Mailman 3 September 2005 - SciPy-User

subversion and installation instructions?
by Giovanni Samaey Sept. 7, 2005

Sept. 7, 2005

Dear all, I have tried to install scipy on ournew university-wide cluster, but I am unsure as to whether the install was completely successful. I checked out scipy from svn, and because that alone gave me "scipy_base not found", I needed to look through the mail on this list to find out that there exists a separate "scipy_core" module, which also has to be checked out and installed separately. Now both of these are installed. However, I only get 246 tests on level=10. I remember that this was much more in the past. Did I forget to install something? I also get one failure, which is listed below. I must say that I am not exactly running on a standard system... We run on a cluster of Opterons, use pathscale as compiler, and the BLAS and LAPACK are from the AMD Core Math Library instead of ATLAS. Once this system is working and validated, I will post detailed installation instructions for this setup. Best, Giovanni ====================================================================== FAIL: check_dot (scipy.lib.blas.test_blas.test_fblas1_simple) ---------------------------------------------------------------------- Traceback (most recent call last): File "/data/home/u0038151/lib/python2.4/site-packages/scipy/lib/blas/tests/test_blas.py", line 75, in check_dot assert_almost_equal(f([3j,-4,3-4j],[2,3,1]),-9+2j) File "/data/home/u0038151/lib/python2.4/site-packages/scipy_test/testing.py", line 662, in assert_almost_equal assert round(abs(desired - actual),decimal) == 0, msg AssertionError: Items are not equal: DESIRED: (-9+2j) ACTUAL: (-9+2.1839129395899578e-317j) ---------------------------------------------------------------------- Ran 246 tests in 1.658s

2 3

Mersenne Twister PRNG
by Robert Kern Sept. 7, 2005

Sept. 7, 2005

I've made a stab at replacing the RANLIB-based PRNG that we currently use in scipy.stats with the superior-in-every-conceivable-way Mersenne Twister. It's currently a separate module, and it has only been tested on Numeric 24.0b2 not the new scipy.base, but it should be able to be almost a drop-in replacement for the module that's currently there. The only distribution I haven't covered is the multivariate normal because I didn't really feel like doing linear algebra in C. But that's easy enough to do at the Python level. The core Mersenne Twister routines come from Jean-Sebastien Roy's RandomKit. Thank you, JS! http://www.jeannot.org/~js/code/index.en.html I would appreciate people putting it through its paces. I've done visual checking of the distributions via Q-Q plots; the script is included as the tests/qq.py and requires matplotlib. I haven't implemented real unit tests via K-S significance tests or Kullback-Leibler distance, but I guess I ought to eventually. The sampling algorithms were implemented from scratch by me from the original literature, so if you see funky numbers, it's probably my fault. AFAICT right now, the numbers are no funkier than those produced by RANLIB. http://cheeseshop.python.org/pypi/mtrand/0.1 -- Robert Kern rkern(a)ucsd.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter

2 4

Upgrading scipy.io.loadmat
by Nick Fotopoulos Sept. 6, 2005

Sept. 6, 2005

Greetings, A couple months ago, I posted to scipy-user asking if anyone knew how to fix scipy.io.loadmat to read Matlab 7 (R14) mat-files. Receiving no response, I hacked the mio.py myself and can now read in the new version of mat-files. While I was tinkering, I fixed the in-place-but-broken support for complex arrays; it returned only the real parts before. scipy-users, this is just letting you know that if you need these features, there is a working solution. scipy-devs, what is the proper channel for submitting patches? Take care, Nick Fotopoulos

2 1

No module named __cvs_version__
by Yaroslav Bulatov Sept. 6, 2005

Sept. 6, 2005

I get that warning when I execute scipy.special.chebyt(1) The error comes from somewhere inside of gen_roots_and_weights What might be causing this? Also, how can I go about tracking down the source? I tried by pasting various bits of code from various scipy files and seeing if error is reproduced, but is there a more efficient method? -- Yaroslav Bulatov bulatov(a)cs.oregonstate.edu Dearborn 102 Oregon State University Corvallis, OR

1 0

scipy can't find Numeric header files during install
by Yaroslav Bulatov Sept. 6, 2005

