[Biopython-dev] coverage of function testing

[Marshall Hampton]

Hi,

I noticed some discussion of the coverage and automation of testing for 
functions in biopython, and thought I would suggest folks check out the 
testing and coverage tools in Sage (www.sagemath.org).  Testing of 
functions in Sage is done by testing examples in their docstrings - there 
are comments to opt out of testing or to indicate if they will take a long 
time.  They also have scripts for checking which functions have at least 
one such testable example.  So you can do something like this:


sage -coverage PATH_TO_SAGE/sage/geometry/polyhedra.py

and get

SCORE
/Volumes/D/sage-3.2.alpha0/devel/sage-main/sage/geometry/polyhedra.py:
100% (21 of 21)

to see if anything is untested.

Now that biopython is converting to numpy, I will start arguing for its 
inclusion as a standard part of Sage (right now it is an optional 
package).


Cheers,

Marshall Hampton
Integrated Biosciences Program and
Department of Mathematics and Statistics
University of Minnesota, Duluth