Mailman 3 May 2008 - SciPy-Dev

SLSQP Constrained Optimizer Status
by Rob Falck 24 Nov '13

24 Nov '13

I'm currently implementing the Sequential Least Squares Quadratic Programming (SLSQP) optimizer, by Dieter Kraft, for use in Scipy. The Fortran code being wrapped with F2PY is here: http://www.netlib.org/toms/733 (its use within Scipy has been cleared) SLSQP provides for bounds on the independent variables, as well as equality and inequality constraint functions, which is a capability that doesn't exist in scipy.optimize. Currently the code works, although the constraint normals are being generated by approximation. I'm working on a way to pass these in. I think the most elegant way will be a single function that returns the matrix of constraint normals. For a demonstration of what the code can do, here is an optimization of f(x,y) = 2xy + 2x - x**2 - 2y**2 Example 14.2 in Chapra & Canale gives the maximum as x=2.0, y=1.0. The unbounded optimization tests find this solution. As expected, its faster when derivatives are provided rather than approximated. Unbounded optimization. Derivatives approximated. Elapsed time: 1.45792961121 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] Unbounded optimization. Derivatives provided. Elapsed time: 1.03211402893 ms Results [[1.9999999515712266, 0.99999996181577444], -1.9999999999999984, 4, 0, 'Optimization terminated successfully.'] The following example uses an equality constraint to find the optimal when x=y. Bound optimization. Derivatives approximated. Elapsed time: 1.384973526 ms Results [[0.99999996845920858, 0.99999996845920858], -0.99999999999999889, 4, 0, 'Optimization terminated successfully.'] I've tried to conform to the syntax used by the other optimizers in scipy.optimize. The function definition and doc string are below. If anyone is interested in testing it out, let me know. def fmin_slsqp( func, x0 , eqcons=[], f_eqcons=None, ieqcons=[], f_ieqcons=None, bounds = [], fprime = None, fprime_cons=None,args = (), iter = 100, acc = 1.0E-6, iprint = 1, full_output = 0, epsilon = _epsilon ): """ Minimize a function using Sequential Least SQuares Programming Description: Python interface function for the SLSQP Optimization subroutine originally implemented by Dieter Kraft. Inputs: func - Objective function (in the form func(x, *args)) x0 - Initial guess for the independent variable(s). eqcons - A list of functions of length n such that eqcons[j](x0,*args) == 0.0 in a successfully optimized problem f_eqcons - A function of the form f_eqcons(x, *args) that returns an array in which each element must equal 0.0 in a successfully optimized problem. If f_eqcons is specified, eqcons is ignored. ieqcons - A list of functions of length n such that ieqcons[j](x0,*args) >= 0.0 in a successfully optimized problem f_ieqcons - A function of the form f_ieqcons(x0, *args) that returns an array in which each element must be greater or equal to 0.0 in a successfully optimized problem. If f_ieqcons is specified, ieqcons is ignored. bounds - A list of tuples specifying the lower and upper bound for each independent variable [ (xl0, xu0), (xl1, xu1), ...] fprime - A function that evaluates the partial derivatives of func fprime_cons - A function of the form f(x, *args) that returns the m by n array of constraint normals. If not provided, the normals will be approximated. Equality constraint normals precede inequality constraint normals. args - A sequence of additional arguments passed to func and fprime iter - The maximum number of iterations (int) acc - Requested accuracy (float) iprint - The verbosity of fmin_slsqp. iprint <= 0 : Silent operation iprint == 1 : Print summary upon completion (default) iprint >= 2 : Print status of each iterate and summary full_output - If 0, return only the minimizer of func (default). Otherwise, output final objective function and summary information. epsilon - The step size for finite-difference derivative estimates. Outputs: ( x, { fx, gnorm, its, imode, smode }) x - The final minimizer of func. fx - The final value of the objective function. its - The number of iterations. imode - The exit mode from the optimizer, as an integer. smode - A string describing the exit mode from the optimizer. Exit modes are defined as follows: -1 : Gradient evaluation required (g & a) 0 : Optimization terminated successfully. 1 : Function evaluation required (f & c) 2 : Number of equality constraints larger than number of independent variables 3 : More than 3*n iterations in LSQ subproblem 4 : Inequality constraints incompatible 5 : Singular matrix E in LSQ subproblem 6 : Singular matrix C in LSQ subproblem 7 : Rank-deficient equality constraint subproblem HFTI 8 : Positive directional derivative for linesearch 9 : Iteration limit exceeded -- - Rob Falck

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Question about Kaiser Implementation in firwin
by Buehler, Eric (AGRE) 04 Oct '08

04 Oct '08

Hello, I have been using the signal.firwin FIR design tool and I have a question about the implementation. Scipy-0.4.8 Numpy-0.9.6 I am generating a kaiser window with the following parameters: N = 128 Cutoff = ~4e7 width = .3 All of the special kaiser generation parameters in the function follow Oppenheim and Schafer well. Even the sinc function for linear phase is follows exactly. However, the last line of the firwin function is causing me some heartburn. filter_design.py 1538 win = get_window(window,N,fftbins=1) 1539 alpha = N//2 1540 m = numpy.arange(0,N) 1541 h = win*special.sinc(cutoff*(m-alpha)) 1542 return h / sum(h) Line 1542 of filter_design.py, "return h / sum(h)", normalizes the function where it doesn't seem necessary, at least in the kaiser window case. Without the normalization, the kaiser window already returns a value of 1 at the zero frequency point. This normalization scales all of the data, making the window difficult to use in the frequency domain. Can someone point me to the rationale for this line? Looking at the code, this seems to be a pretty recent change (within the last year/year and a half). Thanks, Eric Buehler eric <dot> buehler <at> smiths-aerospace <dot> com ****************************************** The information contained in, or attached to, this e-mail, may contain confidential information and is intended solely for the use of the individual or entity to whom they are addressed and may be subject to legal privilege. If you have received this e-mail in error you should notify the sender immediately by reply e-mail, delete the message from your system and notify your system manager. Please do not copy it for any purpose, or disclose its contents to any other person. The views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of the company. The recipient should check this e-mail and any attachments for the presence of viruses. The company accepts no liability for any damage caused, directly or indirectly, by any virus transmitted in this email. ******************************************

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[SciPy-user] ANN: NumPy/SciPy Documentation Marathon 2008
by Johann Cohen-Tanugi 10 Jun '08

10 Jun '08

Great! I am onboard : wiki username JohannCohenTanugi - review docstrings - test examples - write some? I have not developed any core numpy/scipy functions, but I use python extensively at work. - I am not a native English speaker, but I lived a good 6 years in the U.S.A, so I can make do if needed. ;) Sunday is perfect to start diving in... See you all "there". best, Johann

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Re: [SciPy-dev] Error building from svn on Intel Macs.
by Viral Shah 04 Jun '08

