updating NumPy in EPD
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From: Nick Matzke on 8 Jun 2010 20:05 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 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(a)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 ====================================================
From: Nick Matzke on 8 Jun 2010 20:10 Oh yes -- 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. Cheers! Nick 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 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(a)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 ====================================================
From: Robert Kern on 8 Jun 2010 23:13 On 6/8/10 8:05 PM, 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? EPD support questions should be directed to the EPD-Users mailing list: https://mail.enthought.com/mailman/listinfo/epd-users But basically, you would remove the numpy package that is installed and reinstall numpy from source. -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco
From: Nick Matzke on 8 Jun 2010 23:32
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(a)berkeley.edu > <mailto:matzke(a)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(a)scipy.org <mailto:NumPy-Discussion(a)scipy.org> > http://mail.scipy.org/mailman/listinfo/numpy-discussion > > > > ------------------------------------------------------------------------ > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)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 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(a)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 ==================================================== |