Mailman 3 June 2008 - NumPy-Discussion

Bug in numpy.histogram?
by Tommy Grav June 9, 2008

June 9, 2008

With the most recent change in numpy 1.1 it seems that numpy.histogram was broken when wanting a normalized histogram. I thought the idea was to leave the functionality of histogram as it was in 1.1 and then break the api in 1.2? import numpy a = [0,1,2,3,4,5,6,7,8] numpy.histogram(a) /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site- packages/numpy/lib/function_base.py:166: FutureWarning: The semantics of histogram will be modified in release 1.2 to improve outlier handling. The new behavior can be obtained using new=True. Note that the new version accepts/ returns the bin edges instead of the left bin edges. Please read the docstring for more information. Please read the docstring for more information.""", FutureWarning) (array([1, 1, 1, 1, 0, 1, 1, 1, 1, 1]), array([ 0. , 0.8, 1.6, 2.4, 3.2, 4. , 4.8, 5.6, 6.4, 7.2])) data, bins = numpy.histogram(a) len(data) 10 len(bins) 10 b = [1,3,5,6,9] data, bins = numpy.histogram(a,b) /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site- packages/numpy/lib/function_base.py:193: FutureWarning: The semantic for bins will change in version 1.2. The bins will become the bin edges, instead of the left bin edges. """, FutureWarning) data array([2, 2, 1, 3, 0]) bins array([1, 3, 5, 6, 9]) data, bins = numpy.histogram(a,b,normed=True) Traceback (most recent call last): File "<console>", line 0, in <module> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/numpy/lib/function_base.py", line 189, in histogram raise ValueError, 'Use new=True to pass bin edges explicitly.' ValueError: Use new=True to pass bin edges explicitly.

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Installation info
by Peter Creasey June 9, 2008

June 9, 2008

Is numpy v1.1 going to come out in egg format? I ask because I only see the superpack installers on the sourceforge page, and we have users who we are delivering to via egg - requires. thanks, Peter 2008/5/23 <numpy-discussion-request(a)scipy.org>: > Send Numpy-discussion mailing list submissions to > numpy-discussion(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://projects.scipy.org/mailman/listinfo/numpy-discussion > or, via email, send a message with subject or body 'help' to > numpy-discussion-request(a)scipy.org > > You can reach the person managing the list at > numpy-discussion-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Numpy-discussion digest..." > > > Today's Topics: > > 1. Re: f2py errors: any help interpreting? (Mark Miller) > 2. Re: f2py errors: any help interpreting? (Robert Kern) > 3. Re: f2py errors: any help interpreting? (Mark Miller) > 4. Re: f2py errors: any help interpreting? (Robert Kern) > 5. Re: f2py errors: any help interpreting? (Mark Miller) > 6. Re: f2py errors: any help interpreting? (Mark Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 May 2008 14:48:47 -0700 > From: "Mark Miller" <markperrymiller(a)gmail.com> > Subject: Re: [Numpy-discussion] f2py errors: any help interpreting? > To: "Discussion of Numerical Python" <numpy-discussion(a)scipy.org> > Message-ID: > <d1eaff10805231448i69fe8589v18062ef0f737f85(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Super...I'll give it a try. Or should I just wait for the numpy 1.1 > release? > > thanks, > > -Mark > > On Fri, May 23, 2008 at 2:45 PM, Robert Kern <robert.kern(a)gmail.com> wrote: > >> On Fri, May 23, 2008 at 4:00 PM, Mark Miller <mark.miller(a)usu.edu> wrote: >> >> > File "C:\Python25\lib\site-packages\numpy\f2py\rules.py", line 1222, in >> > buildmodule >> > for l in '\n\n'.join(funcwrappers2)+'\n'.split('\n'): >> > TypeError: cannot concatenate 'str' and 'list' objects >> > >> > >> > Any thoughts? Please let me know if more information is needed to >> > troubleshoot. >> >> This is a bug that was fixed in SVN r4335. >> >> http://projects.scipy.org/scipy/numpy/changeset/4335 >> >> -- >> Robert Kern >> >> "I have come to believe that the whole world is an enigma, a harmless >> enigma that is made terrible by our own mad attempt to interpret it as >> though it had an underlying truth." >> -- Umberto Eco >> _______________________________________________ >> Numpy-discussion mailing list >> Numpy-discussion(a)scipy.org >> http://projects.scipy.org/mailman/listinfo/numpy-discussion >> >

