Bumped dependencies, added github workflow, logback.

.github/workflows/maven.yml

@@ -0,0 +1,26 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+name: Java CI with Maven
+
+on:
+  push:
+    branches: 
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build-20:
+    runs-on: ubuntu-latest
+    env:
+      JDK_JAVA_OPTIONS: "--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-java@v3
+        with:
+          java-version: 20
+          distribution: 'temurin'
+          cache: maven
+      - name: Build with Maven and JDK-20
+        run: mvn --batch-mode --update-snapshots package

pom.xml

@@ -47,27 +47,28 @@
     </issueManagement>
 
     <ciManagement>
-        <system>Travis CI</system>
-        <url>https://travis-ci.org/PathwayCommons/${project.name}</url>
+        <system>GitHub</system>
+        <url>https://github.com/PathwayCommons/${project.name}/actions/workflows/maven.yml</url>
     </ciManagement>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <paxtools.version>5.0.1</paxtools.version>
-        <slf4j.version>1.7.7</slf4j.version>
+        <paxtools.version>5.3.0</paxtools.version>
+        <slf4j.version>2.0.11</slf4j.version>
         <github.global.server>github</github.global.server>
+        <jvm.options>--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED</jvm.options>
     </properties>
 
     <build>
         <pluginManagement>
             <plugins>
                 <plugin>
                     <artifactId>maven-compiler-plugin</artifactId>
-                    <version>3.5.1</version>
+                    <version>3.11.0</version>
                     <configuration>
-                        <source>1.8</source>
-                        <target>1.8</target>
+                        <source>11</source>
+                        <target>11</target>
                     </configuration>
                 </plugin>
             </plugins>
@@ -88,7 +89,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>
-                <version>2.4</version>
+                <version>3.5.1</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -221,29 +222,33 @@
             <artifactId>jcl-over-slf4j</artifactId>
             <version>${slf4j.version}</version>
             <scope>runtime</scope>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>jul-to-slf4j</artifactId>
             <version>${slf4j.version}</version>
             <scope>runtime</scope>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>log4j-over-slf4j</artifactId>
             <version>${slf4j.version}</version>
             <scope>runtime</scope>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>1.1.2</version>
+            <version>1.4.12</version>
             <scope>runtime</scope>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.12</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

src/main/resources/logback.xml

@@ -12,7 +12,6 @@
     </encoder>
   </appender>
 
-  <!--<logger name="org.biopax.paxtools" level="warn" />-->
   <logger name="edu.mit.broad.vdb.msigdb" level="info" />
 
   <root level="warn">

src/test/resources/logback-test.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration>
+
+  <contextListener class="ch.qos.logback.classic.jul.LevelChangePropagator">
+    <resetJUL>true</resetJUL>
+  </contextListener>
+
+  <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+    <encoder>
+      <pattern>%d %-5level [%thread] %logger{25} - %msg%n</pattern>
+      <outputPatternAsHeader>true</outputPatternAsHeader>
+    </encoder>
+  </appender>
+
+  <root level="info">
+    <appender-ref ref="console" />
+  </root>
+
+</configuration>