Merge pull request medbioinf#205 from julianu/main

updating dependencies
julianu · Jul 2, 2024 · 79b00bf · 79b00bf
2 parents 8817dfb + 5c6a2ec
commit 79b00bf
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diff --git a/.github/workflows/maven-and-docker.yml b/.github/workflows/maven-and-docker.yml
@@ -25,7 +25,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up JDK 17
+    - name: Set up JDK 21
       uses: actions/setup-java@v3
       with:
         java-version: '21'

diff --git a/.gitignore b/.gitignore
@@ -52,4 +52,10 @@ log/
 logs/
 target/
 .idea/
-.externalToolBuilders/
+.externalToolBuilders/
+/.apt_generated/
+/.apt_generated_tests/
+
+# VSCode files #
+###########################
+/.vscode
diff --git a/LICENSE b/LICENSE
@@ -3,7 +3,7 @@
 --------------------------------------------------------------------------------
 Copyright Ruhr University Bochum - Medical Bioinformatics,
 Ruhr University Bochum - Medizinisches Proteom-Center and European
-Bioinformatics Institute (EMBL-EBI), 2013-2023
+Bioinformatics Institute (EMBL-EBI), 2013-2024
 
 This software is released under a three-clause BSD license:
 

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.5.0</version>
+	<version>1.5.1</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 
@@ -39,30 +39,32 @@
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
-		<log4j2.version>2.22.0</log4j2.version>
+		<log4j2.version>2.23.1</log4j2.version>
 		<junit.version>4.13.2</junit.version>
 		<commons-collections.version>4.4</commons-collections.version>
-		<commons-text.version>1.11.0</commons-text.version>
+		<commons-text.version>1.12.0</commons-text.version>
 		<jmzidentml.version>1.2.13</jmzidentml.version>
 		<jmztab.version>3.0.8</jmztab.version>
 		<pride-mod.version>2.1.12</pride-mod.version>
 		<pride-jaxb.version>1.0.22</pride-jaxb.version>
 		<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>5.1.5</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>
+		<compomics-utilities.version>5.1.12</compomics-utilities.version>
+		<biojava-ontology.version>7.1.1</biojava-ontology.version>
+		<gson.version>2.11.0</gson.version>
+		<picocli.version>4.7.6</picocli.version>
 		<sqlite4java.version>1.0.392</sqlite4java.version>
-		<sqlite-jdbc.version>3.44.1.0</sqlite-jdbc.version>
+		<sqlite-jdbc.version>3.46.0.0</sqlite-jdbc.version>
 		<xercesImpl.version>2.12.2</xercesImpl.version>
 
 		<!-- override dependencies from some packages to avoid vulnarabilities  -->
-		<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>
+		<logback.version>1.5.6</logback.version>
+		<jackson-annotations.version>2.17.1</jackson-annotations.version>
+		<guava.version>33.2.1-jre</guava.version>
+		<commons-codec.version>1.17.0</commons-codec.version>
+		<commons-compress.version>1.26.2</commons-compress.version>
+		<aircompressor.version>0.27</aircompressor.version>
 
 		<!-- these are "internal" dependencies, the jar files are delivered together with the source -->
 		<BaseLib.version>0.0.1-SNAPSHOT</BaseLib.version>
@@ -124,20 +126,20 @@
 		<!-- JAXB needs to be added for Java >= 9 -->
     	<dependency>
 			<groupId>javax.xml.bind</groupId>
-			<artifactId>jaxb-api</artifactId>
-			<version>2.3.1</version>
+   			<artifactId>jaxb-api</artifactId>
+    		<version>2.3.1</version>
 		</dependency>
 
 		<dependency>
 			<groupId>com.sun.xml.bind</groupId>
 			<artifactId>jaxb-impl</artifactId>
-			<version>2.3.1</version>
+			<version>2.3.9</version>
 		</dependency>
 
 		<dependency>
 			<groupId>com.sun.xml.bind</groupId>
 			<artifactId>jaxb-core</artifactId>
-			<version>2.3.0</version>
+			<version>4.0.5</version>
 		</dependency>
 		<!-- JAXB additions --> 
 
@@ -208,7 +210,7 @@
 			<artifactId>utilities</artifactId>
 			<version>${compomics-utilities.version}</version>
 			<exclusions>
-			<!-- these packages break Java 17 dependencies -->
+				<!-- these packages break Java 17 dependencies -->
 				<exclusion> 
 					<groupId>org.ogce</groupId>
 					<artifactId>xpp3</artifactId>
@@ -217,6 +219,11 @@
 					<groupId>org.apache.axis</groupId>
 					<artifactId>axis-jaxrpc</artifactId>
 				</exclusion>
+				<!-- not needed (only visualization) and highly deprecated -->
+				<exclusion>
+					<groupId>umontreal.iro.lecuyer.gof</groupId>
+					<artifactId>ssj</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 
@@ -288,11 +295,6 @@
 			<artifactId>logback-classic</artifactId>
 			<version>${logback.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>poi</artifactId>
-			<version>${poi.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-annotations</artifactId>
@@ -303,6 +305,21 @@
 			<artifactId>guava</artifactId>
 			<version>${guava.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>commons-codec</groupId>
+			<artifactId>commons-codec</artifactId>
+			<version>${commons-codec.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-compress</artifactId>
+			<version>${commons-compress.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>io.airlift</groupId>
+			<artifactId>aircompressor</artifactId>
+			<version>${aircompressor.version}</version>
+		</dependency>
 	</dependencies>
 
 	<build>