Update to JDK 25, bump dependencies

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/setup-java@v5
         with:
           distribution: "temurin"
-          java-version: "17"
+          java-version: "25"
           cache: "maven"
           cache-dependency-path: "pom.xml"
       - run: mvn compile

.github/workflows/docs.yml

@@ -19,7 +19,7 @@ jobs:
       - uses: actions/setup-java@v5
         with:
           distribution: "temurin"
-          java-version: "17"
+          java-version: "25"
           cache: "maven"
           cache-dependency-path: "pom.xml"
       - run: mvn compile

.jitpack.yml

@@ -1,6 +1,7 @@
-language: java  
-jdk:  
-  - openjdk17
+language: java
+jdk:
+  - openjdk25
 before_install:
-  - sdk install java 17.0.2-open
-  - sdk use java 17.0.2-open
+  - sdk install java 25.0.3-tem
+  - sdk use java 25.0.3-tem
+  - sdk install maven

pom.xml

@@ -2,7 +2,7 @@
   xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <properties>
-    <maven.compiler.release>17</maven.compiler.release>
+    <maven.compiler.release>25</maven.compiler.release>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
   </properties>
   <groupId>com.github.jasmineRepo</groupId>
@@ -21,14 +21,6 @@
     </dependencies>
   </dependencyManagement>
 
-  <distributionManagement>
-    <repository>
-      <id>github</id>
-      <name>GitHub Packages</name>
-      <url>https://maven.pkg.github.com/jasmineRepo/JAS-mine-core</url>
-    </repository>
-  </distributionManagement>
-
   <build>
     <plugins>
       <plugin>
@@ -42,13 +34,13 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-surefire-plugin</artifactId>
-        <version>3.5.4</version>
+        <version>3.5.6</version>
       </plugin>
 
       <plugin>
         <groupId>org.jacoco</groupId>
         <artifactId>jacoco-maven-plugin</artifactId>
-        <version>0.8.14</version>
+        <version>0.8.15</version>
         <executions>
           <execution>
             <goals>
@@ -102,7 +94,7 @@
           <extension>
               <groupId>org.apache.maven.wagon</groupId>
               <artifactId>wagon-ssh</artifactId>
-              <version>2.4</version>
+              <version>3.5.3</version>
           </extension>
       </extensions>
   </build>
@@ -111,13 +103,14 @@
     <dependency>
       <groupId>org.junit.jupiter</groupId>
       <artifactId>junit-jupiter</artifactId>
+      <version>6.1.0</version>
       <scope>test</scope>
     </dependency>
 
     <dependency>
-      <groupId>log4j</groupId>
-      <artifactId>log4j</artifactId>
-      <version>1.2.17</version>
+      <groupId>org.apache.logging.log4j</groupId>
+      <artifactId>log4j-core</artifactId>
+      <version>2.26.0</version>
       <type>jar</type>
     </dependency>
     <dependency>
@@ -129,76 +122,73 @@
     <dependency>
       <groupId>commons-beanutils</groupId>
       <artifactId>commons-beanutils</artifactId>
-      <version>20030211.134440</version>
+      <version>1.11.0</version>
     </dependency>
     <dependency>
       <groupId>commons-logging</groupId>
       <artifactId>commons-logging</artifactId>
-      <version>1.2</version>
+      <version>1.3.6</version>
     </dependency>               
     <dependency>
       <groupId>org.apache.poi</groupId>
       <artifactId>poi</artifactId>
-      <version>5.2.2</version>
+      <version>5.5.1</version>
     </dependency>
     <dependency>
       <groupId>org.apache.poi</groupId>
       <artifactId>poi-ooxml</artifactId>
-      <version>5.2.2</version>
+      <version>5.5.1</version>
     </dependency>
-    <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-collections4 -->
     <dependency>
         <groupId>org.apache.commons</groupId>
         <artifactId>commons-collections4</artifactId>
-        <version>4.4</version>
+        <version>4.5.0</version>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-math3</artifactId>
       <version>3.6.1</version>
     </dependency>
-    <!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
     <dependency>
-        <groupId>commons-io</groupId>
-        <artifactId>commons-io</artifactId>
-        <version>2.14.0</version>
-    </dependency>       
-    <!-- https://mvnrepository.com/artifact/xerces/xercesImpl -->
-        <dependency>
-            <groupId>xerces</groupId>
-            <artifactId>xercesImpl</artifactId>
-            <version>2.12.2</version>
-        </dependency>
-        <dependency>
-            <groupId>org.javassist</groupId>
-            <artifactId>javassist</artifactId>
-            <version>3.29.1-GA</version>
-        </dependency>
+      <groupId>commons-io</groupId>
+      <artifactId>commons-io</artifactId>
+      <version>2.22.0</version>
+    </dependency>
+    <dependency>
+      <groupId>xerces</groupId>
+      <artifactId>xercesImpl</artifactId>
+      <version>2.12.2</version>
+    </dependency>
+    <dependency>
+      <groupId>org.javassist</groupId>
+      <artifactId>javassist</artifactId>
+      <version>3.31.0-GA</version>
+    </dependency>
 
     <dependency>
       <groupId>jakarta.enterprise</groupId>
       <artifactId>jakarta.enterprise.cdi-api</artifactId>
-      <version>4.0.1</version>
+      <version>4.1.0</version>
     </dependency>
     <dependency>
       <groupId>jakarta.ws.rs</groupId>
       <artifactId>jakarta.ws.rs-api</artifactId>
-      <version>3.1.0</version>
+      <version>4.0.0</version>
     </dependency>
     <dependency>
       <groupId>org.hibernate.orm</groupId>
       <artifactId>hibernate-core</artifactId>
-      <version>6.1.2.Final</version>
+      <version>6.1.7.Final</version>
     </dependency>
     <dependency>
       <groupId>com.h2database</groupId>
       <artifactId>h2</artifactId>
-      <version>2.2.220</version>
+      <version>2.4.240</version>
     </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.18.0</version>
+            <version>3.20.0</version>
             <scope>compile</scope>
         </dependency>
   </dependencies>

src/main/java/microsim/data/ExperimentManager.java

@@ -10,7 +10,8 @@
 import microsim.data.db.Experiment;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 /**
  * Singleton. Utility used to create ana manage experiment setup.
@@ -22,7 +23,7 @@
  */
 public class ExperimentManager {
 
-    private static final Logger log = Logger.getLogger(ExperimentManager.class);
+    private static final Logger log = LogManager.getLogger(ExperimentManager.class);
 
     /**
      * The flag determines if the tool must copy input resources into output folder.

src/main/java/microsim/data/ExportCSV.java

@@ -15,9 +15,6 @@
 
 import jakarta.persistence.Transient;
 
-import org.apache.log4j.Logger;
-
-import microsim.data.db.DatabaseUtils;
 import microsim.data.db.PanelEntityKey;
 import microsim.engine.SimulationEngine;
 
@@ -31,7 +28,6 @@
  */
 public class ExportCSV {
 
-    private static Logger log = Logger.getLogger(DatabaseUtils.class);
     public static Long autoincrementSeed = 1000000L;
 
     // Fields for exporting tables to output .csv files

src/main/java/microsim/data/db/DatabaseUtils.java

@@ -7,19 +7,20 @@
 import java.util.List;
 import java.util.Map;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import jakarta.persistence.*;
 
 import microsim.annotation.GUIparameter;
 import microsim.data.MultiKeyCoefficientMap;
 import microsim.data.MultiKeyCoefficientMapFactory;
 import microsim.engine.SimulationEngine;
 
-import org.apache.log4j.Logger;
-
 @SuppressWarnings("deprecation")
 public class DatabaseUtils {
 
-    private static Logger log = Logger.getLogger(DatabaseUtils.class);
+    private static Logger log = LogManager.getLogger(DatabaseUtils.class);
 
     private static EntityManagerFactory entityManagerFactory = null;
     private static EntityManagerFactory outEntityManagerFactory = null;

src/main/java/microsim/engine/SimulationEngine.java

@@ -18,7 +18,8 @@
 import microsim.exception.SimulationRuntimeException;
 
 import org.apache.commons.math3.random.RandomGenerator;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 /**
  * The simulation engine. The engine keeps a reference to an EventQueue object
@@ -59,7 +60,7 @@
  */
 public class SimulationEngine extends Thread {
 
-    private static Logger log = Logger.getLogger(SimulationEngine.class);
+    private static Logger log = LogManager.getLogger(SimulationEngine.class);
 
     private int eventThresold = 0;
 

src/main/java/microsim/statistics/TimeSeries.java

@@ -7,13 +7,14 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import microsim.engine.SimulationEngine;
 import microsim.event.CommonEventType;
 import microsim.event.EventListener;
 import microsim.reflection.ReflectionUtils;
 
-import org.apache.log4j.Logger;
-
 import cern.colt.list.DoubleArrayList;
 import cern.colt.list.FloatArrayList;
 import cern.colt.list.IntArrayList;
@@ -50,7 +51,7 @@
  * @author Michele Sonnessa
  */
 public class TimeSeries implements EventListener, IUpdatableSource {
-    private static Logger log = Logger.getLogger(TimeSeries.class);
+    private static Logger log = LogManager.getLogger(TimeSeries.class);
 
     /** A custom event identifier for perfomAction method. Save to disk. */
     public static final int EVENT_SAVE = 1;

src/main/java/microsim/statistics/reflectors/DoubleInvoker.java

@@ -6,11 +6,12 @@
 import java.util.Collection;
 import java.util.Iterator;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import microsim.reflection.ReflectionUtils;
 import microsim.statistics.IDoubleSource;
 
-import org.apache.log4j.Logger;
-
 /**
  * Not of interest for users. It uses java reflection to call objects' methods
  * which return double values. It is used by Statistics objects.
@@ -42,7 +43,7 @@
  * @author Michele Sonnessa
  */
 public class DoubleInvoker implements IDoubleSource {
-    private static Logger log = Logger.getLogger(DoubleInvoker.class);
+    private static Logger log = LogManager.getLogger(DoubleInvoker.class);
 
     protected Method method;
     protected Field field;

src/main/java/microsim/statistics/reflectors/FloatInvoker.java

@@ -4,11 +4,12 @@
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import microsim.reflection.ReflectionUtils;
 import microsim.statistics.IFloatSource;
 
-import org.apache.log4j.Logger;
-
 /**
  * Not of interest for users. It uses java reflection to call objects' methods
  * which return double values. It is used by Statistics objects.
@@ -40,7 +41,7 @@
  * @author Michele Sonnessa
  */
 public class FloatInvoker implements IFloatSource {
-    private static Logger log = Logger.getLogger(FloatInvoker.class);
+    private static Logger log = LogManager.getLogger(FloatInvoker.class);
 
     protected Method method;
     protected Field field;