Mailman 3 February 2010 - NumPy-Discussion

datetime uses API deprecated in python3.1
by Charles R Harris Feb. 23, 2010

Feb. 23, 2010

Hi Travis, The warning is dep.py:6: PendingDeprecationWarning: The CObject API is deprecated as of Python 3.1. Please convert to using the Capsule API. np.dtype('M8[3M/40]') This doesn't happen with the old dtypes, so I assume it is associated with something introduced for datetime. Any ideas? I've attached a script that shows the warning. Chuck

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random.uniform documentation bug?
by Alan G Isaac Feb. 23, 2010

Feb. 23, 2010

This behavior does not match the current documentation. >>> np.random.uniform(low=0.5,high=0.5) 0.5 >>> np.random.uniform(low=0.5,high=0.4) 0.48796883601707464 I assume this behavior is intentional and it is the documentation that is in error (for the case when high<=low)? fwiw, Alan Isaac

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numpy + ubuntu 9.10 (karmic) + unladen swallow
by Valery Khamenya Feb. 23, 2010

Feb. 23, 2010

Hi all, I know the formula works, but fail to reproduce it :) Issue #1. the following entry from numpy installation docs is perhaps out-of-date, at least as for ubuntu karmic: sudo apt-get install gcc g77 python-dev atlas3-base-dev Neither g77 nor atlas3-base-dev are available. Perhaps, g77 from previous ubuntu distro could work, but it would be good to see what installation docs says about this trick. Issue #2. The following definition of include_dirs in site.cfg doesn't seem to be used by gcc: [DEFAULT] include_dirs = /usr/local/include:/home/me/wrk/unladen-trunk/Include I build numpy like that: PYTHONPATH= ~/wrk/unladen-trunk/python setup.py build Where the python executable is the one from the great "unladen-swallow" project. Such invocation leads fast to the following error: ... compile options: '-Inumpy/core/src -Inumpy/core/include -IInclude -I/home/vak/me/unladen-trunk -c' gcc: _configtest.c _configtest.c:1:20: error: Python.h: No such file or directory ... Indeed, the directory /home/me/wrk/unladen-trunk/Include isn't listed for "-I" flag Any hints? thanks in advance :) best regards -- Valery

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SciPy2010 Call for Papers
by Stéfan van der Walt Feb. 23, 2010

Feb. 23, 2010

========================== SciPy 2010 Call for Papers ========================== SciPy 2010, the 9th Python in Science Conference, will be held from June 28th - July 3rd, 2010 in Austin, Texas. At this conference, novel applications and breakthroughs made in the pursuit of science using Python are presented. Attended by leading figures from both academia and industry, it is an excellent opportunity to experience the cutting edge of scientific software development. The conference is preceded by two days of paid tutorials, during which community experts provide training on several scientific Python packages. We invite you to take part by submitting a talk abstract on the conference website at: http://conference.scipy.org Talk/Paper Submission ===================== We solicit talks and accompanying papers (either formal academic or magazine-style articles) that discuss topics regarding scientific computing using Python, including applications, teaching, development and research. Papers are included in the peer-reviewed conference proceedings, published online. Please note that submissions primarily aimed at the promotion of a commercial product or service will not be considered. Important dates for authors include: * 11 April: Talk abstracts due * 20 April: Notification of acceptance * 13 June: Papers due * 15 August: Publication of proceedings Further detail will be made available on http://conference.scipy.org Conference Dates ================ * Friday, 10 May: Early registration ends * Monday-Tuesday, 28-29 June: Tutorials * Wednesday-Thursday, June 30-July 1: Conference * Friday-Saturday, July 2-3: Coding Sprints Executive Committee =================== * Conference: Jarrod Millman & Eric Jones * Program: Stefan van der Walt & Ondrej Certik * Student Sponsorship: Travis Oliphant For more information on Python, visit http://www.python.org.

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double free or corruption after calling a Slicot routine wrapped with f2py
by enrico avventi Feb. 23, 2010

Feb. 23, 2010

hello, first of all, as i'm new here, i would like to greet everyone in the list and thank the developers of numpy/scipy. i'm transitioning my work from matlab to python and this software is very helpfull indeed. the reason i'm writing is that i got to a stumbling block last week. i tried wrote some wrappers of Slicot routines aided by f2py that i keep on github (http://github.com/avventi/Slycot). the latest routine i tried to wrap, SB02OD, make python to crash with the glibc error double free or corruption. precisely i get this error if the wrapper slycot.sb02od is called within a method, i.e Python 2.5.2 (r252:60911, Jan 24 2010, 14:53:14) [GCC 4.3.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import slycot >>> slycot.examples.sb02od_example() --- Example for sb01od ... The solution X is [[ 1. 0.] [ 0. 2.]] rcond = 0.632455532034 *** glibc detected *** python: double free or corruption (!prev): 0x082ec3b8 *** as you can see the routine does indeed return the correct output but make python crash afterwards. On the other hand if i type ieach step interactively Python 2.5.2 (r252:60911, Jan 24 2010, 14:53:14) [GCC 4.3.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from numpy import * >>> import slycot >>> A = array([[0,1],[0,0]]) >>> B = array([[0],[1]]) >>> C = array([[1,0],[0,1],[0,0]]) >>> Q = dot(C.T,C) >>> R = zeros((1,1)) >>> L = zeros((2,1)) >>> out = slycot.sb02od('D',2,1,3,A,B,Q,R,L) >>> out[1] array([[ 1., 0.], [ 0., 2.]]) >>> out[0] 0.63245553203367577 >>> out = slycot.sb02od('D',2,1,3,A,B,Q,R,L) *** glibc detected *** python: double free or corruption (!prev): 0x0832b428 *** it works the first time but not the second. i tried Debian lenny 32/64bit and a virtualized Fedora 12 32bit and the error persists. do you have any ideas why this happens or where should i look to start solving it? thanks in advance. regards, /Enrico

