Mailman 3 August 2013 - SciPy-Dev

Re: [SciPy-Dev] cubature license (Warren Weckesser)
by Saullo Castro Aug. 27, 2013

Aug. 27, 2013

Dear all, due to the BSD and GPL licenses incompatibilities the cubature package will not be included in SciPy. Steven Johnson replied explaining that the code is directly derived from Hintlib, and GNU GSL libraries, both of which are GPL. The wrapper is already available in GitHub and soon I will include one link in PyPI. https://github.com/saullocastro/cubature if anyone is interested. Greetings, Saullo 2013/8/25 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: cubature license (Warren Weckesser) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 25 Aug 2013 08:01:32 -0400 > From: Warren Weckesser <warren.weckesser(a)gmail.com> > Subject: Re: [SciPy-Dev] cubature license > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: > < > CAGzF1udYnngzyzjS2ezp2h3joYkzLib9jXiZSKpjSZSPz3RHhw(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On 8/25/13, Saullo Castro <saullogiovani(a)gmail.com> wrote: > > @Warren > > > > from the good disccusion here ( > > http://matplotlib.org/devel/license.html#license-discussion) > > it seems that the biggest difference between the GPL and the BSD is that > > the former requires you to distribute your source code, and the BSD > allows > > you to do whatever you want... > > > > I don't see the problem to include it in SciPy, since the source code is > > always distributed. > > > The issue is the restriction placed on anyone who wants to > *redistribute* software that uses scipy. For example, currently a > third party could build and sell a commercial application that uses > scipy without having to distribute the source code for the application > or their modified version of scipy. That would not be possible with > a GPL license. > > More reading: http://www.freebsd.org/doc/en/articles/bsdl-gpl/article.html > > Warren > > > > Even if third part companies like Enthought are using > > it, it is more like a module, isn't it? and the core code behind it can > > still be BSD based. > > > > Anyway, the software has a `clencurt_gen.c` stand-alone program which > does > > not have to be used unless the user whant a `p-adaptive` cubature with > more > > than 8193 points per dimension, this type of cubature applies > > "p-refinement" (increase of interpolation function order) instead of > > "h-refinement" (splitting the interval). I don't see a need to include > this > > program in the SciPy cubature. We can implement this restriction in the > > wrapper. > > > > I will ask Steven Johnson about this, if removing this part could make > > cubature re-licensable to BSD. > > > > Greetings! > > Saullo > > > > > > 2013/8/24 <scipy-dev-request(a)scipy.org> > > > >> Send SciPy-Dev mailing list submissions to > >> scipy-dev(a)scipy.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://mail.scipy.org/mailman/listinfo/scipy-dev > >> or, via email, send a message with subject or body 'help' to > >> scipy-dev-request(a)scipy.org > >> > >> You can reach the person managing the list at > >> scipy-dev-owner(a)scipy.org > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of SciPy-Dev digest..." > >> > >> > >> Today's Topics: > >> > >> 1. Re: cubature license (Robert Kern) > >> 2. Re: cubature license (Warren Weckesser) > >> 3. Re: cubature license (Warren Weckesser) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sat, 24 Aug 2013 16:53:10 +0200 > >> From: Robert Kern <robert.kern(a)gmail.com> > >> Subject: Re: [SciPy-Dev] cubature license > >> To: SciPy Developers List <scipy-dev(a)scipy.org> > >> Message-ID: > >> < > >> CAF6FJivScnjqnAZO8OJ0XZpJ48+KsC5rdOmE+5z-EWWJn7iH_g(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> On Sat, Aug 24, 2013 at 4:47 PM, Warren Weckesser < > >> warren.weckesser(a)gmail.com> wrote: > >> > > >> > On 8/24/13, Saullo Castro <saullogiovani(a)gmail.com> wrote: > >> > > @Alex, > >> > > > >> > > you are right, "it uses some GPL code from other projects (Hintlib > >> > > and > >> > > GSL). > >> > > " > >> > > > >> > > But is it really impossible to include it in SciPy because of that? > >> > > >> > Yes. We do not include GPL-licensed code in SciPy. I haven't looked > >> > at the Cubature code, so I don't know the extent to which it uses > >> > HIntLib and GSL, but based on the comment on the web page, it is > >> > unlikely that Steven Johnson can re-license his code with a license > >> > that is compatible with SciPy. The GPL is viral that way (insert the > >> > usual "I am not a lawyer" disclaimer here). > >> > >> It's not quite as viral as that. He can license the code that he himself > >> wrote under whatever license he likes as long as it is compatible with > >> the > >> GPL license of the other libraries that he is combining his code with. > If > >> the code that he wrote is separable from HIntLib and GSL by rewriting > >> that > >> functionality, he can distribute his code under the BSD license for > >> inclusion in SciPy. > >> > >> -- > >> Robert Kern > >>

