Update to use Java 17 (#1315)

* Update to use Java 17
* change to gradle 8.0.2
* minor changes to support java 17
* remove test module configuration and use gradle test platform instead
* update configuration reference from defalt -> runtimeClasspath, also change some 11's to 17s
* remove broken proguard stuff

.github/workflows/gradle_test.yml

@@ -7,13 +7,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up JDK 11
-        uses: actions/setup-java@v1
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
         with:
-          java-version: 11
+          java-version: 17
+          distribution: temurin 
       - name: Cache Gradle packages
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             ~/.gradle/caches
@@ -30,4 +31,4 @@ jobs:
         # Restoring these files from a GitHub Actions cache might cause problems for future builds.
         run: |
           rm -f ~/.gradle/caches/modules-2/modules-2.lock
-          rm -f ~/.gradle/caches/modules-2/gc.properties
+          rm -f ~/.gradle/caches/modules-2/gc.properties

build.gradle

@@ -27,26 +27,25 @@ apply plugin: 'application'
 
 import org.apache.tools.ant.filters.ReplaceTokens
 
-//import proguard.gradle.ProGuardTask
-
 mainClassName = 'org.broad.igv.ui.Main'
 ext.moduleName = 'org.igv'
 
-// Build sourceset for ProGuard
 buildscript {
     repositories {
         mavenCentral()
     }
-    dependencies {
-        [group: 'net.sf.proguard', name: 'proguard-gradle', version: '6.1.1']
-        classpath 'net.sf.proguard:proguard-gradle:6.1.1'
-    }
 }
 
 repositories {
     mavenCentral()
 }
 
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
+}
+
 sourceSets {
     main {
         resources {
@@ -128,10 +127,13 @@ dependencies {
     )
 
     testImplementation(
-            [group: 'junit', name: 'junit', version: '4.12'],
+            [group: 'junit', name: 'junit', version: '4.13'],
             [group: 'com.sparkjava', name: 'spark-core', version: '2.2'],
             [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.22.4']
     )
+    testRuntimeOnly(
+           [group: 'org.junit.vintage', name:'junit-vintage-engine', version:'5.8.2']
+    )
 }
 
 
@@ -179,35 +181,7 @@ tasks.withType(Test) {
     systemProperties['org.xerial.snappy.tempdir'] = 'build/tmp'
     maxHeapSize = '2g'
     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
-}
-
-compileTestJava {
-    inputs.property("moduleName", moduleName)
-    doFirst {
-        options.compilerArgs = [
-                '--module-path', classpath.asPath,
-                '--add-modules', 'junit',
-                '--patch-module', "$moduleName=" + files(sourceSets.test.java.srcDirs).asPath,
-        ]
-        classpath = files()
-    }
-}
-
-test {
-    inputs.property("moduleName", moduleName)
-
-    doFirst {
-        jvmArgs = [
-                '-Dcom.sun.xml.bind.v2.bytecode.ClassTailor.noOptimize',
-                '--module-path', classpath.asPath,
-                '--add-modules', 'junit',
-                '--add-modules', 'ALL-MODULE-PATH',
-                '--add-reads', "$moduleName=junit",
-                '@scripts/test_suite.args',
-                '--patch-module', "$moduleName=" + files(sourceSets.test.java.outputDir, sourceSets.main.output.resourcesDir).asPath,
-        ]
-        classpath = files()
-    }
+    useJUnitPlatform()
 }
 
 task createDist(type: Copy, dependsOn: jar) {
@@ -229,10 +203,11 @@ task createDist(type: Copy, dependsOn: jar) {
     }
     // Copies all Maven-fetched dependency jars
     with copySpec {
-        from configurations.default {
+        from configurations.runtimeClasspath {
             exclude '**/*log4j*.jar' 
         }
         into "lib"
+        duplicatesStrategy DuplicatesStrategy.EXCLUDE
     }
     with copySpec { from("genomes/sizes") {} into "lib/genomes" }
 
