Mailman 3 October 2002 - SciPy-User

New to scipy and having problems getting started
by Mariska, John Oct. 17, 2002

Oct. 17, 2002

I'm running Active Python 2.1.1, wxPython, Numeric 20.2.0, and gnuplot. All were installed some time ago and work fine. I installed SciPy-0.2.0_alpha_144.4373.win32-py2.1.exe with no error messages. When I try to get into scipy and run the test program, however, I get the following traceback. Is there something else I need to do to configure scipy? John M. PythonWin 2.1.1 (#20, Jul 26 2001, 11:38:51) [MSC 32 bit (Intel)] on win32. Portions Copyright 1994-2001 Mark Hammond (MarkH(a)ActiveState.com) - see 'Help/About PythonWin' for further copyright information. >>> from scipy import * Traceback (most recent call last): File "<interactive input>", line 1, in ? File "E:\Python21\scipy\__init__.py", line 36, in ? from scipy_base import * File "E:\Python21\scipy_base\__init__.py", line 109, in ? import limits File "E:\Python21\scipy_base\limits.py", line 45, in ? float_epsilon = epsilon(Numeric.Float32) File "E:\Python21\scipy_base\limits.py", line 28, in epsilon x = x * cast(.5) ArithmeticError: Integer overflow in multiply. >>>

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SciPy setup, Atlas3.4.1
by Ly Johnny Oct. 17, 2002

Oct. 17, 2002

Hi, I'm trying to get SciPy 0.2 up and running. I've read through the install.txt file from the source. I tried installing Atlas 3.4.1 yesterday, the install was not complete as if took over 9 hours and I lost my patients and aborted the install. I was wondering is there a quicker way to get SciPy working? Regards, Johnny

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Nonlinear programming codes in scipy
by Nils Wagner Oct. 17, 2002

Oct. 17, 2002

Hi, I wonder if scipy will support nonlinear programming codes like Spellucci's mixed SQP/ECQP-method for general continuous nonlinear programming problems. See http://plato.la.asu.edu/donlp2.html for further details. Nils

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ANNOUNCE: Class -- Building C/C++ Extensions for Python
by eric jones Oct. 16, 2002

Oct. 16, 2002

Building C/C++ Extensions for Python Description: Enthought is proud to announce "Building C/C++ extensions for Python," an intense 3 day course taught by David Beazley, David Abrahams, and Eric Jones, the lead authors of SWIG, Boost.Python, and Weave. This hands-on course is geared toward C/C++ programmers and teaches the start-to-finish process of exposing C/C++ libraries for use in Python. Students are sure to benefit from this opportunity to learn from three of the leading experts in the field. The class teaches the fundamentals of designing and building Python extensions and addresses the common problems that arise during the process. Boost.Python, SWIG, and Weave are central to the discussion, and each is covered in depth. Fundamental topics such as handling reference counts and building Python 2.2 style extension types by hand are also covered. Other topics discussed include Pyrex, distributing extensions using distutils, debugging extensions, and solving shared library issues. The course is divided equally between lectures and hands-on programming sessions. Users will need to bring either a Linux or a Windows NT/2000/XP, network enabled, laptop to the class with Python 2.2 and a C++ compiler installed for the programming sessions. More information about setup requirements is available at the website. Space is limited. Website: http://www.enthought.com/training/building_extensions.html Signup Information: Call (512) 536-1057 to reserve your place. Dates: December 9th, 10th, and 11th, 2002 (Monday through Wednesday) Instruction Hours: Instruction runs from 9am-9pm on the first two days (with breaks for lunch, dinner, and between sessions), and 9am-6pm on the final day of the class. Location: The Driskill Hotel www.driskillhotel.com 604 Brazos Street Austin, Texas The Driskill is conveniently located in the heart of downtown Austin. And, yes, it has high speed internet connections in the guest rooms. What's Included: 3 nights of lodging All meals and snacks Unlimited caffeinated drinks Class materials 3 days of instruction Cost: $2400.00 US. About the Authors: David Beazley David is an assistant professor in the Department of Computer Science at the University of Chicago. He has worked on Python extension building since 1996 and is the creator of SWIG (www.swig.org). He is also the author of the "Python Essential Reference." David holds a PhD in Computer Science from the University of Utah. David Abrahams David is a founding member and moderator of Boost (www.boost.org) and heads Boost Consulting, a company dedicated to providing professional support and development services for the Boost C++ libraries and associated tools. He has been an ANSI/ISO C++ committee member since 1996, when he contributed a theory, specification, and implementation of exception handling for the C++ standard library. In his 14-year career he has developed applications for the desktop and embedded devices in the fields of music software, speech recognition, and circuit simulation. David holds a BSE in Computer Science from the University of Pennsylvania. Eric Jones Eric has a broad background in engineering and software development and leads Enthought's product engineering and software design. Eric is a lead developer on the SciPy (www.scipy.org) and Weave projects and has taught numerous courses about Python and how to leverage it for scientific computing. Prior to co-founding Enthought, Eric worked in the fields of numerical electromagnetics and genetic optimization. Eric holds a PhD degree in Electrical Engineering from Duke University. ---------------------------------------------- eric jones 515 Congress Ave www.enthought.com Suite 1614 512 536-1057 Austin, Tx 78701

