[Numpy-discussion] updating NumPy in EPD

Nick Matzke matzke@berkeley....
Tue Jun 8 22:31:07 CDT 2010



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@berkeley.edu 
> <mailto:matzke@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
> 
> 
> 
>     --
>     ====================================================
>     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
>     http://ib.berkeley.edu/courses/ib200a/index.shtml
> 
>     Lab websites:
>     http://ib.berkeley.edu/people/lab_detail.php?lab=54
>     http://fisher.berkeley.edu/cteg/hlab.html
>     Dept. personal page:
>     http://ib.berkeley.edu/people/students/person_detail.php?person=370
>     Lab personal page:
>     http://fisher.berkeley.edu/cteg/members/matzke.html
>     Lab phone: 510-643-6299
>     Dept. fax: 510-643-6264
>     Cell phone: 510-301-0179
>     Email: matzke@berkeley.edu <mailto:matzke@berkeley.edu>
> 
>     Mailing address:
>     Department of Integrative Biology
>     3060 VLSB #3140
>     Berkeley, CA 94720-3140
> 
>     -----------------------------------------------------
>     "[W]hen people thought the earth was flat, they were wrong.
>     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."
> 
>     Isaac Asimov (1989). "The Relativity of Wrong." The
>     Skeptical Inquirer, 14(1), 35-44. Fall 1989.
>     http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
>     ====================================================
> 
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-- 
====================================================
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
http://ib.berkeley.edu/courses/ib200a/index.shtml

Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke@berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong. 
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."

Isaac Asimov (1989). "The Relativity of Wrong." The 
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
====================================================


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