Mailman 3 August 2005 - SciPy-Dev

Submitting Patches
by harkal＠sylphis3d.com 01 Sep '05

01 Sep '05

Hello, what is the appropriate procedure to submit patches? I sended to the list a patch for RQ decomposition a month ago but got no responce. Will is be commited? Will it not? Best regards, Harry

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natural neighber interpolation
by Alan G Isaac 30 Aug '05

30 Aug '05

Just noticed http://dilbert.engr.ucdavis.edu/~suku/nem/thesis.html#CODE which provides public domain Fortran code. Cheers, Alan Isaac

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Utility to pad a matrix
by Tim Cera 26 Aug '05

26 Aug '05

Hello, Please find at http://www.scipy.org/Members/timcera/pad-0.1.tar.gz/download a utility to pad an n-dimensional matrix. You can pad with the mean, median, maximum, or minimum of each vector along each axis or just use a portion of the vector near the edges. You can also assign a constant to the pad values, or ramp from the edge value to a constant, or mirror along the edge values, or pad with values wrapped from the other end of the vector. I had an earlier version that I was using for rank-1 matrices, but I have extended the padding functions to n-dimensions. Now that pad can work with n-dimensional matrics, I have hopes that pad (or something like it) could be a utility used by FFT, convolution, and filter functions. Some of these functions support some forms of padding internally, most do not. Kindest regards, Tim Cera

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Re: [SciPy-dev] Restructuring of SciPy
by Joe Harrington 23 Aug '05

23 Aug '05

On this thread from last week, I thought we had already decided to move in the direction of modules and well-written intro docs that point you to a specific graphics package (while letting you know that others exist and pointing you to more info). The concept was laid out in the ASP doc and ensuing discussion, for which see the wiki. We also introduced the idea of umbrella packages, which are (nearly-)empty packages that depend on (and therefore cause your package manager to download and install) useful sets of modules. For example, we could have a scipy-astro-all that got scipy-core, scipy-docs, scipy-astro, scipy-matplotlib, and so on, but not scipy-bio-molecules or scipy-em-whatever. For that matter, we could (should) have a scipy-all, that gets everything. --jh--

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Restructuring of SciPy
by Travis Oliphant 21 Aug '05

21 Aug '05

After the 0.3.2 release, scipy will be getting a face-lift. As part of that, I'm wondering about the restructuring process. For a long time, we've been operating under the "big-scipy-package" with capability for small packages to be released separately model. It has had limited success and I don't know of any small packages actually being released like that. With things like Enthon out there that act as the "batteries included super distribution" anyway. It makes me wonder if we shouldn't move scipy to the "scipy-modules" perspective directly and develop and think about scipy has a collection of modules that work together smoothly (i.e. naming conventions, etc.) scipy_core + available instructions could provide all the infrastructure someone needs to contribute packages to scipy. This would also allow people to develop (and maintain) their own modules (which they seem to like to do anyway). If we could just get them to play nice with the rest of scipy_core, it would all be for benefit. We already have the infrastructure in place for modules to play nicely with the overall package. I'm just wondering if we shouldn't emphasize more the modular approach by the way the svn tree is layed out (so individual modules can be checked out independently, for example). I've also spoken to people who find it hard to rely on their scipy in their code they pass on because you have to get the whole package, even if you only use a few parts. Matlab also uses modules effectively. I think we should take advantage of the restructuring process to think about this. Comments? -Travis

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stats._support and stats.anova ... SVN
by Perry, Alexander (GE Infrastructure) 19 Aug '05

19 Aug '05

I've just spent some time looking through the call heirarchy that underlies scipy.stats.anova() and there is considerable bitrot from years of neglect. Does anybody know when this was last known to work ? It looks like it would be easier to take an old working version and update it to the current python and scipy versions, than to fix the subtle interactions and side effects. Separately to that, can someone suggest a timeline on which the SVN tree will be up and able to build itself again? With the project repository broken, maybe I should fork (it'd be a branch, if we had a repository), fix up the stuff I need using local CVS, wait for the SVN to become stable, migrate my fork to become a branch, then merge the branch. Anybody disagree?

