Mailman 3 August 2012 - SciPy-Dev

SciPy.org Website Move and Redesign
by Kyle Mandli Aug. 26, 2012

Aug. 26, 2012

At the scipy conference this year there were a number of people who expressed interest in moving the scipy.org website off of the current server and migrate away from using MoinMoinWiki. It turns out there have been a number of attempts at this over the past couple of years but nothing has ever stuck (as can be seen in the github org page). After discussing a number of approaches it sounds like the best strategy is one similar to what IPython and many other packages are using, namely using github pages and sphinx. The plan would be: 1) Mailing lists - Leave these as there's a lot of content there and we are worried about losing history and users if we even attempted to move this (plus we don't have a good alternative). 2) Scipy.org (and numpy.org) - Move the content to a repository under the Scipy organization on github that would contain a sphinx representation of the content that people can make pull requests to. There would be another repository that the built content would then be pushed to and that github would show as the website. David Warde-Farley has made an attempt at converting many of the scipy pages over to sphinx but it was never used (https://github.com/dwf/scipy-website). I noticed there were a few attempts at this a while ago (> 2 years). 3) Trac Projects - Numpy is in the process (or so we thought) of moving all the trac issues to github issues and as far as we are aware represents really the last reason these trac projects are still being used. Once this is done we can dispense with these as well. The scipy trac pages have not been moved at all and would also have to be done. These represent some effort but the website could make the transition before this is complete anyway. 4) Anything else? I am hoping that we can move the content quickly and set up the system first to get it off the ground and update the pages as we can. Hopefully we can get something going quickly and avoid the fates of previous attempts at this. Kyle

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scipy.ndimage.measurements.label
by Sarah Mount Aug. 25, 2012

Aug. 25, 2012

Hi there, sorry if this is a bit of a daft and random question, but I couldn't figure it out from reading the source. What algorithm does scipy.ndimage.measurements.label implement? Many thanks, Sarah -- Sarah Mount, Senior Lecturer, University of Wolverhampton website: http://www.snim2.org/ twitter: @snim2

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Re: [SciPy-Dev] Mountain Lion Scipy-dev build fails (Ralf Gommers)
by Aaron Andalman Aug. 24, 2012

Aug. 24, 2012

Ralf, Thanks for the information. You were correct; the -msse4 flag does appear to be coming from the brew installation of python. Grep reveals the flag in a Makefile, and editing the makefile altered the results of scipy python setup.py configure. Thus scipy now compiles! Thank you. However, I'm hoping to understand how and why scipy gets the -msse4 flag from the Makefile? Should this be modified? Or should the brew python formula be modified somehow? Thanks, Aaron

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scipy-0.10.1 compilation on 64 bit windows in debug mode
by Santosh Pratap Singh Aug. 16, 2012

Aug. 16, 2012

Hi All, I am trying to compile a debug version of the scipy-0.10.1 extension on 64 bit windows. I have also compiled the python-2.7.3 and numpy-1.6.2 in debug mode. When I am building scipy, I ran into the problem C:\cpython\Debug\scipy\0_10_1\scipy-0.10.1>python_d setup.py config --compiler=msvc --fcompiler=intelvem build --debug compile options: '-g -IC:\cpython\Debug\CPython\2_7_3\winx64\Debug\python\lib\site-packages\numpy\core\include -c' ifort.exe:f77: scipy\fftpack\src\dfftpack\dcosqb.f ifort: command line warning #10131: extension 'M' not supported ignored in optio n '/Qax' *ifort: command line error: option '/g' is ambiguous* error: Command "C:\Program Files (x86)\Intel\Compiler\11.1\060\Bin\intel64\ifort.exe -FI -w90 -w95 /nologo /MD /nbs /Qlowercase /us /O1 /QaxM -g -IC:\cpython\Debug\CPython\2_7_3\winx64\Debug\python\lib\site-packages\numpy\core\include -c /c scipy\fftpack\src\dfftpack\dcosqb.f /Fobuild\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcosqb.o" failed with exit status 1 Can some one help me in this? Am I missing something? Thanks. Santosh

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Re: [SciPy-Dev] Suggested Change to io.wavfile
by Brian Hone Aug. 13, 2012

Aug. 13, 2012

I'm in the process of spinning up a technical team that is using scipy for audio signal processing, so I expect that we'll be finding lots of issues with wavfile. I'll take a look at the bug list and see if we knock off a few of them as we go. Happy to do the test and pull request. Stupid question though - I haven't yet made the jump from good old svn to git. Can anyone give me the right sequence of commands so I don't mess it up? Brian On 8/11/2012 1:00 PM, scipy-dev-request(a)scipy.org wrote: > > Thanks for posting. I see we don't have a nominated maintainer for > io.wavfile - Ralf - is that right? > > https://github.com/scipy/scipy/blob/master/doc/MAINTAINERS.rst.txt > > Does anyone who uses wav files feel able to comment here? > > Brian - please consider a test and a pull request? Please do email > again if that's hard to do. Do you think we should omit a warning or > make this fix optional, perhaps with the fix set as the default > behavior? > > Thanks again, > > Matthew > > > ------------------------------ > > Message: 2 > Date: Fri, 10 Aug 2012 22:02:07 +0200 > From: Ralf Gommers<ralf.gommers(a)gmail.com> > Subject: Re: [SciPy-Dev] Suggested Change to io.wavfile > To: SciPy Developers List<scipy-dev(a)scipy.org> > Message-ID: > <CABL7CQimy=nGtzPmYR46a-n1yrwQf0gaNzD+BzByvfv=UMzaKw(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > On Fri, Aug 10, 2012 at 9:51 PM, Matthew Brett<matthew.brett(a)gmail.com>wrote: > >> Hi, >> >> On Thu, Aug 9, 2012 at 8:08 AM, Brian Hone<brianhone(a)gmail.com> wrote: >>> Hi folks, >>> >>> I'm running into a wavfile read error which appears to be caused by >>> slight problems in wavfile meta-data. (Specifically, the meta-data >>> mis-reports the number of frames). Unfortunately, 2/3 of the wav files >>> I've randomly sampled have this problem, and most audio packages just >>> deal with it. >>> >>> I notice from a search that a lot of people have this problem with >>> io.wavfile.read: >>> >>> /usr/lib/python2.7/site-packages/scipy/io/wavfile.pyc in read(file) >>> 125 else: >>> 126 fmt = '<i' >>> --> 127 size = struct.unpack(fmt, data)[0] >>> 128 fid.seek(size, 1) >>> 129 fid.close() >>> >>> >>> Here's a fix - just calculate the actual file length and use the minimum >>> or the file length and the meta-data reported length. >>> >>> 113,121c113 >>> < >>> < ## Calculate the actual file length in case meta-data is incorrect >>> < current_pos = fid.tell() >>> < fid.seek(0,2) >>> < actual_file_length = fid.tell() >>> < fid.seek( current_pos ) >>> < total_length = min( fsize, actual_file_length ) >>> < >>> < while (fid.tell()< total_length): >>> --- >>> > while (fid.tell()< fsize): >> Thanks for posting. I see we don't have a nominated maintainer for >> io.wavfile - Ralf - is that right? >> > Yes, unfortunately. I count 7 open tickets for wavfile, some of which are > quite old. Wavfile is<200 lines of Python code, so fixing most of these > probably won't be very difficult. If there's someone who is interested in > this code and would be willing to put in some time, that would be great. > > Ralf > > >> https://github.com/scipy/scipy/blob/master/doc/MAINTAINERS.rst.txt >> >> Does anyone who uses wav files feel able to comment here? >> >> Brian - please consider a test and a pull request? Please do email >> again if that's hard to do. Do you think we should omit a warning or >> make this fix optional, perhaps with the fix set as the default >> behavior? >> >> Thanks again, >> >> Matthew >> _______________________________________________ >> SciPy-Dev mailing list >> SciPy-Dev(a)scipy.org >> http://mail.scipy.org/mailman/listinfo/scipy-dev >>

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Suggested Change to io.wavfile
by Brian Hone Aug. 10, 2012

