Mailman 3 January 2009 - NumPy-Discussion

List of Lists in C
by Hanni Ali 26 Jan '09

26 Jan '09

Hi, Quick question, I've been doing a fair bit of extension writing in C recently, but wondered how best to implement: >>> l = [[]] * 5 to create a list of a given length containing the initialization variable desired. A loop seems the straight forward manner, but I would have thought there was a more efficient way... Currently I just do it in Python and pass through the already initialized list as it seems perfectly efficient. Cheers, Hanni

2 4

How to remove pages from the wiki ?
by Pierre GM 26 Jan '09

26 Jan '09

All, How can I remove pages from the wiki ? I ran into some that are clearly unrelated to numpy, scipy or programming... Thanks a lot in advance, P

1 0

Academic citation ?
by Pierre GM 26 Jan '09

26 Jan '09

All, What is the most up-to-date way to cite Numpy and Scipy in an academic journal ? Thanks a lot in advance P.

2 2

glibc error
by Gideon Simpson 25 Jan '09

25 Jan '09

Having built an up to date lapack and ATLAS against gcc 4.3.2, I tried installing numpy 1.2.1 on Python 2.5.4. When testing I get: Python 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.test() Running unit tests for numpy NumPy version 1.2.1 NumPy is installed in /usr/local/nonsystem/simpson/lib/python2.5/site- packages/numpy Python version 2.5.4 (r254:67916, Jan 24 2009, 00:27:20) [GCC 4.3.2] nose version 0.10.4 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................F ................K ........................................................................ ........................................................................ ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................*** glibc detected *** python: free(): invalid next size (fast): 0x000000001196b550 *** I then have to kill python to get control again. -gideon

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Having trouble installing Numpy on OS X
by Nat Wilson 25 Jan '09

25 Jan '09

Would anyone be willing to help me interpret an error while trying to build and install Numpy? I've searched around, and haven't seen this elsewhere. I've been running into this wall for about half the day now. I've tried reinstalling Python, using numpy 1.2.0 and 1.2.1. I have Python 2.6.1, running on OS X 10.4.11, with a G4 PPC processor. Here's the print out: Ganymede:~/Desktop/numpy-1.2.1 username$ python setup.py build Running from numpy source directory. Traceback (most recent call last): File "setup.py", line 96, in <module> setup_package() File "setup.py", line 68, in setup_package from numpy.distutils.core import setup File "/Users/username/Desktop/numpy/numpy/distutils/__init__.py", line 6, in <module> File "/Users/username/Desktop/numpy/numpy/distutils/ccompiler.py", line 11, in <module> File "/Users/username/Desktop/numpy/numpy/distutils/log.py", line 7, in <module> File "/Users/username/Desktop/numpy/numpy/distutils/misc_util.py", line 8, in <module> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ python2.6/tempfile.py", line 34, in <module> from random import Random as _Random File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ python2.6/random.py", line 871, in <module> _inst = Random() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ python2.6/random.py", line 96, in __init__ self.seed(x) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/ python2.6/random.py", line 115, in seed super(Random, self).seed(a) SystemError: error return without exception set Any ideas? I've had numpy/scipy installed in the past, but recently had to wipe everything and start from scratch. Everything should be pretty clean right now. Am I missing something obvious? Thanks, NJW

5 14

Suggested change for NaN, Infs float->int conversion
by Matthew Brett 25 Jan '09

25 Jan '09

Hi, When converting arrays from float to ints, I notice that NaNs, Infs, and -Infs all get the minimum integer value: >>> flts = np.array([np.nan, np.inf, -np.inf]) >>> flts.astype(np.int16) array([-32768, -32768, -32768], dtype=int16) However, setting NaNs into integer arrays gives a value of 0 >>> ints = np.array([1]) >>> ints.dtype dtype('int32') >>> ints[0] = np.nan >>> ints array([0]) whereas Inf or -Inf raise an error (as Josef pointed out recently): >> ints[0] = np.inf ------------------------------------------------------------ Traceback (most recent call last): File "<ipython console>", line 1, in <module> OverflowError: cannot convert float infinity to long >>> ints[0] = -np.inf ------------------------------------------------------------ Traceback (most recent call last): File "<ipython console>", line 1, in <module> OverflowError: cannot convert float infinity to long Matlab seems more consistent and sensible here: >> flts = [NaN Inf -Inf]; >> int32(flts) ans = 0 2147483647 -2147483648 >> ints = int32([1 1 1]); >> ints(:) = [NaN Inf -Inf] ints = 0 2147483647 -2147483648 Is there a route to change towards the matlab behavior? Or at least make numpy behavior self-consistent? Best, Matthew

3 2

numpy and the ACML
by Gideon Simpson 25 Jan '09

25 Jan '09

Does anyone have a guide on how to get numpy to use the ACML as its blas/lapack backend? -gideon

