Update to gradle 8.5 (#1697)

* update shadow plugin to 8.1.1
* 8.5 is necessary for running against java 21

build.gradle

@@ -10,7 +10,7 @@ plugins {
     id 'signing'
     id 'jacoco'
     id 'com.palantir.git-version' version '0.11.0'
-    id 'com.github.johnrengelman.shadow' version '7.1.2'
+    id 'com.github.johnrengelman.shadow' version '8.1.1'
     id 'com.github.spotbugs' version "5.0.13"
 }
 
@@ -62,11 +62,11 @@ group = 'com.github.samtools'
 
 defaultTasks 'jar'
 
-tasks.withType(JavaCompile) {
+tasks.withType(JavaCompile).configureEach {
     options.encoding = 'UTF-8'
 }
 
-tasks.withType(Javadoc) {
+tasks.withType(Javadoc).configureEach {
     options.addStringOption('encoding', 'UTF-8')
     options.addStringOption('Xdoclint:none', '-quiet')
 }
@@ -81,7 +81,7 @@ jar {
 
 import org.gradle.internal.os.OperatingSystem;
 
-tasks.withType(Test) { task ->
+tasks.withType(Test).configureEach { task ->
     task.outputs.upToDateWhen { false } // tests will always rerun
 
     // Always run serially because there are some very badly behaved tests in HTSJDK that
@@ -99,8 +99,8 @@ tasks.withType(Test) { task ->
 
     beforeTest { descriptor ->
         count++
-        if( count % 200 == 0) {
-            logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
+        if (count % 200 == 0) {
+            logger.lifecycle("Finished " + Integer.toString(count++) + " tests")
         }
     }
 
@@ -118,7 +118,7 @@ tasks.withType(Test) { task ->
 
 }
 
-task testWithDefaultReference(type: Test) {
+tasks.register('testWithDefaultReference', Test) {
     description = "Run tests with a default reference File"
     jvmArgs += '-Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa'
 
@@ -127,7 +127,7 @@ task testWithDefaultReference(type: Test) {
     }
 }
 
-task testWithOptimisticVCF4_4(type: Test) {
+tasks.register('testWithOptimisticVCF4_4', Test) {
     description = "Run tests with optimistic VCF 4.4 reading"
     jvmArgs += '-Dsamjdk.optimistic_vcf_4_4=true'
 
@@ -149,15 +149,15 @@ test {
 } dependsOn testWithDefaultReference, testWithOptimisticVCF4_4
 
 
-task testFTP(type: Test) {
+tasks.register('testFTP', Test) {
     description = "Runs the tests that require connection to a remote ftp server"
     useTestNG {
         includeGroups "ftp"
         excludeGroups "slow", "broken"
     }
 }
 
-task testExternalApis(type: Test) {
+tasks.register('testExternalApis', Test) {
     description = "Run the SRA, ENA, and HTTP tests (tests that interact with external APIs)"
     jvmArgs += '-Dsamjdk.sra_libraries_download=true'
 
@@ -169,7 +169,7 @@ task testExternalApis(type: Test) {
 
 if(project == rootProject) {
     wrapper {
-        gradleVersion = '7.6'
+        gradleVersion = '8.5'
     }
 }
 
@@ -249,8 +249,4 @@ signing {
     sign publishing.publications.htsjdk
 }
 
-gradle.taskGraph.beforeTask { Task task ->
-    println "executing $task ..."
-}
-
-task install(dependsOn:publishToMavenLocal)
+tasks.register('install') { dependsOn publishToMavenLocal }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+networkTimeout=10000
 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/.
@@ -80,10 +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=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 # 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"'
@@ -143,12 +143,16 @@ fi
 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