Release notes

5.0.1

Bugs

#550: Erroneous index check for Sample.argAt(int) method in io.jenetics.prog.regression package.
#554: ClassCastException in io.jenetics.prog.regression.Regression class.

5.0.0

Improvements

#534: Generify Regression classes so it can be used for regression analysis of arbitrary types.
#529: Implementation of Hybridizing PSM and RSM mutation operator (HPRM)
#518: Implementation of Symbolic Regression classes. This makes it easier to solve such optimization problems.
#515: Rename Tree.getIndex(Tree) to Tree.indexOf(Tree).
#509: Allow to collect the nth best optimization results.

final ISeq<EvolutionResult<DoubleGene, Double>> best = engine.stream()
    .limit(Limits.bySteadyFitness(50))
    .flatMap(MinMax.toStrictlyIncreasing())
    .collect(ISeq.toISeq(10));

#504: Rename Tree.getChild(int) to Tree.childAt(int).
#500: Implementation of Reverse Sequence mutation operator (RSM).
#497: Implement Boolean operators for GP.
#496: Implement GT operator for GP.
#493: Add dotty tree formatter
#488: Implement new tree formatter TreeFormatter.LISP. This allows to create a Lisp string representation from a given Tree.
#487: Re-implementation of 'MathTreePruneAlterer'. The new implementation uses the newly introduced Tree Rewriting API, implemented in #442.
#486: Implement TreeRewriteAlterer, based on the new Tree Rewriting API.
#485: Cleanup of MathExpr class.
#484: The Tree.toString() now returns a parentheses string.
#481: The parentheses tree representation now only escapes "protected" characters.
#469: Implementation of additional Evaluator factory methods.
#465: Remove fitness scaler classes. The fitness scaler doesn't carry its weight.
#455: Implementation of CompletableFutureEvaluator.
#450: Improvement of FutureEvaluator class.
#449: The Engine.Builder constructor is now public and is the most generic way for creating engine builder instances. All other builder factory methods are calling this primary constructor.
#447: Remove evolution iterators. The whole evolution is no performed via streams.
#442: Introduce Tree Rewriting API, which allows to define own rewrite rules/system. This is very helpful when solving GP related problems.

final TRS<String> trs = TRS.parse(
    "add(0,$x) -> $x",
    "add(S($x),$y) -> S(add($x,$y))",
    "mul(0,$x) -> 0",
    "mul(S($x),$y) -> add(mul($x,$y),$y)"
);

// Converting the input tree into its normal form.
final TreeNode<String> tree = TreeNode.parse("add(S(0),S(mul(S(0),S(S(0)))))");
trs.rewrite(tree);
assert tree.equals(TreeNode.parse("S(S(S(S(0))))"));

#372: Allow to define the chromosome index an Alterer is allowed to change. This allows to define alterers for specific chromosomes in a genotype.

// The genotype prototype, consisting of 4 chromosomes
final Genotype<DoubleGene> gtf = Genotype.of(
    DoubleChromosome.of(0, 1),
    DoubleChromosome.of(1, 2),
    DoubleChromosome.of(2, 3),
    DoubleChromosome.of(3, 4)
);

// Define the GA engine.
final Engine<DoubleGene, Double> engine = Engine
    .builder(gt -> gt.getGene().doubleValue(), gtf)
    .selector(new RouletteWheelSelector<>())
    .alterers(
        // The `Mutator` is used on chromosome with index 0 and 2.
        SectionAlterer.of(new Mutator<DoubleGene, Double>(), 0, 2),
        // The `MeanAlterer` is used on chromosome 3.
        SectionAlterer.of(new MeanAlterer<DoubleGene, Double>(), 3),
        // The `GaussianMutator` is used on all chromosomes.
        new GaussianMutator<>()
    )
    .build();

#368: Remove deprecated code.
#364: Clean implementation of async fitness functions.
#342: The Tree accessor names are no longer in a Java Bean style: getChild(int) -> childAt(int). This corresponds to the childAtPath(path) methods.
#331: Remove hashCode and equals method from Selector and Alterer.
#314: Add factory method for AdaptiveEngine, which simplifies its creation.
#308: General improvement of object serialization.
#50: Improve Genotype validation. The new Constraint interface, and its implementation RetryConstraint, now allows a finer control of the validation and recreation of individuals.

