Mailman 3 January 2008 - NumPy-Discussion

Test failure with latest SVN
by Robin Jan. 18, 2008

Jan. 18, 2008

I am on OS X 10.5.1 and get a test failure with the latest numpy svn. (Previously ran with no errors with svn as of a few weeks ago). test_zero_probability (numpy.tests.test_random.TestMultinomial) ... ok ====================================================================== ERROR: Ticket #396 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/tests/test_regression.py", line 600, in check_poly1d_nan_roots self.failUnlessRaises(np.linalg.LinAlgError,getattr,p,"r") File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/unittest.py", line 320, in failUnlessRaises callableObj(*args, **kwargs) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py", line 623, in __getattr__ return roots(self.coeffs) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py", line 124, in roots roots = _eigvals(A) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/polynomial.py", line 37, in _eigvals return eigvals(arg) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py", line 378, in eigvals return eig(a,b=b,left=0,right=0,overwrite_a=overwrite_a) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/scipy/linalg/decomp.py", line 128, in eig a1 = asarray_chkfinite(a) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/function_base.py", line 398, in asarray_chkfinite raise ValueError, "array must not contain infs or NaNs" ValueError: array must not contain infs or NaNs ---------------------------------------------------------------------- Ran 713 tests in 0.697s FAILED (errors=1) Out[3]: <unittest._TextTestResult run=713 errors=1 failures=0> Robin

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Ctypes reference counting
by Ryan May Jan. 18, 2008

Jan. 18, 2008

Hi, Can someone explain the reference counting wrt using ctypes and numpy. Specifically, I have code like: from ctypes import * import numpy as N class Data(Structure): _fields_=[('var',POINTER(c_float))] d = Data() d.var = N.arange(100., dtype=N.float32).ctypes.data_as(POINTER(c_float)) print d.var[5] #Should be 5.0 Instead it prints 0.0. (On my bigger code, it just segfaults.) Obviously, the array going in get's collected b/c its reference count goes to 0. Why does getting the data as a pointer not add a reference? Is there a "correct" way to do what I'm attempting? Overall, I'm trying to create arrays using Numpy that are saved into structures and passed into ctypes-wrapped C code that does the heavy lifting. However, this heavy lifting is done in a different (ie. separate and higher) scope than the code that creates the arrays. Thanks, Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

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PyArray_FromAny min/max dims
by Neal Becker Jan. 18, 2008

Jan. 18, 2008

Why are 0 values of min_depth/max_depth ignored? Why not allow 0, which is a scalar array, and use -1 to mean ignore?

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numpy Intel ICC build help?
by Ray Schumacher Jan. 18, 2008

Jan. 18, 2008

We've just built Python 2.4 in the lab with Intel ICC and MS VS 2005, but had problems building 2.5, and also numpy, with the MKL. Would someone be willing to share their build experience or project files? Ray -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.5.516 / Virus Database: 269.19.2/1222 - Release Date: 1/13/2008 12:23 PM

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casting
by Neal Becker Jan. 17, 2008

Jan. 17, 2008

numpy frequently refers to 'casting'. I'm not sure if that term is ever defined. I believe it has the same meaning as in C. In that case, it is unfortunately used to mean 2 different things. There are casts that do not change the underlying bits (such as a pointer cast), and there are casts that actually convert to different bits (such as float -> double). I think numpy means the latter. When an array where the underlying data is one type, a cast to another type means actually reallocating and converting the data. It often occurs that I have an algorithm that can take any integral type, because it is written with c++ templates. In that case, I don't want to use PyArray_FROMANY, because I don't want to unecessarily convert the array data. Instead, I'd like to inquire what is the preferred type of the data. The solution I'm exploring is to use a function I call 'preferred_array_type'. This uses the __array_struct__ interface to find the native data type. I chose to use this interface, because then it will work with both numpy arrays and other array-like types. Any thoughts on all of this? Particularly, my observation that numpy seems to want me to tell it what data type of array my algorithm wants, but doesn't seem to provide a good mechanism to allow me to inquire what is the native type to avoid conversion.

