Mailman 3 September 2012 - NumPy-Discussion

John Hunter's memorial service
by Fernando Perez Sept. 7, 2012

Sept. 7, 2012

Hi all, I have just received the following information from John's family regarding the memorial service: John's memorial service will be held on Monday, October 1, 2012, at 11.a.m. at Rockefeller Chapel at the University of Chicago. The exact address is 5850 S. Woodlawn Ave, Chicago, IL 60615. The service is open to the public. The service will be fully planned and scripted with no room for people to eulogize, however, we will have a reception after the service, hosted by Tradelink, where people can talk. Regards, f

1 1

FWIW: "regressions" of dependees of nukmpy 1.7.0b1
by Yaroslav Halchenko Sept. 6, 2012

Sept. 6, 2012

Recently Sandro uploaded 1.7.0b1 into Debian experimental so I decided to see if this bleeding edge version doesn't break some of its dependees... Below is a copy of http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… first FAILED/ok column is when building against sid numpy version 1.6.2-1 and the second one is against 1.7.0~b1. I think some 'ok -> FAILED' might be indicative of regressions (myself looking into two new funny failures in pymvpa2's master). Some FAILED->FAILED could be ignored (e.g. I forgotten to provide /dev/shm so multiprocessing was failing)... Enjoy Testing builds against python-numpy_1.7.0~b1-1.dsc aster_10.6.0-1-4.dsc FAILED FAILED aster_10.6.0-1-4_amd64.build avogadro_1.0.3-5.dsc FAILED ok babel_1.4.0.dfsg-8.dsc ok ok basemap_1.0.3+dfsg-2.dsc ok ok biosig4c++_1.3.0-2.dsc ok ok brian_1.3.1-1.dsc ok ok cfflib_2.0.5-1.dsc ok ok cmor_2.8.0-2.dsc ok ok connectomeviewer_2.1.0-1.dsc ok ok cython_0.15.1-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… dballe_5.18-1.dsc ok ok dipy_0.5.0-3.dsc ok ok dolfin_1.0.0-7.dsc FAILED ok flann_1.7.1-4.dsc ok ok fonttools_2.3-1.dsc ok ok gamera_3.3.3-2.dsc ok ok gdal_1.9.0-3.dsc ok ok getfem++_4.1.1-10.dsc FAILED ok gnudatalanguage_0.9.2-4.dsc ok ok gnuradio_3.6.1-1.dsc FAILED ok guiqwt_2.1.6-4.dsc FAILED ok h5py_2.0.1-2.dsc ok ok joblib_0.6.4-3.dsc ok ok lazyarray_0.1.0-1.dsc ok ok libfreenect_0.1.2+dfsg-6.dsc ok ok libgetdata_0.7.3-6.dsc ok ok libmpikmeans_1.5-1.dsc ok ok libvigraimpex_1.7.1+dfsg1-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… lintian_2.5.10.1.dsc FAILED ok magics++_2.14.11-4.dsc ok ok mathgl_1.11.2-14.dsc FAILED ok matplotlib_1.1.1~rc2-1.dsc FAILED ok mayavi2_4.1.0-1.dsc FAILED ok mdp_3.2+git78-g7db3c50-3.dsc ok ok mgltools-bhtree_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-dejavu_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-geomutils_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-gle_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-molkit_1.5.6~rc3~cvs.20120206-1.dsc ok ok mgltools-opengltk_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-pyglf_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-sff_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-utpackages_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-vision_1.5.6~rc3~cvs.20120601-1.dsc ok ok mgltools-visionlibraries_1.5.6~rc3~cvs.20120601-1.dsc ok ok mlpy_2.2.0~dfsg1-2.dsc ok ok mmass_5.2.0-2.dsc ok ok model-builder_0.4.1-6.dsc ok ok mpi4py_1.3+hg20120611-1.dsc ok ok mypaint_1.0.0-1.dsc ok ok necpp_1.5.0+cvs20101003-2.1.dsc ok ok neo_0.2.0-1.dsc ok ok nexus_4.2.1-svn1614-1.dsc FAILED ok nibabel_1.2.2-1.dsc ok ok nipy_0.2.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… nitime_0.4-2.dsc ok ok nlopt_2.2.4+dfsg-2.dsc ok ok numexpr_2.0.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… numm_0.4-1.dsc FAILED ok opencv_2.3.1-11.dsc ok ok openmeeg_2.0.0.dfsg-5.dsc FAILED ok openopt_0.38+svn1589-1.dsc ok ok pandas_0.8.1-1.dsc ok ok pdb2pqr_1.8-1.dsc ok ok pebl_1.0.2-2.dsc ok ok plplot_5.9.9-5.dsc FAILED ok psignifit3_3.0~beta.20120611.1-1.dsc ok ok pycuda_2012.1-1.dsc ok ok pydicom_0.9.6-1.dsc ok ok pyentropy_0.4.1-1.dsc ok ok pyepr_0.6.1-2.dsc ok ok pyevolve_0.6~rc1+svn398+dfsg-2.dsc ok ok pyfai_0.3.5-1.dsc ok ok pyfits_3.0.8-2.dsc ok ok pyformex_0.8.6-4.dsc ok ok pygame_1.9.1release+dfsg-6.dsc FAILED ok pygrib_1.9.3-1.dsc ok ok pygtk_2.24.0-3.dsc ok ok pylibtiff_0.3.0~svn78-3.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… pymca_4.6.0-2.dsc ok ok pymol_1.5.0.1-2.dsc ok ok pymvpa_0.4.8-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… pymvpa2_2.1.0-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… pynifti_0.20100607.1-4.dsc ok ok pynn_0.7.4-1.dsc ok ok pyopencl_2012.1-1.dsc ok ok pyqwt3d_0.1.7~cvs20090625-9.dsc FAILED ok pyqwt5_5.2.1~cvs20091107+dfsg-6.dsc FAILED ok pysparse_1.1-1.dsc ok ok pysurfer_0.3+git15-gae6cbb1-1.1.dsc ok ok pytables_2.3.1-3.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… pytango_7.2.3-2.dsc ok ok python-ase_3.6.0.2515-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… python-biggles_1.6.6-1.dsc ok ok python-biom-format_1.0.0-1.dsc ok ok python-biopython_1.59-1.dsc ok ok python-chaco_4.1.0-1.dsc ok ok python-cogent_1.5.1-2.dsc ok ok python-cpl_0.3.6-1.dsc ok ok python-csa_0.1.0-1.1.dsc ok ok python-enable_4.1.0-1.dsc ok ok python-fabio_0.0.8-1.dsc ok ok python-fftw_0.2.2-1.dsc ok ok python-gnuplot_1.8-1.1.dsc ok ok python-networkx_1.7~rc1-3.dsc ok ok python-neuroshare_0.8.5-1.dsc ok ok python-pywcs_1.11-1.dsc ok ok python-scientific_2.8-3.dsc ok ok python-scipy_0.10.1+dfsg1-4.dsc ok ok python-shapely_1.2.14-1.dsc ok ok python-visual_5.12-1.4.dsc ok ok pytools_2011.5-2.dsc ok ok pywavelets_0.2.0-5.dsc ok ok pyzmq_2.2.0-1.dsc ok ok qiime_1.5.0-2.dsc ok ok rdkit_201203-3.dsc ok ok rpy_1.0.3-22.dsc ok ok rpy2_2.2.6-1.dsc ok ok scikit-learn_0.11.0-2.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… shogun_1.1.0-6.dsc FAILED ok skimage_0.6.1-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… spherepack_3.2-4.dsc ok ok statsmodels_0.4.2-1.dsc ok FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… stimfit_0.10.18-1.1.dsc ok ok syfi_1.0.0.dfsg-1.dsc ok ok taurus_3.0.0-1.dsc FAILED ok tifffile_20120421-1.dsc ok ok uncertainties_1.8-1.dsc ok ok veusz_1.15-1.dsc FAILED ok vistrails_2.0.alpha~1-3.dsc ok ok wrapitk-python_3.20.1.5.dsc FAILED FAILED http://www.onerussian.com/Linux/deb/logs/python-numpy_1.7.0~b1-1_amd64.test… wsjt_5.9.7.r383-1.6.dsc ok ok yade_0.80.1-2.dsc FAILED ok yp-svipc_0.14-2.dsc ok ok -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik

4 8

encounter error while it's testing
by 心如烛光 Sept. 5, 2012

Sept. 5, 2012

Hi,everybody. I have installed scipy with commend:"pip install scipy" (OSX lion 10.7.4) But I encounter error while testing.BTW,the test of numpy is OK. I input: >>> import scipy >>> scipy.test() And this is the respond: Running unit tests for scipy NumPy version 1.8.0.dev-e60c70d NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy SciPy version 0.12.0.dev-858610f SciPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy Python version 2.7.3 (default, Apr 19 2012, 00:55:09) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] nose version 1.1.2 .....................................................................................................................................................................................F.FFPython(334,0x7fff7d1a2960) malloc: *** error for object 0x7fa0544e7f28: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6

2 1

Question Regarding numpy.i and 2-dimensional input array
by Dylan Temple Sept. 5, 2012

Sept. 5, 2012

Hello, I am trying to use numpy.i to move a function from python to C that takes a 2-D array as an input and am having difficulty. The code is pretty long so I've made a simple example that recreates the error. example.c: #include <stdio.h> #include "example.h" void matrix_example (int n, int m, double *x0, \ int p, double *x) { int i; int j; int k; for (i = 0; i < n; ++i) { for (j=0; j < 0; ++j) { x[k] = 2 * x0[i][j]; ++k; } } } example.h: void matrix_example (int n, int m, double *x0, int p, double *x); example.i: %module example %{ #define SWIG_FILE_WITH_INIT #include "example.h" %} %include "numpy.i" %init %{ import_array(); %} %apply (int DIM1, int DIM2, double *IN_ARRAY2) {(int n, int m, double *x0)}; %apply (int DIM1, double *ARGOUT_ARRAY1) {(int p, double *x)}; I then use prompts: $ swig -python example.i $ python setup.py build_ext --inplace However I get the error: example.c: In function ‘matrix_example’: example.c:12: error: subscripted value is neither array nor pointer error: command 'gcc' failed with exit status 1 It seems as though x0 is not actually being passed to the function as a 2-D array. Any help on why this error is happening would be great! Thank you, Dylan Temple -- Dylan Temple Graduate Student, University of Michigan NA&ME Department B.E. Naval Architecture M.S.E Naval Architecture 121 NA&ME Department, 2600 Draper Dr. 607-592-1749

2 1

ANN: scikit-learn 0.12 Released
by Andreas Mueller Sept. 4, 2012

Sept. 4, 2012

Dear fellow Pythonistas. I am pleased to announce the release of scikit-learn 0.12 <http://scikit-learn.org/stable/>. This release adds several new features, for example multidimensional scaling (MDS), multi-task Lasso and multi-output decision and regression forests. There has also been a lot of progress in documentation and ease of use. Details can be found on the what's new page <cid:part2.04060304.01070404@ais.uni-bonn.de>. Sources and windows binaries are available on sourceforge, through pypi (http://pypi.python.org/pypi/scikit-learn/0.12) or can be installed directly using pip: pip install -U scikit-learn I want to thank all of the developers who made this release possible and welcome our new contributors. Keep on learning, Andy

