Mailman 3 September 2010 - NumPy-Discussion

Matlab IO Warning in mio5.py
by Ben Longstaff 22 Nov '10

22 Nov '10

Is the warning message produced by the test script below an issue I need to address if I am to use the numpy and scipy libraries? The script below gives me the warning below on both windows 7 and vista Thanks for your time Ben Python Script #!/path/to/python import re, string, sys from numpy import * import scipy.weave print "Hello, World!" Warning Message C:\Python26\lib\site-packages\scipy\io\matlab\mio5.py:90: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from mio5_utils import VarReader5 Hello, World!

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Test failures on 2.6
by T J 18 Nov '10

18 Nov '10

Hi, I'm getting a couple of test failures with Python 2.6, Numpy 1.2.0, Nose 0.10.4: nose version 0.10.4 ..........................................................................................................................................................................................................................................................................................................................................................................................................................................F................K........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./share/home/me/usr/lib/python2.6/site-packages/numpy/lib/tests/test_io.py:68: SyntaxWarning: assertion is always true, perhaps remove parentheses? assert(c.readlines(), ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................./share/home/me/usr/lib/python2.6/site-packages/numpy/ma/tests/test_core.py:1315: SyntaxWarning: assertion is always true, perhaps remove parentheses? assert(store._mask, True) /home/me/usr/lib/python2.6/site-packages/numpy/ma/tests/test_core.py:1322: SyntaxWarning: assertion is always true, perhaps remove parentheses? assert(store._mask, True) /home/me/usr/lib/python2.6/site-packages/numpy/ma/tests/test_core.py:1989: SyntaxWarning: assertion is always true, perhaps remove parentheses? assert(test.mask, [0,1,0,0,0,0,0,0,0,0]) ...............................................E................................................................................................................................................................................ ====================================================================== ERROR: Tests the min/max functions with explicit outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/me/usr/lib/python2.6/site-packages/numpy/ma/tests/test_core.py", line 653, in test_minmax_funcs_with_output result = npfunc(xm,axis=0,out=nout) File "/home/me/usr/lib/python2.6/site-packages/numpy/core/fromnumeric.py", line 1525, in amin return amin(axis, out) File "/home/me/usr/lib/python2.6/site-packages/numpy/ma/core.py", line 2978, in min np.putmask(out, newmask, np.nan) ValueError: cannot convert float NaN to integer ====================================================================== FAIL: test_umath.TestComplexFunctions.test_against_cmath ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/me/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/case.py", line 182, in runTest self.test(*self.arg) File "/home/me/usr/lib/python2.6/site-packages/numpy/core/tests/test_umath.py", line 268, in test_against_cmath assert abs(a - b) < atol, "%s %s: %s; cmath: %s"%(fname,p,a,b) AssertionError: arcsin 2: (1.57079632679-1.31695789692j); cmath: (1.57079632679+1.31695789692j) ---------------------------------------------------------------------- Ran 1726 tests in 8.856s FAILED (KNOWNFAIL=1, errors=1, failures=1) <nose.result.TextTestResult run=1726 errors=1 failures=1>

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Trouble cloning numpy Github repo over HTTP
by Scott Sinclair 09 Nov '10

09 Nov '10

Hi, I'm behind a firewall that doesn't allow me to use the git protocol so I can't use the git:// URL. I see the following problem: $ git clone http://github.com/numpy/numpy.git numpy Initialized empty Git repository in /home/scott/external_repos/numpy/.git/ error: RPC failed; result=22, HTTP code = 417 I never have trouble cloning other repos off of Github over HTTP. See http://support.github.com/discussions/repos/4323-error-rpc-failed-result22-… Does anyone else see this problem? Thanks, Scott

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DataArray fixes
by Lluís 18 Oct '10

18 Oct '10

I started writing some fixes for DataArray, but some others need discussion on whether they should be implemented as I describe. To this extent, please see issues at http://github.com/fperez/datarray/issues and comment on them, so that I'll know if I should implement these. Thanks, Lluis -- "And it's much the same thing with knowledge, for whenever you learn something new, the whole world becomes that much richer." -- The Princess of Pure Reason, as told by Norton Juster in The Phantom Tollbooth

