Mailman 3 July 2007 - SciPy-Dev

Deprecating packages
by David Cournapeau July 27, 2007

July 27, 2007

Hi, In the context of releasing soon a new scipy tarball, I was wondering what is the most appropriate approach to deprecate toolboxes (in sandbox, not standard packages of course). 4 packages in scipy.sandbox are now in scikits.learn (pyem, svm, ann and ga). What I did for pyem is to throw an import error in the __init__ with instructions on where to get the new code. Can I do the same for other packages (those were not "mine", so I didn't want to change anything before feedback) ? cheers, David

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ticket 464
by dmitrey July 26, 2007

July 26, 2007

hi all, Nils proposed me to fix the ticket 464 http://projects.scipy.org/scipy/scipy/ticket/464 I found the problem is here: rank = len(x0.shape)# So matrix(0.3) yields shape (1,1) here => rank = 2 if not -1 < rank < 2: raise ValueError, "Initial guess must be a scalar or rank-1 sequence." I propose to fix it in the way: rank = len(x.shape) if not -1 < rank < 2: if x.shape == (1,1): x = x.flatten()#matrix(0.3) for example else: raise ValueError, "Initial guess must be a scalar or rank-1 sequence." If you don't mind (no other opinions during several hours) I will commit the change to svn. I found the same change should be done for optimize.fmin Regards, D.

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scipy.stats: test for handling nan values
by David Cournapeau July 26, 2007

July 26, 2007

Hi, Trying to solve a few tickets related to nanmean and co, I wanted to add tests for those functions, as well as general behaviour of basic statistics function with nan. Part of the test suite (in test_stats.py) is based on the Statistical quiz for Wilkinson; missing values are not supported. If I finish the test suite by implemenging MISSING by nan values, is this conceptually correct or not ? I wanted to be sure before committing the change in the test suite (actually, only adding originally disabled tests) cheers, David

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BoF on 3D visualization
by Prabhu Ramachandran July 26, 2007

July 26, 2007

Hello, Gael Varoquaux and myself are planning on holding a "Pythonic 3D visualization" BoF at SciPy07 on Thursday evening. We'd like to know if any of you would be interested in this. If you are, please do let us know. Please also let us know if you have anything in particular you'd like to discuss. Thanks. Cheers, -- Prabhu Ramachandran http://www.aero.iitb.ac.in/~prabhu

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copy on write?
by Nathan Bell July 26, 2007

July 26, 2007

Is there any support for copy on write behavior in numpy? I haven't seen anything to suggest that it does or doesn't exist. The particular application I have in mind is as follows: Sparse matrices, such as csr_matrix, are represented by three dense 1D arrays. Two of these arrays encode the structure of the matrix, while one records the nonzero values. Many operations like __abs__ and __neg__ require only a change to the data array and leave the structure arrays unchanged. Therefore, when performing B = abs(A), the two sparse matrices could share the same structure arrays. This sort of optimization is nearly always desirable, especially when B is short-lived (e.g. abs(A).sum(0)). Unfortunately, the user may occasionally decide to change A or B's sparsity structure directly (e.g. an inplace sort on the column indices). Hence, in general one must copy for complete safety. If the CSR structure data was COW, then one could apply such optimizations frequently without fear of atypical usage. Short of COW, can one easily get the refcount of an ndarray (in Python)? -- Nathan Bell wnbell(a)gmail.com

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Trouble with optimize.fmin_ncg
by Nils Wagner July 25, 2007

July 25, 2007

Hi all, I have some trouble with fmin_ncg. IIRC the attached code worked for me before (line 44-48) but it hangs with recent svn. Any pointer would be appreciated. Nils

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Trouble with fmin_ncg
by Nils Wagner July 25, 2007

July 25, 2007

Hi, I guess I traced the problem with ncg down to the Hessian. The results between the sparse and the dense version differ. Nils

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Making numpy test work in scikits
by David Cournapeau July 24, 2007

July 24, 2007

Hi, I had a hard time to get the usual numpy tests working inside a scikits (because of setuptools): I wanted to keep the usual numpy tests infrastructure (each package has a tests directory where all the tests are), while being able to use them with python setup.py test. Below is a an quick explanation how I did it: - foo/scikits/foo -> this is a typical "scipy package", in the sense that you can use the same layout for tests as in a scipy package. - foo/setup.py -> use the test_suite argument of the setup function, with the value "tester" - foo/tester.py -> this defines a function additional_tests, which is supposed to return a unittest.TestSuite. I use NumpyTest to find all the tests in the package foo, and make a TestSuite from it; I had to use a private function, though, but maybe adding public API in numpy would be possible. The module tester boils down to this: from numpy.testing import NumpyTest def additional_tests(): # XXX: does this guarantee that the package is the one in the dev trunk, and # not scikits.foo installed somewhere else ? import scikits.foo np = NumpyTest(scikits.foo) return np._test_suite_from_all_tests(np.package, level = 1, verbosity = 1) With this, you can call all the tests with python setup.py test (which is the point of all this, actually), but: - I don't know much about unittest, though, so this may be not ideal but is the only way I found to make is work without touching anything else than the setup.py file. - There may be a way to make this a bit more automatic (I don't like the fact that I have to give the name of the package in additional_tests, for example) - I didn't find a way to give argumements for tests in command line (setuptools does not seem to support it for the test command). cheers, David

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Astronomy / PyFITS BOF at SciPy
by Christopher Hanley July 24, 2007

July 24, 2007

Hi, It looks like we have more than enough interest for an astronomy BOF Thursday evening after dinner. I look forward to seeing everyone. Cheers, Chris

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SciPy 2007 Conference BOF
by Christopher Hanley July 23, 2007

July 23, 2007

Greetings, I have a question for those planning on attending the SciPy 2007 conference in a few weeks. I have been approached regarding the possibility about having a BOF meeting to discuss PyFITS. I was wondering if there would be an interest in this, or more generally, about astronomy software development. We at the Space Telescope Science Institute could talk about our future plans. Please let me know if you are interested in having a BOF meeting. If there is enough interest I will arrange a session for Thursday evening. Cheers, Chris Hanley -- Christopher Hanley Systems Software Engineer Space Telescope Science Institute 3700 San Martin Drive Baltimore MD, 21218 (410) 338-4338

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