Repository: commons-math Updated Branches: refs/heads/master 9f42f18f1 -> 09129d536
prepared release notes for version 3.4 Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/09129d53 Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/09129d53 Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/09129d53 Branch: refs/heads/master Commit: 09129d536726fac7f94f6b641e34a34a49c9a012 Parents: 9f42f18 Author: Luc Maisonobe <l...@apache.org> Authored: Sat Dec 13 22:04:33 2014 +0100 Committer: Luc Maisonobe <l...@apache.org> Committed: Sat Dec 13 22:04:33 2014 +0100 ---------------------------------------------------------------------- RELEASE-NOTES.txt | 273 ++++++++++++------------------------------- src/changes/changes.xml | 9 +- 2 files changed, 82 insertions(+), 200 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/commons-math/blob/09129d53/RELEASE-NOTES.txt ---------------------------------------------------------------------- diff --git a/RELEASE-NOTES.txt b/RELEASE-NOTES.txt index 16bfcde..7930ea8 100644 --- a/RELEASE-NOTES.txt +++ b/RELEASE-NOTES.txt @@ -1,24 +1,24 @@ - Apache Commons Math 3.3 RELEASE NOTES + Apache Commons Math 3.4 RELEASE NOTES -The Apache Commons Math team is pleased to announce the release of commons-math3-3.3. +The Apache Commons Math team is pleased to announce the release of commons-math3-3.4-SNAPSHOT -The Apache Commons Math project is a library of lightweight, self-contained mathematics -and statistics components addressing the most common practical problems not immediately -available in the Java programming language or commons-lang. +The Apache Commons Math project is a library of lightweight, self-contained mathematics and statistics components addressing the most common practical problems not immediately available in the Java programming language or commons-lang. 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.x JAR file. +way such as to allow drop-in replacement of the v3.3 JAR file. Most notable among the new features are: -Framework for creating artificial neural nets, self organizing feature maps, -computational geometry algorithms (convex hull, enclosing ball), performance -improvements of the linear simplex solver, refactoring of curve fitters, -low-discrepancy random generators (sobol, halton), least-squares fitting. +new distributions (Gumbel, Laplace, Logistic, Nakagami), and +improvements on percentiles algorithms (better handling for NaNs +in the regular algorithm, plus a new storeless implementation). +Bicubic splines interpolators have been fixed and new implementations +added. There have been numerous bug fixes and several improvements +on performances or robustness. See below for a full list) -The minimum version of the Java platform required to compile and use -Commons Math is Java 5. + The minimum version of the Java platform required to compile and use +Apache 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 @@ -32,203 +32,80 @@ Caveat: 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). - 3. A few methods/constructors in the package o.a.c.m.geometry.partitioning - have changed their signature in a non backwards-compatible way. The respective - classes are intended to be package private only and are not supposed to be - used for other purposes. Changes in this version include: New features: -o N/A: Added an order 6 fixed-step ODE integrator designed by H. A. Luther in 1968. -o MATH-1110: Added new constructor to "OLSMultipleLinearRegression" to be able - to specify a custom singularity threshold for QR decomposition. Thanks to Edward Segall. -o MATH-1119: Added a fast single-step method for fixed-step Runge-Kutta integrators. -o MATH-1101: Improved documentation of QR decomposition handling of singular matrices. -o MATH-1053: QR decomposition can compute pseudo-inverses for tall matrices. Thanks to Sean Owen. -o MATH-820: Field vectors now implement the visitor pattern just like real vectors. -o MATH-749: Added MonotoneChain algorithm to compute the convex hull of a collection of - points in 