Mailman 3 December 2002 - SciPy-User

buglets in stats/morestats.py
by Staelin, Carl Dec. 17, 2002

Dec. 17, 2002

There are a number of buglets in stats/morestats.py which make the routine wilcoxon unusable. I have attached a patch, which can be integrated by: cd scipy/stats patch < morestats.diff If you have any questions or concerns, please do not hesitate to contact me. Cheers, Carl <<morestats.diff>> _________________________________________________ [(hp)] Carl Staelin Senior Research Scientist Hewlett-Packard Laboratories Technion City Haifa, 32000 ISRAEL +972(4)823-1237x221 +972(4)822-0407 fax staelin(a)hpl.hp.com _______http://www.hpl.hp.com/personal/Carl_Staelin_______

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new Mandrake Source RPMs
by RA Dec. 17, 2002

Dec. 17, 2002

I've updated some files linked on <http://www.scipy.org/Members/RalfA/packages/Mandrake-9.0-RPM/index_html/view> (see list below). Now, weave is included as a seperate package (it depends on python-scipy-core). I've only added the date of the cvs version, because I couldn't find any related version number like in scipy/__cvs__version_.py. Please give me a hint or change setup_weave.py ... Chako has remained as a ToDo. Ralf. ### http://www.scipy.org/Members/RalfA/packages/Mandrake-9.0-RPM/python-f2py-2.… http://www.scipy.org/Members/RalfA/packages/Mandrake-9.0-RPM/python-weave-0… http://www.scipy.org/Members/RalfA/packages/Mandrake-9.0-RPM/python-scipy-c… http://www.scipy.org/Members/RalfA/packages/Mandrake-9.0-RPM/python-scipy-0…

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PyQwt upgrade
by Gerard Vermeulen Dec. 17, 2002

Dec. 17, 2002

Announcing PyQwt-3.5 PyQwt = FAST and EASY data plotting for Python, Numeric and Qt! PyQwt is a set of Python bindings for the Qwt C++ class library. The Qwt library extends the Qt framework with widgets for Scientific and Engineering applications. PyQwt requires and extends PyQt, a set of Python bindings for Qt. PyQwt requires Numeric. Numeric extends the Python language with new data types that make Python an ideal language for numerical computing and experimentation. PyQwt runs on Windows and Unix/Linux. The home page of PyQwt is http://gerard.vermeulen.free.fr New in PyQwt-3.5: 1. Upgraded to PyQt-3.5/sip-3.5 and Qt-3.1.0. 2. Builds by default with Qwt-2002-08-07 or optionally with Qwt-2002-10-13. 3. setup.py installs now also the documentation for the Qwt library. 4. The LATEST change in version numbering scheme :-) From now on I will track the PyQt/sip version numbers with a possible extra a, b, c, ... for bugfix releases. Gerard Vermeulen

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Re: [SciPy-user] fastumath import error
by Costas Malamas Dec. 16, 2002