04 Jun '08

I did 'rm -rf build', and here's the output from scratch. I'm building with "python setup.py build". Since the log file is large, I am putting it up here: http://gauss.cs.ucsb.edu/~viral/scipy-build.log -viral > Message: 2 > Date: Fri, 30 May 2008 16:12:42 -0500 > From: "Robert Kern" <robert.kern(a)gmail.com> > Subject: Re: [SciPy-dev] Error building from svn on Intel Macs. > To: "SciPy Developers List" <scipy-dev(a)scipy.org> > Message-ID: > <3d375d730805301412t37517289x91e4b7e9d27f816b(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Fri, May 30, 2008 at 3:53 PM, Viral Shah > <vshah(a)interactivesupercomputing.com> wrote: >> I am using an Intel Mac, and trying to build scipy following the >> instructions at: http://www.scipy.org/Installing_SciPy/Mac_OS_X >> >> I was able to successfully build numpy (from svn) without any extra >> configuration. For scipy, even though I have installed the gfortran >> compiler, setup doesn't seem to like the fact that I have 4.2.3. I am >> using gcc 4.0.1 that is supplied by Apple. I get the following: >> >> customize G95FCompiler >> customize GnuFCompiler >> customize Gnu95FCompiler >> Couldn't match compiler version for 'GNU Fortran (GCC) >> 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU >> Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou >> may redistribute copies of GNU Fortran\nunder the terms of the GNU >> General Public License.\nFor more information about these matters, >> see >> the file named COPYING\n' >> >> After searching around on scipy-dev, I resorted to doing this: >> >> $ python setup.py config_fc --fcompiler=gnu95 build >> >> That allowed me to get further, but left me with the following error >> that I don't understand. I can help update the instructions page with >> info about compilers, if I can get this process working. Thanks in >> advance. > > Please provide the full output. The error that you see is a result of > a failure to correctly configure the Fortran compiler earlier. The > current numpy SVN should be able to handle the version string you give > above. > > > In [37]: from numpy.distutils.fcompiler import gnu > > In [38]: fc = gnu.Gnu95FCompiler() > > In [39]: v = 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free > Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to > the extent permitted by law.\nYou may redistribute copies of GNU > Fortran\nunder the terms of the GNU General Public License.\nFor more > information about these matters, see the file named COPYING\n' > > In [40]: print v > GNU Fortran (GCC) 4.2.3 > Copyright (C) 2007 Free Software Foundation, Inc. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > > > In [41]: fc.version_match(v) > Out[41]: '4.2.3' > > -- > Robert Kern > > "I have come to believe that the whole world is an enigma, a harmless > enigma that is made terrible by our own mad attempt to interpret it as > though it had an underlying truth." > -- Umberto Eco > > > ------------------------------ > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.org > http://projects.scipy.org/mailman/listinfo/scipy-dev > > > End of Scipy-dev Digest, Vol 55, Issue 29 > *****************************************

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Re: [SciPy-dev] ANN: NumPy/SciPy Documentation Marathon 2008
by Joe Harrington 03 Jun '08

03 Jun '08

I'm excited that so many talented people are signing up to contribute to the docs! Now I'm wishing that I had turned my debate with Stefan about the number who would play into a bet for ice cream...ah well. A quick comment about getting started. Please do read the front page of the wiki and the docs it refers to. We spent considerable time fine-tuning these to respond to exactly the questions that have been raised regarding import format, how to sign up, ReST conventions, etc. I'll provide rationale for some of these below. 1. I signed up on the wiki but can't edit; why? Post your name and wait a day. We're trying to avoid wiki spam by having the wiki chieftains approve editors by adding them to EditorGroup. We don't have huge resources so we're trying to pre-empt management problems like cleaning up wiki spam. Then we can spend more of our limited time writing docs. 2. Workflow? How do I know what to edit, review, or proof? We also don't have a workflow yet, though we have a utilitarian hack in mind that should show the status of each function. Right now they're all in need of editing, so we have a few weeks. Part of the problem is that the wiki gets torn down and rebuilt every time Stefan checks the docs in, and it's not a full web ap. If you have interest in helping solve this problem *and you have no interest in writing*, please let us know. Otherwise, please write, write, write! We have like 1000 proofed pages to produce, maybe more. 3. import convention? >>> 1) Assume 'from numpy import *' >>> 2) Assume 'import numpy'?????? >>> 3) Assume 'import numpy as np' For consistency in the docs, and likely to make doctests work, we need to have just one set of assumptions for imports. It will confuse new users and look very unprofessional if one docstring assumes "import numpy", another "import numpy as np", another "from numpy import thefunctionbeingdocumented" and so forth. We want to be clear and to make the examples cut-and-pasteable for as many people as possible. This is why we have asked people (in the doc instructions and example) to assume "import numpy" for numpy docs, to assume that and "import scipy" for scipy docs, and to make all other imports explicitly in the examples (e.g., if you want to plot in an example). We can discuss alternatives here, but we saw recently a variety of opinion (my own perhaps too loudly expressed) on how best to abbreviate, so I think that we'll probably end up in a religious war about how we want to tell people to import. Since it should always be ok simply to "import numpy", and since that is the simplest form of the import command, my personal take is that this is the appropriate assumption to make in the docs. The "assume import numpy" convention is at the very least understood by all, as you have to do it to access the package. My second preference, which looks more like other programming languages and is briefest, is to assume the user has done "from whatever import foo" on every function in the example. Sadly, this looks suspiciously like "from whatever import *", and we definitely don't want to encourage that practice. It's also not likely to be true. I'm still debating with myself over whether we should put that explicit import at the start of each example. It's an extra line, but it makes for the clearest and briefest rest of the example, which is the interesting part. (Allow me to show my silly side by saying that I usually lose these debates with myself...by not deciding.) --jh--

