[SciPy-Dev] cubature license

Warren Weckesser warren.weckesser@gmail....
Sat Aug 24 09:47:01 CDT 2013


On 8/24/13, Saullo Castro <saullogiovani@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).

But don't let that stop you from creating a python wrapper as a
separate project.  That's a great idea, and I'm sure a lot of folks
will appreciate it.

Warren


>
> Saullo
>
> 2013/8/24 <scipy-dev-request@scipy.org>
>
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>>    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@gmail.com>
>> Subject: Re: [SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 32
>> To: Scipy-Dev <scipy-dev@scipy.org>
>> Message-ID:
>>         <CAHbwRz50dGBAp50xPXvcG+HV=
>> XQotXJFdU0YqQQdbTMNLru8_Q@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@scipy.org>
>>
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>> > 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@ncsu.edu>
>> > Subject: [SciPy-Dev] cubature license
>> > To: scipy-dev@scipy.org
>> > Message-ID:
>> >         <CAE5GFc+F+gxTctEcJLxO_wRadVLOE=
>> > o0XGDEVNy0hb0qu0ip0g@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@mit.edu>
>> > Subject: Re: [SciPy-Dev] cubature license
>> > To: SciPy Developers List <scipy-dev@scipy.org>
>> > Message-ID:
>> >         <
>> > CABTWFhGzjRPgDRmc5Q3csTAiN3yLMk8H6qP_Rvxo15RPRNo0Mg@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@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@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@scipy.org
>> > >> http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > >>
>> > >
>> > >
>> > >
>> > > --
>> > > Matthew Redmond
>> > > Massachusetts Institute of Technology
>> > > Department of Mathematics, Course 18C
>> > > Class of 2013
>> > >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL:
>> >
>> http://mail.scipy.org/pipermail/scipy-dev/attachments/20130823/c51a46f9/attachment-0001.html
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Fri, 23 Aug 2013 14:27:45 -0400
>> > From: alex <argriffi@ncsu.edu>
>> > Subject: Re: [SciPy-Dev] cubature license
>> > To: SciPy Developers List <scipy-dev@scipy.org>
>> > Message-ID:
>> >         <
>> > CAE5GFcJdW_4iW5Fbqe+7uAhGO2nMmN2+aDxTJSsz9DubFDeAeA@mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > On Fri, Aug 23, 2013 at 2:18 PM, Matt Redmond <mrdmnd@mit.edu> wrote:
>> > > 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@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@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@scipy.org
>> > >>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > >>
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Matthew Redmond
>> > >> Massachusetts Institute of Technology
>> > >> Department of Mathematics, Course 18C
>> > >> Class of 2013
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > SciPy-Dev mailing list
>> > > SciPy-Dev@scipy.org
>> > > http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > >
>> >
>> > Even if he would personally be on board with this usage, the following
>> > bit makes it complicated.
>> >
>> > "Our code is based in part on code borrowed from the HIntLib
>> > numeric-integration library by Rudolf Sch?rer and from code for
>> > Gauss-Kronrod quadrature (for 1d integrals) from the GNU Scientific
>> > Library, both of which are free software under the GNU GPL."
>> >
>> > Alex
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Fri, 23 Aug 2013 13:09:15 -0600
>> > From: Charles R Harris <charlesr.harris@gmail.com>
>> > Subject: Re: [SciPy-Dev] cubature license
>> > To: SciPy Developers List <scipy-dev@scipy.org>
>> > Message-ID:
>> >         <CAB6mnxKaknribvOT7U8qGLnt_sfXpXkvVZKbviksqHH1U=
>> > NFQA@mail.gmail.com>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Ah, memories. It might not be too hard to replace the Gauss-Kronrad
>> > quadrature, it was the first algorithm I implemented on a 80186 3MHz PC
>> > back in the days when Microsoft offered a Fortran compiler ;) I don't
>> know
>> > about the rest of the dependencies.
>> >
>> >
>> > On Fri, Aug 23, 2013 at 12:27 PM, alex <argriffi@ncsu.edu> wrote:
>> >
>> > > On Fri, Aug 23, 2013 at 2:18 PM, Matt Redmond <mrdmnd@mit.edu> wrote:
>> > > > 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@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@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@scipy.org
>> > > >>> http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > > >>
>> > > >>
>> > > >>
>> > > >>
>> > > >> --
>> > > >> Matthew Redmond
>> > > >> Massachusetts Institute of Technology
>> > > >> Department of Mathematics, Course 18C
>> > > >> Class of 2013
>> > > >
>> > > >
>> > > >
>> > > > _______________________________________________
>> > > > SciPy-Dev mailing list
>> > > > SciPy-Dev@scipy.org
>> > > > http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > > >
>> > >
>> > > Even if he would personally be on board with this usage, the
>> > > following
>> > > bit makes it complicated.
>> > >
>> > > "Our code is based in part on code borrowed from the HIntLib
>> > > numeric-integration library by Rudolf Sch?rer and from code for
>> > > Gauss-Kronrod quadrature (for 1d integrals) from the GNU Scientific
>> > > Library, both of which are free software under the GNU GPL."
>> > >
>> > > Alex
>> > > _______________________________________________
>> > > SciPy-Dev mailing list
>> > > SciPy-Dev@scipy.org
>> > > http://mail.scipy.org/mailman/listinfo/scipy-dev
>> > >
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL:
>> >
>> http://mail.scipy.org/pipermail/scipy-dev/attachments/20130823/efc1ee20/attachment-0001.html
>> >
>> > ------------------------------
>> >
>> > Message: 5
>> > Date: Fri, 23 Aug 2013 19:58:31 -0400
>> > From: Jack Howarth <howarth@bromo.med.uc.edu>
>> > Subject: Re: [SciPy-Dev] ANN: Scipy 0.13.0 beta 1 release
>> > To: SciPy Developers List <scipy-dev@scipy.org>
>> > Message-ID: <20130823235831.GA6527@bromo.med.uc.edu>
>> > Content-Type: text/plain; charset=us-ascii
>> >
>> > On Thu, Aug 22, 2013 at 03:12:21PM +0200, Ralf Gommers wrote:
>> > > Hi all,
>> > >
>> > > I'm happy to announce the availability of the first beta release of
>> Scipy
>> > > 0.13.0. Please try this beta and report any issues on the scipy-dev
>> > mailing
>> > > list.
>> > >
>> > > Source tarballs and release notes can be found at
>> > > https://sourceforge.net/projects/scipy/files/scipy/0.13.0b1/. Windows
>> > and
>> > > OS X installers will follow later (we have a minor infrastructure
>> > > issue
>> > to
>> > > solve, and I'm at EuroScipy now).
>> > >
>> > > Cheers,
>> > > Ralf
>> >
>> > Ralf,
>> >    FYI, if the proposed elimination of support for the Accelerate
>> > framework on
>> > darwin was implemented in scipy 0.13, you will definietely want to
>> > consider reverting that
>> > change. It appears that the issues in the Accelerate framework (at
>> > least
>> as
>> > tested with scipy 0.12.0) are resolved in the next darwin release...
>> >
>> > Ran 6134 tests in 88.016s
>> >
>> > OK (KNOWNFAIL=15, SKIP=36)
>> >
>> > compared to darwin12...
>> >
>> > Ran 6134 tests in 96.886s
>> >
>> > FAILED (KNOWNFAIL=15, SKIP=36, failures=63)
>> >
>> > and darwin11...
>> >
>> > Ran 6134 tests in 118.346s
>> >
>> > FAILED (KNOWNFAIL=15, SKIP=36, failures=65)
>> >
>> >              Jack
>> > ps I have looked at the proposed replacement of using openblas and it
>> > is
>> > rather suboptimal. Please
>> > don't inflict that on us.
>> >
>> > > _______________________________________________
>> > > SciPy-Dev mailing list
>> > > SciPy-Dev@scipy.org
>> > > http://mail.scipy.org/mailman/listinfo/scipy-dev
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 6
>> > Date: Sat, 24 Aug 2013 10:29:12 +0200
>> > From: Saullo Castro <saullogiovani@gmail.com>
>> > Subject: Re: [SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 31
>> > To: Scipy-Dev <scipy-dev@scipy.org>
>> > Message-ID:
>> >         <CAHbwRz4ihS6YzevgPdDZ131=
>> > QgOrSRjJBjRn1t8saN4L0sq-JA@mail.gmail.com>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > @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@scipy.org>
>> >
>> > > Send SciPy-Dev mailing list submissions to
>> > >         scipy-dev@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@scipy.org
>> > >
>> > > You can reach the person managing the list at
>> > >         scipy-dev-owner@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@gmail.com>
>> > > Subject: Re: [SciPy-Dev] Loss of precision using lsoda f2py interface
>> > >         or ode  class
>> > > To: SciPy Developers List <scipy-dev@scipy.org>
>> > > Message-ID: <504DC808-6E3E-436B-A936-696B51834882@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@gmail.com>
>> > > Subject: Re: [SciPy-Dev] Need some help to wrap the cubature package
>> > >         in      scipy/integrate
>> > > To: SciPy Developers List <scipy-dev@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@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.pyx
>> > >
>> > > 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
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