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<?xml version="1.0"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<!--
This file is used by the maven-changes-plugin to generate the release notes.
Useful ways of finding items to add to this file are:
1. Add items when you fix a bug or add a feature (this makes the
release process easy :-).
2. Do a JIRA search for tickets closed since the previous release.
3. Use the report generated by the maven-changelog-plugin to see all
SVN commits.
To generate the file RELEASE-NOTES.txt from this file:
mvn changes:announcement-generate -Prelease-notes [-Dchanges.version]
The <action> type attribute can be add,update,fix,remove.
-->
<!-- NOTE:
The description attribute entries below are specially formatted
so as to improve the layout of the generated text release notes.
The parsing process removes all line feeds, replacing them with a single space.
The Velocity template in src/changes/release-notes.vm has been enhanced to replace pairs of adjacent spaces
with a new-line in the release notes. (These spaces are ignored when displaying HTML).
If the output is not quite correct, check for invisible trailing spaces!
-->
<document>
<properties>
<title>Commons Math Release Notes</title>
</properties>
<body>
<release version="3.2" date="2013-04-03" description="
This is a minor release: It combines bug fixes and new features.
Changes to existing features were made in a backwards-compatible
way such as to allow drop-in replacement of the v3.1[.1] JAR file.
Most notable among the new features are: Framework for automatic
differentiation, Lévy distribution, prime numbers, enumerated
distributions, real field allowing to use several algorithms
(solvers, linear algebra, 3D geometry) with different real-like
classes (high accuracy or automatic differentiation), spherical
coordinates with gradients and Hessians, reorganized clustering
package with different distance implementations.
The minimum version of the Java platform required to compile and use
Commons Math is Java 5.
Users are encouraged to upgrade to this version as this release not
only includes bug fixes but also deprecates numerous classes and
methods that will be deleted from the next major release (4.0).
Caveat:
1. The implementation of the BOBYQA optimization algorithm is in alpha
state (cf. MATH-621): Many code paths are untested, and we are looking
for volunteers to improve the code readability, robustness and performance
and to extend the unit tests suite.
2. A few methods in the FastMath class are in fact slower that their
counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
">
<action dev="luc" type="fix" issue="MATH-961" >
Fixed wrong array dimensions in secondary equations handling in some cases.
</action>
<action dev="luc" type="fix" issue="MATH-960" >
Fixed missing side effects of secondary equations on main state in
Ordinary Differential Equations integration.
</action>
<action dev="luc" type="fix" issue="MATH-957" due-to="Evan Ward">
Fixed inverse cumulative probability for uniform distribution.
</action>
<action dev="tn" type="add" issue="MATH-917,MATH-918,MATH-919,MATH-920" due-to="Reid Hochstedler">
All contents of package "o.a.c.m.stat.clustering" refactored into
new package "o.a.c.m.ml.clustering" and added support for additional
distance measures in package "o.a.c.m.ml.distance": "CanberraDistance",
"ChebyshevDistance", "EuclideanDistance" and "ManhattanDistance".
</action>
<action dev="tn" type="fix" issue="MATH-891">
"SpearmansCorrelation" now works correctly in case of a provided
"NaturalRanking" with a "NaNStrategy.REMOVED" strategy and the input
data contains NaN values. From version 4.0 onwards this strategy will
not be supported anymore.
</action>
<action dev="erans" type="update" issue="MATH-956">
Replaced hard-coded numbers in "LevenbergMarquardtOptimizer".
</action>
<action dev="luc" type="update" issue="MATH-955" due-to="Evan Ward">
Fixed loading of test file when path contains a space.
</action>
<action dev="luc" type="update" issue="MATH-954" due-to="Charles Cooper">
Improved speed of FastMath.abs methods for all signatures, by removing branching.
</action>
<action dev="luc" type="update" issue="MATH-953" due-to="Charles Cooper">
Improved speed of several FastMath methods.
</action>
<action dev="luc" type="fix" issue="MATH-934">
Fixed Complex.reciprocal() for zero argument.
</action>
<action dev="luc" type="update" issue="MATH-951" due-to="Charles Cooper">
Improved speed of FastMath copysign methods.
</action>
<action dev="erans" type="add" issue="MATH-817" due-to="Jared Becksfort">
Added Multivariate Normal Mixture Model Fitting by Expectation Maximization.
</action>
<action dev="tn" type="fix" issue="MATH-862">
AbstractRealMatrix will now check for rectangular input arrays in
its copySubMatrix methods.
</action>
<action dev="erans" type="fix" issue="MATH-949">
Increment iteration counter in optimization algorithms.
</action>
<action dev="luc" type="add" issue="MATH-811" >
Added a way to trigger only increasing or decreasing events in ODE integration.
</action>
<action dev="luc" type="fix" issue="MATH-950" >
Fixed missing update in ODE event handlers, when a RESET_STATE is triggered.
</action>
<action dev="psteitz" type="update" issue="MATH-671">
Made EmpiricalDisribution smoothing kernel pluggable.
</action>
<action dev="psteitz" type="add" issue="MATH-946" due-to="Jared Becksfort">
Added array-scaling methods to MathArrays.
</action>
<action dev="luc" type="update" issue="MATH-877" due-to="Peter Andrews">
Allow direct use of SummaryStatistics in one-way ANOVA.
</action>
<action dev="luc" type="fix" issue="MATH-947" >
Fixed infinite loop when NaN occurs in singular value decomposition.
</action>
<action dev="luc" type="add" issue="MATH-460" due-to="Andrew Waterman">
Added the Lévy distribution.