Bugs

#520: Fix tree-rewriting for Const values. This leads to non-matching nodes when trying to simplify the GP tree.
#475: Level function returns different results depending on whether the iterator is iterating through a ProgramGene or TreeNode.
#473: DynamicGenotype example causes IllegalArgumentException.

4.4.0

Improvements

#316: Improve implementation of tree rewriting. This is a preparations tep for #442.
#414: Use Gradle 'implementation' instead of 'compile' dependency
#426: Relax final restriction on some Alterer implementations. All alterers can now be sub-classed.
#430: Codec for numeric 2d matrices.
#433: Upgrade Gradle to 5.x.
#443: Precondition check for XXXChromosome.of(Gene...) factory methods.
#445: Mark Phenotype.newInstance methods as deprecated.
#457: Add <A> A[] Seq.toArray(IntFunction<A[]> generator) method.

Bugs

#425: Manual fixes.

4.3.0

Improvements

#347: Improve hashCode and equals methods.
#349: Cleanup of chromosome constructors. Make the constructors more regular.
#355: Simplify implementation of numeric genes.
#361: Add NumericChromosome.primitiveStream() methods.
#366: Deprecate reference to fitness function property from Phenotype. Preparation step for generalizing the fitness evaluation.
#377: Add Tree.childAt method. Lets you fetch deeply nested child nodes.
#378: Convert tree to parentheses tree string.
#379: Parse parentheses tree string to tree object.
#380: Add TreeNode.map method.
#400: Codec for mapping source- and target objects.
#406: Make the library compilable under Java 11.
#411: Improve the behaviour of the MathExpr.format method.

Bugs

#357: Invalid length of selected population in MonteCarloSelector.
#420: Limits.byFitnessThreshold termination strategy is missing best generation.

4.2.1

Bugs

416: Method internal comb.subset doesn't create all possible combinations. The PermutationChromosome is therefore not able to create solutions for the whole search space.

4.2.0

Improvements

#325: Allow customization of fitness evaluation execution for bundling calculations
#327: Improve CPU utilization during fitness evaluation.
#335: Seq view wrapper for List and T[] types.

Bugs

#317: Fix links of Javadoc images.
#318: NULL result from engine.stream() after upgrade from 4.0.0 to 4.1.0.
#336: Errornous default implementation of 'Seq.indexWhere'.
#341: Error in internal 'bit.increment' method.
#345: Assumption for 'Genotype.newInstance(ISeq)' no longer holds.

4.1.0

Improvements

#223: Implementation of Multi-Objective Optimization.
#259: Pruning GP program tree.
#285: Population exchange between different Engines.
#294: Cleanup of Jenetics examples.
#295: Upgrade Gradle version 4.5.
#297: Compile JMH test on test execution.
#306: Improve Javadoc on how to extend chromosomes.
#307: Enable @apiNote, @implSpec and @implNote Javadoc tag.

Bugs

#290: User's manual fixes.
#298: Fix GP load/save of generated tree.

