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The following are links to scientific software libraries that have
been recommended by Python users.

=== Number Crunching and Related Tools ===

This page lists a number of packages related to numerics, number crunching, signal processing,
financial modeling, linear programming, statistics, data structures, date-time processing,
random number generation, and crypto.

==== Data Structures ====

  * PyPolyhedron

  Calculate polyhedron's V- and H-representation. This is a Python
  interface to a C-library cddlib (Pearu Peterson)

  * avl_tree

  AVL module provide a hybrid between a dictionary and a list which
  can come in handy. AVL trees (named after the inventors,
  Adel'son-Vel'skii and Landis) are balanced binary search trees.
  (Sam Rushing)

  * bplustree

  Classical compsci B+trees, implemented entirely in Python: Fast,
  portable file based indexing with range queries and including a
  dbm-compatibility mode. (Aaron Watters)

  * fsm

  FiniteStateMachine module. (Skip Montanaro)

  * graph_lib

  This module defines the Python class Graph. Graph is loosely
  modelled after the Library of Efficient Data types and Algorithms
  (LEDA). It includes methods for constructing graphs, BFS and DFS
  traversals, topological sort, etc.

  * kjbuckets

  kjbuckets is a C extension to python which defines three Python data
  types kjSet, kjGraph, and kjDict, implemented using a fast and space
  efficient hash table strategy. The types are tightly coupled and
  may be combined and manipulated using a collection of fast "set at a
  time" operations written in C. If you need to manipulate
  collections and mappings quickly take a look at this module. It
  comes with no warrantee of course, but it has been pounded pretty
  heavily and I consider it fairly solid. (Aaron Watters)

  * npstruct

  An extension module useful for parsing and unparsing binary data
  structures. Somewhat like the standard struct module, but with a few
  extra features (bitfields, user-function-fields, byte order
  specification, etc...) and a different API more convenient for
  streamed and context-sensitive formats like network protocol
  packets, image and sound files, etc. (Sam Rushing)

==== Date/Time ====

  * mxDateTime

  These types were created to provide a consistent way of transferring
  date and time data between Python and databases. Apart from handling
  date before the Unix epoch (1.1.1970) they also correctly work with
  dates beyond the Unix time limit (currently with Unix time values
  being encoded using 32bit integers, the limit is reached in 2038)
  and thus is Year 2000 and Year 2038 safe. (M.-A. Lemburg)

  * Mayalib
  [FTP://www.pauahtun.org/pub/mayalib.zip [source]]

  Mayan dates and numbers (math) for Python. (Ivan Van Laningham)

  * normalDate

  NormalDate is a specialized class to handle dates without all the
  excess baggage (time zones, daylight savings, leap seconds, etc.) of
  other date structures. (Jeff Bauer)

==== FFT ====

  * SciPy -- http://www.scipy.org

  * fourier

  A set of routines to perform Fourier transforms using pure
  (Numerical) Python. These are slower by a factor of 2-10 than pure C
  version in the FFT module (which is pretty good for a pure Python
  solution), but they make an interesting example. (Tom Hochberg)

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx

==== Finance ====

  * pyfi

  pyfi provides a set of functions that perform commonly used financial calculations.
  ([[http://hobbiton.thisside.net|[Rupert Scammell]]])

  * pyFinancials

  A collection of algorithms for advanced financial calculations.
  (G. P. Ciceri)

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx --
  Includes many standard financial calculations plus many other general functions used in finance.

  * MibianLib -- Options Pricing Library

==== Geometry ====

  * PyGTS - http://pygts.sourceforge.net/ -- PyGTS is a python package used to construct, manipulate, and perform computations on triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library (http://gts.sourceforge.net/).

==== Interface ====

  * SciPy -- http://www.scipy.org

  * SAML

  Interface to the "Simple Algebraic Math Library", a C library for
  computer algebra, together with some application programs: a desktop
  calculator, a spreadsheet (sort of) and a program to factorize
  integers. (Thierry Bousch)

  * pymat

  PyMat is an interface between NumPy and a MATLAB engine
  session. It can be used to support NumPy's functionality with the
  features of MATLAB. An example module is included that presents a very
  simple interface to MATLAB's plotting functions. This allows you to, for
  example, plot NumPy arrays in a MATLAB plot window. (Andrew Sterian)

  * PYML

  PYML is an interface between the computer language Python and
  Mathematica. Mathematica expressions can be written in Python code,
  evaluated, and their results returned to Python. Support for postscript
  graphics returned from Mathematica exists.
  (David Konerding)

==== Mixed Integer and Linear Programming ====

  * Coopr

  A COmmon Optimization Python Repository that includes Pyomo: a Pythonic Algebraic Modeling Language for mixed integer and linear programming.