</action>
<action dev="luc" type="update" >
Normal distribution now uses a direct implementation of the
inverse error function to compute inverse cumulative probability
instead of relying on a numerical solver. This is much faster,
more accurate and does not need convergence threshold.
</action>
<action dev="luc" type="add" issue="MATH-948" >
Implementations for inverse error function and inverse complementary
error functions have been added.
</action>
<action dev="luc" type="fix" issue="MATH-580" >
Extended ranges for FastMath performance tests.
</action>
<action dev="luc" type="fix" issue="MATH-925" >
Finalized implementation of diagonal matrix.
</action>
<action dev="luc" type="fix" issue="MATH-630" due-to="Christopher Nix" >
Added rank revealing QR decomposition.
</action>
<action dev="luc" type="fix" issue="MATH-570" due-to="Arne Plöse" >
ArrayFieldVector can now be constructed from any FieldVector.
</action>
<action dev="luc" type="fix" issue="MATH-861" due-to="Sébastien Brisard" >
Improved checking of null vector elements.
</action>
<action dev="luc" type="add" issue="MATH-845" due-to="Sébastien Riou" >
Added utilities for prime numbers.
</action>
<action dev="luc" type="fix" issue="MATH-936" >
Fixed generation of long random numbers between two bounds.
</action>
<action dev="luc" type="fix" issue="MATH-942" due-to="Piotr Wydrych" >
Fixed creation of generic array.
</action>
<action dev="luc" type="add" issue="MATH-914" >
Check bounds in multi-start vector optimizers.
</action>
<action dev="luc" type="add" issue="MATH-941" due-to="Piotr Wydrych" >
Added discrete distributions.
</action>
<action dev="luc" type="fix" issue="MATH-940" due-to="Piotr Wydrych" >
Fixed abstract test class naming that broke ant builds.
</action>
<action dev="luc" type="fix" issue="MATH-939" due-to="Piotr Wydrych" >
Allow covariance to be computed for one-dimensional variables.
</action>
<action dev="luc" type="fix" issue="MATH-938" >
Fixed accuracy of 3D Line.revert().
</action>
<action dev="luc" type="fix" issue="MATH-937" >
Improved javadoc to explain how switching functions should
behave across events in ODE events detection.
</action>
<action dev="luc" type="add" >
Added Hermite interpolator for RealFieldElement instances.
</action>
<action dev="luc" type="add" >
Added RealFieldElement interface to represent anything that is
real number like, implemented by both Decimal64, Dfp and DerivativeStructure.
</action>
<action dev="luc" type="add" >
Added partial derivatives computation for 3D vectors and rotations.
</action>
<action dev="luc" type="fix" issue="MATH-935" >
Fixed DerivativeStructure.atan2 for special cases when both arguments are +/-0.
</action>
<action dev="luc" type="add" >
Added accurate linear combination of DerivativeStructure instances,
avoiding cancellation.
</action>
<action dev="erans" type="update" issue="MATH-933">
Throw "MathUnsupportedOperationException" from optimizers that do
not support constraints (previous behaviour was to silently ignore
the "SimpleBounds" argument).
</action>
<action dev="luc" type="add" >
Added conversion of gradients and Hessians from spherical to Cartesian
coordinates in 3D.
</action>
<action dev="erans" type="update" issue="MATH-931" due-to="Sean Owen">
Greater efficiency in "UnitSphereRandomVectorGenerator".
</action>
<action dev="tn" type="fix" issue="MATH-930">
Improved class javadoc wrt convergence criteria and added
additional constructors to override the default epsilon and cut-off
values in class "SimplexSolver".
</action>
<action dev="erans" type="fix" issue="MATH-929" due-to="Piotr Wydrych">
Fixed truncated value in "MultivariateNormalDistribution".
</action>
<action dev="erans" type="fix" issue="MATH-927" due-to="Dennis Hendriks">
Made "BitStreamGenerator" implement the "Serializable" interface.
</action>
</release>
<release version="3.1.1" date="2013-01-14" description="
This is a point release: It fixes a bug that renders version 3.1 unusable
in some situations (see details below).
">
<action dev="erans" type="fix" issue="MATH-924">
Added a (minimal) "DiagonalMatrix" implementation, such that the
case of a large number of uncorrelated observations is handled
efficiently.
</action>
</release>
<release version="3.1" date="2012-12-23" description="
This is a minor release: It combines bug fixes and new features.
Changes to existing features were made in a backwards-compatible
way such as to allow drop-in replacement of the v3.0 JAR file.
Most notable among the new features are: Framework for automatic
differentiation, multivariate mixture model distribution, quaternions,
Gauss integration framework, Hermite polynomial interpolation,
eigenvalue decomposition of non-symmetric matrices, DBSCAN clustering.
Most notable among the changes are: Greatly improved precision in
the implementation of the Gamma and Beta special functions, optimizers
API, deprecation of the sparse vector implementation.
The minimal version of the Java platform required to compile and use
Commons Math is Java 5.
Users are encouraged to upgrade to this version as this release not
only includes bug fixes but also deprecates numerous classes and
methods that will be deleted from the next major release (4.0).
Caveat:
1. The implementation of the BOBYQA optimization algorithm is in alpha
state (cf. MATH-621): Many code paths are untested, and we are looking
for volunteers to improve the code readability, robustness and performance
and to extend the unit tests suite.
2. A few methods in the FastMath class are in fact slower that their
counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
">
<action dev="erans" type="add" issue="MATH-874">
All contents of package "o.a.c.m.optimization" refactored into
new packages "o.a.c.m.optimization" and "o.a.c.m.fitting".
