Mailman 3 August 2007 - SciPy-Dev

superlu sources and Debian
by Ondrej Certik Aug. 29, 2007

Aug. 29, 2007

Hi, I adopted the scipy package in debian, it will be fixed soon. And definitely I'll be available to test the new release so that it works in Debian. In the process of polishing the package I noticed there are sources of SuperLU included, but not of the umfpack. I think either there should be both sources of superlu and umfpack, or nothing. I personally am for nothing, since they are already in Debian as separate packages, so it is better to link against already installed packages - saves space and it is the cleaner solution. Also if there are some bugs discovered and fixed by upstream (superlu, umfpack) or the maintainer of the respective debian package, all I need is to recompile the scipy package, so I am using the work made by others (contrary to distributing the sources of superlu ourselves, in which case we need to fix everything). Ondrej

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Requiring Python 2.4
by Stefan van der Walt Aug. 28, 2007

Aug. 28, 2007

Hi all, I noticed that some Python 2.4-only features crept into parts of SciPy (yes, I'm guilty, too). Has Python 2.5 been out for long enough that we can drop support for 2.3? Stéfan

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I will branch SciPy 0.6.x tomorrow night (8/29)
by Jarrod Millman Aug. 28, 2007

Aug. 28, 2007

Hello, Given the amount of work that was done today, I am going to wait another day before branching. The "soft-freeze" is still in effect, so (until I make the branch) please don't check anything in unless it is a bugfix. You can check out the roadmap here: http://projects.scipy.org/scipy/scipy/milestone/0.6 Please let me know if you have any questions/comments/concerns. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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some problems with optimize.py docstrings
by dmitrey Aug. 28, 2007

Aug. 28, 2007

Hi all, unfortunately some days ago I had a problems with internet connection and that's why I didn't committed updated docstrings to optimize.py. That time I encountered some problems and that's why I switched to other tasks assigned to me, and forgot to do this one in-time. The problems that I mentioned are related to lack of documentation, and, moreover, to incorrect documentation. So, 1. def line_search(...) """... Outputs: (alpha, gc, fc) ...""" ... return alpha_star, _ls_fc, _ls_gc, fval_star, old_fval, fprime_star 1) is (gc, fc) really equal to _ls_fc, _ls_gc? Maybe vise versa? As for me, I don't know what are those return params mean. 2) documentation has the line "For the zoom phase it uses an algorithm by" (so what should be here?) 3) Description misses meanings of amax, old_fval, old_old_fval (same to line_search_BFGS) 2. def line_search_BFGS(...) """... Outputs: (alpha, fc, gc)""" ... if (phi_a0 <= phi0 + c1*alpha0*derphi0): return alpha0, fc, 0, phi_a0 #NOTE: 4 params instead of 3 ... if (phi_a1 <= phi0 + c1*alpha1*derphi0): return alpha1, fc, 0, phi_a1 #same: 4 params instead of 3 ... if (phi_a2 <= phi0 + c1*alpha2*derphi0): return alpha2, fc, 0, phi_a2 #same So, as you see, 1) it has incorrect output - 4 values instead of 3 2) it doesn't describe what are those fc and gc 3) output gc is always equal to zero On the other hand, almost noone uses the funcs except some other funcs from optimize.py (elseware lots of tickets would be filed). The same to some other funcs from optimize.py (i.e. they are used only from other optimize.py funcs). So I suppose it could wait. Are you agree? So do you want me to commit the changes I done to svn right now, before tomorrow scipy 0.6 release? Let me attach to the letter links to optimize.py file as well as epydoc output. Regards, D. optimize.py http://www.box.net/shared/3bi5n8jtln html-file http://www.box.net/shared/0l44js08jj

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I need help with a couple of tickets
by Jarrod Millman Aug. 28, 2007

Aug. 28, 2007

Hello, There are a few tickets that I need some help with: http://projects.scipy.org/scipy/scipy/ticket/238 =================================== My understanding is that the issues raised by this ticket are solved. There is a patch attached that fixes the problem in scipy.linalg; but the patch needs to be generalized to apply to scipy.lib as well. Please let me know if that isn't correct. Also, what is the best way to detect whether something has been compiled with veclib? http://projects.scipy.org/scipy/scipy/ticket/325 =================================== It seems like this ticket should be closed. Is anyone still having this issue? http://projects.scipy.org/scipy/scipy/ticket/401 =================================== It seems like this ticket should be closed. Is anyone still having this issue? Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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Reminder: upcoming SciPy 0.6.x branch
by Jarrod Millman Aug. 26, 2007

Aug. 26, 2007

Hello, This is a reminder that I will be branching for the 0.6 release on Monday. So (until I make the branch) please don't check anything in unless it is a bugfix. You can check out the roadmap here: http://projects.scipy.org/scipy/scipy/milestone/0.6 I am also putting together some notes about making releases here: http://projects.scipy.org/scipy/scipy/wiki/MakingReleases Please let me know if you have any questions. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/

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Maskedarray implementations : new developer zone wiki page
by Pierre GM Aug. 26, 2007

