Mailman 3 January 2008 - SciPy-Dev

Sage/Scipy Days 8 reminder: Feb 29-March 4.
by Fernando Perez Jan. 22, 2008

Jan. 22, 2008

Hi all, Just a quick reminder for all about the upcoming Sage/Scipy Days 8 at Enthought collaborative meeting: http://wiki.sagemath.org/days8 Email me directly (Fernando.Perez(a)Colorado.edu) if you plan on coming, so we can have a proper count and plan accordingly. Cheers, f

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Status of weave
by C. Ball Jan. 21, 2008

Jan. 21, 2008

Hi, Recently I asked a question on the Scipy-User list about using weave with numpy arrays of dtype=object (http://article.gmane.org/gmane.comp.python.scientific.user/14642). There has been no reply, so now I'd like to find out the status of weave. I see that various bugs have been fixed recently, and that there has been some work on the converters (e.g. r3309 from the svn log), so I guess someone is working on weave. Are there any plans to allow arrays with dtype=object to be converted? Thanks very much, Chris

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sparse solvers in scipy rock
by Ondrej Certik Jan. 21, 2008

Jan. 21, 2008

Hi, yesterday I wrote some solver for 1D time dependent schrodinger equation to my school, using explicit and implicit methods and using scipy sparse solvers, because I was lazy to use some fortran routines for inverting the tridiagonal matrix, and I was surprised how nice it works in scipy. You did a great job. I am convinced that is the way to call all sparse solvers. Here is the code: http://hg.certik.cz/schrod1D/ I based it on the example: http://www.scipy.org/Cookbook/SchrodingerFDTD which uses central differences explicit method, but I wrote it my way, using complex numbers directly and Cython to speed it up. I also implemented euler differences explicit method, which totally blows up after a few iterations, and also an implicit method, which works really well. Where do you think I could put it together with some documentation how to play with it? to the above wiki, or should I create a new wiki for that? It's an example how to use Cython+Numpy+scipy sparse solvers (superlu currently). Ondrej

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WxPython required?
by Gabriel Gellner Jan. 21, 2008

Jan. 21, 2008

Upon a recent svn update, I get this error when I run scipy.test(): ====================================================================== ERROR: Failure: <type 'exceptions.RuntimeError'>(Could not locate wxPython base directory.) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/nose-0.10.0b1-py2.5.egg/nose/loader.py", line 344, in loadTestsFromName addr.filename, addr.module) File "/usr/lib/python2.5/site-packages/nose-0.10.0b1-py2.5.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/lib/python2.5/site-packages/nose-0.10.0b1-py2.5.egg/nose/importer.py", line 84, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/home/ggellner/lib/python/lib/python2.5/site-packages/scipy/weave/tests/test_wx_spec.py", line 13, in <module> from scipy.weave import ext_tools, wx_spec File "/home/ggellner/lib/python/lib/python2.5/site-packages/scipy/weave/wx_spec.py", line 20, in <module> wx_base = find_base_dir() File "/home/ggellner/lib/python/lib/python2.5/site-packages/scipy/weave/wx_spec.py", line 16, in find_base_dir raise RuntimeError("Could not locate wxPython base directory.") RuntimeError: Could not locate wxPython base directory. ---------------------------------------------------------------------- Upon installing wxpython this error disappears, does this mean scipy depends on wxpython now? Gabriel

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numpy and scipy required for weave?
by C. Ball Jan. 21, 2008

Jan. 21, 2008

> Hi, I'm trying to use the latest SVN version of weave, but I find I can't use it unless I have both numpy and scipy installed. First I tried checking out weave alone, but I got the following error when I tried to install: $ svn update At revision 3852. $ python setup.py install Traceback (most recent call last): File "setup.py", line 16, in ? from numpy.distutils.core import setup ImportError: No module named numpy.distutils.core A reply to someone else having this problem mentions that weave should work alone: http://thread.gmane.org/gmane.comp.python.scientific.user/9096/focus=9097 Installing numpy is easy, so weave depending on it is not really a problem from my point of view. After installing numpy, however, I find that scipy is also required: $ python [...] >>> import weave Traceback (most recent call last): File "<stdin>", line 1, in <module> File "[...]/lib/python2.5/site-packages/weave/__init__.py", line 21, in <module> from scipy.testing.pkgtester import Tester ImportError: No module named scipy.testing.pkgtester >>> In the past, weave did not require scipy. To prevent this error, all I have to do is comment out the last two lines of weave/__init__.py: # from scipy.testing.pkgtester import Tester # test = Tester().test Our software depends on weave, but we cannot require our users to install scipy. Can I file a tracker item about this, or is the plan for weave to become inseparably dependent on scipy? Thanks, Chris

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scikits: mailing list for tickets, etc...
by David Cournapeau Jan. 20, 2008

Jan. 20, 2008

Hi, Since the deprecation of the sandboxes, I think it is reasonable to expect more people getting scikits. Would it be possible to get at least a ML for the tickets and svn commit ? Ideally, a ML for users/dev would be good, too, cheers, David

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Status of arpack
by Matthieu Brucher Jan. 18, 2008

Jan. 18, 2008

Hi, Did someone take the job of putting it into the trunk in some place, patch it and test it ? I'd like to use it in the near future :) Matthieu -- French PhD student Website : http://matthieu-brucher.developpez.com/ Blogs : http://matt.eifelle.com and http://blog.developpez.com/?blog=92 LinkedIn : http://www.linkedin.com/in/matthieubrucher

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32bit vs 64bit doctest differences
by Nathan Bell Jan. 18, 2008

Jan. 18, 2008

It appears that numpy prints the 'dtype=intXX' part only when the size of int differs from the machine word size. For example, consider the following test run on a 64-bit machine: File "/usr/lib/python2.5/site-packages/scipy/stsci/convolve/Convolve.py", line 295, in scipy.stsci.convolve.Convolve.boxcar Failed example: boxcar(num.array([10, 0, 0, 0, 0, 0, 1000]), (3,), mode="wrap").astype(num.longlong) Expected: array([336, 3, 0, 0, 0, 333, 336], dtype=int64) Got: array([336, 3, 0, 0, 0, 333, 336]) Should we just use dtype=int to avoid this issue? It appears dtype=int chooses the native size. -- Nathan Bell wnbell(a)gmail.com http://graphics.cs.uiuc.edu/~wnbell/

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SyntaxError in scikits/learn arffread.py
by Nils Wagner Jan. 18, 2008

Jan. 18, 2008

Hi all, I have installed the scikits package learn from scratch. Compiling /usr/lib/python2.4/site-packages/scikits/learn/utils/arffread.py ... File "/usr/lib/python2.4/site-packages/scikits/learn/utils/arffread.py", line 401 finally: ^ SyntaxError: invalid syntax Cheers, Nils

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Scipy website and svn down?
by Brian Granger Jan. 17, 2008

Jan. 17, 2008

Hi, I look like all of the scipy/numpy stuff is down. I can't reach the website/repo for numpy/scipy/ipython/mpi4py/etc. Brian

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