Hi, Ed Schofield has created a patch for NumPy to work with BioPython (see below).
Bruce
---------- Forwarded message ---------- From: bugzilla-daemon@portal.open-bio.org bugzilla-daemon@portal.open-bio.org Date: Mar 27, 2007 8:08 AM Subject: [Biopython-dev] [Bug 2251] New: [PATCH] NumPy support for BioPython To: biopython-dev@biopython.org
http://bugzilla.open-bio.org/show_bug.cgi?id=2251
Summary: [PATCH] NumPy support for BioPython Product: Biopython Version: Not Applicable Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: edschofield@gmail.com
The following patch adds support for NumPy in addition to Numeric. It does so with a thin wrapper layer at the C level and Python level, similar in purpose to (but less ambitious than) the numerix wrapper layer used by matplotlib.
The patch is designed to prevent imports of incompatible compiled C modules in the case one installs Numeric after installing BioPython with NumPy support.
It also changes the following: - C #include statements - Python import statements - references to obsoleted function names - the width of the dimension data types in cluster.c from int to intp (for 64-bit architectures) - the distutils setup.py file to supply the correct NumPy header locations. - the documentation (updating references to NumPy)
It also fixes array boolean operators in MarkovModel.py, which were silently broken before.
It applies to BioPython 1.43, as follows:
$ tar xzvf biopython-1.43.tar.gz $ cd biopython-1.43 $ patch -p1 < /path/to/biopython-1.43-numpy-support-v5.patch
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Bruce Southey