</action>
<action dev="psteitz" type="update" issue="MATH-672">
Added methods to EmpiricalDistribution to implement the RealDistribution
interface.
</action>
<action dev="tn" type="add" issue="MATH-897" due-to="Reid Hochstedler">
DBSCAN clustering algorithm (in package "o.a.c.m.stat.clustering").
</action>
<action dev="erans" type="add" issue="MATH-910">
Added element-by-element addition, subtraction, multiplication and division
(in class "o.a.c.m.util.MathArrays").
</action>
<action dev="erans" type="fix" issue="MATH-904" due-to="Jeff Hain">
Fixed "pow" method in class "FastMath".
</action>
<action dev="erans" type="update" issue="MATH-902" due-to="Bruce A. Johnson">
Created a "maximum number of iterations" stopping criterion in the
convergence checkers (package "o.a.c.m.optimization") that allows the
optimizers to return the "current best point" even if the convergence
criteria are not met.
</action>
<action dev="erans" type="fix" issue="MATH-905" due-to="Jeff Hain">
Fixed overflow in "sinh" and "cosh" methods in class "FastMath".
</action>
<action dev="celestin" type="update" issue="MATH-849">
Accuracy improvements of Gamma.logGamma, and implementation of
Gamma.gamma. Both new implementations are based on the NSWC
Library of Mathematical Functions.
</action>
<action dev="erans" type="add" issue="MATH-902">
New constructor in the custom checker classes (package
"o.a.c.m.optimization") for passing the number of iterations
after which the "convergence test" will return true.
This allows an algorithm to return the best solution found (after
the user-defined number of iterations) even if it does not meet the
other convergence criteria.
</action>
<action dev="tn" type="update" issue="MATH-906" due-to="Patrick Meyer">
Use "NaNStrategy#FAILED" as default strategy in "NaturalRanking".
</action>
<action dev="erans" type="add" issue="MATH-899">
Added a new "SynchronizedRandomGenerator" that wraps another
"RandomGenerator" with all methods being synchronized, thus
rendering the code thread-safe (at some efficiency cost).
</action>
<action dev="tn" type="add" issue="MATH-893" due-to="Patrick Meyer">
Add new "NaNStrategy": FAILED, used in "RankingAlgorithm" implementations.
Any encountered input value that succeeds a "Double#isNaN" check, results in a
"NotANumberException".
</action>
<action dev="tn" type="add" issue="MATH-892">
Add new constructor to "SpearmansCorrelation" class which allows to specify the
"RankingAlgorithm" to be used.
</action>
<action dev="luc" type="fix" issue="MATH-890">
Fixed naming inconsistencies between Interval and IntervalsSet classes.
</action>
<action dev="luc" type="add" issue="MATH-889">
Added a method to check points in the Interval class, with a tolerance for boundary.
</action>
<action dev="psteitz" type="add" issue="MATH-878" due-to="Radoslav Tsvetkov">
Added G-test statistics.
</action>
<action dev="erans" type="add" issue="MATH-883">
New "getSquareRoot" method in class "EigenDecomposition" (package
"o.a.c.m.linear").
</action>
<action dev="erans" type="update" issue="MATH-884">
Added "isSymmetric" and "checkSymmetric" in "MatrixUtils" (package
"o.a.c.m.linear").
</action>
<action dev="psteitz" type="update" issue="MATH-885">
Moved private array argument validation methods from ChiSquareTest to MathArrays.
</action>
<action dev="erans" type="add" issue="MATH-816" due-to="Jared Becksfort">
New class for generic multivariate mixture model distributions.
</action>
<action dev="tn" type="fix" issue="MATH-759" due-to="sebb">
Use getter/setter methods of super class for access to field "windowSize" in
"ListUnivariateImpl".
</action>
<action dev="luc" type="fix" issue="MATH-880">
Improved construction of polygons with an additional constructor, more robust numerically.
</action>
<action dev="tn" type="add" issue="MATH-474" due-to="Dan Checkoway">
Added new methods "merge(Frequency)", "merge(Collection<Frequency>)",
"incrementValue(Comparable<?>, long)" and "entrySetIterator()" to the "Frequency" class.
</action>
<action dev="tn" type="fix" issue="MATH-778" due-to="Sébastien Brisard">
Allow unlimited input values for "Dfp#multiply(int)".
</action>
<action dev="luc" type="fix" issue="MATH-641" due-to="Curtis Jensen">
Added distance to point to 2D Line and Segment.
</action>
<action dev="erans" type="fix" issue="MATH-783">
"PowellOptimizer" (package "o.a.c.m.optimization.direct") uses
"BrentOptimizer" as its internal line search optimizer. The fix
forces the convergence criterion of "BrentOptimizer" to use
function values (instead of domain values).
</action>
<action dev="erans" type="fix" issue="MATH-865,MATH-867,MATH-868" due-to="Nikolaus Hansen, Frank Hess">
Numerical accuracy problems arose in "CMAESOptimizer" (in package
"o.a.c.m.optimization.direct") when large finite boundaries were
specified, because the interval of allowed values was mapped to
[0, 1]. This mapping was not necessary and its removal allows
finite and infinite boundaries to be used together.
</action>
<action dev="luc" type="fix" >
Fixed some issues in nth root derivatives at 0.
</action>
<action dev="tn" type="fix" issue="MATH-848">
Fixed transformation to a Schur matrix for certain input matrices.
</action>
<action dev="erans" type="add" issue="MATH-860">
Added matrix "block inversion" (in "o.a.c.m.linear.MatrixUtils").
</action>
<action dev="erans" type="fix" issue="MATH-864" due-to="Frank Hess">
"CMAESOptimizer": Solution was not constrained to lie within the
provided boundaries.