2D. Additionally, the AklToussaintHeuristic can be used to speed up the generation. -o MATH-1095: Added Emo Welzl algorithm to find the smallest enclosing ball of a collection of points. -o MATH-1072: Added a constructor to "AbstractListChromosome" that does not copy the input argument. -o MATH-1091: BSP tree now provides an API to compute a global signed distance from - a test point to the region. The distance is positive if the point is - outside of the region, negative if the point is inside, and zero - when the point is at the boundary. The distance is continuous - everywhere, so it can be used with a root solver to identify accurately - boundary crossings. This API is available for all BSP trees, in - Euclidean and spherical geometries, and in all dimensions. -o N/A: Added new geometry sub-packages: spherical.oned which deals with geometry - on the 1-sphere (i.e. the circle) and spherical.twod which deals with the - 2-sphere (i.e. the regular sphere). BSP trees can be used in these new - spaces, so one can build arcs sets and spherical polygons sets with all - the regular operations (inside/outside/boundary checks, union, intersection, - symetric difference, complement ...). -o MATH-1090: IntervalsSet now implements Iterable<double[]>, so one can iterate - over the sub-intervals without building a full list containing a copy of everything beforehand. -o MATH-923: Utilities for creating artificial neural networks (package "o.a.c.m.ml.neuralnet"). - Implementation of Kohonen's Self-Organizing Feature Map (SOFM). -o MATH-1014: Refactoring of curve fitters (package "o.a.c.m.fitting"). -o MATH-970: Added possibility to retrieve the best found solution of the "SimplexSolver" in case - the iteration limit has been reached. The "optimize(OptimizationData...)" method now - supports a "SolutionCallback" which provides access to the best solution if - a feasible solution could be found (phase 2 of the Two-Phase simplex method has been reached). -o MATH-1061: Added InsufficientDataException. -o MATH-983: Added a graphical overview of available continuous distributions to the userguide. -o MATH-1051: Added Kendall's tau correlation (KendallsCorrelation). Thanks to Matt Adereth,devl. -o MATH-1036: Added SparseGradient to deal efficiently with first derivatives when the number - of variables is very large but most computations depend only on a few of the - variables. Thanks to Ajo Fod. -o MATH-1038: Added ConfidenceInterval class and BinomialConfidenceInterval providing several - estimators for confidence intervals for binomial probabilities. Thanks to Thorsten Schäfer. -o MATH-1004: Added new methods to compute the inverse of a matrix to "DiagonalMatrix" - and "MatrixUtils". Thanks to Ajo Fod. -o MATH-1041: "Pair": added factory method and "toString" method. Thanks to Sean Owen. -o MATH-1002: "AbstractUnivariateStatistic.test(...)" methods have uses outside subclasses; - implementation moved to MathArrays.verifyValues(...). -o MATH-1034: Added exact binomial test implementation. Thanks to Thorsten Schäfer. -o MATH-1018: Added overloaded constructors for subclasses of "RealDistribution" implementations - which do not require an explicit "inverseCumulativeAccuracy". The default accuracy will - be used instead. Thanks to Ajo Fod. -o MATH-1001: Added overloaded methods for "Frequency#incrementValue(Comparable, long)" with - int, long and char primitive arguments. Thanks to sebb. -o MATH-1030: Added a section to the userguide for the new package o.a.c.m.ml with an - overview of available clustering algorithms and a code example. Thanks to Thorsten Schäfer. -o MATH-1028: Added new distance metric "EarthMoversDistance". Thanks to Thorsten Schäfer. -o MATH-1025: Added CombinatoricsUtils to the util package, moving binomial - coefficients, factorials and Stirling numbers there and adding - a combinations iterator. -o MATH-991: "PolynomialSplineFunction": added method "isValidPoint" that - checks whether a point is within the interpolation range. -o MATH-989: "BicubicSplineInterpolatingFunction": added method "isValidPoint" that - checks whether a point is within the interpolation range. -o MATH-1010: Utility to shuffle an array. -o MATH-1008: Created package ("o.a.c.m.fitting.leastsquares") for least-squares - fitting, with implementations of "LevenbergMarquardtOptimizer" and - "GaussNewtonOptimizer" adapted to a new ("fluent") API. -o MATH-1007: Add mode function to StatUtils class. -o MATH-1000: Add mode function to Frequency class. -o MATH-997: Implemented Gauss-Hermite quadrature scheme (in package "o.a.c.m.analysis.integration.gauss"). -o MATH-967: Added midpoint integration method. Thanks to Oleksandr Kornieiev. -o MATH-851: Added method "MathArrays#convolve(double[], double[])" to compute the - discrete, linear convolution of two sequences. Thanks to Clemens Novak. -o MATH-977: Added low-discrepancy random generator "HaltonSequenceGenerator". -o MATH-826: Added low-discrepancy random generator "SobolSequenceGenerator". Thanks to Sam Halliday. -o MATH-973: Added "GeometricDistribution" to "o.a.c.m.distribution" package. Thanks to Mauro Tortonesi. -o MATH-968: Added "ParetoDistribution" to "o.a.c.m.distribution" package. Thanks to Alex Gryzlov. -o MATH-898: Added "FuzzyKMeansClusterer" to "o.a.c.m.ml.clustering" package. +o MATH-1166: New classes "BicubicInterpolatingFunction" and "BicubicInterpolator" to + replace "BicubicSplineInterpolatingFunction" and "BicubicSplineInterpolator". +o Boundary attributes in regions now provides the BSP tree nodes that + were used to split the sub-hyperplane forming the boundary part of the facet. +o MATH-1144: Interface to allow parameter validation in "o.a.c.m.fitting.leastsquares": + the point computed by by the optimizer can be modified before evaluation. +o MATH-1154: Changed classes in the inference package that instantiate distributions to + pass null RandomGenerators to avoid initialization overhead for the default + generator. +o MATH-1156: Added all Java 8 StrictMath methods to FastMath, so FastMath remains compatible + with newer Java versions. +o MATH-1139: Added Gumbel, Laplace, Logistic and Nakagami distributions. Thanks to Alexey Volkov. +o MATH-1120: Added several different estimation types and NaN handling strategies for Percentile. Thanks to Venkatesha Murthy. +o MATH-418: Added implementation of PSquare algorithm to estimate percentiles without + storing data in memory (i.e. as StorelessUnivariateStatistic). Thanks to Venkatesha Murthy. Fixed Bugs: -o N/A: Fixed an issue with noisy functions for ODE events detection. -o MATH-1092: Extracted class "LineSearch" from "PowellOptimizer", to be used in - "NonLinearConjugateGradientOptimizer" (in place of the implementation that triggered this issue). -o MATH-1115: Build properly empty polyhedrons set when given equal min/max boundaries. Also explained - better in the javadoc about some wrong usage of PolyhedronsSet constructor. -o MATH-1117: Build properly empty polygons set when given equal min/max boundaries. Also explained - better in the javadoc about some wrong usage of PolygonsSet constructor. -o MATH-1118: "Complex": Fixed compatibility of "equals(Object)" with "hashCode()". - Added new methods for testing floating-point equality between the real - (resp. imaginary) parts of two complex numbers. -o MATH-1107: Prevent penalties to grow multiplicatively in CMAES for out of bounds points. Thanks to Bruce A Johnson. -o MATH-875: Un-deprecated RealVector.sparseIterator, documenting explicitly that entries - not iterated above are the zero ones. -o MATH-821: Relaxed specification for function mapping on vectors, thus allowing straightforward - implementation for sparse vectors. -o MATH-1065: Calculating the inverse cumulative probability of an "EnumeratedRealDistribution" - will now return the correct result according to the selected enumerated probability - mass function. Thanks to matteodg. -o MATH-976: Create additional artifact "commons-math3-x.y.z-tools.jar" as part of the - release process. This artifact contains useful tools, e.g. for performance testing. -o MATH-990: Improved performance of "MathArrays#sortInPlace(...)". -o MATH-1044: Clarify javadoc of "DecompositionSolver#getInverse()" and corresponding implementations - wrt the actually returned inverse. Several decomposition implementations are able - to return a pseudo-inverse in case of a singular matrix. Thanks to Sean Owen. -o MATH-985: Fixed an indexing problem in "BicubicSplineInterpolatingFunction" which - resulted in wrong interpolations. Thanks to Johnathan Kool. -o MATH-1089: "Precision#round(double, ...)" will now return negative zero for negative - values rounded to zero, similar to the float variant. -o MATH-1088: The iterator returned by "MultiDimensionalCounter#iterator()" will now - correctly throw a "NoSuchElementException" when calling "next()" and the iterator is already exhausted. -o MATH-1082: The cutOff mechanism of the "SimplexSolver" in package o.a.c.math3.optim.linear - could lead to invalid solutions. The mechanism has been improved in a way that - the tableau does not need to be updated anymore. Additionally, a new check will - prevent impossible solutions to be returned as valid. -o MATH-1079: Improved performance of "SimplexSolver" in package o.a.c.math3.optim.linear by - directly performing row operations and keeping track of the current basic variables. -o MATH-842: Added support for different pivot selection rules to the "SimplexSolver" by introducing - the new "OptimizationData" class "PivotSelectionRule". Currently supported rules are: - Dantzig (default) and Bland (avoids cycles). -o MATH-1070: Fix "Precision#round(float, int, int)" when using rounding mode "BigDecimal.ROUND_UP" - and the discarded fraction is zero. Thanks to Oleksandr Muliarevych. -o MATH-1059: Use "FastMath" instead of "Math" within Commons Math. -o MATH-1068: Avoid overflow when calculating Kendall's correlation for large arrays. Thanks to Gal Lalouche. -o MATH-1067: Avoid infinite recursion in "Beta.regularizedBeta" (package "o.a.c.m.special"). Thanks to Florian Erhard. -o MATH-1056: Fixed unintended integer division error in PoissonDistribution sampling method. Thanks to Sean Owen. -o MATH-1057: Fixed failing unit tests for "BOBYQAOptimizer" when executed with a Oracle/Sun JVM 1.5. -o MATH-1062: A call to "KalmanFilter#correct(...)" may have resulted in "NonSymmetricMatrixException" - as the internally used matrix inversion method was using a too strict symmetry check. -o MATH-1058: Precision improvements (for small values of the argument) in "Beta" function - and in "LogNormalDistribution" and "WeibullDistribution". Thanks to Sean Owen. -o MATH-1055: Fixed some invalid links inside javadoc and added missing deprecated annotations. Thanks to Sean Owen. -o MATH-1051: "EigenDecomposition" may have failed to compute the decomposition for certain - non-symmetric matrices. Port of the respective bugfix in Jama-1.0.3. -o MATH-1047: Check for overflow in methods "pow" (class "o.a.c.m.util.ArithmeticUtils"). -o MATH-1045: "EigenDecomposition": Using tolerance for detecting whether a matrix is singular. Thanks to Sean Owen. -o MATH-1035: Simplified and improved performance of "ArithmeticUtils#addAndCheck(long, long)". Thanks to derphead. -o MATH-1029: The "BigFraction" constructor will throw a "FractionConversionException" - also in case negative values are provided which exceed the allowed range (+/- Integer.MAX_VALUE). -o MATH-1033: The "KalmanFilter" wrongly enforced a column dimension of 1 for - the provided control and measurement noise matrix. Thanks to Yuan Qu. -o MATH-1037: Fix a typo in the test class of "GeometricDistribution" and ensure that a meaningful - tolerance value is used when comparing test results with expected values. Thanks to Aleksei Dievskii. -o MATH-996: Creating a "Fraction" or "BigFraction" object with a maxDenominator parameter - does not throw a "FractionConversionException" anymore in case the value is - very close to fraction. Thanks to Tim Allison. -o MATH-999: Improve performance of "DiagonalMatrix#preMultiply(RealVector)". Thanks to Ajo Fod. -o MATH-1021: Fixed overflow in "HypergeometricDistribution". Thanks to Brian Bloniarz. -o MATH-1020: Fixed "nextPermutation" method (in "o.a.c.m.random.RandomDataGenerator"). - This bug does not affect applications using a previous version of Commons Math. -o MATH-1019: Buggy (private) method "shuffle" in "o.a.c.m.random.RandomDataGenerator" - superseded by "MathArrays.shuffle" (cf. MATH-1010). -o MATH-1012: Created "RandomGeneratorFactory" (package "o.a.c.m.random") to reduce - code duplication in "RandomDataGenerator". -o MATH-1005: Fixed "MathArrays.linearCombination" when array length is 1. Thanks to Roman Werpachowski. -o MATH-993: In "GaussNewtonOptimizer", check for convergence before updating the - parameters estimation for the next iteration. -o MATH-988: Fixed NullPointerException in 2D and 3D sub-line intersections. Thanks to Andreas Huber. -o MATH-962: Added clarification to the javadoc of "VectorFormat" and derived classes - in case "," is used as a separator. -o MATH-965: Fixed inconsistent dimensions preventing use of secondary states in ODE events. +o MATH-1178: Fixed example in userguide ("stat" section). Thanks to Dmitriy. +o MATH-1175: Fixed inverse cumulative probability of 0 in "LaplaceDistribution". Thanks to Karsten Loesing. +o MATH-1174: Fixed a problem with too thin polygons considered to have infinite size. +o MATH-1162: Fixed a problem with vanishing cut sub-hyperplanes during BSP tree merging. +o MATH-1167: "o.a.c.m.stat.regression.OLSMultipleLinearRegression": Use threshold + when performing "QRDecomposition". Thanks to Neil Ireson. +o MATH-1165: "FuzzyKMeansClusterer" has thrown an exception in case one of the data + points was equal to a cluster center. Thanks to Pashutan Modaresi. +o MATH-1160: Provide access to state derivatives in ContinuousOutputModel. +o MATH-1138: Fixed bicubic spline interpolator, using Akima splines. Thanks to Hank Grabowski. +o MATH-1147: Added statistics missing from toString method in SummaryStatistics. +o MATH-1152: Improved performance of "EnumeratedDistribution#sample()" by caching + the cumulative probabilities and using binary rather than a linear search. Thanks to Andras Sereny. +o MATH-1148: "MonotoneChain" did not take the tolerance factor into account when + sorting the input points. In case of collinear points this could result + in a "ConvergenceException" when computing the hull. Thanks to Guillaume Marceau. +o MATH-1151: Interface "ValueAndJacobianFunction" is a precondition for lazy + evaluation (in "o.a.c.m.fitting.leastsquares"). +o MATH-1145: Fix potential integer overflows in "MannWhitneyUTest" when providing + large sample arrays. Thanks to Anders Conbere. +o MATH-1149: Fixed potential null pointer dereferencing in constructor of + "DummyStepInterpolator(DummyStepInterpolator)". Thanks to M Kim. +o MATH-1136: Fixed BinomialDistribution to deal with degenerate cases correctly. Thanks to Aleksei Dievskii. +o MATH-1135: "MonotoneChain" failed to generate a convex hull if only a minimal hull + shall be created (includeCollinearPoints=false) and collinear hull points + were present in the input. Thanks to Guillaume Marceau. +o MATH-1131: Improve performance of "KolmogorovSmirnovTest#kolmogorovSmirnovTest(...)" for + large samples. Also changed implementation for large n to use Pelz-Good + approximation. Thanks to Schalk W. Cronjé. +o MATH-1134: "BicubicSplineInterpolatingFunction": all fields made final and initialized in + the constructor. Added flag to request initialization, or not, of the internal + data needed for partial derivatives. +o MATH-984: Constrained EmpiricalDistribution sample/getNextValue methods to return + values within the range of the data; correctly linked RandomGenerator to + superclass so that RealDistribution reseedRandomGenerator method works. +o MATH-1129: "Percentile": wrong sorting in the presence of NaN. +o MATH-1127: Fixed overflow in Precision.equals with ulps (both double and float versions). +o MATH-1125: Performance improvements for Student's t-distribution. Thanks