[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 #3 from bsouthey at gmail.com  2008-09-18 23:01 EST -------
(In reply to comment #1)
> 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__

24.2

Based on a Google search, this is a 64bit problem with Python 2.5 and Numeric. 

So either do:
1) Drop the [:] from the left-hand side: 
lp_initial = lp_arcout_t[:,0]

2) Do a loop:
for bi in range(lp_initial.shape[0]):
    lp_initial[bi] = lp_arcout_t[bi,0]

3) Support NumPy - oh, wait already done... :-)

> 
> 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

Excellent! It is also good promo on what BioPython can do.

> 
> 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)."

I did not see where GFF is mentioned so a link would be worthwhile. Also, this
is probably the wrong place for the test or it should not be referenced unless
asked.

> 
> 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?

test_BioSQL ... skipping. Connection failed, check settings in
Tests/setup_BioSQL.py if you plan to use BioSQL: (2002, "Can't connect to local
MySQL server through socket '/var/lib/mysql/mysql.sock' (2)")
ok
test_BioSQL_SeqIO ... skipping. Connection failed, check settings in
Tests/setup_BioSQL.py if you plan to use BioSQL: (2002, "Can't connect to local
MySQL server through socket '/var/lib/mysql/mysql.sock' (2)")
ok

I initially thought to note these in the installation but after looking at the
BioSQL page, these MySQL tests should not be run to test BioPython. These are
BioSQL tests such they should be run after MySQL and BioSQL have been setup. So
these should not be tested unless asked for.  


> 
> Thanks,
> 
> Peter
> 

No, thanks to all the developers as this is too minor.

Bruce


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.