Mailman 3 August 2009 - SciPy-User

Intro tutorial checklist failure
by Gökhan Sever 15 Aug '09

15 Aug '09

Hello, As posted below the output of the script seemingly there is something wrong with the matplotlib tests. I have matplotlib installed and working properly however the script fails to test this. Manual testing of the test plot functions work properly as expected. I don't have scipy and mayavi installed yet since there are two bizarre installation issues that I have had and posted on the lists, and still couldn't figure out. All were working extremely nicely on Fedora 10 (The source code installations) but there must be somethings wrong with some critical libraries or some tools' being so up-to-date. [gsever@ccn python-repo]$ python intro_tut_checklist.py Running tests: __main__.test_imports('setuptools', None) ... MOD: setuptools, version: 0.6c9 ok __main__.test_imports('IPython', None) ... MOD: IPython, version: 0.11.bzr.r1205 ok __main__.test_imports('numpy', None) ... MOD: numpy, version: 1.4.0.dev ok __main__.test_imports('scipy', None) ... ERROR __main__.test_imports('scipy.io', None) ... ERROR __main__.test_imports('matplotlib', <function validate_mpl at 0xb7a83614>) ... ERROR __main__.test_imports('pylab', None) ... ERROR __main__.test_imports('enthought.mayavi.api', None) ... ERROR __main__.test_loadtxt(array([[ 0., 1.], ... ok __main__.test_loadtxt(array([('M', 21, 72.0), ('F', 35, 58.0)], ... ok __main__.test_loadtxt(array([ 1., 3.]), array([ 1., 3.])) ... ok __main__.test_loadtxt(array([ 2., 4.]), array([ 2., 4.])) ... ok Simple plot generation. ... ERROR Plots with math ... ERROR ====================================================================== ERROR: __main__.test_imports('scipy', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named scipy ====================================================================== ERROR: __main__.test_imports('scipy.io', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named scipy.io ====================================================================== ERROR: __main__.test_imports('matplotlib', <function validate_mpl at 0xb7a83614>) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 106, in check_import validator(m) File "intro_tut_checklist.py", line 69, in validate_mpl m.use('Agg') AttributeError: 'module' object has no attribute 'use' ====================================================================== ERROR: __main__.test_imports('pylab', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> File "/home/gsever/Desktop/python-repo/matplotlib/lib/pylab.py", line 1, in <module> from matplotlib.pylab import * ImportError: No module named pylab ====================================================================== ERROR: __main__.test_imports('enthought.mayavi.api', None) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 91, in check_import exec "import %s as m" % mnames File "<string>", line 1, in <module> ImportError: No module named mayavi.api ====================================================================== ERROR: Simple plot generation. ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 166, in test_plot from matplotlib import pyplot as plt ImportError: cannot import name pyplot ====================================================================== ERROR: Plots with math ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/nose/case.py", line 182, in runTest self.test(*self.arg) File "intro_tut_checklist.py", line 175, in test_plot_math from matplotlib import pyplot as plt ImportError: cannot import name pyplot ---------------------------------------------------------------------- Ran 14 tests in 0.539s FAILED (errors=7) Cleanup - removing temp directory: /home/gsever/Desktop/python-repo/tmp-testdata-h_qN8x *************************************************************************** TESTS FINISHED *************************************************************************** If the printout above did not finish in 'OK' but instead says 'FAILED', copy and send the *entire* output, including the system information below, for help. We'll do our best to assist you. You can send your message to the Scipy user mailing list: http://mail.scipy.org/mailman/listinfo/scipy-user but feel free to also CC directly: Fernando.Perez(a)berkeley.edu ================== System information ================== os.name : posix os.uname : ('Linux', 'ccn', '2.6.29.6-217.2.3.fc11.i686.PAE', '#1 SMP Wed Jul 29 16:05:22 EDT 2009', 'i686') platform : linux2 platform+ : Linux-2.6.29.6-217.2.3.fc11.i686.PAE-i686-with-fedora-11-Leonidas prefix : /usr exec_prefix : /usr executable : /usr/bin/python version_info : (2, 6, 0, 'final', 0) version : 2.6 (r26:66714, Jun 8 2009, 16:07:26) [GCC 4.4.0 20090506 (Red Hat 4.4.0-4)] -- Gökhan

