Target java17

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 22]
+        java_version: [17, 21, 22]
 
     steps:
       - name: Environment
@@ -115,7 +115,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 21]
+        java_version: [17, 21]
         test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout

build.gradle

@@ -73,12 +73,12 @@ allprojects {
     }
 
     compileJava {
-        options.release.set(11)
+        options.release.set(17)
     }
 
     tasks.withType(GroovyCompile) {
-        sourceCompatibility = '11'
-        targetCompatibility = '11'
+        sourceCompatibility = '17'
+        targetCompatibility = '17'
     }
 
     idea {
@@ -147,7 +147,6 @@ allprojects {
     // Required to run tests on Java 9 and higher in compatibility mode
     tasks.withType(Test) {
         jvmArgs ([
-            '-Dorg.spockframework.mock.ignoreByteBuddy=true',
             '--enable-preview',
             '--add-opens=java.base/java.lang=ALL-UNNAMED',
             '--add-opens=java.base/java.io=ALL-UNNAMED',

modules/nextflow/build.gradle

@@ -54,10 +54,10 @@ dependencies {
 
     // test configuration
     testFixturesApi ("org.apache.groovy:groovy-test:4.0.22") { exclude group: 'org.apache.groovy' }
-    testFixturesApi ("cglib:cglib-nodep:3.3.0")
-    testFixturesApi ("org.objenesis:objenesis:3.2")
-    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testFixturesApi ("org.objenesis:objenesis:3.4")
+    testFixturesApi ("net.bytebuddy:byte-buddy:1.14.17")
+    testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }
+    testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy' }
     testFixturesApi 'com.google.jimfs:jimfs:1.2'
 
 }

modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy

@@ -93,7 +93,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
     List<BranchInfo> getBranches() {
         // https://docs.microsoft.com/en-us/rest/api/azure/devops/git/refs/list?view=azure-devops-rest-6.0#refs-heads
         final url = "$endpointUrl/refs?filter=heads&api-version=6.0"
-        this.<BranchInfo>invokeAndResponseWithPaging(url, { Map branch ->
+        this.invokeAndResponseWithPaging(url, { Map branch ->
             new BranchInfo(strip(branch.name), branch.objectId as String)
         })
     }
@@ -104,7 +104,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
     List<TagInfo> getTags() {
         // https://docs.microsoft.com/en-us/rest/api/azure/devops/git/refs/list?view=azure-devops-rest-6.0#refs-tags
         final url = "$endpointUrl/refs?filter=tags&api-version=6.0"
-        this.<TagInfo>invokeAndResponseWithPaging(url, { Map tag ->
+        this.invokeAndResponseWithPaging(url, { Map tag ->
             new TagInfo(strip(tag.name), tag.objectId as String)
         })
     }
@@ -118,9 +118,10 @@ final class AzureRepositoryProvider extends RepositoryProvider {
                 .replace('refs/heads/','')
     }
 
+    // NOTE: @Memoized with <T> does not work with bytebuddy
     @Memoized
-    protected <T> List<T> invokeAndResponseWithPaging(String url, Closure<T> parse) {
-        final result = new ArrayList<T>(50)
+    protected List invokeAndResponseWithPaging(String url, Closure parse) {
+        final result = new ArrayList(50)
         do {
             final resp = invokeAndParseResponse(url)
             final tags = resp.value as List<Map>

modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy

@@ -241,8 +241,9 @@ abstract class RepositoryProvider {
         }
     }
 
+    // NOTE: @Memoized with <T> does not work with bytebuddy
     @Memoized
-    protected <T> List<T> invokeAndResponseWithPaging(String request, Closure<T> parse) {
+    protected List invokeAndResponseWithPaging(String request, Closure parse) {
         int page = 0
         final result = new ArrayList()
         while( true ) {

plugins/nf-azure/src/main/nextflow/cloud/azure/nio/AzFileSystem.groovy

@@ -527,16 +527,17 @@ class AzFileSystem extends FileSystem {
      * @param cond A predicate that determines when a retry should be triggered
      * @return The {@link dev.failsafe.RetryPolicy} instance
      */
+    // NOTE: @Memoized with <T> does not work with bytebuddy
     @Memoized
-    protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+    protected RetryPolicy retryPolicy(Predicate<? extends Throwable> cond) {
         final cfg = AzConfig.getConfig().retryConfig()
         final listener = new EventListener<ExecutionAttemptedEvent>() {
             @Override
             void accept(ExecutionAttemptedEvent event) throws Throwable {
                 log.debug("Azure I/O exception - attempt: ${event.attemptCount}; cause: ${event.lastFailure?.message}")
             }
         }
-        return RetryPolicy.<T>builder()
+        return RetryPolicy.builder()
                 .handleIf(cond)
                 .withBackoff(cfg.delay.toMillis(), cfg.maxDelay.toMillis(), ChronoUnit.MILLIS)
                 .withMaxAttempts(cfg.maxAttempts)