[Biopython-dev] NumPy conversion roadmap

[Michiel de Hoon]

Hi everybody,

Now that Biopython 1.48 is out (thanks Peter!), we can now start to consider the conversion from Numerical Python to NumPy.

I'd like to propose the following steps:

1) Let's wait for a week or so before making any NumPy-related commits to see if any serious problems show up with the 1.48 release.

2) Three modules use Numerical Python at the C-level: Bio.Cluster, Bio.KDTree, and Bio.Affy. I have a NumPy-based module ready for Bio.Cluster. For Bio.KDTree and Bio.Affy, see my next mails.

3) Once these three modules are converted, Biopython can be compiled again. We can then consider the modules that use Numerical Python at the Python-level. There are about ten of those. Some of them are heavily used (such as Bio.PDB), whereas others are more obscure. Conversion is usually trivial, but I'd like to suggest that we take this opportunity also to review each of these modules to see if any should be deprecated.

Comments, anybody?

--Michiel.