On Feb 11, 9:45 am, William Stein <wst...@gmail.com> wrote:
> On Wed, Feb 11, 2009 at 6:52 AM, Simon King <k...@mathematik.uni-jena.de>
> wrote:
Hi,
> > Dear sage developers,
>
> > some people, including myself, believe that Sage should contain more
> > tools for topology. E.g., there was a thread
> >http://groups.google.com/group/sage-devel/browse_thread/thread/5bd11c...
> > about simplicial complexes and their homology.
>
> > John Palmieri has sent a post to some algebraic topology list (https://
> > lists.lehigh.edu/mailman/listinfo/algtop-l), pointed the people to
> > Sage and asked for contribution. Thank you, John!
>
> I very much hope Algebraic Topology will be a theme at Sage Days 15:
>
> http://wiki.sagemath.org/days15
>
> Simon -- any chance you will be able to go to that?
>
> > Being subscriber of that list, I added that one way to contribute is
> > to point us to existing software packages. So far, there was one
> > answer (concerning "plex", see below).
>
> > My question: How should the work on inclusion of topology software be
> > organized? Should one open a single trac ticket (essentially
> > complaining that there is not enough topology around), on which
> > suggestions for inclusions are collected?
>
> No! A wiki.sagemath.org page and email discussion would be much
> better for that.
Yes, and any spkg would need to make the journey from experimental to
optional to finally standard in case they are portable and voted in.
> > Or should the collection be
> > on this thread, with one separate ticket for each suggestion?
>
> Yes.
Well, without an spkg don't open a ticket.
> > Here are three suggestions:
> > 1. Simplicial complexes / Homology (see thread above)
> > I asked Frank Lutz, and he said that Polymake had a module 'topaz'
> > that can compute homology. However, in a recent Polymake upgrade,
> > topaz was removed from the distribution, due to some compiler problem.
> > So, it might make sense to wait for on upgrade of topaz.
Polymake does not have a chance to become standard in Sage as long as
they use C++ template meta programming (it is code that compiles quite
a long time) and they keep on with theit plan to build future releases
on something that runs via a shared memory interface to Perl. The code
is just not portable and after some discussion last year pointing out
various problems with that approach I don't see the developers
changing their minds on that.
> > 2. SnapPea
> > SnapPea is a program for creating and studying hyperbolic 3-manifolds
> > (http://www.geometrygames.org/SnapPea-old/index.html). It seems to be
> > widely used by computational topologists. AFAIK it can deal with ideal
> > triangulations, compute volume, has a census of hyperbolic manifolds,
> > can also work with hyperbolic knots, etc.
> > If I understand correctly, it is under GNU GPL and may be used as a
> > Python module.
>
> A longtime Sage user -- Nathan Dunfield -- I think wrote the Python
> interface, and uses SnapPea from Sage for his research.
>
> > 3. Plex (suggestion of Ryan Lewis from the above-mentioned topology
> > list)
> > Plex is a software package for computing persistent homology of finite
> > simplicial complexes, often generated from point cloud data (http://
> > comptop.stanford.edu/programs/jplex/index.html).
>
> > 4. I found a link to a list of topology related software:
> >http://www.math.uiuc.edu/~nmd/computop/
> > Some of these might be interesting.
>
> > I am not sure if Plex really is an option for Sage. Previous versions
> > were written for Matlab. The current version is written in Java and
> > can also run in a standalone mode, using an integrated Java
> > interpreter, called Beanshell. Dunno if that works for Sage.
>
> It's an option as an optional package. I doubt it will be standard,
> but I doubt anything big will be added to standard sage anytime _this_
> year due to porting being the number one goal.
Well, the main problem is not that we are porting Sage, the main
problem is that any piece of software out there does not work out of
the box on the platforms we want it to and in most cases upstream is
content with the platform support that they have. Often enough their
build systems have issues that need to be fixed to bring it up to the
standard we want in Sage.
> But that shouldn't
> stop anybody from writing good interfaces between Sage and other
> software. There's no a priori reason that there shouldn't be an
> excellent Sage <--> X interface for all math software X.
+1
> -- William
Cheers,
Michael
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