@@ -244,32 +219,32 @@ tasks.distTar.enabled = false
 tasks.startScripts.enabled = false
 
 task createDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_${version}.zip"
+    archiveFileName = "IGV_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist")
-    into "IGV_${version}"
+    into "IGV_${archiveVersion}"
 }
 
 task createLinuxDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Linux_${version}.zip"
+    archiveFileName = "IGV_Linux_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*.command"
         exclude 'igvtools*'
         exclude 'lib/genomes'
     }
-    into "IGV_Linux_${version}"
+    into "IGV_Linux_${archiveVersion}"
 }
 
 task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Linux_${version}_WithJava.zip"
-    with copySpec { from jdkBundleLinux into "jdk-11" }
+    archiveFileName = "IGV_Linux_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleLinux into "jdk-17" }
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*.command"
         exclude 'igvtools*'
         exclude 'lib/genomes'
     }
-    into "IGV_Linux_${version}"
+    into "IGV_Linux_${archiveVersion}"
     doLast {
         if (jdkBundleLinux == "") {
             throw new GradleException("Required property not set: jdkBundleLinux");
@@ -278,26 +253,27 @@ task createLinuxWithJavaDistZip(type: Zip, dependsOn: createDist) {
 }
 
 task createMacDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Mac_${version}.zip"
+    archiveFileName = "IGV_Mac_${archiveVersion}.zip"
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*_hidpi*"
         exclude "igvtools*"
         exclude 'lib/genomes'
     }
-    into "IGV_Mac_${version}"
+
+    into "IGV_Mac_${archiveVersion}"
 }
 
 task createMacWithJavaDistZip(type: Zip, dependsOn: createDist) {
-    archiveName = "IGV_Mac_${version}_WithJava.zip"
-    with copySpec { from jdkBundleMac into "jdk-11" }
+    archiveFileName = "IGV_Mac_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleMac into "jdk-17" }
     from("${buildDir}/IGV-dist") {
         exclude "*.bat"
         exclude "*_hidpi*"
         exclude "igvtools*"
         exclude 'lib/genomes'
     }
-    into "IGV_Mac_${version}"
+    into "IGV_Mac_${archiveVersion}"
     doLast {
         if (jdkBundleMac == "") {
             throw new GradleException("Required property not set: jdkBundleMac");
@@ -339,7 +315,7 @@ task createMacAppDist(type: Copy, dependsOn: createDist) {
 }
 
 task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) {
-    archiveName = "IGV_MacApp_${version}.zip"
+    archiveFileName = "IGV_MacApp_${archiveVersion}.zip"
     from("${buildDir}/IGV-MacApp-dist")
 
     doLast {
@@ -348,8 +324,8 @@ task createMacAppDistZip(type: Zip, dependsOn: createMacAppDist) {
 }
 
 task createMacAppWithJavaDistZip(type: Zip, dependsOn: createMacAppDist) {
-    archiveName = "IGV_MacApp_${version}_WithJava.zip"
-    with copySpec { from jdkBundleMac into "IGV_${version}.app/Contents/jdk-11" }
+    archiveFileName = "IGV_MacApp_${archiveVersion}_WithJava.zip"
+    with copySpec { from jdkBundleMac into "IGV_${archiveVersion}.app/Contents/jdk-17" }
     from("${buildDir}/IGV-MacApp-dist")
 
     doLast {
@@ -383,7 +359,7 @@ task createWinDist(type: Copy, dependsOn: createDist) {
 }
 
 task createWinWithJavaDist(type: Copy, dependsOn: createWinDist) {
-    with copySpec { from jdkBundleWindows into "IGV_${version}/jdk-11" }
+    with copySpec { from jdkBundleWindows into "IGV_${version}/jdk-17" }
     with copySpec {
         from("${buildDir}/IGV-WinExe-dist/IGV_${version}") { exclude 'installer.nsi' }
         into "IGV_${version}"
@@ -465,7 +441,8 @@ task fullJar(type: Jar, dependsOn: jar) {
                 "Application-Name": "IGV",
                 "Built-By": System.getProperty('user.name'),
                 "Main-Class": mainClassName,
-                "Class-Path": configurations.default.collect { it.getName() }.join(' ')
+
+                "Class-Path": configurations.runtimeClasspath.collect { it.getName() }.join(' ')
         )
     }
 }
@@ -475,16 +452,3 @@ task fullJar(type: Jar, dependsOn: jar) {
 //if (!makensisCommand == "" && !signcodeCommand == "") {
 //    dependsOn signWinExeDist
 //}
-
-// XXX: META-INF versions support (Java11) seem to clash with proguard at this point in time:
-// https://sourceforge.net/p/proguard/bugs/665/
-// https://sourceforge.net/p/proguard/discussion/182456/thread/8c56b22dc2/?limit=25
-//task myproguard(type: ProGuardTask) {
-////    configuration 'proguard.txt'
-//
-//    injars "${buildDir}/IGV-dist/lib"
-//    outjars "${buildDir}/libs/igv-proguard.jar"
-//
-//    //libraryjars "${buildDir}/IGV-dist/lib", jarfilter:"lib/**.jar(!META-INF/**)"
-//    //libraryjars "${System.getProperty('java.home')}/lib/rt.jar"
-//}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.5.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.0.2-bin.zip
+networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists