updating NumPy in EPD

Tue Jun 8 23:32:36 EDT 2010

Hi again,

I got the solution on the NumPy list, I thought I would 
share for posterity...

Jeff Hsu wrote:
 > Check which version of numpy python is importing with 
"import numpy;
 > printnumpy.__file__".  I had a similar question and this 
worked after I
 > removed that installation of numpy.  I think the 
enthought distro
 > installs it somewhere else that has priority.

Ah, this was totally the trick!  To summarize for posterity:

=================================
Fix for an old version of NumPy installed with the EPD 
Enthough Python Distribution:

0. Figure out, what's your current version, and where is it 
located?

ipython
import numpy
print numpy.__file__
numpy.__version__

1. Download newest Numpy.tar.gz (1.4.1) from sourceforge, unzip

2. Install with:
cd ~/Desktop/downloads/numpy-1.4.1
python setup.py (3 times -- configure, build, install)

3. delete or rename old Numpy, redirect IPython's location 
to new install:

cd 
/Library/Frameworks/Python.framework/Versions/2.5.2001/lib/python2.5/site-packages/numpy-1.0.4.0004-py2.5-macosx-10.3-fat.egg

mv numpy numpy_old

ln -s 
/Library/Frameworks/Python.framework/Versions/2.5.2001/lib/python2.5/site-packages/numpy 
numpy

Manual install of PyCogent:

1. download from sourceforge
2. working install:

cd /bioinformatics/pythonstuff/PyCogent-1.4.1/
python setup.py build
sudo python setup.py install
python setup.py build_ext -if

(no NumPy version error this time!)

Finally:

ipython
import numpy
dir(numpy)
========================

Thanks!
Nick

 > On Tue, Jun 8, 2010 at 10:30 PM, Nick Matzke 
<matzke at berkeley.edu
 > <mailto:matzke at berkeley.edu>> wrote:
 >
 >     Hi NumPy gurus,
 >
 >     I have a slightly weird question.  I would like to 
install
 >     the PyCogent python library.  However, this requires 
NumPy
 >     1.3 or higher.  I only have NumPy 1.1.1, because I 
got it as
 >     part of the Enthought Python Distribution (4.1) back 
in 2008.
 >
 >     Now, when I download & install a new version of 
NumPy, the
 >     install seems to work.  However, the PyCogent 
installer can
 >     still only see the NumPy 1.1.1 version.
 >
 >     Any advice on what I might do to fix this?
 >
 >     I would just update my version of EPD, which is
 >     where my NumPy came from -- however, Enthought only has
 >     available for academic download a version of EPD that 
works
 >     on OS X 10.5 or later, and my Mac is a 10.4.11 and I'd
 >     rather not completely reinstall the OS just to get one
 >     little library to work.
 >
 >     Any help much appreciated!!
 >
 >     Cheers!
 >     Nick
 >

 >     _______________________________________________
 >     NumPy-Discussion mailing list
 >     NumPy-Discussion at scipy.org 
<mailto:NumPy-Discussion at scipy.org>
 >     http://mail.scipy.org/mailman/listinfo/numpy-discussion
 >
 >
 >
 > 
------------------------------------------------------------------------
 >
 > _______________________________________________
 > NumPy-Discussion mailing list
 > NumPy-Discussion at scipy.org
 > http://mail.scipy.org/mailman/listinfo/numpy-discussion

Nick Matzke wrote:
> Hi all,
> 
> I have a slightly weird question.  I would like to install the PyCogent 
> library.  However, this requires NumPy 1.3 or higher.  I only have NumPy 
> 1.1.1, because I got it as part of the Enthought Python Distribution 
> (4.1) back in 2008.
> 
> Now, when I download & install a new version of NumPy, it seems to 
> work.  However, the PyCogent installer can only see the NumPy 1.1.1 
> version.
> 
> Any advice on what I might do to fix this?
> 
> Cheers!
> Nick
> 
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Graduate Student Instructor, IB200A
Principles of Phylogenetics: Systematics
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Email: matzke at berkeley.edu

Mailing address:
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3060 VLSB #3140
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When people thought the earth was spherical, they were 
wrong. But if you think that thinking the earth is spherical 
is just as wrong as thinking the earth is flat, then your 
view is wronger than both of them put together."

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====================================================