Mailman 3 October 2009 - SciPy-Dev

Numpy_Example_List_With_Doc page
by Gökhan Sever 08 Oct '09

08 Oct '09

Hello, http://www.scipy.org/Numpy_Example_List_With_Doc This page doesn't tell anything different than the original numpy documentation. Also causes confusion in my opinion because of this statement: "To update this page just follow the instructions<http://www.scipy.org/Numpy_Example_List_With_Doc/script>. " Has it left intentionally or forgotten? -- Gökhan

2 1

Re: [SciPy-dev] numpy.distutils: passing config_fc options in setup.py
by Prabhu Ramachandran 08 Oct '09

08 Oct '09

On Monday 05 October 2009 03:50 PM, Pearu Peterson wrote: >> passing config_fc={...} to either Extension or setup does not work. >> The numpy version is 1.4.0.dev6976. > > A hackish solution would be to insert the following code to the > beginning of the setup.py file: > > import sys > sys.argv[:] = sys.argv[:1] + ['config_fc'. "--f90flags='-ffree-form > -fno-underscoring'"] + sys.argv[1:] > ) Thanks for the suggestion. I was hoping for a cleaner solution but this will work too. cheers, prabhu

2 1

scipy.test() segfaults
by Nils Wagner 08 Oct '09

08 Oct '09

Hi, Is this a known issue ? >>> import scipy >>> scipy.test() Running unit tests for scipy NumPy version 1.4.0.dev7507 NumPy is installed in /home/nwagner/local/lib64/python2.6/site-packages/numpy SciPy version 0.8.0.dev5964 SciPy is installed in /home/nwagner/local/lib64/python2.6/site-packages/scipy Python version 2.6 (r26:66714, Feb 3 2009, 20:49:49) [GCC 4.3.2 [gcc-4_3-branch revision 141291]] nose version 0.10.4 Program received signal SIGSEGV, Segmentation fault. PyArray_NeighborhoodIterNew (x=0x0, bounds=0x7ffff7ac2330, mode=-161985568, fill=0x7ffff7ac2330) at numpy/core/src/multiarray/iterators.c:1935 1935 array_iter_base_init((PyArrayIterObject*)ret, x->ao); (gdb) bt #0 PyArray_NeighborhoodIterNew (x=0x0, bounds=0x7ffff7ac2330, mode=-161985568, fill=0x7ffff7ac2330) at numpy/core/src/multiarray/iterators.c:1935 #1 0x00007fffee5d7e98 in init_path () at /home/nwagner/local/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1206 Nils

4 10

Note on changeset 5878: Add old_behavior arg for convolve2d and correlate2d
by Pearu Peterson 07 Oct '09

07 Oct '09

Hi, Currently scipy.signal.convolve gives the following warning by default: """ Current default behavior of convolve and correlate functions is deprecated. Convolve and corelate currently swap their arguments if the second argument has dimensions larger than the first one, and the mode is relative to the input with the largest dimension. The new behavior is to never swap the inputs, which is what most people expects, and is how correlation is usually defined. You can control the behavior with the old_behavior flag - the flag will disappear in scipy 0.9.0, and the functions will then implement the new behavior only. """ The problem right now is that it is difficult to write a stable application that would not give this warning. Using old_behavior=False argument means that when upgrading to scipy 0.9.0, the application will become broken because the kw argument will be removed. In my application the old and new behaviors are identical. My suggestion is to raise the deprecation warning only when the old and the new behavior are in conflict. For example, consider the diff below. What do you think? Pearu $ svn diff signaltools.py Index: signaltools.py =================================================================== --- signaltools.py (revision 5953) +++ signaltools.py (working copy) @@ -100,10 +100,11 @@ val = _valfrommode(mode) if old_behavior: - warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) if np.iscomplexobj(in2): + # hmm, how is this related to deprecation warning? in2 = in2.conjugate() if in1.size < in2.size: + warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) swp = in2 in2 = in1 in1 = swp @@ -210,8 +211,8 @@ slice_obj = [slice(None,None,-1)]*len(kernel.shape) if old_behavior: - warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) if (product(kernel.shape,axis=0) > product(volume.shape,axis=0)): + warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) temp = kernel kernel = volume volume = temp @@ -383,11 +384,8 @@ """ if old_behavior: - warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) - - if old_behavior: - warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) if (product(np.shape(in2),axis=0) > product(np.shape(in1),axis=0)): + warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) temp = in1 in1 = in2 in2 = temp @@ -436,8 +434,8 @@ cross-correlation of in1 with in2. """ - if old_behavior: - warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) + #if old_behavior: + # warnings.warn(DeprecationWarning(_SWAP_INPUTS_DEPRECATION_MSG)) val = _valfrommode(mode) bval = _bvalfromboundary(boundary)

3 3

Re: [SciPy-dev] [SciPy-Dec] scipy.weave crashes for pure inline
by Emmanuel Lambert 06 Oct '09

06 Oct '09

For the record of the archives/mailinglist, I just want to mention that there is a patch avaialble for the problem described below. It can be found at : http://projects.scipy.org/scipy/ticket/855 > > > On Tue, 2009-09-22 at 14:47 -0700, Thomas Robitaille wrote: > > Hi, > > > > I'm using a recent svn revision of scipy (5925). After installing it I went > > to scipy/weave/examples and ran 'python array3d.py'. I get the following > > error message (below). Can other people reproduce this problem? If not, > > maybe it's some local installation issue. > > > > Thanks, > > > > Thomas > > > > --- > > > > numpy: > > [[[ 0 1 2 3] > > [ 4 5 6 7] > > [ 8 9 10 11]] > > > > [[12 13 14 15] > > [16 17 18 19] > > [20 21 22 23]]] > > Pure Inline: > > Traceback (most recent call last): > > File "array3d.py", line 105, in <module> > > main() > > File "array3d.py", line 98, in main > > pure_inline(arr) > > File "array3d.py", line 57, in pure_inline > > weave.inline(code, ['arr']) > > File > > "/Users/tom/Library/Python/2.6/site-packages/scipy/weave/inline_tools.py", > > line 324, in inline > > results = attempt_function_call(code,local_dict,global_dict) > > File > > "/Users/tom/Library/Python/2.6/site-packages/scipy/weave/inline_tools.py", > > line 392, in attempt_function_call > > function_list = function_catalog.get_functions(code,module_dir) > > File "/Users/tom/Library/Python/2.6/site-packages/scipy/weave/catalog.py", > > line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/Users/tom/Library/Python/2.6/site-packages/scipy/weave/catalog.py", > > line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File > > "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/shelve.py", > > line 110, in __contains__ > > return key in self.dict > > File > > "/Users/tom/Library/Python/2.6/site-packages/scipy/io/dumbdbm_patched.py", > > line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > ------------------------------------------------------------------- > > On Mon, 2009-09-21 at 16:46 +0200, Emmanuel Lambert wrote: > > Hi, > > > > I compiled SciPy and Numpy on a machine with Scientific Linux. > > > > We detected a problem with Weave and after > > investigation, it turns out that some of the unit tests delivered > > with Scipy-Weave also fail ! Below is a list of tests that fail in for > > example the "test_c_spec" file. They all raise a KeyError. > > > > This is with SciPy 0.7.1 on Python 2.6. I also downloaded the latest > > Weave code again from the SVN repository, but the problem is not > > resolved. > > > > Any idea on how to tackle this problem? There are no posts that help > > me further. I don't have this problem with the same standard scipy > > package that was is available for Ubuntu 9.04 (apparently the weave > > version number is the same). > > > > It looks like the compilation works fine, see sample stdout also > > below. > > > > What could cause this? > > > > thanks for any help. > > Emmanuel > > > > ******************* SAMPLE OF STDOUT ****************** > > > > -------------------- >> begin captured stdout << --------------------- > > <weave: compiling> > > running build_ext > > running build_src > > building extension "sc_d133102ab45193e072f8dbb5a1f6848513" sources > > customize UnixCCompiler > > customize UnixCCompiler using build_ext > > customize UnixCCompiler > > customize UnixCCompiler using build_ext > > building 'sc_d133102ab45193e072f8dbb5a1f6848513' extension > > compiling C++ sources > > C compiler: g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 - > > Wall -fPIC > > > > compile options: '-I/user/home/gent/vsc401/vsc40157/scipy-runtime/ > > scipy/weave -I/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/ > > weave/scxx -I/user/home/gent/vsc401/vsc40157/numpy-runtime/numpy/core/ > > include -I/apps/gent/gengar/harpertown/software/Python/2.6.2- > > gimkl-0.5.0/include/python2.6 -c' > > g++: /user/home/gent/vsc401/vsc40157/.python26_compiled/ > > sc_d133102ab45193e072f8dbb5a1f6848513.cpp > > g++ -pthread -shared /tmp/vsc40157/python26_intermediate/ > > compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/ > > vsc40157/.python26_compiled/sc_d133102ab45193e072f8dbb5a1f6848513.o / > > tmp/vsc40157/python26_intermediate/ > > compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/ > > vsc40157/scipy-runtime/scipy/weave/scxx/weave_imp.o -o /user/home/gent/ > > vsc401/vsc40157/.python26_compiled/ > > sc_d133102ab45193e072f8dbb5a1f6848513.so > > running scons > > > > --------------------- >> end captured stdout << ---------------------- > > > > > > ********************** TESTS THAT FAIL *********************** > > > > -bash-3.2$ python ./test_c_spec.py > > E..........EE.................EEEE......E..........EE.................EEEE.............. > > ====================================================================== > > ERROR: test_call_function (test_c_spec.CallableConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 296, in test_call_function > > compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_file_to_py (test_c_spec.FileConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 262, in test_file_to_py > > force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_py_to_file (test_c_spec.FileConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 246, in test_py_to_file > > inline_tools.inline(code,['file'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_dict (test_c_spec.SequenceConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 305, in test_convert_to_dict > > inline_tools.inline("",['d'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_list (test_c_spec.SequenceConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 309, in test_convert_to_list > > inline_tools.inline("",['l'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_string (test_c_spec.SequenceConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 313, in test_convert_to_string > > inline_tools.inline("",['s'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_tuple (test_c_spec.SequenceConverter) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 317, in test_convert_to_tuple > > inline_tools.inline("",['t'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_call_function (test_c_spec.TestCallableConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 296, in test_call_function > > compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_file_to_py (test_c_spec.TestFileConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 262, in test_file_to_py > > force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_py_to_file (test_c_spec.TestFileConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 246, in test_py_to_file > > inline_tools.inline(code,['file'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_dict (test_c_spec.TestSequenceConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 305, in test_convert_to_dict > > inline_tools.inline("",['d'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_list (test_c_spec.TestSequenceConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 309, in test_convert_to_list > > inline_tools.inline("",['l'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_string (test_c_spec.TestSequenceConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 313, in test_convert_to_string > > inline_tools.inline("",['s'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ====================================================================== > > ERROR: test_convert_to_tuple (test_c_spec.TestSequenceConverterUnix) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > tests/test_c_spec.py", line 317, in test_convert_to_tuple > > inline_tools.inline("",['t'],compiler=self.compiler,force=1) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > inline_tools.py", line 301, in inline > > function_catalog.add_function(code,func,module_dir) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 648, in add_function > > self.cache[code] = self.get_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 615, in get_functions > > function_list = self.get_cataloged_functions(code) > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/ > > catalog.py", line 529, in get_cataloged_functions > > if cat is not None and code in cat: > > File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/ > > lib/python2.6/shelve.py", line 110, in __contains__ > > return key in self.dict > > File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/ > > dumbdbm_patched.py", line 73, in __getitem__ > > pos, siz = self._index[key] # may raise KeyError > > KeyError: 0 > > > > ---------------------------------------------------------------------- > > Ran 88 tests in 32.581s > > > > FAILED (errors=14)

1 0

Volunteer for Scipy Project
by Arkapravo Bhaumik 05 Oct '09

05 Oct '09

> Dear Sir/Ma'am > > I was in e-mail contact with one of your colleagues , Travis ; I am very > interested in contributing to scipy project as a volunteer. I believe that I > can contribute in > > (1) Documentation > (2) Suggesting and developing newer functionality > (3) Study similar software as Matlab, Mathematica, Maple etc trying to look > for inspiration for possible improvements in scipy > > Some of my dabbling python are discussed in my blogspot, > http://programming-unlimited.blogspot.com/ and I am eager to be a part of > scipy : a revolution in the making. > > I look forward to your reply. > > Kind regards > > Arkapravo >

5 12

Re: [SciPy-dev] Scipy-dev Digest, Vol 72, Issue 6
by Arkapravo Bhaumik 05 Oct '09

05 Oct '09

Hi My immediate plan was to try out scipy for some of those 'exotic' integrals which can only be sought through the route of contour integration ( http://programming-unlimited.blogspot.com/2009/10/exotic-integrals-in-scipy…). My immediate observation has been the comments made in scipy along with the output is not very consistent. I will soon post my detailed observations. Comparing with Matlab etc , I am sure we cannot 'copy' a module (and I doubt that may help). My plan was to used Matlab as a motivation , I guess that in about 3-5 years scipy will take over all the numerical/scientific software. I was wondering that employing some Pythonic-GUI (wx, tk,turtle, frog etc) is it possible to develop software as Simulink ? Best regards Arkapravo 2009/10/6 <scipy-dev-request(a)scipy.org> > Send Scipy-dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Scipy-dev digest..." > > > Today's Topics: > > 1. Re: Volunteer for Scipy Project (Anne Archibald) > 2. Re: Volunteer for Scipy Project (David Goldsmith) > 3. Re: Volunteer for Scipy Project (Anne Archibald) > 4. Re: Volunteer for Scipy Project (Charles R Harris) > 5. Re: Volunteer for Scipy Project (Anne Archibald) > 6. Re: Volunteer for Scipy Project (Charles R Harris) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 5 Oct 2009 16:40:46 -0400 > From: Anne Archibald <peridot.faceted(a)gmail.com> > Subject: Re: [SciPy-dev] Volunteer for Scipy Project > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: > <ce557a360910051340l2e5af73es5b7498abf677db7(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > 2009/10/5 David Cournapeau <david(a)ar.media.kyoto-u.ac.jp>: > > Hi Arkapravo, > > > > Arkapravo Bhaumik wrote: > >> > >> ? ? Dear Sir/Ma'am > >> > >> ? ? I was in e-mail contact with one of your colleagues , Travis ; ?I > >> ? ? am very interested in contributing to scipy project as a > >> ? ? volunteer. I believe that I can contribute in > >> > >> ? ? (1) Documentation > >> ? ? (2) Suggesting and developing newer functionality > >> ? ? (3) Study similar software as Matlab, Mathematica, Maple etc > >> ? ? trying to look for inspiration for possible improvements in scipy > >> > > > > Thanks for your help. As in most open source projects, the best way to > > contribute is to work on something that you actually need for yourself, > > be it code enhancement, bug fixes, documentation, etc... > > > > Depending on your interests and proficiency in python vs. C vs. Fortran, > > there are several things that could be worked on: the ones which need > > the most work ATM are scipy.special and scipy.interpolate. > > > > Please note also that you should be careful when 'studying' proprietary > > software - reimplementing from scratch a similar functionality is OK, > > re-using the implementation is almost never ok. > > I would add a mode of working that is definitely okay: find a > reference to a journal article on how to compute the thing you're > interested in (possibly by finding the reference in > matlab/r/maple/mathematica/whatever source ordoumentation) and > implementing what is described in the research paper. This is a great > way to fill gaps in scipy with good, well-thought-out algorithms. > > Anne > > > ------------------------------ > > Message: 2 > Date: Mon, 5 Oct 2009 13:54:11 -0700 > From: David Goldsmith <d.l.goldsmith(a)gmail.com> > Subject: Re: [SciPy-dev] Volunteer for Scipy Project > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: > <45d1ab480910051354m3cc0f210hdb49b5a281948807(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Just curious, Anne: have you anything in particular in mind (i.e., are > there > some small - or gaping - holes in scipy (IYO, of course) which you know > could be filled by a careful implementation of something(s) extant in the > literature)? > > DG > > On Mon, Oct 5, 2009 at 1:40 PM, Anne Archibald <peridot.faceted(a)gmail.com > >wrote: > > > 2009/10/5 David Cournapeau <david(a)ar.media.kyoto-u.ac.jp>: > > > Hi Arkapravo, > > > > > > Arkapravo Bhaumik wrote: > > >> > > >> Dear Sir/Ma'am > > >> > > >> I was in e-mail contact with one of your colleagues , Travis ; I > > >> am very interested in contributing to scipy project as a > > >> volunteer. I believe that I can contribute in > > >> > > >> (1) Documentation > > >> (2) Suggesting and developing newer functionality > > >> (3) Study similar software as Matlab, Mathematica, Maple etc > > >> trying to look for inspiration for possible improvements in scipy > > >> > > > > > > Thanks for your help. As in most open source projects, the best way to > > > contribute is to work on something that you actually need for yourself, > > > be it code enhancement, bug fixes, documentation, etc... > > > > > > Depending on your interests and proficiency in python vs. C vs. > Fortran, > > > there are several things that could be worked on: the ones which need > > > the most work ATM are scipy.special and scipy.interpolate. > > > > > > Please note also that you should be careful when 'studying' proprietary > > > software - reimplementing from scratch a similar functionality is OK, > > > re-using the implementation is almost never ok. > > > > I would add a mode of working that is definitely okay: find a > > reference to a journal article on how to compute the thing you're > > interested in (possibly by finding the reference in > > matlab/r/maple/mathematica/whatever source ordoumentation) and > > implementing what is described in the research paper. This is a great > > way to fill gaps in scipy with good, well-thought-out algorithms. > > > > Anne > > _______________________________________________ > > Scipy-dev mailing list > > Scipy-dev(a)scipy.org > > http://mail.scipy.org/mailman/listinfo/scipy-dev > > >

1 0

numpy.distutils: passing config_fc options in setup.py
by Prabhu Ramachandran 03 Oct '09

03 Oct '09

Hi, I've been using f2py to generate an extension module for someone's free-form f90 code. I need to pass extra arguments to config_fc and right now to get everything working I do this: python setup.py config_fc --f90flags='-ffree-form -fno-underscoring' build_ext --inplace Is there an easy way to set the --f90flags set by default to what I want in the setup.py script itself? I.e. I'd like users to be able to do: python setup.py build_ext --inplace This doesn't seem documented anywhere, is there some place I should look? This is how my setup.py looks currently: #---- from numpy.distutils.core import Extension, setup setup(ext_modules = [Extension("varsha", ["varsha.pyf", "s2p.f", "fft.c", "invLeg.c"], define_macros=[('NO_APPEND_FORTRAN', None)], ) ], ) #---- passing config_fc={...} to either Extension or setup does not work. The numpy version is 1.4.0.dev6976. Thanks! cheers, prabhu

1 0

Doc edit rights
by Michael Droettboom 03 Oct '09

03 Oct '09

I've been improving the chararray functionality (see this thread [1]). It would be helpful to get edit rights to the documentation editor so I can comment on and mark some docstrings for review. (FWIW, I think Travis O. is giving me SVN commit rights, so that's taken care of.) [1] http://www.nabble.com/Re%3A--SciPy-dev--Deprecate-chararray--was-Plea-for-h… Cheers, Mike -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA

3 3

Volunteer for Scipy Project
by Arkapravo Bhaumik 02 Oct '09

02 Oct '09

> Dear Sir/Ma'am > > I was in e-mail contact with one of your colleagues , Travis ; I am very > interested in contributing to scipy project as a volunteer. I believe that I > can contribute in > > (1) Documentation > (2) Suggesting and developing newer functionality > (3) Study similar software as Matlab, Mathematica, Maple etc trying to look > for inspiration for possible improvements in scipy > > Some of my dabbling python are discussed in my blogspot, > http://programming-unlimited.blogspot.com/ and I am eager to be a part of > scipy : a revolution in the making. > > I look forward to your reply. > > Kind regards > > Arkapravo >

1 0