Mailman 3 September 2003 - SciPy-Dev

Problems with latest cvs
by Nils Wagner Sept. 18, 2003

Sept. 18, 2003

Dear experts, /usr/local/bin/python setup.py install failed with the following message usr/local/lib/python2.1/site-packages/scipy/traits/traits.py:518: SyntaxWarning: local name 'object' in 'sync_trait' shadows use of 'object' as global in nested scope 'lambda' def sync_trait ( self, trait_name, object, alias = None, mutual = True ): /usr/local/lib/python2.1/site-packages/scipy/traits/traits.py:518: SyntaxWarning: local name 'self' in 'sync_trait' shadows use of 'self' as global in nested scope 'lambda' def sync_trait ( self, trait_name, object, alias = None, mutual = True ): /usr/local/lib/python2.1/site-packages/scipy/traits/traits.py:518: SyntaxWarning: local name 'trait_name' in 'sync_trait' shadows use of 'trait_name' as global in nested scope 'lambda' def sync_trait ( self, trait_name, object, alias = None, mutual = True ): /usr/local/lib/python2.1/site-packages/scipy/traits/traits.py:518: SyntaxWarning: local name 'alias' in 'sync_trait' shadows use of 'alias' as global in nested scope 'lambda' def sync_trait ( self, trait_name, object, alias = None, mutual = True ): byte-compiling /usr/local/lib/python2.1/site-packages/scipy/traits/tests/test_timing.py to test_timing.pyc byte-compiling /usr/local/lib/python2.1/site-packages/scipy/traits/tests/test_traits.py to test_traits.pyc Traceback (most recent call last): File "setup.py", line 113, in ? setup_package() File "setup.py", line 103, in setup_package url = "http://www.scipy.org", File "scipy_core/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/local/lib/python2.1/distutils/core.py", line 138, in setup dist.run_commands() File "/usr/local/lib/python2.1/distutils/dist.py", line 899, in run_commands self.run_command(cmd) File "/usr/local/lib/python2.1/distutils/dist.py", line 919, in run_command cmd_obj.run() File "/usr/local/lib/python2.1/distutils/command/install.py", line 484, in run self.run_command(cmd_name) File "/usr/local/lib/python2.1/distutils/cmd.py", line 328, in run_command self.distribution.run_command(command) File "/usr/local/lib/python2.1/distutils/dist.py", line 919, in run_command cmd_obj.run() File "/usr/local/lib/python2.1/distutils/command/install_lib.py", line 93, in run self.byte_compile(outfiles) File "/usr/local/lib/python2.1/distutils/command/install_lib.py", line 130, in byte_compile verbose=self.verbose, dry_run=self.dry_run) File "/usr/local/lib/python2.1/distutils/util.py", line 439, in byte_compile compile(file, cfile, dfile) File "/usr/local/lib/python2.1/py_compile.py", line 62, in compile codeobject = __builtin__.compile(codestring, dfile or file, 'exec') OverflowError: ('integer literal too large', ('/usr/local/lib/python2.1/site-packages/scipy/traits/tests/test_traits.py', 839, None, "[ '000-000-000', '999-9999-999', '1234-567-8769', '[123] 456-7890',\n")) Nils

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test failures with current CVS
by bhoel＠web.de Sept. 16, 2003

Sept. 16, 2003

Hello, Building and installing the current CVS version of SciPy, import scipy scipy.test() gives 4 errors on SuSE 8.2 with Python 2.3 and gcc3.3: ... ====================================================================== ERROR: check_cdf (test_distributions.test_foldnorm) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.3/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 586, in __call__ return self.rvs(*args, **kwds) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 338, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 1100, in _rvs return abs(norm(loc=c,size=self._size)) TypeError: __call__() got an unexpected keyword argument 'loc' ====================================================================== ERROR: check_cdf (test_distributions.test_nct) ---------------------------------------------------------------------- Traceback (most recent call last): File "<string>", line 5, in check_cdf File "/usr/local/lib/python2.3/site-packages/scipy/stats/stats.py", line 1521, in kstest vals = sb.sort(rvs(*args,**kwds)) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 586, in __call__ return self.rvs(*args, **kwds) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 338, in rvs vals = reshape(self._rvs(*args),size) File "/usr/local/lib/python2.3/site-packages/scipy/stats/distributions.py", line 1704, in _rvs return norm(loc=nc,size=self._size)*sqrt(df) / sqrt(chi2(df,size=self._size)) TypeError: __call__() got an unexpected keyword argument 'loc' ====================================================================== ERROR: check_chebyc (test_basic.test_chebyc) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 214, in check_chebyc chebc = chebyc(1)(.2) File "/usr/local/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 398, in chebyc p = p * 2.0/p(2) File "/usr/local/lib/python2.3/site-packages/scipy_base/polynomial.py", line 445, in __getattr__ raise KeyError KeyError ====================================================================== ERROR: check_chebys (test_basic.test_chebys) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib/python2.3/site-packages/scipy/special/tests/test_basic.py", line 220, in check_chebys chebs = chebys(1)(.2) File "/usr/local/lib/python2.3/site-packages/scipy/special/orthogonal.py", line 429, in chebys p = p * (n+1.0)/p(2) File "/usr/local/lib/python2.3/site-packages/scipy_base/polynomial.py", line 445, in __getattr__ raise KeyError KeyError ---------------------------------------------------------------------- Ran 739 tests in 3.045s FAILED (errors=4) <unittest.TextTestRunner object at 0x4075bf8c> >>> Greetings Berthold -- bhoel(a)web.de / http://starship.python.net/crew/bhoel/ It is unlawful to use this email address for unsolicited ads (USC Title 47 Sec.227). I will assess a US$500 charge for reviewing and deleting each unsolicited ad.

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Contour plots in scipy
by Nils Wagner Sept. 16, 2003

Sept. 16, 2003

Dear experts, I am interested in a plot of equipotential curves. If desired, the regions between contours should be shaded or colored to indicate their magnitude. Is this feature already available in scipy ? Any comments or suggestions ? Nils

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powm for scipy
by Nils Wagner Sept. 16, 2003

Sept. 16, 2003

Dear experts, I wonder, if powm will become a part of scipy in the near future. Nils

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Earth Science Markup Language
by Rahul Ramachandran Sept. 10, 2003

Sept. 10, 2003

All: We have implemented a Python wrapper for the ESML data reader library. This allows users to read any kind of unstructured files formats in Binary or ASCII and formats such as HDF-EOS, netCDF, GRIB in Python. I think it will be extremely useful to the SciPy community. Details about ESML can be found at: http://esml.itsc.uah.edu <http://esml.itsc.uah.edu/> Thnx, -Rahul **************************************** Rahul Ramachandran, Ph.D. Information Technology and Systems Center University of Alabama in Huntsville Huntsville, AL 35899 Tel: (256)-824-5157 Fax: (256)-824-5149 email: rramachandran(a)itsc.uah.edu <mailto:rramachandran@itsc.uah.edu>

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Compile failure of CVS version
by bhoel＠web.de Sept. 10, 2003

Sept. 10, 2003

Hello, Trying to compile the latest CVS version of SciPy I get: gcc -fno-strict-aliasing -DNDEBUG -g -O3 -Wstrict-prototypes -O3 -fstrict-aliasing -funroll-loops -fschedule-insns2 -ffast-math -fno-math-errno -funsafe-math-optimizations -fno-trapping-math -march=athlon-xp -mfpmath=sse -msse -mmmx -m3dnow -fPIC -I/home/devel/CVS/scipy/Lib_chaco/agg2/include -I/home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/include -I/usr/local/include/python2.3 -c /home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/agg_wrap.cxx -o build/temp.linux-i686-2.3/home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/agg_wrap.o In file included from /home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/agg_wrap.cxx:982: /home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/kiva_graphics_context.h:515: error: invalid type `agg::rgba' for default argument to `agg::rgba&' /home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/agg_wrap.cxx: In function ` PyObject* _wrap__GraphicsContextArray_clear(PyObject*, PyObject*)': /home/devel/CVS/scipy/Lib_chaco/kiva/agg/swig_src/agg_wrap.cxx:5182: error: could not convert `rgba(1.0e+0, 1.0e+0, 1.0e+0, 1.0e+0)' to `agg::rgba&' error: command 'gcc' failed with exit status 1 I am on a SuSE 8.2 but with gcc --version gcc (GCC) 3.3 (SuSE Linux) Copyright (C) 2003 Free Software Foundation, Inc. instead of the original delivered prerelease version and a self compiled Python 2.3. Sorry, but I don't know enough about C++ to provide a patch. Greetings Berthold -- bhoel(a)web.de / http://starship.python.net/crew/bhoel/ It is unlawful to use this email address for unsolicited ads (USC Title 47 Sec.227). I will assess a US$500 charge for reviewing and deleting each unsolicited ad.