to Ajo Fod. +o MATH-1123: Fixed NullPointerException when chopping-off a sub-hyperplane + that is exactly at a region boundary. Thanks to Aurélien Labrosse. +o MATH-1121: "BrentOptimizer": increment base class iteration counter. Thanks to Ajo Fod. Changes: -o N/A: Bracketing utility for univariate root solvers returns a tighter interval than before. - It also allows choosing the search interval expansion rate, supporting both linear - and asymptotically exponential rates. -o MATH-437: Added KolmogorovSmirnovTest class, deprecating KolmogorovSmirnovDistribution. -o MATH-1099: Make QR the default in GaussNewtonOptimizer. Thanks to Evan Ward. -o MATH-1099: Add Cholesky option to GaussNewtonOptimizer. Thanks to Evan Ward. -o MATH-1099: Make QR in GaussNewton faster and more accurate. Thanks to Evan Ward. -o MATH-870: The sparse vector and matrix classes have been un-deprecated. This is a reversal - of a former decision, as we now think we should adopt a generally accepted - behavior which is ... to ignore the problems of NaNs and infinities in - sparse linear algebra entities. -o MATH-1050: Deprecated "ArithmeticUtils#pow(int, long)" and "ArithmeticUtils#pow(long, long)" - in favor of corresponding methods "ArithmeticUtils#pow(..., int)". -o MATH-1080: The "LinearConstraintSet" will now return the enclosed collection of "LinearConstraint" - objects in the same order as they have been added. -o MATH-1031: Added new class "ClusterEvaluator" to evaluate the result of a clustering algorithm - and refactored existing evaluation code in "MultiKMeansPlusPlusClusterer" - into separate class "SumOfClusterVariances". Thanks to Thorsten Schäfer. -o MATH-1039: Added logDensity methods to AbstractReal/IntegerDistribution with naive default - implementations and improved implementations for some current distributions. Thanks to Aleksei Dievskii. -o MATH-1011: Improved implementation of "sample" method of "UniformIntegerDistribution". -o MATH-1006: Enabled LaTeX expressions in javadoc and site docs via MathJax. -o MATH-995: Documented limitation of "IterativeLegendreGaussIntegrator" (added warning about potential wrong usage). -o MATH-987: Added append method to SimpleRegression, making this class map/reducible. Thanks to Ajo Fod. -o MATH-978: Added append method to StorelessCovariance, making this class map/reducible. Thanks to Ajo Fod. +o Spurious vertices in the middle of otherwise straight edges are now + filtered out when rebuilding polygons boundaries from BSP trees. +o MATH-1128: Added lazy evaluation to "LeastSquaresFactory" (in "o.a.c.m.fitting.leastsquares") + to avoid evaluating the model when the optimization algorithm does not actually + require it. For complete information on Apache Commons Math, including instructions on how to submit bug reports, patches, or suggestions for improvement, see the Apache Commons Math website: http://commons.apache.org/proper/commons-math/ + + http://git-wip-us.apache.org/repos/asf/commons-math/blob/09129d53/src/changes/changes.xml ---------------------------------------------------------------------- diff --git a/src/changes/changes.xml b/src/changes/changes.xml index d241c57..22a5143 100644 --- a/src/changes/changes.xml +++ b/src/changes/changes.xml @@ -53,10 +53,15 @@ If the output is not quite correct, check for invisible trailing spaces! <release version="3.4" date="TBD" 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.x JAR file. + way such as to allow drop-in replacement of the v3.3 JAR file. Most notable among the new features are: - XXX + new distributions (Gumbel, Laplace, Logistic, Nakagami), and + improvements on percentiles algorithms (better handling for NaNs + in the regular algorithm, plus a new storeless implementation). + Bicubic splines interpolators have been fixed and new implementations + added. There have been numerous bug fixes and several improvements + on performances or robustness. See below for a full list) The minimum version of the Java platform required to compile and use Apache Commons Math is Java 5.
