225 lines
15 KiB
Plaintext
225 lines
15 KiB
Plaintext
|
|
Apache Commons Math 4.0-beta1 RELEASE NOTES
|
|
|
|
The Apache Commons Math team is pleased to announce the release of commons-math4-parent-4.0-beta1
|
|
|
|
The Apache Commons Math project is a library of lightweight mathematics
|
|
and statistics components addressing common practical problems.
|
|
|
|
This is a major release that requires source changes in applications.
|
|
Lower-level functionality has been split off to new components, often
|
|
with bug-fixes, performance enhancements and improved API:
|
|
Commons RNG,
|
|
Commons Numbers,
|
|
Commons Geometry,
|
|
Commons Statistics.
|
|
Functionality still within Commons Math has been modularized and
|
|
partly refactored.
|
|
This is a work-in-progress (help welcome).
|
|
Codes for which the refactoring has not been undertaken (or was
|
|
deemed incomplete) have been moved to 'legacy' modules.
|
|
The minimum version of the Java platform required to compile and use
|
|
Commons Math is Java 8.
|
|
Users are encouraged to upgrade to this version, and to the new
|
|
components listed above (they are now Commons Math's dependencies).
|
|
For code now located in the 'commons-math-legacy' module, upgrading
|
|
will be a matter of changing the top-level package name:
|
|
From 'org.apache.commons.math3' to 'org.apache.commons.math4.legacy'.
|
|
Code in the 'commons-math-legacy-core' module comprise classes that
|
|
moved from package 'org.apache.commons.math3' and package
|
|
'org.apache.commons.math3.util' (e.g. 'MathArrays') to package
|
|
'org.apache.commons.math4.legacy.core'.
|
|
Notes:
|
|
Class 'FastMath' was renamed 'AccurateMath' (now located in package
|
|
'org.apache.commons.math4.legacy.core.jdkmath').
|
|
Caveat:
|
|
Although hundreds of issues have been fixed (see 'git log' and the
|
|
reports in the bug-tracking system of all the listed components),
|
|
many remain due to the lack of human resources necessary in order
|
|
to support the whole codebase (it was one of the main reasons for
|
|
creating more focused components).
|
|
|
|
Changes in this version include:
|
|
|
|
New features:
|
|
o MATH-1648: "BicubicInterpolator": Provide partial derivatives of interpolating functions. Thanks to Alessandro Moscatelli.
|
|
o MATH-1371: Add "ElkanKMeansPlusPlusClusterer" clustering algorithm. Thanks to Artem Barger.
|
|
o MATH-1622: Update class "SimplexOptimizer" (in package "o.a.c.m.legacy.optim.nonlinear.scalar.noderiv")
|
|
to support simulated annealing.
|
|
o MATH-1551: "Percentile": Partial support for weighted data. Thanks to Allen Yu.
|
|
o MATH-1529: "AkimaSplineInterpolator": Option to use alternative weights.
|
|
o MATH-1509: Add "MiniBatchKMeansClusterer" clustering algorithm. Thanks to Chen Tao.
|
|
o MATH-1519: Add "Calinski-Harabsz" clustering evaluator. Thanks to Chen Tao.
|
|
o MATH-1516: Interface for ranking a list of clusters.
|
|
o MATH-1477: "MillerUpdatingRegression": Fixed "ArrayIndexOutOfBounds" exception. Thanks to Chee Sing Lee.
|
|
o MATH-1459: Create a way to automatically calculate a Jacobian matrix using a differentiator. Thanks to Adrian Porter.
|
|
o MATH-1426: "DescriptiveStatistics": allow "Double[]" as initializer. Thanks to Karl Richter.
|
|
o MATH-1383: Dependency toward the "Commons Rng" component.
|
|
o MATH-1015: Gauss-Laguerre quadrature. Thanks to Thomas Neidhart.
|
|
o MATH-1350: Improved code coverage (unit tests). Thanks to Rob Tompkins.
|
|
o MATH-1336: New 64-bits RNG implementations. On 64-bits systems, they are ~35% faster than
|
|
"java.util.Random" for generating "long" or "double" values. They also guarantee
|
|
much better randomness than "Random" (cf. MATH-1327).
|
|
o MATH-1335: Refactoring of uniform random number generator functionality: new API
|
|
implemented in package "o.a.c.m.rng".
|
|
o MATH-1337: Adaptor class from new API ("o.a.c.m.rng.RandomSource") to old API
|
|
("o.a.c.m.random.RandomGenerator").
|
|
o MATH-1327: Report on performance and correctness of the new RNG implementations.
|
|
o MATH-1314: Javadoc of the new RNG API ("o.a.c.m.rng") mentions the "seed problem".
|
|
o MATH-1158: New interface for sampling from distribution (package "o.a.c.m.distribution").
|
|
o MATH-1351: New sampler API for "MultivariateRealDistribution".
|
|
o MATH-1348: Adaptor for using one of the new RNG implementations where an instance of
|
|
"java.util.Random" is required.
|
|
o MATH-1295: "FactorialLog": Cache-based computation of the "log factorial" function (implemented
|
|
as an inner class of "CombinatoricsUtils" in package "o.a.c.m.util"). Thanks to Aleksei Dievskii.
|
|
o MATH-1271: Added divideUnsigned and remainderUnsigned to ArithmeticUtils. Thanks to Qualtagh.
|
|
o Added a fast implementation of IEEEremainder in FastMath.
|
|
o MATH-945: Added method "T log10()" to interface "RealFieldElement".
|
|
o MATH-1039: Added logDensity(double) to RealDistribution and logProbability(int)
|
|
to IntegerDistribution interface. The implementations have already been
|
|
updated in release 3.3. Thanks to Aleksei Dievskii.
|
|
|
|
Fixed Bugs:
|
|
o MATH-1647: "HaltonSequenceGenerator": Raise exception when precondition is not met. Thanks to Maksym Bohachov.
|
|
o MATH-1462: "EmpiricalDistribution": Use constant kernel for bins that contain up to 3 values.
|
|
o MATH-1379: Fix "LoessInterpolator" (in package "o.a.c.m.legacy.analysis.interpolation"). Thanks to Richard Wilkinson.
|
|
o MATH-1617: Class "BigReal": Fix equality check. Thanks to Ng Tsz Sum.
|
|
o MATH-1613: Decrease maximum number of iterations in "SimpsonIntegrator" and
|
|
"TrapezoidIntegrator" (due to the available range of the internal
|
|
counter of function evaluations).
|
|
o MATH-1431: "EmpiricalDistribution" handles empty bin. Thanks to Artem Onuchin.
|
|
o MATH-1565: Add context to "OutOfRangeException". Thanks to Randy Strauss.
|
|
o MATH-1558: "MidPointIntegrator": Fix iterative procedure in order to actually benefit
|
|
from evaluations performed at earlier stages. Thanks to Sam Ritchie.
|
|
o MATH-1555: "Atan2": Documentation issue. Thanks to Laurent Galluccio.
|
|
o MATH-1549: "SimplexTableau": Internally "scale down" the problem definition when the
|
|
constraints are defined with large numbers, in order to avoid spurious
|
|
exceptions caused by floating-point accuracy errors. Thanks to Mohammad Rezaei.
|
|
o MATH-1548: Avoid inefficiencies in computing the standard quality measures of a SOFM.
|
|
o MATH-1537: Clean-up (typos and unused "import" statements). Thanks to Jin Xu.
|
|
o MATH-1531: "EmpiricalDistribution": Workaround to avoid spurious exception.
|
|
o MATH-1511: Issue in site generation and developers documentation.
|
|
o MATH-1518: Remove code duplication by moving method to class "Cluster".
|
|
o MATH-1388: Avoid overflow.
|
|
o MATH-1401: "ClopperPearsonInterval": Missing cases. Thanks to Michele De Stefano.
|
|
o MATH-1463: "IntegerSequence.incrementor": Throw "NoSuchElementException" from "next" method.
|
|
o MATH-1458: "SimpsonIntegrator": Fixed iteration. Thanks to Alex Herbert.
|
|
o MATH-1419: "PolynomialSplineFunction": incorrect usage of exception. Thanks to Hang Park.
|
|
o MATH-1413: add generics to the Frequency class
|
|
o MATH-1417: "RRQRDecomposition": bug in method "performHouseholderReflection". Thanks to Jean-Francois Lecomte.
|
|
o MATH-1381: Fix "BinomialTest": P-value larger than 1. Thanks to Kexin Xie.
|
|
o MATH-1382: "MultivariateNormalDistribution": performance improvement (by
|
|
removing unnecessary copying). Thanks to Stefan Bunk.
|
|
o MATH-1405: "KolmogorovSmirnovTest": bug in "fixTies". Thanks to Daniil Finkel.
|
|
o MATH-1376: "SimplexOptimizer": Wrong value of iteration number was passed to the convergence checker. Thanks to Thomas Weise.
|
|
o MATH-1319: Major refactoring of package "o.a.c.m.random".
|
|
o MATH-1366: Removed obsolete RNG API (replaced by classes under "o.a.c.m.rng").
|
|
o MATH-1340: Avoid exception swallowing (in class "TestUtils").
|
|
o MATH-1339: Avoid redundant object creation.
|
|
o MATH-1356: "HypergeometricDistribution": Handle special cases that produced NaN.
|
|
o MATH-1343: "BetaDistribution": Removed unnecessary recomputation.
|
|
o MATH-1124: "JDKRandomGenerator": Method "nextInt(int)" now throws a "NotStrictlyPositiveException".
|
|
The class now delegates to (rather inherits from) "java.util.Random".
|
|
o MATH-1300: "AbstractRandomGenerator" and "BitsStreamGenerator": Remove a redundant call
|
|
to the random data provider. Thanks to Rostislav Krasny.
|
|
o MATH-1231: Lifted unnecessary restriction on constructor's argument of
|
|
"MicrosphereInterpolator" (package "o.a.c.m.analysis.interpolation").
|
|
o MATH-1230: The "SimplexSolver" will now throw a "DimensionMismatchException"
|
|
when calling "optimize(...)" with linear constraints whose dimension
|
|
does not match the dimension of the objective function.
|
|
o MATH-1222: Use Double.isNaN rather than x != x in FastMath. Thanks to Benedikt Ritter.
|
|
o MATH-1143: Added helper methods to FunctionUtils for univariate and multivariate differentiable functions conversion.
|
|
o MATH-964: Removed unused package private class PollardRho in package primes.
|
|
o MATH-1221: Improve performance of "ZipfDistribution" by caching the nth generalized harmonic.
|
|
o MATH-1205: Methods "evaluate(...)" of class "Variance" changed the internal state
|
|
although it was stated differently in the javadoc.
|
|
o MATH-1191: Fixed ignored method parameters in QRDecomposition protected methods.
|
|
o MATH-1212: Changed javadoc as the RandomDataGenerator class does not implement
|
|
an interface anymore (the previous interface has been deprecated in
|
|
3.X and removed in 4.0).
|
|
|
|
Changes:
|
|
o MATH-1653: Remove class "CombinatoricsUtils" (in package "o.a.c.m.util").
|
|
Functionality is in "Commons Numbers" combinatorics package.
|
|
o MATH-1640: Do not change caller's arguments in "KMeansPlusPlusClusterer":
|
|
A negative value for "maxIterations" will raise an exception.
|
|
o MATH-1629: Throw "ArithmeticException" instead of "MathArithmeticException".
|
|
o MATH-1630: Introduce "JdkMath" class for redirecting calls to either JDK or CM
|
|
implementations of the functions defined in "java.lang.Math".
|
|
o Simplify assertions with simpler equivalent. Thanks to Arturo Bernal.
|
|
o MATH-1573: Remove redundant local variables. Thanks to Arturo Bernal.
|
|
o MATH-1572: Simplify conditional expressions. Thanks to Arturo Bernal.
|
|
o MATH-1616: Refactor "EmpiricalDistribution" class (in package "o.a.c.m.legacy.distribution").
|
|
o MATH-1595: Clean up "o.a.c.math4.legacy.random" package.
|
|
o MATH-1615: Remove class "StableRandomGenerator" (in package "o.a.c.m.legacy.random").
|
|
o MATH-1614: Refactor "SimplexOptimizer" (in package "o.a.c.m.legacy.optim.nonlinear.scalar.noderiv").
|
|
o MATH-1582: Transforms codes moved into a dedicated maven module.
|
|
o MATH-1578: ANN codes moved into a dedicated maven module.
|
|
o MATH-1575: Modularization set-up: All codes were moved into a "legacy" maven module.
|
|
WIP: Functionalities should gradually be moved into dedicated modules.
|
|
o MATH-1562: Add "Automatic-Module-Name" entry to JAR manifest file. Thanks to Frank Ulbricht.
|
|
o MATH-1554: Remove package "o.a.c.math4.geometry".
|
|
o MATH-1547: More flexible ranking of SOFM.
|
|
o MATH-1530: "SplineInterpolator": Improved performance. Thanks to Yassine Damerdji.