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importing scipy.stats generates exception on deprecate decorator
by Damian Eads 03 Jun '08

03 Jun '08

Hi, I just encountered a rather puzzling exception I have never seen before, which is generated when scipy.stats is imported. It occurs regardless if I use scipy from the latest SVN checkout or Fedora 8-yum. [redfox@localhost chestnut]$ python Python 2.5.1 (r251:54863, Oct 30 2007, 13:54:11) [GCC 4.1.2 20070925 (Red Hat 4.1.2-33)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy.stats Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/tmp/qq/lib/python2.5/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/tmp/qq/lib/python2.5/site-packages/scipy/stats/stats.py", line 192, in <module> import scipy.linalg as linalg File "/tmp/qq/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 13, in <module> from iterative import * File "/tmp/qq/lib/python2.5/site-packages/scipy/linalg/iterative.py", line 5, in <module> from scipy.sparse.linalg import isolve File "/tmp/qq/lib/python2.5/site-packages/scipy/sparse/__init__.py", line 5, in <module> from base import * File "/tmp/qq/lib/python2.5/site-packages/scipy/sparse/base.py", line 45, in <module> class spmatrix(object): File "/tmp/qq/lib/python2.5/site-packages/scipy/sparse/base.py", line 139, in spmatrix @deprecate TypeError: deprecate() takes exactly 3 arguments (1 given) >>> Any ideas? Damian

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Re: [SciPy-dev] Error building from svn on Intel Macs.
by Viral Shah 31 May '08

