bump dependencies

build.gradle

@@ -8,7 +8,7 @@ buildscript {  // for "com.github.ben-manes.versions" plugin
         }
     }
     dependencies {
-        classpath "com.github.ben-manes:gradle-versions-plugin:0.50.0"
+        classpath "com.github.ben-manes:gradle-versions-plugin:0.51.0"
     }
 }
 
@@ -164,7 +164,7 @@ tasks.named("dependencyUpdates").configure {
 
 dependencies {
 
-    implementation 'org.apache.groovy:groovy:4.0.17' // 4.0.5-9,13 are buggy - probems with Ligands.groovy @CompileStatic
+    implementation 'org.apache.groovy:groovy:4.0.18' 
 
     implementation 'org.codehaus.gpars:gpars:1.2.1'
     implementation 'org.apache.commons:commons-lang3:3.14.0'
@@ -174,7 +174,7 @@ dependencies {
     implementation 'com.google.code.gson:gson:2.10.1'
     implementation 'com.univocity:univocity-parsers:2.9.1' // csv parser
     implementation 'org.apache.commons:commons-csv:1.10.0'
-    implementation 'org.zeroturnaround:zt-zip:1.16'
+    implementation 'org.zeroturnaround:zt-zip:1.17'
     implementation 'org.apache.commons:commons-compress:1.25.0'
     implementation 'org.tukaani:xz:1.9'
     implementation 'com.github.luben:zstd-jni:1.5.5-11'
@@ -196,6 +196,6 @@ dependencies {
 
     implementation fileTree(dir: 'lib', include: '*.jar')
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-engine:5.10.1'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.10.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter-engine:5.10.2'
+    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.10.2'
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -145,15 +145,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -202,11 +202,11 @@ 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
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+# 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" \