Hi Bruce,

The test_MarkovModel problem looks serious, but improvements to the messages
from skipped tests are also worthwhile.

test_MarkovModel
================
This is interesting, I've not seen this before.  What version of Numeric do you
have?  You can find out at the python prompt with:

import Numeric
print Numeric.__version__

test_PopGen_FDist and test_PopGen_SimCoal
=========================================
These are 3rd party population genetics tools.  Do you think they should be
listed under http://biopython.org/wiki/Download#Optional_Software

test_GFF
========
This unit test requires a GFF wormbase MySQL database to be setup, plus an
environment variable for the password.  This is fairly complicated to explain,
hence "Environment is not configured for this test (not important if you do not
plan to use Bio.GFF)."

test_BioSQL and test_BioSQL_SeqIO
=================================
These require a BioSQL database with python driver to be installed plus the
username and password etc to be given in setup_BioSQL.py. What message did you
get exactly, and how would you suggest improving the message given?

Thanks,

Peter


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