Mailman 3 May 2006 - SciPy-Dev

Wrapping band matrices
by Arnd Baecker 01 Jun '06

01 Jun '06

Hi, I would like to contribute f2py generated wrappers for the LAPACK routines dgbrfs, dgbtrf, dgbtrs, dsbev, dsbevd, dsbevx which deal with symmetric band matrices. Originally they were developed with Numeric and the old f2py. At this point I have two questions: a) before the function signature looked like: dsbev - Function signature: w,z,info = dsbev(ab,[compute_v,lower,ldab,overwrite_ab]) but now it is dsbev - Function signature: w,z,info = dsbev(ab,[compute_v,lower,ldab]) I.e.: `overwrite_ab` is missing. What has to be done to get this again? b) What would be the best approach for the integration into scipy? The present status is at http://www.physik.tu-dresden.de/~baecker/python/band.zip The routines work "stand-alone" python setup.py build python tests/test_band.py and (after more clean-up/documentation)_ might_ be a good example/framework for others to add further LAPACK routines. In particular I think it is easier to test new stuff separately than to directly integrate it into scipy/Lib/linalg/generic_flapack.pyf Would it make sense to add this to the scipy sandbox at some point? (I would prefer to leave the final integration into scipy/Lib/linalg/* to a real expert...) In any case, before this, the next steps are: - do the <tchar=s,d>sbev stuff for all routines in generic_band.pyf - address FIXMEs in generic_band.pyf - add unit tests for all routines (only one example is given at the moment) Many thanks, Arnd

2 4

ATLAS vs Lapack
by Friedrich, Robin K 30 May '06

30 May '06

Hi, I'm having a little trouble building the scipy package on our Linux system. (RH EL 3) We have ATLAS 3.6.0 installed and it appears that the setup found it and used it to build. However at runtime the resulting lapack_lite module could not find a symbol. The symbol is defined in the blas_lite.c but maybe the ATLAS build messed up the lapack_lite stuff.??? >From the setup run: creating build/temp.linux-i686-2.4/scipy/corelib/lapack_lite compile options: '-DATLAS_INFO="\"3.6.0\"" -I/ips/fd/cm/cmg/rel/csw/oss/include/ATLAS -Iscipy/base/in clude -Ibuild/src/scipy/base -Iscipy/base/src -I/ips/fd/cm/cmg/rel/csw/oss/include/python2.4 -c' gcc: scipy/corelib/lapack_lite/lapack_litemodule.c gcc -pthread -shared build/temp.linux-i686-2.4/scipy/corelib/lapack_lite/lapack_litemodule.o -L/ips/f d/cm/cmg/rel/csw/oss/lib/ATLAS -llapack -lf77blas -lcblas -latlas -o build/lib.linux-i686-2.4/scipy/l ib/lapack_lite.so From the test attempt: ...lib/python2.4/site-packages/scipy $ python setup.py test Traceback (most recent call last): File "setup.py", line 26, in ? from scipy.distutils.core import setup File "/ips/fd/sw/csw/oss/lib/python2.4/site-packages/scipy/__init__.py", line 35, in ? import scipy.basic.linalg as linalg File "/ips/fd/sw/csw/oss/lib/python2.4/site-packages/scipy/basic/linalg.py", line 1, in ? from basic_lite import * File "/ips/fd/sw/csw/oss/lib/python2.4/site-packages/scipy/basic/basic_lite.py", line 7, in ? import scipy.lib.lapack_lite as lapack_lite ImportError: /ips/fd/sw/csw/oss/lib/python2.4/site-packages/scipy/lib/lapack_lite.so: undefined symbol: s_wsfe

2 1

neural nets
by Gary Ruben 28 May '06

28 May '06

Just looking at which summer of code projects got up and saw the Neural Nets in SciPy one by Frederic Mailhot mentored by Robert Kern. Congratulations. I just wanted to draw their attention to an ANN library which they may already know about but which may be useful for reference purposes: http://fann.sourceforge.net/fann.htm It already has Python bindings but is LGPL. Gary R.