</action>
<action dev="erans" type="add" issue="MATH-863" due-to="Julien Anxionnat">
New "Quaternion" class (package "o.a.c.m.complex").
</action>
<action dev="erans" type="add" issue="MATH-866" due-to="Yannick Tanguy">
Added method to test for floating-point numbers equality with a
relative tolerance (class "o.a.c.m.util.Precision").
</action>
<action dev="tn" type="fix" issue="MATH-666">
Deprecated "FieldVector#getData()" in favor of "toArray()".
</action>
<action dev="luc" type="fix" issue="MATH-789">
Fixed an error in rectangular Cholesky decomposition.
</action>
<action dev="psteitz" type="update" issue="MATH-859">
Clarified definition of isSupportXxxBoundInclusive in RealDistribution
interface, made code consistent with the definition, and deprecated
these methods, marking for removal in 4.0.
</action>
<action dev="erans" type="update" issue="MATH-841" due-to="Sebastien Riou">
Performance improvement in computation of the greatest common divisor
(in class "o.a.c.m.util.ArithmeticUtils").
</action>
<action dev="erans" type="fix" issue="MATH-855">
Added a check so that the returned point will always be the best one.
</action>
<action dev="luc" type="add" >
Added a NewtonRaphsonSolver that uses the new differentiation package
to define the function to solve. This class is intended to replace the
former NewtonSolver which is deprecated.
</action>
<action dev="psteitz" type="update" issue="MATH-850">
Added RandomDataGenerator to replace RandomDataImpl and deprecated
RandomData interface and RandomDataImpl class. Deprecated
nextInversionDeviate methods from RandomDataImpl class. Ensured that
all nextXxx methods in RandomDataImpl/RandomDataGenerator use the
configured RandomGenerator.
</action>
<action dev="erans" type="fix" issue="MATH-844">
Generate an exception for rare ill-conditioned cases in "HarmonicFitter"
guessing procedure (package "o.a.c.m.optimization.fitting").
</action>
<action dev="erans" type="add" issue="MATH-815" due-to="Jared Becksfort">
New interface for multivariate distributions.
Added multivariate normal distribution.
</action>
<action dev="luc" type="add" >
Added a utility method to compute Stirling numbers of the second kind.
</action>
<action dev="luc" type="add" >
Added a new package dealing with differentials, for one or more free
parameters and derivation order 1 or higher.
</action>
<action dev="tn" type="add" issue="MATH-777" due-to="Reid Hochstedler">
Added additional crossover policies: "CycleCrossover", "NPointCrossover",
"OrderedCrossover" and "UniformCrossover".
</action>
<action dev="tn" type="fix" issue="MATH-828">
Improved numerical stability of "SimplexSolver" by introducing Bland's rule
to prevent cycling and a cutoff threshold to zero out very small values.
</action>
<action dev="tn" type="fix" issue="MATH-836" due-to="Baste Nesse Buanes">
Fixed overflow detection for negative values in constructor of class "Fraction".
</action>
<action dev="erans" type="fix" issue="MATH-835" due-to="Baste Nesse Buanes">
Fixed overflow in method "percentageValue" in class "Fraction".
</action>
<action dev="erans" type="fix" issue="MATH-622">
Raised (to 10) the default number of fractional digits to print out.
</action>
<action dev="erans" type="fix" issue="MATH-762">
Removed duplicate code.
</action>
<action dev="tn" type="add" issue="MATH-831">
Added a new "RealMatrixFormat" class for input/output of RealMatrix instances.
Default formatter instances for commons-math and octave have been added to
"MatrixUtils".
</action>
<action dev="erans" type="add" issue="MATH-827">
New "IterativeLegendreGaussIntegrator" that performs the same automatic
subdivision of the integration interval as "LegendreGaussIntegrator",
but uses the classes from package "o.a.c.m.analysis.integration.gauss"
to perform the Gauss integration on the sub-interval.
Deprecated "LegendreGaussIntegrator".
</action>
<action dev="tn" type="fix" issue="MATH-578">
Improve performance of quantile evaluation in "Percentile" class for cases
with lots of equal values.
</action>
<action dev="erans" type="add" issue="MATH-797">
New framework for Gauss integration schemes (in package
"o.a.c.m.analysis.integration.gauss").
Gauss-Legendre quadrature rules (of unlimited order) implemented in
double precision, and high precision (using "BigDecimal").
</action>
<action dev="erans" type="add" issue="MATH-764,MATH-823">
For all distribution classes (in package "o.a.c.m.distribution"), a new
constructor takes a "RandomGenerator" parameter.
The "RandomDataImpl" instance has been superseded by this RNG.
All "sample()" methods have been modified to use this RNG instead of
delegating to the methods in "RandomData".
</action>
<action dev="tn" type="add" issue="MATH-235">
Added support for real asymmetric matrices to "EigenDecomposition".
</action>
<action dev="erans" type="add" issue="MATH-768">
Re-instated methods to find all complex roots of a polynomial (class
"LaguerreSolver" in package "o.a.c.m.analysis.solvers").
</action>
<action dev="erans" type="add" issue="MATH-810">
Added accessors to the "Pair" class (package "o.a.c.m.util").
</action>
<action dev="tn" type="add" issue="MATH-822" due-to="Jared Becksfort">
Added new constructors in "EigenDecomposition" and deprecated two constructors
with unused parameters.
</action>
<action dev="erans" type="fix" issue="MATH-798">
Added overridden method in "PolynomialFitter" (package
"o.a.c.m.optimization.fitting") to limit the number of evaluations.