1 0

Mysterious test_pareto failure on Travis
by Nathaniel Smith Sept. 4, 2012

Sept. 4, 2012

The last two Travis builds of master have failed consistently with the same error: http://travis-ci.org/#!/numpy/numpy/builds It looks like a real failure -- we're getting the same error on every build variant, some sort of problem in test_pareto. Example: http://travis-ci.org/#!/numpy/numpy/jobs/2328823 The obvious culprit would be the previous commit, which regenerated mtrand.c with Cython 0.17: http://github.com/numpy/numpy/commit/cd9092aa71d23359b33e89d938c55fb14b9bf6… What's weird, though, is that that commit passed just fine on Travis: http://travis-ci.org/#!/numpy/numpy/builds/2313124 It's just the two commits since then that failed. But these commits have been 1-line docstring changes, so I don't see how they could have possibly created the problem. Also, the test passes fine with python 2.7 on my laptop with current master. Can anyone reproduce this failure? Any ideas what might be going on? -n

6 13

Re: [Numpy-discussion] [SciPy-User] [ANN] New free tool for TSP solving
by Dmitrey Sept. 3, 2012

Sept. 3, 2012

--- Исходное сообщение --- От кого: "Niki Spahiev" <niki.spahiev(a)gmail.com> Кому: scipy-user(a)scipy.org Дата: 3 сентября 2012, 13:57:49 Тема: Re: [SciPy-User] [ANN] New free tool for TSP solving > > > New free tool for TSP solving is available (for downloading as well) - > OpenOpt TSP class: TSP (traveling salesman problem). Hello Dmitrey, Can this tool solve ATSP problems? Thanks, Niki > Hi, yes - asymmetric (see examples with networkx DiGraph), including multigraphs (networkx MultiDiGraph) as well. > _______________________________________________ SciPy-User mailing listSciPy-User@scipy.orghttp://mail.scipy.org/mailman/listinfo/scipy-user

1 0

[ANN] New free tool for TSP solving
by Dmitrey Sept. 2, 2012

Sept. 2, 2012

Hi all, New free tool for TSP solving is available (for downloading as well) - OpenOpt TSP class: TSP (traveling salesman problem). It is written in Python, uses NetworkX graphs on input (another BSD-licensed Python library, de-facto standard graph lib for Python language programmers), can connect to MILP solvers like glpk, cplex, lpsolve, has a couple of other solvers - sa (simulated annealing, Python code by John Montgomery) and interalg If someone is interested, I could implement something from (or beyound) its future plans till next OpenOpt stable release 0.41, that will be 2 weeks later (Sept-15). Regards, D.

1 0

encounter many warnings while it's installing scipy
by 心如烛光 Sept. 2, 2012

Sept. 2, 2012

Hi,everybody. I encounter many warnings while it's installing scipy with the commend:pip install scipy Such as " warning:XX variable is uninitialized before used [-Wuninitialized]" What makes these warnings? And will they make something wrong with scipy?How can I fix it ?? Thank you so much for your help!

2 1

How to debug reference counting errors
by Ondřej Čertík Sept. 1, 2012

Sept. 1, 2012

Hi, There is segfault reported here: http://projects.scipy.org/numpy/ticket/1588 I've managed to isolate the problem and even provide a simple patch, that fixes it here: https://github.com/numpy/numpy/issues/398 however the patch simply doesn't decrease the proper reference, so it might leak. I've used bisection (took the whole evening unfortunately...) but the good news is that I've isolated commits that actually broke it. See the github issue #398 for details, diffs etc. Unfortunately, it's 12 commits from Mark and the individual commits raise exception on the segfaulting code, so I can't pin point the problem further. In general, how can I debug this sort of problem? I tried to use valgrind, with a debugging build of numpy, but it provides tons of false (?) positives: https://gist.github.com/3549063 Mark, by looking at the changes that broke it, as well as at my "fix", do you see where the problem could be? I suspect it is something with the changes in PyArray_FromAny() or PyArray_FromArray() in ctors.c. But I don't see anything so far that could cause it. Thanks for any help. This is one of the issues blocking the 1.7.0 release. Ondrej

4 5