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fftpack.convolve.convolve
by Clemens Novak Aug. 26, 2013

Aug. 26, 2013

Hi, I've been working on extending the fftpack tutorial page (you can see the current status here: https://github.com/ClemensFMN/scipy/blob/tut_fft/doc/source/tutorial/fftpac… ) and I stumbled across the function fftpack.convolve.convolve . Sorry the blunt question, but what does this function do? From the name I'd assume that it calculates the convolution of two sequences (as convolve in scipy.signal does) using the fft (since it is part of fftpack), but appearently it doesn't: import numpy as np import scipy.fftpack.convolve as conv import scipy as sp import scipy.signal as sig x = np.array([1.0, 0.0, 0.0]) h = np.array([1.0, 2.0, 3.0]) y1 = conv.convolve(x, h) [ 5. -1. -1.] y2 = sig.convolve(x, h) [ 1. 2. 3. 0. 0.] y3 = sp.ifft(sp.fft(x) * sp.fft(h)) [ 1.+0.j 2.+0.j 3.+0.j] Does the function extend its first and/or second argument to a periodic sequence and perform then the convolution (I tried some ideas but that didn'twork either)? It would be great if someone could please provide some insight... Regards - Clemens

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sprint mini-report
by Ralf Gommers Aug. 25, 2013

Aug. 25, 2013

Hi all, Today we had 18 people in the room at the EuroScipy sprint - many of which made their first contribution to scipy today - plus Josef joining remotely and David C hiding out in the scikit-learn room. Some statistics on what we managed to do: - 21 scipy PRs - 9 scipy PRs merged - 5 scipy issues closed, and many more discussed - 2 numpy commits - 2 scipy.org PRs Thanks everyone for joining (keep those PRs coming...:) ), and Pierre for the coffee runs and pizza! Cheers, Ralf

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Re: [SciPy-Dev] cubature license
by Saullo Castro Aug. 25, 2013

Aug. 25, 2013

@Warren from the good disccusion here ( http://matplotlib.org/devel/license.html#license-discussion) it seems that the biggest difference between the GPL and the BSD is that the former requires you to distribute your source code, and the BSD allows you to do whatever you want... I don't see the problem to include it in SciPy, since the source code is always distributed. Even if third part companies like Enthought are using it, it is more like a module, isn't it? and the core code behind it can still be BSD based. Anyway, the software has a `clencurt_gen.c` stand-alone program which does not have to be used unless the user whant a `p-adaptive` cubature with more than 8193 points per dimension, this type of cubature applies "p-refinement" (increase of interpolation function order) instead of "h-refinement" (splitting the interval). I don't see a need to include this program in the SciPy cubature. We can implement this restriction in the wrapper. I will ask Steven Johnson about this, if removing this part could make cubature re-licensable to BSD. Greetings! Saullo 2013/8/24 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: cubature license (Robert Kern) > 2. Re: cubature license (Warren Weckesser) > 3. Re: cubature license (Warren Weckesser) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Aug 2013 16:53:10 +0200 > From: Robert Kern <robert.kern(a)gmail.com> > Subject: Re: [SciPy-Dev] cubature license > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: > < > CAF6FJivScnjqnAZO8OJ0XZpJ48+KsC5rdOmE+5z-EWWJn7iH_g(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Sat, Aug 24, 2013 at 4:47 PM, Warren Weckesser < > warren.weckesser(a)gmail.com> wrote: > > > > On 8/24/13, Saullo Castro <saullogiovani(a)gmail.com> wrote: > > > @Alex, > > > > > > you are right, "it uses some GPL code from other projects (Hintlib and > > > GSL). > > > " > > > > > > But is it really impossible to include it in SciPy because of that? > > > > Yes. We do not include GPL-licensed code in SciPy. I haven't looked > > at the Cubature code, so I don't know the extent to which it uses > > HIntLib and GSL, but based on the comment on the web page, it is > > unlikely that Steven Johnson can re-license his code with a license > > that is compatible with SciPy. The GPL is viral that way (insert the > > usual "I am not a lawyer" disclaimer here). > > It's not quite as viral as that. He can license the code that he himself > wrote under whatever license he likes as long as it is compatible with the > GPL license of the other libraries that he is combining his code with. If > the code that he wrote is separable from HIntLib and GSL by rewriting that > functionality, he can distribute his code under the BSD license for > inclusion in SciPy. > > -- > Robert Kern >

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Re: [SciPy-Dev] License compatibility SciPy -> MIT -> GPL
by Saullo Castro Aug. 25, 2013

Aug. 25, 2013

@Robert Kern maybe you misunderstood me, I am not trying to find a workaround to include GPL code in scipy, actually I just found it interesting that SciPy is compatible to MIT and MIT to GPL, but not Scipy to GPL. Your answer has clarified it so far... I will keep in touch with the cubature author (Steven Johnson) to see if relicensing is an alternative, and moving on with the wrapper (testing and documentation now). Thank you! Saullo 2013/8/25 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: cubature license (Saullo Castro) > 2. License compatibility SciPy -> MIT -> GPL (Saullo Castro) > 3. Re: License compatibility SciPy -> MIT -> GPL (Matthieu Brucher) > 4. Re: License compatibility SciPy -> MIT -> GPL (Robert Kern) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 25 Aug 2013 08:40:09 +0200 > From: Saullo Castro <saullogiovani(a)gmail.com> > Subject: Re: [SciPy-Dev] cubature license > To: Scipy-Dev <scipy-dev(a)scipy.org> > Message-ID: > <CAHbwRz7Uy_=5o3Dvk=_ > M-3oKCAFuckZBHwBd+D6sKx4bTBP5OA(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > @Warren > > from the good disccusion here ( > http://matplotlib.org/devel/license.html#license-discussion) > it seems that the biggest difference between the GPL and the BSD is that > the former requires you to distribute your source code, and the BSD allows > you to do whatever you want... > > I don't see the problem to include it in SciPy, since the source code is > always distributed. Even if third part companies like Enthought are using > it, it is more like a module, isn't it? and the core code behind it can > still be BSD based. > > Anyway, the software has a `clencurt_gen.c` stand-alone program which does > not have to be used unless the user whant a `p-adaptive` cubature with more > than 8193 points per dimension, this type of cubature applies > "p-refinement" (increase of interpolation function order) instead of > "h-refinement" (splitting the interval). I don't see a need to include this > program in the SciPy cubature. We can implement this restriction in the > wrapper. > > I will ask Steven Johnson about this, if removing this part could make > cubature re-licensable to BSD. > > Greetings! > Saullo > > > 2013/8/24 <scipy-dev-request(a)scipy.org> > > > Send SciPy-Dev mailing list submissions to > > scipy-dev(a)scipy.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mail.scipy.org/mailman/listinfo/scipy-dev > > or, via email, send a message with subject or body 'help' to > > scipy-dev-request(a)scipy.org > > > > You can reach the person managing the list at > > scipy-dev-owner(a)scipy.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of SciPy-Dev digest..." > > > > > > Today's Topics: > > > > 1. Re: cubature license (Robert Kern) > > 2. Re: cubature license (Warren Weckesser) > > 3. Re: cubature license (Warren Weckesser) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 24 Aug 2013 16:53:10 +0200 > > From: Robert Kern <robert.kern(a)gmail.com> > > Subject: Re: [SciPy-Dev] cubature license > > To: SciPy Developers List <scipy-dev(a)scipy.org> > > Message-ID: > > < > > CAF6FJivScnjqnAZO8OJ0XZpJ48+KsC5rdOmE+5z-EWWJn7iH_g(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > On Sat, Aug 24, 2013 at 4:47 PM, Warren Weckesser < > > warren.weckesser(a)gmail.com> wrote: > > > > > > On 8/24/13, Saullo Castro <saullogiovani(a)gmail.com> wrote: > > > > @Alex, > > > > > > > > you are right, "it uses some GPL code from other projects (Hintlib > and > > > > GSL). > > > > " > > > > > > > > But is it really impossible to include it in SciPy because of that? > > > > > > Yes. We do not include GPL-licensed code in SciPy. I haven't looked > > > at the Cubature code, so I don't know the extent to which it uses > > > HIntLib and GSL, but based on the comment on the web page, it is > > > unlikely that Steven Johnson can re-license his code with a license > > > that is compatible with SciPy. The GPL is viral that way (insert the > > > usual "I am not a lawyer" disclaimer here). > > > > It's not quite as viral as that. He can license the code that he himself > > wrote under whatever license he likes as long as it is compatible with > the > > GPL license of the other libraries that he is combining his code with. If > > the code that he wrote is separable from HIntLib and GSL by rewriting > that > > functionality, he can distribute his code under the BSD license for > > inclusion in SciPy. > > > > -- > > Robert Kern > >

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License compatibility SciPy -> MIT -> GPL
by Saullo Castro Aug. 25, 2013

Aug. 25, 2013

Well, we've been discussion the license combatility for the cubature module. >From the links @Warren gave me: http://wiki.scipy.org/License_Compatibility http://matplotlib.org/devel/license.html#license-discussion it states that the MIT license is compatible with SciPy, and in the MIT description in Wikipedia (http://en.wikipedia.org/wiki/MIT_License) it states that this license is compatible with the GPL. So... is there a crack here where we could place a GPL software in SciPy? Thank you, Saullo

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Re: [SciPy-Dev] cubature license
by Saullo Castro Aug. 24, 2013

Aug. 24, 2013

@Alex, you are right, "it uses some GPL code from other projects (Hintlib and GSL). " But is it really impossible to include it in SciPy because of that? Saullo 2013/8/24 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: SciPy-Dev Digest, Vol 118, Issue 32 (Saullo Castro) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Aug 2013 10:39:03 +0200 > From: Saullo Castro <saullogiovani(a)gmail.com> > Subject: Re: [SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 32 > To: Scipy-Dev <scipy-dev(a)scipy.org> > Message-ID: > <CAHbwRz50dGBAp50xPXvcG+HV= > XQotXJFdU0YqQQdbTMNLru8_Q(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I already contacted Steven Johnson about this matter and he told me > that "relicensing > the Cubature code is not feasible", but he agrees on including this in > SciPy if the SciPy community agrees to include a GNU GPL licensed software > there. > > Otherwise I will probably create a separate Python package for it, ideally > with a pip installer, as suggested by him. > > Greetings, > Saullo > > > 2013/8/24 <scipy-dev-request(a)scipy.org> > > > Send SciPy-Dev mailing list submissions to > > scipy-dev(a)scipy.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://mail.scipy.org/mailman/listinfo/scipy-dev > > or, via email, send a message with subject or body 'help' to > > scipy-dev-request(a)scipy.org > > > > You can reach the person managing the list at > > scipy-dev-owner(a)scipy.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of SciPy-Dev digest..." > > > > > > Today's Topics: > > > > 1. cubature license (alex) > > 2. Re: cubature license (Matt Redmond) > > 3. Re: cubature license (alex) > > 4. Re: cubature license (Charles R Harris) > > 5. Re: ANN: Scipy 0.13.0 beta 1 release (Jack Howarth) > > 6. Re: SciPy-Dev Digest, Vol 118, Issue 31 (Saullo Castro) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 23 Aug 2013 13:20:19 -0400 > > From: alex <argriffi(a)ncsu.edu> > > Subject: [SciPy-Dev] cubature license > > To: scipy-dev(a)scipy.org > > Message-ID: > > <CAE5GFc+F+gxTctEcJLxO_wRadVLOE= > > o0XGDEVNy0hb0qu0ip0g(a)mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > I noticed on the mailing list that someone wants to put cubature into > > scipy. You will need to ask Steven Johnson before this can happen > > because scipy is licensed in a way that does not allow it to accept > > GPL code. Actually now that I read more, this will probably not > > happen anyway because cubature itself depends on multiple GPL-licensed > > codes. > > http://mail.scipy.org/pipermail/scipy-dev/2013-August/thread.html > > http://ab-initio.mit.edu/wiki/index.php/Cubature > > > > Alex > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 23 Aug 2013 11:18:09 -0700 > > From: Matt Redmond <mrdmnd(a)mit.edu> > > Subject: Re: [SciPy-Dev] cubature license > > To: SciPy Developers List <scipy-dev(a)scipy.org> > > Message-ID: > > < > > CABTWFhGzjRPgDRmc5Q3csTAiN3yLMk8H6qP_Rvxo15RPRNo0Mg(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > I took a number of his classes at MIT, and I'm fairly sure he'd be on > board > > with this usage. He seemed pretty supportive of SciPy. > > > > > > On Fri, Aug 23, 2013 at 10:28 AM, Matt Redmond <mttrdmnd(a)gmail.com> > wrote: > > > > > I'll ask him - I took his classes at MIT and I'm fairly sure he'd be > okay > > > with this. > > > > > > > > > On Fri, Aug 23, 2013 at 10:20 AM, alex <argriffi(a)ncsu.edu> wrote: > > > > > >> I noticed on the mailing list that someone wants to put cubature into > > >> scipy. You will need to ask Steven Johnson before this can happen > > >> because scipy is licensed in a way that does not allow it to accept > > >> GPL code. Actually now that I read more, this will probably not > > >> happen anyway because cubature itself depends on multiple GPL-licensed > > >> codes. > > >> http://mail.scipy.org/pipermail/scipy-dev/2013-August/thread.html > > >> http://ab-initio.mit.edu/wiki/index.php/Cubature > > >> > > >> Alex > > >> _______________________________________________ > > >> SciPy-Dev mailing list > > >> SciPy-Dev(a)scipy.org > > >> http://mail.scipy.org/mailman/listinfo/scipy-dev > > >> > > > > > > > > > > > > -- > > > Matthew Redmond > > > Massachusetts Institute of Technology > > > Department of Mathematics, Course 18C > > > Class of 2013 > > > > >

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Re: [SciPy-Dev] Need some help to wrap the cubature package in scipy/integrate
by Saullo Castro Aug. 24, 2013

Aug. 24, 2013

Just to update you guys, since the matter regarding the Cubature license incompatility is not closed, I decided to move the wrapper development from my scipy forked repository to a new one. Here is the link: https://github.com/saullocastro/cubature if you wish to keep track of it. The wrapper is working so far and now I will start writing all the testing functions, some scripts for benchmarking and the documentation. Please, let's try to include it in scipy/integrate. Greetings, Saullo 2013/8/23 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: Loss of precision using lsoda f2py interface or ode class > (Joris Vankerschaver) > 2. Re: Need some help to wrap the cubature package in > scipy/integrate (Nathan Woods) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Aug 2013 14:56:49 +0200 > From: Joris Vankerschaver <jvankers(a)gmail.com> > Subject: Re: [SciPy-Dev] Loss of precision using lsoda f2py interface > or ode class > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: <504DC808-6E3E-436B-A936-696B51834882(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > On 23-aug-2013, at 02:15, Juan Luis Cano wrote: > > I fear odeint/ode bugs are starting to pile up (gh-1567, gh-1801, > > gh-1976, gh-2515, gh-2570), and as many have suggested in the past a > > rewrite or redesign would be quite helpful. > > This may have been pointed out before, but one inconsistency that should > be fixed in an eventual redesign is that scipy.integrate.ode expects an RHS > of the form `f(t, y0, ...)` whereas odeint expects an RHS with the first > two parameters reversed, i.e. of the form `f(y0, t, ...)`. The former > convention is the standard in Matlab and Sage. > > All the best, > Joris > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 23 Aug 2013 10:22:01 -0600 > From: Nathan Woods <charlesnwoods(a)gmail.com> > Subject: Re: [SciPy-Dev] Need some help to wrap the cubature package > in scipy/integrate > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: <-1837672449859755872@unknownmsgid> > Content-Type: text/plain; charset="iso-8859-1" > > We just had a multidimensional integrator (nquad) wrapped into the latest > beta version of scipy. How does cubature compare? I've been kicking around > the idea of improving the speed of nquad by moving more of the code to a > compiled language. How would that compare? > > Nate > > > On Aug 23, 2013, at 5:35 AM, Saullo Castro <saullogiovani(a)gmail.com> > wrote: > > I am wrapping the Cubature package for multi-dimensional integration that > supports vector-valued functions and offers both fixed and adaptive > integration schemes. > > Please, see more details here: > http://ab-initio.mit.edu/wiki/index.php/Cubature > > I've forked the scipy repository and my current attempt can be directly > accessed here: > > > https://github.com/saullocastro/scipy/blob/master/scipy/integrate/_cubature… > > When compiling the cython code I am getting the error: > > _cubature.obj : error LNK2019: unresolved external symbol hcubature > referenced in function __pyx_pf_9_cubature_fhcubature > C:\usr\scipy\scipy\integrate\_cubature.pyd : fatal error LNK1120: 1 > unresolved externals > error: command 'link.exe' failed with exit status 1120 > > Could you please have a look? > > Thank you very much! > Saullo > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev >

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Re: [SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 32
by Saullo Castro Aug. 24, 2013

Aug. 24, 2013

Dear all, I already contacted Steven Johnson about this matter and he told me that "relicensing the Cubature code is not feasible", but he agrees on including this in SciPy if the SciPy community agrees to include a GNU GPL licensed software there. Otherwise I will probably create a separate Python package for it, ideally with a pip installer, as suggested by him. Greetings, Saullo 2013/8/24 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. cubature license (alex) > 2. Re: cubature license (Matt Redmond) > 3. Re: cubature license (alex) > 4. Re: cubature license (Charles R Harris) > 5. Re: ANN: Scipy 0.13.0 beta 1 release (Jack Howarth) > 6. Re: SciPy-Dev Digest, Vol 118, Issue 31 (Saullo Castro) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Aug 2013 13:20:19 -0400 > From: alex <argriffi(a)ncsu.edu> > Subject: [SciPy-Dev] cubature license > To: scipy-dev(a)scipy.org > Message-ID: > <CAE5GFc+F+gxTctEcJLxO_wRadVLOE= > o0XGDEVNy0hb0qu0ip0g(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > I noticed on the mailing list that someone wants to put cubature into > scipy. You will need to ask Steven Johnson before this can happen > because scipy is licensed in a way that does not allow it to accept > GPL code. Actually now that I read more, this will probably not > happen anyway because cubature itself depends on multiple GPL-licensed > codes. > http://mail.scipy.org/pipermail/scipy-dev/2013-August/thread.html > http://ab-initio.mit.edu/wiki/index.php/Cubature > > Alex > > > ------------------------------ > > Message: 2 > Date: Fri, 23 Aug 2013 11:18:09 -0700 > From: Matt Redmond <mrdmnd(a)mit.edu> > Subject: Re: [SciPy-Dev] cubature license > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: > < > CABTWFhGzjRPgDRmc5Q3csTAiN3yLMk8H6qP_Rvxo15RPRNo0Mg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I took a number of his classes at MIT, and I'm fairly sure he'd be on board > with this usage. He seemed pretty supportive of SciPy. > > > On Fri, Aug 23, 2013 at 10:28 AM, Matt Redmond <mttrdmnd(a)gmail.com> wrote: > > > I'll ask him - I took his classes at MIT and I'm fairly sure he'd be okay > > with this. > > > > > > On Fri, Aug 23, 2013 at 10:20 AM, alex <argriffi(a)ncsu.edu> wrote: > > > >> I noticed on the mailing list that someone wants to put cubature into > >> scipy. You will need to ask Steven Johnson before this can happen > >> because scipy is licensed in a way that does not allow it to accept > >> GPL code. Actually now that I read more, this will probably not > >> happen anyway because cubature itself depends on multiple GPL-licensed > >> codes. > >> http://mail.scipy.org/pipermail/scipy-dev/2013-August/thread.html > >> http://ab-initio.mit.edu/wiki/index.php/Cubature > >> > >> Alex > >> _______________________________________________ > >> SciPy-Dev mailing list > >> SciPy-Dev(a)scipy.org > >> http://mail.scipy.org/mailman/listinfo/scipy-dev > >> > > > > > > > > -- > > Matthew Redmond > > Massachusetts Institute of Technology > > Department of Mathematics, Course 18C > > Class of 2013 > > >

