org.apache.groovy

quiltdata · Dec 6, 2024 · a2d0ccd · a2d0ccd
1 parent b8ae03c
commit a2d0ccd
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Showing 5 changed files with 27 additions and 53 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-24.10.0
+24.11.0-edge
diff --git a/build.gradle b/build.gradle
@@ -35,7 +35,7 @@ if (groovyVer) {
 
         configurations.all {
             resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-                if (details.requested.group == 'org.codehaus.groovy') {
+                if (details.requested.group == 'org.apache.groovy') {
                     if (groovyVer.contains(':')) {
                         details.useTarget(groovyVer)
                     }
@@ -90,18 +90,18 @@ allprojects {
 
     configurations {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-all'
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-cli-picocli'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-all'
+        all*.exclude group: 'org.apache.groovy', module: 'groovy-cli-picocli'
         // groovydoc libs
         groovyDoc.extendsFrom runtime
     }
 
-    groovyVer= '3.0.23'
+    groovyVer= '4.0.24'
 
     dependencies {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
         implementation 'com.github.groovy-wslite:groovy-wslite:1.1.3'
-        implementation "org.codehaus.groovy:groovy-all:${groovyVer}"
+        implementation "org.apache.groovy:groovy-all:${groovyVer}"
         implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.1'
         implementation 'com.upplication:s3fs:2.2.2'
 
@@ -110,8 +110,8 @@ allprojects {
         }
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.1'
-        groovyDoc "org.codehaus.groovy:groovy-groovydoc:${groovyVer}"
-        groovyDoc "org.codehaus.groovy:groovy-ant:${groovyVer}"
+        groovyDoc "org.apache.groovy:groovy-groovydoc:${groovyVer}"
+        groovyDoc "org.apache.groovy:groovy-ant:${groovyVer}"
     }
 
     test {

diff --git a/gradle-groovysh-init.gradle b/gradle-groovysh-init.gradle
@@ -3,7 +3,6 @@ gradle.projectsLoaded {
         afterEvaluate { project ->
             if (!project.repositories.any { it.name == 'MavenRepo' }) {
                 project.repositories {
-                    // To be able to load org.codehaus.groovy:groovy-groovysh
                     mavenCentral()
                 }
         }
@@ -13,8 +12,8 @@ gradle.projectsLoaded {
             }
 
             project.dependencies {
-                groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") {
-                    exclude group: 'org.codehaus.groovy'
+                groovyshdependencies("org.apache.groovy:groovy-groovysh:${GroovySystem.version}") {
+                    exclude group: 'org.apache.groovy'
                 }
             }
 
@@ -31,7 +30,7 @@ gradle.projectsLoaded {
                         groovyObjectClassLoader.addURL(file.toURL())
                     }
                     Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader)
-                    groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader)
+                    groovyshClass = Class.forName('org.apache.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader)
 
                     if (groovyshClass) {
                         groovyShell = groovyshClass.newInstance()

diff --git a/plugins/nf-quilt/build.gradle b/plugins/nf-quilt/build.gradle
@@ -16,33 +16,16 @@
 
 plugins {
     // Apply the groovy plugin to add support for Groovy
-    id 'groovy'
+    id 'groovy' // io.nextflow.groovy-library-conventions?
     id 'idea'
     id 'se.patrikerdes.use-latest-versions' version '0.2.18'
     id 'com.github.ben-manes.versions' version '0.51.0'
     id 'jacoco'
 }
 
-useLatestVersions {
-    // A blacklist of dependencies to update, in the format of group:name
-    updateBlacklist = [
-        'com.quiltdata:quiltcore',
-        'org.codehaus.groovy:groovy',
-        'org.codehaus.groovy:groovy-nio',
-        'org.codehaus.groovy:groovy-test',
-        'org.spockframework:spock-core',
-        'org.spockframework:spock-junit4',
-    ]
-}
-
 group = 'io.nextflow'
 // DO NOT SET THE VERSION HERE
 // THE VERSION FOR PLUGINS IS DEFINED IN THE `/resources/META-INF/MANIFEST.NF` file
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(17)
-    }
-}
 
 idea {
     module.inheritOutputDirs = true
@@ -71,45 +54,37 @@ sourceSets {
 
 ext {
     nextflowVersion = rootProject.file('VERSION').text.trim()
-    groovyVer = '3.0.23'
+    groovyVer = '4.0.18'
 }
 
 
 dependencies {
-    // quiltcore
     implementation 'com.quiltdata:quiltcore:0.1.5'
+    implementation "org.apache.groovy:groovy-all:$groovyVer"
 
     // This dependency is exported to consumers, that is to say found on their compile classpath.
     compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.1.0-alpha1'
-    compileOnly 'org.pf4j:pf4j:3.12.1'
+    compileOnly 'org.slf4j:slf4j-api:1.7.10'
+    compileOnly 'org.pf4j:pf4j:3.4.1'
     // add here plugins depepencies
-    compileOnly 'org.slf4j:slf4j-simple:2.1.0-alpha1'
-    compileOnly 'black.ninia:jep:4.2.1'
-    runtime 'black.ninia:jep:4.2.1'
-    runtimeOnly 'org.junit.platform:junit-platform-launcher:1.11.3'
-    implementation 'commons-io:commons-io:2.17.0'
-    implementation 'black.ninia:jep:4.2.1'
-    testImplementation 'black.ninia:jep:4.2.1'
-    //testImplementation(testFixtures('black.ninia:jep:4.0.3'))
 
     // test configuration
-    testImplementation "org.codehaus.groovy:groovy:$groovyVer"
-    testImplementation "org.codehaus.groovy:groovy-nio:$groovyVer"
+    testImplementation "org.apache.groovy:groovy:$groovyVer"
+    testImplementation "org.apache.groovy:groovy-nio:$groovyVer"
     testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation("org.codehaus.groovy:groovy-test:$groovyVer") { exclude group: 'org.codehaus.groovy' }
-    testImplementation('cglib:cglib-nodep:3.3.0')
-    testImplementation('org.objenesis:objenesis:3.4')
-    testImplementation('org.spockframework:spock-core:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation('org.spockframework:spock-junit4:2.3-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation('com.google.jimfs:jimfs:1.3.0')
+    testImplementation ("org.apache.groovy:groovy-all:$groovyVer") { exclude group: 'org.apache.groovy' }
+    testImplementation ("cglib:cglib-nodep:3.3.0")
+    testImplementation ("org.objenesis:objenesis:3.1")
+    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ('com.google.jimfs:jimfs:1.1')
 
     testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
     testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
 
     // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
     modules {
-        module('commons-logging:commons-logging') { replacedBy('org.slf4j:jcl-over-slf4j') }
+        module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
     }
 }
 

diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy b/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
@@ -178,7 +178,7 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
         provider.copy(remoteFile, tempFile)
 
         then:
-        thrown org.codehaus.groovy.runtime.powerassert.PowerAssertionError
+        thrown org.apache.groovy.runtime.powerassert.PowerAssertionError
     }
 
     void 'should do nothing when copying a path to itself'() {
@@ -205,7 +205,7 @@ class QuiltFileSystemProviderTest extends QuiltSpecification {
         provider.move(remoteFile, tempFile)
 
         then:
-        thrown org.codehaus.groovy.runtime.powerassert.PowerAssertionError
+        thrown org.apache.groovy.runtime.powerassert.PowerAssertionError
     }
 
     void 'should recognize when path isHidden'() {