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Problems with Scipy and Fedora Core 4
by Greg Novak 18 Aug '05

18 Aug '05

I'm having trouble getting Scipy to run on Fedora Core 4. The latest release (0.3.2) fails to compile with errors in the source, probably related to the switch to GCC 4.0. I'm not summarizing them here because the problems don't exist in the Subversion code. After checking out the latest code from svn, Scipy compiles but I get the following error: ImportError: /usr/lib/python2.4/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv I'm using Fedora Cora 4, with RPMS blas-3.0-29, lapack-3.0-29, and atlas-3.6.0-0.fdr.2 installed. I've also installed compat-gcc-33-g77 to get g77 and libg2c.a. This... ahem... would seem to have the effect of mixing GCC 3.3 and 4.0 code, which strikes me as dicey at best. Are my worries justified? I've attached a complete traceback and the output of scipy_distutils/system_info.py. Any tips are appreciated, including (if necessary) "It doesn't work right now." Thanks, Greg

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scipy via svn
by Nils Wagner 17 Aug '05

17 Aug '05

Hi all, Finally I have installed scipy via svn. svn co http://svn.scipy.org/svn/scipy/trunk scipy and in ~/scipy svn co http://svn.scipy.org/svn/scipy_core/trunk/ scipy_core Python 2.4 (#1, May 30 2005, 19:23:06) [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import scipy No module named __cvs_version__ ====================================================================== ERROR: check_integer (scipy.io.array_import.test_array_import.test_read_array) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.4/site-packages/scipy/io/tests/test_array_import.py", line 57, in check_integer a = stats.randint.rvs(1,20,size=(3,4)) File "/usr/lib/python2.4/site-packages/scipy_base/ppimport.py", line 303, in __getattr__ module = self._ppimport_importer() File "/usr/lib/python2.4/site-packages/scipy_base/ppimport.py", line 258, in _ppimport_importer raise ImportError,self.__dict__.get('_ppimport_exc_info')[1] ImportError: No module named __cvs_version__ ---------------------------------------------------------------------- Ran 245 tests in 0.304s FAILED (errors=1) <unittest.TextTestRunner object at 0xb771998c> Some obsolote cvs related problems arise. Nils

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SciPy SVN reorganization
by Joe Cooper 17 Aug '05

17 Aug '05

Hi all, A concensus seems to have been reached on the re-organization of the SciPy repository, and it also has been agreed that a new release will be rolled immediately (or some approximation of immediately) based on the old layout. To that end I have tagged both scipy and scipy_core repositories with a "pre_org" tag: http://svn.scipy.org/svn/scipy_core/tags/pre_org/ http://svn.scipy.org/svn/scipy/tags/pre_org/ The immediate release should be built from this tag. If you need to make changes, please branch this tag, and work on the branch. I will not commit the re-organized repository until tomorrow, as I want folks to have a chance to be aware of the changes and make any commits they want to make before the re-organization. The changes are sweeping and /will/ certainly require a fresh checkout, as I'm moving scipy_core into scipy...so one repo will disappear. So, do whatever you have to do /now/, or let me know that you need more time. If anyone involved in the release wants me to re-tag in a few hours after some commits, I can probably do that too. If anyone needs assistance with using branches or tags in Subversion please let me know.

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SciPy 2005 Conference: Preliminary Schedule of Presentations
by Travis N. Vaught 13 Aug '05

13 Aug '05

All, I've posted a preliminary schedule of presentations at: http://www.scipy.org/wikis/scipy05/ConferenceSchedule Please feel free to provide comments or corrections--either to the list or directly to me. If you haven't registered, you may do so at: https://www.enthought.com/scipy05/ More information about the conference is at: http://www.scipy.org/wikis/scipy05/ Regards, Travis (Vaught)

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