Update to JDK21 and Gradle 9

.github/workflows/ci-build-manual-crf.yml

@@ -18,10 +18,10 @@ jobs:
       with:
         fetch-tags: true
         fetch-depth: 0
-    - name: Set up JDK 17
+    - name: Set up JDK 21
       uses: actions/setup-java@v4
       with:
-        java-version: '17.0.10+7'
+        java-version: '21'
         distribution: 'temurin'
         cache: 'gradle'
     - name: Build with Gradle

.github/workflows/ci-build-manual-eval.yml

@@ -20,10 +20,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up JDK 17
+    - name: Set up JDK 21
       uses: actions/setup-java@v4
       with:
-        java-version: '17.0.10+7'
+        java-version: '21'
         distribution: 'temurin'
         cache: 'gradle'
     - name: Build with Gradle

.github/workflows/ci-build-manual-full.yml

@@ -18,10 +18,10 @@ jobs:
       with:
         fetch-tags: true
         fetch-depth: 0
-    - name: Set up JDK 17
+    - name: Set up JDK 21
       uses: actions/setup-java@v4
       with:
-        java-version: '17.0.10+7'
+        java-version: '21'
         distribution: 'temurin'
         cache: 'gradle'
     - name: Build with Gradle

.github/workflows/ci-build-unstable.yml

@@ -13,11 +13,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 11
+      - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
-          java-version: '11'
-          distribution: 'adopt'
+          java-version: '21'
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Build with Gradle
         run: ./gradlew clean assemble --info --stacktrace --no-daemon

Dockerfile.crf

@@ -13,7 +13,7 @@
 # -------------------
 # build builder image
 # -------------------
-FROM eclipse-temurin:17.0.15_6-jdk AS builder
+FROM eclipse-temurin:21-jdk AS builder
 
 USER root
 
@@ -66,7 +66,7 @@ RUN rm -rf grobid-source
 # -------------------
 # build runtime image
 # -------------------
-FROM eclipse-temurin:17.0.15_6-jre
+FROM eclipse-temurin:21-jre
 
 RUN apt-get update && \
     apt-get -y upgrade && \

Dockerfile.delft

@@ -15,7 +15,7 @@
 # build builder image
 # -------------------
 
-FROM eclipse-temurin:17.0.15_6-jdk AS builder
+FROM eclipse-temurin:21-jdk AS builder
 
 USER root
 
@@ -122,8 +122,9 @@ COPY --from=builder /opt/java/openjdk ${JAVA_HOME}
 # install jep 
 RUN pip3 install jep==4.0.3
 
-
-ENV LD_LIBRARY_PATH=/usr/local/lib/python3.8/dist-packages/jep:grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep:${LD_LIBRARY_PATH}
+# Get the Python version dynamically and set LD_LIBRARY_PATH accordingly
+ENV PYTHON_VERSION=$(python3 --version | cut -d' ' -f2 | cut -d'.' -f1,2)
+ENV LD_LIBRARY_PATH=/usr/local/lib/python${PYTHON_VERSION}/dist-packages/jep:grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep:${LD_LIBRARY_PATH}
 # remove libjep.so because we are providing our own version in the virtual env above
 RUN rm /opt/grobid/grobid-home/lib/lin-64/jep/libjep.so
 

Dockerfile.evaluation

@@ -12,7 +12,7 @@
 # build builder image
 # -------------------
 
-FROM eclipse-temurin:17.0.15_6-jdk AS builder
+FROM eclipse-temurin:21-jdk AS builder
 
 USER root
 
@@ -115,8 +115,9 @@ COPY --from=builder /opt/java/openjdk ${JAVA_HOME}
 # install jep
 RUN pip3 install jep==4.0.3
 
-
-ENV LD_LIBRARY_PATH=/usr/local/lib/python3.8/dist-packages/jep:grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep:${LD_LIBRARY_PATH}
+# Get the Python version dynamically and set LD_LIBRARY_PATH accordingly
+ENV PYTHON_VERSION=$(python3 --version | cut -d' ' -f2 | cut -d'.' -f1,2)
+ENV LD_LIBRARY_PATH=/usr/local/lib/python${PYTHON_VERSION}/dist-packages/jep:grobid-home/lib/lin-64:grobid-home/lib/lin-64/jep:${LD_LIBRARY_PATH}
 # remove libjep.so because we are providing our own version in the virtual env above
 RUN rm /opt/grobid/grobid-home/lib/lin-64/jep/libjep.so
 

