feat: update to Java 21 and Gradle 8.5 #405

.github/workflows/lapis2.yml

@@ -12,10 +12,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Execute Tests
@@ -39,10 +39,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Login to GitHub Container Registry
@@ -90,10 +90,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Setup Node.js

lapis2/build.gradle

@@ -3,18 +3,26 @@ import org.gradle.api.tasks.testing.logging.TestLogEvent
 import org.jetbrains.kotlin.gradle.dsl.JvmTarget
 
 plugins {
-    id 'org.springframework.boot' version '3.1.5'
+    id 'org.springframework.boot' version '3.2.0'
     id 'io.spring.dependency-management' version '1.1.4'
-    id 'org.jetbrains.kotlin.jvm' version '1.9.20'
-    id 'org.jetbrains.kotlin.plugin.spring' version '1.9.20'
+    id 'org.jetbrains.kotlin.jvm' version '1.9.21'
+    id 'org.jetbrains.kotlin.plugin.spring' version '1.9.21'
     id 'org.jlleitschuh.gradle.ktlint' version "11.6.1"
     id 'org.springdoc.openapi-gradle-plugin' version "1.8.0"
     id 'antlr'
 }
 
 group = 'org.genspectrum'
 version = '0.0.1-SNAPSHOT'
-sourceCompatibility = '19'
+
+java {
+    sourceCompatibility = '21'
+    targetCompatibility = '21'
+}
+
+kotlin {
+    jvmToolchain(21)
+}
 
 repositories {
     mavenCentral()
@@ -69,7 +77,7 @@ tasks.named('test') {
 }
 
 tasks.named('bootBuildImage') {
-    environment["BP_JVM_VERSION"] = "20"
+    environment["BP_JVM_VERSION"] = "21"
     environment["BPE_SPRING_PROFILES_ACTIVE"] = "docker"
     environment["BPE_LAPIS_REFERENCE_GENOME_FILENAME"] = "./reference_genomes.json"
     imageName = "ghcr.io/genspectrum/${project.name}"

lapis2/gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
-networkTimeout=10000
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

lapis2/gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/master/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/.
@@ -80,11 +80,11 @@ do
     esac
 done
 
-# This is normally unused
-# shellcheck disable=SC2034
-APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
+APP_NAME="Gradle"
+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"'
 
@@ -143,16 +143,12 @@ 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

lapis2/gradlew.bat

@@ -26,7 +26,6 @@ if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
 if "%DIRNAME%"=="" set DIRNAME=.
-@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%