[compiler] get rid of BoxedArrayBuilder (#15131)

## Change Description

This PR makes a start at replacing Hail's old custom collection classes
with Scala 2.13 style collections. Here, I just replace all uses of
`BoxedArrayBuilder` with alternatives using the standard library. For
most cases, I either replace it with an `ArrayBuffer` if access to the
contents is needed during construction, and an `ArraySeq.newBuilder`
otherwise.

## Security Assessment

- This change cannot impact the Hail Batch instance as deployed by Broad
Institute in GCP

Author: patrick-schultz

hail/build.mill

@@ -159,6 +159,9 @@ trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { o
     if (scalaVersion().startsWith("2.13")) {
       finalOptions ++
       Seq(
+       // collection types
+        // value ArrayStack in package mutable is deprecated (since 2.13.0): Use Stack instead of ArrayStack; it now uses an array-based implementation
+        "-Wconf:cat=deprecation&msg=value ArrayStack in package mutable is deprecated:s",
       // generic to immutable default
       // collection methods
         // method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated (since 2.13.0): implicit conversions from Array to immutable.IndexedSeq are implemented by copying; use `toIndexedSeq` explicitly if you want to copy, or use the more efficient non-copying ArraySeq.unsafeWrapArray
@@ -328,6 +331,7 @@ trait RootHailModule extends CrossScalaModule with HailModule { outer =>
     Rule.Relocate("org.elasticsearch.**", "is.hail.relocated.@0"),
     Rule.Relocate("org.json4s.**", "is.hail.relocated.@0"),
     Rule.Relocate("org.objectweb.**", "is.hail.relocated.@0"),
+    Rule.Relocate("scala.collection.compat.**", "is.hail.relocated.@0"),
   )
 
   override def scalacPluginMvnDeps: T[Seq[Dep]] = Seq(

hail/hail/src-2.12/is/hail/utils/compat/immutable/ArraySeq.scala

@@ -1,5 +1,6 @@
 package is.hail.utils.compat.immutable
 
+import scala.collection.compat.IterableOnce
 import scala.collection.generic.CanBuildFrom
 import scala.collection.mutable
 import scala.reflect.ClassTag
@@ -13,9 +14,12 @@ object ArraySeq {
   def newBuilder[T: ClassTag]: mutable.Builder[T, ArraySeq[T]] =
     Array.newBuilder[T].mapResult(unsafeWrapArray)
 
-  def apply[T: ClassTag](elems: T*): ArraySeq[T] = elems match {
+  def apply[T: ClassTag](elems: T*): ArraySeq[T] = from(elems)
+
+  def from[T: ClassTag](it: IterableOnce[T]): ArraySeq[T] = it match {
     case a: mutable.WrappedArray[T] => unsafeWrapArray(a.array)
-    case _ => unsafeWrapArray(elems.toArray)
+    case a: ArraySeq[T] => a
+    case _ => unsafeWrapArray(it.toArray)
   }
 
   def unapplySeq[T](seq: ArraySeq[T]): Some[ArraySeq[T]] = Some(seq)
@@ -24,4 +28,10 @@ object ArraySeq {
 
   implicit def canBuildFrom[T: ClassTag]: CanBuildFrom[ArraySeq[_], T, ArraySeq[T]] =
     A.canBuildFrom
+
+  def fill[T: ClassTag](n: Int)(elem: => T): ArraySeq[T] =
+    unsafeWrapArray(Array.fill(n)(elem))
+
+  def tabulate[T: ClassTag](n: Int)(f: Int => T): ArraySeq[T] =
+    unsafeWrapArray(Array.tabulate(n)(f))
 }

hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala

@@ -1,8 +1,6 @@
 package is.hail.utils.compat.mutable
 
-import scala.collection.generic
-
-trait Growable[-A] extends generic.Growable[A] {
+trait GrowableCompat[-A] extends Growable[A] {
   override def +=(elem: A): this.type = addOne(elem)
   protected def addOne(elem: A): this.type
   def knownSize: Int = -1

hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala

@@ -1,8 +1,6 @@
 package is.hail.utils.compat.mutable
 
-import scala.collection.generic
-
-trait Shrinkable[-A] extends generic.Shrinkable[A] {
+trait ShrinkableCompat[-A] extends Shrinkable[A] {
   override def -=(elem: A): this.type = subtractOne(elem)
   protected def subtractOne(elem: A): this.type
 }

hail/hail/src-2.12/is/hail/utils/compat/mutable/package.scala

@@ -0,0 +1,6 @@
+package is.hail.utils.compat
+
+package object mutable {
+  type Growable[-A] = scala.collection.generic.Growable[A]
+  type Shrinkable[-A] = scala.collection.generic.Shrinkable[A]
+}

hail/hail/src-2.12/is/hail/utils/compat/package.scala

@@ -3,9 +3,25 @@ package is.hail.utils
 import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat.Factory
+import scala.collection.mutable.WrappedArray
 import scala.reflect.ClassTag
 
