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Adding notices and readme file etc regarding the derived work of Apache Commons Math library about to be included in JIDT.

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Apache License
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APACHE COMMONS MATH DERIVATIVE WORKS:
The Apache commons-math library includes a number of subcomponents
whose implementation is derived from original sources written
in C or Fortran. License terms of the original sources
are reproduced below.
===============================================================================
For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in
the LevenbergMarquardtOptimizer class in package
org.apache.commons.math3.optimization.general
Original source copyright and license statement:
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
Redistribution and use in source and binary forms, with or
without modification, are permitted provided that the
following conditions are met:
1. Redistributions of source code must retain the above
copyright notice, this list of conditions and the following
disclaimer.
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copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials
provided with the distribution.
3. The end-user documentation included with the
redistribution, if any, must include the following
acknowledgment:
"This product includes software developed by the
University of Chicago, as Operator of Argonne National
Laboratory.
Alternately, this acknowledgment may appear in the software
itself, if and wherever such third-party acknowledgments
normally appear.
4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS"
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SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,
EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
POSSIBILITY OF SUCH LOSS OR DAMAGES.
===============================================================================
Copyright and license statement for the odex Fortran routine developed by
E. Hairer and G. Wanner and translated in GraggBulirschStoerIntegrator class
in package org.apache.commons.math3.ode.nonstiff:
Copyright (c) 2004, Ernst Hairer
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
Copyright and license statement for the original lapack fortran routines
translated in EigenDecompositionImpl class in package
org.apache.commons.math3.linear:
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
- Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer listed
in this license in the documentation and/or other materials
provided with the distribution.
- Neither the name of the copyright holders nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
Copyright and license statement for the original Mersenne twister C
routines translated in MersenneTwister class in package
org.apache.commons.math3.random:
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. The names of its contributors may not be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
The class "org.apache.commons.math3.exception.util.LocalizedFormatsTest" is
an adapted version of "OrekitMessagesTest" test class for the Orekit library
The "org.apache.commons.math3.analysis.interpolation.HermiteInterpolator"
has been imported from the Orekit space flight dynamics library.
Th Orekit library is described at:
https://www.orekit.org/forge/projects/orekit
The original files are distributed under the terms of the Apache 2 license
which is: Copyright 2010 CS Communication & Systèmes
===============================================================================
The initial code for shuffling an array (originally in class
"org.apache.commons.math3.random.RandomDataGenerator", now replaced by
a method in class "org.apache.commons.math3.util.MathArrays") was
inspired from the algorithm description provided in
"Algorithms", by Ian Craw and John Pulham (University of Aberdeen 1999).
The textbook (containing a proof that the shuffle is uniformly random) is
available here:
http://citeseerx.ist.psu.edu/viewdoc/download;?doi=10.1.1.173.1898&rep=rep1&type=pdf
===============================================================================
License statement for the direction numbers in the resource files for Sobol sequences.
-----------------------------------------------------------------------------
Licence pertaining to sobol.cc and the accompanying sets of direction numbers
-----------------------------------------------------------------------------
Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the names of the copyright holders nor the names of the
University of New South Wales and the University of Waikato
and its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
===============================================================================
The initial commit of package "org.apache.commons.math3.ml.neuralnet" is
an adapted version of code developed in the context of the Data Processing
and Analysis Consortium (DPAC) of the "Gaia" project of the European Space
Agency (ESA).
===============================================================================

