Mailman 3 February 2007 - SciPy-User

NameError on scipy import
by Stephen Uhlhorn 02 Feb '07

02 Feb '07

I built numpy/scipy on my OS X 10.4 machine following the instructions at the scipy.org page. I installed ActiveState python 2.4 and had no build errors thru the entire process including numpy 1.0.1 and scipy 0.5.2. The post-install numpy test passed without error, but importing scipy gave this error: >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/scipy/__init__.py", line 33, in ? del lib NameError: name 'lib' is not defined Should I update to the latest svn version? Any suggestions? Thanks- -stephen

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arpack.speigs.ARPACK_gen_eigs
by Nils Wagner 02 Feb '07

02 Feb '07

Hi, The shift must be real in arpack.speigs.ARPACK_gen_eigs. For what reason ? How can I compute the eigenvalues enclosed by the green circle ? Nils

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asanyarray
by Nils Wagner 02 Feb '07

02 Feb '07

Hi, I am confused about the behaviour of asanyarray Python 2.4.1 (#1, Oct 13 2006, 16:51:58) [GCC 4.0.2 20050901 (prerelease) (SUSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy import * >>> A = io.mmread('mhd416a.mtx.gz') >>> A <416x416 sparse matrix of type '<type 'numpy.float64'>' with 8562 stored elements in COOrdinate format> >>> shape(A) (416, 416) >>> A=asanyarray(A) >>> A array(<416x416 sparse matrix of type '<type 'numpy.float64'>' with 8562 stored elements in COOrdinate format>, dtype=object) >>> shape(A) () Help on function asanyarray in module numpy.core.numeric: asanyarray(a, dtype=None, order=None) Returns a as an array, but will pass subclasses through. Why is the shape altered by asanyarray ? Nils

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Release 0.6.1 of pyaudio, renamed pyaudiolab
by David Cournapeau 02 Feb '07

02 Feb '07

Hi There, A few months ago, I posted the first release of pyaudio, a python module to give numpy/scipy environment audio file IO capabilities (ala matlab wavread and co). I recently took time to update it significantly, and as several people showed interest in pyaudio recently, I thought this may interest some people here. The main improvements since last public annoucement: - renamed to pyaudiolab to avoid nameclash with other package pyaudio. - ability to seek into audio files and sync files for flushing IO buffers - matlab-like API: wavread and wavwrite - improvements of the API: more similar to numpy conventions, ability to retrieve most meta-data of a file. - some bug fixing (one bug was quite severe, leading to data corruption on ubuntu with python2.5, due to some weirdness in ubuntu python2.5 packaging) - a real documentation If some people manage to use it on something else than linux, I would happy to hear (particularly Mac OS X, which I cannot test myself). Cheers, David ====== pyaudiolab ====== * WHAT FOR ?: The Goal of pyaudiolab is to give to a numpy/scipy environment some basic audio IO facilities (ala sound, wavread, wavwrite of matlab). With pyaudiolab, you should be able to read and write most common audio files from and to numpy arrays. The underlying IO operations are done using libsndfile from Erik Castro Lopo (http://www.mega-nerd.com/libsndfile/), so he is the one who did the hard work. As libsndfile has support for a vast number of audio files (including wav, aiff, but also htk, ircam, and flac, an open source lossless codec), pyaudiolab enables the import from and export to a fairly large number of file formats. * WHERE TO GET ?: http://www.ar.media.kyoto-u.ac.jp/members/david/softwares/pyaudiolab/index.… bzr archive: http://www.ar.media.kyoto-u.ac.jp/members/david/archives/pyaudiolab/pyaudio… # HOW TO USE ?: http://www.ar.media.kyoto-u.ac.jp/members/david/softwares/pyaudiolab/index.…

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numpy installer not finding ATLAS in spite of correct environment variable
by Anand Patil 01 Feb '07

01 Feb '07

Hi all, I'm trying to install numpy on a machine in which /usr/local/atlas/lib/Linux_HAMMER64SSE2_4 contains: libatlas.a libcblas.a liblapack.a libptcblas.a libtstatlas.a Makefile Make.inc I've set the relevant environment variables as follows: setenv ATLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ setenv BLAS /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ setenv LAPACK /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ setenv BLAS_SRC /usr/local/atlas/src/blas setenv LAPACK_SRC /usr/local/atlas/src/lapack However, numpy's installer does this: atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries lapack,blas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack,blas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib NOT AVAILABLE /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1301: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries blas not found in /usr/local/lib libraries blas not found in /usr/lib NOT AVAILABLE /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1310: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1313: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack,blas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack_atlas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack,blas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries lapack,blas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack_atlas not found in /usr/local/atlas/lib/Linux_HAMMER64SSE2_4/ libraries lapack,blas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack,blas not found in /usr/lib/sse2 libraries lapack_atlas not found in /usr/lib/sse2 libraries lapack,blas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1210: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/usr/local/atlas/lib/Linux_HAMMER64SSE2_4/'] language = f77 /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1234: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) /projects/mangellab/anand/numpy-1.0.1/numpy/distutils/system_info.py:1237: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE Then, even though it apparently found lapack, it builds lapack_lite: gcc: numpy/linalg/dlamch.c gcc: numpy/linalg/lapack_litemodule.c gcc: numpy/linalg/zlapack_lite.c gcc: numpy/linalg/dlapack_lite.c gcc: numpy/linalg/blas_lite.c gcc: numpy/linalg/f2c_lite.c What am I doing wrong? Thanks much, Anand

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Re: [SciPy-user] What it the best way to install on a Mac?
by Chris Fonnesbeck 01 Feb '07

01 Feb '07

Jerry wrote: > I've been mostly lurking here for quite a while and am thinking I > should get some stuff installed and see what all the excitement is > about. I can't help but notice that some of the posts are about > installation problems on various platforms. I also recall (I think) > that someone was keeping an up-to-date installer for the Mac. >Probably Chris Fonnesbeck's Scipy Superpack. > If so, > is this a "proper" Mac installer? >Yes, however, the last release of it was improperly compiled, IIRC. I posted a new build yesterday, which should work. C. -- Chris Fonnesbeck + Atlanta, GA + http://trichech.us

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Re: [SciPy-user] What it the best way to install on a Mac?
by joris＠ster.kuleuven.ac.be 01 Feb '07

01 Feb '07

On Wednesday 31 January 2007 01:27, Robert Kern wrote: >Learn to build from source. Because of the dependency on FORTRAN runtime >libraries, this is the lowest-hassle method. This may be true at the moment, but I hope this will not be the general philosophy for the future? Having to build from source may scare off potential numpy/scipy/matplotlib users... Yesterday someone said that he was trying to install scipy from source for about 2 weeks now. This does not look good for someone who is contemplating whether to use numpy/scipy/matplotlib or not. It's not that I demand other people to make easy-to-install packages, but I think that we're heading in the wrong direction if we don't even think that easy-to-install packages are really necessary and that installing from source works just fine. Perhaps Robert didn't mean it as I put it, but I just wanted to express my concern. J. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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something like GTS??
by Gennan Chen 01 Feb '07

01 Feb '07

Hi! Is there something like GTS (GNU Triangulated Surface Library: http:// gts.sourceforge.net/) in Scipy? I hate to cook my own for all those bookkeeping of vertices and surfaces. Any recommendation will be welcomed.. Gen-Nan Chen

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