Update to MOEAFramework 4.0

Author: dhadka

.classpath

@@ -9,6 +9,7 @@
 	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="optional" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
@@ -22,9 +23,10 @@
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 			<attribute name="test" value="true"/>
+			<attribute name="optional" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java: [ '8', '11', '16', '17', '18', '19', '20' ]
+        java: [ '17', '18', '19', '20', '21' ]
     steps:
       - uses: actions/checkout@v3
       - name: Set up JDK ${{ matrix.java }}

.github/workflows/stage.yml

@@ -25,10 +25,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up JDK 16
+      - name: Set up JDK 17
         uses: actions/setup-java@v3
         with:
-          java-version: 16
+          java-version: 17
           distribution: temurin
       - name: Install required software
         run: |

COPYING

@@ -1,4 +1,4 @@
-Copyright 2009-2022 David Hadka and other contributors.  All rights reserved.
+Copyright 2009-2024 David Hadka and other contributors.  All rights reserved.
 
 The MOEA Framework is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by 

README.md

@@ -24,7 +24,7 @@ Add the following dependency to your `pom.xml`:
 <dependency>
     <groupId>org.moeaframework</groupId>
     <artifactId>gd</artifactId>
-    <version>1.2</version>
+    <version>2.0</version>
 </dependency>
 ```
 
@@ -47,7 +47,7 @@ If unset, it will default to uniformly-spaced points generated using the Normal
 
 ## License
 
-Copyright 2009-2022 David Hadka and other contributors.  All rights reserved.
+Copyright 2009-2024 David Hadka and other contributors.  All rights reserved.
 
 The MOEA Framework is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by

pom.xml

@@ -31,15 +31,15 @@
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<maven.compiler.source>8</maven.compiler.source>
-		<maven.compiler.target>8</maven.compiler.target>
+		<maven.compiler.source>17</maven.compiler.source>
+		<maven.compiler.target>17</maven.compiler.target>
 	</properties>
 
 	<dependencies>
 		<dependency>
 			<groupId>org.moeaframework</groupId>
 			<artifactId>moeaframework</artifactId>
-			<version>3.2</version>
+			<version>4.0</version>
 			<scope>provided</scope>
 		</dependency>
 		<dependency>
@@ -58,13 +58,13 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.11.0</version>
+			<version>2.15.1</version>
 			<scope>provided</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.12.0</version>
+			<version>3.14.0</version>
 			<scope>provided</scope>
 		</dependency>
 		<dependency>

src/main/java/org/moeaframework/gd/Example.java

@@ -1,3 +1,20 @@
+/* Copyright 2009-2024 David Hadka
+ *
+ * This file is part of the MOEA Framework.
+ *
+ * The MOEA Framework is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
+ *
+ * The MOEA Framework is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+ * License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the MOEA Framework.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package org.moeaframework.gd;
 
 import org.moeaframework.Analyzer;
@@ -21,8 +38,8 @@ public static void main(String[] args) {
 				.withAlgorithm("MOEA/D")
 				.runSeeds(50));
 
-		// collect data for MOEA/D with Generalized Decomposition - by targeting the Pareto front
-		// points, we should get extremely close to the optimum
+		// collect data for MOEA/D with Generalized Decomposition - by targeting the Pareto front points, we should
+		// get extremely close to the optimum
 		analyzer.addAll("GD-MOEA/D", executor
 				.withAlgorithm("GD-MOEA/D")
 				.withProperty("targets", "pf/DTLZ2.3D.pf")

src/main/java/org/moeaframework/gd/GDMOEAD.java

@@ -1,22 +1,37 @@
+/* Copyright 2009-2024 David Hadka
+ *
+ * This file is part of the MOEA Framework.
+ *
+ * The MOEA Framework is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
+ *
+ * The MOEA Framework is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+ * License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the MOEA Framework.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package org.moeaframework.gd;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.moeaframework.algorithm.MOEAD;
 import org.moeaframework.core.FrameworkException;
 import org.moeaframework.core.Population;
-import org.moeaframework.core.PopulationIO;
 import org.moeaframework.core.Problem;
 import org.moeaframework.core.Solution;
-import org.moeaframework.core.operator.RandomInitialization;
+import org.moeaframework.core.initialization.RandomInitialization;
 import org.moeaframework.core.spi.OperatorFactory;
 import org.moeaframework.core.variable.RealVariable;
-import org.moeaframework.util.io.CommentedLineReader;
+import org.moeaframework.util.io.Resources;
+import org.moeaframework.util.io.Resources.ResourceOption;
 import org.moeaframework.util.weights.NormalBoundaryDivisions;
 import org.moeaframework.util.weights.NormalBoundaryIntersectionGenerator;
 import org.moeaframework.util.weights.WeightGenerator;
@@ -32,9 +47,8 @@ public GDMOEAD(Problem problem, String targets) {
 	}
 
 	public GDMOEAD(Problem problem, NormalBoundaryDivisions divisions) {
-		this(problem,
-				new GeneralizedDecomposition(new NormalBoundaryIntersectionGenerator(
-						problem.getNumberOfObjectives(), divisions)));
+		this(problem, new GeneralizedDecomposition(new NormalBoundaryIntersectionGenerator(
+				problem.getNumberOfObjectives(), divisions)));
 	}
 
 	public GDMOEAD(Problem problem, WeightGenerator weightGenerator) {
@@ -50,35 +64,22 @@ public GDMOEAD(Problem problem, WeightGenerator weightGenerator) {
 	}
 
 	private static List<double[]> loadTargets(String resource) {
-		Population population = null;
-		
 		try {
-			File file = new File(resource);
+			File file = Resources.asFile(GDMOEAD.class, "/" + resource, ResourceOption.REQUIRED,
+					ResourceOption.TEMPORARY, ResourceOption.FILE);
 
-			if (file.exists()) {
-				population = PopulationIO.readObjectives(file);
-			} else {
-				try (InputStream input = GDMOEAD.class.getResourceAsStream("/" + resource)) {
-					if (input != null) {
-						population = PopulationIO.readObjectives(new CommentedLineReader(new InputStreamReader(input)));
-					}
-				}
+			Population population = Population.loadObjectives(file);
+			
+			List<double[]> targets = new ArrayList<double[]>();
+			
+			for (Solution solution : population) {
+				targets.add(solution.getObjectives());
 			}
+			
+			return targets;
 		} catch (IOException e) {
 			throw new FrameworkException("failed to load " + resource, e);
 		}
-		
-		if (population == null) {
-			throw new FrameworkException("could not find " + resource);
-		}
-		
-		List<double[]> targets = new ArrayList<double[]>();
-		
-		for (Solution solution : population) {
-			targets.add(solution.getObjectives());
-		}
-		
-		return targets;
 	}
 
 }

src/main/java/org/moeaframework/gd/GDMOEADProvider.java

@@ -1,3 +1,20 @@
+/* Copyright 2009-2024 David Hadka
+ *
+ * This file is part of the MOEA Framework.
+ *
+ * The MOEA Framework is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or (at your
+ * option) any later version.
+ *
+ * The MOEA Framework is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+ * License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the MOEA Framework.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package org.moeaframework.gd;
 
 import org.moeaframework.core.Algorithm;

src/main/java/org/moeaframework/gd/GeneralizedDecomposition.java

@@ -1,4 +1,4 @@
-/* Copyright 2009-2022 David Hadka
+/* Copyright 2009-2024 David Hadka
  *
  * This file is part of the MOEA Framework.
  *
@@ -30,15 +30,13 @@
 import com.joptimizer.optimizers.LPPrimalDualMethod;
 
 /**
- * Generates weights used to find solutions near a given set of target points.
- * Generalized decomposition determines the Chebychev scalarizing function
- * weights that are used to attain solutions near the given target points.
+ * Generates weights used to find solutions near a given set of target points.  Generalized decomposition determines
+ * the Chebychev scalarizing function weights that are used to attain solutions near the given target points.
  * <p>
  * References:
  * <ol>
- *   <li>Giagkiozis, I., R. C. Purshouse, and P. J. Fleming (2013).
- *       "Generalized Decomposition."  Evolutionary Multi-Criterion
- *       Optimization, 7th International Conference, pp. 428-442.
+ *   <li>Giagkiozis, I., R. C. Purshouse, and P. J. Fleming (2013).  "Generalized Decomposition."  Evolutionary
+ *       Multi-Criterion Optimization, 7th International Conference, pp. 428-442.
  * </ol>
  */
 public class GeneralizedDecomposition implements WeightGenerator {
@@ -49,8 +47,7 @@ public class GeneralizedDecomposition implements WeightGenerator {
 	private final List<double[]> targets;
 
 	/**
-	 * Constructs a weight generator transforming the given weights into those
-	 * defined by generalized decomposition.
+	 * Constructs a weight generator transforming the given weights into those defined by generalized decomposition.
 	 * 
 	 * @param generator the weight generator
 	 */
@@ -59,8 +56,8 @@ public GeneralizedDecomposition(WeightGenerator generator) {
 	}
 
 	/**
-	 * Constructs a weight generator transforming the given target points into
-	 * the required Chebychef scalaring function weights.
+	 * Constructs a weight generator transforming the given target points into the required Chebychef scalarizing
+	 * function weights.
 	 * 
 	 * @param targets the target points normalized on the unit hypervolume
 	 */
@@ -86,8 +83,7 @@ public List<double[]> generate() {
 	}
 
 	private static double[] solve_chebychev(double[] x) {
-		// This function uses JOptimizer to solve the following convex
-		// optimization problem:
+		// This function uses JOptimizer to solve the following convex optimization problem:
 		//
 		//   minimize norm_inf(X*w)
 		//   subject to
@@ -97,8 +93,7 @@ private static double[] solve_chebychev(double[] x) {
 		//      X is an n x n diagonal matrix
 		//      w is a n x 1 vector
 		//
-		// norm_inf(X*w) is solved by introducing a slack variable, t, and 
-		// adding constraints X*w <= t and X*w >= -t.
+		// norm_inf(X*w) is solved by introducing a slack variable, t, and adding constraints X*w <= t and X*w >= -t.
 
 		// setup the standard form matrices for LP
 		double[] c = new double[x.length + 1];
@@ -134,8 +129,7 @@ private static double[] solve_chebychev(double[] x) {
 		}
 
 		// use JOptimizer to solve the LP
-		ConvexMultivariateRealFunction[] inequalities =
-				new ConvexMultivariateRealFunction[4 * x.length];
+		ConvexMultivariateRealFunction[] inequalities = new ConvexMultivariateRealFunction[4 * x.length];
 
 		for (int i = 0; i < 4 * x.length; i++) {
 			inequalities[i] = new LinearMultivariateRealFunction(G[i], -h[i]);