Aug. 26, 2007

On Saturday 25 August 2007 15:48:00 Eric Firing wrote: > I've made a couple of small "emergency" edits, but a separate page would > make things much more visible and less confusing. So here it is: http://projects.scipy.org/scipy/numpy/wiki/MaskedArrayAlternative Please note the section : Optimizing maskedarray. You'll find the quick description of a test case (three implementations of divide) that emerged from on off-list discussion with Eric Firing. The problem can be formulated as "do we need to fill masked arrays before processing or not ?". Eric is in favor of the second solution (prefilling according to the domain mask), while the more it goes, the more I'm leaning towards the third one "bah, let numpy take care of that." I would be very grateful if you could post your comments/ideas/suggestions about the three implementations on that list. This is an issue I'd like to solve ASAP. Thanks a lot in advance Pierre

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GSoC weekly report
by dmitrey Aug. 25, 2007

Aug. 25, 2007

Hi all, this week 2 solvers were implemented in optimizers module: - based on cubic interpolation - Barzalai and Borwein (monotone and non-monotone versions) Unfortunately, as I had informed Matthieu, cubic interpolation algorithm contained a mistake (after block "h>0?", "No" branch, there should be added "phi1', phi2' = phi2', phi1'"), and it took a significant time for me to find and fix the one. but when I tried my examples it turned out that as for Barzalai and Borwein (nonmonotone), the book I'm following doesn't provide default values of all those initial settings (sigma, sigma1, sigma2, alpha_min, alpha_max, pho). Ok, I know that 0 < sigma1 < sigma2 < 1 and 0<pho<1, sigma>0, 0<eps<<1, but I don't know any suggestions about alpha_min and alpha_max. I took alpha_min =1e-6 and alpha_max=2, but alpha_max=1e6 works much better (on the other hand, maybe my func was very badly scaled and that's the matter). Web search "Barzalai and Borwein" also doesn't yield me suggestions about alpha_min and alpha_max. Now I'm working on second order Armijo step rule and second order Wolfe-Powell step rules. These ones, as well as some other steps assigned to me, require Cholesky factorization. I intend to use that one from scipy/numpy (don't write by myself, despite there is a little bit modified alg), because that one from the book will require sufficient of time to be implemented (and that one is not vectoriezed). Regards, D.

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Maskedarray implementations
by Pierre GM Aug. 25, 2007

Aug. 25, 2007

All, As you might be aware, there are currently two concurrent implementations of masked arrays in numpy: * numpy.ma is the official implementation, but it is unclear whether it is still actively maintained. * maskedarray is the alternative I've been developing initially for my own purpose from numpy.ma. It is available in the scipy svn sandbox, but is already fully functional The main difference between numpy.ma and maskedarray is that the objects created by numpy.ma are NOT ndarrays, while maskedarray.MaskedArray is a full subclass of ndarrays. For example: >>>import numpy, maskedarray >>>x = numpy.ma.array([1,2], mask=[0,1]) >>>isinstance(x, numpy.ndarray) False >>>numpy.asanyarray(x) array([1,2]) Note that we just lost the mask... >>>x = maskedarray.array([1,2], mask=[0,1]) >>>isinstance(x, numpy.ndarray) True >>>numpy.asanyarray(x) masked_array(data = [1 --], mask = [False True], fill_value=999999) Note that the mask is conserved. Having the masked array be a subclass of ndarray makes masked arrays easier to mix with other ndarray types and to subclass. An example of application is the TimeSeries package, where the main TimeSeries class is a subclass of maskedarray.MaskedArray. * Does anyone see any *disadvantages* to this aspect of maskedarray relative to numpy.ma? * What would be the requisites to move maskedarray out of the sandbox ? We hope to be able in the short term to either replace or at least merge the two implementations, once a couple of issues are addressed (but we can talk about that later...) Thanks a lot in advance for your feedback Pierre

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EMPython site is dead...delete from Topical?
by Joe Harrington Aug. 22, 2007

Aug. 22, 2007

A user just complained to me that the link to www.empython.org on the topical software page took him to a porn site. It appears that www.empython.org is not a live site, and instead gives you one of those IP registrar ad sites. After a while it sometimes redirects you into neverland, and maybe neverland has some porn sites. At any rate, does EM python still exist anywhere as a project? Do we want to archive the code somewhere (presuming someone has it)? We should either archive the code and link to it, or delete the link entirely if we don't have that code or don't want to archive it. I found the note below from April, but when I tried emailing rob (at) empython.org, it bounced. Thoughts? We'll see this happen again, so we should decide some sort of consistent treatment of sites that just vanish. --jh-- [SciPy-user] EMPython Robert Kern robert.kern@gmail.... Wed Apr 11 14:05:31 CDT 2007 * Previous message: [SciPy-user] EMPython * Next message: [SciPy-user] Building SciPy * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] ________________________________________________________________________ lorenzo bolla wrote: > Dear all, > does anyone know who is responsible for the website: > http://www.empython.org/? > if I get it right, he should be Robert Lytle, former responsible for > www.electromagneticpython.org <http://www.electromagneticpython.org>, > now dismissed. > do you know an e-mail address I can write to? He's posted on enthought-dev recently. rob (at) empython.org -- Robert Kern "I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco ________________________________________________________________________

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