Dec. 16, 2002

I've run into the same exact problem on Cygwin (Linux for all intends and purposes). I am an old hand at Python but new at SciPy. Here's what fixed it (and I cannot still figure out why, for the life of me). I cd'ed into site-packages/scipy_base, fired up python. At the prompt, I did: import fastumath Then, I went into site-packages, fired up python and run: from scipy_base import fastumath Neither gave me an importing error and since "from scipy import *" has worked everywhere. Which of course makes no sense (unless, it needed some .pyc file or something). C. >From: Pearu Peterson <pearu(a)cens.ioc.ee> >Reply-To: scipy-user(a)scipy.net >To: scipy-user(a)scipy.net >Subject: Re: [SciPy-user] fastumath import error >Date: Mon, 16 Dec 2002 13:37:38 +0200 (EET) > > >On Mon, 16 Dec 2002, Oscar López wrote: > > > >> > > >> Run python somewhere from your home directory and then import scipy. > > > > > > > That is quite strange, If I move to $HOME > > % cd $HOME > > %python > > >>> import scipy > > __file__= scipy/scipy_base/__init__.pyc > > Traceback (most recent call last): > > File "<stdin>", line 1, in ? > > File "scipy/__init__.py", line 36, in ? > > from scipy_base import * > > File "/usr/lib/python2.1/site-packages/PIL/__init__.py", line 107 > > # ;-) > > ImportError: No module named fastumath > > scipy cannot be imported from its source directory. > > Change to another directory and try again. > > >>> > > > > Now If I move to $HOME/tmp and > > %python > > >>> import scipy > > >>> > > > > > > How is it possible? The only difference is that cvs directory scipy is > > at $HOME. So i must run python at a directory that is not the parent of > > the directory of the scipy cvs directory, mustn't I? > >That's right. > > > Please could you enlighten me in the resason for this behaviour? > >When you run python from $HOME that also contains scipy cvs source tree, >then importing scipy will pick up scipy source instead of the installed >scipy. I suggest that you make a directory cvs and move scipy source >directory there: > >cd $HOME >mkdir cvs >mv scipy cvs > >Then you can use scipy also from your home directory. > >Regards, > Pearu > >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.net >http://www.scipy.net/mailman/listinfo/scipy-user _________________________________________________________________ Tired of spam? Get advanced junk mail protection with MSN 8. http://join.msn.com/?page=features/junkmail

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fastumath import error
by Oscar López Dec. 16, 2002

Dec. 16, 2002

Dear all I am newbie to python and scipy so perhaps this is a common problem but I have checked the archives and despite there exist some similar problem reports i wasn't able to find out a proper workaround. After i installed the scipy from cvs i got: neptuno:~$ python Python 2.1.1 (#1, Aug 30 2001, 17:36:05) [GCC 2.96 20000731 (Mandrake Linux 8.1 2.96-0.61mdk)] on linux-i386 Type "copyright", "credits" or "license" for more information. >>> import scipy __file__= scipy/scipy_base/__init__.pyc Traceback (most recent call last): File "<stdin>", line 1, in ? File "scipy/__init__.py", line 36, in ? from scipy_base import * File "/usr/lib/python2.1/site-packages/PIL/__init__.py", line 107, in ? # ;-) ImportError: No module named fastumath scipy cannot be imported from its source directory. Change to another directory and try again. >>> therefore i changed to: % cd /usr/lib/python2.1/site-packages/scipy_base % python >>> import scipy >>> I guess that it meant the scipy was imported. Thus, I tried to add this path to PYTHONPATH in my .bashrc MYPYTHON=/usr/lib/python2.1/site-packages export PYTHONPATH=$PYTHONPATH:$MYPYTHON/scipy_base:$MYPYTHON/scipy and now I got stuck with Python 2.1.1 (#1, Aug 30 2001, 17:36:05) [GCC 2.96 20000731 (Mandrake Linux 8.1 2.96-0.61mdk)] on linux-i386 Type "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "scipy/__init__.py", line 36, in ? from scipy_base import * File "/usr/lib/python2.1/site-packages/scipy_base/__init__.py", line 111, in ? import limits File "scipy/scipy_base/limits.py", line 10, in ? import scipy_base.fastumath File "/usr/lib/python2.1/site-packages/scipy_base/__init__.py", line 111, in ? import limits File "/usr/lib/python2.1/site-packages/scipy_base/limits.py", line 11, in ? reload(scipy_base.fastumath) ImportError: reload(): module fastumath not in sys.modules >>> It seems to me that there exist a problem in the environment variables Please how could i setup the environment variables to import properly scipy from elsewhere ? Am i missing something important? Any help is really appreciated Thanks a lot for your help Best wishes -- http://www.iit.upco.es/~oscar I tell ya, I was an ugly kid. I was so ugly that my dad kept the kid's picture that came with the wallet he bought. -- Rodney Dangerfield

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Problems compiling scipy/sparse (more)
by Costas Malamas Dec. 15, 2002

Dec. 15, 2002

Also, I forgot: I run scipy/sparse/setup_sparse.py, with the following traceback: building 'sparse._zsuperlu' extension gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -DUSE_DL_IMPORT -I/usr/include/py hon2.2 -c /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c -o build/temp.cygwin 1.3.17-i686-2.2/_zsuperlumodule.o In file included from /d/Projects/scipy/scipy/sparse/SuperLU/SRC/zsp_defs.h:23, from /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c:26: /d/Projects/scipy/scipy/sparse/SuperLU/SRC/supermatrix.h:19: parse error before numeric constant /d/Projects/scipy/scipy/sparse/SuperLU/SRC/supermatrix.h:21: parse error before numeric constant In file included from /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c:27: /d/Projects/scipy/scipy/sparse/SuperLU/SRC/util.h:95: warning: function declara ion isn't a prototype /d/Projects/scipy/scipy/sparse/SuperLU/SRC/util.h:101: warning: function declar tion isn't a prototype /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c: In function `NRFormat_from_sp atrix': /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c:46: warning: implicit declarat on of function `zCreate_CompRow_Matrix' /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c: In function `Py_zgssv': /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c:163: warning: implicit declara ion of function `superlu_delete_allkeys' /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c: At top level: /d/Projects/scipy/scipy/sparse/_zsuperlumodule.c:190: warning: function declara ion isn't a prototype error: command 'gcc' failed with exit status 1 >From: "Costas Malamas" <costasm(a)hotmail.com> >Reply-To: scipy-user(a)scipy.net >To: scipy-user(a)scipy.net >Subject: [SciPy-user] Problems compiling scipy/sparse >Date: Sun, 15 Dec 2002 15:54:06 +0000 > >After my recent inquiry into scipy/sparse, I bit the bullet, downloaded >SciPy CVS and started compiling everything to get scipy/sparse working. I >got through ATLAS, LAPACK, f2py, NumPy and most of sparsekit itself fine, >but then run into two really bizarre issues: > >a) Scipy/sparse/Makefile requires the target _sparsemodule.so (and .o). >Yet, such a module is not compiled by any component in the directory (the >closest is _sparsekit.pyf). What gives? > >b) After taking out the _sparsemodule.so target from the Makefile, I am >getting this error which I can't explain (disclaimer: my C is very rusty): >gcc -c -I/usr/include/python2.2 -I./SuperLU/SRC -fpic -O2 _zsuperlumodule.c >cc1: warning: -fpic ignored for target (all code is position independent) >In file included from SuperLU/SRC/zsp_defs.h:23, > from _zsuperlumodule.c:26: >SuperLU/SRC/supermatrix.h:19: parse error before numeric constant >SuperLU/SRC/supermatrix.h:21: parse error before numeric constant >make: *** [_zsuperlumodule.o] Error 1 > >All this is compiled on cygwin, gcc 3.2. Ideas? > >Thanks in advance, > >Costas > > > > >_________________________________________________________________ >MSN 8 with e-mail virus protection service: 2 months FREE* >http://join.msn.com/?page=features/virus > >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.net >http://www.scipy.net/mailman/listinfo/scipy-user _________________________________________________________________ STOP MORE SPAM with the new MSN 8 and get 2 months FREE* http://join.msn.com/?page=features/junkmail

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Problems compiling scipy/sparse
by Costas Malamas Dec. 15, 2002

Dec. 15, 2002

After my recent inquiry into scipy/sparse, I bit the bullet, downloaded SciPy CVS and started compiling everything to get scipy/sparse working. I got through ATLAS, LAPACK, f2py, NumPy and most of sparsekit itself fine, but then run into two really bizarre issues: a) Scipy/sparse/Makefile requires the target _sparsemodule.so (and .o). Yet, such a module is not compiled by any component in the directory (the closest is _sparsekit.pyf). What gives? b) After taking out the _sparsemodule.so target from the Makefile, I am getting this error which I can't explain (disclaimer: my C is very rusty): gcc -c -I/usr/include/python2.2 -I./SuperLU/SRC -fpic -O2 _zsuperlumodule.c cc1: warning: -fpic ignored for target (all code is position independent) In file included from SuperLU/SRC/zsp_defs.h:23, from _zsuperlumodule.c:26: SuperLU/SRC/supermatrix.h:19: parse error before numeric constant SuperLU/SRC/supermatrix.h:21: parse error before numeric constant make: *** [_zsuperlumodule.o] Error 1 All this is compiled on cygwin, gcc 3.2. Ideas? Thanks in advance, Costas _________________________________________________________________ MSN 8 with e-mail virus protection service: 2 months FREE* http://join.msn.com/?page=features/virus

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"New" bug tracker for SciPy/Weave/Chaco
by eric jones Dec. 13, 2002

Dec. 13, 2002

Hey group, We've had a Roundup bug tracker for a while now, but haven't really announced it as we were working out the hitches in it. I believe it is in good enough shape now for us to start using it. Please start submitting bugs to the bugtracker. http://www.scipy.net/roundup/scipy/index Roundup handles its own login management, so unfortunately it doesn't integrate seamlessly with the scipy.org site yet (any volunteers?). You'll have to register as a Roundup user if you want to benefit from its email system of keeping the bug submitter informed of progress. Sorry about this, but please do take the time to do this. It'll help with communication. It is also possible to submit bugs anonymously. There will likely be some bugs in the actual bugtracker.:-| Let us know when you see something that needs to be fixed, and we'll try and accommodate. We really could use a Roundup/Zope expert from the community to pitch in on this. Joe: Is there a link to point people at for a quick tutorial? If so, could you place it on the bugtracker side bar. If not, could you write up a quick-start guide. Thanks, eric ---------------------------------------------- eric jones 515 Congress Ave www.enthought.com Suite 1614 512 536-1057 Austin, Tx 78701

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numarray complex comparisons
by Perry Greenfield Dec. 12, 2002

Dec. 12, 2002

The questions just keep coming... We need to decide whether or not complex comparisons work. They do not work for Python scalars. Consistency would argue for them not working for numarray arrays. However some argue: 1) not allowing them defeats more generic programming. We agreed until we found that IDL doesn't support them either, and we never noticed. We are skeptical of this claim and would like to see real-life examples. 2) it is useful to allow comparisons since that would result in repeatable, sorting of values (e.g., to find duplicate values) for ordering purposes. Cannot this just be handled by the sort routines themselves? Why must this result in comparison operators working? In the absence of good examples for 1) or good arguments for 2) we propose to make complex comparisons generate exceptions. Perry Greenfield

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Re: [SciPy-user] Sparse Matrices (SciPy or elsewhere)?
by Costas Malamas Dec. 11, 2002

Dec. 11, 2002

Well, it's not in the auto-build. I downloaded the CVS tree, but my C is years behind me. Is it compilable on win32 (VC++)? will I have better luck with cygwin? Any tips, or howtos (even general ones) that can be of help? Thanks, Costas >From: Travis Oliphant <oliphant.travis(a)ieee.org> >Reply-To: scipy-user(a)scipy.net >To: scipy-user(a)scipy.net >Subject: Re: [SciPy-user] Sparse Matrices (SciPy or elsewhere)? >Date: 09 Dec 2002 12:02:02 -0700 > >On Mon, 2002-12-09 at 00:36, Costas Malamas wrote: > > I use SciPy, mostly for fun (check out my toy at memigo.com). For a new > > project, I am looking for a way to do sparse matrix algebra in >NumPy/SciPy. > > I notice that SciPy/sparse has been pretty much abandoned. Is it > > functional? if not, are there alternatives? > >It's not been abandoned. It's there and compiles for me. It has not >been extensively tested. It's fairly complete and is built on top of >other well tested libraries. > >Getting it to work on win32 has not been tested entirely. > >-Travis O. > > >_______________________________________________ >SciPy-user mailing list >SciPy-user(a)scipy.net >http://www.scipy.net/mailman/listinfo/scipy-user _________________________________________________________________ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963

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