Updating to java 21

* replacing use of deprecated function
* making some methods final and Suppressing some 'this-escape' warnings
* update github actions to use java 21

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java: [ 17 ]
+        java: [ 21 ]
         experimental: [false]
       fail-fast: false
     continue-on-error: ${{ matrix.experimental }}

build.gradle

@@ -11,8 +11,9 @@ wrapper {
 }
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_17
-    targetCompatibility = JavaVersion.VERSION_17
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
 }
 
 group = 'org.broadinstitute'

src/main/java/org/broadinstitute/barclay/argparser/ArgumentDefinition.java

@@ -53,7 +53,7 @@ public ArgumentDefinition(final Object containingObject, final Field underlyingF
      * Get the underlying {@code Field} for this argument
      * @return the {@code Field} for this argument
      */
-    public Field getUnderlyingField() { return underlyingField; }
+    public final Field getUnderlyingField() { return underlyingField; }
 
     /**
      * Get the parent {@code Object} containing the {@code Field} for this argument.
@@ -77,7 +77,7 @@ public ArgumentDefinition(final Object containingObject, final Field underlyingF
      * Get the {@code Object} representing the current value of the field for this object.
      * @return A boxed value even if the underlying field is a primitive. will not be null.
      */
-    public Object getArgumentValue() {
+    public final Object getArgumentValue() {
         try {
             return getUnderlyingField().get(getContainingObject());
         } catch (final IllegalAccessException e) {
@@ -158,7 +158,7 @@ public List<String> getOriginalCommandLineValues() {
      * constructors can be found.
      * @return {@code Class<?>} for this field
      */
-    protected Class<?> getClassForUnderlyingField() {
+    protected final Class<?> getClassForUnderlyingField() {
         final Field field = getUnderlyingField();
         if (isCollectionField(field)) {
             final ParameterizedType clazz = (ParameterizedType) (field.getGenericType());

src/main/java/org/broadinstitute/barclay/argparser/ClassFinder.java

@@ -10,6 +10,7 @@
 import java.net.URLClassLoader;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Paths;
 import java.util.Enumeration;
 import java.util.LinkedHashSet;
 import java.util.Set;
@@ -44,7 +45,7 @@ public ClassFinder(final File jarFile) throws IOException {
         // but the jarPath is remembered so that the iteration over the classpath skips anything other than
         // the jarPath.
         jarPath = jarFile.getCanonicalPath();
-        final URL[] urls = {new URL("file", "", jarPath)};
+        final URL[] urls = {Paths.get(jarPath).toUri().toURL()};
         loader = new URLClassLoader(urls, Thread.currentThread().getContextClassLoader());
     }
 

src/main/java/org/broadinstitute/barclay/argparser/NamedArgumentDefinition.java

@@ -42,6 +42,7 @@ public class NamedArgumentDefinition extends ArgumentDefinition {
      *                                      {@code CommandLinePluginDescriptor} itself are not contained in a plugin,
      *                                      and will not have a {@code descriptorForControllingPlugin}. can be null.
      */
+    @SuppressWarnings("this-escape")
     public NamedArgumentDefinition(
             final Argument argumentAnnotation,
             final Object containingObject,

src/main/java/org/broadinstitute/barclay/argparser/PositionalArgumentDefinition.java

@@ -22,6 +22,7 @@ public class PositionalArgumentDefinition extends ArgumentDefinition {
      * @param containingObject the parent {@code Object} containing this argument. cannot be null.
      * @param argField the {@code Field} for this argument. cannot be null.
      */
+    @SuppressWarnings("this-escape")
     public PositionalArgumentDefinition(
             final PositionalArguments positionalArgumentsAnnotation,
             final Object containingObject,

src/main/java/org/broadinstitute/barclay/help/DocWorkUnit.java

@@ -48,6 +48,7 @@ public class DocWorkUnit implements Comparable<DocWorkUnit> {
      * @param clazz
      * @param documentedFeatureAnnotation
      */
+    @SuppressWarnings("this-escape")
     public DocWorkUnit(
             final DocWorkUnitHandler workUnitHandler,
             final Element docElement,