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int-ifying a float array
by David Goldsmith Feb. 23, 2010

Feb. 23, 2010

Hi! Is there a less cumbersome way (e.g., one that has a "cast-like" syntax and/or leverages broadcasting) than what follows to convert an array of floats to an array of ints? Here's what works: >>> import numpy as N >>> t = N.array([0.0, 1.0]); t.dtype dtype('float64') >>> t = N.array(t, dtype=int); t; t.dtype array([0, 1]) dtype('int32') Here's three ways that don't: >>> t = N.array([0.0, 1.0]) >>> int(t) Traceback (most recent call last): File "<input>", line 1, in <module> TypeError: only length-1 arrays can be converted to Python scalars >>> N.int(t) Traceback (most recent call last): File "<input>", line 1, in <module> TypeError: only length-1 arrays can be converted to Python scalars >>> t.dtype = N.int >>> t array([ 0, 0, 0, 1072693248]) It doesn't really surprise me that none of these cast-like (or attribute change in the last case) ways work (though it might be nice if at least one of them did), but perhaps I'm just not guessing the syntax right... Thanks, DG

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Request for testing
by Charles R Harris Feb. 22, 2010

Feb. 22, 2010

Hi All, I would be much obliged if some folks would run the attached script and report the output, numpy version, and python version. It just runs np.isinf(np.inf), which raises an "invalid value" warning with current numpy. As far as I can see the function itself hasn't changed since numpy1.3, yet numpy1.3 & python2.5 gives no such warning. Chuck

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ask.scipy.org
by Gökhan Sever Feb. 22, 2010

Feb. 22, 2010

Hello, Since after Robert Kern showed http://advice.mechanicalkern.com/ on SciPy09 there are many similar initiatives that uses stackoverflow.com (SO) layout. Some smart guys come up with this site http://stackexchange.com/ to those who want to have a simple but a paid solution. I don't have an intention of creating controversial discussion. It just to my eyes SO has a very appealing and easy to use interface and it's getting some number of posts related to scientific Python tools. I usually suggest my friends to use the mailing lists first and SO for their questions. Some prefer mailing lists some not. Mailing lists require more steps to get in however SO register step is much easier due to OpenID logging. Without belabouring further, It would be good to link R. Kern's advice site to either ask.scipy or advice.scipy or another alternative to attract new-comers easily. I am more in favor of the ask.scipy.org option. Thus I can refer the people (hear I mean mostly non-programmers or students/programmers without Python experience), simply to go ask.scipy.orgfor their first questions instead of telling them to search answers at many different mediums. What do you think? -- Gökhan

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numpy.test() failures in 2.0.0.dev8233
by Nils Wagner Feb. 21, 2010

Feb. 21, 2010

====================================================================== FAIL: test_multiarray.TestNewBufferProtocol.test_export_endian ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/tests/test_multiarray.py", line 1582, in test_export_endian assert y.format in '>l' AssertionError ====================================================================== FAIL: test_multiarray.TestNewBufferProtocol.test_export_record ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/tests/test_multiarray.py", line 1561, in test_export_record assert y.format == 'T{b:a:=h:b:=l:c:=q:d:B:e:=H:f:=L:g:=Q:h:=d:i:=d:j:=g:k:4s:l:=4w:m:3x:n:?:o:}' AssertionError ====================================================================== FAIL: test_multiarray.TestNewBufferProtocol.test_export_simple_1d ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/tests/test_multiarray.py", line 1514, in test_export_simple_1d assert y.format == '=l' AssertionError ====================================================================== FAIL: test_multiarray.TestNewBufferProtocol.test_export_subarray ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/nwagner/local/lib64/python2.6/site-packages/nose-0.11.2.dev-py2.6.egg/nose/case.py", line 183, in runTest self.test(*self.arg) File "/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/tests/test_multiarray.py", line 1576, in test_export_subarray assert y.itemsize == 16 AssertionError ---------------------------------------------------------------------- Ran 2519 tests in 21.494s FAILED (KNOWNFAIL=4, failures=4) <nose.result.TextTestResult run=2519 errors=0 failures=4>

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ABI changes complete in trunk
by Travis Oliphant Feb. 21, 2010

Feb. 21, 2010

I've made the ABI changes I think are needed in the SVN trunk. Please feel free to speak up if you have concerns or problems (and if you want to change white-space, just do it...). If the release schedule needs to be delayed by several weeks in order to get Py3k support in NumPy 2.0, that seems like a worthwhile thing. I wish I had time to help, but Pauli and Chuck are doing a great job. Best, -Travis

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