Sept. 6, 2005

I'm trying to install scipy with --prefix=~/usr option I've installed Numeric and headers went to " ~/usr/include/python2.3/Numeric/" But now when I install SciPy by doing "python setup.py install --prefix=~/usr", it says Lib/cluster/src/vq_wrap.cpp:563:33: Numeric/arrayobject.h: No such file or directory How can I tell it to look in "~/usr/include/python2.3/Numeric/" for Numeric headers? -- Yaroslav Bulatov bulatov(a)cs.oregonstate.edu Dearborn 102 Oregon State University Corvallis, OR

2 2

SciPy 2005 Conference: Preliminary Schedule of Presentations
by Travis N. Vaught Sept. 5, 2005

Sept. 5, 2005

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)

3 2

Re: [SciPy-dev] scipy core (Numeric3) win32 binaries to play with
by Alan G Isaac Sept. 5, 2005

Sept. 5, 2005

On Fri, 02 Sep 2005, Travis Oliphant apparently wrote: > http://numeric.scipy.org/files/scipy_core-0.4.0.win32-py2.4.exe So far so good. Thanks! Alan Isaac

2 1

New Lyx Version eas(ier) to install on Windows.
by Travis Oliphant Sept. 3, 2005

Sept. 3, 2005

There is a new Lyx Version that works on Windows quite well -- windows is now officially supported. So, those of you who have been hesitant to try LyX because it supposedly doesn't work on Windows, have no more excuse ;-) An executable installer is available at http://www.lyx.org The setup process guides you through the other programs that are needed (ImageMagick, Ghostscript, a minimal shell like minsys, Python, and optionally Perl) to run lyx well. -Travis

2 1

RE: [SciPy-user] Matplotlib fonts
by Howey, David A Sept. 3, 2005

Sept. 3, 2005

Wicked. This is just what I needed. Thanks. I will try and join the matplotlib list now! Dave -----Original Message----- From: scipy-user-bounces(a)scipy.net [mailto:scipy-user-bounces@scipy.net] On Behalf Of John Hunter Sent: 01 September 2005 16:06 To: SciPy Users List Subject: Re: [SciPy-user] Matplotlib fonts >>>>> "Howey," == Howey, David A <d.howey(a)imperial.ac.uk> writes: David> Does anyone know any easy way to set the 'global' font David> sizes for eg. tick mark labels, titles, xlabels, ylabels David> for matplotlib? I would rather not use the matplotlibrc David> file since I want the code to be platform independent. Can David> I set something in my code that will then affect all David> subsequent figures? This question is more appropriate on matplotlib-users (attempting to set followups). You can subscribe at http://lists.sourceforge.net/mailman/listinfo/matplotlib-users . You can also set the rc params from within a script, and this will affect all subsequent figures. There are two ways to do it. * Use rcParams; this is a dictionary where the keys are the same as in the rc file from matplotlib import rcParams rcParams.update( { 'font.family' : 'serif', 'font.style' : 'normal', 'font.variant' : 'normal', 'font.weight' : 'bold', 'font.stretch' : 'normal', 'font.size' : 'large', }) from pylab import * plot([1,2,3]) show() or use the "rc" command, which may be syntactically nicer but is equivalent; see http://matplotlib.sourceforge.net/matplotlib.pylab.html#-rc from matplotlib import rc rc('font', family='serif', style='normal', variant='normal', weight='bold', stretch='normal', size='large') from pylab import * plot([1,2,3]) show() Note that changing these in the rc file is almost as portable. matplotlib respects per directory rc files, so you can make your customizations in the rc file and distribute it with your script/application and this will override the user's default configuration. JDH _______________________________________________ SciPy-user mailing list SciPy-user(a)scipy.net http://www.scipy.net/mailman/listinfo/scipy-user

2 1

Matplotlib fonts
by Howey, David A Sept. 1, 2005

Sept. 1, 2005

Does anyone know any easy way to set the 'global' font sizes for eg. tick mark labels, titles, xlabels, ylabels for matplotlib? I would rather not use the matplotlibrc file since I want the code to be platform independent. Can I set something in my code that will then affect all subsequent figures? Dave

2 1