Enable the use of Java 22 (#4970) [ci fast]

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Dr Marco Claudio De La Pierre <[email protected]>

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 17, 21]
+        java_version: [11, 17, 22]
 
     steps:
       - name: Environment

docs/install.md

@@ -6,7 +6,7 @@
 
 ## 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 21)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. 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 11 (or later, up to 22)](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

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-rc-2-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,11 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
+# This is normally unused
+# shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +131,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,18 +198,28 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
         org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
 # Use "xargs" to parse quoted args.
 #
 # With -n1 it outputs one arg per line, with the quotes and backslashes removed.

gradlew.bat

@@ -14,7 +14,7 @@
 @rem limitations under the License.
 @rem
 
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -25,7 +25,8 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,13 +41,13 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
+if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -56,11 +57,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -75,13 +76,15 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal

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)"
+version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22)"
 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"
     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) ]] && 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"
+[[ $JAVA_VER =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22) ]] && 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
 

nextflow

@@ -311,7 +311,7 @@ else
     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)"
+    version_check="^(1.8|9|10|11|12|13|14|15|16|17|18|19|20|21|22)"
     version_message="Java 8 or later (up to 21)"
   fi
   if [[ ! $JAVA_VER =~ $version_check ]]; then
@@ -323,8 +323,8 @@ else
       fi
       exit 1
   fi
-  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21) ]]; then
-      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 21\n"
+  if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18|19|20|21|22) ]]; then
+      echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 22\n"
   fi
   mkdir -p "$(dirname "$JAVA_KEY")"
   [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
@@ -346,7 +346,7 @@ if [[ $cmd == console ]]; then bg=1;
 else JAVA_OPTS+=(-Djava.awt.headless=true)
 fi
 
-[[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
+[[ "$JAVA_VER" =~ ^(21|22) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 [[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
 [[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
 [[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
@@ -417,7 +417,7 @@ else
     [[ "$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 [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21) ]]; then
+    if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18|19|20|21|22) ]]; 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)
@@ -437,7 +437,7 @@ else
       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) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
+        elif [[ ! "$JAVA_VER" =~ ^(21|22) ]]; then die "Virtual threads require Java 19 or later - current version $JAVA_VER"
         fi
       fi
       launcher+=("${cmd_tail[@]}")