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Setting up Scipy
by Johnny boi Oct. 15, 2002

Oct. 15, 2002

Hi there, I'm new to Scipy, and I'm having some possibly minor problems in regards to setting it up on a RH 7.2 Linux box. My question is, should I simple tar the Scipy file into the directory of python/site-packages? I noticed that it extracted 4 directories, do i have to run any setup scripts? Many thanks, Johnny --------------------------------- Yahoo! Messenger for SMS- Always be connected to your Messenger Friends

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scipy.test(1) FAIL: check_basic (test_morestats.test_shapiro)
by My VDI Freemail Oct. 15, 2002

Oct. 15, 2002

Hi, I am using latest CVS that is >>> scipy.__version__ '0.2.0_alpha_144.4360' Running scipy.test(1) gives the following messages BTW some information concerning my OS SuSE 8.1 Python 2.2.1 (#1, Sep 10 2002, 17:49:17) [GCC 3.2] on linux2 creating test suite for: scipy.linalg.matfuncs !! FAILURE building test for scipy.linalg.matfuncs <string>:1: ImportError: No module named test_matfuncs (in ?) ====================================================================== FAIL: check_basic (test_morestats.test_shapiro) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.2/site-packages/scipy/stats/tests/test_morestats.py", line 30, in check_basic assert_almost_equal(w,0.90047299861907959,8) File "/usr/lib/python2.2/site-packages/scipy_test/testing.py", line 335, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: DESIRED: 0.900472998619 ACTUAL: 0.900472939014 Any idea ? Nils

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Can't find atlas for scipy install
by Stephen Boulet Oct. 15, 2002

Oct. 15, 2002

I've installed atlas (atlas-3.2.1 and atlas-c++-0.4.5). "/usr/lib" is in my "/etc/ld.so.conf" and I've run "ldconfig". When I try installing scipy (cvs), I get the messages below. Can someone tell me what I'm doing wrong? (I did notice that there is a "/usr/bin/atlas-config" executable in the atlas distribution; I'm not sure how to use it though.) -- Stephen # python setup.py install atlas_info: NOT AVAILABLE linalg/setup_linalg.py:36: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: NOT AVAILABLE linalg/setup_linalg.py:40: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the scipy_distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 130, in ? install_package() File "setup.py", line 95, in install_package config.extend([get_package_config(x,parent_package)for x in standard_packages]) File "setup.py", line 45, in get_package_config config = mod.configuration(parent) File "linalg/setup_linalg.py", line 43, in configuration raise BlasSrcNotFoundError,BlasSrcNotFoundError.__doc__ scipy_distutils.system_info.BlasSrcNotFoundError: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the scipy_distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable.