4.0.0

Improvements

#28: Immutable population class. The original Population class has been replaced by Seq<Phenotype<G, C>>. This points to a more functional implementation of the library.
#119: Chromosome implementations are now fully immutable. This is an internal change only.
#121: Mutator class is easier now to extend. It has been extended with additional mutate methods which serves as extension points for onw Mutator implementations.
#123: Chromosome with variable number of genes: Most chromosomes can now be created with a variable number of genes. DoubleChromosome.of(0.0, 1.0, IntRange.of(5, 16)).
#172: io.jenetics.prngine library replaces the existing PRNG implementations in the io.jenetics.base module.
#175: Align random int range generation with io.jenetics.prngine library. This is an internal change only.
#180: Change library namespace from org.jenetics to io.jenetics. This is the most invasive change of this release. Users have to adopt the imports in all their code.
#183: Change copyright email address to ...@gmail.com
#200: Implementation of gene convergence termination: A termination method that stops the evolution when a user-specified percentage of the genes that make up a Genotype are deemed as converged. A gene is deemed as converged when the average value of that gene across all of the genotypes in the current population is less than a user-specified percentage away from the maximum gene value across the genotypes.
#253: Removal of deprecated code and classes: mainly JAXB marshalling and the LCG64ShiftRandom class.
#260: Clean room implementation of internal subset function. This method was a port from the C++ source written by John Burkardt. The original source has been published under the LGPL licence, which is not compatible to tha Apache 2 licence. To avoid legal issues, the affected method has been reimplemented using the Clean Room method, based on the original book, Combinatorial Algorithms for Computers and Calculators, by Albert Nijenhuis and Herbert Wilf. The io.jenetics.internal.math.comb.subset method is now fully compatible with the Apache 2 licence.
#262: Filter for duplicate individuals: It is now possible to intercept the stream of EvolutionResults of the evolution Engine:

final Engine<DoubleGene, Integer> engine = Engine.builder(problem)
	.mapping(EvolutionResult.toUniquePopulation())
	.build();

#264: Upgrade Gradle to version 4.3.
#266: The Seq serialization should be more robust in the case of implementation changes.
#268: Implementation of an EliteSelector.
#269: Cleanup of internal, mathematical helper functions.
#272: Obey Java naming convention. Two helper classes have been renamed to obey the Java naming conventions. codecs -> Codecs and limits -> Limits.
#279: Additional MSeq.swap method.

Bugs

#247: Fix the classpath of the jrun helper script.
#256: Buggy type signature of AnyChromosome.of method.

3.9.0

Improvements

#26: Extend Gradle scripts for multi-module releases.
#27: Parallel EvolutionStream.
#64: Implementation of TreeGene/Chromosome.
#181: XML marshaling module: org.jenetics.xml.
#199: Termination: Population convergence.
#201: Simplify Gradle build scripts.
#204: Remove internal 'Stack' container class.
#207: Add missing BitChromosome factory methods.
#216: Restructuring of User's Manual.
#218: Mark LCG64ShiftRandom class as deprecated.
#219: Mark JAXB marshaling as deprecated.
#227: Genetic Programming module: org.jenetics.prog.
#228: Upgrade Gradle to 4.0.2.
#229: Define stable module names.
#236: Rename module jenetix to org.jenetics.ext
#238: Align project directories with maven artifact names.

Bugs

#212: Fix Seq.toArray(Object[]) method.
#226: Incorrect MinMax.toString() output.
#233: Engine.java Comment Grammar Fix.
#234: Population.empty() isn't empty

3.8.0

Improvements

#157: Add LineCrossover class.
#158: Add IntermediateCrossover class.
#168: Remove dependency to java.desktop module.
#169: Describe how to configure (μ, λ) and (μ + λ) Evolution Strategies in manual.
#177: Additional 'Seq' conversion functions:
- Seq.asISeq()
- Seq.asMSeq()
#182: Rename build script to default names. All build scripts are now named build.gradle.
#188: Additional Engine.Builder methods
#189: TruncationSelector is now able to globally limit best selected individuals. This is used for (μ, λ) and (μ + λ) Evolution Strategies.
#197: Improve CPU utilization for long running fitness functions. The original concurrent fitness function evaluation where assumed to be quite fast.

3.7.0

Improvements

#127: Change the maven group and artifact ID from org.bitbucket:org.jenetics to io.jenetics:jenetics.
#142: Jenetics now compiles without warnings with Java 9 EA.
#145: Add additional Engine.stream(...) and Engine.iterator(...) methods:
#150: Implement fitness convergence termination strategy.
#152: Remove hashCode and replace equals method with sameState(T) for mutable objects.
#156: Implementation of an UniformCrossover.
#162: Update and improve User's Manual.

Bug fixes

#143: Fix serialization of EvolutionResult class.
#146: NPE in EvolutionResult.toBestEvolutionResult() when collecting empty EvolutionStreams.
#159: The User's Manual build fails for Lyx version 2.2.2.

3.6.0

Improvements

#103: Add MSeq.sort method.
#114: Alterer implementations are now able to handle Chromosomes of different length.
#135: Add Codec.decode(Genotype) default method.
#140: Additional EvolutionResult.toBestResult collectors.

Bug fixes

#129: Fix Javadoc encoding.

Updates

#134: Update Gradle to 3.1.
#138: Update TestNG to 6.9.13.

3.5.1

Bug fixes

#111: Dead lock for single-threaded executors.

3.5.0

Improvement

#81: It is now easier to register user-defined JAXB marshallings -- org.jenetics.util.IO.JAXB.register
#90, #91: The manual contains now a section where the performance of the MonteCarloSelector and an evolutionary Selector is compared (fig. 6.8, page 52).
#96: Merge branch with incubation module org.jenetix, which contains experimental classes.
#101: Add manual example for solving the Rastrigin function.

Bug fixes

#92: Fix example code in user manual.
#94: Inconsistent pre-condition check of Engine.Builder.build method.
#99: EvolutionResult was not completely immutable.

3.4.0

Improvement

#68: Improve implementations of Seq interfaces. Note: The changes of this issue changes the Java serialization of the Genes and Chromosomes. Gene/Chromosomes which has been serialized with version 3.3 can't be loaded with version 3.4. As a workaround, it is still possible to write the Genes/Chromosomes in XML format and load it with version 3.4.
#73: Add additional methods to Seq interface: Seq.append and Seq.prepend.
#79: Improve evolution performance measuring. Code resides now in (experimental) org.jenetics.tool module.
#85: Add support for fixed-sized subsets in PermutationChromosome class. See also codecs.ofSubSet(ISeq, int).

3.3.0

Improvement

#43: Add Evolving images example.
#62: Two or more Codec interfaces can be combined into a single one.
#66: Add AnyGene and AnyChromosome for arbitrary allele types.

Bug fixes

#52: Immutability of ISeq violated.
#55: Fixing example-run script for Mac.

3.2.0

Improvements

#24: Stabilize statistical selector tests.
#25: Remove testng.xml file. The test classes are now determined automatically.
#40: Introduce Codec interface for defining problem encodings.
Add Internal section in manual, which describes implementation details.

Bug fixes

#33: Selectors must not change the input population. This occasionally caused ConcurrentModificationException. Such selectors are now creating a defensive copy of the input population.
#34: IndexOutOfBoundsException when selecting populations which are too short.
#35: IndexOutOfBoundsException when altering populations which are too short.
#39: Numerical instabilities of ProbabilitySelector.
#47: Engine deadlock for long running fitness functions.

3.1.0

Improvements

Additional termination strategies in org.jenetics.engine.limit class.
Add EvolutionStream.of factory method. This allows to use other evolution functions than the Engine class.
org.jenetics.stat.Quantile has now a combine method which lets them use in a parallel stream.
#12: Fix typos in user manual.
#13: Add link to Javadoc and manual to README file.
#14: Remove Serializable interface from Gene and Chromosome.
#16: Make code examples in Javadoc standard conform.
#17: Improve recombination section in manual.
#20: Advance Genotype validity checks.

3.0.1

Fixes: #2, #7

3.0.0

Rewrite of engine classes to make use of Java 8 Stream API.

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