Replace Deprecated classes like Stack/Stream

- remove TransientParam class, replace with just @transient
- replace deprecated Stream with LazyList
- rename iterator to eventIterator since Iterator trait now defines iterator field
- .toIterator -> .iterator
- update collection converters for 2.13, add compat class to enable for 2.12
- remove additional implicitCoversions/reflectiveCalls imports since it causes an unused import error in 2.13
- replace mutable.ArrayStack/Stack with custom Stack class that is backed by ListBuffer
- replace deprecated Proxy class with overrides to toString, hashCode and equals
- non-explicit implicit return types are deprecated in 2.13
- parseString is required for 2.13 extenders of Numeric, set to None
- add comments about code not covered by tests

DAFFODIL-2152

Author: olabusayoT

daffodil-cli/bin.NOTICE

@@ -167,3 +167,19 @@ The following NOTICE information applies to binary components distributed with t
   Portions of this code are derived from classes placed in the
   public domain by Arbortext on 10 Apr 2000. See:
   http://www.arbortext.com/customer_support/updates_and_technical_notes/catalogs/docs/README.htm
+
+- org.scala-lang.scala-collection-compat_2.13-<VERSION>.jar
+  scala-collection-compat
+  Copyright (c) 2002-2025 EPFL
+  Copyright (c) 2011-2025 Lightbend, Inc. dba Akka
+
+  Scala includes software developed at
+  LAMP/EPFL (https://lamp.epfl.ch/) and
+  Akka (https://akka.io/).
+
+  Licensed under the Apache License, Version 2.0 (the "License").
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.

daffodil-cli/src/main/scala/org/apache/daffodil/cli/debugger/CLIDebuggerRunner.scala

@@ -20,8 +20,8 @@ package org.apache.daffodil.cli.debugger
 import java.io.File
 import java.io.InputStream
 import java.io.PrintStream
-import scala.collection.JavaConverters._
 import scala.io.Source
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.runtime1.debugger._
 

daffodil-cli/src/test/scala/org/apache/daffodil/cli/cliTest/Util.scala

@@ -31,8 +31,8 @@ import java.nio.file.Path
 import java.nio.file.Paths
 import java.security.MessageDigest
 import java.util.concurrent.TimeUnit
-import scala.collection.JavaConverters._
 import scala.collection.mutable
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.cli.Main
 import org.apache.daffodil.cli.Main.ExitCode

daffodil-codegen-c/src/main/scala/org/apache/daffodil/codegen/c/DaffodilCCodeGenerator.scala

@@ -21,7 +21,7 @@ import java.io.File
 import java.net.JarURLConnection
 import java.nio.file.Files
 import java.nio.file.Paths
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 import scala.util.Properties.isWin
 
 import org.apache.daffodil.codegen.c.generators.AlignmentFillCodeGenerator

daffodil-codegen-c/src/main/scala/org/apache/daffodil/codegen/c/generators/CodeGeneratorState.scala

@@ -21,7 +21,7 @@ import java.io.ByteArrayInputStream
 import java.io.ByteArrayOutputStream
 import java.io.InputStreamReader
 import java.nio.charset.StandardCharsets
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.core.util.TestUtils
 import org.apache.daffodil.lib.util._

daffodil-core/src/test/scala/org/apache/daffodil/core/layers/TestLayers.scala

@@ -22,10 +22,10 @@ import java.io.ByteArrayInputStream
 import java.io.ByteArrayOutputStream
 import java.nio.charset.StandardCharsets
 import java.util.Scanner
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.lib.exceptions.Assert
 
-import collection.JavaConverters._
 import org.apache.commons.io.IOUtils
 import org.junit.Assert._
 import org.junit.Test

daffodil-io/src/test/scala/org/apache/daffodil/layers/TestJavaIOStreams.scala

@@ -21,7 +21,7 @@ import java.io.File
 import java.net.URI
 import java.nio.channels.ReadableByteChannel
 import java.nio.channels.WritableByteChannel
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.core.compiler.{ Compiler => SCompiler }
 import org.apache.daffodil.core.compiler.{ InvalidParserException => SInvalidParserException }

daffodil-japi/src/main/scala/org/apache/daffodil/japi/Daffodil.scala

@@ -39,7 +39,7 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
-import scala.collection.JavaConverters;
+import scala.jdk.javaapi.CollectionConverters;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
@@ -1357,7 +1357,7 @@ public void testJavaAPIBlob1() throws IOException, ClassNotFoundException, Inval
             output.setBlobAttributes(blobDir, "pre-", ".suf");
 