Aug. 10, 2012

Hi folks, I'm running into a wavfile read error which appears to be caused by slight problems in wavfile meta-data. (Specifically, the meta-data mis-reports the number of frames). Unfortunately, 2/3 of the wav files I've randomly sampled have this problem, and most audio packages just deal with it. I notice from a search that a lot of people have this problem with io.wavfile.read: /usr/lib/python2.7/site-packages/scipy/io/wavfile.pyc in read(file) 125 else: 126 fmt = '<i' --> 127 size = struct.unpack(fmt, data)[0] 128 fid.seek(size, 1) 129 fid.close() Here's a fix - just calculate the actual file length and use the minimum or the file length and the meta-data reported length. 113,121c113 < < ## Calculate the actual file length in case meta-data is incorrect < current_pos = fid.tell() < fid.seek(0,2) < actual_file_length = fid.tell() < fid.seek( current_pos ) < total_length = min( fsize, actual_file_length ) < < while (fid.tell() < total_length): --- > while (fid.tell() < fsize):

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ANN: SciPy 0.11.0 release candidate 1
by Ralf Gommers Aug. 10, 2012

Aug. 10, 2012

Hi, I am pleased to announce the availability of the first release candidate of SciPy 0.11.0. For this release many new features have been added, and over 120 tickets and pull requests have been closed. Also noteworthy is that the number of contributors for this release has risen to over 50. Some of the highlights are: - A new module, sparse.csgraph, has been added which provides a number of common sparse graph algorithms. - New unified interfaces to the existing optimization and root finding functions have been added. Sources and binaries can be found at https://sourceforge.net/projects/scipy/files/scipy/0.11.0rc1/, release notes are copied below. Please try this release candidate and report any problems on the scipy mailing lists. Cheers, Ralf ========================== SciPy 0.11.0 Release Notes ========================== .. note:: Scipy 0.11.0 is not released yet! .. contents:: SciPy 0.11.0 is the culmination of 8 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. Highlights of this release are: - A new module has been added which provides a number of common sparse graph algorithms. - New unified interfaces to the existing optimization and root finding functions have been added. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Our development attention will now shift to bug-fix releases on the 0.11.x branch, and on adding new features on the master branch. This release requires Python 2.4-2.7 or 3.1-3.2 and NumPy 1.5.1 or greater. New features ============ Sparse Graph Submodule ---------------------- The new submodule :mod:`scipy.sparse.csgraph` implements a number of efficient graph algorithms for graphs stored as sparse adjacency matrices. Available routines are: - :func:`connected_components` - determine connected components of a graph - :func:`laplacian` - compute the laplacian of a graph - :func:`shortest_path` - compute the shortest path between points on a positive graph - :func:`dijkstra` - use Dijkstra's algorithm for shortest path - :func:`floyd_warshall` - use the Floyd-Warshall algorithm for shortest path - :func:`breadth_first_order` - compute a breadth-first order of nodes - :func:`depth_first_order` - compute a depth-first order of nodes - :func:`breadth_first_tree` - construct the breadth-first tree from a given node - :func:`depth_first_tree` - construct a depth-first tree from a given node - :func:`minimum_spanning_tree` - construct the minimum spanning tree of a graph ``scipy.optimize`` improvements ------------------------------- The optimize module has received a lot of attention this release. In addition to added tests, documentation improvements, bug fixes and code clean-up, the following improvements were made: - A unified interface to minimizers of univariate and multivariate functions has been added. - A unified interface to root finding algorithms for multivariate functions has been added. - The L-BFGS-B algorithm has been updated to version 3.0. Unified interfaces to minimizers ```````````````````````````````` Two new functions ``scipy.optimize.minimize`` and ``scipy.optimize.minimize_scalar`` were added to provide a common interface to minimizers of multivariate and univariate functions respectively. For multivariate functions, ``scipy.optimize.minimize`` provides an interface to methods for unconstrained optimization (`fmin`, `fmin_powell`, `fmin_cg`, `fmin_ncg`, `fmin_bfgs` and `anneal`) or constrained optimization (`fmin_l_bfgs_b`, `fmin_tnc`, `fmin_cobyla` and `fmin_slsqp`). For univariate functions, ``scipy.optimize.minimize_scalar`` provides an interface to methods for unconstrained and bounded optimization (`brent`, `golden`, `fminbound`). This allows for easier comparing and switching between solvers. Unified interface to root finding algorithms ```````````````````````````````````````````` The new function ``scipy.optimize.root`` provides a common interface to root finding algorithms for multivariate functions, embeding `fsolve`, `leastsq` and `nonlin` solvers. ``scipy.linalg`` improvements ----------------------------- New matrix equation solvers ``````````````````````````` Solvers for the Sylvester equation (``scipy.linalg.solve_sylvester``, discrete and continuous Lyapunov equations (``scipy.linalg.solve_lyapunov``, ``scipy.linalg.solve_discrete_lyapunov``) and discrete and continuous algebraic Riccati equations (``scipy.linalg.solve_continuous_are``, ``scipy.linalg.solve_discrete_are``) have been added to ``scipy.linalg``. These solvers are often used in the field of linear control theory. QZ and QR Decomposition ```````````````````````` It is now possible to calculate the QZ, or Generalized Schur, decomposition using ``scipy.linalg.qz``. This function wraps the LAPACK routines sgges, dgges, cgges, and zgges. The function ``scipy.linalg.qr_multiply``, which allows efficient computation of the matrix product of Q (from a QR decompostion) and a vector, has been added. Pascal matrices ``````````````` A function for creating Pascal matrices, ``scipy.linalg.pascal``, was added. Sparse matrix construction and operations ----------------------------------------- Two new functions, ``scipy.sparse.diags`` and ``scipy.sparse.block_diag``, were added to easily construct diagonal and block-diagonal sparse matrices respectively. ``scipy.sparse.csc_matrix`` and ``csr_matrix`` now support the operations ``sin``, ``tan``, ``arcsin``, ``arctan``, ``sinh``, ``tanh``, ``arcsinh``, ``arctanh``, ``rint``, ``sign``, ``expm1``, ``log1p``, ``deg2rad``, ``rad2deg``, ``floor``, ``ceil`` and ``trunc``. Previously, these operations had to be performed by operating on the matrices' ``data`` attribute. LSMR iterative solver --------------------- LSMR, an iterative method for solving (sparse) linear and linear least-squares systems, was added as ``scipy.sparse.linalg.lsmr``. Discrete Sine Transform ----------------------- Bindings for the discrete sine transform functions have been added to ``scipy.fftpack``. ``scipy.interpolate`` improvements ---------------------------------- For interpolation in spherical coordinates, the three classes ``scipy.interpolate.SmoothSphereBivariateSpline``, ``scipy.interpolate.LSQSphereBivariateSpline``, and ``scipy.interpolate.RectSphereBivariateSpline`` have been added. Binned statistics (``scipy.stats``) ----------------------------------- The stats module has gained functions to do binned statistics, which are a generalization of histograms, in 1-D, 2-D and multiple dimensions: ``scipy.stats.binned_statistic``, ``scipy.stats.binned_statistic_2d`` and ``scipy.stats.binned_statistic_dd``. Deprecated features =================== ``scipy.sparse.cs_graph_components`` has been made a part of the sparse graph submodule, and renamed to ``scipy.sparse.csgraph.connected_components``. Calling the former routine will result in a deprecation warning. ``scipy.misc.radon`` has been deprecated. A more full-featured radon transform can be found in scikits-image. ``scipy.io.save_as_module`` has been deprecated. A better way to save multiple Numpy arrays is the ``numpy.savez`` function. The `xa` and `xb` parameters for all distributions in ``scipy.stats.distributions`` already weren't used; they have now been deprecated. Backwards incompatible changes ============================== Removal of ``scipy.maxentropy`` ------------------------------- The ``scipy.maxentropy`` module, which was deprecated in the 0.10.0 release, has been removed. Logistic regression in scikits.learn is a good and modern alternative for this functionality. Minor change in behavior of ``splev`` ------------------------------------- The spline evaluation function now behaves similarly to ``interp1d`` for size-1 arrays. Previous behavior:: >>> from scipy.interpolate import splev, splrep, interp1d >>> x = [1,2,3,4,5] >>> y = [4,5,6,7,8] >>> tck = splrep(x, y) >>> splev([1], tck) 4. >>> splev(1, tck) 4. Corrected behavior:: >>> splev([1], tck) array([ 4.]) >>> splev(1, tck) array(4.) This affects also the ``UnivariateSpline`` classes. Behavior of ``scipy.integrate.complex_ode`` ------------------------------------------- The behavior of the ``y`` attribute of ``complex_ode`` is changed. Previously, it expressed the complex-valued solution in the form:: z = ode.y[::2] + 1j * ode.y[1::2] Now, it is directly the complex-valued solution:: z = ode.y Minor change in behavior of T-tests ----------------------------------- The T-tests ``scipy.stats.ttest_ind``, ``scipy.stats.ttest_rel`` and ``scipy.stats.ttest_1samp`` have been changed so that 0 / 0 now returns NaN instead of 1. Other changes ============= The SuperLU sources in ``scipy.sparse.linalg`` have been updated to version 4.3 from upstream. The function ``scipy.signal.bode``, which calculates magnitude and phase data for a continuous-time system, has been added. The two-sample T-test ``scipy.stats.ttest_ind`` gained an option to compare samples with unequal variances, i.e. Welch's T-test. ``scipy.misc.logsumexp`` now takes an optional ``axis`` keyword argument. Authors ======= This release contains work by the following people (contributed at least one patch to this release, names in alphabetical order): * Jeff Armstrong * Chad Baker * Brandon Beacher + * behrisch + * borishim + * Matthew Brett * Lars Buitinck * Luis Pedro Coelho + * Johann Cohen-Tanugi * David Cournapeau * dougal + * Ali Ebrahim + * endolith + * Bjørn Forsman + * Robert Gantner + * Sebastian Gassner + * Christoph Gohlke * Ralf Gommers * Yaroslav Halchenko * Charles Harris * Jonathan Helmus + * Andreas Hilboll + * Marc Honnorat + * Jonathan Hunt + * Maxim Ivanov + * Thouis (Ray) Jones * Christopher Kuster + * Josh Lawrence + * Denis Laxalde + * Travis Oliphant * Joonas Paalasmaa + * Fabian Pedregosa * Josef Perktold * Gavin Price + * Jim Radford + * Andrew Schein + * Skipper Seabold * Jacob Silterra + * Scott Sinclair * Alexis Tabary + * Martin Teichmann * Matt Terry + * Nicky van Foreest + * Jacob Vanderplas * Patrick Varilly + * Pauli Virtanen * Nils Wagner + * Darryl Wally + * Stefan van der Walt * Liming Wang + * David Warde-Farley + * Warren Weckesser * Sebastian Werk + * Mike Wimmer + * Tony S Yu + A total of 55 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

