Mailman 3 September 2005 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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Install of scipy core for current scipy users
by Travis Oliphant Oct. 6, 2005

Oct. 6, 2005

If you are a current user of scipy and want to try out the new scipy core. You can do so. However, the default install will change four __init__.py files on your system (which will probably "break" the rest of scipy). Hopefully we will get scipy as a whole to work with the new system shortly. There has also been talk of putting together a simple install to fixup the __init__ files so that old scipy and new scipy_core can live together peacefully (anyone who can help with that is welcomed). scipy\__init__.py scipy\linalg\__init__.py scipy\fftpack\__init__.py scipy\stats\__init__.py are the affected files. The ones from scipy can just be copied back, but then you won't get the functions from new scipy. -Travis

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Array functions
by Howey, David A Oct. 5, 2005

Oct. 5, 2005

I guess this is a numpy question, but how do I do truth tests on arrays? I'm trawling around the documentation but struggling to find an answer.. I want to test if any array contains ONLY zeros. Originally I had: if a == 0: # code in here I need this to be true both for a = 0 # ie a is just a number and for a = array((0,0,0,0,0)) It must return false for any array with any nonzero elements anywhere At the moment python does this (which is wrong): >>> vin = array((1.,0,0)) >>> vin array([ 1., 0., 0.]) >>> if vin == 0: print "yes" yes >>> Thanks Dave

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Release of SciPy Core 0.4 (Beta)
by Travis Oliphant Oct. 5, 2005

Oct. 5, 2005

This is to announce the release of SciPy Core 0.4.X (beta) It is available at sourceforge which you can access by going to http://numeric.scipy.org Thanks to all who helped me with this release, especially Robert Kern Pearu Peterson Now, let's start getting this stable.... -Travis Oliphant

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Scipy with Python 2.4 on Windows - solution
by rainman Oct. 5, 2005

Oct. 5, 2005

Hello scipy-user, To succesfully build SciPy with Python 2.4, replace file \SciPy_complete-0.3.2\scipy_core\scipy_distutils\mingw32_support.py with http://home.uic.tula.ru/~s001180/scipy-py24/mingw32ccompiler.py Those who do not believe their spirit is bold enough to face tremendous nightmares of compiling tons of sources, may take a chance with this (beware, downloading is slow): http://home.uic.tula.ru/~s001180/scipy-py24/SciPy_complete-0.3.2.win32-py2.… Note that this is UNofficial bugfix and UNofficial build. Just a quick hack for those who lost all hope. -- Best regards, rainman mailto:rainman.rocks@gmail.com

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Re: [SciPy-user] Release of SciPy Core 0.4 (Beta)
by Brian Granger Sept. 30, 2005