31 May '08

Attaching full output. $ python setup.py build Warning: No configuration returned, assuming unavailable. mkl_info: libraries mkl,vml,guide not found in /System/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 NOT AVAILABLE fftw3_info: libraries fftw3 not found in /System/Library/Frameworks/ Python.framework/Versions/2.5/lib libraries fftw3 not found in /usr/local/lib libraries fftw3 not found in /usr/lib fftw3 not found NOT AVAILABLE fftw2_info: libraries rfftw,fftw not found in /System/Library/Frameworks/ Python.framework/Versions/2.5/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 /System/Library/Frameworks/ Python.framework/Versions/2.5/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 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 /System/Library/Frameworks/ Python.framework/Versions/2.5/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/ python/numpy/distutils/system_info.py:401: 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_fc 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._hierarchy_wrap" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-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-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/scipy/interpolate/dfitpack- f2pywrappers.f' to sources. building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/lapack/ clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-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-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize._slsqp" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-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-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-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-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- 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-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.stats.statlib" sources f2py options: ['--no-wrap-functions'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.stats.futil" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.stats.mvn" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/scipy/stats/mvn- f2pywrappers.f' to sources. building extension "scipy.ndimage._nd_image" sources building extension "scipy.ndimage._segment" sources building extension "scipy.ndimage._register" 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 scipy/__svn_version__.py -> build/lib.macosx-10.5-i386-2.5/scipy copying build/src.macosx-10.5-i386-2.5/scipy/__config__.py -> build/ lib.macosx-10.5-i386-2.5/scipy running build_clib customize UnixCCompiler customize UnixCCompiler using build_clib customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler Could not locate executable g77 Could not locate executable f77 Could not locate executable f95 customize GnuFCompiler customize Gnu95FCompiler Couldn't match compiler version for 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou may redistribute copies of GNU Fortran\nunder the terms of the GNU General Public License.\nFor more information about these matters, see the file named COPYING\n' customize G95FCompiler customize GnuFCompiler customize Gnu95FCompiler Couldn't match compiler version for 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou may redistribute copies of GNU Fortran\nunder the terms of the GNU General Public License.\nFor more information about these matters, see the file named COPYING\n' customize NAGFCompiler customize NAGFCompiler using build_clib running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize NAGFCompiler customize AbsoftFCompiler customize IbmFCompiler customize GnuFCompiler customize Gnu95FCompiler Couldn't match compiler version for 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou may redistribute copies of GNU Fortran\nunder the terms of the GNU General Public License.\nFor more information about these matters, see the file named COPYING\n' customize G95FCompiler customize GnuFCompiler customize Gnu95FCompiler Couldn't match compiler version for 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou may redistribute copies of GNU Fortran\nunder the terms of the GNU General Public License.\nFor more information about these matters, see the file named COPYING\n' warning: build_ext: fcompiler=nag is not available. building 'scipy.fftpack._fftpack' extension compiling C sources C compiler: gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp - mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall -DMACOSX -I/ usr/include/ffi -DENABLE_DTRACE -arch i386 -arch ppc -pipe compile options: '-Ibuild/src.macosx-10.5-i386-2.5 -I/System/Library/ Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/ include -I/System/Library/Frameworks/Python.framework/Versions/2.5/ include/python2.5 -c' Traceback (most recent call last): File "setup.py", line 92, in <module> setup_package() File "setup.py", line 84, 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/lib/ python2.5/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) 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' > On Fri, May 30, 2008 at 3:53 PM, Viral Shah > <vshah(a)interactivesupercomputing.com> wrote: >> I am using an Intel Mac, and trying to build scipy following the >> instructions at: http://www.scipy.org/Installing_SciPy/Mac_OS_X >> >> I was able to successfully build numpy (from svn) without any extra >> configuration. For scipy, even though I have installed the gfortran >> compiler, setup doesn't seem to like the fact that I have 4.2.3. I am >> using gcc 4.0.1 that is supplied by Apple. I get the following: >> >> customize G95FCompiler >> customize GnuFCompiler >> customize Gnu95FCompiler >> Couldn't match compiler version for 'GNU Fortran (GCC) >> 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU >> Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou >> may redistribute copies of GNU Fortran\nunder the terms of the GNU >> General Public License.\nFor more information about these matters, >> see >> the file named COPYING\n' >> >> After searching around on scipy-dev, I resorted to doing this: >> >> $ python setup.py config_fc --fcompiler=gnu95 build >> >> That allowed me to get further, but left me with the following error >> that I don't understand. I can help update the instructions page with >> info about compilers, if I can get this process working. Thanks in >> advance. > > Please provide the full output. The error that you see is a result of > a failure to correctly configure the Fortran compiler earlier. The > current numpy SVN should be able to handle the version string you give > above. > > > In [37]: from numpy.distutils.fcompiler import gnu > > In [38]: fc = gnu.Gnu95FCompiler() > > In [39]: v = 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free > Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to > the extent permitted by law.\nYou may redistribute copies of GNU > Fortran\nunder the terms of the GNU General Public License.\nFor more > information about these matters, see the file named COPYING\n' > > In [40]: print v > GNU Fortran (GCC) 4.2.3 > Copyright (C) 2007 Free Software Foundation, Inc. > > GNU Fortran comes with NO WARRANTY, to the extent permitted by law. > You may redistribute copies of GNU Fortran > under the terms of the GNU General Public License. > For more information about these matters, see the file named COPYING > > > In [41]: fc.version_match(v) > Out[41]: '4.2.3' > > -- > Robert Kern > > "I have come to believe that the whole world is an enigma, a harmless > enigma that is made terrible by our own mad attempt to interpret it as > though it had an underlying truth." > -- Umberto Eco