  * pulp-or Mixed Integer Programming (MIP) and LP
  PuLP is an LP modeler written in python. PuLP can generate MPS or LP files
  and call GLPK, COIN CLP/CBC, CPLEX, Gurobi and XPRESS to solve linear problems.
  PuLP can be installed from pypi via
$easy_install pulp-or

  * cvxopt
  CVXOPT supports linear, quadratic and other advanced types of convex programming. It also has a interface to blas and lapack and is compatible with NumPy.

  * lpsolvpy

  An interface to the LGPL'd numerical linear program solver lp_solve.
  (Michael Pronath)
  * Lp_solve5 (5.1 and 5.5) Mixed Integer Programming (MIP) and LP - New ones, NO python binding yet. Volunteers needed for python bindings.
  CPLEX, LINDO, AMPL/MathProg, LP etc. formats supported. (Noli Sicad)

  * pycplex
  Python interface to the ILOG CPLEX Callable Library.

  * GLPK (GNU Linear Programming Kit) MIP and LP
    Python bindings [[http://rpm.pbone.net/index.php3/stat/4/idpl/1709746/com/python-glpk-0.4-2mdk.i586.rpm.html|[source]]]
  Has python bindings for 4.7 and can be used for 4.8. No debian package (use RPM then Alien for debian)
  CPLEX, LINDO, AMPL/MathProg, LP etc. formats supported as well. (Noli Sicad)

  * SciPy -- http://www.scipy.org

  * pySimplex
  [[http://starship.python.net/crew/aaron_watters/pysimplex/|[pysimplex]]] (broken link)
  [[http://www.pythonpros.com/arw/pysimplex/|[details]]] (broken link)
  [[http://www.pythonpros.com/arw/pysimplex/pysimplex.tgz|[source]]] (broken link)

  Pysimplex provides some basic symbolic programming tools for
  constructing, solving and optimizing systems of linear equations and
  inequalities. It includes an implementation of the classical SIMPLEX
  linear optimization algorithm as well as a filter for parsing and
  optimizing linear models encoded using the standard MPS format.
  (Aaron Watters)

  * Simplex

  Simplex minimizes an arbitrary nonlinear function of N variables by
  the Nedler-Mead Simplex method. (Vivake Gupta)

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx

==== Matrix/Vector ====

  * matrix

  Yet Another Matrix Module. This one leans more toward the flexible
  end of the spectrum, sacrificing performance for correctness. For
  example, it can correctly handle rationals and other strange things
  being inserted into it. Also implemented: LU[P] decomposition, and a
  simultaneous linear equation solving capability. Most of the
  standard matrix ops: transpose, determinant, inverse, etc.. along
  with some functional-style methods for mapping and iteration. (Sam

  * SciPy -- http://www.scipy.org

  * Sparsemodule (Links are broken )

  An extension module wrapping the sparse library. It can be used for
  solving large systems of linear equations. (Neil Schemenauer)

  * MatPy

  A Python package for numerical computation and plotting with a
  MatLab-like interface. It currently consists of wrappers around the
  Numeric, Gnuplot and SpecialFuncs packages. It provides an
  alternative interface to NumPy that is somewhat more convenient for
  matrix and vector computation. Eventually both will be based
  directly on the same low level routines. We are also looking for the
  possibility of interface to Octave. (H. Zhu)

==== Music ====

  * ratio

  For those who are big fans of Just Intonation, one tedious aspect of
  this is that you end up fondling ratios a lot. The math gets boring
  after a while, though I do believe you should be able to do the math
  on your own to get a feel for what it is you're doing. Having said
  that, I decided I needed some help because I got sick of reducing
  multiplied ratios. I've written a quick Python module, ratio.py,
  which handles a lot of the tedium. In particular, building up JI
  tetrachords and scales based on justly intuned chords or by
  katapyknosis is pretty simple with this module. (William Annis)

==== Neural Networks ====

  * bpnn

  A simple back-propagation neural network module.
  (Neil Schemenauer)

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx

==== Numerics ====

  * numberTheory
  [details !? FIXME: was same as source]
  [[http://www.dorb.com/python/numberTheory.py|[source FIXME: broken link]]]

  Collection of functions from the book numberTheory.
  Darrell Gallion.

  * FixedPoint
  [[http://sunsite.compapp.dcu.ie/pub/linux/redhat/DMA/|[details: FIXME: broken link]]]

  Fixed decimal precision arithmetic.

  * Fraction

  Simple class implemented in pure Python that does fraction arithmetic.
  (Mike Hostetler)

  * SILOON ((FIXME: both link broken))

  SILOON (Scripting Interface Languages for Object-Oriented Numerics)
  gives users the ability to rapidly prototype their scientific codes
  in a simple yet elegant fashion using the popular scripting
  languages Python and Perl. While programming in these flexible and
  dynamic languages, SILOON users maintain the capability of accessing
  the full power and complexity of C++ and FORTRAN (coming soon)
  libraries executed on high-performance parallel computers. (SILOON

  * surd ((FIXME: both link broken))

  Irrational numbers (surds) as objects.