Sept. 30, 2005

Which version of gccc are you using? As I understand it, g77 3.4 is not compatible with gcc 4.0 (the default on OS X). Switching to gcc 3.4 might help: gcc_select 3.3 I will soon try scipy_core on Tiger with Python 2.4.1. Brian Brian Granger, Ph.D. Assistant Professor of Physics Santa Clara University bgranger(a)scu.edu Phone: 408-551-1891 Fax: 408-554-6965 >>> managan(a)llnl.gov 09/30/05 11:21 AM >>> OK, I am giving this a go. I seem to be not setting a flag about some math functions availability. Here are the details (aorry about the length of it but I snipped a lot!): OSX 10.3.9, Python 2.4.1 Installed g77v3.4-bin.tar.gz from http://hpc.sourceforge.net/ as described into /usr/local/... Installed fftw-3.0.1-fma.tar.gz from http://www.fftw.org/download.html into ~/Documents/local/... where I have other libraries I have installed. Got scipy_core-0.4.1.tar.gz from http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=6222, wanted to try out the new replacement for Numeric tar -zxvf scipy_core-0.4.1.tar.gz cd scipy_core-0.4.1 python setup.py build Assuming default configuration (scipy/distutils/command/{setup_command,setup}.py was not found) Appending scipy.distutils.command configuration to scipy.distutils Assuming default configuration (scipy/distutils/fcompiler/{setup_fcompiler,setup}.py was not found) ... Appending scipy.base configuration to scipy blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] Appending scipy.lib configuration to scipy Assuming default configuration (scipy/fftpack/{setup_fftpack,setup}.py was not found) ... scipy_core version 0.4.1 running build running config_fc running build_src building extension "scipy.base.multiarray" sources creating build creating build/src creating build/src/scipy creating build/src/scipy/base Generating build/src/scipy/base/config.h customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler Could not locate executable f77 customize GnuFCompiler customize GnuFCompiler ... compiling C sources gcc options: '-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes' creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base creating build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base/src compile options: '-Ibuild/src/scipy/base/src -Iscipy/base/include -Ibuild/src/scipy/base -Iscipy/base/src -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c' gcc: build/src/scipy/base/src/umathmodule.c In file included from build/src/scipy/base/src/umathmodule.c:8: scipy/base/include/scipy/arrayobject.h:84: warning: redefinition of `ushort' /usr/include/sys/types.h:82: warning: `ushort' previously declared here scipy/base/include/scipy/arrayobject.h:85: warning: redefinition of `uint' /usr/include/sys/types.h:83: warning: `uint' previously declared here build/src/scipy/base/src/umathmodule.c: In function `nc_floor_quotl': build/src/scipy/base/src/umathmodule.c:1257: warning: implicit declaration of function `floorl' build/src/scipy/base/src/umathmodule.c: In function `nc_sqrtl': build/src/scipy/base/src/umathmodule.c:1269: warning: implicit declaration of function `sqrtl' ... build/src/scipy/base/__umath_generated.c:171: error: initializer element is not constant build/src/scipy/base/__umath_generated.c:171: error: (near initialization for `arccosh_data[2]') error: Command "gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dy namic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -Ibuild/src/scipy/base/src -Iscipy/base/include -Ibuild/s rc/scipy/base -Iscipy/base/src -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 -c b uild/src/scipy/base/src/umathmodule.c -o build/temp.darwin-7.9.0-Power_Macintosh-2.4/build/src/scipy/base /src/umathmodule.o" failed with exit status 1 At 12:59 AM -0600 9/30/05, Travis Oliphant wrote: >This is to announce the release of SciPy Core 0.4.X (beta) > >It is available at sourceforge which you can access by going to > >http://numeric.scipy.org > >Thanks to all who helped me with this release, especially > >Robert Kern >Pearu Peterson > >Now, let's start getting this stable.... > >-Travis Oliphant > > > >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.net >http://www.scipy.net/mailman/listinfo/scipy-user -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Rob Managan email managan at llnl.gov LLNL phone: 925-423-0903 P.O. Box 808, L-095 FAX: 925-422-3389 Livermore, CA 94551-0808 _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user This message scanned for viruses and SPAM at SCU (MGW2)

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Problems Installing SciPy on OS X 10.4.2 w/ python 2.3.5
by Zane Crawford Sept. 30, 2005

Sept. 30, 2005

With much frustration, and some patient help from Chris Fonnesbeck, I have been trying to get SciPy installed on my Mac. I am running OS X 10.4.2, and am attempting to use the stock python (2.3.5) which is installed by the Apple developer tools. I believe I have all of the underlying dependencies installed and functioning (Numeric 24.0b2, AquaTerm 1.0b2, fftw, GnuPlot 4.0.0, F2PY, and probably other things I installed along the way), and am now running into problems with the actual build of SciPy itself. I have just tried three different ways: 1) I installed a binary package which Chris created for me, built on python 2.3.5. It installs fine, and I can "import scipy" without issues, however, I can't use anything from it, because of the __cvs_version__ bug, which is referred to in the mailing list archives, but which was apparently not fixed in a persistent way. (it seems there was some clever code which allowed the software to keep track of its own version based on the CVS versions of the files, but this became broken when the source was migrated to SVN?) 2) I tried to build the last CVS version of SciPy, from July 29th, 2005. This fails almost immediately, regardless of whether I'm using GCC 3.3 or GCC 4.0, with an error from posixpath.py, line 77: i = p.rfind('/') + 1 AttributeError: 'NoneType' object has no attribute 'rfind' 3) I tried pulling the most recent version of the source from SVN. This seems to get much further than the CVS build, but fails eventually: In file included from Lib/xplt/src/play/all/hash0.c:8: build/temp.darwin-8.2.0-Power_Macintosh-2.3/config_pygist/config.h:3:3: #error destroy this config.h and rerun configure script However, there are many many warnings prior to this failure, and I don't know what the acutal problem is I've completely removed (as far as I can tell) all installed SciPy packages (from Chris' build) and think I have a clean 2.3.5 python environment ready to install SciPy. If anyone has any other sources they would recommend building from, I'm happy to try. My initial attempt to install SciPy (prior to this mess) was via Fink, which seemed to result in its own problems. -- Zane A. Crawford . + zane(a)ideotrope.org Amateur Human * , * https://ideotrope.org Boulder, Colorado __o work : 303.735.3729 _`\<,_ "Here we are, trapped in the cell : 303.815.6866 (*)/ (*) amber of the moment. There PGP : 0x55E0815F is no why." -- Kurt Vonnegut

