Mailman 3 December 2013 - SciPy-Dev

ANN: Scipy 0.13.2 release
by Ralf Gommers 13 Dec '13

13 Dec '13

Hi, I'm happy to announce the availability of the scipy 0.13.2 release. This is a bugfix only release; it contains fixes for ndimage and optimize, and most importantly was compiled with Cython 0.19.2 to fix memory leaks in code using Cython fused types. Source tarballs, binaries and release notes can be found at http://sourceforge.net/projects/scipy/files/scipy/0.13.2/ Cheers, Ralf ========================== SciPy 0.13.2 Release Notes ========================== SciPy 0.13.2 is a bug-fix release with no new features compared to 0.13.1. Issues fixed ------------ - 3096: require Cython 0.19, earlier versions have memory leaks in fused types - 3079: ``ndimage.label`` fix swapped 64-bitness test - 3108: ``optimize.fmin_slsqp`` constraint violation

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search in docs
by josef.pktd＠gmail.com 06 Dec '13

06 Dec '13

Is it intentional that the documentation doesn't have a search field ? http://docs.scipy.org/doc/scipy/reference/index.html although, Google seems to have indexed it very well, at least searching by function names. Josef

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adding linear fitting routine
by David J Pine 06 Dec '13

06 Dec '13

I would like to get some feedback and generate some discussion about a least squares fitting routine I submitted last Friday [please see adding linear fitting routine<http://comments.gmane.org/gmane.comp.python.scientific.devel/18442> (29 Nov 2013)]. I know that everybody is very busy, but it would be helpful to get some feedback and, I hope, eventually to get this routine added to one of the basic numpy/scipy libraries. David Pine

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Re: [SciPy-Dev] SciPy-Dev Digest, Vol 122, Issue 4
by Matt Newville 05 Dec '13

05 Dec '13

Hi Daniele, > A named tuple would be much preferable over a dictionary IMHO. It is a > much leaner structure and it still support unpacking if someone is > inclined to do that. The Python standard library returns named tuples > in a few places as well. > > Cheers, > Daniele > Perhaps you could enlighten me on this? I don't claim to know one way or the other whether a named tuple is "a much leaner structure" than a dict or a Bunch or an instance of an empty class. Is this is an important consideration for how to structure a collection of return values of high-level scipy functions? Named tuple can be accessed either by index or by field name. Any future changes to such a return argument *must* be made by appending to the existing values, and would probably cause a lot of grief anyway (for those relying on there being exactly 8 return values, say, it would break code). Since none of the other approaches even have an order, it would seem that the point of advocating for named tuple would be because order was important. If that were the case, I would think everyone you asked would immediately come up with the same answers to these questions: a) should the set of return values be ordered? b) what is the right order? c) are you confident this order s not only right but will always be right? If you were writing divmod(), I think you could get such answers (and probably just use a tuple). I would have a harder time answering these for minimize(), curve_fit(), or linfit(). The discussion here about linfit() was not so much working out the right order for outputs, but about what the right outputs were. David expressed the idea of just sticking with two outputs at least partly (I think) because those two (best_values, covariance) had an obvious order and everything else could derived from them, and it was hard to decide what a right order for any possibly useful derived values might be. To me, that sort of suggests that an ordered output is not the best choice I'm happy to be shown why named tuples would be the way to go, but I'm not seeing it right now. I hope you can help me out. Cheers, --Matt Newville

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Savitzky-Golay and other smoothing filters
by Jonathan Stickel 04 Dec '13

04 Dec '13

On 11/27/13 11:00 , scipy-dev-request(a)scipy.org wrote: > It took a while, but eventually a Savitzky-Golay filter made it into > scipy:https://github.com/scipy/scipy/pull/470 Smoothing filters continue to be of interest to scipy users. I wrote a regularization-based smoothing method a few years ago: https://github.com/jjstickel/scikit-datasmooth/ https://pypi.python.org/pypi/scikits.datasmooth/0.61 and suggested then that several smoothing methods be co-located inside or outside scipy but did not get enough traction to make this happen. Any further interest in this now? It seems that a subbranch of scipy.signal would be logical (e.g. scipy.signal.smoothing). Or perhaps a single function interface to several smoothing methods (spline, S-G, wavelet, regularization, others). I have limited time, but I would be willing to work on a pull request or such with some coaching (it would be my first). Thanks, Jonathan

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thLib: package for 3D kinematics and data analysis (including Savitzky-Golay filter)
by Haslwanter Thomas 04 Dec '13

04 Dec '13

I have compiled a package that should be useful for many researchers, especially in the field of movement analysis. It can be installed with pip install thLib and documentation is provided under http://work.thaslwanter.at/thLib/html/ I would be happy to contribute any of the functions in this package to SciPy. Especially, I believe that a Savitzky-Golay filter is overdue for Scipy. Please provide feedback, which of the functions may be relevant for SciPy, and which functions are faulty or missing. Thanks thomas --- Prof. (FH) PD Dr. Thomas Haslwanter School of Applied Health and Social Sciences University of Applied Sciences Upper Austria FH OÖ Studienbetriebs GmbH Garnisonstraße 21 4020 Linz/Austria Tel.: +43 (0)5 0804 -52170 Fax: +43 (0)5 0804 -52171 E-Mail: Thomas.Haslwanter(a)fh-linz.at<mailto:Thomas.Haslwanter@fh-linz.at> Web: me-research.fh-linz.at<http://work.thaslwanter.at> or work.thaslwanter.at

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Callback for SLSQP minimization
by Matthias Kümmerer 04 Dec '13

04 Dec '13

Hi, in scipy.optimize, there is at the moment no possibility to add a callback function when minimizing using the SLSQP method. I was wondering whether there is some deeper reason for that. If there are no reasons against that, I would like to implement a callback for this method. Guessing from the code, it should be quite easy. I thought, the callback should be called after each function evaluation in _minimize_slsqp, that is around [1]. By the way: Is it better to discuss this kind of question on the mailing list, or should I open an issue in GitHub for such things? Best, Matthias [1] https://github.com/scipy/scipy/blob/v0.13.0/scipy/optimize/slsqp.py#L353

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0.13.2 release plan
by Ralf Gommers 03 Dec '13

03 Dec '13

Hi all, I plan to do a 0.13.2 release this week, due to a memory leak in griddata with the Cython version used to release 0.13.1: https://github.com/scipy/scipy/issues/2388. 0.13.x also contains a fix for another ndimage.label regression. Is there anything else that should go into 0.13.2? Ralf

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