Update gradle to 8.5 (#195)

* gradle 8.5 is the first gradle that officially runs on java 21

build.gradle

@@ -7,11 +7,13 @@ plugins {
 }
 
 wrapper {
-    gradleVersion = '7.4.2'
+    gradleVersion = '8.5'
 }
 
-sourceCompatibility = 1.17
-targetCompatibility = 1.17
+java {
+    sourceCompatibility = JavaVersion.VERSION_17
+    targetCompatibility = JavaVersion.VERSION_17
+}
 
 group = 'org.broadinstitute'
 
@@ -88,18 +90,19 @@ test {
 
 }
 
-task javadocJar(type: Jar, dependsOn: javadoc) {
+tasks.register('javadocJar', Jar) {
+    dependsOn javadoc
     archiveClassifier = 'javadoc'
     from 'build/docs/javadoc'
 }
 
-task sourcesJar(type: Jar) {
+tasks.register('sourcesJar', Jar) {
     from sourceSets.main.allSource
     archiveClassifier = 'sources'
 }
 
 // This is a hack to disable the default javadoc lint until we fix the html formatting
-tasks.withType(Javadoc) {
+tasks.withType(Javadoc).configureEach {
     options.addStringOption('Xdoclint:none', '-quiet')
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-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 +80,11 @@ 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"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +131,29 @@ 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 $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,18 +198,28 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# 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
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# 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, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
         org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
 # Use "xargs" to parse quoted args.
 #
 # With -n1 it outputs one arg per line, with the quotes and backslashes removed.