Sage /home/files/files-old/spkg/archive Packages

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

A software package for algebraic, geometric and combinatorial problems on linear spaces. Available at www.4ti2.de.

A software package for algebraic, geometric and combinatorial problems on linear spaces. Available at www.4ti2.de.

A software package for algebraic, geometric and combinatorial problems on linear spaces. Available at www.4ti2.de.

This spkg builds ATLAS for Sage. It is build per default on Linux and
Solaris, but should also work on OSX and Cygwin.

About

This is an optional spkg to build ATLAS for Sage. It mostly intended 
for Linux, but should also work on OSX and Unixes.

ChangeLog

* 20070815: Michael Abshoff <mashoff@fsmath.mathematik.uni-dortmund.de>
 + new upstream release (3.7.37), initial release

ToDo

* compile threading support confitionally
* break out the "make check"

About

This is an optional spkg to build ATLAS for Sage. It mostly intended 
for Linux, but should also work on OSX and Unixes.

Maintainer: Michael Abshoff

ChangeLog

* 20071006: Michael Abshoff <mashoff@fsmath.mathematik.uni-dortmund.de>
 + update to 3.7.38

* 20070815: Michael Abshoff <mashoff@fsmath.mathematik.uni-dortmund.de>
 + new upstream release (3.7.37), initial release
 + "make check" added in spkg-check

ToDo

* compile threading support confitionally

This package contains a recent version of Texinfo, GNU m4, and help2man.
It contains the git repository of autoconf, automake and libtool.

For the latter 3 packages (commonly referred to as "autotools"),
many different versions are installed, by checking out the versions
from the git repo and building/installing them separately. Since the
complete git repository is shipped in the spkg, this does not require
internet access.

For Texinfo, m4 and help2man, just one version is installed. These are
prerequisites for autotools. Moreover, Texinfo is often needed for
bootstrapping packages. Even though m4 is already a prerequisite of
Sage, autoconf requires an up-to-date version of GNU m4.

The package makes wrapper scripts in $SAGE_LOCAL/bin for the various
autotools, which call the "correct" version. This means that, if a file
"configure" already exists in the current directory, the same autoconf
version is run which created the original file. Otherwise, the latest
version is run. The goal of all this is to make it easier to patch
configure.ac or Makefile.am files inside a spkg. By using the same
version of autotools as originally used, the patch files should be
relatively small. The environment variables AUTOCONF_VERSION,
AUTOMAKE_VERSION and LIBTOOL_VERSION can be used to override the
chosen version.

This version of the axiom4sage package is built using a variant of the FriCAS fork of the Axiom project that uses hardware independent cached Lisp files to generate the executables.

Bill Page
July 29, 2007.

Benzene is a program for the efficient generation of all nonisomorphic fusenes and benzenoids with a given number of faces. Fusenes are planar polycyclic hydrocarbons with all bounded faces hexagons. Benzenoids are fusenes that are subgraphs of the hexagonal lattice.

1. Download from the web. (insert addresses here)

    
2.  Delete all the pdf's from egenix:

        rm egenix/mx/*/*.pdf egenix/mx/*/Doc/*

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.

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.

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.

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.

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.

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.

The Boehm-Demers-Weiser conservative garbage collector.

Describe the package here. 

Boost provides free peer-reviewed portable C++ source libraries.

We emphasize libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

We aim to establish "existing practice" and provide reference implementations so that Boost libraries are suitable for eventual standardization. Ten Boost libraries are already included in the C++ Standards Committee's Library Technical Report (TR1) and will be in the new C++0x Standard now being finalized. C++0x will also include several more Boost libraries in addition to those from TR1. More Boost libraries are proposed for TR2.

Website: http://www.boost.org/

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.

Buckygen is a program for the efficient generation of all nonisomorphic fullerenes. These are triangulations where all vertices have degree 5 or 6. Or if the dual representation is used: cubic plane graphs where all faces are pentagons or hexagons. 

Buckygen is a program for the efficient generation of all nonisomorphic fullerenes. These are triangulations where all vertices have degree 5 or 6. Or if the dual representation is used: cubic plane graphs where all faces are pentagons or hexagons. 

bzip2 is a freely available, patent free, high-quality data compressor.
It typically compresses files to within 10% to 15% of the best available
techniques (the PPM family of statistical compressors), whilst being
around twice as fast at compression and six times faster at
decompression.

The Computational Infrastructure for Operations Research (COIN-OR**,
or simply COIN)  project is an initiative to spur the development of
open-source software for the operations research community.

The COIN Branch and Cut solver (CBC) is an open-source
mixed-integer program (MIP) solver written in C++. CBC is intended to
be used primarily as a callable library to create customized
branch-and-cut solvers. A basic, stand-alone executable version is
also available. CBC is an active open-source project led by John
Forrest at www.coin-or.org.

The Computational Infrastructure for Operations Research (COIN-OR**,
or simply COIN)  project is an initiative to spur the development of
open-source software for the operations research community.

The COIN Branch and Cut solver (CBC) is an open-source
mixed-integer program (MIP) solver written in C++. CBC is intended to
be used primarily as a callable library to create customized
branch-and-cut solvers. A basic, stand-alone executable version is
also available. CBC is an active open-source project led by John
Forrest at www.coin-or.org.

The Computational Infrastructure for Operations Research (COIN-OR**,
or simply COIN)  project is an initiative to spur the development of
open-source software for the operations research community.

The COIN Branch and Cut solver (CBC) is an open-source
mixed-integer program (MIP) solver written in C++. CBC is intended to
be used primarily as a callable library to create customized
branch-and-cut solvers. A basic, stand-alone executable version is
also available. CBC is an active open-source project led by John
Forrest at www.coin-or.org.

Includes ccache to allow for fast recompiles

Includes ccache to allow for fast recompiles

The C-library cddlib is a C implementation of the Double Description 
Method of Motzkin et al. for generating all vertices (i.e. extreme points)
and extreme rays of a general convex polyhedron in R^d given by a system 
of linear inequalities:

   P 

Cephes Mathematical Library. Latest Linux distribution, dated
6/4/00. Special functions and other goodies in C, including long
double precision routines for 68K, 386, and sparc processors. This is
the most complete distribution package of the function library (but
not the most up-to-date one). It includes these sections-- double: all
functions in 64-bit double precision; single: all available functions
in 32-bit single precision; long double: all available functions in
80-bit extended precision; 128bit: all available functions in 128-bit
long double precision; qlib: all functions in q-type extended (44 to
106 decimal) precision, includes a C++ class for the binary floating
point arithmetic and a q-type calculator program; c9x-complex: new C
language standard C9X data type for complex variables, header
complex.h for GNU C and functions in float complex, double complex,
and long double complex precisions.

Website: http://www.moshier.net/

Download: http://www.moshier.net/cephes-math-28.tar.gz

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

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

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

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

Cliquer is a set of C routines for finding cliques in an arbitrary
weighted graph. It uses an exact branch-and-bound algorithm recently
developed by Patr Ostergard.

Contains a small database of Conway polynomials.

Cremona's programs for enumerating and computating with elliptic curves
defined over the rational numbers.   (This is the culmination of over
30 years of hard work and careful polish.)

MAINTAINTERS: 
   * William Stein
   * John Cremona
   * Ralph Philip Weinmann


TODO:
   * must get rid of the -DLONG_IS_64_BIT -- see what is done in FLINT.
   * 
   

CryptoMiniSat is a SAT solver that aims to become a premiere SAT
  solver with all the features and speed of successful SAT solvers,
  such as MiniSat and PrecoSat. The long-term goals of CryptoMiniSat
  are to be an efficient sequential, parallel and distributed
  solver. There are solvers that are good at one or the other,
  e.g. ManySat (parallel) or PSolver (distributed), but we wish to
  excel at all.

  CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted
  by researchers and industry.