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polyeig
by Nils Wagner Oct. 15, 2002

Oct. 15, 2002

Hi, I wonder, if the matlab function polyeig will be available in scipy. Nils

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conversion of c++ vector in weave
by Michael Sorich Oct. 14, 2002

Oct. 14, 2002

Hi I wish to convert a small part of my code to C++ for speed. The code is not amenable to numeric arrays and uses lists extensively. I am thinking about using c++ vectors in place of python lists (I presume that this will be a lot faster than using Py::List). What little experience I have in extending python with C/C++ is limited to using weave. If I use vectors, is there any method to automatically convert my result (vector< vector<int> >) to something that can be returned to python (tuple/list/array). I believe that Boost can do this (at least the upcoming v2, see http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/*checkout*/boost/boost/li bs/python/doc/v2/faq.html), however I am not sure how I would be able to integrate this with weave.inline. It does not appear obvious that there is anything in CXX that will do this. Any help would be appreciated. Thanks Michael Sorich PhD Student School of Pharmaceutical, Molecular and Biomedical Sciences University of South Australia Email: michael.sorich(a)postgrads.unisa.edu.au mike_sorich(a)hotmail.com --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.393 / Virus Database: 223 - Release Date: 30/09/2002

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Problems installing CVS version of scipy
by Francesc Alted Oct. 14, 2002

Oct. 14, 2002

Hi, I've installed the CVS version of scipy following directions stated on this mailing list, and everything compiled ok (apparently!). But, when I try to import scipy, I get the next error: $ python2.2 Python 2.2.1 (#1, Apr 21 2002, 08:38:44) [GCC 2.95.4 20011002 (Debian prerelease)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy exceptions.ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/_fli nalg.so: undefined symbol: dlaswp_ Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.2/site-packages/scipy/__init__.py", line 49, in ? import special, io, linalg, stats, fftpack File "/usr/local/lib/python2.2/site-packages/scipy/special/__init__.py", line 328, in ? import orthogonal File "/usr/local/lib/python2.2/site-packages/scipy/special/orthogonal.py", lin e 59, in ? from scipy.linalg import eig File "/usr/local/lib/python2.2/site-packages/scipy/linalg/__init__.py", line 4 2, in ? from basic import * File "/usr/local/lib/python2.2/site-packages/scipy/linalg/basic.py", line 17, in ? import calc_lwork ImportError: /usr/local/lib/python2.2/site-packages/scipy/linalg/calc_lwork.so: undefined symbol: ieeeck_ and, curiously enough, if I try to import again, it succeeds!: >>> import scipy >>> scipy.test(10) creating test suite for: scipy_base.type_check No test suite found for scipy_base.polynomial creating test suite for: scipy_base.shape_base creating test suite for: scipy_base.function_base No test suite found for scipy_base.scimath No test suite found for scipy_base.__cvs_version__ creating test suite for: scipy_base.limits creating test suite for: scipy_base.index_tricks No test suite found for scipy_base.scipy_base_version creating test suite for: scipy_base.matrix_base ................................................................................ ................................... ---------------------------------------------------------------------- Ran 115 tests in 0.323s OK <unittest.TextTestRunner instance at 0x8289a8c> The CVS version I'm using is: >>> scipy.__cvs_version__.cvs_version (1, 144, 1520, 4350) Using Debian 3.0 Linux here, and installed Numeric 22.0, Atlas 3.4.1 and F2PY 2.23.190-1369. The rest of the packages are from distribution. Any hint? -- Francesc Alted PGP KeyID: 0x61C8C11F Aplications developer Public PGP key available: http://www.openlc.org/falted_at_openlc.asc Key fingerprint = 1518 38FE 3A3D 8BE8 24A0 3E5B 1328 32CC 61C8 C11F

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