Mailman 3 May 2009 - SciPy-User

addressing 1d array
by Ross Williamson 18 May '09

18 May '09

Hi everyone I'm currently writing some code where I read in a data file - Generally there are > 1 entry and I check certain parameters for example if data[0]['date'] == something: Which is fine until I get a single element and the above gives: '0-d arrays cannot be indexed' which makes sense , however, is there any easy way of just using the above code without having to check each time to see if it is only a single element - i.e. transparent (similar to idl) and just assumes that data[0] is the only element if there is only one in there. Cheers Ross

2 3

Chaco question
by Jochen Schroeder 17 May '09

17 May '09

Hi all, I'm trying to write a small application using chaco to check some of my simulation results. It's actually also a bit of an exercise to learn chaco. Currently what I have is something like this: class ContainerTest(HasTraits): plot = Instance(VPlotContainer) traits_view = View(Item('plot', editor=ComponentEditor(), show_label=False), width=800, height=800, resizable=True, title='spectrum') def __init__(self): super(ContainerTest, self).__init__() I,f,z = load_field('test.h5') plotdata = ArrayPlotData(spectrum=Is) imageplot = Plot(self.plotdata) im = imageplot.img_plot("spectrum", xbounds=t, ybounds=z, colormap=jet)[0] LI = LineInspector(component=self.imageplot, write_metadata=True, inspect_mode='indexed', axis='index_y') imageplot.overlays.append(LI) line = ArrayPlotData(field=I[0],frequency=f) lp = Plot(self.line) lineplot = lp.plot(("frequency","field"), type="line") container = VPlotContainer(imageplot,lp) self.plot = container I is a spectrum of a field depending on frequency f and propagation distance z. So on top i have an imageplot of the spectral evolution, while at the bottom I have just the spectrum at one point of the evolution. What I'm trying to do with the LineInspector is that I'd like to be able to move it up and down and choose which spectrum to display in the bottom plot. I've looked at some of the examples and I understand I need to at an event handler using on_trait_change, however I can't find which object gets written the metadata to. Another (slight) problem I found is that if I change the interpolation to bilinear I have a white gradient overlaying at the top and bottom of the image. Can anyone point me in the right direction? As I'm a bit stuck atm. Cheers Jochen

2 2

Looking for a way to cluster data
by Gary Ruben 16 May '09

16 May '09

Hi all, I'm looking for some advice on how to order data points so that I can visualise them. I've been looking at scipy.cluster for this purpose but I'm not sure whether it is suitable so I thought I'd see whether anyone had suggestions for a simpler suggestion of how to order the coordinates. I have a binary 3D array containing 1's that form a shape in a 3D volume against a background of 0's - they form a skeleton of a connected, branched structure. Furthermore, the points are all 26-connected to each other, i.e. there are no gaps in the skeleton. The longest chains may be 1000's of points long. It would be nice to visualise these using the mayavi mlab plot3d function, which draws tubes and which requires ordered coordinates as input, so I need to get ordered coordinate lists that traverse the points along the branches of the skeleton. It would also be nice to preferentially cluster long chains since then I can cull very short chains from the visualisation. scipy.cluster seems to be able to cluster the points but I'm not sure how to get the x,y,z coordinates of the original points out of its linkage data. This may not be possible. Maybe the scipy.spatial module is a better match to my problem. Any suggestions? Gary

4 7

Is numpy's argsort lying about its numpy.int32 types?
by Rob Clewley 15 May '09

15 May '09

Hi, I'm having a problem comparing some types when using numpy's argsort. I'm using numpy 1.0.2. I can reproduce it simply: Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] << snip >> In [1]: from numpy import argsort, sort, int32, array In [2]: x=array([1,3,2]) In [3]: aa=argsort(x) In [4]: as=sort(x) In [5]: type(aa[0]) Out[5]: <type 'numpy.int32'> In [6]: type(as[0]) Out[6]: <type 'numpy.int32'> In [7]: int32 Out[7]: <type 'numpy.int32'> In [8]: type(as[0])==int32 Out[8]: True In [9]: type(aa[0])==int32 Out[9]: False Any of the three indices in aa give me the same problem. Can someone explain if I should be doing this a different way, and if this is a bug?! Thanks, Rob