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scipy.signal.ss2tf nests numerator 1 deeper, is this a bug ?
by Stef Mientki 15 Aug '09

15 Aug '09

hello, creating a module that accepts any LTI representation, my program didn't work, because ss2tf nests the numerator 1 deeper. Is this a bug ? from scipy import signal from scipy.signal import tf2ss, ss2tf print '======== HighPass Filter ========' print 'Filter-1: IIR (Butterworth), 0.06*fn, -50dB' filt = signal.iirdesign( 0.06, 0.002, 1, 50, 0, 'butter') Space_State = tf2ss ( *filt ) filt2 = ss2tf ( *Space_State ) print 'orginal transfer function', filt print 'tf --> Space_State --> tf', filt2 OUTPUT: ======== HighPass Filter ======== Filter-1: IIR (Butterworth), 0.06*fn, -50dB orginal transfer function (array([ 0.92410511, -1.84821022, 0.92410511]), array([ 1. , -1.84244187, 0.85397858])) tf --> Space_State --> tf (array([[ 0.92410511, -1.84821022, 0.92410511]]), array([ 1. , -1.84244187, 0.85397858])) Is there a handy work around ? One of things I want to do is to calculate the frequency response (but I guess more things that I want will raise problems :-) So this generates an error: h, w = signal.freqz ( *filt2 ) And I have to use this statement: h, w = signal.freqz ( filt2 [0] [0], filt2 [1] ) thanks, Stef Mientki

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Problems installing scipy [was: Sanity checklist for SciPy'09 tutorials]
by David Goldsmith 15 Aug '09