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FAIL: Tests mask_rowcols
by Nils Wagner June 8, 2008

June 8, 2008

Hi all, I found one failure in numpy.test() with numpy 1.2.0.dev5257 ====================================================================== FAIL: Tests mask_rowcols. ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/lib64/python2.5/site-packages/numpy/ma/tests/test_extras.py", line 211, in check_mask_rowcols assert(mask_rowcols(x).all()) AssertionError ---------------------------------------------------------------------- Ran 1298 tests in 1.845s FAILED (failures=1) <unittest._TextTestResult run=1298 errors=0 failures=1> >>> numpy.__version__ '1.2.0.dev5257' Nils

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Keywords in wrapped functions
by Pierre GM June 8, 2008

June 8, 2008

All, is there a reason why in some functions (min, max...) optional parameters are parsed by position instead of by keyword ? OK, let me give you an example: #----------------------------------------------- def amin(a, axis=None, out=None): try: amin = a.min except AttributeError: return _wrapit(a, 'min', axis, out) return amin(axis, out) #----------------------------------------------- * Why using amin(axis,out) instead of amin(axis=axis,out=out) ? * Would it be possible to add some optional keywords to amin/amax, so that a "fill_value" parameter would be recognized by numpy.min when dealing with masked arrays ? A modified amin would then be like: def amin(a, axis=None, out=None, **kwargs): try: amin = a.min except AttributeError: return _wrapit(a, 'min', axis=axis, out=out, **kwargs) return amin(axis=axis, out=out, **kwargs) Am I missing something ?

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Ticket #812 - numpy.sum, numpy.std, numpy.var fail on masked arrays
by Pierre GM June 8, 2008

June 8, 2008

Folks, I recently revamped some of the functions of numpy.ma to handle explicit output parameters (eg, sum, std, var...). As a consequence, ticket #812 should be solved. Could anybody give a recent SVN (>=5259) a try and let me know if I can close the ticket ? Thanks a lot in advance. P.

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umath ufunc docstrings
by Pauli Virtanen June 8, 2008

June 8, 2008

Hi, I'd like to adjust the way numpy.core.umath ufunc docstrings are defined to make them more easy to handle in the ongoing documentation marathon: - Remove the signature magic in ufunc_get_doc - Define ufunc docstrings in a separate module instead of in generate_umath.py, in the same format as in add_newdocs.py Suggested patch is attached; it passes numpy tests. Any thoughts on whether it should go in? I was also thinking about the problem with pydoc.help and ufuncs: would making PyUFuncObject a subclass of PyFunctionObject be a reasonable fix? Pauli

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SCons install fails with rev 5258
by Alan McIntyre June 8, 2008

June 8, 2008

I just updated my NumPy tree from svn trunk, and the SCons install now fails with the following message: ImportError: Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python intepreter from there.: File "/home/alan/numpy/numpy/linalg/SConstruct", line 18: mlib = scons_get_mathlib(env) File "/usr/local/lib/python2.5/site-packages/numscons-0.7.1-py2.5.egg/numscons/__init__.py", line 37: from numpy.distutils.misc_util import get_mathlibs File "/home/alan/numpy/numpy/__init__.py", line 84: raise ImportError(msg) status is 512 error: Error while executing scons command /usr/local/bin/python2.5 "/usr/local/lib/python2.5/site-packages/numscons-0.7.1-py2.5.egg/numscons/scons-local/scons.py" -f numpy/linalg/SConstruct -I. scons_tool_path="" src_dir="numpy/linalg" pkg_name="numpy.linalg" distutils_libdir="build/lib.linux-i686-2.5" cc_opt=gcc cc_opt_path="/usr/bin" f77_opt=gfortran f77_opt_path="/usr/bin" cxx_opt=g++ cxx_opt_path="/usr/bin" include_bootstrap=numpy/core/include:build/scons/numpy/core silent=0 bootstrapping=1 (see above)