1 0

Summer of Code: pylibsvm accepted!
by Albert Strasheim 24 May '06

24 May '06

Hello all I just received confirmation from Google that my proposal for adding Support Vector Machine support to SciPy has been accepted. :-) Thanks very much to Robert Kern and Dave Kammeyer for their help so far. Dave will also be mentoring the project (thanks also to the other volunteers). The original proposal is here: http://students.ee.sun.ac.za/~albert/pylibsvm/ I've done quite a bit of work on the code since posting the proposal, so the timeline might change slightly, but I am still planning to have a first cut of the code in the SciPy sandbox by the end of June, with the final code done by the middle of August. If you're interested to see how this project progresses, check the URL mentioned above, starting in a day or two. Regards, Albert

2 1

Fail in building numpy(svn).
by Wenjie He 24 May '06

24 May '06

I just follow the tutorial in http://www.scipy.org/Installing_SciPy/Windows to build numpy step by step, and everything is OK except building numpy. I use cygwin with gcc to compile them all, and use pre-compiler python-2.4 in windows xp sp2. I try build in both windows native command line and cygwin with: python.exe setup.py config --compiler=mingw32 build --compiler=mingw32 bdist_wininst And the result is the same with the error which is attached below. It is my first time to build a python module, and I don't know where to start to fix the error. Can anyone show me the way, plz? Wenjie -- I'm lazy, I'm coding. http://my.donews.com/henotii -- I'm lazy, I'm coding. http://my.donews.com/henotii

2 1

Next SciPy release
by Ed Schofield 24 May '06

24 May '06

Hi all, Now that NumPy 0.9.8 is out, I'd like to make a new SciPy release (0.4.9) early next week. Now's the time for any last-minute fixes or documentation improvements (hint, hint!) -- Ed

3 3

Ticket #128
by Nils Wagner 24 May '06

24 May '06

Ticket #128 is already fixed in svn isn't it ? http://projects.scipy.org/scipy/numpy/ticket/128 Nils

1 0

Network maintenace complete
by Jeff Strunk 20 May '06

20 May '06

Good afternoon. Thank you for allowing today's maintenance. I apologize for it taking longer than expected. Everything should be in order now. If you notice that something no longer works, please let me know and I will take care of it as soon as possible. Thank you for your patience, Jeff Strunk IT Administrator Enthought Inc.

1 0

Sandbox setup change
by cookedm＠physics.mcmaster.ca 19 May '06

19 May '06

For those working with packages in scipy.sandbox, I've added a feature to the setup.py that will mean you won't have to edit it (and run the risk of committing your change in). Simply make a file Lib/sandbox/enabled_packages.txt with the subpackages you want to enable, one per line. Since that file doesn't exist in svn, you won't check it in. cheers! -- |>|\/|< /--------------------------------------------------------------------------\ |David M. Cooke http://arbutus.physics.mcmaster.ca/dmc/ |cookedm(a)physics.mcmaster.ca

1 0

Using randomkit in extensions
by Tom Loredo 18 May '06

18 May '06

Hi folks, There's been talk here in the last few months about the need to link to some numpy/scipy libraries in user's extensions. As far as I can follow the discussion, no solution to this problem has been found yet. Clue me in if I'm wrong! The recommended workaround has been to just duplicate code. It's inefficient but it works! That's what I've been doing. But it's a problematic solution for extensions that use random numbers. Code should produce reproducible results. Robert added the ability to save/restore state to numpy.random specifically to support reproducibility. Simply copying randomkit.[ch] or mtrand.c breaks this. So far my extensions have needed a deterministic number of uniform or normal samples, so I've written them to accept a numpy array of samples as input (the Python wrapper around the extension code hides this). But now I'm writing an extension that internally uses a rejection technique, with the expected # of rejections varying widely from case to case. So it's not possible to send it an array with the needed samples. A possible workaround would be to grab mtrand's state in Python and communicate it to my extension's copy of *rand*. The Python wrapper around the extension call could get the state back after the call and update numpy's mtrand state appropriately. Does this sound sensible? Is there a better way? If this would work, how should I proceed (I've never used Pyrex---will it be necessary)? I can write the extension in Fortran, C or C++. Thanks, Tom ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

2 1