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Re: [SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 31
by Saullo Castro Aug. 24, 2013

Aug. 24, 2013

@Nate, I don't know all the details about this algorithm, but based on the tests I've performed here it requires much fewer function evaluations than dblquad or tplquad, since it is NOT a recursive call of 1D-integrands. It offers two refinement options: h-cubature which refines by including more integration points p-cubature which refines by increasing the approximation order (better for smooth functions) I will keep working on that and I hope to give you a better feedback very soon. Please, see more details here: http://ab-initio.mit.edu/wiki/index.php/Cubature Greetings, Saullo 2013/8/23 <scipy-dev-request(a)scipy.org> > Send SciPy-Dev mailing list submissions to > scipy-dev(a)scipy.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://mail.scipy.org/mailman/listinfo/scipy-dev > or, via email, send a message with subject or body 'help' to > scipy-dev-request(a)scipy.org > > You can reach the person managing the list at > scipy-dev-owner(a)scipy.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SciPy-Dev digest..." > > > Today's Topics: > > 1. Re: Loss of precision using lsoda f2py interface or ode class > (Joris Vankerschaver) > 2. Re: Need some help to wrap the cubature package in > scipy/integrate (Nathan Woods) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Aug 2013 14:56:49 +0200 > From: Joris Vankerschaver <jvankers(a)gmail.com> > Subject: Re: [SciPy-Dev] Loss of precision using lsoda f2py interface > or ode class > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: <504DC808-6E3E-436B-A936-696B51834882(a)gmail.com> > Content-Type: text/plain; charset=us-ascii > > On 23-aug-2013, at 02:15, Juan Luis Cano wrote: > > I fear odeint/ode bugs are starting to pile up (gh-1567, gh-1801, > > gh-1976, gh-2515, gh-2570), and as many have suggested in the past a > > rewrite or redesign would be quite helpful. > > This may have been pointed out before, but one inconsistency that should > be fixed in an eventual redesign is that scipy.integrate.ode expects an RHS > of the form `f(t, y0, ...)` whereas odeint expects an RHS with the first > two parameters reversed, i.e. of the form `f(y0, t, ...)`. The former > convention is the standard in Matlab and Sage. > > All the best, > Joris > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 23 Aug 2013 10:22:01 -0600 > From: Nathan Woods <charlesnwoods(a)gmail.com> > Subject: Re: [SciPy-Dev] Need some help to wrap the cubature package > in scipy/integrate > To: SciPy Developers List <scipy-dev(a)scipy.org> > Message-ID: <-1837672449859755872@unknownmsgid> > Content-Type: text/plain; charset="iso-8859-1" > > We just had a multidimensional integrator (nquad) wrapped into the latest > beta version of scipy. How does cubature compare? I've been kicking around > the idea of improving the speed of nquad by moving more of the code to a > compiled language. How would that compare? > > Nate > > > On Aug 23, 2013, at 5:35 AM, Saullo Castro <saullogiovani(a)gmail.com> > wrote: > > I am wrapping the Cubature package for multi-dimensional integration that > supports vector-valued functions and offers both fixed and adaptive > integration schemes. > > Please, see more details here: > http://ab-initio.mit.edu/wiki/index.php/Cubature > > I've forked the scipy repository and my current attempt can be directly > accessed here: > > > https://github.com/saullocastro/scipy/blob/master/scipy/integrate/_cubature… > > When compiling the cython code I am getting the error: > > _cubature.obj : error LNK2019: unresolved external symbol hcubature > referenced in function __pyx_pf_9_cubature_fhcubature > C:\usr\scipy\scipy\integrate\_cubature.pyd : fatal error LNK1120: 1 > unresolved externals > error: command 'link.exe' failed with exit status 1120 > > Could you please have a look? > > Thank you very much! > Saullo > > _______________________________________________ > SciPy-Dev mailing list > SciPy-Dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev >

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