             ParseResult res = dp.parse(input, output);
-            List<Path> blobPaths = JavaConverters.seqAsJavaList(output.getBlobPaths());
+            List<Path> blobPaths = CollectionConverters.asJava(output.getBlobPaths());
 
             try {
                 assertFalse(res.isError());

daffodil-japi/src/test/java/org/apache/daffodil/example/TestJavaAPI.java

@@ -20,7 +20,6 @@ package org.apache.daffodil.lib
 import java.io.{ BufferedInputStream, ByteArrayInputStream }
 import scala.language.implicitConversions
 import scala.language.reflectiveCalls
-import scala.language.{ implicitConversions, reflectiveCalls } // silences scala 2.10 warnings
 
 import org.apache.daffodil.lib.exceptions.Assert
 import org.apache.daffodil.lib.xml.NS

daffodil-lib/src/main/scala/org/apache/daffodil/lib/Implicits.scala

@@ -69,7 +69,7 @@ object ValidationResult {
   val empty: ValidationResult = ValidationResult(Seq.empty, Seq.empty)
 
   def apply(w: Seq[ValidationWarning], e: Seq[ValidationFailure]): ValidationResult = {
-    import scala.collection.JavaConverters.asJavaCollectionConverter
+    import scala.jdk.CollectionConverters._
     new ValidationResult {
       val warnings: java.util.Collection[ValidationWarning] = w.asJavaCollection
       val errors: java.util.Collection[ValidationFailure] = e.asJavaCollection

daffodil-lib/src/main/scala/org/apache/daffodil/lib/api/Validator.scala

@@ -19,6 +19,7 @@ package org.apache.daffodil.lib.util
 
 import java.util.concurrent.ArrayBlockingQueue
 import java.util.concurrent.Executors
+import scala.collection.compat.immutable.LazyList
 import scala.concurrent.ExecutionContext
 import scala.concurrent.Future
 import scala.util.Failure
@@ -212,13 +213,14 @@ final class InvertControl[S](body: => Unit) extends MainCoroutine[Try[S]] with I
 
   private val dummy: Try[S] = Success(null.asInstanceOf[S])
 
-  private def gen: Stream[S] = {
+  private def gen: LazyList[S] = {
     val x = resume(
       producer,
       dummy
     ) // producer isn't sent anything. It's just resumed to get another value.
     x match {
-      case EndOfData => Stream.Empty
+      // TODO: no test coverage
+      case EndOfData => LazyList.empty
       case Success(v) => v #:: gen
       case Failure(e) => {
         failed = true
@@ -227,14 +229,16 @@ final class InvertControl[S](body: => Unit) extends MainCoroutine[Try[S]] with I
     }
   }
 
-  private lazy val iterator = gen.toIterator
+  private lazy val eventIterator = gen.iterator
 
   override def hasNext: Boolean = {
-    !failed && iterator.hasNext
+    // TODO: no test coverage
+    !failed && eventIterator.hasNext
   }
   override def next(): S = {
     if (failed) throw new IllegalStateException()
-    else iterator.next()
+    // TODO: no test coverage
+    else eventIterator.next()
   }
 
 }

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/Coroutines.scala

@@ -553,7 +553,7 @@ object DecimalUtils {
         }
 
         val allDigits = opl match {
-          case OverpunchLocation.Start => digit + num.substring(1)
+          case OverpunchLocation.Start => digit.toString + num.substring(1)
           case OverpunchLocation.End => num.substring(0, opindex) + digit
           case _ => Assert.impossible()
         }
@@ -603,7 +603,7 @@ object DecimalUtils {
         }
 
         val convertedNum = opl match {
-          case OverpunchLocation.Start => digit + inStr.substring(1)
+          case OverpunchLocation.Start => digit +: inStr.substring(1)
           case OverpunchLocation.End => inStr.substring(0, opindex) + digit
           case _ => Assert.impossible()
         }

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/DecimalUtils.scala

@@ -32,8 +32,8 @@ import java.nio.charset.StandardCharsets
 import java.nio.charset.{ Charset => JavaCharset }
 import java.nio.file.Files
 import java.nio.file.Paths
-import scala.collection.JavaConverters._
 import scala.io.Source
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.lib.equality._
 import org.apache.daffodil.lib.exceptions.Assert
@@ -272,8 +272,9 @@ object Misc {
     }
   }
 
-  def initialUpperCase(s: String): String = s.head.toUpper + s.substring(1)
-  def initialLowerCase(s: String): String = s.head.toLower + s.substring(1)
+  // TODO: no test coverage
+  def initialUpperCase(s: String): String = s.head.toUpper +: s.substring(1)
+  def initialLowerCase(s: String): String = s.head.toLower +: s.substring(1)
 
   /**
    * Convert FooBar to fooBar, but leave FOOBAR as FOOBAR.
@@ -284,7 +285,7 @@ object Misc {
     // At this point we know the first letter is uppercase
     //
     if (isAllUpper(s, 1)) s
-    else s(0).toLower + s.substring(1)
+    else s(0).toLower +: s.substring(1)
   }
 
   def isAllUpper(s: String, start: Int): Boolean = {

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/Misc.scala

@@ -17,8 +17,8 @@
 
 package org.apache.daffodil.lib.util
 
-import scala.collection.JavaConverters._
 import scala.collection.mutable
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.lib.exceptions.Assert
 