build.gradle

@@ -1,19 +1,9 @@
-buildscript {
-    repositories {
-        mavenLocal()
-        mavenCentral()
-        maven {
-            url 'https://plugins.gradle.org/m2/'
-        }
-        gradlePluginPortal()
-    }
-    dependencies {
-        classpath 'gradle.plugin.org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.12.0'
-        classpath "gradle.plugin.com.github.jengelman.gradle.plugins:shadow:7.0.0"
-        classpath 'com.adarshr:gradle-test-logger-plugin:2.0.0'
-        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:1.8.21"
-        classpath "net.researchgate:gradle-release:3.0.2"
-    }
+plugins {
+    id 'org.jetbrains.kotlin.jvm' version '2.0.0' apply false
+    id 'com.gradleup.shadow' version '8.3.8' apply false
+    id 'com.adarshr.test-logger' version '4.0.0' apply false
+    id 'com.github.kt3k.coveralls' version '2.12.2' apply false
+    id 'net.researchgate.release' version '3.1.0' apply false
 }
 
 repositories {
@@ -59,6 +49,7 @@ def getJavaLibraryPath = {
 }
 
 apply plugin: 'jacoco'
+apply plugin: 'com.github.kt3k.coveralls'
 
 jacoco {
     toolVersion = '0.8.8'
@@ -70,7 +61,7 @@ def getGitRevision() {
     try {
         def stdout = new ByteArrayOutputStream()
         println("Checking git under ${rootProject.rootDir}")
-        exec {
+        project.exec {
             workingDir rootProject.rootDir
             commandLine 'git', 'describe', '--tags', '--always', '--first-parent'
             standardOutput = stdout
@@ -94,11 +85,6 @@ tasks.register('collectGitRevision') {
 }
 
 allprojects {
-    apply plugin: 'java-library'
-    apply plugin: 'base'
-    apply plugin: 'com.github.kt3k.coveralls'
-    apply plugin: 'com.adarshr.test-logger'
-    apply plugin: 'org.jetbrains.kotlin.jvm'
     apply plugin: 'net.researchgate.release'
 
     group = "org.grobid"
@@ -114,6 +100,8 @@ allprojects {
 subprojects {
     apply plugin: 'java'
     apply plugin: 'maven-publish'
+    apply plugin: 'org.jetbrains.kotlin.jvm'
+    apply plugin: 'com.adarshr.test-logger'
 
     publishing {
         publications {
@@ -127,14 +115,15 @@ subprojects {
         }
     }
 
-    sourceCompatibility = 1.11
-    targetCompatibility = 1.11
+    java {
+        toolchain {
+            languageVersion = JavaLanguageVersion.of(21)
+        }
+    }
 
-    tasks.withType(KotlinCompile).configureEach {
-        sourceCompatibility = JavaVersion.VERSION_11
-        targetCompatibility = JavaVersion.VERSION_11
+    tasks.withType(org.jetbrains.kotlin.gradle.tasks.KotlinCompile).configureEach {
         kotlinOptions {
-            jvmTarget = JavaVersion.VERSION_11
+            jvmTarget = "21"
         }
     }
 
@@ -149,7 +138,6 @@ subprojects {
     configurations {
         all*.exclude group: 'org.slf4j', module: "slf4j-log4j12"
         all*.exclude group: 'log4j', module: "log4j"
-        implementation.setCanBeResolved(true)
     }
 
     ext {
@@ -173,9 +161,9 @@ subprojects {
             because("Only needed to run tests in a version of IntelliJ IDEA that bundles older versions")
         }
         testImplementation('org.junit.jupiter:junit-jupiter')
-        testImplementation 'org.easymock:easymock:5.1.0'
-        testImplementation "org.powermock:powermock-api-easymock:2.0.7"
-        testImplementation "org.powermock:powermock-module-junit4:2.0.7"
+        testImplementation 'org.easymock:easymock:5.6.0'
+        testImplementation "org.powermock:powermock-api-easymock:2.0.9"
+        testImplementation "org.powermock:powermock-module-junit4:2.0.9"
         testImplementation "org.xmlunit:xmlunit-matchers:2.10.0"
         testImplementation "org.xmlunit:xmlunit-legacy:2.10.0"
         testImplementation "org.hamcrest:hamcrest-all:1.3"
@@ -203,15 +191,15 @@ subprojects {
     tasks.register('sourceJar', Jar) {
         description = 'A jar that contains source code'
         archiveClassifier = 'sources'
-        from project.sourceSets.main.java
+        from sourceSets.main.allSource
     }
 
     artifacts {
         archives sourceJar
         archives jar
     }
 
-    test {
+    tasks.withType(Test) {
         useJUnitPlatform()
 
         testLogging.showStandardStreams = true
@@ -223,7 +211,11 @@ subprojects {
 
         if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
             jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED",
-                "--add-opens", "java.base/java.io=ALL-UNNAMED", "--add-opens", "java.xml/jdk.xml.internal=ALL-UNNAMED"
+                "--add-opens", "java.base/java.io=ALL-UNNAMED", 
+                "--add-opens", "java.xml/jdk.xml.internal=ALL-UNNAMED",
+                // PowerMock compatibility with Java 21 - TODO: Replace PowerMock with Mockito/JUnit Jupiter
+                "--add-opens", "java.base/java.lang=ALL-UNNAMED",
+                "--add-opens", "java.base/java.util=ALL-UNNAMED"
         }
 
         systemProperty "java.library.path", "${javaLibraryPath}"
@@ -233,7 +225,7 @@ subprojects {
 /** SUBPROJECTS **/
 
 project("grobid-core") {
-    apply plugin: 'com.github.johnrengelman.shadow'
+    apply plugin: 'com.gradleup.shadow'
     apply plugin: 'jacoco'
 
     configurations {
@@ -351,9 +343,11 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 project(":grobid-service") {
     apply plugin: 'application'
     apply plugin: 'jacoco'
-    apply plugin: 'com.github.johnrengelman.shadow'
+    apply plugin: 'com.gradleup.shadow'
 
