Update Gradle to 8.5 (#1930)

* update to use configuration api
* remove no longer relevant bits about the parser settings
* update to automatically configure javadoc/source jars and the toolchain

build.gradle

@@ -83,16 +83,19 @@ dependencies {
     testImplementation 'org.testng:testng:7.7.0'
 }
 
-configurations.all {
+configurations.configureEach {
     resolutionStrategy {
         // force the htsjdk version so we don't get a different one transitively
         force 'com.github.samtools:htsjdk:' + htsjdkVersion
     }
 }
 
 java {
-    sourceCompatibility = 1.17
-    targetCompatibility = 1.17
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
+    withJavadocJar()
+    withSourcesJar()
 }
 
 final isRelease = Boolean.getBoolean("release")
@@ -104,20 +107,9 @@ group = 'com.github.broadinstitute'
 
 defaultTasks 'all'
 
-task all(dependsOn: ['jar', 'distZip', 'javadoc', 'shadowJar', 'currentJar', 'picardDoc'])
-
-// Source file names for the picard command line properties file. We select and include only one of
-// these two files in each jar, renamed to "picardCmdLine.properties", depending on which parser we
-// want enabled.
-final String legacySourcePropertyFile = 'legacyParserProperties.properties'
-final String barclaySourcePropertyFile = 'barclayParserProperties.properties'
-
-// Target name/location for the picard command line properties file; one of the above source
-// files will be included at this path/location for runtime access
-final String picardTargetPropertiesPath = 'picard'
-final String picardTargetPropertyFile = 'picardCmdLine.properties'
+tasks.register('all') { dependsOn 'jar', 'distZip', 'javadoc', 'shadowJar', 'currentJar', 'picardDoc' }
 
-tasks.withType(Jar){
+tasks.withType(Jar).configureEach {
     manifest {
         attributes 'Main-Class': 'picard.cmdline.PicardCommandLine',
                 'Implementation-Title': 'Picard',
@@ -128,7 +120,7 @@ tasks.withType(Jar){
     }
 }
 
-tasks.withType(Javadoc) {
+tasks.withType(Javadoc).configureEach {
     // do this for all javadoc tasks, including gatkDoc
     options.addStringOption('Xdoclint:none')
 }
@@ -138,7 +130,8 @@ javadoc {
 }
 
 // Generate Picard Online Doc
-task picardDoc(type: Javadoc, dependsOn: ['cleanPicardDoc', classes]) {
+tasks.register('picardDoc', Javadoc) {
+    dependsOn 'cleanPicardDoc', classes
     final File picardDocDir = file("build/docs/picarddoc")
     doFirst {
         // make sure the output folder exists or we can create it
@@ -176,10 +169,10 @@ task picardDoc(type: Javadoc, dependsOn: ['cleanPicardDoc', classes]) {
     options.noTimestamp(false)
 }
 
-task currentJar(type: Copy){
+tasks.register('currentJar', Copy) {
     from shadowJar
     into file("$buildDir/libs")
-    rename { string -> "picard.jar"}
+    rename { string -> "picard.jar" }
 }
 
 shadowJar {
@@ -188,13 +181,13 @@ shadowJar {
 
 // Run the tests using the legacy parser only. Assumes that test code is written using
 // legacy command line parser syntax.
-task legacyTest(type: Test) {
+tasks.register('legacyTest', Test) {
     systemProperty 'picard.useLegacyParser', 'true'
 }
 
 // Run the tests using the Barclay command line parser (useLegacyParser=false), which requires
 // conversion of test command lines from Picard-style command line syntax to Barclay-style syntax.
-task barclayTest(type: Test) {
+tasks.register('barclayTest', Test) {
     systemProperty 'picard.convertCommandLine', 'true'
 }
 
@@ -203,7 +196,7 @@ test {
     dependsOn barclayTest
 }
 
-tasks.withType(Test) {
+tasks.withType(Test).configureEach {
     outputs.upToDateWhen { false } // tests will always rerun
     description = "Runs the unit tests"
 
@@ -214,7 +207,7 @@ tasks.withType(Test) {
 
     useTestNG {
         List excludes = ["slow", "broken"]
-        if( !OperatingSystem.current().isUnix() ) {
+        if (!OperatingSystem.current().isUnix()) {
             excludes << "unix"
         }
         String TEST_TYPE = "$System.env.TEST_TYPE"
@@ -239,8 +232,8 @@ tasks.withType(Test) {
 
         beforeTest { descriptor ->
             count++
-            if( count % 100 == 0) {
-                logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
+            if (count % 100 == 0) {
+                logger.lifecycle("Finished " + Integer.toString(count++) + " tests")
             }
         }
     } else {
@@ -252,7 +245,7 @@ tasks.withType(Test) {
 
         // listen to standard out and standard error of the test JVM(s)
         onOutput { descriptor, event ->
-            logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
+            logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message)
         }
     }
 
@@ -282,25 +275,7 @@ jacocoTestReport {
 }
 
 wrapper {
-    gradleVersion = '8.2.1'
-}
-
-task javadocJar(type: Jar) {
-    archiveClassifier.set('javadoc')
-    from 'build/docs/javadoc'
-}
-
-task sourcesJar(type: Jar) {
-    from sourceSets.main.allSource
-    archiveClassifier.set('sources')
-}
-
-/**
- * This specifies what artifacts will be built and uploaded when performing a maven upload.
- */
-artifacts {
-    archives javadocJar
-    archives sourcesJar
+    gradleVersion = '8.5'
 }
 
 /**
@@ -375,18 +350,21 @@ publish {
 ext.htmlDir = file("build/docs/html")
 
 //update static web docs
-task copyJavadoc(dependsOn: ['javadoc', 'picardDoc'], type: Copy) {
+tasks.register('copyJavadoc', Copy) {
+    dependsOn 'javadoc', 'picardDoc'
     from 'build/docs/javadoc'
     into "$htmlDir/javadoc"
 }
 
-task copyPicardDoc(dependsOn: 'picardDoc', type: Copy){
+tasks.register('copyPicardDoc', Copy) {
+    dependsOn 'picardDoc'
     from 'build/docs/picarddoc'
     into "$htmlDir/picarddoc"
 }
 
-task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){
-  outputs.dir htmlDir
+tasks.register('updateGhPages') {
+    dependsOn 'copyJavadoc', 'copyPicardDoc'
+    outputs.dir htmlDir
 }
 
 updateGhPages.finalizedBy gitPublishPush

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,10 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
+# This is normally unused
+# shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +130,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,6 +197,10 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
 # Collect all arguments for the java command;
 #   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
 #     shell script including quotes and variable substitutions, so put them in