Mailman 3 May 2011 - SciPy-Dev

Tests not running for scipy.constants?
by Warren Weckesser May 23, 2011

May 23, 2011

It appears that the tests for scipy.constants are not running. Here's what I get with trunk: $ python -c "import scipy.constants; scipy.constants.test('full')" Running unit tests for scipy.constants NumPy version 1.5.1 NumPy is installed in /Library/Frameworks/Python.framework/Versions/7.0/lib/python2.7/site-packages/numpy SciPy version 0.10.0.dev SciPy is installed in /Users/warren/local_tmp/lib/python2.7/site-packages/scipy Python version 2.7.1 |EPD 7.0-1 (32-bit)| (r271:86832, Dec 3 2010, 15:41:32) [GCC 4.0.1 (Apple Inc. build 5488)] nose version 1.0.0 ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK I get the same with 0.9.0rc2, so the problem may have been around for awhile. The tests for other packages run as expected, and if I run nosetests in the constants/tests directory, the test run: $ nosetests .............. ---------------------------------------------------------------------- Ran 14 tests in 0.451s OK Does anyone else see this? Warren

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Building the docs: need "plot_directive" extension
by Warren Weckesser May 22, 2011

May 22, 2011

I'm trying to build the HTML docs. Running 'make html' in the doc/ directory first resulted in: Extension error: Could not import extension numpydoc (exception: No module named numpydoc) so I installed the numpydoc package from pypi. Now I get this: Extension error: Could not import extension plot_directive (exception: No module named plot_directive) How do I install the 'plot_directive' extension? I'm using python 2.7, numpy 1.5.1, matplotlib 1.0.1. Warren

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scipy.special.expi complex test failure with scipy 0.9, numpy 1.6.1dev
by Christoph Gohlke May 21, 2011

May 21, 2011

Hello, I am getting the following scipy.special.expi failure when testing scipy 0.9, which was built against numpy 1.6.1dev (these are Windows/msvc9/MKL builds). E.g. scipy.special.expi(1e-99+0j) returns -227.3787085+6.2831855j, not -227.3787085+0j. This is not Python 2/3 version or 32/64 bit specific. Scipy 0.9 built against numpy 1.5.1 passes the test. Christoph ====================================================================== FAIL: test_mpmath.test_expi_complex ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python32\lib\site-packages\nose\case.py", line 188, in runTest self.test(*self.arg) File "C:\Python32\lib\site-packages\numpy\testing\decorators.py", line 147, in skipper_func return f(*args, **kwargs) File "C:\Python32\lib\site-packages\scipy\special\tests\test_mpmath.py", line 48, in test_expi_complex FuncData(sc.expi, dataset, 0, 1).check() File "C:\Python32\lib\site-packages\scipy\special\tests\testutils.py", line 224, in check assert_(False, "\n".join(msg)) File "C:\Python32\lib\site-packages\numpy\testing\utils.py", line 34, in assert_ raise AssertionError(msg) AssertionError: Max |adiff|: 3.86856e+25 Max |rdiff|: 0.304157 Bad results for the following points (in output 0): (1e-99+0j) => (-227.37870854150898+6.283185307179586j) != (-227.37870854150898+0j) (rdiff 0.02763312953742352) (1.668100537200083e-88+0j) => (-201.5385869423536+6.283185307179586j) != (-201.53858694235356+0j) (rdiff 0.03117609090400528) (2.7825594022071145e-77+0j) => (-175.6984653431982+6.283185307179586j) != (-175.6984653431982+0j) (rdiff 0.03576118490794107) (4.6415888336126776e-66+0j) => (-149.8583437440428+6.283185307179586j) != (-149.8583437440428+0j) (rdiff 0.041927497329819895) (7.742636826811214e-55+0j) => (-124.01822214488739+6.283185307179586j) != (-124.01822214488739+0j) (rdiff 0.050663404123299706) (1.2915496650148721e-43+0j) => (-98.178100545732+6.283185307179586j) != (-98.178100545732+0j) (rdiff 0.06399782917222806) (2.1544346900318602e-32+0j) => (-72.3379789465766+6.283185307179586j) != (-72.3379789465766+0j) (rdiff 0.08685873449436396) (3.5938136638045226e-21+0j) => (-46.49785734742121+6.283185307179586j) != (-46.49785734742121+0j) (rdiff 0.13512849119547773) (5.994842503189323e-10+0j) => (-20.657735747666305+6.283185307179586j) != (-20.657735747666308+0j) (rdiff 0.30415653409107984)

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ttest_1samp strange behaviour
by James Bergstra May 20, 2011

May 20, 2011

I was trying to make sure that ttest_1samp did what I thought and came across the following... In [41]: for i in range(10): ....: print scipy.stats.ttest_1samp([0]*i, 0) ....: ....: (nan, nan) (1.0, nan) (1.0, 0.49999999999999956) (1.0, 0.42264973081037427) (1.0, 0.39100221895577053) (1.0, 0.37390096630005898) (1.0, 0.36321746764912255) (1.0, 0.35591768374958205) (1.0, 0.35061666282020748) (1.0, 0.34659350708733416) Am I interpreting this correctly that the null-hypothesis is decreasing in probability as we actually observe it more times?? James -- http://www-etud.iro.umontreal.ca/~bergstrj

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maybe a bug into scipy.interpolate.Rbf?
by Luca Penasa May 17, 2011

