[Numpy-discussion] Numerics vs. numpy

Bruce Southey bsouthey@gmail....
Fri Apr 27 14:45:02 CDT 2007


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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