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Error building from svn on Intel Macs.
by Viral Shah 30 May '08

30 May '08

I am using an Intel Mac, and trying to build scipy following the instructions at: http://www.scipy.org/Installing_SciPy/Mac_OS_X I was able to successfully build numpy (from svn) without any extra configuration. For scipy, even though I have installed the gfortran compiler, setup doesn't seem to like the fact that I have 4.2.3. I am using gcc 4.0.1 that is supplied by Apple. I get the following: customize G95FCompiler customize GnuFCompiler customize Gnu95FCompiler Couldn't match compiler version for 'GNU Fortran (GCC) 4.2.3\nCopyright (C) 2007 Free Software Foundation, Inc.\n\nGNU Fortran comes with NO WARRANTY, to the extent permitted by law.\nYou may redistribute copies of GNU Fortran\nunder the terms of the GNU General Public License.\nFor more information about these matters, see the file named COPYING\n' After searching around on scipy-dev, I resorted to doing this: $ python setup.py config_fc --fcompiler=gnu95 build That allowed me to get further, but left me with the following error that I don't understand. I can help update the instructions page with info about compilers, if I can get this process working. Thanks in advance. <snip> building 'scipy.fftpack._fftpack' extension compiling C sources C compiler: gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp - mno-fused-madd -fno-common -dynamic -DNDEBUG -g -Os -Wall -DMACOSX -I/ usr/include/ffi -DENABLE_DTRACE -arch i386 -arch ppc -pipe compile options: '-Ibuild/src.macosx-10.5-i386-2.5 -I/System/Library/ Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/ include -I/System/Library/Frameworks/Python.framework/Versions/2.5/ include/python2.5 -c' Traceback (most recent call last): File "setup.py", line 92, in <module> setup_package() File "setup.py", line 84, 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/lib/ python2.5/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) 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' -viral

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Tutorials at Scipy 2008
by Fernando Perez 29 May '08

29 May '08

[ This is meant as a heads-up here, please keep the discussion on the SciPy user list so we can focus the conversation in one list only. ] Hi all, Travis Oliphant and myself have signed up to coordinate the tutorials sessions at this year's SciPy conference. Our tentative plan is described here: http://scipy.org/SciPy2008/Tutorials but it basically consists of holding in parallel: 1. A 2-day hands-on tutorial for beginners. 2. A set of 2 or 4 hour sessions on special topics. We need input from people on: - Do you like this idea? - If yes for #1, any suggestions/wishes? Eric Jones, Travis O and myself have all taught similar things and could potentially do it again, but none of us is trying to impose it. If someone else wants to do it, by all means mention it. The job could be split across multiple people once an agenda is organized. - For #2, please go to the wiki and fill in ideas for topics and/or presenters. We'll need a list of viable topics with actual presenters before we start narrowing down the schedule into something more concrete. Feel free to either discuss things here or to just put topics on the wiki. I find wikis to be a poor place for conversation but excellent for summarizing items. I'll try to update the wiki with ideas that arise here, but feel free to directly edit the wiki if you just want to suggest a specific topic or brief piece of info, do NOT feel like you have to vet anything on list. Cheers, Travis and Fernando.

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ANN: NumPy 1.1.0
by Jarrod Millman 29 May '08

29 May '08

I'm pleased to announce the release of NumPy 1.1.0. NumPy is the fundamental package needed for scientific computing with Python. It contains: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * basic linear algebra functions * basic Fourier transforms * sophisticated random number capabilities * tools for integrating Fortran code. Besides it's obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide-variety of databases. This is the first minor release since the 1.0 release in October 2006. There are a few major changes, which introduce some minor API breakage. In addition this release includes tremendous improvements in terms of bug-fixing, testing, and documentation. For information, please see the release notes: http://sourceforge.net/project/shownotes.php?release_id=602575&group_id=1369 Thank you to everybody who contributed to this release. Enjoy, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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