15 Aug '09

Hi! Problem(s) installing "bleeding edge" svn checkout (done just now; no checkout problems reported) of scipy using "python setup.py install" on the (DOS Terminal) command line. Platform: Windows Vista Home Premium SP1 Python: 2.6.2 (Numpy 1.3.0rc2 already installed and run successfully numerous times). Output: (lengthy; questions follow) C:\Python26\Lib\site-packages\scipy>python setup.py install setup.py:63: UserWarning: --- Could not run svn info --- warnings.warn(" --- Could not run svn info --- ") Warning: No configuration returned, assuming unavailable. blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in C:\Python26\lib libraries mkl,vml,guide not found in C:\ libraries mkl,vml,guide not found in C:\Python26\libs NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS NOT AVAILABLE atlas_blas_info: NOT AVAILABLE C:\Python26\lib\site-packages\numpy\distutils\system_info.py:1383: 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 C:\Python26\lib libraries blas not found in C:\ libraries blas not found in C:\Python26\libs NOT AVAILABLE C:\Python26\lib\site-packages\numpy\distutils\system_info.py:1392: 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 C:\Python26\lib\site-packages\numpy\distutils\system_info.py:1395: 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__) Traceback (most recent call last): File "setup.py", line 160, in <module> setup_package() File "setup.py", line 152, in setup_package configuration=configuration ) File "C:\Python26\lib\site-packages\numpy\distutils\core.py", line 150, in set up config = configuration() File "setup.py", line 118, in configuration config.add_subpackage('scipy') File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 852, i n add_subpackage caller_level = 2) File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 835, i n get_subpackage caller_level = caller_level + 1) File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 782, i n _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy\setup.py", line 8, in configuration config.add_subpackage('integrate') File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 852, i n add_subpackage caller_level = 2) File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 835, i n get_subpackage caller_level = caller_level + 1) File "C:\Python26\lib\site-packages\numpy\distutils\misc_util.py", line 782, i n _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy\integrate\setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "C:\Python26\lib\site-packages\numpy\distutils\system_info.py", line 303, in get_info return cl().get_info(notfound_action) File "C:\Python26\lib\site-packages\numpy\distutils\system_info.py", line 454, in get_info raise self.notfounderror,self.notfounderror.__doc__ numpy.distutils.system_info.BlasNotFoundError: 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. Does one need to install BLAS separately? If so, that should be added to the Pre-requisites on http://conference.scipy.org/intro_tutorial. Also vague from that page: Are iPython, matplotlib, and Mayavi separate download/installs (i.e., not part of scipy? I thought, at least, matplotlib was included with scipy, no?) Do they need to be installed in the order listed? In particular, can EPD or Python(x,y) be installed before the others? Finally, a comment/question: this is *a lot* of stuff - how necessary is it all, really? In particular, I signed up for the "advanced" track ('cause, based on the advertised content, that's where I am vis-a-vis the numpy content, which appears to be a substantial portion of the tutorials), but I'm "intermediate" w/ matplotlib and "novice" w/ everything else on the list - is this going to be a problem? DG --- On Sun, 8/9/09, Fernando Perez <fperez.net(a)gmail.com> wrote: > From: Fernando Perez <fperez.net(a)gmail.com> > Subject: [Numpy-discussion] Sanity checklist for those attending the SciPy'09 tutorials > To: "Discussion of Numerical Python" <numpy-discussion(a)scipy.org>, "SciPy Users List" <scipy-user(a)scipy.org> > Date: Sunday, August 9, 2009, 2:12 AM > Hi all, > > [ sorry for spamming the list, but even though I sent this > to all the > email addresses I have on file for tutorial attendees, I > know I am > missing a few, so I hope they see this message. ] > > In order to make your experience at the scipy tutorials as > smooth as > possible, we strongly recommend that you take a little time > to install > the necessary tools in advance. > > For both introductory and advanced tutorials: > > http://conference.scipy.org/intro_tutorial > http://conference.scipy.org/advanced_tutorials > > you will find instructions on what to install and where to > download it > from. In addition (this is also mentioned on those > pages), we > encourage you to run according to your tutorial of choice, > a little > checklist script: > > https://cirl.berkeley.edu/fperez/tmp/intro_tut_checklist.py > https://cirl.berkeley.edu/fperez/tmp/adv_tut_checklist.py > > This will try to spot any problems early, and we'll > do our best to > help you with them before you arrive to the conference. > > Best regards, > > Dave Peterson and Fernando Perez. > > ps - for those of you who may find fixes for the checklist > scripts, > the sources are hosted on github: > > http://github.com/fperez/scipytut/ > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion >

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lnpymath cannot find error during scipy installation
by Gökhan Sever 15 Aug '09

