Mailman 3 March 2010 - SciPy-Dev

[burtscher@mpia-hd.mpg.de: Dead links on scipy Download page]
by Joe Harrington March 30, 2010

March 30, 2010

>From an Alert Reader... > From: Leonard Burtscher <burtscher(a)mpia-hd.mpg.de> > To: jharring(a)physics.ucf.edu > Subject: Dead links on scipy Download page > Date: Thu, 25 Mar 2010 21:04:37 +0100 > Joe, > Just wanted to let you know that the two links to macinscience.org on http://www.scipy.org/Download > are not working anymore. > Best, > Leonard Burtscher Chris F., are you out there? Else, does anyone know what's up with that site? --jh--

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Regenerating Swig-generated files with Swig 1.3.40 ?
by David Cournapeau March 29, 2010

March 29, 2010

Hi, I would like to know if there is any objection to regenerate the swig source files with the last SWIG ? I have started working on py3 support for scipy, and the recent SWIG have added support for py3 compatibility (>= 1.3.37, we currently use 1.3.36). The main drawback I can see is that it would require people to build their own swig if they want to modify the code, as few distributions support such recent swig releases. cheers, David

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scipy.misc.ppimport
by Warren Weckesser March 24, 2010

March 24, 2010

Hi, A new ticket on the scipy trac (http://projects.scipy.org/scipy/ticket/1136) reports a problem with scipy.misc.ppimport. Not long ago I fixed a couple blatant typos in ppimport.py (because of another ticket, http://projects.scipy.org/scipy/ticket/1133), but I didn't actually try to use the ppimport() function. I think this code has problems. There was code in there that could never have worked, and there are no tests. I'm not going to have time to work on ppimport, and after a little searching, I wonder if anyone should bother. In scipy trunk, the only actual use of anything related to ppimport is in the info() function in misc.helpmod.py, and it just checks if the object for which info is being requested has attributes assigned by ppimport. But if nothing else in scipy actually uses ppimport, the code in info() is moot. All the info.py files of the various scipy packages contain 'postpone_import = 1', but I don't see any code that actually uses this variable. What's the history of ppimport? Why does it exist in scipy? Pearu Peterson worked on this several years ago, but it is not clear to me how it is currently used. Can we simply get rid of it, or am I missing something? Warren

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Patch review request: adding hadamard function to scipy.linalg
by Warren Weckesser March 24, 2010

March 24, 2010

I submitted a patch to ticket #675: http://projects.scipy.org/scipy/ticket/675 It adds a function that generates Hadamard matrices. The code is a slightly modified version of the code submitted by Ivo in the ticket. If anyone has a moment, take a look and let me know what you think. The function is only a few lines, so a review shouldn't take long. I'd like to have at least one other set of eyes on the code before checking it in. Cheers, Warren

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Installing scipy on OS 10.6.2
by Paul Fuoss March 24, 2010

March 24, 2010

I have been unsuccessful at installing scipy on OS 10.6. When I try to build from the distribution, I get a huge number of library architecture errors. I've tried to build both against the python that comes with the system (2.6.1) and against the MacPort python (2.6.5) (see test summary at end of message). When I try to install via MacPort, it appears to install but much functionality is missing (e.g. curve_fit) that I assume is because the BLAS and LAPACK libraries aren't being linked to correctly. I'm using OS 10.6.2 on an Intel iMac. The latest Xcode is installed (3.2.1) with: i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5646) (dot 1) gfortran from research.att.acom: GNU Fortran (GCC) 4.2.3 I would appreciate suggestions. ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/fftpack/_fftpack.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/fftpack/_fftpack.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/special/_cephes.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/special/_cephes.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: test_integer (test_array_import.TestReadArray) ---------------------------------------------------------------------- ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pytho n2.6/site-packages/scipy/special/_cephes.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/special/_cephes.so: no matching architecture in universal wrapper ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/lib/blas/fblas.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/lib/blas/fblas.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/lib/lapack/calc_lwork.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/lib/lapack/calc_lwork.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/linalg/flapack.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/linalg/flapack.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/sparse/linalg/isolve/_iterative.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/optimize/minpack2.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/optimize/minpack2.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/odr/__odrpack.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/odr/__odrpack.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/optimize/minpack2.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/optimize/minpack2.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/special/_cephes.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/special/_cephes.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/sparse/linalg/isolve/_iterative.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/sparse/linalg/isolve/_iterative.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/sparse/linalg/isolve/_iterative.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/special/_cephes.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/special/_cephes.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== ERROR: Failure: ImportError (dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/pyth on2.6/site-packages/scipy/special/_cephes.so, 2): no suitable image found. Did find: /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/si te-packages/scipy/special/_cephes.so: no matching architecture in universal wrapper) ---------------------------------------------------------------------- ====================================================================== FAIL: test_mio.test_warnings(<type 'exceptions.FutureWarning'>, <function loadmat at 0x1048f61b8>, '/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/s ite-packages/scipy/io/matlab/tests/data/testdouble_7.1_GLNX86.mat') ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/s ite-packages/nose/case.py", line 183, in runTest self.test(*self.arg) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/s ite-packages/numpy/testing/utils.py", line 693, in assert_raises return nose.tools.assert_raises(*args,**kwargs) AssertionError: FutureWarning not raised ---------------------------------------------------------------------- Ran 1382 tests in 428.657s FAILED (KNOWNFAIL=6, SKIP=3, errors=16, failures=1) Out[3]: <nose.result.TextTestResult run=1382 errors=16 failures=1>