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help from OS X 10.5 users wanted
by Ralf Gommers 16 Oct '10

16 Oct '10

Hi, There have been many reports from OS X 10.5(.8) users that the provided binaries on Sourceforge for numpy versions >= 1.4.0 do not work, see http://projects.scipy.org/numpy/ticket/1322. If you're an OS X 10.5 user I would like your help to test if the same issue occurs for the following binary: http://sourceforge.net/projects/numpy/files/Temporary/numpy-2.0.0.dev-py2.6… Please comment on the above ticket. Thanks, Ralf

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inversion of large matrices
by Daniel Elliott 12 Oct '10

12 Oct '10

Hello, I am new to Python (coming from R and Matlab/Octave). I was preparing to write my usual compute pdf of a really high dimensional (e.g. 10000 dimensions) Gaussian code in Python but I noticed that numpy had a function for computing the log determinant in these situations. Is there a function for performing the inverse or even the pdf of a multinomial normal in these situations as well? Thank you. Numpy and scipy look pretty awesome. - dan

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datarray repositories have diverged
by Rob Speer 09 Oct '10

09 Oct '10

There's some DataArray code that I've had for a while, but I just finished it up and tested it today. Most notably, it includes a new __str__ for DataArrays that does some nice layout and includes ticks: In [9]: print d_arr country year --------- ------------------------------------------------- 1994 1998 2002 2006 2010 Netherlan -0.505758 0.096597 1.083148 -0.450156 0.172754 Uruguay 1.772182 -0.113394 -0.781307 1.002416 -0.64925 Germany -2.013874 0.283947 1.170848 -0.504823 0.448497 Spain -0.725844 0.909713 -1.191371 -0.465167 -1.518764 (The layout functions in datarray.print_grid actually work with any ndarray, so you can use it as an alternative to the __str__ in NumPy.) However, I notice that all the new development on datarray is happening on Fernando Perez's branch, which mine diverged from long ago. I forked from Lluis (jesusabdullah)'s branch, which was the most active at the time, and I got all but the most recent changes merged back in. But that branch in turn was never merged back into fperez's. The divergence point is even before I added the syntax for named axes and ticks by name (such as arr.named['Spain', 1994:2010] or arr.year.named[2010]). Does it make sense to merge my branch into the main one? http://github.com/rspeer/datarray -- Rob

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NPZ format
by Francesc Alted 03 Oct '10

03 Oct '10

Hi, I'm going to give a seminar about serialization, and I'd like to describe the .npy format. I noticed that there is a variant of it called .npz that can pack several arrays in one single file. However, .npz does not use compression at all and I'm wondering what's the reason. I suppose that this is because you don't want to loose the possibility to memmap saved arrays, but can someone confirm this? Thanks, -- Francesc Alted

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constant shaded triangle mesh in mayavi2
by Geoffrey Irving 01 Oct '10

01 Oct '10

Hello, I'm not sure where the correct place to ask questions about Mayavi, so feel free to redirect me elsewhere. I have a triangle mesh with a bunch of data on each face. The only color-relevant argument to triangular_mesh I know about is scalars, which is one value per vertex. Is there a way to set color per triangle, ideally with control over rgb separately so I can visualize three different fields at once? Thanks, Geoffrey

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Re: [Numpy-discussion] numpydoc: "Other Parameters" section
by Joe Harrington 01 Oct '10

01 Oct '10

> It seems that the "Other parameters" section is not > getting included in the output. The "Other parameters" is not often used in numpy because there are not generally dozens of "tweaking" parameters in its basic numerical routines. It will probably be more common in certain scipy pages, and if other packages adopted the format, it could get used a lot. Plotting packages, for example, often have a ton of "tweaking" parameters (line width, line color, line pattern, major axis tick interval, minor axis tick interval, x axis label, y axis label, title, axis font, title font, tick strings, etc.) and could use this section to good effect to sort those out from the parameters of primary interest. This would keep the output section and so forth near the top of the docstring for easy reading. So, it would be better to fix the problem than deprecate the section. --jh--

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