CryptoMiniSat is a SAT solver that aims to become a premiere SAT
  solver with all the features and speed of successful SAT solvers,
  such as MiniSat and PrecoSat. The long-term goals of CryptoMiniSat
  are to be an efficient sequential, parallel and distributed
  solver. There are solvers that are good at one or the other,
  e.g. ManySat (parallel) or PSolver (distributed), but we wish to
  excel at all.

  CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted
  by researchers and industry.

This is a fast SDP solver written in C, with a callable library

MAINTAINERS:
   * William Stein
   * Josh Kantor

----------------------------

Downloaded from 
   www.ee.ucla.edu/~vandenbe/cvxopt/

Removed the examples and doc directory to save 0.5MB space.

CVXOPT is a free software package for convex optimization based on the
Python programming language. It can be used with the interactive
Python interpreter, on the command line by executing Python scripts,
or integrated in other software via Python extension modules. Its main
purpose is to make the development of software for convex optimization
applications straightforward by building on Python's extensive
standard library and on the strengths of Python as a high-level
programming language.

Cython is a language that makes writing C extensions for the Python language as
easy as Python itself. Cython is based on the well-known Pyrex, but supports
more cutting edge functionality and optimizations.

The Cython language is very close to the Python language, but Cython additio-
nally supports calling C functions and declaring C types on variables and class
attributes. This allows the compiler to generate very efficient C code from
Cython code.

This makes Cython the ideal language for wrapping for external C libraries, and
for fast C modules that speed up the execution of Python code.

Website: http://www.cython.org/

John Cremona's huge database of elliptic curves

See:
http://www.warwick.ac.uk/staff/J.E.Cremona/ftp/data/
and
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

John Cremona's huge database of elliptic curves

See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

John Cremona's huge database of elliptic curves

See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

John Cremona's huge database of elliptic curves

See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

John Cremona's huge database of elliptic curves

See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

John Cremona's huge database of elliptic curves

See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
http://sage.math.washington.edu/cremona/INDEX.html

This is an optional package, not included by default.

GAP's databases of finite groups and table of marks.

The databases of GAP: finite groups and tables of marks

The databases of GAP: finite groups and tables of marks

The databases of GAP: finite groups and tables of marks

The databases of GAP: finite groups and tables of marks

The collection of optional PARI packages elldata, seadata, galpol,
nftables (galdata is included in the standard PARI spkg).
See http://pari.math.u-bordeaux.fr/packages.html

Docutils is a modular system for processing documentation into useful
formats, such as HTML, XML, and LaTeX. For input Docutils supports
reStructuredText, an easy-to-read, what-you-see-is-what-you-get
plaintext markup syntax.

dot2tex is a python module, whose purpose is to give graphs generated
by Graphviz a more LaTeX friendly look and feel. This is accomplished
by converting xdot output from Graphviz to a series of PSTricks or
PGF/TikZ commands.

http://www.fauskes.net/code/dot2tex/

dot2tex is a Python module, whose purpose is to give graphs generated
by Graphviz a more LaTeX friendly look and feel. This is accomplished
by converting xdot output from Graphviz to a series of PSTricks or
PGF/TikZ commands.

See http://www.fauskes.net/code/dot2tex/
or http://dot2tex.googlecode.com/

ECL is an implementation of the Common Lisp language as defined by the
ANSI X3J13 specification. The most relevant features:

 * A bytecodes compiler and interpreter.
 * Compiles Lisp also with any C/C++ compiler.
 * It can build standalone executables and libraries.
 * ASDF, Sockets, Gray streams, MOP, and other useful components.
 * Extremely portable.
 * A reasonable license.

ECL supports the operating systems Linux, FreeBSD, NetBSD, OpenBSD,
Solaris and Windows, running on top of the Intel, Sparc, Alpha and
PowerPC processors. Porting to other architectures should be rather
easy.

Website: http://ecls.sourceforge.net/

John Cremona's programs for enumerating and computing with elliptic
curves defined over the rational numbers. This is the culmination of
over 25 years of hard work.

MAINTAINER: 
    -- William Stein

I obtained the package from http://gforge.inria.fr/projects/ecm/

GMP-ECM - Elliptic Curve Method for Integer Factorization

Sources can be obtained from http://gforge.inria.fr/projects/ecm/

Includes two databases:

 * A small subset of the data in John Cremona's database of elliptic curves up
   to conductor 10000. See http://www.warwick.ac.uk/~masgaj/ftp/data/ or
   http://sage.math.washington.edu/cremona/INDEX.html
 * William Stein's database of interesting curves

FFLAS-FFPACK is a LGPL-2.1+ source code library for dense linear
algebra over word-size finite fields.

http://linalg.org/projects/fflas-ffpack

Obtained from:
  svn export https://flint.svn.sourceforge.net/svnroot/flint/trunk

Upstream maintainer: Bill Heart
Website: www.flintlib.org

2007-12-19 (Michael Abshoff):
  + update to FLINT 1.03
  + reenable mandatory "make check"

2007-12-16 (Michael Abshoff):
  + disable mandatory "make check"
  + remove -B flag in make check since it breaks make 2.79 and earlier

2007-12-10 (Michael Abshoff): Update to FLINT 1.02

2007-12-08 (Michael Abshoff): Update to FLINT 1.01

2007-12-06 (Michael Abshoff): Update to FLINT 1.00

2007-11-25 (Michael Abshoff): add "flint_stack_release();" in fmpz_poly.c:1485
           to avoid a memory leak. Deteced and fixed by Bill Hart

2007-11-24 (Michael Abshoff): upgraded to svn r1075

2007-10-02 (William Stein): upgraded to svn 1012

2007-10-02 (Robert Bradshaw): upgraded to svn r1068

Obtained from:
  svn export https://flint.svn.sourceforge.net/svnroot/flint/trunk

FLINT is a C library for doing number theory, written by William Hart and David Harvey.

Website: www.flintlib.org

FLINT is a C library for doing number theory, maintained by William Hart.

Website: www.flintlib.org

Renamed gfortran to gfortran-64 and added script called gfortran that injects "-m64" into the commandline.

This version of the axiom4sage package is built using a variant of the FriCAS fork of the Axiom project that uses hardware independent cached Lisp files to generate the executables.

Bill Page
July 29, 2007.

FriCAS is an advanced computer algebra system. Its capabilities range from calculus (integration and differentiation) to abstract algebra. It can plot functions and has an integrated help system.

FriCAS is a fork of the Axiom project -- its starting point was the wh-sandbox branch of the Axiom project. 

This version of the fricas package is built using hardware independent cached Lisp files to generate the executables.

FriCAS is an advanced computer algebra system. Its capabilities range from calculus (integration and differentiation) to abstract algebra. It can plot functions and has an integrated help system.

FriCAS is a fork of the Axiom project -- its starting point was the wh-sandbox branch of the Axiom project. 

This version of the fricas package is built using hardware independent cached Lisp files to generate the executables.

FriCAS is an advanced computer algebra system. Its capabilities range
from calculus (integration and differentiation) to abstract algebra. 
It can plot functions and has an integrated help system.

FriCAS is a fork of the Axiom project -- its starting point was the
wh-sandbox branch of the Axiom project.

This version of the fricas package is built using hardware independent
cached Lisp files to generate the executables.

FriCAS is an advanced computer algebra system. This package adds an
interface to the Aldor (http://www.aldor.org) compiler.

In addition to extending the FriCAS by writing new library code in the
builtin SPAD language, this package allows to compile Aldor code for
FriCAS.

Note that this package does not include the Aldor compiler itself and
can only be installed if Aldor is already available on the system.

The software package Frobby provides a number of computations on
monomial ideals. The current main feature is the socle of a monomial
ideal, which is largely equivalent to computing the maximal standard
monomials, the Alexander dual or the irreducible decomposition.

Operations on monomial ideals are much faster than algorithms designed
for ideals in general, which is what makes a specialized library for
these operations on monomial ideals useful.

The software package Frobby provides a number of computations on
monomial ideals. The current main feature is the socle of a monomial
ideal, which is largely equivalent to computing the maximal standard
monomials, the Alexander dual or the irreducible decomposition.