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Problem controlling temp dir usage and verbose output for scipy_distutils vs. distutils
by Robert Clewley Sept. 29, 2005

Sept. 29, 2005

Hi, I've just got scipy_distutils and SWIG to successfully build a C extension module that uses Fortran sources (after surprisingly little additional effort from the pure-C case -- nice job Pearu), but I'm having trouble with two things that I didn't have trouble with using Python's original distutils: 1) Controlling the stderr warnings and info from the compilers and 2) Controlling the temp directories that the build uses. The libraries I'm building are numerical ODE integrators which are selected in my software by the user. I want to keep the filespace tidy and not require any additional admin by the user. In the past I've been building pure C extensions and provided arguments to my (regular Python distutils) setup command like the following, which solved both of the above problems: setup(name = "integrator in pure c", author = "me", script_args = ['-q', 'build', '--build-lib=.', '--build-platlib=.', '-t'+tempdirname], ext_modules = [Extension("modC", sources=modfilelist, include_dirs=incdirs, extra_compile_args=['-w'])]) The script args placed all of the temporary files in the same place which is automatically chosen by my software according to the user's choice of integrator. The -w argument used to shut up the C compiler nicely! However, when I switched to scipy_distutils in order to access the Fortran compiler, these options no longer seem to have any effect. This is what the modules that use Fortran libraries are set up with: setup(name = "integrator with fortran lib", author = "me", script_args = ['-q', 'build', '--build-lib=.', '--build-platlib=.', '-t'+tempdirname], ext_modules = [Extension("modfort", sources=modfilelist, include_dirs=incdirs, libraries=['myfortlib'], extra_compile_args=['-w'])], libraries=[('myfortlib',{'sources': fortfilelist})]) I now end up with a deep tree of temp directories (such as I used to have in the pure C case before I discovered the --build-lib options) inside my desired compilation temporary directory, as well as a separate 'build' directory beside my temp compilation dir that holds my final .py interface file (in ./build/src/modfort_temp/). I looked at the API and I cannot see additional options that I could be passing. I can see a install_libbase attribute being inherited from Python's distutils/command/install.py module's install class into SciPy's overriding class, but I don't get why it's not being used in the same way. I'm having the same problems on both Win32 and Linux platform using Python 2.3.5 and SciPy 0.3.2. My problem is also not specific to using Fortran libraries, as my old pure-C module suffers problem (2) when I use scipy_distutils on it (although the compiler stays quiet). Any ideas please? Thanks, Rob Clewley

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Gamma distribution questions
by Jinsheng you Sept. 29, 2005

Sept. 29, 2005

I have some projects related to the gamma distribution. would you please help me with these: 1) Assuming that I have a gamma distribution dataset, how can I estimate parameters such as alpha, beta from the dataset. 2) assuming that I know the alpha and beta of the distribution, how can I get the value for a given probability. 3) assuming that I know the alpha and beta of the distribution, how can I get the probability for a given x. Thank you so much. _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

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3d plotting question
by Yaroslav Bulatov Sept. 29, 2005

Sept. 29, 2005

There are so many 3d plotting packages, but I'm looking for something simple that'll resemble 3d plots of Gnuplot/Mathematica, can someone recommend one? -- Yaroslav Bulatov bulatov(a)cs.oregonstate.edu Dearborn 102 Oregon State University Corvallis, OR

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