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Issue #3236 has been updated by Peter Cock.
<ul>
<li><strong>Status</strong> changed from <i>In Progress</i> to <i>Closed</i></li>
<li><strong>% Done</strong> changed from <i>20</i> to <i>100</i></li>
</ul>
<p>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.</p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/3236#change-15294">Feature #3236: Make Biopython work in PyPy 1.5</a></h1>
<ul><li>Author: Eric Talevich</li>
<li>Status: Closed</li>
<li>Priority: Low</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: </li>
<li>Target version: </li>
<li>URL: </li></ul>
<p>PyPy is now roughly as production-ready as Jython:<br /><a class="external" href="http://morepypy.blogspot.com/2011/04/pypy-15-released-catching-up.html">http://morepypy.blogspot.com/2011/04/pypy-15-released-catching-up.html</a></p>
<p>Let's make Biopython work on PyPy 1.5.</p>
<p>To make the pure-Python core of Biopython work, I did this:</p>
<ul>
<li>Download and unpack the pre-compiled Linux tarball from pypy.org</li>
<li>Copy the header file <code>marshal.h</code> from the CPython 2.X installation into the <code>pypy-c-.../include/</code> directory</li>
<li>pypy setup.py build; pypy setup.py install</li>
<li>Delete pypy-c-.../site-packages/Bio/cpairwise2*.so</li>
</ul>
<p>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 <code>cpairwise2</code> in the CPython 2.6 installation.</p>
<p>Numpy isn't available on PyPy yet, and it may be some time before it does.</p>
<p>Observations from <code>pypy setup.py test</code>:</p>
<ul>
<li>test_BioSQL triggers tons of RuntimeWarnings related to sqlite3 functions</li>
<li>test_BioSQL_SeqIO fails -- attempts to retrieve P01892 instead of Q29899 (?)</li>
<li>test_Restriction triggers a TypeError, somehow (also causing test_CAPS to err)</li>
<li>test_Entrez fails with many noisy errors -- looks related to expat, may be just my installation</li>
<li>importing <code>Bio.trie</code> fails, probably due to a <code>marshal.h</code> issue with compilation</li>
</ul>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1647/pypy1.5-setup.diff">pypy1.5-setup.diff</a>
(1.15 KB)<br />
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