Mailman 3 January 2009 - SciPy-Dev

An interesting exercise - reproduce R analysis using python.
by Alan Jackson Jan. 27, 2009

Jan. 27, 2009

A quite good online book, "Using R for Data Analysis and Graphics" by John Maindonald has been updated and has all the data and exercises posted on the net. Relevance to this group? I think it might be quite fun and instructive to work through the 'R' exercises with numpy/matplotlib/scipy instead. I'm considering doing it, partly just to broaden my numpy/matplotlib skillset, but I thought I would post this here in case anyone else might find it an interesting challenge. Exercises and datasets can be found from links here : http://blog.revolution-computing.com/2009/01/using-r-for-data-analysis-and-… -- ----------------------------------------------------------------------- | Alan K. Jackson | To see a World in a Grain of Sand | | alan(a)ajackson.org | And a Heaven in a Wild Flower, | | www.ajackson.org | Hold Infinity in the palm of your hand | | Houston, Texas | And Eternity in an hour. - Blake | -----------------------------------------------------------------------

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ANN: SciPy 0.7.0rc2 (release candidate)
by Jarrod Millman Jan. 24, 2009

Jan. 24, 2009

I'm pleased to announce the second release candidate for SciPy 0.7.0. Due to an issue with the Window's build scripts, the first release candidate wasn't announced. SciPy is a package of tools for science and engineering for Python. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more. This release candidate comes almost one year after the 0.6.0 release and contains many new features, numerous bug-fixes, improved test coverage, and better documentation. Please note that SciPy 0.7.0rc2 requires Python 2.4 or greater and NumPy 1.2.0 or greater. For information, please see the release notes: http://sourceforge.net/project/shownotes.php?group_id=27747&release_id=6556… You can download the release from here: http://sourceforge.net/project/showfiles.php?group_id=27747&package_id=1953… Thank you to everybody who contributed to this release. Enjoy, Jarrod Millman

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is PySparse required for scipy.maxentropy
by josef.pktd＠gmail.com Jan. 24, 2009

Jan. 24, 2009

historic artifact or not? I saw a reference to PySparse in scipy.maxentropy.maxentutils.sparsefeatures. Is this still required or covered by scipy.sparse? Josef def sparsefeatures(f, x, format='csc_matrix'): """ Returns an Mx1 sparse matrix of non-zero evaluations of the scalar functions f_1,...,f_m in the list f at the point x. If format='ll_mat', the PySparse module (or a symlink to it) must be available in the Python site-packages/ directory. A trimmed-down version, patched for NumPy compatibility, is available in the SciPy sandbox/pysparse directory. """ m = len(f) if format == 'll_mat': import spmatrix sparsef = spmatrix.ll_mat(m, 1)

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Parallel cKDTree for SciPy
by Sturla Molden Jan. 24, 2009

Jan. 24, 2009

This is a follow up to my post on scipy-user this morning. As shown, using OpenMP with cKDTree works very well. But it remained that I hand-edited the output from Cython. Therefore, I rewrote Anne Archibald's cKDTree sliglity, putting all the OpenMP calls in a separate C file. Now it works without having to modify the Cython output. I have also made sure that: - The GIL is released around the time-consuming loop in cKDTree.query. - If a single query is made, OpenMP threads is not used in cKDTree.query. - The number of OpenMP threads can be specified when calling cKDTree.query. For compilation I used GCC 4.4 with -O3 and -fopenmp, and linked -lgomp and -lpthread. I have attached the C and Cython code, and a speed test. In the benchmark, the black line is SciPy's 0.7.0rc2 cKDTree, green line is mine using one OpenMP thread, and the red is letting OpenMP pick the number of threads. I have a dual core laptop so OpenMP used two threads. The code is donated to SciPy if you want it. I think it is substantially better than the present version in SciPy SVN, as speed is the sole purpose of using kd-trees; otherwise, we could just as well do O(N**2) brute force search. Code and benchmark is available here: http://folk.uio.no/sturlamo/kdtree/ Windows binary compiled for Python 2.5 can be uploaded on request. Regards, Sturla Molden

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C++ in scipy: enforcing extension
by David Cournapeau Jan. 24, 2009

Jan. 24, 2009

Hi, I noticed that several scipy modules now use C++ (at least scipy.sparse and scipy.interpolate). I think it would be better if we could agree on one file extension, instead of something using cxx (scipy.sparse.sparsetools) and sometimes cpp (scipy.interpolate). I don't care which one - I thought .cc was the recommended one for some time, but I am not following C++ anymore, so I am not the best person to make the choice, David

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Scipy Trac broken?
by Pauli Virtanen Jan. 23, 2009

Jan. 23, 2009

Hi, Scipy Trac complains about "database disk image is malformed", at http://scipy.org/scipy/scipy/query?status=new&status=assigned&status=reopen… -- Pauli Virtanen

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scipy.org down
by Pauli Virtanen Jan. 23, 2009

Jan. 23, 2009

Hi, As mentioned in the other thread, scipy.org is down. It was down also last Friday. A coincidence? -- Pauli Virtanen

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manifold_learning
by Nils Wagner Jan. 21, 2009

Jan. 21, 2009

Hi all, The example regression.py in manifold_learning requires openopt. Is it recommended to install Openopt from its new location http://www.openopt.org/Install ? python -i regression.py Traceback (most recent call last): File "regression.py", line 21, in <module> from scikits.learn.machine.manifold_learning import regression File "build/bdist.linux-x86_64/egg/scikits/learn/machine/manifold_learning/__init__.py", line 9, in <module> # See the README file for information on usage and redistribution. File "build/bdist.linux-x86_64/egg/scikits/learn/machine/manifold_learning/compression/__init__.py", line 10, in <module> # File "build/bdist.linux-x86_64/egg/scikits/learn/machine/manifold_learning/compression/geodesic_mds.py", line 14, in <module> ImportError: No module named openopt.solvers.optimizers Cheers, Nils

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FAIL: test_pbdv (test_basic.TestCephes)
by Xavier Gnata Jan. 17, 2009

Jan. 17, 2009

Hi, On kubuntu 64bits, scipy svn: This issue is still open on my box: FAIL: test_pbdv (test_basic.TestCephes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/scipy/special/tests/test_basic.py", line361, in test_pbdv assert_equal(cephes.pbdv(1,0),(0.0,0.0)) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 176, in assert_equal assert_equal(actual[k], desired[k], 'item=%r\n%s' % (k,err_msg), verbose) File "/usr/lib/python2.5/site-packages/numpy/testing/utils.py", line 183, in assert_equal raise AssertionError(msg) AssertionError: Items are not equal: item=1 ACTUAL: 1.0 DESIRED: 0.0 Can you reproduce that? What else should I test to help to kill this bug? Xavier

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scipy.org down
by Pauli Virtanen Jan. 16, 2009

Jan. 16, 2009

(Sorry for the noise if you already know this.) Hi, Scipy.org web server seems to be down. The machine itself seems to be up, though (apache dossed?): $ nc -v scipy.org 80 scipy.org [216.62.213.231] 80 (www) open GET [never returns anything] Let's see if the mailing list works... -- Pauli Virtanen

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