15 Aug '09

/usr/bin/ld: cannot find -lnpymath collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-i686-2.6/scipy/special/_cephesmodule.o build/temp.linux-i686-2.6/scipy/special/amos_wrappers.o build/temp.linux-i686-2.6/scipy/special/specfun_wrappers.o build/temp.linux-i686-2.6/scipy/special/toms_wrappers.o build/temp.linux-i686-2.6/scipy/special/cdf_wrappers.o build/temp.linux-i686-2.6/scipy/special/ufunc_extras.o -L/usr/lib/python2.6/site-packages/numpy/core/lib -L/usr/lib -Lbuild/temp.linux-i686-2.6 -lsc_amos -lsc_toms -lsc_c_misc -lsc_cephes -lsc_mach -lsc_cdf -lsc_specfun -lnpymath -lm -lpython2.6 -lg2c -o scipy/special/_cephes.so" failed with exit status 1 Did a python setupegg.py develop install for numpy and when I tried to do the same for scipy I stuck at that error. I know there is a libnpymath file under one of the numpy build dirs, however not sure how to show that path for the linker. Any ideas? Thank you ############################################## python -c 'from numpy.f2py.diagnose import run; run()' ############################################## ------ os.name='posix' ------ sys.platform='linux2' ------ sys.version: 2.6 (r26:66714, Jun 8 2009, 16:07:26) [GCC 4.4.0 20090506 (Red Hat 4.4.0-4)] ------ sys.prefix: /usr ------ sys.path=':/usr/lib/python2.6/site-packages/foolscap-0.4.2-py2.6.egg:/usr/lib/python2.6/site-packages/Twisted-8.2.0-py2.6-linux-i686.egg:/home/gsever/Desktop/python-repo/ipython:/home/gsever/Desktop/python-repo/numpy:/home/gsever/Desktop/python-repo/matplotlib/lib:/usr/lib/python2.6/site-packages/Sphinx-0.6.2-py2.6.egg:/usr/lib/python2.6/site-packages/docutils-0.5-py2.6.egg:/usr/lib/python2.6/site-packages/Jinja2-2.1.1-py2.6-linux-i686.egg:/usr/lib/python2.6/site-packages/Pygments-1.0-py2.6.egg:/usr/lib/python2.6/site-packages/xlwt-0.7.2-py2.6.egg:/usr/lib/python2.6/site-packages/spyder-1.0.0beta1-py2.6.egg:/usr/lib/python26.zip:/usr/lib/python2.6:/usr/lib/python2.6/plat-linux2:/usr/lib/python2.6/lib-tk:/usr/lib/python2.6/lib-old:/usr/lib/python2.6/lib-dynload:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/Numeric:/usr/lib/python2.6/site-packages/PIL:/usr/lib/python2.6/site-packages/gst-0.10:/usr/lib/python2.6/site-packages/gtk-2.0:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/wx-2.8-gtk2-unicode' ------ Failed to import numarray: No module named numarray Found Numeric version '24.2' in /usr/lib/python2.6/site-packages/Numeric/Numeric.pyc Found new numpy version '1.4.0.dev' in /home/gsever/Desktop/python-repo/numpy/numpy/__init__.pyc Found f2py2e version '2' in /home/gsever/Desktop/python-repo/numpy/numpy/f2py/f2py2e.pyc Found numpy.distutils version '0.4.0' in '/home/gsever/Desktop/python-repo/numpy/numpy/distutils/__init__.pyc' ------ Importing numpy.distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: GnuFCompiler instance properties: archiver = ['/usr/bin/g77', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/g77', '-g', '-Wall', '-fno-second- underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = None compiler_fix = None libraries = ['g2c'] library_dirs = [] linker_exe = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall'] linker_so = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall', '- shared'] object_switch = '-o ' ranlib = ['/usr/bin/g77'] version = LooseVersion ('3.4.6') version_cmd = ['/usr/bin/g77', '--version'] Gnu95FCompiler instance properties: archiver = ['/usr/bin/gfortran', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = ['/usr/bin/gfortran', '-Wall', '-fno-second-underscore', '-fPIC', '-O3', '-funroll-loops'] compiler_fix = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno- second-underscore', '-Wall', '-fno-second-underscore', '- fPIC', '-O3', '-funroll-loops'] libraries = ['gfortran'] library_dirs = [] linker_exe = ['/usr/bin/gfortran', '-Wall', '-Wall'] linker_so = ['/usr/bin/gfortran', '-Wall', '-Wall', '-shared'] object_switch = '-o ' ranlib = ['/usr/bin/gfortran'] version = LooseVersion ('4.4.0') version_cmd = ['/usr/bin/gfortran', '--version'] Fortran compilers found: --fcompiler=gnu GNU Fortran 77 compiler (3.4.6) --fcompiler=gnu95 GNU Fortran 95 compiler (4.4.0) Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=compaq Compaq Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pg Portland Group Fortran Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler Compilers not available on this platform: --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing numpy.distutils.cpuinfo ... ok ------ CPU information: CPUInfoBase__get_nbits getNCPUs has_mmx has_sse has_sse2 has_sse3 has_ssse3 is_32bit is_Intel is_i686 ------ -- Gökhan

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Behavioral science BoF?
by Dav Clark 15 Aug '09