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Problem during build of scipy: - TypeError: can only concatenate list (not "str") to list
by Hans-Joachim Ehlers Jan. 17, 2008

Jan. 17, 2008

Given: AIX 5.3 xlc v8 xlf v10 essl v4.2 Build and installed: numpy 1.0.4 Build and installed: lapack 3.1.1 with CCI and essl support Task: Trying to build scipy 0.6.0 Get the following error which seems to be numpy related: .... extending extension 'scipy.linsolve._csuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] extending extension 'scipy.linsolve._ssuperlu' defined_macros with [('USE_VENDOR_BLAS', 1)] customize UnixCCompiler customize UnixCCompiler using build_ext Traceback (most recent call last): File "setup.py", line 53, in <module> setup_package() File "setup.py", line 45, in setup_package configuration=configuration ) File "/usr/local/lib/python2.5/site-packages/numpy/distutils/core.py", line 176, in setup return old_setup(**new_attr) File "/usr/local/lib/python2.5/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/local/lib/python2.5/distutils/dist.py", line 974, in run_commands self.run_command(cmd) File "/usr/local/lib/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/usr/local/lib/python2.5/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/usr/local/lib/python2.5/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/local/lib/python2.5/distutils/dist.py", line 994, in run_command cmd_obj.run() File "/usr/local/lib/python2.5/site-packages/numpy/distutils/command/build_ext.py", line 166, in run self._cxx_compiler = compiler.cxx_compiler() File "/usr/local/lib/python2.5/site-packages/numpy/distutils/ccompiler.py", line 303, in CCompiler_cxx_compiler + cxx.linker_so[2:] TypeError: can only concatenate list (not "str") to list Any tips ? tia Hajo

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Re: [Numpy-discussion] numpy quit workinge
by Kevin Christman Jan. 16, 2008

Jan. 16, 2008

That's it. I had named one of my files new.py. Thanks so much; now I have one less evidence that I'm going crazy. Kevin ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs

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numpy quit working
by Kevin Christman Jan. 16, 2008

Jan. 16, 2008

I've started to use numpy (1.0.4) and matplotlib but it suddenly quit working. Now when I import a simple test script: import numpy numpy.linspace(0,1) it gives the following error: >>> Traceback (most recent call last): File "D:/anothertest.py", line 1, in <module> import numpy File "C:\Python25\lib\site-packages\numpy\__init__.py", line 37, in <module> import testing File "C:\Python25\lib\site-packages\numpy\testing\__init__.py", line 3, in <module> from numpytest import * File "C:\Python25\lib\site-packages\numpy\testing\numpytest.py", line 19, in <module> from numpy.distutils.exec_command import splitcmdline File "C:\Python25\lib\site-packages\numpy\distutils\__init__.py", line 6, in <module> import ccompiler File "C:\Python25\lib\site-packages\numpy\distutils\ccompiler.py", line 46, in <module> replace_method(CCompiler, 'spawn', CCompiler_spawn) File "C:\Python25\lib\site-packages\numpy\distutils\ccompiler.py", line 24, in replace_method m = new.instancemethod(func, None, klass) AttributeError: 'module' object has no attribute 'instancemethod' >>> However, other import statements, like "import time" work ok. The problem first started when a script would only run if on the root of the drive (e.g. D:\), but now even if I run it from there it doesn't work. What's going on? Kevin ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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gcc not g++ for build numpy on mac 10.4 ?
by denis bzowy Jan. 16, 2008

Jan. 16, 2008

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RFC: out of range slice indexes
by Neal Becker Jan. 16, 2008

Jan. 16, 2008

I've never liked that python silently ignores slices with out of range indexes. I believe this is a source of bugs (it has been for me). It goes completely counter to the python philosophy. I vote to ban them from numpy. >>> from numpy import array >>> x = array (xrange (10)) >>> x[11] Traceback (most recent call last): File "<stdin>", line 1, in <module> IndexError: index out of bounds >>> x[:12] = 2 >>> x array([2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) >>> len (x) 10 Silently ignoring the error x[:12] is a bad idea, IMO. If it meant to _extend_ x to have lenght 12, at least _that_ would be reasonable (but I'm not advocating that position). I believe that out of bounds indexes should always throw IndexError. We can't change that in Python now, but maybe we can in numpy.

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