Mailman 3 November 2008 - SciPy-Dev

default matlab file format
by Jarrod Millman Nov. 11, 2008

Nov. 11, 2008

I think that the savemat function should default to version 5 rather than 4: http://projects.scipy.org/scipy/scipy/browser/trunk/scipy/io/matlab/mio.py I know that there has been an increasing sense that changing the API should be done via deprecation warnings; but, in this particular case, it seems that it would be much more useful to end users to change the behavior without a deprecation. I seriously doubt that there are many (if any) Matlab users with such old versions of Matlab that they can't read version 5 files. What do other people think? Does anyone have a need for keeping version 4 as the default format for saving Matlab files? -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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"intent(aux)" does not honor "depend(..)"
by berthold＠despammed.com Nov. 11, 2008

Nov. 11, 2008

I try to wrap the lapack zheevr routine for a project of ours. Doing this I try to determine the optimal workspace in the wrapper routine. The generated code does work when put into correct order, but inspite ow writing:: integer intent(aux), depend(n) :: nb1 = __ilaenv(1, "ZHETRD", uplo, n, -1, -1, -1) integer intent(aux), depend(n) :: nb2 = __ilaenv(1, "ZUNMTR", uplo, n, -1, -1, -1) integer intent(aux), depend(nb1, nb2) :: nb = MAX(nb1, nb2) the generated code for calculating nb1, nb2, and nb is inserted directly after `PyArg_ParseTupleAndKeywords` is called, instead at a point after `uplo` and `n` are set. I guess this is a bug? Kind regards Berthold -- __ Address: G / \ L Germanischer Lloyd phone: +49-40-36149-7374 -+----+- Vorsetzen 35 P.O.Box 111606 fax : +49-40-36149-7320 \__/ D-20459 Hamburg D-20416 Hamburg

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recursion error in tests
by Christopher Hanley Nov. 11, 2008

Nov. 11, 2008

Hi, I am running scipy.test() for version 0.7.0.dev5042. When I do so I receive the following error: .......................................................................................................................................................................................................................................... ====================================================================== ERROR: Regression test for #653. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/chanley/dev/site-packages/lib/python/nose/case.py", line 182, in runTest self.test(*self.arg) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/tests/test_mio.py", line 343, in test_regression_653 savemat(StringIO(), {'d':{1:2}}, format='5') File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio.py", line 159, in savemat MW.put_variables(mdict) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 996, in put_variables mat_writer.write() File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 855, in write MW.write() File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 855, in write MW.write() <snip> ... </snip> File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 855, in write MW.write() File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 855, in write MW.write() File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 849, in write self.write_header(mclass=mxCELL_CLASS) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 757, in write_header self.write_element(np.array(shape, dtype='i4')) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 704, in write_element self.write_smalldata_element(arr, mdtype, byte_count) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 714, in write_smalldata_element self.write_dtype(tag) File "/Users/chanley/dev/site-packages/lib/python/scipy/io/matlab/mio5.py", line 696, in write_dtype self.file_stream.write(arr.tostring()) File "/usr/stsci/pyssgdev/Python-2.5.1/lib/python2.5/StringIO.py", line 213, in write _complain_ifclosed(self.closed) RuntimeError: maximum recursion depth exceeded ---------------------------------------------------------------------- Ran 2547 tests in 33.578s FAILED (SKIP=28, errors=1) Chris -- Christopher Hanley Senior Systems Software Engineer Space Telescope Science Institute 3700 San Martin Drive Baltimore MD, 21218 (410) 338-4338

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License review / weave bsd-ification
by Jarrod Millman Nov. 10, 2008

Nov. 10, 2008

Hey, I have been working to ensure that all the code in scipy is correctly licensed. One of the main issues was the blitz code in weave. I contacted the authors and we were given permission to use the code with a BSD license: http://scipy.org/scipy/scipy/ticket/649 I just finished most of the changes in: http://scipy.org/scipy/scipy/changeset/4949 http://scipy.org/scipy/scipy/changeset/4949 I found one file in blitz that I am not sure what to do about: http://scipy.org/scipy/scipy/browser/trunk/scipy/weave/blitz/blitz/rand-mt.h Any ideas? thought? suggestions? Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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Memory error in interpolate.sproot
by Nils Wagner Nov. 10, 2008