May 17, 2011

scipy version 0.9.0-r1 I am trying to use scipy.interpolate.Rbf to interpolate a multidimensional function. I see the Rbf class permits to use a callable function as radial basis function, but gives me an error, see below: My self defined rbf: def ElasticDeformationRBF(this, r): ratio = ((r**2) / this.epsilon) out = ratio * np.log(ratio) + 1 - ratio return out interpolator = scipy.interpolate.Rbf(somex, somey, function=ElasticDeformationRBF) The error is: /usr/lib64/python2.6/site-packages/scipy/interpolate/rbf.pyc in __init__(self, *args, **kwargs) 195 setattr(self, item, value) 196 --> 197 self.A = self._init_function(r) - eye(self.N)*self.smooth 198 self.nodes = linalg.solve(self.A, self.di) 199 /usr/lib64/python2.6/site-packages/scipy/interpolate/rbf.pyc in _init_function(self, r) 159 self._function = self.function 160 elif argcount == 2: --> 161 if sys.version_info[0] >= 3: 162 self._function = function.__get__(self, Rbf) 163 else: NameError: global name 'sys' is not defined Maybe a missing import sys?? test_function_is_callable() from rbf's tests does not give any error. help docs say, about callable function: "If callable, then it must take 2 arguments (self, r). The epsilon parameter will be available as self.epsilon." So i cannot understand if it is my fault. Any idea? Thank you -- --------------------------- Luca Penasa Student at Geosciences Dpt. University of Padua (IT) luca.penasa(a)email.it ---------------------------

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User Acceptance Testing
by Joshua Grant May 15, 2011

May 15, 2011

Hi everyone. So I notice that for Scipy, there's some fairly extensive unit tests, which are great for the actual development of the library code. Are there any forms of user acceptance testing, automated or otherwise? Ways to simulate user behaviour and larger blocks of code, beyond single methods/functions?

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Fwd: For certain arrays scipy.interpolate.fitpack.bisplrep fails,
by Paul Kuin May 14, 2011

May 14, 2011

From: Paul Kuin <npkuin(a)gmail.com> To: scipy-dev(a)scipy.org Date: Tue, 10 May 2011 22:23:34 +0100 Subject: For certain arrays scipy.interpolate.fitpack.bisplrep fails, For certain arrays scipy.interpolate.fitpack.bisplrep fails, since the fortran code called expects an integer for the dimension size of certain arrays: line 760-761 of fitpack.py should be modified to if nxest is None: nxest=int(kx+sqrt(m/2)) if nyest is None: nyest=int(ky+sqrt(m/2)) to make sure nxest, and nyest are integer. Please make a patch.

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distributions.ncf.fit -- never converges?
by Yaroslav Halchenko May 6, 2011

May 6, 2011

Since 0.9.0 (not present in 0.7.2), distributions.ncf.fit seems to never converge. could anyone check in development tree if the below call ever returns (I was waiting for minutes... with 0.7.2 it was taking just a moment): python -c 'import scipy.stats.distributions as ssd, numpy as np; d=ssd.ncf; d.fit(np.array([-0.03756533, 0.18115522, 0.06605958, -0.09195276, 0.06162608, 0.07139736, -0.1570828 , -0.11967677, -0.19186652, 0.29411319]));' Thanks in advance! -- =------------------------------------------------------------------= Keep in touch www.onerussian.com Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic

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The state of weave.accelerate?
by Helio Perroni Filho May 5, 2011

May 5, 2011

Dera all, I have been looking for ways to speed up some portions of Python code in my current scipy project. The ideal solution would allow me to keep writing all my code in Python 2.7 – even if the "accelerated" parts had to written in a subset of the language, as in PyPy's Restricted Python – and be easily turned off for debugging. When I learned of scipy.weave.inline, my first thought was "now if only there was a Python-to-C++ translator I could hook up to this!" I was intrigued when I found that cryptic reference about sicpy.weave.accelerate providing "automatic acceleration of Python code"; all the more after searching for more information on it, and finding none. So I decided to take a look at the code. The API seemed simple enough (just a decorator for top-level functions), so I tried it on some toy scripts I keep around. After hacking around a couple simple bugs (two incorrect assertions in bytecodecompiler, a typo defining the one-argument form of the range function and the need to add weave's directory to the compiler include-path in accelerate_tools) I got stuck on the many not-yet-implemented instructions in bytecodecompiler: it seems even basic arithmetic is still to be included. I find this frustrating. From the tests I've run it seems accelerate() already does an adequate work of generating the necessary C++ boilerplate code, compiling it to an extension and then wiring the result back to the executing script. The only thing missing is getting the C++ translation to work – not trivial, I know, but not very hard either, considering what's already in place. Is a lack of manpower holding accelerate() back? If that's the case, I volunteer to work on bytecodecompiler, and get it to at least an RPython-level of functionality. I have read the documentation on the Developer Zone, but didn't find how do I create a Trac account. And besides that, is there anything else not on that page that I should know? -- Ja ne, Helio Perroni Filho http://machineawakening.blogspot.com/

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w prefix in fortran bindings
by Fabian Pedregosa May 5, 2011

May 5, 2011

Hi all. I've been backing lately on the LAPACK bindings and there's something I don't understand . Sometimes the fortranname statement is prefixed with `w`, like in fortranname w<prefix2c>dotc Someone could tell me why the w is needed? Thanks, Fabian

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