15 Aug '09

I know a number of neuroscience types will be coming, but we already talk. So this may not be the best use of conference time. But, I figured I'd see if anyone were interested in issues like: - Stimulus presentation (What do people use / need - I can share my experience creating a more semantic framework for this stuff on top of VisionEgg) - Data collection (I'd be happy to talk about my experiences with the excellent LabJack I/O box - this wouldn't have to be for behavioral data). - Data marshalling, storage, retrieval, visualization, analysis - I'm having great success dealing with glitchy data using an HDF5 container and a TraitsUI visualization tool to rapidly look through the many things that went wrong. I'd be happy talking to people about ecologies or toothpaste or Luan or whatever, if they felt they had similar computational problems. So don't take the "behavioral science" aspect too seriously. Any takers? Dav

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SciPy 2009 website suggestions
by Andrew Straw 14 Aug '09

14 Aug '09

1. Add a link to the schedule in the left-side navigation bar. 2. At the top of each day in the schedule page, list the location of the events.

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Astronomy BoF meeting at SciPy?
by James Turner 14 Aug '09

14 Aug '09

Hi everyone, I haven't heard anything regarding an astronomy BoF session since Joe's AstroPy post on 26 June regarding astronomy libraries. However, at least Joe, Perry and I are interested in talking and I suspect there are others (AplPy people?). Up for discussion will be issues like co-ordinating library development, as different groups help ramp up the functionality available to match IRAF or IDL. Who else is interested? Do you have existing plans to meet at SciPy? What days are you available? So far I believe the three of us are available on Thursday and Friday. How about Thursday evening? Does anyone know what time the dinner on Thursday is? Thanks, James.

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how to use stats.kruskal correctly?
by Chung, Tae-Hoon 14 Aug '09

14 Aug '09

Hi, All; What's the correct way to put something into the stats.kruskal function? Any examples? I tried one list with multiple lists as input or several lists separately but none succeeded. The reference contains only the following description, with no explanation on input arguments: scipy.stats.kruskal(*args) The Kruskal-Wallis H-test is a non-parametric ANOVA for 2 or more groups, requiring at least 5 subjects in each group. This function calculates the Kruskal-Wallis H and associated p-value for 2 or more independent samples. Returns: H-statistic (corrected for ties), associated p-value Thanks in advance, Tae-Hoon Chung

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machine learning/probabilistic modeling BOF?
by David Warde-Farley 14 Aug '09

14 Aug '09

Since David Cournapeau noted that no one had proposed a BOF he was excited about attending (tsk tsk), I wonder if there'd be interest in a machine learning/probabilistic modeling BOF session. What I'm interested in is primarily reusable tools for doing {maximum likelihood, Bayesian} probabilistic modeling in Python. Lately a lot of options have popped up for quickly specifying and fitting/ simulating models, including: - PyMC 2.0 - http://pymc.googlecode.com/ - Infer.NET - http://research.microsoft.com/en-us/um/cambridge/projects/infernet/ - Hierarchical Bayesian Compiler - http://www.cs.utah.edu/~hal/HBC/ Obviously PyMC is the most promising given our preferred programming language but the others include interesting ideas too, for example Infer.NET features a compilatio Some possible topics might include: - The learn scikit - what's it good at, what's it missing? - The maxentropy module - it took me a while to stumble upon it and recognize it as what I know as exponential family models. Could this code be reused, expanded, made more flexible? - The old idea of porting Kevin Murphy's Bayes net toolbox, which DavidC got permission for but none of us actually got around to doing. :) - Things that make complicated models easier to implement and test, i.e. automatic differentiation - New algorithms that might deserve a place in scipy.cluster, ways of improving the existing implementations - Package interoperability, data formats - ??? (your idea here) David

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Re: [SciPy-User] Checklist script
by Fernando Perez 14 Aug '09

14 Aug '09

Hi David, On Thu, Aug 13, 2009 at 11:29 AM, David Kim<davidkim05(a)gmail.com> wrote: > Can I get a little help? see output below... > I'll send in a minute an email with some instructions regarding this, you're not the only one seeing the issue. Cheers, f

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