[Numpy-discussion] Numerics vs. numpy
Fri Apr 27 14:45:02 CDT 2007
Ed Schofield has created a patch for NumPy to work with BioPython (see below).
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From: firstname.lastname@example.org <email@example.com>
Date: Mar 27, 2007 8:08 AM
Subject: [Biopython-dev] [Bug 2251] New: [PATCH] NumPy support for BioPython
Summary: [PATCH] NumPy support for BioPython
Version: Not Applicable
Component: Main Distribution
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
- 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
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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