[Biopython-dev] [Biopython - Feature #3236] Make Biopython work in PyPy 1.5

[redmine at redmine.open-bio.org]

Issue #3236 has been updated by Peter Cock.


A couple of nights ago the unit tests were passing under PyPy 1.9 (Mac OS and Windows tested). There have been some more "Too many open files" failures since though, so we are probably still close to the limit and might benefit from more explicit handle closure.
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Feature #3236: Make Biopython work in PyPy 1.5
https://redmine.open-bio.org/issues/3236

Author: Eric Talevich
Status: In Progress
Priority: Low
Assignee: Biopython Dev Mailing List
Category: 
Target version: 
URL: 


PyPy is now roughly as production-ready as Jython:
http://morepypy.blogspot.com/2011/04/pypy-15-released-catching-up.html

Let's make Biopython work on PyPy 1.5.

To make the pure-Python core of Biopython work, I did this:

* Download and unpack the pre-compiled Linux tarball from pypy.org
* Copy the header file @marshal.h@ from the CPython 2.X installation into the @pypy-c-.../include/@ directory
* pypy setup.py build; pypy setup.py install
* Delete pypy-c-.../site-packages/Bio/cpairwise2*.so

Benchmarking a script that leans heavily on Bio.pairwise2, I see about a 2x speedup between Pypy 1.5 and CPython 2.6 -- yes, that's with the compiled C extension @cpairwise2@ in the CPython 2.6 installation.

Numpy isn't available on PyPy yet, and it may be some time before it does.

Observations from @pypy setup.py test@:

* test_BioSQL triggers tons of RuntimeWarnings related to sqlite3 functions
* test_BioSQL_SeqIO fails -- attempts to retrieve P01892 instead of Q29899 (?)
* test_Restriction triggers a TypeError, somehow (also causing test_CAPS to err)
* test_Entrez fails with many noisy errors -- looks related to expat, may be just my installation
* importing @Bio.trie@ fails, probably due to a @marshal.h@ issue with compilation



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