4 7

whohas command
by Ondrej Certik 24 Jan '09

24 Jan '09

Hi, I just discovered a new whohas command in Debian, that can show a package in virtually all important distributions (Arch, Debian, Fedora, Gentoo, openSUSE, Slackware (and linuxpackages.net), Source Mage, Ubuntu, FreeBSD, NetBSD, OpenBSD, Fink and MacPorts distributions). So for example SymPy is in a lot of them already: $ whohas sympy Arch python-sympy-git 20090121-1 unsupported http://aur.archlinux.org/packages.php?ID=23341 MacPorts py-sympy 0.5.15 http://trac.macports.org/browser/trunk/dports/python/py-sympy/Portfile MacPorts py25-sympy 0.6.3 http://trac.macports.org/browser/trunk/dports/python/py25-sympy/Portfile FreeBSD py25-sympy 0.6.3 math http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-sympy NetBSD py-sympy 0.5.15 math http://pkgsrc.se/math/py-sympy Ubuntu python-sympy 0.4.2-1 universe http://packages.ubuntu.com/gutsy/python-sympy Ubuntu python-sympy 0.5.8-1 universe http://packages.ubuntu.com/hardy/python-sympy Ubuntu python-sympy 0.5.15-1~hardy1 universe http://packages.ubuntu.com/hardy-backports/python-sympy Ubuntu python-sympy 0.5.15-1 universe http://packages.ubuntu.com/intrepid/python-sympy Ubuntu python-sympy 0.6.3-1 universe http://packages.ubuntu.com/jaunty/python-sympy Debian python-sympy 0.6.1-1 testing http://packages.debian.org/lenny/python-sympy Fink sympy-py24 0.5.6-1 http://pdb.finkproject.org/pdb/package.php/sympy-py24 Fink sympy-py25 0.5.6-1 http://pdb.finkproject.org/pdb/package.php/sympy-py25 Gentoo sympy 0.6.3 http://gentoo-portage.com/dev-python/sympy Gentoo sympy 0.6.2 http://gentoo-portage.com/dev-python/sympy openSUSE python-sympy 0.6.3 science http://packages.opensuse-community.org/packageinfo.jsp?checksum=a2258d3deae… It's also interesting to click on the links to get to the pages of sympy for each distribution. And numpy: $ whohas numpy Arch python-numexpr 1.1.1-1 unsupported http://aur.archlinux.org/packages.php?ID=23380 Arch python-numpy 1.2.1-3 community http://aur.archlinux.org/packages.php?ID=8497 Arch scikits-audiolab-svn 1491-1 unsupported http://aur.archlinux.org/packages.php?ID=21018 FreeBSD py25-numpy 1.2.1,1 math http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-numpy FreeBSD py25-symeig 1.4_1 math http://www.freebsd.org/cgi/pds.cgi?ports/math/py25-symeig NetBSD py-numpy 1.1.0 wip http://pkgsrc.se/wip/py-numpy NetBSD py-numpy 1.1.0 math http://pkgsrc.se/math/py-numpy Ubuntu python-numpy 1:1.0.1-8ubuntu1 universe http://packages.ubuntu.com/feisty/python-numpy Ubuntu python-numpy 1:1.0.3-1ubuntu2 universe http://packages.ubuntu.com/gutsy/python-numpy Ubuntu python-numpy 1:1.0.4-6ubuntu3 universe http://packages.ubuntu.com/hardy/python-numpy Ubuntu python-numpy 1:1.1.1-1 http://packages.ubuntu.com/intrepid/python-numpy Ubuntu python-numpy 1:1.1.1-2ubuntu1 http://packages.ubuntu.com/jaunty/python-numpy Ubuntu python-numpy-dbg 1:1.0.1-8ubuntu1 universe http://packages.ubuntu.com/feisty/python-numpy-dbg Ubuntu python-numpy-dbg 1:1.0.3-1ubuntu2 universe http://packages.ubuntu.com/gutsy/python-numpy-dbg Ubuntu python-numpy-dbg 1:1.0.4-6ubuntu3 universe http://packages.ubuntu.com/hardy/python-numpy-dbg Ubuntu python-numpy-dbg 1:1.1.1-1 http://packages.ubuntu.com/intrepid/python-numpy-dbg Ubuntu python-numpy-dbg 1:1.1.1-2ubuntu1 http://packages.ubuntu.com/jaunty/python-numpy-dbg Ubuntu python-numpy-dev 1:1.0.1-8ubuntu1 universe http://packages.ubuntu.com/feisty/python-numpy-dev Ubuntu python-numpy-dev 1:1.0.3-1ubuntu2 universe http://packages.ubuntu.com/gutsy/python-numpy-dev Ubuntu python-numpy-dev http://packages.ubuntu.com/hardy/python-numpy-dev Ubuntu python-numpy-doc 1:1.0.1-8ubuntu1 universe http://packages.ubuntu.com/feisty/python-numpy-doc Ubuntu python-numpy-doc 1:1.0.3-1ubuntu2 universe http://packages.ubuntu.com/gutsy/python-numpy-doc Ubuntu python-numpy-doc 1:1.0.4-6ubuntu3 universe http://packages.ubuntu.com/hardy/python-numpy-doc Ubuntu python-numpy-doc 1:1.1.1-1 http://packages.ubuntu.com/intrepid/python-numpy-doc Ubuntu python-numpy-doc 1:1.1.1-2ubuntu1 http://packages.ubuntu.com/jaunty/python-numpy-doc Ubuntu python-numpy-ext 1:1.0.1-8ubuntu1 universe http://packages.ubuntu.com/feisty/python-numpy-ext MacPorts py-numpy 1.2.1 http://trac.macports.org/browser/trunk/dports/python/py-numpy/Portfile MacPorts py25-numpy 1.2.1 http://trac.macports.org/browser/trunk/dports/python/py25-numpy/Portfile MacPorts py26-numpy 1.2.1 http://trac.macports.org/browser/trunk/dports/python/py26-numpy/Portfile Debian python-numpy 1:1.0.1-1 stable http://packages.debian.org/etch/python-numpy Debian python-numpy-dev 1:1.0.1-1 stable http://packages.debian.org/etch/python-numpy-dev Debian python-numpy-doc 1:1.0.1-1 stable http://packages.debian.org/etch/python-numpy-doc Debian python-numpy-ext 1:1.0.1-1 stable http://packages.debian.org/etch/python-numpy-ext Debian python-numpy 1:1.1.0-3 testing http://packages.debian.org/lenny/python-numpy Debian