</action>
<action dev="celestin" type="add" issue="MATH-807">
Added a new constructor to o.a.c.m.utils.IterationManager, allowing
for the specification of a callback function in case the maximum
number of iteration is reached.
</action>
<action dev="luc" type="add">
A new HermiteInterpolator class allows interpolation of vector-valued
functions using both values and derivatives of the function at sample
points.
</action>
<action dev="erans" type="fix" issue="MATH-804">
Parameterized "CurveFitter" class (package "o.a.c.m.optimization.fitting")
with the type of the fitting function. Updated subclasses "PolynomialFitter",
"HarmonicFitter", "GaussianFitter".
</action>
<action dev="luc" type="fix" issue="MATH-801">
Fixed a problem when building rotations from two pairs of vectors. In very rare cases,
due to numerical inaccuracies the computed quaternion was not normalized (some examples
went as high as 1.0e8) and even after normalization, the quaternion was plain wrong.
</action>
<action dev="celestin" type="remove" issue="MATH-796">
Removed unused fields LocalizedFormats.ALPHA and LocalizedFormats.BETA. This is
an acceptable compatibility break, as these fields are only meant for internal use.
</action>
<action dev="tn" type="fix" issue="MATH-644" due-to="marzieh">
Fix computation of upperCumulativeProbability in "HypergeometricDistribution" and
cleanup of duplicate probability mass function.
</action>
<action dev="celestin" type="fix" issue="MATH-791">
In GammaDistribution, deprecated getAlpha() and getBeta(). Replaced with
getShape() and getScale(), respectively.
</action>
<action dev="luc" type="fix" issue="MATH-793" due-to="Sebb">
Use inline computation for OrderedTuple hash code.
</action>
<action dev="tn" type="fix" issue="MATH-718" >
Use modified Lentz-Thompson algorithm for continued fraction evaluation to avoid
underflows.
</action>
<action dev="luc" type="fix" issue="MATH-780" >
Fixed a wrong assumption on BSP tree attributes when boundary collapses to a too
small polygon at a non-leaf node.
</action>
<action dev="luc" type="fix" issue="MATH-787" >
Put serialization back for PointValuePair and PointVectorValuePair.
</action>
<action dev="tn" type="fix" issue="MATH-627" due-to="Arne Plöse">
Avoid superfluous null check when using iterators in RealVector and ArrayRealVector.
</action>
<action dev="tn" type="fix" issue="MATH-781" due-to="Scheiber Ernő">
Use epsilon instead of ulp in floating-point comparison when dropping columns after
phase 1 in SimplexSolver.
</action>
<action dev="luc" type="fix" issue="MATH-721">
Added a workaround for an OpenJDK issue on sparc solaris with too small constants.
</action>
<action dev="tn" type="fix" issue="MATH-779" due-to="Reid Hochstedler">
Fixed ListPopulation#iterator to return an unmodifiable iterator.
</action>
<action dev="tn" type="fix" issue="MATH-775" due-to="Reid Hochstedler">
Cleanup of ListPopulation to consistently enforce the population limit.
</action>
<action dev="tn" type="fix" issue="MATH-776" due-to="Reid Hochstedler">
Use same range check in constructor for ElitisticListPopulation as in corresponding setter.
</action>
<action dev="tn" type="fix" issue="MATH-767" due-to="Dennis Hendriks">
Fixed unbalanced use of code tags in javadoc of several classes.
</action>
<action dev="tn" type="add" issue="MATH-773" due-to="Reid Hochstedler">
Added class FixedElapsedTime (new StoppingCondition for evolution of generations) to genetics package.
</action>
<action dev="celestin" type="add" issue="MATH-756">
Added classes Decimal64 and Decimal64Field, which are wrapper classes around primitive doubles.
These classes implement FieldElement and Field, respectively.
</action>
</release>
<release version="3.0" date="2012-03-07" description="
This is a major release: It combines bug fixes, new features and
changes to existing features.
Most notable among the new features are: Iterative solvers, Kalman filter,
ISAAC RNG, Illinois and Pegasus root finders, enhanced ODE framework,
refactored geometry package, Binary Space Partition trees.
Most notable among the changes are: Exclusive use of unchecked exceptions,
removal of interfaces for which a single implementation is assumed to exist,
improved coding and API consistency across packages, performance (matrix
product, FFT) and robustness (SVD).
Because of the base package name change, this release can be used together
with earlier versions of Commons Math.
The minimal version of the Java platform required to compile and use
Commons Math is Java 5.
Users are encouraged to upgrade to this version as, in addition to new
features, this release includes numerous bug fixes.
Users of Commons Math 2.0-2 should recompile their code against the 3.0 JAR
file and must adjust the import statements to use the appropriate
org.apache.commons.math3 base package.
Most of the compilation errors users will encounter after the switch will
be due to moved or deleted classes/interfaces resulting from package
reorganization.
Caveat:
1. The implementation of the BOBYQA optimization algorithm is in alpha state
(cf. MATH-621): Many code paths are untested, and we are looking
for volunteers to improve the code readability, robustness and performance
and to extend the unit tests suite.
2. A few methods in the FastMath class are in fact slower that their
counterpart in either Math or StrictMath (cf. MATH-740).
">
<action dev="mikl" type="add" issue="MATH-431">
Added statistical hypothesis tests "MannWhitneyUTest" and
"WilcoxonSignedRankTest".
</action>
<action dev="erans" type="update" issue="MATH-698">
Classes "CMAESOptimizer" and "BOBYQAOptimizer" inherit from
"BaseAbstractMultivariateSimpleBoundsOptimizer" (in package
"o.a.c.m.optimization.direct").