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test_qz_double_sort seg fault - upgrade mingw for binaries?
by Skipper Seabold Aug. 9, 2012

Aug. 9, 2012

Hi, There is a failure that's holding up the release reported here. projects.scipy.org/scipy/ticket/1717 AFAIK, this test seg faults only on the official SSE2/SSE3 windows 32-bit binaries that are built using mingw 3.14 with gcc 3.4. It's only the double precision test that has a callback function that break. https://github.com/numpy/vendor The suspicion is that it's a compiler issue since the tests pass on other architectures and with msvc/mkl on windows as reported by Christoph. I didn't see anything in the LAPACK change sets to suggest it's an issue with the ATLAS/LAPACK, though I suppose this is still possible. How difficult would it be for someone to upgrade mingw/gcc and see if the seg fault goes away? I could try though I'm not set up for this and am not that familiar with cygwin/mingw. Are there any other mingw issues on windows to be aware of that prevents using a newer compiler? Any other way to resolve this? Skipper

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Mountain Lion Scipy-dev build fails
by Aaron Andalman Aug. 9, 2012

Aug. 9, 2012

Dear scipy-dev list, Scipy is failing to build on Mountain Lion, despite my using the latest fixes on github. I'm using pip install -e git+ https://github.com/scipy/scipy#egg=scipy-dev The installation crashes on the line: /usr/bin/llvm-gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -O3 -w -pipe -march=core2 -msse4 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC -I/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -c scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c -o build/temp.macosx-10.5-intel-2.7/scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.o" failed with exit status 1 With the error: In file included from /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:43, from /System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:20, from scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2: /System/Library/Frameworks/vecLib.framework/Headers/vfp.h:51:23: error: immintrin.h: No such file or directory In file included from /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:43, from /System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:20, from scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2: /System/Library/Frameworks/vecLib.framework/Headers/vfp.h: In function ‘vceilf’: /System/Library/Frameworks/vecLib.framework/Headers/vfp.h:53: error: incompatible types in return ... I can compile veclib_cabi.c.c, if I change the -msse4 compilation flag to -msse3 (or if I use clang, but this causes other errors). Thus my questions are: 1) how can I change the compilations flags used by python setup.py to include -msse3 instead of -msse4? 2) why is -msse4 being selected by python setup.py in the first place? 3) is this a bug with setup.py on mountain lion, or is this a problem with my installation? Below is the information requested by the scipy installation readme. python -c 'from numpy.f2py.diagnose import run; run()' ------ os.name='posix' ------ sys.platform='darwin' ------ sys.version: 2.7.2 (default, Jan 14 2012, 15:51:45) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] ------ sys.prefix: /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/.. ------ sys.path=':/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages/pip-1.1-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python27.zip:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.0.2-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-darwin:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-mac:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-mac/lib-scriptpackages:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-tk:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-old:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-dynload:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages:/Users/andalman/.local/lib/python2.7/site-packages:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info' ------ Found new numpy version '1.6.2' in /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.pyc Found f2py2e version '2' in /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/f2py2e.pyc Found numpy.distutils version '0.4.0' in '/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/__init__.pyc' ------ Importing numpy.distutils.fcompiler ... ok ------ Checking availability of supported Fortran compilers: Gnu95FCompiler instance properties: archiver = ['/usr/local/bin/gfortran', '-cr'] compile_switch = '-c' compiler_f77 = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-form', '- fno-second-underscore', '-arch', 'i686', '-arch', 'x86_64', '-fPIC', '-O3', '-funroll-loops'] compiler_f90 = ['/usr/local/bin/gfortran', '-Wall', '-fno-second- underscore', '-arch', 'i686', '-arch', 'x86_64', '-fPIC', '-O3', '-funroll-loops'] compiler_fix = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-form', '- fno-second-underscore', '-Wall', '-fno-second-underscore', '-arch', 'i686', '-arch', 'x86_64', '-fPIC', '-O3', '- funroll-loops'] libraries = ['gfortran'] library_dirs = [] linker_exe = ['/usr/local/bin/gfortran', '-Wall', '-Wall'] linker_so = ['/usr/local/bin/gfortran', '-Wall', '-arch', 'i686', '- arch', 'x86_64', '-Wall', '-undefined', 'dynamic_lookup', '-bundle'] object_switch = '-o ' ranlib = ['/usr/local/bin/gfortran'] version = LooseVersion ('4.2.1') version_cmd = ['/usr/local/bin/gfortran', '--version'] Fortran compilers found: --fcompiler=gnu95 GNU Fortran 95 compiler (4.2.1) Compilers available for this platform, but not found: --fcompiler=absoft Absoft Corp Fortran Compiler --fcompiler=g95 G95 Fortran Compiler --fcompiler=gnu GNU Fortran 77 compiler --fcompiler=ibm IBM XL Fortran Compiler --fcompiler=intel Intel Fortran Compiler for 32-bit apps --fcompiler=nag NAGWare Fortran 95 Compiler --fcompiler=pg Portland Group Fortran Compiler Compilers not available on this platform: --fcompiler=compaq Compaq Fortran Compiler --fcompiler=hpux HP Fortran 90 Compiler --fcompiler=intele Intel Fortran Compiler for Itanium apps --fcompiler=intelem Intel Fortran Compiler for 64-bit apps --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps --fcompiler=intelvem Intel Visual Fortran Compiler for 64-bit apps --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler --fcompiler=mips MIPSpro Fortran Compiler --fcompiler=none Fake Fortran compiler --fcompiler=pathf95 PathScale Fortran Compiler --fcompiler=sun Sun or Forte Fortran 95 Compiler --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler For compiler details, run 'config_fc --verbose' setup command. ------ Importing numpy.distutils.cpuinfo ... ok ------ CPU information: CPUInfoBase__get_nbits getNCPUs is_64bit is_i386 ------ (main_projects)Aaron-Andalmans-MacBook-Pro:scipy andalman$ #################################### ython /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py lapack_info: libraries lapack not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack not found in /usr/local/lib FOUND: libraries = ['lapack'] library_dirs = ['/usr/lib'] language = f77 lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] wx_info: Could not locate executable wx-config File not found: None. Cannot determine wx info. NOT AVAILABLE lapack_atlas_info: libraries lapack_atlas,f77blas,cblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib __main__.lapack_atlas_info NOT AVAILABLE umfpack_info: libraries umfpack not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib amd_info: libraries amd not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib FOUND: libraries = ['amd'] library_dirs = ['/usr/local/lib'] swig_opts = ['-I/usr/local/include'] define_macros = [('SCIPY_AMD_H', None)] include_dirs = ['/usr/local/include'] FOUND: libraries = ['umfpack', 'amd'] library_dirs = ['/usr/local/lib'] swig_opts = ['-I/usr/local/include', '-I/usr/local/include'] define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)] include_dirs = ['/usr/local/include'] _pkg_config_info: Found executable /usr/local/bin/pkg-config NOT AVAILABLE lapack_atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib __main__.lapack_atlas_threads_info NOT AVAILABLE x11_info: /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538: UserWarning: Specified path /usr/X11R6/lib64 is invalid. warnings.warn('Specified path %s is invalid.' % d) /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538: UserWarning: Specified path /usr/X11/lib64 is invalid. warnings.warn('Specified path %s is invalid.' % d) /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538: UserWarning: Specified path /usr/lib64 is invalid. warnings.warn('Specified path %s is invalid.' % d) FOUND: libraries = ['X11'] library_dirs = ['/usr/X11R6/lib'] include_dirs = ['/usr/X11R6/include'] blas_info: libraries blas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries blas not found in /usr/local/lib FOUND: libraries = ['blas'] library_dirs = ['/usr/lib'] language = f77 fftw_info: libraries fftw3 not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib fftw3 not found libraries rfftw,fftw not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries rfftw,fftw not found in /usr/local/lib libraries rfftw,fftw not found in /usr/lib fftw2 not found NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib __main__.atlas_threads_info NOT AVAILABLE f2py_info: FOUND: sources = ['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c'] include_dirs = ['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src'] gdk_pixbuf_xlib_2_info: NOT AVAILABLE dfftw_threads_info: libraries drfftw_threads,dfftw_threads not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries drfftw_threads,dfftw_threads not found in /usr/local/lib libraries drfftw_threads,dfftw_threads not found in /usr/lib dfftw threads not found NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE fftw3_info: libraries fftw3 not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib fftw3 not found 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'] sfftw_info: libraries srfftw,sfftw not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries srfftw,sfftw not found in /usr/local/lib libraries srfftw,sfftw not found in /usr/lib sfftw not found NOT AVAILABLE xft_info: NOT AVAILABLE fft_opt_info: fftw2_info: libraries rfftw,fftw not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries rfftw,fftw not found in /usr/local/lib libraries rfftw,fftw not found in /usr/lib fftw2 not found NOT AVAILABLE dfftw_info: libraries drfftw,dfftw not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries drfftw,dfftw not found in /usr/local/lib libraries drfftw,dfftw not found in /usr/lib dfftw not found NOT AVAILABLE djbfft_info: NOT AVAILABLE NOT AVAILABLE gdk_x11_2_info: NOT AVAILABLE agg2_info: NOT AVAILABLE numarray_info: NOT AVAILABLE blas_src_info: NOT AVAILABLE fftw_threads_info: libraries rfftw_threads,fftw_threads not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries rfftw_threads,fftw_threads not found in /usr/local/lib libraries rfftw_threads,fftw_threads not found in /usr/lib fftw threads not found NOT AVAILABLE _numpy_info: NOT AVAILABLE gdk_info: NOT AVAILABLE gtkp_x11_2_info: NOT AVAILABLE sfftw_threads_info: libraries srfftw_threads,sfftw_threads not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries srfftw_threads,sfftw_threads not found in /usr/local/lib libraries srfftw_threads,sfftw_threads not found in /usr/lib sfftw threads not found NOT AVAILABLE boost_python_info: NOT AVAILABLE freetype2_info: NOT AVAILABLE gdk_2_info: NOT AVAILABLE lapack_src_info: NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE gtkp_2_info: NOT AVAILABLE gdk_pixbuf_2_info: NOT AVAILABLE blas_mkl_info: libraries mkl,vml,guide not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries lapack_atlas not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib __main__.atlas_info NOT AVAILABLE Numeric_info: NOT AVAILABLE numerix_info: numpy_info: /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538: UserWarning: Specified path /usr/local/include/python2.7 is invalid. warnings.warn('Specified path %s is invalid.' % d) /usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538: UserWarning: Specified path is invalid. warnings.warn('Specified path %s is invalid.' % d) FOUND: define_macros = [('NUMPY_VERSION', '"\\"1.6.2\\""'), ('NUMPY', None)] include_dirs = ['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include'] FOUND: define_macros = [('NUMPY_VERSION', '"\\"1.6.2\\""'), ('NUMPY', None)] include_dirs = ['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include'] lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE

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Re: [SciPy-Dev] [SciPy-User] ANN: SciPy 0.11.0 release candidate 1
by Ralf Gommers Aug. 7, 2012

Aug. 7, 2012

On Sat, Jul 21, 2012 at 7:21 PM, John Hassler <hasslerjc(a)comcast.net> wrote: > > On 7/20/2012 5:00 PM, Pauli Virtanen wrote: > > 20.07.2012 22:24, John Hassler kirjoitti: > >> The offending line is: > >> AA,BB,Q,Z,sdim = qz(A,B,sort=sort) > >> > >> I couldn't find 'sort' defined anywhere, so I arbitrarily changed it to > >> sort='lhp'. Then it runs, although the test fails. > >> > >> Is there something else I can try? > > Seems to be a problem with the callable sort function then. > > > > That it works with sort='lhp' is strange, and probably means that there > > is not a problem with all callback functions, but something goes wrong > > in the algorithm. (Which would be expected, if *gees callbacks work > > without problems.) > > > > If you can/know how to recompile, try recompiling with > > > > set OPT=-g -DDEBUGCFUNCS > > python setup.py ......... > > > > This should make the f2py wrappers spit out extra information on what is > > going on. > > > I'm not set up to recompile. Is there anyone who can reproduce the issue and investigate this further? Alternatively I can build some binaries with the above debug flags. I can't reproduce the issue though, so that may be a painful way to debug. Ralf > I set up a little test program to > reproduce the problem (below). It leads to the Fortran call to gges in > _decomp_qz.py. This crashes if sort_t = 1 (which calls the lambda), but > not for sort_t = 0. I didn't play with it any further. > john > > # Test qz > import numpy as np > from scipy.linalg import qz > > A = np.array([[3.9, 12.5, -34.5, -0.5], > [ 4.3, 21.5, -47.5, 7.5], > [ 4.3, 21.5, -43.5, 3.5], > [ 4.4, 26.0, -46.0, 6.0 ]]) > > B = np.array([[ 1.0, 2.0, -3.0, 1.0], > [1.0, 3.0, -5.0, 4.0], > [1.0, 3.0, -4.0, 3.0], > [1.0, 3.0, -4.0, 4.0]]) > > > #sort = lambda ar,ai,beta : ai == 0 ## crashes > sort = None ## runs > > print(qz(A,B,sort=sort)) > > _______________________________________________ > SciPy-User mailing list > SciPy-User(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-user >

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