Re: r12855 - /1.3/docs/latex/install.tex -- June 09, 2011 - 14:09

That's a good idea, then it is harder to forget.  It will involve a
lot of work, to have relax compile with QUADPACK linked in.  Would you
like to have the honours of opening the task?  :)

Regards,

Edward



On 9 June 2011 13:44, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi Ed,
>
> I don't have time as well at the moment... but it would certainly be a good
> thing to do !
>
> Maybe we should create a task..?
>
>
> Séb  :)
>
>
> On 11-06-07 11:36 AM, Edward d'Auvergne wrote:
> > Hi,
> >
> > I was thinking of developing our own interface to that single function
> > of QUADPACK.  But scipy is under the BSD licence, so we can use their
> > interface directly within relax.  Or at least we could see how they
> > have done it, with compilation, etc.  It would be good to eliminate
> > that one, but I don't have time at the moment to dig deeply into it.
> > I have too many papers to write up at this point ;)
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> >
> >
> > On 7 June 2011 09:57, Sébastien Morin<sebastien.morin.1@xxxxxxxxx>  wrote:
> > > Hi Ed,
> > >
> > > Integrating Scipy as well (or only the part of Scipy needed for relax)
> > > would
> > > be a very good idea and would make our system independent of the future
> > > changes and bugs, etc.
> > >
> > > Since this is a single function being used from Scipy, would a similar
> > > function be available elsewhere ?  As from the Scipy website, "The
> > > package
> > > scipy.integrate does two things: integration (or quadrature), and solving
> > > differential equations." I guess this is pretty general and a similar
> > > function out of Scipy should exist...
> > >
> > > After a quick search, I found a Python module capable of this and named
> > > "FuncDesigner" (http://openopt.org/FuncDesigner).
> > >
> > > Also, what about interfacing directly with the Fortran library QUADPACK ?
> > > Is
> > > this too complicated ?
> > >
> > >
> > > Séb  :)
> > >
> > >
> > > On 11-06-06 6:14 PM, Edward d'Auvergne wrote:
> > > > The following link would be important for this integration:
> > > > http://scipy.org/Installing_SciPy/BuildingGeneral
> > > >
> > > > Regards,
> > > >
> > > > Edward
> > > >
> > > > On 6 June 2011 18:10, Edward d'Auvergne<edward@xxxxxxxxxxxxx>    wrote:
> > > > > Hi,
> > > > >
> > > > > I was hoping to get the numerical integration from Scipy into relax as
> > > > > well, but this is far more complicated.  I only use the
> > > > > scipy.integrate.quad() function, which is simply an interface for a
> > > > > function from the Fortran library QUADPACK
> > > > >
> > > > >
> > > > > (http://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.quad.html).
> > > > >  It is a BSD licence, so it can be legally integrated into relax.  But
> > > > > is will probably require code compilation.  I haven't looked into it
> > > > > in detail, but I'm guessing it could be done.
> > > > >
> > > > > Cheers,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 4 June 2011 08:44, Sébastien Morin<sebastien.morin.1@xxxxxxxxx>
> > > > >  wrote:
> > > > > > Hi Ed,
> > > > > >
> > > > > > That's a very good idea !
> > > > > >
> > > > > > Less dependencies means an easier access for users (and potentially a
> > > > > > more
> > > > > > stable code)..!
> > > > > >
> > > > > > Are there any other dependencies you plan to include into relax's
> > > > > > source
> > > > > > code ???
> > > > > >
> > > > > > Cheers,
> > > > > >
> > > > > >
> > > > > > Séb  :)
> > > > > >
> > > > > >
> > > > > > On 11-06-03 6:34 PM, edward@xxxxxxxxxxxxx wrote:
> > > > > > > Author: bugman
> > > > > > > Date: Fri Jun  3 18:34:53 2011
> > > > > > > New Revision: 12855
> > > > > > >
> > > > > > > URL: http://svn.gna.org/viewcvs/relax?rev=12855&view=rev
> > > > > > > Log:
> > > > > > > Removed Scientific python from the dependency list in the user
> > > > > > > manual.
> > > > > > >
> > > > > > >
> > > > > > > Modified:
> > > > > > >     1.3/docs/latex/install.tex
> > > > > > >
> > > > > > > Modified: 1.3/docs/latex/install.tex
> > > > > > > URL:
> > > > > > >
> > > > > > >
> > > > > > > http://svn.gna.org/viewcvs/relax/1.3/docs/latex/install.tex?rev=12855&r1=12854&r2=12855&view=diff
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > ==============================================================================
> > > > > > > --- 1.3/docs/latex/install.tex (original)
> > > > > > > +++ 1.3/docs/latex/install.tex Fri Jun  3 18:34:53 2011
> > > > > > > @@ -14,7 +14,6 @@
> > > > > > >  \begin{description}
> > > > > > >  \item[\href{http://python.org/}{Python}\index{Python}:]  Version 2.5
> > > > > > > or
> > > > > > > higher.
> > > > > > >  \item[\href{http://numpy.scipy.org/}{NumPy}\index{NumPy}:]  Version
> > > > > > > 1.0.4
> > > > > > > or higher.  This package is used for most of the numerical
> > > > > > > calculations
> > > > > > > within relax.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > -\item[\href{http://starship.python.net/~hinsen/ScientificPython/}{ScientificPython}\index{ScientificPython}:]
> > > > > > >  Version 2.8 or higher.  This is an optional package.  relax has an
> > > > > > > inbuilt
> > > > > > > PDB reader.  However, due to the diversity of the PDB with many files
> > > > > > > not
> > > > > > > conforming to the standard, this reader many not function for all
> > > > > > > files.  An
> > > > > > > alternative is to use the more advanced PDB reader that comes with
> > > > > > > ScientificPython.
> > > > > > >  \item[\href{http://www.scipy.org/}{SciPy}\index{SciPy}:]  Version
> > > > > > > 0.7.1
> > > > > > > or higher.  This package is also optional.  It is required only for
> > > > > > > the
> > > > > > > frame order theory analyses.
> > > > > > >  \item[\href{http://www.scipy.org/}{wxPython}\index{wxPython}:]
> > > > > > >  Version
> > > > > > > 2.8 or higher.  This package is optional.  It is required for the
> > > > > > > operation
> > > > > > > of the graphical user interface (GUI)\index{GUI}.
> > > > > > >  \end{description}
> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > relax (http://nmr-relax.com)
> > > > > > >
> > > > > > > This is the relax-commits mailing list
> > > > > > > relax-commits@xxxxxxx
> > > > > > >
> > > > > > > To unsubscribe from this list, get a password
> > > > > > > reminder, or change your subscription options,
> > > > > > > visit the list information page at
> > > > > > > https://mail.gna.org/listinfo/relax-commits
> > > > > >
> > > > > > --
> > > > > > Sébastien Morin, Ph.D.
> > > > > > Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> > > > > > Department of Structural Biology
> > > > > > Biozentrum, Universität Basel
> > > > > > Klingelbergstrasse 70
> > > > > > 4056 Basel
> > > > > > Switzerland
> > > --
> > > Sébastien Morin, Ph.D.
> > > Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> > > Department of Structural Biology
> > > Biozentrum, Universität Basel
> > > Klingelbergstrasse 70
> > > 4056 Basel
> > > Switzerland
>
> --
> Sébastien Morin, Ph.D.
> Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> Department of Structural Biology
> Biozentrum, Universität Basel
> Klingelbergstrasse 70
> 4056 Basel
> Switzerland