</action>
<action dev="sebb" type="fix" issue="MATH-650" >
Added pre-computed arrays to speed up initial loading time for FastMath.
</action>
<action dev="luc" type="update">
Resources for error messages translations have been moved out of META-INF
folder in the jar, to avoid interferences with some build systems.
</action>
<action dev="erans" type="fix" issue="MATH-744" due-to="Thundre">
Fixed "doubleValue" and "floatValue" method in "BigFraction" when
numerator and denominator are larger than the range of the
corresponding primitive type.
</action>
<action dev="erans" type="update" issue="MATH-488">
Removed "MathException" (from package "o.a.c.math").
</action>
<action dev="erans" type="update" issue="MATH-459">
Removed "MathRuntimeException" (from package "o.a.c.math").
</action>
<action dev="tn" type="fix" issue="MATH-739">
Merged interface and implementation of statistical tests in
o.a.c.m.stat.inference package.
</action>
<action dev="tn" type="update" issue="MATH-670">
Merged interface and implementation of EmpiricalDistribution.
</action>
<action dev="tn" type="fix" issue="MATH-588">
Relaxed test for equality in UnivariateStatisticAbstractTest.
</action>
<action dev="tn" type="update" issue="MATH-575">
Modified the genetics package to use localized exception messages.
</action>
<action dev="tn" type="fix" issue="MATH-652" due-to="Greg Sterijevski">
Fixed a faulty test for zero in TridiagonalTransformer.
</action>
<action dev="erans" type="fix" issue="MATH-664">
Changed algorithm in computation of the covariance matrix in
"AbstractLeastSquares" (package "optimization.general"), from
"LUDecomposition" to "QRDecomposition".
</action>
<action dev="psteitz" type="fix" issue="MATH-724" due-to="Dennis Hendriks">
Fixed rounding error in RandomDataImpl nextInt, nextLong methods causing lower
endpoints to be excluded when negative. Also improved robustness of nextUniform
for extreme values and changed its contract to throw IAE when provided bounds
are infinite or NaN.
</action>
<action dev="erans" type="fix" issue="MATH-728" due-to="Bruce A. Johnson">
Fixed "offset by one" bug in "BOBYQAOptimizer".
</action>
<action dev="luc" type="fix" issue="MATH-727">
Check first step size in embedded Runge-Kutta integrators, and truncate it if needed.
</action>
<action dev="psteitz" type="fix" issue="MATH-723">
Modified setSeed methods in Bitstream generators (MersenneTwister and Well
generators) to clear the cache of normal deviates used by nextGaussian.
</action>
<action dev="luc" type="fix" issue="MATH-716">
Fixed bracketing interval balancing in BracketingNthOrderBrentSolver.
</action>
<action dev="erans" type="fix" issue="MATH-690">
Removed unused or duplicate utility methods from "MathUtils".
Math functions with "double" arguments were moved to class "FastMath".
</action>
<action dev="erans" type="fix" issue="MATH-689">
Broke up bloated "MathUtils" class into "MathArrays", "Precision",
"ArithmeticUtils" classes.
</action>
<action dev="psteitz" type="fix" issue="MATH-704" due-to="Thomas Neidhart">
Fixed array indexing error in Variance evaluate method for
computing the weighted variance of an array segment.
</action>
<action dev="luc" type="fix" issue="MATH-713" due-to="Thomas Neidhart">
Fixed case of unconstrained variables that still occur in the objective function
in simplex solver.
</action>
<action dev="luc" type="add" issue="MATH-710" due-to="Eldar Agalarov">
The fast cryptographically secure pseudorandom number generator ISAAC has been added.
</action>
<action dev="luc" type="add" issue="MATH-714">
The reset method in StepHandler interface has been renamed init and is provided
more information on the integration by the calling integrator. A similar init method
has been added to the EventHandler interface.
</action>
<action dev="luc" type="fix" issue="MATH-705">
Improved accuracy of Runge-Kutta based step interpolators near step start.
</action>
<action dev="psteitz" type="fix" issue="MATH-691">
Fixed errors in SummaryStatistics addValue causing variance, mean, or
geometric mean statistics not to be updated if they have been overridden
using instances of commons-math supplied implementations.
</action>
<action dev="psteitz" type="update" issue="MATH-694">
Removed First, Third, Fourth moments from the public API.
These internally used statistics have non-standard definitions.
The classes remain, but now have package scope.
</action>
<action dev="psteitz" type="update" issue="MATH-693">
Added support for population variance in StatUtils, SummaryStatistics
and DescriptiveStatistics and clarified javadoc to make it clear that
'variance' means sample variance.
</action>
<action dev="luc" type="fix" issue="MATH-709">
Fixed BigFraction percentage method which did not work at all.
</action>
<action dev="erans" type="update" issue="MATH-697">
Added interface and abstract class for supporting optimizers classes
that can take simple constraints into account.
</action>
<action dev="luc" type="fix" due-to="MATH-706" >
Fixed a bad interaction between step handlers and event handlers in
ODE integrators.
</action>
<action dev="luc" type="add" due-to="Jan Kotek" >
Added array constructor and getter for Vector2D and Vector3D.
</action>
<action dev="luc" type="add" due-to="Jan Kotek" >
Added applyTo and applyInverseTo methods in the Rotation class that
handle directly arrays instead of Vector3D instances.
</action>
<action dev="luc" type="fix" issue="MATH-196" >
Added adapters for simple bound constraints optimization that can be
used for all direct optimization methods, including the ones that do not
support constraints by themselves.
</action>
<action dev="luc" type="fix" issue="MATH-702" >
CMA-ES optimizer input sigma is now consistent with boundaries range units.
</action>
<action dev="psteitz" type="add" issue="MATH-462" due-to="Pavel Ryzhof">
Added stable random generator based on Chambers-Mallows-Stuck method.
</action>
<action dev="psteitz" type="update" issue="MATH-701">
Changed the default seed used for RandomDataImpl, AbstractWell and MersenneTwister
PRNGs to add the system identity hash code of the instance to the current system
time, so generators initialized with default seeds within system clock resolution
will generate different sequences. Changed the default non-secure generator used
by RandomDataImpl to Well19937c.
</action>
<action dev="luc" type="fix" issue="MATH-695">
Fixed an event resetting issue in ODE.
</action>
<action dev="erans" type="update" issue="MATH-696">
Default implementation for "addToEntry" and "multiplyEntry" in
"AbstractRealMatrix".
</action>
<action dev="erans" type="add" issue="MATH-685">
Method "addToEntry" in "RealVector".
</action>
<action dev="psteitz" type="update" issue="MATH-612" due-to="Christopher Nix">
Replaced temporary matrices and entry mutators with double[][] arrays to speed computation
in loops within QRDecomposition, Bi- and TriDiagonalTransformer implementations.
</action>
<action dev="luc" type="fix" issue="MATH-679" due-to="Christopher Berner">
Fixed an integer overflow in OpenMapRealMatrix.
</action>
<action dev="erans" type="fix" issue="MATH-688">
"FastMath": Use constant fields instead of recomputing them at method
call.
</action>
<action dev="luc" type="add" issue="MATH-687" due-to="Romain di Costanzo">
Added Jacobi polynomials.
</action>
<action dev="erans" type="add" issue="MATH-683" due-to="Romain di Costanzo">
Added "shift" method to compute the coefficients of a new polynomial
whose values are the same as those of another polynomial but computed
at a shifted point.
</action>
<action dev="erans" type="fix" issue="MATH-676">
Faster "multiply" method in "Array2DRowRealMatrix". Code inspired
from the Jama project.
</action>
<action dev="luc" type="fix" issue="MATH-445" >
Replaced package.html with package-info.java for package documentation.
</action>
<action dev="luc" type="fix" issue="MATH-284" due-to="Klaus Hartlage">
Added a getRuntimeClass method to the Field interface allowing to use a
complete hierarchy of fields sharing a common interface.
</action>
<action dev="luc" type="fix" issue="MATH-457" >
The last remaining uses of OptimizationException have been replaced by unchecked
exceptions (UnboundSolutionException, NoFeasibleSolutionException,
MaxCountExceededException ...)
</action>
<action dev="luc" type="fix" issue="MATH-487" >
The checked ConvergenceException has been replaced by an unchecked ConvergenceException.
</action>
<action dev="luc" type="fix" issue="MATH-381" due-to="Pascal Parraud">
ODE step interpolation with Jacobians is now fully merged with
classical step interpolation.
</action>
<action dev="luc" type="fix" issue="MATH-380" due-to="Pascal Parraud">
Completely revamped the computation of Jacobians in ODE. This computation is now
included in the mainstream class hierarchy, not in a separate package anymore,
and it allows adding other types of equations to a main ODE, not only variational
equations for Jacobians computation.
</action>
<action dev="gregs" type="update" issue="MATH-607">
SimpleRegression implements UpdatingMultipleLinearRegression interface.
</action>
<action dev="gregs" type="update" issue="MATH-675">
Added isMonotone methods in MathUtils. Optimized checkOrder method.
</action>
<action dev="erans" type="fix" issue="MATH-664">
In class "AbstractLeastSquaresOptimizer": Allow to specify a singularity
threshold in call to "getCovariances" method.
</action>
<action dev="gregs" type="update" issue="MATH-649">
Added the ability to suppress the estimation of the intercept in SimpleRegression.
</action>
<action dev="sebb" type="fix" issue="MATH-658" due-to="Yannick TANGUY">
Dead code in FastMath.pow(double, double) and some improvement in test coverage.
</action>
<action dev="erans" type="fix" issue="MATH-663">
Removed "getData()" method from "RealVector" as it was redundant with
"toArray()".
</action>
<action dev="luc" type="update" issue="MATH-195" >
Removed completely MathUserException.
</action>
<action dev="luc" type="update" issue="MATH-488" >
Use the refactored exceptions framework for ODE.
</action>
<action dev="luc" type="add" >
Added a getter to allow retrieving the exception related to an exception context
provider.
</action>
<action dev="psteitz" type="update" issue="MATH-364" due-to="Christian Winter">
Added erf(double,double) to Erf and used this to improve tail probability
accuracy in NormalDistributionImpl.
</action>
<action dev="psteitz" type="fix" issue="MATH-654">
Enabled reseeding of the random generators used by EmpiricalDistributionImpl
and ValueServer. Modified ValueServer to pass its RandomData instance to
the EmpiricalDistributionImpl that it creates when used in DIGEST_MODE, so
reseeding ValueServer works as expected.
</action>
<action dev="erans" type="fix" issue="MATH-653">
Renamed "AbstractRealVector" to "RealVector". The interface was removed
in favour of its unique (abstract) implementation. Also removed several
methods with double[] arguments from AbstractRealVector.
</action>
<action dev="erans" type="add" issue="MATH-646" due-to="Sébastien Brisard">
Unmodifiable view of a "RealVector".
</action>
<action dev="luc" type="fix" issue="MATH-501" >
Refactored integration API for consistency with solvers API. Now the main convergence
parameters are set in the constructor and remain fixed.