-    mainClassName = 'org.grobid.service.main.GrobidServiceApplication'
+    application {
+        mainClass = 'org.grobid.service.main.GrobidServiceApplication'
+    }
 
 
     tasks.run {
@@ -436,7 +430,7 @@ project(":grobid-service") {
 }
 
 project(":grobid-trainer") {
-    apply plugin: 'com.github.johnrengelman.shadow'
+    apply plugin: 'com.gradleup.shadow'
     apply plugin: 'jacoco'
 
     dependencies {
@@ -541,7 +535,7 @@ project(":grobid-trainer") {
 
     trainerTasks.each { taskName, mainClassName ->
         tasks.create(name: taskName, type: JavaExec, group: 'modeltraining') {
-            main = mainClassName
+            mainClass = mainClassName
             classpath = sourceSets.main.runtimeClasspath
             def javaLibraryPath = getJavaLibraryPath()
             if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
@@ -555,7 +549,7 @@ project(":grobid-trainer") {
 
     complexTrainerTasks.each { taskName, mainClassNameAndArgs ->
         tasks.create(name: taskName, type: JavaExec, group: 'modeltraining') {
-            main = mainClassNameAndArgs[0]
+            mainClass = mainClassNameAndArgs[0]
             classpath = sourceSets.main.runtimeClasspath
             def javaLibraryPath = getJavaLibraryPath()
             if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
@@ -580,7 +574,7 @@ project(":grobid-trainer") {
     // ./gradlew PrepareDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 
     // ./gradlew EvaluateDOIMatching -Pp2t=ABS_PATH_TO_PMC/PMC_sample_1943 
     task(jatsEval, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
-        main = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
+        mainClass = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
         classpath = sourceSets.main.runtimeClasspath
         args 'nlm', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0'), getArg('flavor', '')
         def javaLibraryPath = getJavaLibraryPath()
@@ -593,7 +587,7 @@ project(":grobid-trainer") {
     }
 
     task(teiEval, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
-        main = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
+        mainClass = 'org.grobid.trainer.evaluation.EndToEndEvaluation'
         classpath = sourceSets.main.runtimeClasspath
         args 'tei', getArg('p2t', '.'), getArg('run', '0'), getArg('fileRatio', '1.0'), getArg('flavor', '')
         def javaLibraryPath = getJavaLibraryPath()
@@ -607,7 +601,7 @@ project(":grobid-trainer") {
     }
 
     task(PrepareDOIMatching, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
-        main = 'org.grobid.trainer.evaluation.EvaluationDOIMatching'
+        mainClass = 'org.grobid.trainer.evaluation.EvaluationDOIMatching'
         classpath = sourceSets.main.runtimeClasspath
         args 'data', getArg('p2t', '.')
         def javaLibraryPath = getJavaLibraryPath()
@@ -622,7 +616,7 @@ project(":grobid-trainer") {
     }
 
     task(EvaluateDOIMatching, dependsOn: 'classes', type: JavaExec, group: 'modelevaluation') {
-        main = 'org.grobid.trainer.evaluation.EvaluationDOIMatching'
+        mainClass = 'org.grobid.trainer.evaluation.EvaluationDOIMatching'
         classpath = sourceSets.main.runtimeClasspath
         args 'eval', getArg('p2t', '.')
 
@@ -662,24 +656,24 @@ tasks.register("codeCoverageReport", JacocoReport) {
     // XML -> coveralls,
     // HTML -> for manual check
     reports {
-        xml.enabled true
-        html.enabled true
-        csv.enabled true
+        xml.required = true
+        html.required = true
+        csv.required = true
     }
 
 }
 
 /** COVERALLS **/
 coveralls {
-    sourceDirs = files(subprojects.sourceSets.main.allSource.srcDirs).files.absolutePath
+        sourceDirs = files(subprojects.findAll { it.plugins.hasPlugin('java') }.sourceSets.main.allSource.srcDirs).files.absolutePath
 }
 
 tasks.coveralls {
     dependsOn codeCoverageReport
 }
 
 wrapper {
-    gradleVersion "7.2"
+    gradleVersion "9.0.0"
 }
 
 build.dependsOn project.getSubprojects().collect({ it.getTasks().getByName("build") })
@@ -691,4 +685,4 @@ release {
     git {
         requireBranch.set('master')
     }
-}
+}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.0.0-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists