Mailman 3 September 2008 - SciPy-User

Installation from source on OS X: 'NoneType' object has no attribute 'link_shared_object'
by Michael Williams Oct. 5, 2008

Oct. 5, 2008

Hi, I'm having trouble installing scipy-0.6.0.tar.gz according to the instructions on http://www.scipy.org/Installing_SciPy/Mac_OS_X. When I run "python setup.py build_src build_clib --fcompiler=gnu95 build_ext --fcompiler=gnu95 build" I get the following error (email continues below): Traceback (most recent call last): File "setup.py", line 53, in <module> setup_package() File "setup.py", line 45, in setup_package configuration=configuration ) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/core.py", line 174, in setup return old_setup(**new_attr) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_ext.py", line 121, in run self.build_extensions() File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/command/build_ext.py", line 416, in build_extensions self.build_extension(ext) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_ext.py", line 312, in build_extension link = self.fcompiler.link_shared_object AttributeError: 'NoneType' object has no attribute 'link_shared_object' Relevant version information follows: asosx40:~$ gfortran --version GNU Fortran (GCC) 4.3.0 20070810 (experimental) asosx40:~$ gcc --version i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5484) asosx40:~$ python --version Python 2.5.1 (This is the stock OS X 10.5 Python installation.) I get the same error when I try this with the current scipy from svn. I get a different error when I try to build using g77 by doing "python setup.py build_src build_clib --fcompiler=gnu build_ext -- fcompiler=gnu build": creating build/lib.macosx-10.5-i386-2.5/scipy/fftpack /usr/local/bin/g77 -g -Wall -undefined dynamic_lookup -bundle build/ temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/scipy/fftpack/ _fftpackmodule.o build/temp.macosx-10.5-i386-2.5/scipy/fftpack/src/ zfft.o build/temp.macosx-10.5-i386-2.5/scipy/fftpack/src/drfft.o build/ temp.macosx-10.5-i386-2.5/scipy/fftpack/src/zrfft.o build/ temp.macosx-10.5-i386-2.5/scipy/fftpack/src/zfftnd.o build/ temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/ fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0 - Lbuild/temp.macosx-10.5-i386-2.5 -ldfftpack -lg2c -lcc_dynamic -o build/lib.macosx-10.5-i386-2.5/scipy/fftpack/_fftpack.so ld: library not found for -lcc_dynamic collect2: ld returned 1 exit status ld: library not found for -lcc_dynamic collect2: ld returned 1 exit status error: Command "/usr/local/bin/g77 -g -Wall -undefined dynamic_lookup - bundle build/temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/ scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.5-i386-2.5/scipy/ fftpack/src/zfft.o build/temp.macosx-10.5-i386-2.5/scipy/fftpack/src/ drfft.o build/temp.macosx-10.5-i386-2.5/scipy/fftpack/src/zrfft.o build/temp.macosx-10.5-i386-2.5/scipy/fftpack/src/zfftnd.o build/ temp.macosx-10.5-i386-2.5/build/src.macosx-10.5-i386-2.5/ fortranobject.o -L/usr/local/lib/gcc/i686-apple-darwin8.8.1/3.4.0 - Lbuild/temp.macosx-10.5-i386-2.5 -ldfftpack -lg2c -lcc_dynamic -o build/lib.macosx-10.5-i386-2.5/scipy/fftpack/_fftpack.so" failed with exit status 1 I would be very grateful for any suggestions! Thanks, -- Michael Williams http://www-astro.physics.ox.ac.uk/~williams/

4 8

sparse matrices -- slicing and fancy indexing for assignment
by Christopher MacMinn Oct. 1, 2008

Oct. 1, 2008

Hey folks - I installed SciPy 0.7.0.dev4753 from svn yesterday to get access to some of the upcoming improvements to scipy.sparse. In particular, I was excited about the prospect of slicing and fancy indexing for CSC and CSR matrices. Unfortunately, I find now that slicing and fancy indexing are only supported for viewing and copying, not for assignment. E.g.: # Create a sparse CSC matrix A >>> from scipy import sparse >>> A = sparse.eye(10,10,format="csc") # Have a look at the first row of A >>> print A[0,:].todense() [[ 1. 0. 0. 0. 0. 0. 0. 0. 0. 0.]] # Now try to set the first row equal to 5 >>> A[0,:] = 5. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Python/2.5/site-packages/scipy/sparse/ compressed.py", line 601, in __setitem__ raise NotImplementedError("Fancy indexing in assignment not " NotImplementedError: Fancy indexing in assignment not supported for csr matrices. # Fail. Is slicing / fancy indexing for assignment planned for the final 0.7.0 release, or is this (above) the best we're going to get? Best, Chris MacMinn

3 2

unusual fitting problem
by peter websdell Oct. 1, 2008

Oct. 1, 2008

Howdy gang, I have an unusual fitting problem that has me totally stumped. I need to perform a basic interpolation between a few data points, but i need the result to look linear on a loglog scale. Making sense? OK, i'll try again. Imagine you plotted the data points on a loglog scale, then printed it out and joined the dots with a ruler and pencil. That is what I need to achieve. I'm trying to automate an old assessment method at work which requires manually drawing a chart to extrapolate new values between the known data points. It's tedious and there are literally hundreds need doing. :-o Any help will be graciously received. Please let me know if my explanation is nonsense. Cheers, Pete.

3 4

NumpyTest warning after upgrade
by Gary Pajer Sept. 30, 2008

Sept. 30, 2008

I've upgraded numpy and scipy after quite some time. I think I had numpy 1.0.4 and scipy 5.2, but I'm not 100% sure. I'm on winxp, python 2.5.1, and I installed using the windows exe installers on scipy.org I've poked around the scipy-users and numpy-users lists, and learned what I already know: NumpyTest is deprecated. How can I fix this? regards, Gary --------------------------------------------------------------------------------------------------------- C:\Documents and Settings\Gary\My Documents>ipython Python 2.5.1 (r251:54863, Apr 18 2007, 08:51:08) [MSC v.1310 32 bit (Intel)] Type "copyright", "credits" or "license" for more information. IPython 0.9.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import numpy In [2]: import scipy c:\python25\lib\site-packages\scipy\misc\__init__.py:25: DeprecationWarning: NumpyTest will be removed in the next release; please upda te your code to use nose or unittest test = NumpyTest().test In [3]: numpy.__version__ Out[3]: '1.2.0' In [4]: scipy.__version__ Out[4]: '0.6.0' -------------------------------------------------------------------------------