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Doc error in scipy.optimize.fmin and missing info in ref guide
by Rob Clewley March 21, 2010

March 21, 2010

Hi, In both my old version and the one in the svn trunk there is an inconsistency in the docstring of scipy.optimize.fmin. Other Parameters ---------------- xtol : float Relative error in xopt acceptable for convergence. ftol : number Relative error in func(xopt) acceptable for convergence. As you see from the following code snippet from the body of the function, the convergence test is in terms of absolute error for both x and f, as the sim array contains x values and fsim the function values. if (max(numpy.ravel(abs(sim[1:]-sim[0]))) <= xtol \ and max(abs(fsim[0]-fsim[1:])) <= ftol): break Also, optional parameters for any optimize functions are not described in the draft of the Scipy reference manual I came across while googling this issue. For instance, at http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.fmin.htm… fmin does not have the optional arguments detailed. If this is automatically generated is there a reason why the optional parameters aren't being shown in this document? I think they should be, IMO. -Rob

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Another easy patch review: ticket #996
by Warren Weckesser March 21, 2010

March 21, 2010

I added a patch to ticket #996 that implements the change discussed there. The change to the code is trivial; the main issue is that everyone else agrees that the `find` function should return the list of keys instead of printing them. Personally I think it's another no-brainer. Warren

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Reguest for easy patch review--ticket #1113
by Warren Weckesser March 21, 2010

March 21, 2010

Hi, I submitted a patch to ticket #1113 that is just two lines added to the eig() function of scipy.linalg (along with some tests). I think it's a no-brainer, but I'd still like at least one other person to take a look and give it a thumbs up before I commit it. Thanks, Warren

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linalg.toeplitz and ticker #667
by Warren Weckesser March 21, 2010

March 21, 2010

I am going to update linalg.toeplitz to fix the problem reported in ticket #667, but I have some questions about the desired behavior of the function when either `c` (the first column) or `r` (the first row) is complex. The docstring does not say anything about complex values, but the code does some undocumented and unexpected things in this case, one example of which is the bug reported in the ticket #667. I would like to fix this, but I would first like opinions on exactly how it *should* handle complex arguments. I *think* the idea is that if `c` is complex and `r` is not given, then a Hermitian Toeplitz matrix is created. Is that correct? Note that this requires that c[0] be real, since c[0] is the value that will be in the diagonal of the matrix. While I am fixing this, I would like to remove the printed warning that occurs when r[0] != c[0]. I would like to change this to raise a ValueError--that is, adopt the philosophy that either the arguments are correct (and the code handles them as [not yet, but soon to be] documented in the docstring, with no warnings needed), or the arguments are wrong and an exception should be raised. This means that when `r` is not given, an exception would be raised if c[0] is not real. A very different way to handle the case of `r` not being given is to assume it means a square matrix should be created with r[1:] = 0 (i.e. zeros in all the upper off-diagonals). This avoids the whole issue of complex numbers and conjugates, but it is also a more drastic change. Warren

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patches to prepare for 0.7.2rc1
by Ralf Gommers March 20, 2010

March 20, 2010

At http://github.com/rgommers/scipy/tree/release0p7 I have some patches to bump version number, add release notes for 0.7.2, and some updates to the pavement file. Can I ask for a review and if it's all fine, can these be committed to the 0.7.x branch? Thanks, Ralf

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