+package compat {
+  class ArrayOps[A: ClassTag](val a: WrappedArray[A]) {
+    def sortInPlace[B >: A]()(implicit ct: ClassTag[B], ord: Ordering[B])
+      : WrappedArray[A] = {
+      scala.util.Sorting.stableSort(a.array.asInstanceOf[Array[B]])
+      a
+    }
+
+    def sortInPlaceBy[B](f: A => B)(implicit ord: Ordering[B]): WrappedArray[A] =
+      sortInPlace()(implicitly, ord = ord on f)
+  }
+}
+
 package object compat {
   implicit def arraySeqbf[A: ClassTag](ob: ArraySeq.type): Factory[A, ArraySeq[A]] =
     ob.canBuildFrom[A]
+
+  implicit def toArrayOps[A: ClassTag](a: Array[A]): ArrayOps[A] = new ArrayOps(a)
 }

hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala

@@ -2,5 +2,7 @@ package is.hail.utils.compat
 
 package object mutable {
   type Growable[-A] = scala.collection.mutable.Growable[A]
+  type GrowableCompat[-A] = Growable[A]
   type Shrinkable[-A] = scala.collection.mutable.Shrinkable[A]
+  type ShrinkableCompat[-A] = Shrinkable[A]
 }

hail/hail/src/is/hail/annotations/OrderedRVIterator.scala

@@ -12,11 +12,11 @@ object OrderedRVIterator {
   def multiZipJoin(
     sm: HailStateManager,
     its: IndexedSeq[OrderedRVIterator],
-  ): Iterator[BoxedArrayBuilder[(RegionValue, Int)]] = {
-    require(its.length > 0)
+  ): Iterator[collection.IndexedSeq[(RegionValue, Int)]] = {
+    require(its.nonEmpty)
     val first = its(0)
     val flipbooks = its.map(_.iterator.toFlipbookIterator)
-    FlipbookIterator.multiZipJoin(
+    FlipbookIterator.multiZipJoin[RegionValue](
       flipbooks.toArray,
       first.t.joinComp(sm, first.t).compare,
     )

hail/hail/src/is/hail/annotations/RegionPool.scala

@@ -3,6 +3,8 @@ package is.hail.annotations
 import is.hail.expr.ir.LongArrayBuilder
 import is.hail.utils._
 
+import scala.collection.mutable
+
 object RegionPool {
 
   def apply(strictMemoryCheck: Boolean = false): RegionPool = {
@@ -28,8 +30,8 @@ final class RegionPool private (strictMemoryCheck: Boolean, threadName: String,
   protected[annotations] val freeBlocks: Array[LongArrayBuilder] =
     Array.fill[LongArrayBuilder](4)(new LongArrayBuilder(8))
 
-  protected[annotations] val regions = new BoxedArrayBuilder[RegionMemory]()
-  private[this] val freeRegions = new BoxedArrayBuilder[RegionMemory]()
+  protected[annotations] val regions = mutable.ArrayBuffer.empty[RegionMemory]
+  private[this] val freeRegions = mutable.ArrayStack.empty[RegionMemory]
   private[this] val blocks: Array[Long] = Array(0L, 0L, 0L, 0L)
   private[this] var totalAllocatedBytes: Long = 0L
   private[this] var allocationEchoThreshold: Long = 256 * 1024
@@ -103,7 +105,7 @@ final class RegionPool private (strictMemoryCheck: Boolean, threadName: String,
     chunkCache.freeChunkToCache(chunkPointer)
 
   protected[annotations] def getMemory(size: Int): RegionMemory = {
-    if (freeRegions.size > 0) {
+    if (freeRegions.nonEmpty) {
       val rm = freeRegions.pop()
       rm.initialize(size)
       rm

hail/hail/src/is/hail/annotations/WritableRegionValue.scala

@@ -3,7 +3,7 @@ package is.hail.annotations
 import is.hail.backend.HailStateManager
 import is.hail.rvd.RVDContext
 import is.hail.types.physical.{PStruct, PType}
-import is.hail.utils.compat.mutable.Growable
+import is.hail.utils.compat.mutable.GrowableCompat
 
 import scala.collection.mutable.{ArrayBuffer, PriorityQueue}
 
@@ -129,7 +129,7 @@ class RegionValuePriorityQueue(
 }
 
 class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
-    extends Iterable[RegionValue] with Growable[RegionValue] {
+    extends Iterable[RegionValue] with GrowableCompat[RegionValue] {
 
   val value = RegionValue(region, 0)