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Apache Commons Math
Copyright 2001-2014 The Apache Software Foundation
This product includes software developed at
The Apache Software Foundation (http://www.apache.org/).
===============================================================================
The inverse error function implementation in the Erf class is based on CUDA
code developed by Mike Giles, Oxford-Man Institute of Quantitative Finance,
and published in GPU Computing Gems, volume 2, 2010.
===============================================================================
The BracketFinder (package org.apache.commons.math3.optimization.univariate)
and PowellOptimizer (package org.apache.commons.math3.optimization.general)
classes are based on the Python code in module "optimize.py" (version 0.5)
developed by Travis E. Oliphant for the SciPy library (http://www.scipy.org/)
Copyright © 2003-2009 SciPy Developers.
===============================================================================
The LinearConstraint, LinearObjectiveFunction, LinearOptimizer,
RelationShip, SimplexSolver and SimplexTableau classes in package
org.apache.commons.math3.optimization.linear include software developed by
Benjamin McCann (http://www.benmccann.com) and distributed with
the following copyright: Copyright 2009 Google Inc.
===============================================================================
This product includes software developed by the
University of Chicago, as Operator of Argonne National
Laboratory.
The LevenbergMarquardtOptimizer class in package
org.apache.commons.math3.optimization.general includes software
translated from the lmder, lmpar and qrsolv Fortran routines
from the Minpack package
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
===============================================================================
The GraggBulirschStoerIntegrator class in package
org.apache.commons.math3.ode.nonstiff includes software translated
from the odex Fortran routine developed by E. Hairer and G. Wanner.
Original source copyright:
Copyright (c) 2004, Ernst Hairer
===============================================================================
The EigenDecompositionImpl class in package
org.apache.commons.math3.linear includes software translated
from some LAPACK Fortran routines. Original source copyright:
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
===============================================================================
The MersenneTwister class in package org.apache.commons.math3.random
includes software translated from the 2002-01-26 version of
the Mersenne-Twister generator written in C by Makoto Matsumoto and Takuji
Nishimura. Original source copyright:
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved
===============================================================================
The LocalizedFormatsTest class in the unit tests is an adapted version of
the OrekitMessagesTest class from the orekit library distributed under the
terms of the Apache 2 licence. Original source copyright:
Copyright 2010 CS Systèmes d'Information
===============================================================================
The HermiteInterpolator class and its corresponding test have been imported from
the orekit library distributed under the terms of the Apache 2 licence. Original
source copyright:
Copyright 2010-2012 CS Systèmes d'Information
===============================================================================
The creation of the package "o.a.c.m.analysis.integration.gauss" was inspired
by an original code donated by Sébastien Brisard.
===============================================================================
The direction numbers in the resource file for Sobol generation was created
by Frances Y. Kuo and Stephen Joe. Original source copyright:
Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
All rights reserved.
===============================================================================
The complete text of licenses and disclaimers associated with the the original
sources enumerated above at the time of code translation are in the LICENSE.txt
file.

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The classes under the JIDT package infodynamics.utils.commonsmath3 were
originally distributed as part of the Apache Commons
Math3 library, under the Apache License V2.0 (see ApacheCommons-LICENSE.txt).
This Apache 2 software is now included as a derivative
work in the GPLv3 licensed JIDT project, as per:
http://www.apache.org/licenses/GPL-compatibility.html
The original Apache source code has been modified as follows:
-- We have modified package names to sit inside the JIDT structure.
As required by the license, we have:
1. Given a copy of the original Apache License V2.0 in ApacheCommons-LICENSE.txt
2. We have noted how the original classes have been modified in their
header comments.
3. We have kept the original notices in the headers of each class.
4. We included the original notice file as ApacheCommons-NOTICE.txt
Note that the original license and notice files contain text referring to
derived code that is not redistributed in JIDT.

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@ -85,6 +85,15 @@ Several sets of demonstration code are distributed with the toolkit:
g. java/unittests -- the JUnit test cases for the Java toolkit are included in the distribution -- these case also be browsed to see simple use cases for the various calculators in the toolkit -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/JUnitTestCases
=============
Notices
=============
This project includes modified files from the Apache Commons Math library -- http://commons.apache.org/proper/commons-math/
This Apache 2 software is now included as a derivative work in this GPLv3 licensed JIDT project, as per: http://www.apache.org/licenses/GPL-compatibility.html
Notices and license for this software are found in the notices/commons-math directory.
=============
Joseph T. Lizier, @DATE@