3 3

Problems Building / Installing SciPy on OSX Leopard
by luis cota Sept. 30, 2008

Sept. 30, 2008

I first tried installing using the OSX SuperPack. The install seemed to work, though when importing scipy.integrate, Python crashed because of an error with the referenced modules. This probably has something to do with my OSX setup, though I am not sure where to look. I have installed the latest gFortran and the latest FFTW-3 library as well. I have appended my build log at the end of this email. Any help greatly appreciated ... thanks! *When compiling the SVN Trunk version I get the following output: * python setup.py build Warning: No configuration returned, assuming unavailable. mkl_info: libraries mkl,vml,guide not found in /Library/Frameworks/Python.framework/Versions/2.5/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib libraries mkl,vml,guide not found in /opt/local/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /Library/Frameworks/Python.framework/Versions/2.5/lib libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib FOUND: libraries = ['fftw3'] library_dirs = ['/opt/local/lib'] define_macros = [('SCIPY_FFTW3_H', None)] include_dirs = ['/opt/local/include'] djbfft_info: NOT AVAILABLE blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '-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 = ['-msse3'] umfpack_info: libraries umfpack not found in /Library/Frameworks/Python.framework/Versions/2.5/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib libraries umfpack not found in /opt/local/lib /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy-1.3.0.dev5861-py2.5-macosx-10.3-i386.egg/numpy/distutils/system_info.py:414: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building py_modules sources building library "dfftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "fitpack" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "superlu_src" sources building library "arpack" sources building library "c_misc" sources building library "cephes" sources building library "mach" sources building library "toms" sources building library "amos" sources building library "cdf" sources building library "specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.cluster._distance_wrap" sources building extension "scipy.cluster._hierarchy_wrap" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/scipy/interpolate/src/dfitpack-f2pywrappers.f' to sources. building extension "scipy.interpolate._interpolate" sources building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/build/src.macosx-10.3-i386-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/lib/lapack/clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/build/src.macosx-10.3-i386-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/build/src.macosx-10.3-i386-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.macosx-10.3-i386-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.optimize._slsqp" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.optimize._nnls" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.signal.sigtools" sources building extension "scipy.signal.spline" sources building extension "scipy.sparse.linalg.isolve._iterative" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.sparse.linalg.dsolve._zsuperlu" sources building extension "scipy.sparse.linalg.dsolve._dsuperlu" sources building extension "scipy.sparse.linalg.dsolve._csuperlu" sources building extension "scipy.sparse.linalg.dsolve._ssuperlu" sources building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/build/src.macosx-10.3-i386-2.5/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' to sources. building extension "scipy.sparse.sparsetools._csr" sources building extension "scipy.sparse.sparsetools._csc" sources building extension "scipy.sparse.sparsetools._coo" sources building extension "scipy.sparse.sparsetools._bsr" sources building extension "scipy.sparse.sparsetools._dia" sources building extension "scipy.special._cephes" sources building extension "scipy.special.specfun" sources f2py options: ['--no-wrap-functions'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.macosx-10.3-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.3-i386-2.5' to include_dirs. adding 'build/src.macosx-10.3-i386-2.5/scipy/stats/mvn-f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building extension "scipy.stsci.convolve._correlate" sources building extension "scipy.stsci.convolve._lineshape" sources building extension "scipy.stsci.image._combine" sources building data_files sources running build_py copying build/src.macosx-10.3-i386-2.5/scipy/__config__.py -> build/lib.macosx-10.3-i386-2.5/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize NAGFCompiler Could not locate executable f95 customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize IBMFCompiler Could not locate executable xlf90 Could not locate executable xlf customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize GnuFCompiler Could not locate executable g77 customize Gnu95FCompiler Found executable /usr/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_clib building 'dfftpack' library compiling Fortran sources Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops creating build/temp.macosx-10.3-i386-2.5 creating build/temp.macosx-10.3-i386-2.5/scipy creating build/temp.macosx-10.3-i386-2.5/scipy/fftpack creating build/temp.macosx-10.3-i386-2.5/scipy/fftpack/dfftpack compile options: '-c' gfortran:f77: scipy/fftpack/dfftpack/dcosqb.f gfortran:f77: scipy/fftpack/dfftpack/dcosqf.f gfortran:f77: scipy/fftpack/dfftpack/dcosqi.f gfortran:f77: scipy/fftpack/dfftpack/dcost.f gfortran:f77: scipy/fftpack/dfftpack/dcosti.f gfortran:f77: scipy/fftpack/dfftpack/dfftb.f gfortran:f77: scipy/fftpack/dfftpack/dfftb1.f gfortran:f77: scipy/fftpack/dfftpack/dfftf.f gfortran:f77: scipy/fftpack/dfftpack/dfftf1.f gfortran:f77: scipy/fftpack/dfftpack/dffti.f gfortran:f77: scipy/fftpack/dfftpack/dffti1.f scipy/fftpack/dfftpack/dffti1.f: In function 'dffti1': scipy/fftpack/dfftpack/dffti1.f:11: warning: 'ntry' may be used uninitialized in this function gfortran:f77: scipy/fftpack/dfftpack/dsinqb.f gfortran:f77: scipy/fftpack/dfftpack/dsinqf.f gfortran:f77: scipy/fftpack/dfftpack/dsinqi.f gfortran:f77: scipy/fftpack/dfftpack/dsint.f