Mailman 3 March 2005 - SciPy-User

Compiling python C-extensions to 'Enthon' on Win32
by Bryan Cole 09 Mar '05

09 Mar '05

Hi, Can anyone tell me what compilers can be used to build python C-extensions for the current (2.3) Enthought python distribution (on WindowsXP)? I didn't have any luck with the free-to-download MSVC compiler. Do I need the full MS-VisualStudio? Which version and does it matter? Are there any alternatives (BCC or mingw perhaps)? cheers, Bryan

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Re: Future directions for SciPy in light of meeting at Berkeley
by Joe Harrington 09 Mar '05

09 Mar '05

These were exactly the issues we addressed at SciPy04, and which led to the ASP project. All of the issues brought up in the current discussion have already been discussed there, and with largely the same conclusions. The basic gist is this: THERE ARE THOUSANDS OF PEOPLE WAITING FOR SCIPY TO REACH CRITICAL MASS! SciPy will reach the open-source jumping-off point when an outsider has the following experience: They google, find us, visit us, learn what they'll be getting, install it trivially, and read a tutorial that in less than 15 minutes has them plotting their own data. In that process, which will take less than 45 minutes total, they must also gain confidence in the solidity and longevity of the software and find a supportive community. We don't meet all the elements of this test now. Once we do, people will be ready to jump on and work the open-source magic. The goal of ASP (Accessible SciPy) is to meet that test. Some of what we need is being done already, but by a very small number of people. We need everyone's help to reach a meaningful rate of progress. The main points and their status: 1. Resolve the numeric/numarray split and get at least stubs for the basic routines in the Python core. Nothing scares new users more than instability and uncertainty. Travis O. is now attempting to incorporate numarray's added features (including much of the code that implements them) into numeric, and has made a lot of headway. Perry G. has said that he would switch back to numeric if it did the things numarray does. I think we can forsee a resolution to this split in the calendar year IF that effort stays the course. 2. Package it so that it's straightforward to install on all the popular architectures. Joe Cooper has done a lot here, as have others. The basic stuff installs trivially on Red Hat versions of Linux, Windows, and several others (including Debian, I think, and Mac, modulo the inherent problems people report with the Mac package managers, which we can do nothing about). Optimized installs are also available and not all that difficult, particularly if you're willing to issue a one-line command to rebuild a source package. For Linux, it was decided to stick with a core and add-on packages, and to offer umbrella packages that install common groups of packages through the dependency mechanism (e.g., for astronomy or biology). The main issue here is not the packaging, but the documentation, which is trivial to write at this point. I was able to do a "yum install scipy" at SciPy04, once I knew where the repository was. It's: http://www.enthought.com/python/fedora/$releasever We need someone to write installation notes for each package manager. We also need umbrella packages. 3. Document it thoroughly for both new and experienced users. Right now what we have doesn't scratch the surface. I mean no offense to those who have written what we do have. We need to update that and to write a lot more and a lot else. Janet Swisher and several others are ready to dig into this, but we're waiting for the numeric/numarray split to resolve. A list of needed documents is in the ASP proposal. 4. Focus new users on a single selection of packages. The variety of packages available to do a particular task is both a strength and a weakness. While experienced people will want choice, new users need simplicity. We will select a single package each application (like plotting), and will mainly describe those in the tutorial-level docs. We will not be afraid to change the selection of packages. You're only a new user once, so it will not affect you if we switch the docs after you've become experienced. For example, Matplotlib was selected at the SciPy04 BoF, but if Chaco ever reaches that level of new-user friendliness, we might switch. Both packages will of course always be available. Neither needs to be in the core on Linux and other systems that have package management. New users will be steered to the "starter" umbrella package, which will pull in any components that are not in the core. Enthon will continue to include all the packages in the world, I'm sure! 5. Provide a web site that is easy to use and that communicates to each client audience. We (me, Perry, Janet, Jon-Eric) were actually gearing up to solicit proposals for improving the site and making it the go-to place for all things numerical in python when Travis started his work on problem #1. This is the next step, but we're waiting for item 1 to finish so that we don't distract everyone's attention from its resolution. Many developers are interested in contributing here, too. If people feel it's time, we can begin this process. I just don't want to slow Travis and his helpers one tiny bit! 6. Catalog all the add-ons and external web sites so that scipy.org becomes the portal for all things numeric in python. This, at least, is done, thanks to Fernando Perez. See: http://www.scipy.org/wikis/topical_software/TopicalSoftware I'll add one more issue: 7. Do something so people who use SciPy, numeric, and numarray remember that these issues are being worked, and where, and how to contribute. To that end, all I can do is post periodically about ASP and encourage you to remember it whenever someone wonders why we haven't hit critical mass yet. Please visit the ASP wiki. Read the ASP proposal if you haven't, sign up to do something, and do it! Right now, a paltry 6 people have signed up to help out. http://www.scipy.org/wikis/accessible_scipy/AccessibleSciPy The ASP proposal is linked in the first paragraph of the wiki. After giving it some thought, we decided to use scipy-dev(a)scipy.net as our mailing list, to avoid cross-posted discussions on the 4 mailing lists. Please carry on any further discussion there. Thanks, --jh--

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Re: [Numpy-discussion] Future directions for SciPy in light of meeting at Berkeley
by pearu＠cens.ioc.ee 09 Mar '05

09 Mar '05

On Wed, 9 Mar 2005, Michiel Jan Laurens de Hoon wrote: > Travis Oliphant wrote: > > Proposal (just an idea to start discussion): > > > > Subdivide scipy into several super packages that install cleanly but can > > also be installed separately. Implement a CPAN-or-yum-like repository > > and query system for installing scientific packages. > > Yes! If SciPy could become a kind of scientific CPAN for python from > which users can download the packages they need, it would be a real > improvement. In the end, the meaning of SciPy evolve into "the website > where you can download scientific packages for python" rather than "a > python package for scientific computing", and the SciPy developers might > not feel OK with that. Personally, I would be OK with that. SciPy as a "download site" does not exclude it to provide also a "scipy package" as it is now. I am all in favore of refactoring current scipy modules as much as possible. Pearu

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Novice Question on plt.plot
by David Flory 08 Mar '05

08 Mar '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I cannot run plt.plot from a python 2.3.5 shell. I have no problems from inside pycrust. My DOS window look like this: D:\Flory>python ActivePython 2.3.5 Build 236 (ActiveState Corp.) based on Python 2.3.5 (#62, Feb 9 2005, 16:17:08) [MSC v.1200 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import gui_thread >>> gui_thread.start() >>> from scipy import plt >>> plt.plot((1,2,3)) <scipy.plt.wxplt.plot_frame; proxy of C++ wxFrame instance at _a062ff03_p_wxFrame> >>> D:\Flory> After the plt.plot() call I pop up an empty window "Figure 0" and the console give the <scipy.plt.wxplt.plot_frame ...> line above. When I click on the window, it turns white stays blank, and reports (Not responding). When I close it, WinXP reports that the program is not responding and forces a close. I have SciPy 0.3.2 installed and wxPython 2.5.3.1. I have looked in the documentation and not found anything. Suggestions or pointers to help would be appreciated. - -------------------------------------------------- David Flory -----BEGIN PGP SIGNATURE----- Version: PGP 8.1 iQA/AwUBQi3T3Ve2/rcN3lp8EQJqjgCgo9I5JLd9bfiPcRolcvppjFp+nHEAoJwE fjbOFUGIVXnTfH5ISehw4yja =vmCF -----END PGP SIGNATURE-----

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leastsq and Jacobian
by Stephen Walton 08 Mar '05

08 Mar '05

I find that the following script consistently core dumps (scipy latest CVS, Numeric 23.7, ATLAS 3.6.0) on both FC1 and FC3 when I say "python script.py" at the command line. I was trying to test problems others have reported using the Jacobian argument to leastsq, including a message way back in April 2003 from John Hunter. I'm pretty familiar with MINPACK, having used it to fit some functions a while back. Where might I start looking for the problem? from Numeric import * import scipy as S def ros(x): return array([10*(x[0] - x[1]**2), 1-x[1]]) def dros(x): return array([[-20*x[0], 10],[-1,0]]) def dros_trans(x): return array([[-20*x[0], -1],[10,0]]) x0=[-1.2,1.0] print "No Jacobian:" print S.optimize.leastsq(ros,x0) print "With Jacobian, try 1:" print S.optimize.leastsq(ros,x0,Dfun=dros) print "With Jacobian, try 2:" print S.optimize.leastsq(ros,x0,Dfun=dros_trans) print "With Jacobian, try 3:" print S.optimize.leastsq(ros,x0,Dfun=dros,col_deriv=1) print "With Jacobian, try 4:" print S.optimize.leastsq(ros,x0,Dfun=dros_trans,col_deriv=1)

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lognormal distribution
by Stephen Walton 07 Mar '05

07 Mar '05

An application question for a change: I need to produce pseudorandom numbers drawn from a lognormal distribution (see http://www.itl.nist.gov/div898/handbook/eda/section3/eda3669.htm). Does anyone have existing code for this in Numeric or numarray?

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scipy test file error
by Leila baghdadi 07 Mar '05

07 Mar '05

Hi everyone, I have finally managed to build scipy on Opteron (red hat linux enterprise 3), so I can import it in python with no problems but when I go to scipy/tests and try to run any of the tests python test_common.py the following error appears, can anyone give me a hint, File "/usr/lib64/python2.2/unittest.py", line 412, in loadTestsFromTestCase self.getTestCaseNames(testCaseClass))) File "test_common.py", line 20, in __init__ self.z = rand(100,10,20) File "/projects/mice/share/arch/linux64/lib64/python2.2/site-packages/scipy_base/ppimport.py", line 115, in __call__ return self._ppimport_attr(*args,**kwds) File "/projects/mice/share/arch/linux64/lib64/python2.2/site-packages/scipy/stats/distributions.py", line 82, in rand return random(args) File "/projects/mice/share/arch/linux64/lib64/python2.2/site-packages/scipy/stats/distributions.py", line 75, in random return _build_random_array(randfile.sample, (), size) File "/projects/mice/share/arch/linux64/lib64/python2.2/site-packages/scipy/stats/distributions.py", line 66, in _build_random_array s.shape = size ValueError: total size of new array must be unchanged Thanks very much Leila

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Performance question.
by Duncan Child 07 Mar '05

07 Mar '05

I am working on developing algorithms that are usually called with parameters that are Numeric arrays. We have the usual challenge though of trying to craft code that will gracefully accept both floats or arrays. Because of the often discussed problem with the handling of zero length arrays we expend some effort to ensure that we don't make calls on floats that only work on arrays and have ended up with a bunch of code like safe_len() that can be called with either. Today we have a related problem but now it is with performance (see code below). Numeric is faster than NumArray operating on smaller arrays but it is still relatively slow handling regular floats. We could add to the safe_ suite of functions the fast_ series but this still entails a significant performance hit and is not exactly elegant. The problem is larger than just handling sqrt so I would appreciate any feedback or suggestions on how best to proceed. Thanks, Duncan ================================================= def safe_len(a): # Return the length of the input array or 1 if it is a scalar try: safelen = len(a) except: safelen = 1 return safelen ================================================= from scipy import arange, sqrt from math import sqrt as csqrt import time # this is slower ... start_time = time.clock() for i in range(1000): a = sqrt(i) t1 = time.clock() - start_time # this is faster ... start_time = time.clock() for i in range(1000): a = csqrt(i) t2 = time.clock() - start_time print t1, t2, t1 / t2 C:\sqrt.py 0.0537227007132 0.00181048033684 68.6731754663 ================================================= from scipy import sqrt from math import sqrt as csqrt import types def fast_sqrt(arg): if type(arg) == types.FloatType: return csqrt(arg) else: return sqrt(arg)

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Installation Issues
by Jeremy Morris 04 Mar '05

04 Mar '05

I have been trying to install Scipy for the last few days. I run Mandrake 10, and when I run the command: python setup.py build I get the following error: In file included from /usr/include/python2.3/Python.h:8, from Lib/cluster/src/vq_wrap.cpp:176: /usr/include/python2.3/pyconfig.h:847:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/string.h:26, from Lib/cluster/src/vq_wrap.cpp:27: /usr/include/features.h:131:1: warning: this is the location of the previous definition In file included from Lib/cluster/src/vq_wrap.cpp:499: Lib/cluster/src/vq.h:57:7: warning: no newline at end of file Lib/cluster/src/vq_wrap.cpp:563:33: Numeric/arrayobject.h: No such file or directory Lib/cluster/src/vq_wrap.cpp:686: error: syntax error before `*' token Lib/cluster/src/vq_wrap.cpp:690: error: `basetype_string' was not declared in this scope This is just the first few lines. I think the line that is the most important is this one: Lib/cluster/src/vq_wrap.cpp:563:33: Numeric/arrayobject.h: No such file or directory Like I said, I have been trying to build/install for a few days now. I knew when I was altering the source that maybe something was wrong. Can anyone help? I need to get this running for an assignment, and still have to learn Python. The website said that I should include the following info: Platform : posix linux2 uname -a : Linux <my hostname> 2.6.3-7mdk #1 Wed Mar 17 15:56:42 CET 2004 i686 unknown unknown GNU/Linux gcc -v : Reading specs from /usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.2/specs Configured with: ../configure --prefix=/usr --libdir=/usr/lib --with-slibdir=/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --enable-long-long --enable-__cxa_atexit --enable-clocale=gnu --enable-languages=c,c++,ada,f77,objc,java,pascal --host=i586-mandrake-linux-gnu --with-system-zlib Thread model: posix gcc version 3.3.2 (Mandrake Linux 10.0 3.3.2-6mdk) g77 --version : GNU Fortran (GCC) 3.3.2 (Mandrake Linux 10.0 3.3.2-6mdk) Copyright (C) 2002 Free Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent permitted by law. You may redistribute copies of GNU Fortran under the terms of the GNU General Public License. For more information about these matters, see the file named COPYING or type the command `info -f g77 Copying'. Python Version : 2.3.3 (#2, Feb 9 2005, 13:57:58) [GCC 3.3.2 (Mandrakelinux 10.0 3.3.2-9mdk)] Numeric Version : 23.1 f2py Version : 2.45.241_1926 ATLAS Info : Traceback (most recent call last): File "setup_atlas_version.py", line 5, in ? from scipy_distutils.misc_util import get_path, default_config_dict ImportError: No module named scipy_distutils.misc_util And : Traceback (most recent call last): File "<string>", line 1, in ? ImportError: No module named atlas_version Other output : _pkg_config_info: NOT AVAILABLE agg2_info: ( src_dirs = .:/usr/local/src ) NOT AVAILABLE atlas_blas_info: ( library_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/lib:/usr/lib ) ( paths: /root/Linux_ATHLONSSE1/lib/libf77blas.a ) ( paths: /root/Linux_ATHLONSSE1/lib/libcblas.a ) ( paths: /root/Linux_ATHLONSSE1/lib/libatlas.a ) system_info.atlas_blas_info ( include_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/include:/usr/include ) FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/root/Linux_ATHLONSSE1/lib'] language = c atlas_blas_threads_info: ( library_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/lib:/usr/lib ) ( paths: /root/Linux_ATHLONSSE1/lib/libatlas.a ) system_info.atlas_blas_threads_info NOT AVAILABLE atlas_info: ( library_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/lib:/usr/lib ) ( paths: /root/Linux_ATHLONSSE1/lib/libf77blas.a ) ( paths: /root/Linux_ATHLONSSE1/lib/libcblas.a ) ( paths: /root/Linux_ATHLONSSE1/lib/libatlas.a ) ( paths: /root/Linux_ATHLONSSE1/lib/liblapack.a ) system_info.atlas_info ( include_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/include:/usr/include ) FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/root/Linux_ATHLONSSE1/lib'] language = f77 atlas_threads_info: ( library_dirs = /root/Linux_ATHLONSSE1/lib:/usr/local/lib:/usr/lib ) ( paths: /root/Linux_ATHLONSSE1/lib/libatlas.a ) system_info.atlas_threads_info NOT AVAILABLE blas_info: ( library_dirs = /usr/local/lib:/usr/lib ) NOT AVAILABLE blas_opt_info: Traceback (most recent call last): File "scipy_core/scipy_distutils/system_info.py", line 1430, in ? show_all() File "scipy_core/scipy_distutils/system_info.py", line 1427, in show_all r = c.get_info() File "scipy_core/scipy_distutils/system_info.py", line 314, in get_info self.calc_info() File "scipy_core/scipy_distutils/system_info.py", line 972, in calc_info atlas_version = get_atlas_version(**version_info) File "scipy_core/scipy_distutils/system_info.py", line 809, in get_atlas_version from core import Extension, setup File "scipy_core/scipy_distutils/core.py", line 5, in ? from scipy_distutils.dist import Distribution ImportError: No module named scipy_distutils.dist And : python: can't open file 'scipy_core/scipy_distutils/command/build_flib.py' Thanks again. Jeremy

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PyTrilinos - Python interface to Trilinos libraries
by Nils Wagner 04 Mar '05

04 Mar '05

Hi all, A new release of Trilinos is available. It includes a Python interface to Trilinos libraries. http://software.sandia.gov/trilinos/release_5.0_notes.html Regards, Nils

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