[Biopython-dev] Pypy2 on Win7 x64, numpy problem

[Peter Cock]

On Mon, Apr 28, 2014 at 9:09 AM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
> Hi all,
>
> Yesterday, after a short break on compiling, I tried to build my pypy
> 2 stack to run the biopython tests on it, the problem is on numpy, for
> every thing I tried to compile their numpy version I failed, out of
> curiosity I tried to compile numpy on pypy3 but get even worse. In the
> end both don't compile, at this point I stopped after looking my pypy
> envs are sane.
>
> Manlio

NumPy has a ton of C code, and will not work on PyPy.
Attempting to compile/install NumPy under PyPy is a waste
of time.

However, the PyPy team are reimplementing (some of)
NumPy themselves as the NumPyPy project - see e.g.
http://buildbot.pypy.org/numpy-status/latest.html

Currently Biopython ignores NumPy (and NumPyPy) under
PyPy - last time I did a proper test there were still too many
things missing to make it worth the effort.

However, this is something we should review - I would hope
by now that at least the PDB parsing code might work - even
if things like SVD and numpy.linalg are not available on PyPy.

Similarly, NumPy won't work under Jython.

Peter