Mailman 3 October 2007 - SciPy-Dev

latest SVN (3412) build fails on Windows
by Robin 05 Oct '07

05 Oct '07

Hi, I found that having updated scipy to svn 3412 the new io.nifti module fails: creating build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\io creating build\temp.win32-2.5\Release\build\src.win32-2.5\scipy\io\nifti compile options: '-Iscipy\io\nifti -Iscipy\io\nifti\nifticlib\fsliolib -Iscipy\i o\nifti\nifticlib\niftilib -Iscipy\io\nifti\nifticlib\znzlib -Ic:\Python25\lib\s ite-packages\numpy\core\include -Ic:\Python25\include -Ic:\Python25\PC -c' gcc -mno-cygwin -O2 -Wall -Wstrict-prototypes -Iscipy\io\nifti -Iscipy\io\nifti\ nifticlib\fsliolib -Iscipy\io\nifti\nifticlib\niftilib -Iscipy\io\nifti\nifticli b\znzlib -Ic:\Python25\lib\site-packages\numpy\core\include -Ic:\Python25\includ e -Ic:\Python25\PC -c build\src.win32-2.5\scipy\io\nifti\nifticlib_wrap.c -o bui ld\temp.win32- 2.5\Release\build\src.win32-2.5\scipy\io\nifti\nifticlib_wrap.o g++ -mno-cygwin -shared build\temp.win32- 2.5\Release\build\src.win32-2.5\scipy\i o\nifti\nifticlib_wrap.o -Lc:\Python25\libs -Lc:\Python25\PCBuild -Lbuild\temp.w in32-2.5 -lniftiio -lfslio -lznz -lpython25 -lmsvcr71 -o build\lib.win32- 2.5\sci py\io\nifti\_nifticlib.pyd Found executable C:\cygwin\bin\g++.exe build\temp.win32- 2.5\Release\build\src.win32-2.5\scipy\io\nifti\nifticlib_wrap.o :nifticlib_wrap.c:(.text+0x368c): undefined reference to `_znzprintf' collect2: ld returned 1 exit status error: Command "g++ -mno-cygwin -shared build\temp.win32- 2.5\Release\build\src.w in32-2.5\scipy\io\nifti\nifticlib_wrap.o -Lc:\Python25\libs -Lc:\Python25\PCBuil d -Lbuild\temp.win32-2.5 -lniftiio -lfslio -lznz -lpython25 -lmsvcr71 -o build\l ib.win32-2.5\scipy\io\nifti\_nifticlib.pyd" failed with exit status 1 I am using Cygwin gcc 3.4.4 on Windows XP. Should I submit a ticket or is more information required (or is there a simple fix for something in my setup)? Robin

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Nifti support
by Matthieu Brucher 04 Oct '07

04 Oct '07

Hi, I saw that nifti file support was currently in the pipeline. If the license issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago. Matthieu

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adopting Python Style Guide for classes
by Jarrod Millman 03 Oct '07

03 Oct '07

Hello, For those of you not on the Numpy developer's list, we have been talking about adopting the Python class naming convention to conform with Guido's style guide as closely as possible: http://www.python.org/dev/peps/pep-0008/ According to Guido, class names should use the CapWords convention. Most Python projects (eg, ETS, matploltlib) adhere to the Python naming conventions and it is confusing that NumPy and SciPy don't. Currently, both NumPy and SciPy use either lower_underscore_separated or CapWords for class names. NumPy ====== $ grep -r '^class [A-Z]' --include "*.py" * | wc -l 1014 $ grep -r '^class' --include "*.py" * | grep -v 'class [A-Z]' | wc -l 207 SciPy ===== $ grep -r '^class [A-Z]' --include "*.py" * | wc -l 587 $ grep -r '^class' --include "*.py" * | grep -v 'class [A-Z]' | wc -l 565 So far, there is Universal support for the basic idea of conforming to the Python Style Guide. Since it should effect the user API, we have already updated the TestCase classes. First, we checked in a change to allow TestCase classes to be prefixed with either 'test' or 'Test': http://projects.scipy.org/scipy/numpy/changeset/4144 Then, we updated both SciPy and NumPy to use CapWords for TestCase classes: http://projects.scipy.org/scipy/numpy/changeset/4151 http://projects.scipy.org/scipy/scipy/changeset/3388 In order to run the SciPy tests on the trunk you will need to install NumPy from svn revision 4144 or greater. Before SciPy 0.7.0 is released, we will release NumPy 1.0.4. Also, if you are adding a new class to NumPy or SciPy, please use CapWords. Now we need to decide what to do about the remaining lower_underscore_separated class names. Obviously, it is important that we are careful to not break a lot of code just to bring our class names up to standards. Cheers, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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Fwd: Scientific Programmer Position at UC Berkeley
by Jarrod Millman 02 Oct '07

02 Oct '07

Hello everyone, This position will involve a fairly heavy amount of Python programming. Feel free to contact either Fritz or myself if you have any questions. Thanks, Jarrod ---------- Forwarded message ---------- From: Fritz Sommer <fsommer(a)berkeley.edu> Date: Oct 2, 2007 4:04 PM Subject: Fwd: Scientific Programmer Position at UC Berkeley To: Jarrod Millman <millman(a)berkeley.edu> SCIENTIFIC PROGRAMMER POSITION The Sommer lab at UC Berkeley seeks a scientific programmer to assume an integral role in the design and maintenance of the Core Services of the new NSF-Initiative Data-Sharing in Neuroscience, hosted at the Redwood Center for Theoretical Neuroscience and the Helen Wills Neuroscience Institute. Specifically, work involves the design and administration of the data repository and website used for this initiative. This includes the integration and design of these resources, the development and documentation of tools for data sharing, maintaining a data server, design and maintenance of a website, as well as support and interaction with data contributors. Qualifications: *Interest in Neuroscience *Expertise in Python, Matlab, XML and HTML *Experience with content management systems (PLONE) and version control (CVS or SVN) *Experience with binary data formats and hierarchical data formats (HDF5) *Familiarity with different unix-like platforms (Linux and Mac OS X). *Strong problem-solving abilities Salary and start date The monthly salary range is $3987 - $7318, although most offers will not exceed midpoint of the salary range. Open: immediately, with preferred start date 15 Oct 2007 or earlier. Minimum one year commitment preferred. How to apply U.C. Berkeley has an online applicant website. Visit: http://jobs.berkeley.edu/ and search for job #007217. If you have any questions, please contact Fritz Sommer: fsommer(a)berkeley.edu ------------------------------------------------------------------------ ----- Friedrich T. Sommer, Ph.D., Associate Adjunct Professor University of California, Berkeley Redwood Center for Theoretical Neuroscience & HWNI 3210F Tolman Hall MC 3192 Berkeley, CA 94720 phone (510) 642-7251 fax (510) 642-7206 http://redwood.berkeley.edu/wiki/Fritz_Sommer

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