5 6

going through a lot of plots
by David Warde-Farley 14 May '09

14 May '09

I wonder if anyone has a good pattern they'd like to share for how to page through a lot of plots (mayavi.mlab or matplotlib or Chaco or whatever). I find myself in this situation a lot: I'm looking at a sequence of plots, one for each piece of data in a collection. I usually find myself writing a loop with a plot command followed by raw_input()so that I hit enter in the terminal window IPython session to move to the next item. I usually make this conditional so that I can process in batch without looking at the plots if I choose. This has the effect of producing a newline in the terminal every time I want to move on to the next plot, which is far from ideal, especially in the situation where I'm not printing anything else in that window. I figure there probably is a general way of solving this problem satisfactorily that I just haven't thought of, but any toolkit- specific ideas would be appreciated too. I'd rather avoid mucking with event-handlers since it would force control flow to depend on the plotting toolkit, removing the ability to just "turn off" plot-n-wait. Any thoughts? David

6 15

OS x 10.5 Problems with Scipy Installation
by Graham Enos 14 May '09

14 May '09

Hey all, I'm trying to install scipy today, and am having trouble on my intel macbook. I installed numpy, but scipy doesn't wanna go. Relevant details: OS X version 10.5 gcc version 4.2.1 gfortran version 4.2.3 I exported MACOSX_DEPLOYMENT_TARGET=10.5 and then ran py2.5 setup.py build_src build_clib --fcompiler=gfortran build_ext --fcompiler=gfortran build (py2.5 is my .bash_profile alias for python version 2.5.1) and got the following traceback (and previous lines of info): running build_src building py_modules sources building library "dfftpack" sources building library "fftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "dop" sources building library "fitpack" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "superlu_src" sources building library "arpack" sources building library "sc_c_misc" sources building library "sc_cephes" sources building library "sc_mach" sources building library "sc_toms" sources building library "sc_amos" sources building library "sc_cdf" sources building library "sc_specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.cluster._hierarchy_wrap" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.integrate.dop" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/scipy/interpolate/src/ dfitpack-f2pywrappers.f' to sources. building extension "scipy.interpolate._interpolate" sources building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/lapack/ clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize._slsqp" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize._nnls" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.signal.sigtools" sources conv_template:> build/src.macosx-10.5-i386-2.5/scipy/signal/lfilter.inc Traceback (most recent call last): File "setup.py", line 158, in <module> setup_package() File "setup.py", line 150, in setup_package configuration=configuration ) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/core.py", line 174, in setup return old_setup(**new_attr) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 87, in run self.build_sources() File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 106, in build_sources self.build_extension_sources(ext) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 214, in build_extension_sources sources = self.template_sources(sources, ext) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 322, in template_sources outstr = process_c_file(source) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 191, in process_file % (sourcefile, process_str(''.join(lines)))) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 156, in process_str newstr[sub[0]:sub[1]], sub[4]) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 120, in expand_sub for k in range(numsubs): TypeError: range() integer end argument expected, got NoneType. Looks like build_src is failing for some reason, though I don't know why. Any help would be greatly appreciated! Thanks, Graham

2 1

[ANN][Automatic Differentiation] Beta Version of PYADOLC
by Sebastian Walter 13 May '09

13 May '09

I am pleased to announce the release of PYADOLC (beta version). Homepage: http://github.com/b45ch1/pyadolc/ For download and instructions check the homepage. About the package ================= PYADOLC is a wrapper of the C++ software ADOL-C. It computes derivatives of arbitrarily complex algorithms (with loops and if then else) efficiently on the C++ side. 0) easy and pythonic user interface 1) efficient computation of _gradients_ g, _Hessians_ H and _higher_ order tensors T 2) efficient computation of products dot(u.T, H), dot(H,v) as they are needed in optimization algorithms 3) well documented by docstrings. For more information one can read the C++ documentation. 4) extensive unit test and many examples, including constrained optimization by projected gradients, etc ... 5) should be suitable for derivative generation of rather large scale optimization problems. E.g. optimal control problems, inverse problems, This is not tested though. 6) Sparse Jacobian support. Suggestions and Bugs: =================== Please report any bugs or inconveniences that you encounter! E.g. just write me if you have troubles with the installation. Everything *should* work as you expect. Sparse Jacobian support is experimental and the build process needs a little user assistance but should work. The API is not completely fixed. However, changes to the API will be backward compatible. Hope someone can make use of it. regards, Sebastian