gfortran:f77: scipy/fftpack/dfftpack/dsint1.f gfortran:f77: scipy/fftpack/dfftpack/dsinti.f gfortran:f77: scipy/fftpack/dfftpack/zfftb.f gfortran:f77: scipy/fftpack/dfftpack/zfftb1.f gfortran:f77: scipy/fftpack/dfftpack/zfftf.f gfortran:f77: scipy/fftpack/dfftpack/zfftf1.f gfortran:f77: scipy/fftpack/dfftpack/zffti.f gfortran:f77: scipy/fftpack/dfftpack/zffti1.f scipy/fftpack/dfftpack/zffti1.f: In function 'zffti1': scipy/fftpack/dfftpack/zffti1.f:11: warning: 'ntry' may be used uninitialized in this function ar: adding 23 object files to build/temp.macosx-10.3-i386-2.5/libdfftpack.a ranlib:@ build/temp.macosx-10.3-i386-2.5/libdfftpack.a building 'linpack_lite' library compiling Fortran sources Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops creating build/temp.macosx-10.3-i386-2.5/scipy/integrate creating build/temp.macosx-10.3-i386-2.5/scipy/integrate/linpack_lite compile options: '-c' gfortran:f77: scipy/integrate/linpack_lite/dgbfa.f gfortran:f77: scipy/integrate/linpack_lite/dgbsl.f gfortran:f77: scipy/integrate/linpack_lite/dgefa.f gfortran:f77: scipy/integrate/linpack_lite/dgesl.f gfortran:f77: scipy/integrate/linpack_lite/dgtsl.f gfortran:f77: scipy/integrate/linpack_lite/zgbfa.f gfortran:f77: scipy/integrate/linpack_lite/zgbsl.f gfortran:f77: scipy/integrate/linpack_lite/zgefa.f gfortran:f77: scipy/integrate/linpack_lite/zgesl.f ar: adding 9 object files to build/temp.macosx-10.3-i386-2.5/liblinpack_lite.a ranlib:@ build/temp.macosx-10.3-i386-2.5/liblinpack_lite.a building 'mach' library using additional config_fc from setup script for fortran compiler: {'noopt': ('scipy/integrate/setup.pyc', 1)} customize Gnu95FCompiler compiling Fortran sources Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -fPIC Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC creating build/temp.macosx-10.3-i386-2.5/scipy/integrate/mach compile options: '-c' gfortran:f77: scipy/integrate/mach/d1mach.f gfortran:f77: scipy/integrate/mach/i1mach.f gfortran:f77: scipy/integrate/mach/r1mach.f gfortran:f77: scipy/integrate/mach/xerror.f scipy/integrate/mach/xerror.f:1.40: SUBROUTINE XERROR(MESS,NMESS,L1,L2) 1 Warning: Unused dummy argument 'l2' at (1) scipy/integrate/mach/xerror.f:1.37: SUBROUTINE XERROR(MESS,NMESS,L1,L2) 1 Warning: Unused dummy argument 'l1' at (1) ar: adding 4 object files to build/temp.macosx-10.3-i386-2.5/libmach.a ranlib:@ build/temp.macosx-10.3-i386-2.5/libmach.a building 'quadpack' library compiling Fortran sources Fortran f77 compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/local/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops creating build/temp.macosx-10.3-i386-2.5/scipy/integrate/quadpack compile options: '-c' gfortran:f77: scipy/integrate/quadpack/dqag.f gfortran:f77: scipy/integrate/quadpack/dqage.f gfortran:f77: scipy/integrate/quadpack/dqagi.f gfortran:f77: scipy/integrate/quadpack/dqagie.f scipy/integrate/quadpack/dqagie.f: In function 'dqagie': scipy/integrate/quadpack/dqagie.f:154: warning: 'small' may be used uninitialized in this function scipy/integrate/quadpack/dqagie.f:153: warning: 'ertest' may be used uninitialized in this function scipy/integrate/quadpack/dqagie.f:152: warning: 'erlarg' may be used uninitialized in this function scipy/integrate/quadpack/dqagie.f:151: warning: 'correc' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqagp.f gfortran:f77: scipy/integrate/quadpack/dqagpe.f scipy/integrate/quadpack/dqagpe.f: In function 'dqagpe': scipy/integrate/quadpack/dqagpe.f:196: warning: 'k' may be used uninitialized in this function scipy/integrate/quadpack/dqagpe.f:191: warning: 'correc' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqags.f gfortran:f77: scipy/integrate/quadpack/dqagse.f scipy/integrate/quadpack/dqagse.f: In function 'dqagse': scipy/integrate/quadpack/dqagse.f:153: warning: 'small' may be used uninitialized in this function scipy/integrate/quadpack/dqagse.f:152: warning: 'ertest' may be used uninitialized in this function scipy/integrate/quadpack/dqagse.f:151: warning: 'erlarg' may be used uninitialized in this function scipy/integrate/quadpack/dqagse.f:150: warning: 'correc' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqawc.f gfortran:f77: scipy/integrate/quadpack/dqawce.f gfortran:f77: scipy/integrate/quadpack/dqawf.f gfortran:f77: scipy/integrate/quadpack/dqawfe.f scipy/integrate/quadpack/dqawfe.f: In function 'dqawfe': scipy/integrate/quadpack/dqawfe.f:203: warning: 'll' may be used uninitialized in this function scipy/integrate/quadpack/dqawfe.f:200: warning: 'drl' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqawo.f gfortran:f77: scipy/integrate/quadpack/dqawoe.f scipy/integrate/quadpack/dqawoe.f: In function 'dqawoe': scipy/integrate/quadpack/dqawoe.f:208: warning: 'ertest' may be used uninitialized in this function scipy/integrate/quadpack/dqawoe.f:207: warning: 'erlarg' may be used uninitialized in this function scipy/integrate/quadpack/dqawoe.f:206: warning: 'correc' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqaws.f gfortran:f77: scipy/integrate/quadpack/dqawse.f gfortran:f77: scipy/integrate/quadpack/dqc25c.f gfortran:f77: scipy/integrate/quadpack/dqc25f.f scipy/integrate/quadpack/dqc25f.f: In function 'dqc25f': scipy/integrate/quadpack/dqc25f.f:103: warning: 'm' may be used uninitialized in this function gfortran:f77: scipy/integrate/quadpack/dqc25s.f gfortran:f77: scipy/integrate/quadpack/dqcheb.f gfortran:f77: scipy/integrate/quadpack/dqelg.f scipy/integrate/quadpack/dqelg.f: In function 'dqelg': scipy/integrate/quadpack/dqelg.f:1: internal compiler error: vector VEC(tree,base) index domain error, in build_classic_dist_vector_1 at tree-data-ref.c:2725 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://gcc.gnu.org/bugs.html> for instructions. scipy/integrate/quadpack/dqelg.f: In function 'dqelg': scipy/integrate/quadpack/dqelg.f:1: internal compiler error: vector VEC(tree,base) index domain error, in build_classic_dist_vector_1 at tree-data-ref.c:2725 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://gcc.gnu.org/bugs.html> for instructions. error: Command "/usr/local/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -c -c scipy/integrate/quadpack/dqelg.f -o build/temp.macosx-10.3-i386-2.5/scipy/integrate/quadpack/dqelg.o" failed with exit status 1

