Target Java 17 as minimal Java version (#5045)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Co-authored-by: Ben Sherman <[email protected]>

Author: pditommaso

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 23]
+        java_version: [17, 23]
 
     steps:
       - name: Environment
@@ -133,7 +133,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 23]
+        java_version: [17, 23]
         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',

docs/install.md

@@ -6,12 +6,16 @@
 
 ## Requirements
 
-Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). It requires Bash 3.2 (or later) and [Java 11 (or later, up to 23)](http://www.oracle.com/technetwork/java/javase/downloads/index.html). You can see which version you have using the following command:
+Nextflow can be used on any POSIX-compatible system (Linux, macOS, etc), and on Windows through [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux). It requires Bash 3.2 (or later) and [Java 17 (or later, up to 23)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. You can see which version you have using the following command:
 
 ```bash
 java -version
 ```
 
+:::{versionchanged} 24.11.0-edge
+Support for Java versions prior to 17 was dropped.
+:::
+
 If you don't have a compatible version of Java installed in your computer, it is recommended that you install it through [SDKMAN!](https://sdkman.io/), and that you use the latest LTS version of Temurin. See [this website](https://whichjdk.com/) for more information.
 
 To install Java with SDKMAN:

launch.sh

@@ -66,13 +66,13 @@ fi
 JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
 major=${BASH_REMATCH[1]}
 minor=${BASH_REMATCH[2]}
-version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22|23)"
+version_check="^(17|18|19|20|21|23)"
 if [[ ! $JAVA_VER =~ $version_check ]]; then
-    echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 8 or higher is installed"
+    echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 17 or higher is installed"
     exit 1
 fi
 JVM_ARGS+=" -Dfile.encoding=UTF-8 -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
-[[ $JAVA_VER =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22|23) ]] && JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
+JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
 [[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && [[ "$JAVA_VER" =~ ^(19|20) ]] && JVM_ARGS+=" --enable-preview"
 [[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 

modules/nextflow/build.gradle

@@ -54,10 +54,10 @@ dependencies {
 
     // test configuration
     testFixturesApi ("org.apache.groovy:groovy-test:4.0.23") { 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/RepositoryProvider.groovy

@@ -241,8 +241,15 @@ abstract class RepositoryProvider {
         }
     }
 
-    @Memoized
     protected <T> List<T> invokeAndResponseWithPaging(String request, Closure<T> parse) {
+        // this is needed because apparently bytebuddy used by testing framework is not able
+        // to handle properly this method signature using both generics and `@Memoized` annotation.
+        // therefore the `@Memoized` has been moved to the inner method invocation
+        return invokeAndResponseWithPaging0(request, parse)
+    }
+
+    @Memoized
+    protected List invokeAndResponseWithPaging0(String request, Closure parse) {
         int page = 0
         final result = new ArrayList()
         while( true ) {

nextflow

@@ -313,7 +313,7 @@ if [ ! -x "$JAVA_CMD" ] ; then
             JAVA_CMD="$JAVA_HOME/bin/java"
         fi
     elif [ -x /usr/libexec/java_home ]; then
-        JAVA_CMD="$(/usr/libexec/java_home -v 11+ 2>/dev/null)/bin/java" || JAVA_CMD=java
+        JAVA_CMD="$(/usr/libexec/java_home -v 17+ 2>/dev/null)/bin/java" || JAVA_CMD=java
     else
         JAVA_CMD="$(which java)" || JAVA_CMD=java
     fi
@@ -344,14 +344,8 @@ else
   fi
   major=${BASH_REMATCH[1]}
   minor=${BASH_REMATCH[2]}
-  # legacy version - Java 7/8 only
-  if [ $major -eq 0 ] && [ $minor -lt 26 ]; then
-    version_check="^(1.7|1.8)"
-    version_message="Java 7 or 8"
-  else
-    version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22|23)"
-    version_message="Java 8 or later (up to 22)"
-  fi
+  version_check="^(17|18|19|20|21|22|23)"
+  version_message="Java 17 or later (up to 23)"
   if [[ ! $JAVA_VER =~ $version_check ]]; then
       echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
       if [[ "$NXF_JAVA_HOME" ]]; then
@@ -361,9 +355,6 @@ else
       fi
       exit 1
   fi
-  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21|22|23) ]]; then
-      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 23\n"
-  fi
   mkdir -p "$(dirname "$JAVA_KEY")"
   [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
 fi
@@ -461,33 +452,29 @@ else
     [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
     [[ "$remote_debug" ]] && launcher+=(-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=$NXF_REMOTE_DEBUG_PORT)
 
-    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22|23) ]]; then
-      launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
-      launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
-      if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
-        if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
-        elif [[ ! "$JAVA_VER" =~ ^(21|22|23) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
-        fi
+    launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/jdk.internal.vm=ALL-UNNAMED)
+    launcher+=(--add-opens=java.base/java.util.regex=ALL-UNNAMED)
+    if [[ "$NXF_ENABLE_VIRTUAL_THREADS" == 'true' ]]; then
+      if [[ "$JAVA_VER" =~ ^(19|20) ]]; then launcher+=(--enable-preview)
+      elif [[ ! "$JAVA_VER" =~ ^(21|22|23) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
       fi
-      launcher+=("${cmd_tail[@]}")
-    else
-      launcher+=("${cmd_tail[@]}")
     fi
+    launcher+=("${cmd_tail[@]}")
 
     # create the launch file only when using the legacy launcher (capsule)
     if [[ $NXF_LEGACY_LAUNCHER ]]; then

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

@@ -527,16 +527,23 @@ class AzFileSystem extends FileSystem {
      * @param cond A predicate that determines when a retry should be triggered
      * @return The {@link dev.failsafe.RetryPolicy} instance
      */
-    @Memoized
     protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+        // this is needed because apparently bytebuddy used by testing framework is not able
+        // to handle properly this method signature using both generics and `@Memoized` annotation.
+        // therefore the `@Memoized` has been moved to the inner method invocation
+        return (RetryPolicy<T>) retryPolicy0(cond)
+    }
+
+    @Memoized
+    protected RetryPolicy retryPolicy0(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)