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numpy, py2exe, and SSE
by Zachary Pincus June 7, 2008

June 7, 2008

Hello all, I've been toying around with bundling up a numpy-using python program for windows by using py2exe. All in all, it works great, except for one thing: the numpy superpack installer for windows has (correctly) selected SSE3 binary libraries to install on my machine. This causes (of course) crashes when the binary py2exe bundle, which includes the numpy libraries installed on my machine, is run on a non-SSE3 machine. So, two questions: 1) What's the best target for "safe" binaries on i386 machines? No SSE at all? SSE? SSE2? 2) What's the best way to get the libraries desired installed for numpy? E.g. compile if myself with some --no-sse option? (And if so, any clue as to the required options.) Or is there some way to get the numpy windows installer to install a specific kind of binary? Thanks, Zach Pincus

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Re: [Numpy-discussion] Building 64-bit numpy on OSX
by Dan Yamins June 7, 2008

June 7, 2008

>./configure --disable-toolbox-glue --prefix=/Users/mabshoff/64bitnumpy/python-2.5.2-bin --with-gcc="gcc -m64" > Let's build numpy 1.1.0: > > bsd:64bitnumpy mabshoff$ tar xf numpy-1.1.0.tar.gz > bsd:64bitnumpy mabshoff$ cd numpy-1.1.0 > bsd:numpy-1.1.0 mabshoff$ python setup.py install > <SNIP> > > Michael thanks for your help on building 64-bit python/numpy. I followed your instructions, and was able to build the python portion. (I did the test "python -c 'import platform;print platform.architecture()' " suggested by Jon and I got the 64-bit result, so I think it worked properly.) Thanks very much for this! However, I was unable to get the numpy build to work. When running the setup.py install, I get all sorts of permission errors, so I'm forced to run it as su. (Is this a bad idea?) Anyhow, when I do run "sudo python setup.py install" in the numpy-1.1.0 directory I downloaded from SciPy website, the build apparently works. But when I go into python, I'm not able to import numpy. Specifically, I get: daniel-yaminss-mac-pro:Desktop danielyamins$ python Python 2.5.2 (r252:60911, Jun 5 2008, 19:13:50) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python2.5/site-packages/numpy/__init__.py", line 93, in <module> import add_newdocs File "/usr/local/lib/python2.5/site-packages/numpy/add_newdocs.py", line 9, in <module> from lib import add_newdoc File "/usr/local/lib/python2.5/site-packages/numpy/lib/__init__.py", line 4, in <module> from type_check import * File "/usr/local/lib/python2.5/site-packages/numpy/lib/type_check.py", line 8, in <module> import numpy.core.numeric as _nx File "/usr/local/lib/python2.5/site-packages/numpy/core/__init__.py", line 5, in <module> import multiarray ImportError: dlopen(/usr/local/lib/python2.5/site-packages/numpy/core/multiarray.so, 2): no suitable image found. Did find: /usr/local/lib/python2.5/site-packages/numpy/core/multiarray.so: no matching architecture in universal wrapper Does anyone know what this error means, and/or how to fix it? Sorry if it's obvious and I should know it alread.y Thanks! Dan

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Methods accepting out as arguments
by Pierre GM June 6, 2008

June 6, 2008

Folks, Where could I find a list of the ndarray methods accepting out as an argument ? Thx a lot in advance.

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