[Biopython-dev] [Biopython (old issues only) - Feature #3236] (Closed) Make Biopython work in PyPy 1.5

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Fri Jul 22 15:44:41 UTC 2016

Issue #3236 has been updated by Peter Cock.

Status changed from In Progress to Closed
% Done changed from 20 to 100

Biopython has been working pretty well on PyPy 2.4 onwards (a combination of some fixes on our side but mostly progress on the PyPy side), closing this issue.

Feature #3236: Make Biopython work in PyPy 1.5

* Author: Eric Talevich
* Status: Closed
* Priority: Low
* Assignee: Biopython Dev Mailing List
* Category: 
* Target version: 
* URL: 
PyPy is now roughly as production-ready as Jython:

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

pypy1.5-setup.diff (1.15 KB)

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