Bump groovy 4 + nextflow 24.01.x

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

.github/workflows/build.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [8, 11]
+        java_version: [11, 21]
 
     steps:
       - name: Environment

Makefile

@@ -8,6 +8,10 @@ mm =
 endif 
 
 clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
+	rm -rf plugins/*/build
 	./gradlew clean
 
 compile:
@@ -44,6 +48,9 @@ else
 	./gradlew ${mm}test --tests ${class}
 endif
 
+assemble:
+	./gradlew assemble
+
 #
 # generate build zips under build/plugins
 # you can install the plugin copying manually these files to $HOME/.nextflow/plugins
@@ -62,4 +69,4 @@ upload-plugins:
 	./gradlew plugins:upload
 
 publish-index:
-	./gradlew plugins:publishIndex
+	./gradlew plugins:publishIndex

README.md

@@ -77,7 +77,7 @@ To build and test the plugin during development, configure a local Nextflow buil
 
 3. Compile the plugin alongside the Nextflow code:
     ```bash
-    make compile
+    make assemble
     ```
 
 4. Run Nextflow with the plugin, using `./launch.sh` as a drop-in replacement for the `nextflow` command, and adding the option `-plugins nf-hello` to load the plugin:

gradle/wrapper/gradle-wrapper.properties

@@ -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-8.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

plugins/nf-hello/build.gradle

@@ -50,7 +50,7 @@ sourceSets {
 }
 
 ext{
-    nextflowVersion = '23.04.0'
+    nextflowVersion = '24.01.0-edge'
 }
 
 dependencies {
@@ -61,14 +61,14 @@ dependencies {
     // add here plugins depepencies
 
     // test configuration
-    testImplementation "org.codehaus.groovy:groovy:3.0.17"
-    testImplementation "org.codehaus.groovy:groovy-nio:3.0.17"
+    testImplementation "org.apache.groovy:groovy:4.0.18"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.18"
     testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation ("org.codehaus.groovy:groovy-test:3.0.17") { exclude group: 'org.codehaus.groovy' }
+    testImplementation ("org.apache.groovy:groovy-test:4.0.18") { exclude group: 'org.apache.groovy' }
     testImplementation ("cglib:cglib-nodep:3.3.0")
     testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.2-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.2-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    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"))

plugins/nf-hello/src/resources/META-INF/MANIFEST.MF

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
 Plugin-Id: nf-hello
-Plugin-Version: 0.4.0
+Plugin-Version: 0.5.0
 Plugin-Class: nextflow.hello.HelloPlugin
 Plugin-Provider: nextflow
-Plugin-Requires: >=22.10.0
+Plugin-Requires: >=24.01.0-edge

plugins/nf-hello/src/test/nextflow/hello/HelloDslTest.groovy

@@ -1,5 +1,8 @@
 package nextflow.hello
 
+import java.nio.file.Files
+import java.util.jar.Manifest
+
 import nextflow.Channel
 import nextflow.plugin.Plugins
 import nextflow.plugin.TestPluginDescriptorFinder
@@ -35,9 +38,18 @@ class HelloDslTest extends Dsl2Spec{
             @Override
             protected PluginDescriptorFinder createPluginDescriptorFinder() {
                 return new TestPluginDescriptorFinder(){
+
                     @Override
-                    protected Path getManifestPath(Path pluginPath) {
-                        return pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF')
+                    protected Manifest readManifestFromDirectory(Path pluginPath) {
+                        if( !Files.isDirectory(pluginPath) )
+                            return null
+
+                        final manifestPath = pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF')
+                        if( !Files.exists(manifestPath) )
+                            return null
+
+                        final input = Files.newInputStream(manifestPath)
+                        return new Manifest(input)
                     }
                 }
             }

settings.gradle

@@ -14,6 +14,13 @@
  * limitations under the License.
  */
 
+plugins {
+    // required to download the toolchain (jdk) from a remote repository
+    // https://github.com/gradle/foojay-toolchains
+    // https://docs.gradle.org/current/userguide/toolchains.html#sub:download_repositories
+    id("org.gradle.toolchains.foojay-resolver-convention") version "0.7.0"
+}
+
 rootProject.name = 'nf-hello'
 include('plugins')
 include('plugins:nf-hello')