  * yarn ((FIXME: both link broken))

  Yet Another Rational Numbers module.

  * escript - [[http://access.edu.au/content/view/78/|[details]]] -- escript is a python module to define and solve coupled, non-linear, time-dependend partial differential equations (PDEs).

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx

==== Other Tools ====

  * Evol

  Evolutions strategies: Powerful global optimisation Basic class for
  a global optimisation strategie called 'Evolutionsstrategie' by
  Prof. Schwefel. (Tobias Polzin)

  * explore

  Explore Array Data with Gnuplot Interactive Rotating, Zooming of 3D-gnuplot surface plot.
  (Tobias Polzin)

  * emath

  100% Python functions which are based on the famous Numerical
  Recipes -- polynomial evaluation, zero- finding, integration, FFT's,
  and vector operations. "They are loosely modelled after Numerical
  Recipes in C because I needed, at the time, actual source codes
  which I can examine instead of just wrappers around Fortran
  libraries like NumPy and Octave. As evident from the documentations,
  the routines were written with emphasis on clarity rather than on
  runtime efficiency." (William Park)

  * PyClimate

  A Python package designed to accomplish some usual tasks during the
  analysis of climate variability using Python. It provides functions
  to perform some simple IO operations, operations with
  COARDS-compliant netCDF files, EOF analysis, SVD and CCA analysis of
  coupled data sets, some linear digital filters, kernel based
  probabilitydensity function estimation and access to DCDFLIB.C
  library from Python. (Jon Saenz)

  * Pythonica

  A simple version of mathematica for python.
  (Tobias Polzin)

  * graph-tool

  A python module for efficient analysis of graphs (aka. networks), with
  algorithms implemented in C++ with the Boost Graph Library.

  * SciPy -- http://www.scipy.org

  * ScientificPython

  A collection of Python modules that are useful for scientific
  computing. In this collection you will find modules that cover basic
  geometry (vectors, tensors, transformations, vector and tensor
  fields), quaternions, automatic derivatives, (linear) interpolation,
  polynomials, elementary statistics, nonlinear least-squares fits,
  unit calculations, Fortran-compatible text formatting, 3D
  visualization via VRML, two Tk widgets for simple line plots and
  3D wireframe models, and support for ParallelProcessing. (KonradHinsen)

==== Random Number Generators ====

  * ccrandom

  This module is mostly compatible with Python's random module, but
  uses Linux or BSD's /dev/urandom device to generate numbers, thus
  yielding more random output than the default Python module.
  (Christopher A. Craig)

  * crng ((FIXME: both links broken))

  The Python module crng implements random-number generators (RNGs)
  based on several different algorithms producing uniform deviates in
  the open interval (0,1), i.e. exclusive of the end-point values 0
  and 1. A few continuous and integer-valued non-uniform deviates are
  also available. Each RNG algorithm is implemented as a separate
  Python extension type. The RNG types are independent of each other,
  but have very similar interfaces. The entire module is implemented
  as one single C source code file. (Per J. Kraulis)

  * MTRand ((FIXME: both links broken))

  Mersenne Twister random number generator. Far longer period and far
  higher order of equidistribution than any other implemented
  generators. Fast generation and efficient use of memory. (Darrell

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx

==== Special Functions ====

  * SciPy -- http://www.scipy.org

==== Statistics ====

  * scikits.statsmodels


  scikits.statsmodels is a pure python package that provides
  classes and functions for the estimation of several categories
  of statistical models. These currently include linear regression
  models, OLS, GLS, WLS and GLS with AR(p) errors, generalized
  linear models for six distribution families and M-estimators for
  robust linear models. An extensive list of result statistics are
  available for each estimation problem. More models especially for
  time series analysis are available in the development repository
  on launchpad.

  * stats

  A collection of statistical functions, ranging from descriptive
  statistics (mean, median, histograms, variance, skew, kurtosis,
  etc.) to inferential statistics (t-tests, F-tests, chi-square,
  etc.). The functions are defined for operation on lists and, if
  Numeric is installed, also defined for array arguments. REQUIRES
  pstat.py (v0.3 or later) and io.py (v0.1 or later). (Gary

  * Rpy
  RPy is a very simple, yet robust, Python interface to the R Programming Language.
  [[http://www.r-project.org/|[source]]]. It can manage all kinds of R objects and can execute arbitrary R functions (including the graphic functions). All errors from the R language are converted to Python exceptions. Any module installed for the R system can be used from within Python. (Noli Sicad)

  * SciPy -- http://www.scipy.org

For more information on related numeric packages, see the
[[http://www.python.org/pypi|Python Package Index]].

  * PyIMSL -- http://www.roguewave.com/products/imsl-numerical-libraries/pyimsl-studio.aspx
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NumericAndScientific/Libraries (last edited 2014-05-26 15:03:26 by PaulBoddie)

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