[Biopython-dev] Pypy x64 tests Was: Pypy2 on Win7 x64, numpy problem

Manlio Calvi manlio.calvi at gmail.com
Mon Apr 28 18:53:43 UTC 2014

OK the Tests on Pypy 2 passed but a lot was skipped for one reason to another.
After this mail I'll send another with builds and tests log for
archive and lookups


On Mon, Apr 28, 2014 at 3:02 PM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
> I tried to install their Numpy (the Numpypy project) because I read
> about their difficulties about porting Cpython Numpy but even with
> that I get errors everywhere and don't compile it.
> OK giving the tests ignore Numpy(py) I'll try to build biopython against it.
> On Mon, Apr 28, 2014 at 2:51 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 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

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