Mailman 3 November 2008 - SciPy-Dev

Scipy not compiling in OS X 10.4
by Muhammad Alkarouri Dec. 2, 2008

Dec. 2, 2008

Hi everyone, Congratulations on getting the beta version out. When I tried to compile scipy I get the same error as in http://projects.scipy.org/pipermail/scipy-dev/2008-November/010352.html I am using Python 2.6 from python.org and OS X 10.4.11. The error is: error: file '/Users/malkarouri/tmp/scipy-0.7.0b1/ARPACK/FWRAPPERS/veclib_cabi_c.c' does not exist Regards, Muhammad Alkarouri

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ANN: SciPy 0.7.0b1 (beta release)
by Jarrod Millman Dec. 1, 2008

Dec. 1, 2008

I'm pleased to announce the first beta release of SciPy 0.7.0. SciPy is a package of tools for science and engineering for Python. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more. This beta release comes almost one year after the 0.6.0 release and contains many new features, numerous bug-fixes, improved test coverage, and better documentation. Please note that SciPy 0.7.0b1 requires Python 2.4 or greater and NumPy 1.2.0 or greater. For information, please see the release notes: http://sourceforge.net/project/shownotes.php?group_id=27747&release_id=6427… You can download the release from here: http://sourceforge.net/project/showfiles.php?group_id=27747&package_id=1953… 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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Constructing an ndarray around a ctypes array
by James Dominy Nov. 29, 2008

Nov. 29, 2008

Hi, Is there a way to create an ndarray from a ctypes array, such that they both use the same memory space. Thanks, James

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kstest is reporting wrong p-value ??
by josef.pktd＠gmail.com Nov. 27, 2008

Nov. 27, 2008

Looking again at ticket 395 about the Kolmogorov-Smirnov test, I'm quite sure the kstest is wrong. The current implementation uses absolute value of the deviation, therefore it is a two sided test. A one-sided test takes either max or min of the deviations (not of absolute deviations). However, the test distribution that is used to calculate the p-value is ksone, the distribution for the one-sided Kolmogorov-Smirnov test. So, the reported p-value should be off by approximately one half, or maybe double (?). There was a discussion in http://projects.scipy.org/pipermail/scipy-dev/2004-July/002181.html about this, but I'm not sure that conclusion is correct Can a statistics knowledgeable person check this, or someone with access to a good book? If I am correct, then I can fix the test next week. Josef

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scipy.linalg.qr deprecation warning
by Tiziano Zito Nov. 27, 2008

Nov. 27, 2008

Hi guys, when using scipy.linalg.qr without specifying any keyword argument the user gets the following warning: DeprecationWarning: qr econ argument will be removed after scipy 0.7. The economy transform will then be available through the mode='economic' argument. While I appreciate the idea of warning users of future API changes, I think emitting a warning even if the function has been called without specifying the "econ" argument is a bit too much. The user may not even know what "econ" stands for. What about setting "econ=None" by default and - if the user specified "econ" explicitly, emit the warning and set econ according to user preference - if the user did not specify "econ", set it to the current default, i.e. False ? If no one objects, I will do the needed changes myself tomorrow. tiziano

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scipy ticket #800
by Tiziano Zito Nov. 27, 2008

Nov. 27, 2008

hi! I've just added ticket #800 (numpy's test_poly1d_nan_roots is broken if scipy.linalg is imported) and I know how to fix it, but would like to hear your comments. The best solution IMO is to change the numpy behaviour, and that's something that needs discussion (and that I can't do myself) :-)) ciao, tiziano

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Re: [SciPy-dev] Using memoryviews
by Neal Becker Nov. 27, 2008

Nov. 27, 2008

This discussion might be of interest (from python-3000.devel): Antoine Pitrou wrote: > Josiah Carlson <josiah.carlson <at> gmail.com> writes: >> >> From what I understand of the memoryview when I tried to do the same >> thing a few months ago (use memoryview to replace buffer in >> asyncore/asynchat), memoryview is incomplete. It didn't support >> character buffer slicing (you know, the 'offset' and 'size' arguments >> that were in buffer), and at least a handful of other things (that I >> can't remember at the moment). > > You should try again, memoryview now supports slicing (with the usual > Python syntax, e.g. m[2:5]) as well as slice assignment (with the fairly > sensible limitation that you can't resize the underlying buffer). There's > no real doc for it, but you can look at test_memoryview.py in the Lib/test > directory to have a fairly comprehensive list of the things currently > supported. > > I also support the addition of official functions or macros to access the > underlying fields of the Py_buffer struct, rather than access them > directly from 3rd party code. Someone please open an issue for that in the > tracker. > > The big, big limitation of memoryviews right now is that they only support > one-dimensional byte buffers. The people interested in more complex > arrangements (that is, Scipy/Numpy people) have been completely absent > from the python-dev community for many months now, and I don't think > anyone else cares enough to do the job instead of them. > > Regards > > Antoine.

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can we close these tickets?
by Jarrod Millman Nov. 27, 2008

Nov. 27, 2008

I think the following tickets can be closed: http://scipy.org/scipy/scipy/ticket/723 http://scipy.org/scipy/scipy/ticket/795 If I don't hear anything to the contrary, I will assume that this tickets can be closed. 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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Can we close ticket 593?
by Jarrod Millman Nov. 27, 2008

Nov. 27, 2008

Tiziano Zito committed a fix in revision 5193 http://projects.scipy.org/scipy/scipy/changeset/5193 for ticket 593: http://projects.scipy.org/scipy/scipy/ticket/593 Nils reported that it fixed the problem for him. Can anyone else who was having this problem confirm that r5193 fixes it? If I don't hear anything to the contrary I will assume that we can close this ticket? 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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the state of scipy unit tests
by Nathan Bell Nov. 26, 2008

Nov. 26, 2008

In the past, I would always run 'nosetests scipy' before committing changes to SVN. Due to the current state of the unit tests, I don't anymore, and I suspect I'm not alone. Here are the main offenders on my system: scipy.stats. I appreciate the fact that rigorous testing on this module takes time, but 4 minutes on a 2.4GHz Core 2 system is unreasonable. IMO 20 seconds is a reasonable upper bound. Essential tests that don't meet this time constraint should be filtered out of the default test suite. scipy.weave Takes 2.5 minutes and litters my screen with a few hundred lines like, /tmp/tmpcRI5WR/sc_3a5c7ad3ac45a98d03cd9168232f7d8f1.cpp:618: warning: deprecated conversion from and dumps a bunch of .cpp and .so files in the current working directory. Some minor offenders: scipy.interpolate Emits several UserWarnings (should be filtered out with warnings.warnfilter). scipy.io Several DeprecationWarnings scipy.lib A dozen lines like "zcopy:n=3" scipy.linalg Outputs ATLAS info and a dozen lines like "zcopy:n=3". I'd like to be able to run the entire battery of tests in about a minute with minimal unnecessary output. -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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