Operations on monomial ideals are much faster than algorithms designed
for ideals in general, which is what makes a specialized library for
these operations on monomial ideals useful.

The software package Frobby provides a number of computations on
monomial ideals. The current main feature is the socle of a monomial
ideal, which is largely equivalent to computing the maximal standard
monomials, the Alexander dual or the irreducible decomposition.

Operations on monomial ideals are much faster than algorithms designed
for ideals in general, which is what makes a specialized library for
these operations on monomial ideals useful.

This is a stripped-down version of GAP.  The databases, which are arch
independent, are in a separate package and doc and tests are removed.

PACKAGE MAINTAINERS: William Stein, Martin Albrecht, and David Joyner

** IMPORTANT **:
   When you update this package, be sure to put the guava package
   in the package directory!!

DELETED:
   doc -- some of documentation:
 rm *.bbl *.aux *.dvi *.idx *.ilg *.l* *.m* *.pdf *.toc  *.blg *.ind
 rm */*.bbl */*.aux */*.dvi */*.idx */*.ilg */*.l* */*.m* */*.pdf */*.ind */*.toc */*.blg

   tst -- tests
   bin -- some BIG windows programs, which we don't need since GAP
          is only going to be used via expect

DATABASES (separated out):
   small -- small group's database; will distribute separately.
   pkg/tomlib -- just contains the "Table of Marks"; distribute separately.
   prim
   trans

GAP is a system for computational discrete algebra, with particular
emphasis on Computational Group Theory. GAP provides a programming
language, a library of thousands of functions implementing algebraic
algorithms written in the GAP language as well as large data libraries
of algebraic objects. See also the overview and the description of the
mathematical capabilities. GAP is used in research and teaching for
studying groups and their representations, rings, vector spaces,
algebras, combinatorial structures, and more. The system, including
source, is distributed freely. You can study and easily modify or
extend it for your special use.

This is a stripped-down version of GAP.  The databases, which are
architecture-independent, are in a separate package.

NOTES:

 grape -- it hardcodes cc as compiler, which of course doesn't work.  I've changed to hardcode gcc
  as compiler, which is more likely to work.

Prepared by David Joyner (2006-21-05)

This directory contains several "official" and "undeposited"
GAP packages available from 
http://www.gap-system.org/Packages/packages.html. They are
all released under the GPL with the following exception:
(*) grape contains Brendon McKay's nauty program. 

To load a package, for example grape, into SAGE type
sage: gap('LoadPackage("grape")')
All these packages come with documentation in the
doc or htm subdirectory (e.g., for grape, it would be in
SAGEHOME/local/lib/gap-4.4.7/pkg/grape/htm).

A brief description of each package follows:

braid is a GAP package for computing with braids, covering curves, 
and Hurwitz spaces.

CTblLib - The GAP Character Table Library

DESIGN is a package for classifying, partitioning and studying block designs.

FactInt is a package providing routines for factoring integers, in particular:
    * Pollard's p-1
    * Williams' p+1
    * Elliptic Curves Method (ECM)
    * Continued Fraction Algorithm (CFRAC)
    * Multiple Polynomial Quadratic Sieve (MPQS)

GAPDoc is a package containing a definition of a structure for 
GAP documentation, based on XML. It also contains conversion 
programs for producing text-, DVI-, PDF- or HTML-versions of such 
documents, with hyperlinks if possible.

GRAPE is a package for computing with graphs and groups, and is primarily 
designed for constructing and analysing graphs related to groups, 
finite geometries, and designs.

HAP (Homological Algebra Programming) is a GAP package 
providing some functions for group cohomology computation. 

LAGUNA package provides functionality for calculation of the 
normalized unit group of the modular group algebra of the finite 
p-group and for investigation of Lie algebra associated with group 
algebras and other associative algebras.

SONATA ("System Of Nearrings And Their Applications") is a package 
which constructs finite nearrings and related objects.

TORIC is a GAP package for computing with toric varieties.

Several "official" and "undeposited" GAP packages available from 
http://www.gap-system.org/Packages/packages.html

Several "official" and "undeposited" GAP packages available from
http://www.gap-system.org/Packages/packages.html

Several "official" and "undeposited" GAP packages available from
http://www.gap-system.org/Packages/packages.html

Several "official" and "undeposited" GAP packages available from
http://www.gap-system.org/Packages/packages.html

Several "official" and "undeposited" GAP packages available from
http://www.gap-system.org/Packages/packages.html

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

The GNU Compiler Collection, including the C, C++ and Fortran compiler.

GDB, the GNU Project debugger, allows you to see what is going on
"inside" another program while it executes -- or what another program
was doing at the moment it crashed.

GNU dbm is a set of database routines that use extendible hashing and works similar to the standard UNIX dbm routines.

gf2x is a C/C++ software package containing routines for fast arithmetic
in GF(2)[x] (multiplication, squaring, GCD) and searching for
irreducible/primitive trinomials.

Website: http://gf2x.gforge.inria.fr/

From http://www.math.tu-berlin.de/~jensen/software/gfan/gfan.html: 

Gfan is a software package for computing Groebner fans and tropical varieties.
These are polyhedral fans associated to polynomial ideals. The maximal cones
of a Groebner fan are in bijection with the marked reduced Groebner bases of
its defining ideal. The software computes all marked reduced Groebner bases of
an ideal. Their union is a universal Groebner basis. The tropical variety of a
polynomial ideal is a certain subcomplex of the Groebner fan. Gfan contains
algorithms for computing this complex for general ideals and specialized
algorithms for tropical curves, tropical hypersurfaces and tropical varieties
of prime ideals. In addition to the above core functions the package contains
many tools which are useful in the study of Groebner bases, initial ideals and
tropical geometry.

Git is a fast, scalable, distributed revision control system with an
    unusually rich command set that provides both high-operations and
    full access to internals.

    -- `man git`

Git is a fast, scalable, distributed revision control system with an
    unusually rich command set that provides both high-operations and
    full access to internals.

    -- `man git`

MAINTAINER:
   -- Martin Albrecht

-- 2007-11-02 Michael Abshoff
  * apply rpw's work aorund for OSX 10.5
  * add .hgignore

-- 2007-02-03 Martin Albrecht <malb@informatik.uni-bremen.de>
  * new upstream release: 3.2.6
  * Changes to upstream (everything else below is irrelevant): 
   ./src/library/poly1/givpoly1factor.h (2006-10-21 fix)
   ./src/kernel/zpz/givgfq.inl (2006-10-21 fix)
   ./src/kernel/zpz/givgfq.h  (2006-10-21 fix)
   ./aclocal.m4 64-bit (2006-10-29 fix)
   ./src/library/poly1/givpoly1padic.h (2006-11-09 fix)

-- 2006-12-15 William Stein
   I don't know why, but I had to comment out
   Rep& amxy( Rep& r, const Rep& a, const Rep& b, const Rep& c ) const
   { return Integer::amxy(r,a,b,c); }
in
   src/kernel/integer/givinteger.h
in order to get Givaro to compile on my computer.  I'm guessing maybe
amxy was deprecated from the C++ stl?

-- 2006-12-10 Martin Albrecht <malb@informatik.uni-bremen.de>
 * delete[] not delete where new[] in GivaroMM

-- 2006-11-09 Martin Albrecht <malb@informatik.uni-bremen.de>
 * GCC 4.0.0 on OSX PPC boxes doesn't seem to like "using Poly1Dom<Domain,Dense>::_domain" so we work around this
   in givpoly1padic.h

-- 2006-10-29 Martin Albrecht <malb@informatik.uni-bremen.de>
  * replaced macro AC_LIBTOOL_SYS_DYNAMIC_LINKER with same macro from libtool 1.5.23a in aclocal.m4 to fix build
     on x86-64 systems as suggested by Kate Minola

-- 2006-10-21 Martin Albrecht <malb@informatik.uni-bremen.de> 
 * ported constructor with modulus parameter from linbox to givaro
 * added sage_generator() which returns the generator 

Givaro is a C++ library for arithmetic and algebraic computations. Its
main features are implementations of the basic arithmetic of many
mathematical entities: Primes fields, Extensions Fields, Finite
Fields, Finite Rings, Polynomials, Algebraic numbers, Arbitrary
precision integers and rationals (C++ wrappers over gmp) It also
provides data-structures and templated classes for the manipulation of
basic algebraic objects, such as vectors, matrices (dense, sparse,
structured), univariate polynomials (and therefore recursive
multivariate).

