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This commit udates the gradle build. More in details: - Update Gradle to version 7.6 - Update Nextflow runtime to version 22.10.x - Update Groovy runtime to version 3.0.14 - Fixed some failing tests - Update Java min version to 11 - Update GitHub action build Signed-off-by: Paolo Di Tommaso <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| /* | ||
| * This file was generated by the Gradle 'init' task. | ||
| */ | ||
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| plugins { | ||
| // Support convention plugins written in Groovy. Convention plugins are build scripts in 'src/main' that automatically become available as plugins in the main build. | ||
| id 'groovy-gradle-plugin' | ||
| } | ||
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| repositories { | ||
| // Use the plugin portal to apply community plugins in convention plugins. | ||
| gradlePluginPortal() | ||
| } | ||
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11
buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| /* | ||
| * This file was generated by the Gradle 'init' task. | ||
| */ | ||
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| plugins { | ||
| // Apply the common convention plugin for shared build configuration between library and application projects. | ||
| id 'io.nextflow.groovy-common-conventions' | ||
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| // Apply the application plugin to add support for building a CLI application in Java. | ||
| id 'application' | ||
| } |
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28
buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| /* | ||
| * This file was generated by the Gradle 'init' task. | ||
| */ | ||
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| plugins { | ||
| // Apply the groovy Plugin to add support for Groovy. | ||
| id 'groovy' | ||
| } | ||
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| repositories { | ||
| // Use Maven Central for resolving dependencies. | ||
| mavenCentral() | ||
| } | ||
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| java { | ||
| toolchain { | ||
| languageVersion = JavaLanguageVersion.of(17) | ||
| } | ||
| } | ||
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| compileJava { | ||
| options.release.set(11) | ||
| } | ||
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| tasks.withType(GroovyCompile) { | ||
| sourceCompatibility = '11' | ||
| targetCompatibility = '11' | ||
| } |
11 changes: 11 additions & 0 deletions
11
buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| /* | ||
| * This file was generated by the Gradle 'init' task. | ||
| */ | ||
|
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||
| plugins { | ||
| // Apply the common convention plugin for shared build configuration between library and application projects. | ||
| id 'io.nextflow.groovy-common-conventions' | ||
| // Apply the java-library plugin for API and implementation separation. | ||
| id 'java-library' | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| nextflowVersion = 22.10.0 | ||
| groovyVersion = 3.0.14 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| distributionBase=GRADLE_USER_HOME | ||
| distributionPath=wrapper/dists | ||
| distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip | ||
| distributionUrl=https\://services.gradle.org/distributions/gradle-7.6-bin.zip | ||
| zipStoreBase=GRADLE_USER_HOME | ||
| zipStorePath=wrapper/dists |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -23,7 +23,6 @@ ext.github_organization = 'nextflow-io' | |
| ext.github_username = project.findProperty('github_username') ?: 'pditommaso' | ||
| ext.github_access_token = project.findProperty('github_access_token') ?: System.getenv('GITHUB_TOKEN') | ||
| ext.github_commit_email = project.findProperty('github_commit_email') ?: '[email protected]' | ||
| ext.nextflowVersion = '22.08.1-edge' | ||
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| jar.enabled = false | ||
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@@ -59,7 +58,7 @@ subprojects { | |
| apply plugin: 'java' | ||
| apply plugin: 'groovy' | ||
| apply plugin: 'io.nextflow.nf-build-plugin' | ||
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| repositories { | ||
| mavenLocal() | ||
| mavenCentral() | ||
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@@ -95,6 +94,8 @@ subprojects { | |
| "sha512sum": "${computeSha512(zip)}" | ||
| } | ||
| """.stripIndent() | ||
| // cleanup tmp dir | ||
| file("$buildDir/tmp/makeZip").deleteDir() | ||
| } | ||
| outputs.file("$buildDir/libs/${project.name}-${project.version}.zip") | ||
| } | ||
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@@ -138,13 +139,32 @@ subprojects { | |
| skipExisting = true | ||
| } | ||
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| jar { | ||
| from sourceSets.main.allSource | ||
| doLast { | ||
| file("$buildDir/tmp/jar").deleteDir() | ||
| } | ||
| } | ||
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| tasks.withType(GenerateModuleMetadata) { | ||
| enabled = false | ||
| } | ||
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| task upload(dependsOn: [uploadPlugin] ) { } | ||
| } | ||
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| /* | ||
| * Upload all plugins to the corresponding GitHub repos | ||
| */ | ||
| task upload(dependsOn: [subprojects.uploadPlugin]) { } | ||
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| classes.dependsOn subprojects.copyPluginLibs | ||
| /* | ||
| * Copies the plugins required dependencies in the corresponding lib directory | ||
| */ | ||
| classes.dependsOn subprojects.copyPluginLibs | ||
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| /* | ||
| * Merge and publish the plugins index file | ||
| */ | ||
| task publishIndex( type: io.nextflow.gradle.tasks.GithubRepositoryPublisher ) { | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,16 @@ | ||
| package nextflow.validation | ||
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| import java.nio.file.Path | ||
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| import nextflow.plugin.Plugins | ||
| import nextflow.plugin.TestPluginDescriptorFinder | ||
| import nextflow.plugin.TestPluginManager | ||
| import nextflow.plugin.extension.PluginExtensionProvider | ||
| import org.junit.Rule | ||
| import org.pf4j.PluginDescriptorFinder | ||
| import spock.lang.Shared | ||
| import spock.lang.TempDir | ||
| import test.Dsl2Spec | ||
| import test.OutputCapture | ||
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| import java.nio.file.Path | ||
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| /** | ||
| * @author : jorge <[email protected]> | ||
| * | ||
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@@ -398,7 +395,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{ | |
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| then: | ||
| noExceptionThrown() | ||
| stdout.size == 10 | ||
| stdout.size() == 10 | ||
| } | ||
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| def 'should print a help message with argument options' () { | ||
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@@ -424,7 +421,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{ | |
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| then: | ||
| noExceptionThrown() | ||
| stdout.size == 1 | ||
| stdout.size() == 1 | ||
| } | ||
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| def 'should print a help message of one parameter' () { | ||
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@@ -457,7 +454,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{ | |
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| then: | ||
| noExceptionThrown() | ||
| stdout.size == 7 | ||
| stdout.size() == 7 | ||
| } | ||
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| def 'should fail when help param doesnt exist' () { | ||
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@@ -517,7 +514,7 @@ class PluginExtensionMethodsTest extends Dsl2Spec{ | |
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| then: | ||
| noExceptionThrown() | ||
| stdout.size == 11 | ||
| stdout.size() == 11 | ||
| stdout ==~ /.*\[0;34moutdir : .\[0;32moutDir.*/ | ||
| } | ||
| } | ||