Update to Gradle 8.4 which officially supports Java 21, using:

$ ./gradlew wrapper --gradle-version=8.4

.github/workflows/gradle.yml

@@ -9,8 +9,10 @@
 # - Java 17 (LTS; officially supported since Gradle 7.3)
 # - Java 18 (deprecated; officially supported since Gradle 7.5)
 # - Java 19 (deprecated; officially supported since Gradle 7.6)
-# - Java 20 (current; will be deprecated in September 2023; officially supported since Gradle 8.1)
-# - Java 21 (LTS; to be released in September 2023; not officially supported by Gradle)
+# - Java 20 (deprecated; officially supported since Gradle 8.1)
+# - Java 21 (current; LTS; officially supported since Gradle 8.4)
+# - Java 22 (to be released in March 2024; not officially supported by Gradle)
+# - Java 23 (to be released in September 2024; not officially supported by Gradle)
 name: CS321 Bioinformatics CI with Gradle
 
 on:
@@ -26,17 +28,17 @@ jobs:
 
     strategy:
       matrix:
-        java: [ '8', '11', '15', '16', '17', '18', '19', '20' ]
+        java: [ '8', '11', '15', '16', '17', '18', '19', '20', '21' ]
     name: Java version ${{ matrix.Java }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.java }}
         # the distribution can be either 'adopt' or 'zulu'
-        distribution: 'adopt'
+        distribution: 'zulu'
     - name: Grant execute permission for gradlew
       run: chmod +x gradlew
 

README.md

@@ -43,9 +43,13 @@ Use the following command to check our installed JDK version:
 $ javac -version
 ```
 
-This project **does not work** with JDK 21.
+This project **does not work** with JDK 22.
 
-It is recommended to use either JDK 8, JDK 11 or JDK 17 or JDK 19 or 20.
+It is recommended to use any of the following versions:
+- JDK 8 (LTS)
+- JDK 11 (LTS)
+- JDK 17 (LTS)
+- JDK 21 (LTS)
 
 :book: See this [wiki page for additional details regarding the supported Java versions and links to download the correct JDK versions](https://github.com/BoiseState/CS321_Bioinformatics/wiki/Install-the-correct-JDK-version).
 

build.gradle

@@ -8,7 +8,9 @@ plugins {
 group 'cs321'
 version '1.0'
 
-sourceCompatibility = 1.8
+java {
+    sourceCompatibility = JavaVersion.VERSION_1_8
+}
 
 repositories {
     mavenCentral()

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -85,9 +85,6 @@ done
 APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
-# 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"'
-
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
 
@@ -144,15 +141,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -197,6 +194,10 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
+
+# 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, and $GRADLE_OPTS can contain fragments of
 #     shell script including quotes and variable substitutions, so put them in