[Biopython-dev] Bio/cMarkovModelmodule.c

[Michiel de Hoon]

Hi everybody,

I was looking at our C modules to see if they can be made ready for Python 3. I noticed that Bio/cMarkovModelmodule.c currently contains only one function, _logadd, which is used to speed up Bio.MarkovModel. Numpy 1.3 and later contain a function (logaddexp) that does exactly the same as _logadd. Since Bio.MarkovModel itself already uses Numpy, I think we can remove Bio/cMarkovModelmodule.c. For this to work, we either need to require Numpy >= 1.3 in setup.py, or check for logaddexp when importing numpy in Bio.MarkovModel. I think requiring Numpy >= 1.3 in setup.py is better in the long run, so I would prefer that. Any other opinions?

--Michiel