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/NonAllocatingMap.scala

@@ -18,11 +18,10 @@
 package org.apache.daffodil.lib.util
 
 import java.util.regex.Matcher
-import scala.collection.mutable
 
 sealed abstract class LocalStackBase[T](constructorFunc: => T, optionalResetFunc: (T => Unit)) {
 
-  protected def stack: mutable.ArrayStack[T]
+  protected def stack: Stack[T]
 
   /**
    * This must be inlined to achieve what we're trying to achieve with OnStack/LocalStack.
@@ -61,9 +60,9 @@ class OnStack[T](constructorFunc: => T, optionalResetFunc: (T => Unit))
    */
   def this(constructorFunc: => T) = this(constructorFunc, x => {})
 
-  private val tl = new ThreadLocal[mutable.ArrayStack[T]] {
-    protected final override def initialValue(): mutable.ArrayStack[T] = {
-      val stack = new mutable.ArrayStack[T]
+  private val tl = new ThreadLocal[Stack[T]] {
+    protected final override def initialValue(): Stack[T] = {
+      val stack = new Stack[T]
       stack
     }
   }
@@ -94,7 +93,7 @@ class LocalStack[T](constructorFunc: => T, optionalResetFunc: (T => Unit))
    */
   def this(constructorFunc: => T) = this(constructorFunc, x => {})
 
-  final protected val stack = new mutable.ArrayStack[T]
+  final protected val stack = new Stack[T]
 
 }
 

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/OnStack.scala

@@ -17,8 +17,8 @@
 
 package org.apache.daffodil.lib.util
 
-import scala.collection.JavaConverters._
 import scala.collection.mutable.HashMap
+import scala.jdk.CollectionConverters._
 
 import org.apache.daffodil.lib.exceptions.Assert
 

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/Serialize.scala

@@ -17,11 +17,42 @@
 
 package org.apache.daffodil.lib.util
 
-import scala.annotation.meta._
-
-// The @transient annotation on a constructor parameter doesn't work properly
-// in scala >= 2.11, this is because it does not include the @param annotation.
-// This custom annotation extends transient, but adds the @param annotation so
-// construcutor parameters are properly made transient
-@param
-class TransientParam extends scala.transient
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Compatibility class for 2.12 and 2.13 since ArrayStack and Stack
+ * have been deprecated in 2.13. This allows us to maintain the same
+ * functionality as stack while using ListBuffer instead
+ */
+class Stack[T] {
+  def apply(index: Int): T = {
+    _stackLike(index)
+  }
+
+  private val _stackLike: ListBuffer[T] = new ListBuffer[T]
+
+  def pop(): T = {
+    _stackLike.remove(_stackLike.length - 1)
+  }
+
+  def push(item: T): Unit = {
+    _stackLike += item
+  }
+
+  def isEmpty: Boolean = {
+    _stackLike.isEmpty
+  }
+
+  def clear(): Unit = {
+    // TODO: not covered by tests
+    _stackLike.clear()
+  }
+
+  def top(): T = {
+    _stackLike.last
+  }
+
+  def nonEmpty: Boolean = {
+    _stackLike.nonEmpty
+  }
+}

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/ScalaAnnotations.scala daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/Stack.scala

@@ -17,7 +17,7 @@
 
 package org.apache.daffodil.lib.util
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 object Timer {
 
@@ -185,8 +185,10 @@ object TimeTracker {
    * necessary since we often want to track the time each parser takes to
    * complete, but our parsers are nested making that difficult with standard
    * profilers. This makes that much easier.
+   *
+   * TODO: not covered by tests
    */
-  val childrenTimeStack = scala.collection.mutable.Stack[Long]()
+  val childrenTimeStack = new org.apache.daffodil.lib.util.Stack[Long]()
 
   /**
    * Used to measure a section of code that might get called multiple times.

daffodil-lib/src/main/scala/org/apache/daffodil/lib/util/Timer.scala

@@ -20,7 +20,7 @@ package org.apache.daffodil.lib.validation
 import java.net.URI
 import javax.xml.XMLConstants
 import javax.xml.transform.stream.StreamSource
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 import scala.xml.SAXException
 
 import org.apache.daffodil.lib.api.ValidationException

daffodil-lib/src/main/scala/org/apache/daffodil/lib/validation/XercesValidator.scala

@@ -35,7 +35,7 @@ import javax.xml.transform.sax.SAXSource
 import javax.xml.transform.stream.StreamSource
 import javax.xml.validation.Schema
 import javax.xml.validation.SchemaFactory
-import scala.collection.JavaConverters.asScalaBufferConverter
+import scala.jdk.CollectionConverters._
 import scala.xml.SAXParseException
 import scala.xml.SAXParser
 import scala.xml.parsing.NoBindingFactoryAdapter

daffodil-lib/src/main/scala/org/apache/daffodil/lib/xml/DaffodilXMLLoader.scala

@@ -282,7 +282,7 @@ object XMLUtils {
     }
     // we fell out of the loop. So
     processText() // in case there is text left pending when we hit the end
-    ab.result()
+    ab.result().toSeq
   }
 
   val XSD_NAMESPACE = NS(