5 8

Docs for Krogh Interpolator
by Joshua Stults 13 May '09

13 May '09

Hello, The docs for doing Hermite polynomial interpolation (specifying function and derivative values at points), seem a little lacking: http://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.Krogh… I appreciate the explanation it provides and the reference, but it doesn't actually say how to call the function. Are the values specified in several different 1D arrays, or one multidimensional array, in what order, and how do you specify which derivative you're giving? Thanks. -- Joshua Stults Website: http://j-stults.blogspot.com

3 3

ginput() causes error with TkAgg and imshow()
by n.l.o 13 May '09

13 May '09

Hello I am trying to do a ginput() on a imshow() of a image (fits-file, 512x512). When doing it the first time since invoking python I get the error below. I get it when using the TkAgg AND Qt4(Agg) backends, but NOT with the WX backend. Anyone that knows what to do? Is it a bug, if so where do I post it? Cheers Magnus In [6]: pl.ginput() /usr/lib/python2.6/dist-packages/matplotlib/backend_bases.py:1557: DeprecationWarning: functions overriding warnings.showwarning() must support the 'line' argument warnings.warn(str,DeprecationWarning) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (70, 0)) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /home/magnusp/msc/reduction/<ipython console> in <module>() /usr/lib/python2.6/dist-packages/matplotlib/pyplot.pyc in ginput(*args, **kwargs) 356 If *timeout* is negative, does not timeout. 357 """ --> 358 return gcf().ginput(*args, **kwargs) 359 if Figure.ginput.__doc__ is not None: 360 ginput.__doc__ = dedent(Figure.ginput.__doc__) /usr/lib/python2.6/dist-packages/matplotlib/figure.pyc in ginput(self, n, timeout, show_clicks) 1071 blocking_mouse_input = BlockingMouseInput(self) 1072 return blocking_mouse_input(n=n, timeout=timeout, -> 1073 show_clicks=show_clicks) 1074 1075 def waitforbuttonpress(self, timeout=-1): /usr/lib/python2.6/dist-packages/matplotlib/blocking_input.pyc in __call__(self, n, timeout, show_clicks) 256 self.clicks = [] 257 self.marks = [] --> 258 BlockingInput.__call__(self,n=n,timeout=timeout) 259 260 return self.clicks /usr/lib/python2.6/dist-packages/matplotlib/blocking_input.pyc in __call__(self, n, timeout) 102 try: 103 # Start event loop --> 104 self.fig.canvas.start_event_loop(timeout=timeout) 105 finally: # Run even on exception like ctrl-c 106 # Disconnect the callbacks /usr/lib/python2.6/dist-packages/matplotlib/backends/backend_tkagg.pyc in start_event_loop(self, timeout) 320 321 def start_event_loop(self,timeout): --> 322 FigureCanvasBase.start_event_loop_default(self,timeout) 323 start_event_loop.__doc__=FigureCanvasBase.start_event_loop_default.__doc__ 324 /usr/lib/python2.6/dist-packages/matplotlib/backend_bases.pyc in start_event_loop_default(self, timeout) 1555 str = "Using default event loop until function specific" 1556 str += " to this GUI is implemented" -> 1557 warnings.warn(str,DeprecationWarning) 1558 1559 if timeout <= 0: timeout = np.inf /var/lib/python-support/python2.6/pyfits/NP_pyfits.pyc in showwarning(message, category, filename, lineno, file) 74 if file is None: 75 file = sys.stdout ---> 76 _showwarning(message, category, filename, lineno, file) 77 78 def formatwarning(message, category, filename, lineno): /usr/lib/python2.6/warnings.pyc in _show_warning(message, category, filename, lineno, file, line) 27 file = sys.stderr 28 try: ---> 29 file.write(formatwarning(message, category, filename, lineno, line)) 30 except IOError: 31 pass # the file (probably stderr) is invalid - this warning gets lost. TypeError: formatwarning() takes exactly 4 arguments (5 given) -- View this message in context: http://www.nabble.com/ginput%28%29-causes-error-with-TkAgg-and-imshow%28%29… Sent from the Scipy-User mailing list archive at Nabble.com.