Website: http://www-lmc.imag.fr/CASYS/LOGICIELS/givaro/

SPKG Repository: https://bitbucket.org/malb/givaro-spkg

The GLPK (GNU Linear Programming Kit) package is intended for solving
large-scale linear programming (LP), mixed integer programming (MIP),
and other related problems. It is a set of routines written in ANSI C
and organized in the form of a callable library. 

GLPK supports the GNU MathProg modelling language, which is a subset of
the AMPL language. 

The GLPK package includes the following main components:

 * primal and dual simplex methods
 * primal-dual interior-point method
 * branch-and-cut method
 * translator for GNU MathProg
 * application program interface (API)
 * stand-alone LP/MIP solver 

NOTE: When upgrading GMP, don't forget to update the spkg-install
script for polymake.

A database of graphs. Created by Emily Kirkman based on the work of Jason
Grout. Since April 2012 it also contains the ISGCI graph database.

Caution: this code is GPL incompatible, so it cannot become a standard spkg.

Website: http://www.gnu.org/software/gsl/

From the website above: The GNU Scientific Library (GSL) is a numerical 
library for C and C++ programmers. It is free software under the GNU General 
Public License.

The library provides a wide range of mathematical routines such as random 
number generators, special functions and least-squares fitting. There are 
over 1000 functions in total with an extensive test suite. If the variable
SAGE_CHECK is exported to the value "yes" when building Sage, GSL's test suite
is run. 

GNU libiconv is a library that is used to enable different
languages, with different characters to be handled properly.

AUTHORS: 
   -- William Stein (2007-02-14)

Get it from 
  http://www.cs.uwaterloo.ca/~z4chen/iml.html

1. I had to put the built version of src/repl in that directory, since on OS X it won't build.
   It's basically empty, so this seems safe.

2. I had to src/config/install-sh executable.

3. I had to create src/cblas.h since on many systems it isn't installed anywhere!?
   I just used gsl_cblas.h for this purpose, which seems to work fine.

4. Modified some of the examples, and made build scripts that work.

5. *IMPORTANT*: Change lift to iml_lift in padiclift.* and nonsingsolve.*, since otherwise
   on OSX you'll have horrible weird conflict problems. 

IML is a free library of C source code which implements algorithms for
computing exact solutions to dense systems of linear equations over the
integers. IML is designed to be used with the ATLAS/BLAS library and
GMP bignum library. 

Written in portable C, IML can be used on both 32-bit and 64-bit
machines. It can be called from C++. 

Website: http://www.cs.uwaterloo.ca/~astorjoh/iml.html

From the IPython website:

IPython is a multiplatform, Free Software project (BSD licensed) that offers:

 * An enhanced Python shell designed for efficient interactive
   work. It includes many enhancements over the default Python shell,
   including the ability for controlling interactively all major GUI
   toolkits in a non-blocking manner.
 * A library to build customized interactive environments using Python
   as the basic language (but with the possibility of having extended
   or alternate syntaxes).
* A system for interactive distributed and parallel computing (this is
   part of IPython's new development).

Jinja2 is a library for Python 2.4 and onwards that is designed to be
flexible, fast and secure.

If you have any exposure to other text-based template languages, such
as Smarty or Django, you should feel right at home with Jinja2. It's
both designer and developer friendly by sticking to Python's
principles and adding functionality useful for templating
environments.

This updates jar files necessary for Jmol
to operate from the command line and the Notebook.
It does not contain the Notebook javascript library
jmol_lib.js or changes to Notebook or Sage code.

The jsMath image fonts provide a fall-back for rendering TeX
characters in browsers on computers that do not have the TeX fonts
installed.

The jsMath image fonts provide a fall-back for rendering TeX
characters in browsers on computers that do not have the TeX fonts
installed.

The jsMath image fonts provide a fall-back for rendering TeX
characters in browsers on computers that do not have the TeX fonts
installed.

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. 

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. 

MAINTAINERS:
    Josh Kantor
    William Stein

LattE (Lattice point Enumeration) Integrale solves  the problems of counting lattice points in and integration over convex polytopes. 

Michael Rubinstein's L-function calculator.

CoCoALib is a GPL C++ library for doing Computations in Commutative Algebra. 

fplll is a code distributed under the LGPL that LLL-reduces euclidean lattices.
Since version 3, it can also solve the shortest vector problem.

Website: http://perso.ens-lyon.fr/damien.stehle/fplll.html

This is the

M4RI: Library for matrix multiplication, reduction and inversion over
GF(2).  (See also m4ri/README for a brief overview.)

M4RIE: Library for matrix multiplication, reduction and inversion over
GF(2^k) for 2 <

libogg is the official reference library for the Ogg multimedia container format, and the native file and
stream format for the Xiph.org multimedia codecs. As with all Xiph.org technology is it an open format free
for anyone to use.

Website: http://www.xiph.org/ogg

This is libpng.

http://www.libpng.org/pub/png/libpng.html

This is libpng.

http://www.libpng.org/pub/png/libpng.html

libpng is the official PNG reference library. It supports almost all PNG
features, is extensible, and has been extensively tested for over 13 years.
The home site for development versions (i.e., may be buggy or subject to
change or include experimental features) is http://libpng.sourceforge.net/,
and the place to go for questions about the library is the png-mng-implement
mailing list.

Website: http://www.libpng.org/pub/png/libpng.html

libtheora is the official reference library for the Theora video codec.
Theora is a free and open video compression format from the Xiph.org Foundation.

Website: http://www.xiph.org/theora

1. Get it from:

2. Comment out the 
   #include <string.h> 
lines from both of
          * src/lie.h 
          * src/box/closure.c

3. Makefile -- I had to add -lcurses

1. Get it from:

2. Comment out the 
   #include <string.h> 
lines from both of
          * src/lie.h 
          * src/box/closure.c

3. Makefile -- I had to add -lcurses

*20070906: change default to link against ncurses, curses is uncommon on
modern Linux systems. Linking against curses will be better on Solaris.

[mabshoff]

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 )

From http://linalg.org/: LinBox is a C++ template library for exact,
high-performance linear algebra computation with dense, sparse, and
structured matrices over the integers and over finite fields.

*2007-09-03: merged LinBox ChangeSet 2803, which fixes #498 without the 
             performance regression of the initial workaround
             (mabshoff)


1. Modified charpoly.h and commentator.C

2. Added linboxwrap (malb)

3. Change the line in configure so tuning doesn't take like 30 minutes
   and crash the host computer!

       size_t n

Littlewood-Richardson Calculator

http://math.rutgers.edu/~asbuch/lrcalc/

* 2008-05-15 (Marshall Hampton)

*initial build

1. Deleted McGill-specific build stuff from makefile
2. Added SAGE_LOCAL gmp build locations

lrs implements the linear reverse search algorithm of Avis and Fukuda. 

See the homepage (http://cgm.cs.mcgill.ca/~avis/C/lrs.html)  for details.

Macaulay 2 is a software system devoted to supporting research in algebraic geometry and commutative algebra. 

Macaulay 2 is a software system devoted to supporting research in algebraic geometry and commutative algebra. 

CHANGES:

1. I changed M2/Macualay2/packages/Makefile.in to have the following
near the top.  This speeds up the build a lot and lets it complete
on OS X intel where there is a problem with two examples.

RemakeAllDocumentation ?

The following is in the patches subdirectory.  It is copied in during
the build process.

* I replaced setupext.py by a version that adds  
  some SAGE-specific paths so the build doesn't
  fail (since SAGE includes certain libs that
  matplotlib depends on).