Nov. 10, 2008

Hi all, I have some trouble concerning sproot from numpy import linspace, sin from scipy.interpolate import splrep, splev, sproot from pylab import plot, show, legend, savefig x = linspace(0, 10, 10) y = sin(x) tck = splrep(x, y) x2 = linspace(0, 10, 200) y2 = splev(x2, tck) plot(x, y, 'o', x2, y2) legend(('$\sin(x)$',r'Spline')) show() roots = sproot(tck, mest=2) python -i test_interpol.py /data/home/nwagner/local/lib/python2.5/site-packages/matplotlib/__init__.py:367: UserWarning: matplotlibrc text.usetex can not be used with *Agg backend unless dvipng-1.5 or later is installed on your system warnings.warn( 'matplotlibrc text.usetex can not be used with *Agg ' Traceback (most recent call last): File "test_interpol.py", line 12, in <module> roots = sproot(tck, mest=2) File "/data/home/nwagner/local/lib/python2.5/site-packages/scipy/interpolate/fitpack.py", line 576, in sproot z,ier=_fitpack._sproot(t,c,k,mest) MemoryError How can I resolve that problem ? Nils

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Do we care about the LAPACK C interface?
by Travis E. Oliphant Nov. 9, 2008

Nov. 9, 2008

Hi all, I'm sitting here in a BOF with Clint Whaley (the author of ATLAS). He is looking for information about people that care about the C interface to LAPACK. Do we care? I'm not clear on that. Don't we just use the FORTRAN interfaces to ATLAS? If I hear from you soon, I can give Clint the information before I leave the BOF. -Travis

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complex-value remez?
by Neal Becker Nov. 7, 2008

Nov. 7, 2008

I see some posts from 2003 about complex remez. Any news? http://osdir.com/ml/python.scientific.devel/2003-02/msg00008.html

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numerical math consortium
by Neal Becker Nov. 7, 2008

Nov. 7, 2008

Have you guys seen this? http://www.nmconsortium.org/FldFaq/?id=66&page=FAQ

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Re: [SciPy-dev] Technology Previews and Sphinx Docstring Annotations
by jh＠physics.ucf.edu Nov. 6, 2008

Nov. 6, 2008

"Damian Eads" <eads(a)soe.ucsc.edu> wrote: > Technology preview code is new code incorporated into the trunk of > SciPy ... considered production grade and well-tested ... no > guarantees of a stable API to enable further improvements based on > community feedback. Sorry, but I feel this is a poor idea. Scipy is supposed to be stable. We got rid of the sandbox for a reason. We have too many API problems in scipy and even in numpy (median, FFT, and many others) to introduce a sanctioned mechanism for breaking APIs. If code is production-grade, *it has a stable API*. If not, release a separate package, get some use experience, and let the API mature. If the code is add-on code to an existing package in scipy, your package can monkeypatch it into the relevant scipy package as you and interested others test it, or you can import it separately. Then propose to bring it into SciPy as a mature package once it's ready. I would certainly favor a section of the web site devoted to promoting such tests (scipy.org/nursery? scipy.org/testbed? scipy.org/greenhouse?). Putting a markup in the documentation is not nearly sufficient warning since many people exchange code (e.g., Cookbook) without reading the docs for all the functions and classes the code contains. Also, having "Technology Demonstration" labels all over the place will only serve to shake people's faith in the stability of the package, and prevent it from ever getting a reputation for reliability. Numpy and scipy should never be places for experimentation. --jh--

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linalg.eigh tests - commit permissions?
by Tiziano Zito Nov. 6, 2008

Nov. 6, 2008

dear devs, I am working on the integration of symeig in scipy as a replacement for eigh. As a first step I wrote some tests for eigh, which was not tested till now. It would be better if these tests could be committed before anything else, so that even if symeig integration fails for some reason, eigh gets tested anyway. Who should I ask for commit privileges to the scipy svn repo? Alternatively, I can send a patch here or on scipy Track. The two utility functions "symrand" (generate a random symmetric positive definite matrix) and "random_rot" (generate a random rotation matrix) are in test_decomp.py, let me know if you want them available somewhere else in scipy. I think they are useful enough to be put somewhere, what about directly under scipy.linalg? some other random questions: - the signature for eigh currently is: eigh(a, lower=True, eigvals_only=False, overwrite_a=False) because eigh will grow an additional optional argument "b" (the second matrix of a general eigenproblem), the "overwrite_a" argument should become "overwrite": "b" will be also overwritten. Is this too much of an API breakage? - in the eigh code I see snippets like this: if heev.module_name[:7] == 'flapack': lwork = calc_lwork.heev(heev.prefix,a1.shape[0],lower) w,v,info = heev(a1,lwork = lwork,... else # 'clapack' w,v,info = heev(a1,... what is 'clapack'? how can I test it? I work on a debian system with atlas installed and the 'flapack' branch is always run. why has clapack no "lwork" argument? is it important at all? thank you! tiziano

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