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Import problem numpy.ma
by didier rano Sept. 28, 2008

Sept. 28, 2008

Hi all, I am using numpy in trunk subversion (revision 5872). I have an import problem with "import numpy.ma" => "ImportError: No module named ma" I am using macos X 10.5. I don't know dependences with this module. Thanks for your help Didier Rano

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[ Python(x,y) ] New release : 2.1.1
by Pierre Raybaut Sept. 28, 2008

Sept. 28, 2008

Hi all, As you may already know, Python(x,y) is a free scientific-oriented Python Distribution based on Qt and Eclipse providing a self-consistent scientific development environment. Release 2.1.1 is now available on http://www.pythonxy.com. (Full Edition, Basic Edition, Light Edition, Custom Edition and Update) Changes history Version 2.1.1 (09-28-2008) * Added: o Sphinx 0.4.2 o nose 0.10.3 * Updated: o NumPy 1.2.0 o VTK 5.2.0 o Enthought Tool Suite 3.0.2 o GDCM 2.0.9 o setuptools 0.6c9 o xy 1.0.6.1 o IPython 0.9.1.1 o Console 2.0.140.4 * Corrected: o Issues 18, 19, 20 (see 'Issues' section on Python(x,y) Google Code website) Regards, Pierre Raybaut

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[ Python(x,y) ] Next release
by Pierre Raybaut Sept. 27, 2008

Sept. 27, 2008

Hi all, As you may already know, Python(x,y) is a free scientific-oriented Python Distribution based on Qt and Eclipse providing a self-consistent scientific development environment. Release 2.1.0 has introduced a new plugin system allowing easy update (http://www.pythonxy.com/standard.php) and fully customizable installation: http://www.pythonxy.com/_tools/img.php?lang=1&img=/_images/Windows%20Instal… http://www.pythonxy.com/screenshots.php?dir=/Windows%20Installer Third-party plugins are now available (http://www.pythonxy.com/additional.php) - please do not hesitate to contribute and create your own thanks to the SDK. From now on, releases will be scheduled monthly. However, next release will somehow be available continously because future plugins will be available separately. For example, NumPy 1.2.0, VTK 5.2.0 or ETS 3.0.2 are already available at http://www.pythonxy.com/additional.php. Regards, Pierre Raybaut

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Documentation
by Anne Archibald Sept. 26, 2008