From the Matplotlib website: matplotlib is a python 2D plotting
library which produces publication quality figures in a variety of
hardcopy formats and interactive environments across
platforms. matplotlib can be used in python scripts, the python and
ipython shell (ala matlab or mathematica), web application servers,
and six graphical user interface toolkits.

Here's what spkg-dist does:

* Removed the foreign language versions of the info files,
  since they add several MEGS (and they weren't in previous
  versions of Maxima).  This meant making empty directories
  and changing the Makefile.in's

Maxima is a system for the manipulation of symbolic and numerical
expressions, including differentiation, integration, Taylor series,
Laplace transforms, ordinary differential equations, systems of linear
equations, polynomials, and sets, lists, vectors, matrices, and
tensors. Maxima yields high precision numeric results by using exact
fractions, arbitrary precision integers, and variable precision
floating point numbers. Maxima can plot functions and data in two and
three dimensions. 

For more information, see the Maxima web site

http://maxima.sourceforge.net

Maxima is a system for the manipulation of symbolic and numerical
expressions, including differentiation, integration, Taylor series,
Laplace transforms, ordinary differential equations, systems of linear
equations, polynomials, and sets, lists, vectors, matrices, and
tensors. Maxima yields high precision numeric results by using exact
fractions, arbitrary precision integers, and variable precision
floating point numbers. Maxima can plot functions and data in two and
three dimensions. 

For more information, see the Maxima web site

http://maxima.sourceforge.net

Maxima is a system for the manipulation of symbolic and numerical
expressions, including differentiation, integration, Taylor series,
Laplace transforms, ordinary differential equations, systems of linear
equations, polynomials, and sets, lists, vectors, matrices, and
tensors. Maxima yields high precision numeric results by using exact
fractions, arbitrary precision integers, and variable precision
floating point numbers. Maxima can plot functions and data in two and
three dimensions.

For more information, see the Maxima web site

http://maxima.sourceforge.net

MayaVi2 is a general purpose, cross-platform tool for 2-D and 3-D scientific data visualization.

http://code.enthought.com/mayavi2/

https://svn.enthought.com/enthought/wiki/MayaVi

http://www.scipy.org/Cookbook/MayaVi

MayaVi2 is a general purpose, cross-platform tool for 2-D and 3-D scientific data visualization.

http://code.enthought.com/mayavi2/

https://svn.enthought.com/enthought/wiki/MayaVi

http://www.scipy.org/Cookbook/MayaVi

MayaVi2 is a general purpose, cross-platform tool for 2-D and 3-D scientific data visualization.

http://code.enthought.com/mayavi2/

https://svn.enthought.com/enthought/wiki/MayaVi

http://www.scipy.org/Cookbook/MayaVi

* 20070106 (William Stein):
   Modified mercurial/util.py to more intelligently choose the encoding,
   since this was crashing the install on my sage.math chroot jail.

* no changes from default repo, except that there's a sage
  subdirectory with a better .css file that gets copied to
  templates/static during the install.  And another
  that gets copied to templates/.

* Ran this command in the templates directory:

    replace ">manifest<" ">browse all files<" *.tmpl

  I mean, it's *incredibly* unclear what the hecke the
  "manifest" button is supposed to do.

From http://www.multiprecision.org/mpc: The MPC library is a C library for
multiple-precision floating-point computations with correct rounding. MPC has
continuously been supported by the INRIA and the current main authors come
from the CACAO and TANC project-teams at Loria (Nancy, France) and Ecole
Polytechnique (Palaiseau, France) respectively; see more on the web page. MPC
is based on the MPFR multiple-precision library.

From http://www.multiprecision.org/mpc : MPC is  a C library for the arithmetic
of complex numbers with arbitrarily  high precision and correct rounding of the
result. It is built upon and follows the same principles as MPFR.

From http://www.multiprecision.org/mpc:
GNU MPC is a C library for the arithmetic of complex numbers with
arbitrarily high precision and correct rounding of the result. It
extends the principles of the IEEE-754 standard for fixed precision real
floating point numbers to complex numbers, providing well-defined
semantics for every operation. At the same time, speed of operation at
high precision is a major design goal. 

MPFI is a library for interval arithmetic, which is built upon the MPFR
multiple precision floating-point arithmetic.

MPFI is intended to be a portable library written in C for arbitrary
precision interval arithmetic with intervals represented using MPFR
reliable floating-point numbers. It is based on the GNU MP library and
on the MPFR library.  The purpose of an arbitrary precision interval
arithmetic is on the one hand to get "guaranteed" results, thanks to
interval computation, and on the other hand to obtain accurate results,
thanks to multiple precision arithmetic. The MPFI library is built upon
MPFR in order to benefit from the correct rounding provided, for each
operation or function, by MPFR.  Further advantages of using MPFR are
its portability and compliance with the IEEE 754 standard for
floating-point arithmetic.

2006-11-29:

Just took the standard distribution from 

http://www.mpfr.org/mpfr-current/




This is now out of date.
------------------------------------------------
HOW TO MAKE the -2.2.0 PACKAGE:

* applied cummulative patches as of the date of the file:

wget http://www.mpfr.org/mpfr-current/patches

The webpage says download it into the top of mpfr-2.2.0 tree and use
"GNU patch" to patch it:

patch -N -Z -p1 < patches

Then update the configure script:

   autoconf < configure.in > configure

CHANGELONG:
2006-10-15:
   Fix from Mike Rubinstein:
In sage-1.4/spkg/build/mpfr-20060930/spkg-install
there are a couple of options given to ./configure that are specific to
NTL and don't seem to have anything to do with mpfr, namely:
NTL_GMP_LIP

The MPFR library is a C library for multiple-precision floating-point
computations with correct rounding. MPFR has continuously been supported by
the INRIA and the current main authors come from the Caramel and Arénaire
project-teams at Loria (Nancy, France) and LIP (Lyon, France) respectively;
see more on the credit page. MPFR is based on the GMP multiple-precision
library.

The main goal of MPFR is to provide a library for multiple-precision
floating-point computation which is both efficient and has a well-defined
semantics. It copies the good ideas from the ANSI/IEEE-754 standard for
double-precision floating-point arithmetic (53-bit significand).

MPIR is an open source multiprecision integer library derived from
version 5.0.1 of the GMP (GNU Multi Precision) project (which was
licensed LGPL v2+).

See http://www.mpir.org

Mpmath is a pure-Python library for multiprecision floating-point arithmetic. It provides an extensive set of transcendental functions, unlimited exponent sizes, complex numbers, interval arithmetic, numerical integration and differentiation, root-finding, linear algebra, and much more. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, and in many cases mpmath implements asymptotically fast algorithms that scale well for extremely high precision work. If available, mpmath will (optionally) use gmpy to speed up high precision operations.

Nauty has various tools for finding the automorphism group of a graph,
generating non-isomorphic graphs with certain properties, etc.

Nauty has various tools for finding the automorphism group of a graph,
generating non-isomorphic graphs with certain properties, etc.

Ncurses (new curses, pronounced "enn-curses") started as a freely
distributable "clone" of System V Release 4.0 (SVr4) curses. It has
outgrown the "clone" description, and now contains many features which
are not in SVr4 curses. Curses is a pun on the term "cursor
optimization". It is a library of functions that manage an
application's display on character-cell terminals (e.g., VT100).

The name "ncurses" was first used as the name of the curses library in
Pavel Curtis's pcurses, dated 1982. It was apparently developed on a
BSD 4.4 system, at Cornell. Parts of pcurses are readily identifiable
in ncurses, including the basics for the terminfo compiler (named
compile in that package):

  * the Caps, used to define the terminfo capabilities
  * awk scripts MKcaptab.awk, MKnames.awk
  * the library modules used for the terminfo compiler.

Besides ncurses, parts of pcurses still survive in 2010, in
recognizable form in Solaris.

Website: http://invisible-island.net/ncurses

NetworkX (NX) is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. 

Normaliz is a tool for computations in affine monoids, vector configurations, lattice polytopes,  and rational cones.

