[Biopython-dev] NumPy

[Michiel de Hoon]

Hi everybody,

Previously we discussed on this mailing list whether Biopython should adopt the "new" Numerical Python (aka NumPy, currently at version 1.1.1) instead of the "old" Numerical Python (version 24.2). My objections against NumPy were that its documentation is not freely available, it doesn't compile cleanly on all platforms, and some other scientific and computational biology libraries use the old Numerical Python.

Last week, the NumPy documentation did become freely available. Compilation of NumPy is still not perfect on all platforms (e.g. on Cygwin it may fail), however recently I have also noticed that compilation of the "old" Numerical Python may fail on modern systems. As far as I can tell, MMTK and PyMOL are (still?) based on the "old" Numerical Python, but Matplotlib now relies on the "new" Numerical Python.

In my opinion, the balance is now tilting in favor of the new NumPy, and we should consider transitioning Biopython to the new NumPy. Does anybody have a different opinion? If not, I suggest we bring this up on the user mailing list.

--Michiel.