|
|
o MATH-1524: Code reuse. Thanks to Chen Tao.
|
|
o MATH-1522: Remove generic parameter in clustering evaluator interfaces. Thanks to Chen Tao.
|
|
o MATH-1523: Abstract class "ClusterEvaluator" replaced by an interface.
|
|
o MATH-1408: Do not use exceptions for control flow
|
|
o MATH-1362: Removed deprecated class "Incrementor" (replaced by "IntegerSequence.Incrementor").
|
|
o MATH-1506: Removed class "MultidimensionalCounter" (ported to "Commons Numbers").
|
|
o MATH-1504: Removed class "BigFraction" (ported to "Commons Numbers").
|
|
o MATH-1446: Removed class "Fraction" (ported to "Commons Numbers").
|
|
o MATH-1469: Removed most codes in package "o.a.c.m.geometry".
|
|
"Commons Math" now depends on "Commons Geometry".
|
|
o MATH-1481: "SobolSequenceGenerator": Update data file. Thanks to Théophile Charmont.
|
|
o MATH-1389: Performance improvement for Array2DRowRealMatrix.getSubMatrix() Thanks to Christoph Dibak.
|
|
o MATH-1377: "SimplexOptimizer": Slight performance improvement.
|
|
o MATH-1318: "o.a.c.m.special.Gamma.digamma": Improved performance (through the use of
|
|
the reflection formula for negative arguments). Thanks to Eric Prescott-Gagnon.
|
|
o MATH-1305: "AbstractRandomGenerator" and "BitsStreamGenerator": Slight performance
|
|
improvement of the "nextBytes" method (particularly when the number of
|
|
requested bytes is a multiple of 4). Thanks to Rostislav Krasny.
|
|
o MATH-853: "MathRuntimeException" is now the base class for all commons-math
|
|
exceptions (except for "NullArgumentException" which extends
|
|
"NullPointerException").
|
|
o MATH-1205: The abstract class "AbstractStorelessUnivariateStatistic" does not
|
|
extend anymore from "AbstractUnivariateStatistic".
|
|
o MATH-1205: Default implementation of
|
|
"AbstractStorelessUnivariateStatistic#equals(Object)"
|
|
will only return true if both instances have the same type. Previously
|
|
different statistics were considered to be equal if their current state
|
|
happened to be equal.
|
|
o MATH-1205: Default implementations of "AbstractStorelessUnivariateStatistic#evaluate(...)"
|
|
do not alter the internal state anymore. Instead a temporary copy of
|
|
the statistic is created for evaluation purposes.
|
|
o MATH-1206: Added new API methods in "LeastSquaresProblem.Evaluation" (package
|
|
"o.a.c.m.fitting.leastsquares").
|
|
o MATH-1210: "QRDecomposition": include information about the condition that
|
|
triggers a "SingularMatrixException".
|
|
o MATH-757: Removed broken synchronization support in "ResizableDoubleArray".
|
|
o MATH-869: "SpearmansCorrelation" will now throw an "MathIllegalArgumentException"
|
|
if provided with a "NaturalRanking" instance that uses "REMOVED" as "NaNStrategy".
|
|
o MATH-869: "NullArgumentException" extends now "java.lang.NullPointerException"
|
|
instead of "MathIllegalArgumentException".
|
|
o MATH-839: Renamed "cumulativeProbability(double, double)" to "probability(double, double)"
|
|
in "IntegerDistribution" and "RealDistribution". Thanks to Gilles Sadowski.
|
|
o MATH-1155: WELL type pseudo-random number generators have been refactored:
|
|
the cached indirection index tables per instance are now stored
|
|
in a static instance. This reduces the initialization cost when
|
|
creating a new instance.
|
|
o MATH-825: Method "LaguerreSolver#laguerre(...)" has been made private. Thanks to Gilles Sadowski.
|
|
o MATH-760: Field "windowSize" in "DescriptiveStatistics" has been made private. Thanks to sebb.
|
|
|
|
Removed:
|
|
o MATH-1205: Removed methods "test(...)" from "AbstractUnivariateStatistic".
|
|
The already existing methods "MathArrays#verifyValues(...)" shall
|
|
be used instead.
|
|
o MATH-1050: Removed "ArithmeticUtils#pow(int, long)" and "ArithmeticUtils#pow(long, long)".
|
|
|
|
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/
|
|
|
|
|