Sept. 26, 2008

Hi, I've just written a description of how scipy's smoothing splines work (because a friend is publishing a paper that used them). I had to go look up the original research papers, because there isn't really a good description in the python documentation, or even in the FITPACK source. It seems like it would be valuable to have such a description, but I'm not sure where it should go: duplicated in every one of scipy's spline-fitting functions? at the module level? in some automatic docstring transmogrifier that puts it in all relevant docstrings without requiring source code duplication? Anne """ The splines constructed by this code are described in a number of papers (see below). Summarizing based on Dierckx 1982, the goal is to find a spline for which the "smoothness" (sum of squares of jumps in the highest derivative at the joins) is as small as possible given that the (weighted) sum of squares of residuals is S. This can be achieved by choosing one knot per data point, but in the interests of efficiency and smoothness, the algorithm attempts to select the smallest set of knots that can achieve this balance. For any given set of knots, by adjusting the relative importance of smoothness and good fitting the algorithm can go from the least-squares polynomial of degree K (totally smooth) to the least-squares spline (big jumps at each knot). The code tries to find the smallest set of knots for which the least-squares spline gives you residuals better than S, then adjusts the relative importance of smoothing and quality-of-fit to make the curve smoother until the residuals are exactly S. It finds this best set of knots by starting with the bare minimum of knots - a one-segment spline - and checking whether the least-squares spline (with no smoothness constraints) fits the data as well as S. If not, then it subdivides the interval by introducing a knot. The subdivided spline is again checked to see whether it can fit the data with sum of squares of residuals no worse than S. If not, the worst-fitting subintervals are subdivided again. This is repeated until there are enough knots to make it possible to fit with residuals no worse than S. When this is finally achieved - if necessary by having a knot at every data point so the spline interpolates them - the spline is adjusted to make it smoother but the fit worse until a spline is obtained with sum of squares of residuals exactly S. The procedure does not attempt to produce the strictly minimal set of knots, but it does stop introducing new knots as soon as possible. The process is described in detail in: Dierckx P. : An Algorithm for Smoothing, Differentiation and Integ- ration Of Experimental Data Using Spline Functions, J.Comp.Appl.Maths 1 (1975) 165-184. Dierckx P. : A Fast Algorithm for Smoothing Data on a Rectangular Grid While Using Spline Functions, Siam J.Numer.Anal. 19 (1982) 1286-1304. Dierckx P. : An Improved Algorithm for Curve Fitting with Spline Functions, Report TW54, Dept. Computer Science, K.U. Leuven, 1981. Dierckx P. : Curve and Surface Fitting with Splines, Monographs on Numerical Analysis, Oxford University Press, 1993. The code in scipy is a python wrapper of the FITPACK routines written by: P. Dierckx Dept. Computer Science, K.U. Leuven Celestijnenlaan 200a, B-3001 Heverlee, Belgium. e-mail : Paul.Dierckx(a)cs.kuleuven.ac.be """

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Re: [SciPy-user] Documentation (Anne Archibald)
by jh＠physics.ucf.edu Sept. 26, 2008

Sept. 26, 2008

Anne writes: > It seems like it would be valuable to have such a description, > but I'm not sure where it should go: duplicated in every one of > scipy's spline-fitting functions? at the module level? in some > automatic docstring transmogrifier that puts it in all relevant > docstrings without requiring source code duplication? First, thanks for researching and writing this! This is going to become a general issue, particularly for scipy, where there may be need for many of these in certain modules. What we choose for this one should scale to having many of these per sub-module in some cases, and just one or none in others. I would think that the first one or two per sub-module could go in the sub-module's docstring as you suggest, but after that we should separate all of them into either a .doc sub-sub-module for that sub-module (as now exists for numpy itself) or a function called doc_splines (in this case) that contains only the docstring and "pass". Either way, those pages should be referenced in the sub-module docstring so people know they exist. If we do the doc-function, which is admittedly a hack but which may be more convenient than having to do yet another import, the one-line description should say something appropriate to identify it in lists of functions, something like "documentation for spline implementation". If we could make np.info() import anything it needs to in order to access the named docstring, it would make life easier and the .doc sub-sub-module more attractive, since you wouldn't have to import it. In this case, np.info(sp.foo.doc.spline) would import sp.foo.doc automatically. Whatever is decided, a description should go in the doc standards. --jh--

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