</action>
<action dev="luc" type="fix" issue="MATH-464" >
Added a maximal number of function evaluations to the integration method, similar
to what is done in the solvers API.
</action>
<action dev="psteitz" type="update" issue="MATH-449" due-to="Patrick Meyer">
Added storeless covariance implementation.
</action>
<action dev="psteitz" type="update" issue="MATH-648">
Eliminated extraneous constructor from SimpleRegression.
</action>
<action dev="psteitz" type="update" issue="MATH-506">
Eliminated pluggability of ChiSquaredDistribution used by ChiSquaredDistributionTest.
</action>
<action dev="psteitz" type="update" issue="MATH-634">
Made RandomGenerator configurable and reseedable in EmpiricalDistributionImpl.
</action>
<action dev="luc" type="add" issue="MATH-593">
Added a 3D SubLine class.
</action>
<action dev="erans" type="fix" issue="MATH-645">
Fixed exceptions generated by "ebeMultiply" and "ebeDivide" in "OpenMapRealVector".
</action>
<action dev="erans" type="add" issue="MATH-602" due-to="Greg Serijevski">
In "SingularValueDecompositionImpl", added accessor for the inverse of the condition number.
</action>
<action dev="psteitz" type="fix" issue="MATH-601" due-to="Chris Nix and Greg Serijevski">
Made pseudo-inverse consistent with rank computation in SingularValueDecompositionImpl.
</action>
<action dev="psteitz" type="update" issue="MATH-624" due-to="Greg Sterijevski">
Added methods to solve upper and lower triangular systems to MatrixUtils.
</action>
<action dev="psteitz" type="update" issue="MATH-642">
Improved performance of nextInt(int) in BitsStreamGenerator.
</action>
<action dev="luc" type="fix" issue="MATH-639" >
Fixed a wrong detection of rotation axis versus vectors plane in Rotation constructor
using two vectors pairs.
</action>
<action dev="luc" type="add" >
Added a few linearCombination utility methods in MathUtils to compute accurately
linear combinations a1.b1 + a2.b2 + ... + an.bn taking great care to compensate
for cancellation effects. This both improves and simplify several methods in
euclidean geometry classes, including linear constructors, dot product and cross
product.
</action>
<action dev="psteitz" type="fix" issue="MATH-640">
Fixed bugs in AbstractRandomGenerator nextInt() and nextLong() default
implementations. Prior to the fix for this issue, these methods
generated only positive values.
</action>
<action dev="erans" type="add" issue="MATH-637">
Simple benchmark utility (new class "PerfTestUtils" added to test sources in src/test).
</action>
<action dev="luc" type="add" issue="MATH-636" >
Added a solver for Dfp-based (i.e. high accuracy) functions.
</action>
<action dev="luc" type="add" issue="MATH-635" >
Added a Brent-like solver that has higher (user specified) order and does
bracket selection on the result: BracketingNthOrderBrentSolver.
</action>
<action dev="luc" type="add" >
Added a few shortcut methods and predicates to Dfp (abs, isZero,
negativeOrNull, strictlyNegative, positiveOrNull, strictlyPositive).
</action>
<action dev="erans" type="add" issue="MATH-633" due-to="Sébastien Brisard">
"AbstractRealMatrix" inherits from "RealLinearOperator".
</action>
<action dev="erans" type="add" issue="MATH-613" due-to="Sébastien Brisard">
Linear combination of vectors: "RealVector" interface updated, implemented
in "AbstractRealVector" and "ArrayRealVector".
</action>
<action dev="erans" type="update" issue="MATH-623" due-to="Arne Plöse">
Slightly more efficient implementation of basic operations in
"ArrayRealVector".
</action>
<action dev="erans" type="add" issue="MATH-577" due-to="Arne Plöse">
Overloaded methods (add, subtract, multiply, divide) to take a "double" parameter
(as a complex number with zero imaginary part).
Code and Javadoc cleanup.
Added "valueOf" methods.
</action>
<action dev="mikl" type="fix" issue="MATH-585">
Implemented faster generation of random gamma distributed values with
algorithm from Ahrens and Dieter (1972) for shape < 1 and
Marsaglia and Tsang (2001) otherwise.
</action>
<action dev="luc" type="fix" issue="MATH-605" due-to="Dennis Hendriks">
Allow discrete events to be detected by ODE solvers also at step start.
</action>
<action dev="luc" type="fix" issue="MATH-327,MATH-383,MATH-465,MATH-583,MATH-611" due-to="Christopher Nix">
Rewritten SVD decomposition based on JAMA code.
</action>
<action dev="psteitz" type="fix" issue="MATH-618" due-to="Arne Plose">
Complex add javadoc says that if either addend has NaN parts, the result
should be Complex.NaN. Prior to the fix for this issue, NaNs were propagated
only in real and imaginary parts individually.
</action>
<action dev="erans" type="add" issue="MATH-581" due-to="Sébastien Brisard">
Framework for iterative linear solvers.
</action>
<action dev="psteitz" type="update" issue="MATH-609" due-to="Dave Brosius">
Improved efficiency in RandomDataImpl, LaguerreSolver, FastMath and OutlineExtractor by
moving conditional code into blocks where it is needed.
</action>
<action dev="luc" type="fix" issue="MATH-603" due-to="Dennis Hendriks">
Prevent step normalizer to output twice the last point in MULTIPLES mode.
</action>
<action dev="luc" type="fix" issue="MATH-596,MATH-604">
Removed the requiresDenseOutput method from the StepHandler interface. Now integrators always