1 0

Error when install SciPy on OS X 10.5.6
by Chensong Zhang 13 May '09

13 May '09

Mac OS X 10.5.6 svn current version of scipy gcc --version i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5490) gfortran --version GNU Fortran (GCC) 4.3.3 Warning: No configuration returned, assuming unavailable. blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/ vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/ Python.framework/Versions/2.5/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib libraries umfpack not found in /sw/lib /System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/ python/numpy/distutils/system_info.py:401: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/ ) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE running build_src building py_modules sources building library "dfftpack" sources building library "fftpack" sources building library "linpack_lite" sources building library "mach" sources building library "quadpack" sources building library "odepack" sources building library "dop" sources building library "fitpack" sources building library "odrpack" sources building library "minpack" sources building library "rootfind" sources building library "superlu_src" sources building library "arpack" sources building library "sc_c_misc" sources building library "sc_cephes" sources building library "sc_mach" sources building library "sc_toms" sources building library "sc_amos" sources building library "sc_cdf" sources building library "sc_specfun" sources building library "statlib" sources building extension "scipy.cluster._vq" sources building extension "scipy.cluster._hierarchy_wrap" sources building extension "scipy.fftpack._fftpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.fftpack.convolve" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.integrate._quadpack" sources building extension "scipy.integrate._odepack" sources building extension "scipy.integrate.vode" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.integrate.dop" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.interpolate._fitpack" sources building extension "scipy.interpolate.dfitpack" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/scipy/interpolate/src/ dfitpack-f2pywrappers.f' to sources. building extension "scipy.interpolate._interpolate" sources building extension "scipy.io.numpyio" sources building extension "scipy.lib.blas.fblas" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/lib/blas/fblas-f2pywrappers.f' to sources. building extension "scipy.lib.blas.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/blas/cblas.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.flapack" sources f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/lib/lapack/ clapack.pyf' to sources. f2py options: ['skip:', ':'] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.lib.lapack.atlas_version" sources building extension "scipy.linalg.fblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/fblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/fblas-f2pywrappers.f' to sources. building extension "scipy.linalg.cblas" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/cblas.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.flapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/flapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. adding 'build/src.macosx-10.5-i386-2.5/build/src.macosx-10.5- i386-2.5/scipy/linalg/flapack-f2pywrappers.f' to sources. building extension "scipy.linalg.clapack" sources adding 'build/src.macosx-10.5-i386-2.5/scipy/linalg/clapack.pyf' to sources. f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg._flinalg" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.calc_lwork" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.linalg.atlas_version" sources building extension "scipy.odr.__odrpack" sources building extension "scipy.optimize._minpack" sources building extension "scipy.optimize._zeros" sources building extension "scipy.optimize._lbfgsb" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.moduleTNC" sources building extension "scipy.optimize._cobyla" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize.minpack2" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize._slsqp" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.optimize._nnls" sources f2py options: [] adding 'build/src.macosx-10.5-i386-2.5/fortranobject.c' to sources. adding 'build/src.macosx-10.5-i386-2.5' to include_dirs. building extension "scipy.signal.sigtools" sources conv_template:> build/src.macosx-10.5-i386-2.5/scipy/signal/lfilter.inc Traceback (most recent call last): File "setup.py", line 158, in <module> setup_package() File "setup.py", line 150, in setup_package configuration=configuration ) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/core.py", line 174, in setup return old_setup(**new_attr) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 87, in run self.build_sources() File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 106, in build_sources self.build_extension_sources(ext) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 214, in build_extension_sources sources = self.template_sources(sources, ext) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/command/build_src.py", line 322, in template_sources outstr = process_c_file(source) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 191, in process_file % (sourcefile, process_str(''.join(lines)))) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 156, in process_str newstr[sub[0]:sub[1]], sub[4]) File "/System/Library/Frameworks/Python.framework/Versions/2.5/ Extras/lib/python/numpy/distutils/conv_template.py", line 120, in expand_sub for k in range(numsubs): TypeError: range() integer end argument expected, got NoneType. Chensong ==================================== Mathematics Department Penn State University, State College, PA email: zhangchensong(a)gmail.com web: zhangcs.wordpress.com ====================================

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