Sage Optional Packages

        sage -i db-jones-2005-11-02

Beautiful Soup is a Python HTML/XML parser designed for quick turnaround 
projects like screen-scraping. It is designed for handling badly written html,
so it provides a robust foundation to handle html code generated by tinyMCE.

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

Brian is a simulator for spiking neural networks available on almost all 
platforms. The motivation for this project is that a simulator should not only 
save the time of processors, but also the time of scientists.

Brian is easy to learn and use, highly flexible and easily extensible. The Brian
 package itself and simulations using it are all written in the Python 
programming language, which is an easy, concise and highly developed language 
with many advanced features and development tools, excellent documentation and a
 large community of users providing support and extension packages.

CHomP stands for "Computational Homology Project," and it is a
collection of software for homology computation.  It includes both
command-line functions and a C++ library.

Website: http://chomp.rutgers.edu

Contains a database of all exceptional mutation classes of quivers.

 Every file in the database is of the form ``mutation_classes_n.dig6`` for some ``n`` and
 - contains a ``cPickle.dump`` of a dictionary where
   - the keys are tuples representing irreducible exceptional quiver mutation types of rank ``n``, and
   - the values are all quivers in the given mutation class stored in canonical form as ``(dig6,edges)`` where
     - ``dig6`` is the dig6 data of the given ``DiGraph``, and
     - ``edges`` are the non-simply-laced edges thereof.
 - is obtained by running the function
 ``sage.combinat.cluster_algebra_quiver.quiver_mutation_type._save_data_dig6(n, types

This package wraps Fokko Ducloux's Coxeter 3 C++ library

Features:

- General Coxeter groups, implemented through the combinatorics of reduced words;
- Reduced expression and normal form computations;
- Bruhat ordering;
- Ordinary Kazhdan-Lusztig polynomials;
- Kazhdan-Lusztig polynomials with unequal parameters;
- Inverse Kazhdan-Lusztig polynomials;
- Cells and W-graphs;

http://math.univ-lyon1.fr/~ducloux/coxeter/coxeter3/english/coxeter3_e.html

2009/10/18 - version 1.0 - Initial version
* add cunningham_prime_factors

The open source software GINV implements the Gröbner bases method for
systems of equations.

GINV is a C++ module of Python designed for constructing Gröbner bases
of ideals and modules in polynomial, differential and difference
rings.

Gröbner bases are constructed by involutive algorithms. 

Gnuplot.py is a Python package that interfaces to gnuplot. It allows you to use gnuplot from within Python to plot arrays of data from memory, data files, or mathematical functions.

Guppy-PE is a library and programming environment for Python, currently providing in particular the Heapy subsystem, which supports object and heap memory sizing, profiling and debugging. It also includes a prototypical specification language, the Guppy Specificaion Language (GSL), which can be used to formally specify aspects of Python programs and generate tests and documentation from a common source.

Website: http://pypi.python.org/pypi/guppy/0.1.8

Java 3d libraries.

PACKAGE MAINTAINER: Robert Bradshaw

This is a binary of KASH from:  http://www.math.tu-berlin.de/~kant/download.html

It works on OS X and Linux, but nothing else, since that's all that is available for KASH.
The Linux binary is 32-bit only, but will run on 64-bit boxes in 32-bit mode. 

Programming notebook for the web

LiE is the name of a software package that enables mathematicians and
physicists to perform computations of a Lie group theoretic nature. It
focuses on the representation theory of complex semisimple (reductive)
Lie groups and algebras, and on the structure of their Weyl groups and
root systems.

LiE does not compute directly with elements of the Lie groups and
algebras themselves; it rather computes with weights, roots, characters
and similar objects. Some specialities of LiE are: tensor product
decompositions, branching to subgroups, Weyl group orbits, reduced
elements in Weyl groups, distinguished coset representatives and much
more. These operations have been compiled into the program which results
in fast execution: typically one or two orders of magnitude faster than
similar programs written in a general purpose program.

The LiE programming language makes it possible to customise and extend
the package with more mathematical functions. A user manual is provided
containing many examples.

LiE establishes an interactive environment from which commands can be
given that involve basic programming primitives and powerful built-in
functions. These commands are read by an interpreter built into the
package and passed to the core of the system. This core consists of
programs representing some 100 mathematical functions. The interpreter
offers on-line facilities which explain operations and functions, and
which give background information about Lie group theoretical concepts
and about currently valid definitions and values. 

(from http://www-math.univ-poitiers.fr/~maavl/LiE/description.html )

MPI for Python (mpi4py) provides bindings of the Message Passing
Interface (MPI) standard for the Python programming language, allowing
any Python program to exploit multiple processors.

NZMATH is a Python based number theory oriented calculation system. 
It is developed at Tokyo Metropolitan University. It is freely available 
and distributed under the BSD license.

The Open MPI Project is an open source MPI-2 implementation that is
developed and maintained by a consortium of academic, research, and
industry partners. Open MPI is therefore able to combine the
expertise, technologies, and resources from all across the High
Performance Computing community in order to build the best MPI library
available. Open MPI offers advantages for system and software vendors,
application developers and computer science researchers.

A Sage implementation of Ore algebras and Ore polynomials. 

Main features for the most common algebras include basic arithmetic and actions;
gcrd and lclm; D-finite closure properties; natural transformations between
related algebras; guessing; desingularization; solvers for polynomials, rational
functions and (generalized) power series. 

Modular Cohomology Rings of Finite Groups

The documentation of the package is provided at 
http://sage.math.washington.edu/home/SimonKing/Cohomology/

PHCpack: a general-purpose solver for polynomial systems by homotopy continuation.

Website: http://www2.math.uic.edu/~jan/PHCpack/phcpack.html

Pybtex is a drop-in replacement for BibTeX written in Python. That is,
you can run 'pybtex FILE' instead of 'bibtex FILE'.

We use the bazaar trunk because it is less buggy and more feature-rich.
The latest version is available through this command:

    bzr branch lp:pybtex


This package also installs pyparsing and PyYAML which are needed for pybtex.

PyQt is a set of Python bindings for Nokia's Qt application framework and runs on all platforms supported by Qt including Windows, MacOS/X and Linux. This package provides the X11 bindings.

From 

   http://pyx.sourceforge.net/

From the README.txt of Qhull:

Qhull computes convex hulls, Delaunay triangulations, Voronoi diagrams,
furthest-site Voronoi diagrams, and halfspace intersections about a point.
It runs in 2-d, 3-d, 4-d, or higher.  It implements the Quickhull algorithm
for computing convex hulls.   Qhull handles round-off errors from floating
point arithmetic.  It can approximate a convex hull.

The program includes options for hull volume, facet area, partial hulls,
input transformations, randomization, tracing, multiple output formats, and
execution statistics.

SIP is a tool that makes it very easy to create Python bindings for C
and C++ libraries. It was originally developed to create PyQt, the
Python bindings for the Qt toolkit, but can be used to create bindings
for any C or C++ library.

GPL v2

Trac is an enhanced wiki and issue tracking system for software
development projects. Trac uses a minimalistic approach to web-based
software project management. It provides an interface to Subversion
(or other version control systems), an integrated Wiki and convenient
reporting facilities.