For more details see http://www.mathematik.uni-osnabrueck.de/normaliz/

nose extends the test loading and running features of unittest, making
it easier to write, find and run tests.

NTL is a high-performance, portable C++ library providing data structures and
algorithms for manipulating signed, arbitrary length integers, and for vectors,
matrices, and polynomials over the integers and over finite fields.

Website: http://www.shoup.net/ntl/

This package adds numerical linear algebra and other numerical computing
capabilities to python. 

-----------

svn export http://svn.scipy.org/svn/numpy/trunk

----------

NOTES:

The numpy docstrings don't have nearly enough examples yet.
Fortunately the following two websites have tons of examples:

http://scipy.org/Numpy_Example_List_With_Doc
http://www.hjcb.nl/python/Arrays.html
 

From wikipedia: OpenSSL is an open source implementation of the SSL
and TLS protocols. The core library (written in the C programming
language) implements the basic cryptographic functions and provides
various utility functions. Wrappers allowing the use of the OpenSSL
library in a variety of computer languages are available.

From wikipedia: OpenSSL is an open source implementation of the SSL
and TLS protocols. The core library (written in the C programming
language) implements the basic cryptographic functions and provides
various utility functions. Wrappers allowing the use of the OpenSSL
library in a variety of computer languages are available.

From wikipedia: OpenSSL is an open source implementation of the SSL
and TLS protocols. The core library (written in the C programming
language) implements the basic cryptographic functions and provides
various utility functions. Wrappers allowing the use of the OpenSSL
library in a variety of computer languages are available.

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 p-Groups

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

Modular Cohomology Rings of Finite p-Groups

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

Modular Cohomology Rings of Finite Groups

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

Modular Cohomology Rings of Finite Groups

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

Modular Cohomology Rings of Finite Groups

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

Modular Cohomology Rings of Finite Groups

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

Modular Cohomology Rings of Finite Groups

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

A Package for Analyzing Lattice Polytopes (PALP) is a set of C
programs for calculations with lattice polytopes and applications to
toric geometry.

It contains routines for vertex and facet enumeration, computation of
incidences and symmetries, as well as completion of the set of lattice
points in the convex hull of a given set of points. In addition, there
are procedures specialised to reflexive polytopes such as the
enumeration of reflexive subpolytopes, and applications to toric
geometry and string theory, like the computation of Hodge data and
fibration structures for toric Calabi-Yau varieties.  The package is
well tested and optimised in speed as it was used for time consuming
tasks such as the classification of reflexive polyhedra in 4
dimensions and the creation and manipulation of very large lists of
5-dimensional polyhedra.

While originally intended for low-dimensional applications, the
algorithms work in any dimension and our key routine for vertex and
facet enumeration compares well with existing packages.

Here is how to build a new version of the PARI SAGE spkg:

  1) Get the latest stable source code from
           http://pari.math.u-bordeaux.fr/download.html
     (NOTE -- just like last time, at some point the devel version will be
              the way to go, since that's where all the bug fixes are. 
        The PARI stable/devel model is complicated.)

  2) Extract the above code and make it the directory src in the current directory.

  3) Type ./spkg-dist in the above directory.

  4) Extract the file galdata.tgz from http://pari.math.u-bordeaux.fr/download.html
     in the directory pari-*/src/


-----------------------------------

* 2007-09-09: (Michael Abshoff)
   add -fPIC to DCLFLAGS on Linux PPC in src/config/get_dlcflags

* 2007-03-04: included Pablo De Napoli (denapo@gmail.com)'s
   improvement so PARI will build on systems with runpath support.
   See sage/runpath.txt for details.

* 2006-09-28: (William Stein and Justin Walker)
  Modified PARI build scripts so that they build the 
  PARI *shared* library even under OS X, and on OS X intel
  they build the x86/gmp kernel. 
   

* I took the standard PARI tarball, but ran the script spkg-dist on it
  to create this directory.  This script does various things to some
  of the PARI files to make them work better with SAGE, the most
  important being to replace calls to exit() with calls to abort().

* Also, I placed a directory "sage" in this directory with some files
  needed by spkg-install.

* This changed removed -- 09/28/2006
#* I changed a line of config/Makefile.SH to
#      DLLDFLAGS  

Here is how to build a new version of the PARI SAGE spkg:

  1) Get the latest stable source code from
           http://pari.math.u-bordeaux.fr/download.html
     (NOTE -- just like last time, at some point the devel version will be
              the way to go, since that's where all the bug fixes are. 
        The PARI stable/devel model is complicated.)

  2) Extract the above code and make it the directory src in the current directory.

  3) Type ./spkg-dist in the above directory.

  4) Extract the file galdata.tgz from http://pari.math.u-bordeaux.fr/download.html
     in the directory pari-*/src/


-----------------------------------

* 2007-10-31: (Carl Witty)
   disable runpath altogether; we want Sage to be relocatable.
   install gphelp, and required documentation source files.

* 2007-09-09: (Michael Abshoff)
   add -fPIC to DCLFLAGS on Linux PPC in src/config/get_dlcflags

* 2007-03-04: included Pablo De Napoli (denapo@gmail.com)'s
   improvement so PARI will build on systems with runpath support.
   See sage/runpath.txt for details.

* 2006-09-28: (William Stein and Justin Walker)
  Modified PARI build scripts so that they build the 
  PARI *shared* library even under OS X, and on OS X intel
  they build the x86/gmp kernel. 
   

* I took the standard PARI tarball, but ran the script spkg-dist on it
  to create this directory.  This script does various things to some
  of the PARI files to make them work better with SAGE, the most
  important being to replace calls to exit() with calls to abort().

* Also, I placed a directory "sage" in this directory with some files
  needed by spkg-install.

* This changed removed -- 09/28/2006
#* I changed a line of config/Makefile.SH to
#      DLLDFLAGS  

PARI/GP is a widely used computer algebra system designed for fast
computations in number theory (factorizations, algebraic number
theory, elliptic curves...), but also contains a large number of other
useful functions to compute with mathematical entities such as
matrices, polynomials, power series, algebraic numbers etc., and a lot
of transcendental functions. PARI is also available as a C library to
allow for faster computations.

Originally developed by Henri Cohen and his co-workers (Université
Bordeaux I, France), PARI is now under the GPL and maintained by Karim
Belabas with the help of many volunteer contributors.

Website: http://pari.math.u-bordeaux.fr/

'patch' takes a patch file containing a difference listing produced
by the 'diff' program and applies those differences to one
or more original files, producing patched versions.

The version of 'patch' included is the GNU one. Some of the 'diff' files
produced by GNU 'diff' are not acceptble to some versions of the 'patch'
command, such as the 'patch' command that comes with Solaris.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Applies and run tests on open Sage tickets.

Pexpect is a pure Python module for spawning child applications;
controlling them; and responding to expected patterns in their output.

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

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

The core of PolyBoRi is a C++ library, which provides high-level data
types for Boolean polynomials and monomials, exponent vectors, as well
as for the underlying polynomial rings and subsets of the powerset of
the Boolean variables. As a unique approach, binary decision diagrams
are used as internal storage type for polynomial structures. On top of
this C++-library we provide a Python interface. This allows parsing of
complex polynomial systems, as well as sophisticated and extendable
strategies for Gröbner base computation. PolyBoRi features a powerful
reference implementation for Gröbner basis computation.

This package includes lists of 2- and 3-dimensional reflexive polytopes.

The list of polygons is quite easy to get and it has been known for a while.
The list of 3-polytopes was originally obtained by Maximilian Kreuzer and
Harald Skarke using their software PALP, which is included into the standard
distribution of Sage. To work with lattice and reflexive polytopes from Sage
you can use sage.geometry.lattice_polytope module, which relies on PALP for
some of its functionality. To get access to the databases of this package, use
ReflexivePolytope and ReflexivePolytopes commands.

GPL v3+

The Python Cryptography Toolkit describes a package containing various
cryptographic modules for the Python programming language. It is
intended to provide a reliable and stable base for writing Python
programs that require cryptographic functions.

Extension for PyCrypto which provides more ciphers. For details see

  http://wiki.yobi.be/wiki/PyCryptoPlus

Pygments is a syntax highlighting package written in Python.

It is a generic syntax highlighter for general use in all kinds of
software such as forum systems, wikis or other applications that need
to prettify source code.

A modified version of GiNaC that replaces the dependency on CLN by Python.

This is Python from http://www.python.org

This is Python from http://www.python.org

Python is a dynamic object-oriented programming language that can be used for many kinds of software development. It offers strong support for integration with other languages and tools, comes with extensive standard libraries, and can be learned in a few days. Many Python programmers report substantial productivity gains and feel the language encourages the development of higher quality, more maintainable code.

For more details see http://www.python.org

Python bindings for the zeromq networking library.

Python bindings for the zeromq networking library.

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

Updated the rpy package using trac #1427

R is a language and environment for statistical computing and graphics.
It is a GNU project which is similar to the S language and environment
which was developed at Bell Laboratories (formerly AT&T, now Lucent
Technologies) by John Chambers and colleagues. R can be considered as a
different implementation of S. There are some important differences, but
much code written for S runs unaltered under R.

(taken from http://www.r-project.org/)

Michael Stoll's program which searches for rational points on hyperelliptic
curves.

The GNU Readline library provides a set of functions for use by
applications that allow users to edit command lines as they are typed
in. Both Emacs and vi editing modes are available. The Readline
library includes additional functions to maintain a list of
previously-entered command lines, to recall and perhaps reedit those
lines, and perform csh-like history expansion on previous commands.

Website: http://tiswww.case.edu/php/chet/readline/rltop.html

rpy2 is a redesign and rewrite of rpy. It is providing a low-level
interface to R, a proposed high-level interface, including wrappers to
graphical libraries, as well as R-like structures and functions.

Website: http://rpy.sourceforge.net/rpy2.html

There are several programs for working with Rubik's cubes, by three 
different people. Look inside the directories under /src to see 
specific info and licensing. In summary the three contributers are:


Michael Reid (GPL) http://www.math.ucf.edu/~reid/Rubik/optimal_solver.html
    optimal - uses many pre-computed tables to find an optimal 
              solution to the 3x3x3 Rubik's cube


Dik T. Winter (MIT License)
    cube    - uses Kociemba's algorithm to iteratively find a short
              solution to the 3x3x3 Rubik's cube 
    size222 - solves a 2x2x2 Rubik's cube 


Eric Dietz (GPL) http://www.wrongway.org/?rubiksource
    cu2   - A fast, non-optimal 2x2x2 solver
    cubex - A fast, non-optimal 3x3x3 solver
    mcube - A fast, non-optimal 4x4x4 solver

sage-mode provides Emacs Lisp that helps you use Sage in GNU Emacs.

'''Warning!'''  This is alpha code.  This might fail horribly and is not (yet)
easily customizable!

sage-mode provides Emacs Lisp that helps you use Sage in GNU Emacs.

sage-mode provides Emacs Lisp that helps you use Sage in GNU Emacs.
Inspiration was provided by ipython.el originally.

sage-mode provides Emacs Lisp that helps you use Sage in GNU Emacs.
Inspiration was provided by ipython.el originally.

The Sage Notebook is a web-based graphical user interface for
mathematical software.

The SageTeX package allows you to embed code, results of computations,
and plots from Sage into LaTeX documents.

The SageTeX package allows you to embed code, results of computations,
and plots from Sage into LaTeX documents.

SciPy (pronounced "Sigh Pie") is open-source software for mathematics,
science, and engineering. The SciPy library depends on NumPy, which provides
convenient and fast N-dimensional array manipulation. The SciPy library is
built to work with NumPy arrays, and provides many user-friendly and efficient
numerical routines such as routines for numerical integration and optimization.
Together, they run on all popular operating systems, are quick to install, and
are free of charge. NumPy and SciPy are easy to use, but powerful enough to be
depended upon by some of the world's leading scientists and engineers.

* William Stein 
 * Josh Kantor
 * Jason Grout

* Josh Kantor
 * Michael Abshoff

SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software. 

Website: http://www.scons.org/

setuptools is a collection of enhancements to the Python distutils (for Python 2.3.5 and up on most platforms; 64-bit platforms require a minimum of Python 2.4) that allow you to more easily build and distribute Python packages, especially ones that have dependencies on other packages.

Website: http://pypi.python.org/pypi/setuptools/

The present spkg is based on the fork of setuptools known as distribute.
Website: http://pypi.python.org/pypi/distribute

setuptools is a collection of enhancements to the Python distutils (for Python 2.3.5 and up on most platforms; 64-bit platforms require a minimum of Python 2.4) that allow you to more easily build and distribute Python packages, especially ones that have dependencies on other packages.

 * http://pypi.python.org/pypi/setuptools/

* 20070823 Juan M. Bello Rivas <jmbr@superadditive.com>
 + dropped dependencies on flex and bison

* 20070802 Martin Albrecht <malb@informatik.uni-bremen.de>
 + new upstream release (3-0-3)
 + adapted new spkg structure (all changes in patches subdirectory)

* 20070506 Martin Albrecht <malb@informatik.uni-bremen.de>
 + build script improvements
 + changes to libsingular.h

* 20070326 Martin Albrecht <malb@informatik.uni-bremen.de>
 + rewrote spkg-install
 + added first alpha of libsingular.so
 + removed stand-alone libfactory

* 20070105 William Stein
 + included Singular/Singular.rc.in which was missing for some
   reason and is needed by the cygwin build.

* 20060825 Martin Albrecht <malb@informatik.uni-bremen.de>
 + removed hannes-sprueche.txt (not funny anyway)
 + removed ntl subdirectory (we ship NTL already)
 + removed modules subdirectory (not needed)
 + removed Tst subdirectory (not needed)
 + wrote (very simple) spkg-install from scratch

* 20060831 William Stein and Justin Walker -- fine tuning
  for OS X.

* 20060831 William Stein -- put a lot of the workarounds from the previous
   Singular spkg-install script in here, since they are in fact needed
   in order for Singular to work after you type, e.g., make clean, or if
   you move the install directory.

* Martin Albrecht -- add fix to libcf:
Yes, It's a (new?) bug in libcf I've fixed just yesterday but got no word from 
the Singular people yet. They free a char ptr they are not supposed to free 
if I understand the ostrstring docs correctly. I've attached the 
one-line-fixed int_poly.cc which belongs in the factory subdirectory of 
Singular.

 * Martin Albrecht -- 2006-09-17:
This looks to me as if I didn't remove all references to boost:
/usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:1098: error: exception
I've attached an updated configure.in and configure (created with autoconf 
2.60) with Boost checks disabled which should fix the problem. These belong 
in the Singular subdirectory:
   singular-3-0-2-2006-09-09/Singular

deprecated, use 'hg log' instead

* 20070823 Juan M. Bello Rivas <jmbr@superadditive.com>
 + dropped dependencies on flex and bison

* 20070802 Martin Albrecht <malb@informatik.uni-bremen.de>
 + new upstream release (3-0-3)
 + adapted new spkg structure (all changes in patches subdirectory)

* 20070506 Martin Albrecht <malb@informatik.uni-bremen.de>
 + build script improvements
 + changes to libsingular.h

* 20070326 Martin Albrecht <malb@informatik.uni-bremen.de>
 + rewrote spkg-install
 + added first alpha of libsingular.so
 + removed stand-alone libfactory

* 20070105 William Stein
 + included Singular/Singular.rc.in which was missing for some
   reason and is needed by the cygwin build.

* 20060825 Martin Albrecht <malb@informatik.uni-bremen.de>
 + removed hannes-sprueche.txt (not funny anyway)
 + removed ntl subdirectory (we ship NTL already)
 + removed modules subdirectory (not needed)
 + removed Tst subdirectory (not needed)
 + wrote (very simple) spkg-install from scratch

* 20060831 William Stein and Justin Walker -- fine tuning
  for OS X.

* 20060831 William Stein -- put a lot of the workarounds from the previous
   Singular spkg-install script in here, since they are in fact needed
   in order for Singular to work after you type, e.g., make clean, or if
   you move the install directory.

* Martin Albrecht -- add fix to libcf:
Yes, It's a (new?) bug in libcf I've fixed just yesterday but got no word from 
the Singular people yet. They free a char ptr they are not supposed to free 
if I understand the ostrstring docs correctly. I've attached the 
one-line-fixed int_poly.cc which belongs in the factory subdirectory of 
Singular.

 * Martin Albrecht -- 2006-09-17:
This looks to me as if I didn't remove all references to boost:
/usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:1098: error: exception
I've attached an updated configure.in and configure (created with autoconf 
2.60) with Boost checks disabled which should fix the problem. These belong 
in the Singular subdirectory:
   singular-3-0-2-2006-09-09/Singular

* assert.h: logic seems to be broken on some platforms
 * src.Singular.Makefile.in: adding SunOS for libSingular
 * kernel.rmodulon.cc: simple bugfix
 * mminit.cc: Work around problem with the wrong free being picked causing double frees

Singular is a computer algebra system for polynomial computations,
with special emphasis on commutative and non-commutative algebra,
algebraic geometry, and singularity theory.

Sphinx is a tool that makes it easy to create intelligent and
beautiful documentation for Python projects (or other documents
consisting of multiple reStructuredText sources), written by Georg
Brandl. It was originally created to translate the new Python
documentation, but has now been cleaned up in the hope that it will be
useful to many other projects.

SQLite is a software library that implements a self-contained,
serverless, zero-configuration, transactional SQL database engine.

MAINTAINER: 
   Mike Hansen


SOURCE:
   http://www.mathe2.uni-bayreuth.de/axel/symneu_engl.html


we include index.html, which is the above web site, which officially states
that Symmetrica is PUBLIC DOMAIN.

MAINTAINER: 
   Mike Hansen


SOURCE:
   http://www.mathe2.uni-bayreuth.de/axel/symneu_engl.html


we include index.html, which is the above web site, which officially states
that Symmetrica is PUBLIC DOMAIN.

MAINTAINER: 
   Mike Hansen


SOURCE:
   http://www.mathe2.uni-bayreuth.de/axel/symneu_engl.html


we include index.html, which is the above web site, which officially states
that Symmetrica is PUBLIC DOMAIN.

Symmetrica is a program developed by Lehrstuhl Mathematik II of the
University of Bayreuth. It has routines to handle the following topics

 * ordinary representation theory of the symmetric group and related groups (2/11/04) 
 * ordinary representation theory of the classical groups 
 * modular representation theory of the symmetric group 
 * projective representation theory of the symmetric group 
 * combinatorics of tableaux 
 * symmetric functions and polynomials (7/22/04) 
 * commutative and non commutative Schubert polynomials 
 * operations of finite groups.  
 * ordinary representation theory of Hecke algebras of type A_n

For more details check http://www.symmetrica.de (currently redirects
to http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA)

SYMPOW is a package to compute special values of symmetric power elliptic 
curve L-functions. It can compute up to about 64 digits of precision. 

SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries, except optionally for plotting support.

Tachyon is a raytracer developed by John E. Stone. Tachyon supports
the typical ray tracer features, most of the common geometric
primitives, shading and texturing modes, etc. It also supports less
common features such as HDR image output, ambient occlusion lighting,
and support for various triangle mesh and volumetric texture formats
beneficial for molecular visualization (e.g. rendering VMD scenes).

Currently not all of Tachyon's functionality is exported by the Sage
interface.

GPL v2

This is an optional spkg. It is Linux x86, x86-64, ppc and ppc64 only.

Website: http://www.valgrind.org/

From the above website: Valgrind is an award-winning instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.

The Valgrind distribution currently includes five production-quality tools: a memory error detector, a thread error detector, a cache and branch-prediction profiler, a call-graph generating cache profiler, and a heap profiler. It also includes two experimental tools: a data race detector, and an instant mem

This is an optional spkg. It is Linux x86, x86-64, ppc and ppc64 only.

Website: http://www.valgrind.org/

From the above website: Valgrind is an award-winning instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.

The Valgrind distribution currently includes five production-quality tools: a memory error detector, a thread error detector, a cache and branch-prediction profiler, a call-graph generating cache profiler, and a heap profiler. It also includes two experimental tools: a data race detector, and an instant mem

This is an optional spkg. It supports Linux on x86, x86-64, ppc, ppc64 and ARM
as well as Darwin (Mac OS X 10.5 and 10.6) on x86 and x86-64.

Valgrind is an instrumentation framework for building dynamic analysis tools.
There are Valgrind tools that can automatically detect many memory management
and threading bugs, and profile your programs in detail. You can also use
Valgrind to build new tools.

The Valgrind distribution currently includes six production-quality tools:
a memory error detector, two thread error detectors, a cache and
branch-prediction profiler, a call-graph generating cache and branch-prediction
profiler, and a heap profiler. It also includes three experimental tools: a
heap/stack/global array overrun detector, a second heap profiler that examines
how heap blocks are used, and a SimPoint basic block vector generator. It runs
on the following platforms: X86/Linux, AMD64/Linux, ARM/Linux, PPC32/Linux,
PPC64/Linux, S390X/Linux, ARM/Android (2.3.x), X86/Darwin and AMD64/Darwin
(Mac OS X 10.6 and 10.7).

This is an optional spkg. It supports Linux on x86, x86-64, ppc, ppc64 and ARM
as well as Darwin (Mac OS X 10.5 and 10.6) on x86 and x86-64.

Valgrind is an instrumentation framework for building dynamic analysis tools.
There are Valgrind tools that can automatically detect many memory management
and threading bugs, and profile your programs in detail. You can also use
Valgrind to build new tools.

The Valgrind distribution currently includes six production-quality tools:
a memory error detector, two thread error detectors, a cache and
branch-prediction profiler, a call-graph generating cache and branch-prediction
profiler, and a heap profiler. It also includes three experimental tools: a
heap/stack/global array overrun detector, a second heap profiler that examines
how heap blocks are used, and a SimPoint basic block vector generator. It runs
on the following platforms: X86/Linux, AMD64/Linux, ARM/Linux, PPC32/Linux,
PPC64/Linux, S390X/Linux, ARM/Android (2.3.x), X86/Darwin and AMD64/Darwin
(Mac OS X 10.6 and 10.7).

This is an optional spkg. It is Linux x86, x86-64, ppc and ppc64 only.

Website: http://www.valgrind.org/

From the above website: Valgrind is an award-winning instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.

The Valgrind distribution currently includes five production-quality tools: a memory error detector, a thread error detector, a cache and branch-prediction profiler, a call-graph generating cache profiler, and a heap profiler. It also includes two experimental tools: a data race detector, and an instant mem

Maintainer: Michael Abshoff

* 2007-10-08: update to 3.3.0svn-r6959

* Initial version: 3.3.0svn-r6814

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.

 * http://www.vtk.org/
 * http://www.vtk.org/what-is-vtk.php

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.

 * http://www.vtk.org/
 * http://www.vtk.org/what-is-vtk.php

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.

 * http://www.vtk.org/
 * http://www.vtk.org/what-is-vtk.php

The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.

 * http://www.vtk.org/
 * http://www.vtk.org/what-is-vtk.php

A modern networking library. Also known as 0mq or zmq. The same API is
provided by http://www.crossroads.io, though we currently use the
http://www.zeromq.org implementation.

A modern networking library. Also known as 0mq or zmq. The same API is
provided by http://www.crossroads.io, though we currently use the
http://www.zeromq.org implementation.

Massively Spiffy Yet Delicately Unobtrusive Compression Library (Also
Free, Not to Mention Unencumbered by Patents)

zn_poly is a C library for polynomial arithmetic in Z/nZ[x], where n is any
modulus that fits into an unsigned long.

Website: http://cims.nyu.edu/~harvey/zn_poly/

* bump spkg due to python now using ucs4