From a2d0ccd4b60d21bb7a7c493d049a97ac6fe18338 Mon Sep 17 00:00:00 2001 From: "Dr. Ernie Prabhakar" <19791+drernie@users.noreply.github.com> Date: Thu, 5 Dec 2024 20:54:39 -0800 Subject: [PATCH] org.apache.groovy --- VERSION | 2 +- build.gradle | 14 ++--- gradle-groovysh-init.gradle | 7 ++- plugins/nf-quilt/build.gradle | 53 +++++-------------- .../nio/QuiltFileSystemProviderTest.groovy | 4 +- 5 files changed, 27 insertions(+), 53 deletions(-) diff --git a/VERSION b/VERSION index 21651351..c97fb1cb 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -24.10.0 +24.11.0-edge \ No newline at end of file diff --git a/build.gradle b/build.gradle index a6cd4e17..fc87cfa3 100644 --- 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 index 4c36259c..b533e20f 100644 --- 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 index 83b9b73f..2d70d48f 100644 --- 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 index b302091f..eb8b826e 100644 --- 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'() {