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Hankel, Toeplitz why not Vandermonde
by Nils Wagner Sept. 10, 2003

Sept. 10, 2003

Hi all, I found Hankel and Toeplitz matrices in scipy - why not Vandermonde matrices ? Nils

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problem installing weave under Win ME
by Jean-Baptiste Richet - AREAS Sept. 8, 2003

Sept. 8, 2003

Hello, weave could be highly usefull to me, but I can't have it work correctly on my PC, and I don't know what to do. Could you help me ? I installed the latest zip package by "python setup.py install", on a python 2.3 installation (OS = Windows ME), and here is a result when trying it : ========================= IDLE 1.0 >>> import weave >>> a = 123 >>> weave.inline('printf("%d\\n",a);',['a']) Exception exceptions.AttributeError: "DbfilenameShelf instance has no attribute 'writeback'" in Traceback (most recent call last): File "<pyshell#2>", line 1, in -toplevel- weave.inline('printf("%d\\n",a);',['a']) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\ext_tools.py", line 349, in compile verbose = verbose, **kw) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\build_tools.py", line 194, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "c:\developpement\python23\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) CompileError: error: command 'g++' failed with exit status 1 >>> =========================== The gcc I use comes from MinGW and is version 3.2. I tried out gcc 2.95, and it was nearly the same (error at the same place, but 'cc' was blaimed). I tried cygwin, and it was not different. I tried python 2.2, and the result was similar. Any idea ? thanks a lot for your help. -- Jean-Baptiste Richet AREAS _________________________________ Association régionale pour l'étude et l'amélioration des sols 2, avenue Foch 76460 Saint Valéry en Caux tél : +33 2 35 97 25 12 fax : +33 2 35 97 25 73 _________________________________

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Low-level code integration discussion at scipy'03?
by Fernando Perez Sept. 3, 2003

Sept. 3, 2003

Hi everyone, as I mentioned before, I think it would be great to have a bit of an open discussion on methods and techniques for plugging low-level code into python at Scipy'03. I don't mean to teach people how to write an extension module, but rather what the best/easiest approaches are for writing time-critical code which manipulates Numpy/numarray arrays. A brief summary of the alternatives: * Scipy's weave relies on blitz, which is extremely nice and maps surprisingly well to python arrays. Blitz arrays have slices, ranges, overloaded arithmetic operators and math functions, etc. In fact, writing blitz C++ feels almost like writing python code, with the caveats of handling compile-time type information. But blitz development seems to be rather slow these days, and the issue of access to Blas/lapack from blitz isn't fully settled (i.e., it's not out-of-the box easy). * The ublas library (http://www.boost.org/libs/numeric/ublas/doc/overview.htm). It has direct blas support, but it seems to focus strictly on vectors and matrices, and as far as I see it doesn't support higher rank objects (I could be wrong, though: I've been using blitz for 'real' and only looked at the ublas webpage). * Writing low-level code in fortran and using Pearu's f2py. I love f2py, but I'd prefer my low-level code to have the ability to also use more information from the python side of things if needed. I think f2py is a great tool for wrapping existing fortran codes, but not so much for extending a python program with a few low-level routines. And there is always the potential need for transposition operations when going to Fortran because of the row/column memory ordering discrepancy between C and Fortran. * Complete roll-your-own solutions using the Numarray C api. This is doable, but after using blitz arrays, it feels really low-level. Call me lazy, but after using python I've become fully enamored of writing code which reads as cleanly as possible. What I'd like to know is if there is any interest in organizing a bit of a discussion on this. If an hour can be squeezed in for this in the schedule, great (and I volunteer to moderate if nobody else wants to). If not, perhaps some of people involved with these topics (Eric, Travis, Konrad, Todd and Perry at least, plus whoever else is interested) might be willing to commit to a lunch/dinner to be spent talking about this. It would be nice to know something in advance, because one of blitz's current developers (Julian Cummings) is at Caltech. Perhaps we could ask him to come in and answer some questions about Blitz's future. Blitz feels like the lowest-impedance fit to python's semantics, but I'd like to know more about its long-term feasibility before committing to use it too much. If we set any kind of schedule for this discussion, I can try to contact Julian. Regards, Fernando.

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RE: [SciPy-dev] Re: [SciPy-user] Low-level code integrationdiscussionat scipy'03?
by Chuck Harris Sept. 3, 2003

Sept. 3, 2003

>> >> >> > >> > Are you just talking about C macros to do the indexing >> (including strides? >> >> Well, anything which allows me to say in C/C++: >> >> A(i,j,k,l,m,n) = some_function_of(i,j,k,l,m,n); >> >> square brackets would also work, though >> >> A[i][j][k][l][m][n] >> >> starts to feel ugly real quick. >> >Well, since C is not blessed with convenient handling of multidimensional >array indexing, it would have to be a macro or a function to do this. >A function probably brings in about a factor of 3 penalty for data >access (at least it did a couple years ago when we benchmarked that >approach--hmmm, makes me wonder if blitz resorts to that for large numbers >of dimensions). Mind you, for numarray instances where byteswapped or >nonaligned data are involved, I think a function for indexing is a >necessity. In a temporary moment of madness, I started to write my own version of Numeric. Indexing was a small loop implementing a mixed radix counter that was passed a structure containing the slice info and some function pointers that were called in certain parts of the loop. The overhead I measured was of the order of 10% over a straight loop with embedded function calls on my machine (PIII). So I think it is possible to build pretty efficient functions for this sort of thing. I was most surprised at how low the function call overhead was. Chuck

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