python-numpy-dbg 1:1.1.0-3 testing http://packages.debian.org/lenny/python-numpy-dbg Debian python-numpy-dev testing http://packages.debian.org/lenny/python-numpy-dev Debian python-numpy-doc 1:1.1.0-3 testing http://packages.debian.org/lenny/python-numpy-doc Debian python-numpy-ext 1:1.1.0-3 testing http://packages.debian.org/lenny/python-numpy-ext Fink dap-py25 2.2.6.6-1 http://pdb.finkproject.org/pdb/package.php/dap-py25 Fink dap-py26 2.2.6.6-1 http://pdb.finkproject.org/pdb/package.php/dap-py26 Fink pytables-py24 2.0.3-1 http://pdb.finkproject.org/pdb/package.php/pytables-py24 Fink pytables-py25 2.0.3-1 http://pdb.finkproject.org/pdb/package.php/pytables-py25 Fink scipy-core-py23 1.1.1-1 http://pdb.finkproject.org/pdb/package.php/scipy-core-py23 Fink scipy-core-py24 1.1.1-1 http://pdb.finkproject.org/pdb/package.php/scipy-core-py24 Fink scipy-core-py25 1.1.1-1 http://pdb.finkproject.org/pdb/package.php/scipy-core-py25 Fink scipy-core-py26 1.1.1-1 http://pdb.finkproject.org/pdb/package.php/scipy-core-py26 Gentoo numpy 1.2.1 http://gentoo-portage.com/dev-python/numpy Gentoo numpy 1.1.1 http://gentoo-portage.com/dev-python/numpy Gentoo numpy 1.0.4-r2 http://gentoo-portage.com/dev-python/numpy openSUSE python-numpy 1.2.1 packman http://packages.opensuse-community.org/packageinfo.jsp?checksum=f3f9a6df3da… openSUSE python-numpy-debuginfo 1.2.1 packman http://packages.opensuse-community.org/packageinfo.jsp?checksum=fc6af8293ae… openSUSE python-numpy-debugsource 1.2.1 packman http://packages.opensuse-community.org/packageinfo.jsp?checksum=68c2cade8c8… openSUSE python-numpy 1.2.1 games http://packages.opensuse-community.org/packageinfo.jsp?checksum=dd9071d749b… openSUSE python-numpy 1.2.0 hamradio http://packages.opensuse-community.org/packageinfo.jsp?checksum=574963a98ba… openSUSE python-numpy-devel 1.2.0 hamradio http://packages.opensuse-community.org/packageinfo.jsp?checksum=528c925b696… openSUSE python-numpy 1.2.1 ferichter/o http://packages.opensuse-community.org/packageinfo.jsp?checksum=22490d0f9d0… openSUSE python-numpy-devel 1.2.1 ferichter/o http://packages.opensuse-community.org/packageinfo.jsp?checksum=03018ce7d36… openSUSE python-numpy 1.2.1 MadCAD/open http://packages.opensuse-community.org/packageinfo.jsp?checksum=73f10047cc2… openSUSE python-numpy-devel 1.2.1 MadCAD/open http://packages.opensuse-community.org/packageinfo.jsp?checksum=0642cae514f… openSUSE python-numpy 1.2.1 werner2101/ http://packages.opensuse-community.org/packageinfo.jsp?checksum=99c6af1da69… openSUSE python-numpy-devel 1.2.1 werner2101/ http://packages.opensuse-community.org/packageinfo.jsp?checksum=0cd24f243e5… openSUSE python-numpy 1.2.1 science http://packages.opensuse-community.org/packageinfo.jsp?checksum=1f1197793b0… openSUSE python-numpy-devel 1.2.1 science http://packages.opensuse-community.org/packageinfo.jsp?checksum=4ad91bcb9f9… openSUSE python-numpy 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=a82655e40db… openSUSE python-numpy-devel 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=0bd33a0c8c8… openSUSE python-numpy-debuginfo 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=d079da08ab5… openSUSE python-numpy-debugsource 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=ba9fd6e9352… openSUSE python-numpy 1.2.1 anubisg1/op http://packages.opensuse-community.org/packageinfo.jsp?checksum=10d1efb1265… openSUSE python-numpy-debuginfo 1.2.1 anubisg1/op http://packages.opensuse-community.org/packageinfo.jsp?checksum=6439aa8a322… openSUSE python-numpy-debugsource 1.2.1 anubisg1/op http://packages.opensuse-community.org/packageinfo.jsp?checksum=ebc7ecee464… openSUSE python-numpy 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=f47f40d1377… openSUSE python-numpy-debuginfo 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=b027d798f58… openSUSE python-numpy-debugsource 1.2.1 Education http://packages.opensuse-community.org/packageinfo.jsp?checksum=d8c4d6aa5bc… openSUSE python-numpy 1.2.1 thomas-schr http://packages.opensuse-community.org/packageinfo.jsp?checksum=412bc59b5f6… openSUSE python-numpy-devel 1.2.1 thomas-schr http://packages.opensuse-community.org/packageinfo.jsp?checksum=22b703695a8… openSUSE python-numpy 1.2.0 cyberorg http://packages.opensuse-community.org/packageinfo.jsp?checksum=569e248766d… openSUSE python-numpy-devel 1.2.0 cyberorg http://packages.opensuse-community.org/packageinfo.jsp?checksum=bc8e52b109d… openSUSE python-numpy-devel 1.2.1 science http://packages.opensuse-community.org/packageinfo.jsp?checksum=5d70fb2f388… openSUSE python-numpy 1.2.1 science http://packages.opensuse-community.org/packageinfo.jsp?checksum=84e24a6f7ff… Source Mage numpy 1.2.1 test Source Mage numpy 1.2.1 stable Fedora numpy 1.2.0-1 2.2M 30-10-2008 OpenBSD py-numpy 1.0.4p0 http://www.openbsd.org/4.4_packages/i386/py-numpy-1.0.4p0.tgz-long.html Which reminds me that I still haven't packaged the new numpy for Debian (any help is appreciated). Ondrej

1 0

failure
by Gideon Simpson 24 Jan '09

24 Jan '09

Installing on a Sun machine with Red Hat linux, I got the following error: ====================================================================== FAIL: test_umath.TestComplexFunctions.test_against_cmath ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/nonsystem/simpson/lib/python2.5/site-packages/nose/ case.py", line 182, in runTest self.test(*self.arg) File "/usr/local/nonsystem/simpson/lib/python2.5/site-packages/ numpy/core/tests/test_umath.py", line 268, in test_against_cmath assert abs(a - b) < atol, "%s %s: %s; cmath: %s"%(fname,p,a,b) AssertionError: arcsinh -2j: (-1.31695789692-1.57079632679j); cmath: (1.31695789692-1.57079632679j) ---------------------------------------------------------------------- Ran 1740 tests in 9.839s FAILED (KNOWNFAIL=1, failures=1) <nose.result.TextTestResult run=1740 errors=0 failures=1> How would you recommend I troubleshoot this? How seriously should I take it? This is with a fresh Python 2.5.4 installation too. -gideon

2 1

Pattern for reading non-simple binary files
by Ryan May 23 Jan '09

23 Jan '09

Hi, I'm trying to read in a data from a binary-formatted file. I have the data format, (available at: http://www1.ncdc.noaa.gov/pub/data/documentlibrary/tddoc/td7000.pdf if you're really curious), but it's not what I would consider simple, with a lot of different blocks and messages, some that are optional and some that have different formats depending on the data type. My question is, has anyone dealt with data like this using numpy? Have you found a good pattern for how to construct a numpy dtype dynamically to decode the different parts of the file appropriately as you go along? Any insight would be appreciated. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

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