[SciPy-Dev] SciPy-Dev Digest, Vol 118, Issue 32

Saullo Castro saullogiovani@gmail....
Sat Aug 24 03:39:03 CDT 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@scipy.org>

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> 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
> >
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> ------------------------------
>
> 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
> >
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> ------------------------------
>
> 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
> >
> > _______________________________________________
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