Merge pull request #202 from julianu/main

Updating Java to 21 and critical dependencies

.github/workflows/maven-and-docker.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:
-        java-version: '17'
+        java-version: '21'
         distribution: 'temurin'
         cache: maven
     - name: Build with Maven

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17-jre-jammy
+FROM eclipse-temurin:21-jre-jammy
 
 LABEL MAINTAINERS="Julian Uszkoreit <julian.uszkoreit@rub.de>"\
       description="Docker image for command line execution of PIA - Protein Inference Algorithms"

pom.xml

@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.4.9</version>
+	<version>1.4.10</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 
@@ -50,7 +50,7 @@
 		<xxindex.version>0.23</xxindex.version>
 		<mascotdatfile.version>3.6.1</mascotdatfile.version>
 		<xtandem-parser.version>1.13.0</xtandem-parser.version>
-		<compomics-utilities.version>5.0.41</compomics-utilities.version>
+		<compomics-utilities.version>5.1.5</compomics-utilities.version>
 		<biojava-ontology.version>7.0.2</biojava-ontology.version>
 		<gson.version>2.10.1</gson.version>
 		<picocli.version>4.7.5</picocli.version>
@@ -59,9 +59,10 @@
 		<xercesImpl.version>2.12.2</xercesImpl.version>
 
 		<!-- override dependencies from some packages to avoid vulnarabilities  -->
-		<logback.version>1.4.13</logback.version>
+		<logback.version>1.4.14</logback.version>
 		<jackson-annotations.version>2.16.0</jackson-annotations.version>
 		<poi.version>5.2.5</poi.version>
+		<guava.version>32.1.3-jre</guava.version>
 
 		<!-- these are "internal" dependencies, the jar files are delivered together with the source -->
 		<BaseLib.version>0.0.1-SNAPSHOT</BaseLib.version>
@@ -291,6 +292,11 @@
 			<artifactId>jackson-annotations</artifactId>
 			<version>${jackson-annotations.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<version>${guava.version}</version>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -307,7 +313,7 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.11.0</version>
 				<configuration>
-					<release>17</release>
+					<release>21</release>
 				</configuration>
 			</plugin>
 
@@ -356,7 +362,7 @@
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.8.8</version>
+				<version>0.8.11</version>
 				<executions>
 					<execution>
 						<goals>
@@ -376,7 +382,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>3.1.2</version>
+				<version>3.2.2</version>
 				<configuration>
 					<argLine>${argLine} -Xmx2560m</argLine>
 				</configuration>