Mailman 3 October 2003 - SciPy-User

SciPy'03 proceeding.
by Andrea Riciputi 29 Oct '03

29 Oct '03

Hi there, any news about slides presented at SciPy'03? Are they available on-line at last? If not, when will they be put on-line? Thanks in advance, Andrea. --- Andrea Riciputi "Science is like sex: sometimes something useful comes out, but that is not the reason we are doing it" -- (Richard Feynman)

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RE: [SciPy-user] weave build errors
by Christopher Fonnesbeck 29 Oct '03

29 Oct '03

Running weave.test() results in the output below, where it seems to have trouble finding most of the tests. This is why I thought the warning about not finding __init__.py in tests was important. I have installed scipy_distutils, scipy_test and scipy_base; scipy_core and the full scipy cause problems, seemingly related to gcc3.4, as unrecognized symbols pop up. >>> weave.test() Found 2 tests for weave.blitz_tools !! No test file 'test_vtk_spec.py' found for <module 'weave.vtk_spec' from '...te-packages/weave/vtk_spec.pyc'> Found 0 tests for weave.c_spec !! No test file 'test_base_spec.py' found for <module 'weave.base_spec' from '...e-packages/weave/base_spec.pyc'> Found 16 tests for weave.slice_handler Found 3 tests for weave.standard_array_spec Found 12 tests for weave.build_tools !! No test file 'test_common_info.py' found for <module 'weave.common_info' from '...packages/weave/common_info.pyc'> !! No test file 'test_converters.py' found for <module 'weave.converters' from '...-packages/weave/converters.pyc'> !! No test file 'test_base_info.py' found for <module 'weave.base_info' from '...e-packages/weave/base_info.pyc'> !! FAILURE importing tests for <module 'weave.wx_spec' from '...ite-packages/weave/wx_spec.pyc'> /System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/ site-packages/weave/tests/test_wx_spec.py:17: ImportError: No module named wxPython (in ?) !! No test file 'test_swigptr.py' found for <module 'weave.swigptr' from '...ite-packages/weave/swigptr.pyc'> building extensions here: /Users/chris/.python23_compiled/m3 Found 1 tests for weave.ext_tools Found 26 tests for weave.catalog !! No test file 'test_info_weave.py' found for <module 'weave.info_weave' from '...-packages/weave/info_weave.pyc'> !! No test file 'test_blitz_spec.py' found for <module 'weave.blitz_spec' from '...-packages/weave/blitz_spec.pyc'> Found 85 tests for weave.size_check !! No test file 'test_platform_info.py' found for <module 'weave.platform_info' from '...ckages/weave/platform_info.pyc'> Found 1 tests for weave.ast_tools !! No test file 'test_accelerate_tools.py' found for <module 'weave.accelerate_tools' from '...ges/weave/accelerate_tools.pyc'> !! No test file 'test___cvs_version__.py' found for <module 'weave.__cvs_version__' from '...ages/weave/__cvs_version__.pyc'> !! No test file 'test_weave_version.py' found for <module 'weave.weave_version' from '...ckages/weave/weave_version.pyc'> !! No test file 'test_dumbdbm_patched.py' found for <module 'weave.dumbdbm_patched' from '...ages/weave/dumbdbm_patched.pyc'> Found 0 tests for weave.inline_tools !! No test file 'test_dumb_shelve.py' found for <module 'weave.dumb_shelve' from '...packages/weave/dumb_shelve.pyc'> !! No test file 'test___init__.py' found for <module 'weave' from '...te-packages/weave/__init__.pyc'> !! No test file 'test_bytecodecompiler.py' found for <module 'weave.bytecodecompiler' from '...ges/weave/bytecodecompiler.pyc'> .....................warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations .....warning: specified build_dir '_bad_path_' does not exist or is not writable. Trying default locations ........................................................................ ................................................ ---------------------------------------------------------------------- Ran 146 tests in 2.674s OK <unittest.TextTestRunner object at 0x13cfff0> -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia

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RE: [SciPy-user] weave build errors
by Christopher Fonnesbeck 28 Oct '03

28 Oct '03

OK, done that. I do get the following error, however that prevents weave from running its tests: package init file '/Users/chris/Development/python/scipy_core/scipy_base/tests/ __init__.py' not found (or not a regular file) Thanks again, cjf -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia

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SWIG required for scipy setup?
by Christopher Fonnesbeck 28 Oct '03

28 Oct '03

OSX nightmares continue: It now appears that swig is required to build scipy on OSX 10.3 -- building scipy from cvs gives the following error: building agg swig: swig -c++ -python -shadow -I/Users/chris/Development/python/scipy/Lib_chaco/agg2/include agg.i sh: line 1: swig: command not found I thought scipy was independent of swig. Should I be avoiding the scipy cvs for this platform? Sorry for the hassles, but I either need to get scipy running to continue development of my own code, or move on without it. Thanks, Chris -- Christopher J. Fonnesbeck ( c h r i s @ f o n n e s b e c k . o r g ) Georgia Cooperative Fish & Wildlife Research Unit, University of Georgia

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weave build errors
by Christopher Fonnesbeck 27 Oct '03

27 Oct '03

I'm trying to build and install weave on OSX 10.3 using python 2.3, but get the following build error that I cannot interpret: Goldeneye:~/Development/python/weave chris$ python setup_weave.py build Traceback (most recent call last): File "setup_weave.py", line 52, in ? setup(**configuration()) File "setup_weave.py", line 9, in configuration local_path = get_path(__name__,parent_path2) TypeError: get_path() takes exactly 1 argument (2 given) I'm not sure why this is happening, so advice is welcome. Note that calling setup.py instead of setup_weave.py yields a similar result. Chris Fonnesbeck

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sqrtm
by Nils Wagner 27 Oct '03

27 Oct '03

Hi all, Just another sqrtm implementation based on Pade iteration... def sqrtm2(A,p): # # Pade Iteration # m,n = shape(A) i=arange(1,p+1) xi = 0.5*(1.+cos(0.5*(2*i-1)*pi/p)) ai2 = 1.0/xi-1. Y0 = A Z0 = identity(n) maxiter = 5 for k in arange(0,maxiter): sum1= zeros((n,n),Complex) sum2= zeros((n,n),Complex) for j in arange(0,p): sum1 = sum1 + linalg.inv(dot(Z0,Y0)+ai2[j]*identity(n))/xi[j] sum2 = sum2 + linalg.inv(dot(Y0,Z0)+ai2[j]*identity(n))/xi[j] Y1 = dot(Y0,sum1)/p Z1 = dot(Z0,sum1)/p Y0 = Y1 Z0 = Z1 return Y1,Z1 # # test matrix # A=rand(5,5) # # Modify the spectrum # A = dot(A,A)/25.0+identity(5) # Y2,Z2 = sqrtm2(A,4) print linalg.norm(dot(Y2,Y2)-A) print linalg.norm(dot(Z2,Z2)-linalg.inv(A)) Any suggestions ? Nils

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More matrix functions
by Nils Wagner 27 Oct '03

27 Oct '03

Dear experts, Please find enclosed two algorithms for the computation of the matrix square root. It would be great to have this function in scipy. Any comments ? Nils Reference Nick Higham How and how not to compute the matrix square root Numerical Algorithms 15(2) 227--242 (1997)

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output format
by Nils Wagner 27 Oct '03

27 Oct '03

Dear experts, Is it possible to remove e+xx in the output generated by io.write_array(file,B4,...) Actually, the entries of B4 are integers. >>> B4 array([[ 4.25424070e+10, 3.81028483e+10, 2.12712035e+10], [ 3.36632897e+10, 3.01503208e+10, 1.68316448e+10], [ 8.87911734e+09, 7.95252750e+09, 4.43955867e+09]]) Nils

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cluster module
by Barry Drake 26 Oct '03

26 Oct '03

The vq.py example tries to import the scipy.cluster.vq module, which raises an import exception. Does anyone know where this module can be downloaded? It wasn't installed with the Enthought distro of Python 2.3 and I couldn't find it in a search of the SciPy site or mail list. Thanks. Barry Drake

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Weave problem
by Barry Drake 25 Oct '03

25 Oct '03

When I try to run the fibonacci.py that came installed with Enthought Python 2.3 dist., I get the following: Traceback (most recent call last): File "C:\Python23\Lib\site-packages\weave\examples\fibonacci1.py", line 71, in ? build_fibonacci() File "C:\Python23\Lib\site-packages\weave\examples\fibonacci1.py", line 66, in build_fibonacci mod.compile() File "..\ext_tools.py", line 340, in compile verbose = verbose, **kw) File "..\build_tools.py", line 240, in build_extension compiler_dir = platform_info.get_compiler_dir(compiler_name) File "..\platform_info.py", line 110, in get_compiler_dir compiler_obj = create_compiler_instance(dist) File "..\platform_info.py", line 50, in create_compiler_instance compiler = new_compiler(compiler=compiler_name) File ".\distutils\ccompiler.py", line 1173, in new_compiler File ".\distutils\msvccompiler.py", line 212, in __init__ distutils.errors.DistutilsPlatformError: Python was built with version 6 of Visual Studio, and extensions need to be built with the same version of the compiler, but it isn't installed. Does this mean I have to go out and buy MCVC 6.0 and uninstall MSVC 7.1 or rebuild Python 2.3 from the ground up using my MSVC 7.1? Is there some reason that Python 2.3 was not built with mingw32, which is supplied with the Enthought Python 2.3 dist.? It seems to me that the latter would make the use of weave and other tools seamless regardless of which MS*^(*&(* is installed. Does anyone know of a less painless way to get around the above problem? Please tell me I'm missing something real simple; so far all of my searching and digging has yieled nothing. Thanks. Barry

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