hail-is · hail-ci-robot · Nov 13, 2025 · Aug 26, 2025 · Aug 26, 2025 · Sep 25, 2025
diff --git a/hail/build.mill b/hail/build.mill
@@ -147,27 +147,6 @@ trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { o
     if (scalaVersion().startsWith("2.13")) {
       finalOptions ++
       Seq(
-      // collection types
-        // type Traversable in package scala is deprecated (since 2.13.0): Use Iterable instead of Traversable
-        "-Wconf:cat=deprecation&msg=type Traversable in package scala is deprecated:s",
-        // type TraversableOnce in package scala is deprecated (since 2.13.0): Use IterableOnce instead of TraversableOnce
-        "-Wconf:cat=deprecation&msg=type TraversableOnce:s",
-        // type BufferedIterator in package scala is deprecated (since 2.13.0): Use scala.collection.BufferedIterator instead of scala.BufferedIterator
-        "-Wconf:cat=deprecation&msg=type BufferedIterator in package scala is deprecated:s",
-        // class Stream in package immutable is deprecated (since 2.13.0): Use LazyList (which is fully lazy) instead of Stream (which has a lazy tail only)
-        "-Wconf:cat=deprecation&msg=Stream:s",
-        // type Growable in package generic is deprecated (since 2.13.0): Growable was moved from collection.generic to collection.mutable
-        "-Wconf:cat=deprecation&msg=type Growable in package generic is deprecated:s",
-        // type GenTraversableOnce in package collection is deprecated (since 2.13.0): Gen* collection types have been removed
-        "-Wconf:cat=deprecation&msg=type GenTraversableOnce in package collection is deprecated:s",
-        // trait MultiMap in package mutable is deprecated (since 2.13.0): Use a scala.collection.mutable.MultiDict in the scala-collection-contrib module
-        "-Wconf:cat=deprecation&msg=trait MultiMap in package mutable is deprecated:s",
-        // inheritance from class HashMap in package mutable is deprecated (since 2.13.0): HashMap will be made final; use .withDefault for the common use case of computing a default value
-        "-Wconf:cat=deprecation&msg=inheritance from class HashMap in package mutable is deprecated:s",
-        // object JavaConverters in package collection is deprecated (since 2.13.0): Use `scala.jdk.CollectionConverters` instead
-        "-Wconf:cat=deprecation&msg=object JavaConverters in package collection is deprecated:s",
-        // object ImplicitConversions in package convert is deprecated (since 2.13.0): Use `scala.jdk.CollectionConverters` instead
-        "-Wconf:cat=deprecation&msg=object ImplicitConversions in package convert 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
@@ -317,7 +296,6 @@ trait RootHailModule extends CrossScalaModule with HailModule { outer =>
     Rule.Exclude("META-INF/INDEX.LIST"),
     Rule.ExcludePattern("scala/(?!collection/compat).*"),
     Rule.AppendPattern("META-INF/services/.*", "\n"),
-//    Rule.Relocate("scala.collection.compat.**", "is.hail.relocated.@0"),
     Rule.Relocate("breeze.**", "is.hail.relocated.@0"),
     Rule.Relocate("com.google.cloud.**", "is.hail.relocated.@0"),
     Rule.Relocate("com.google.common.**", "is.hail.relocated.@0"),

diff --git a/hail/hail/src-2.12/is/hail/utils/compat/ShrinkableCompat.scala b/hail/hail/src-2.12/is/hail/utils/compat/ShrinkableCompat.scala
diff --git a/...is/hail/utils/compat/GrowableCompat.scala → ...utils/compat/mutable/GrowableCompat.scala b/...is/hail/utils/compat/GrowableCompat.scala → ...utils/compat/mutable/GrowableCompat.scala
@@ -1,8 +1,8 @@
-package is.hail.utils.compat
+package is.hail.utils.compat.mutable
 
-import scala.collection.generic.Growable
+import scala.collection.generic
 
-trait GrowableCompat[-A] extends Growable[A] {
+trait Growable[-A] extends generic.Growable[A] {
   override def +=(elem: A): this.type = addOne(elem)
   protected def addOne(elem: A): this.type
   def knownSize: Int = -1

diff --git a/hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala b/hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala
@@ -0,0 +1,8 @@
+package is.hail.utils.compat.mutable
+
+import scala.collection.generic
+
+trait Shrinkable[-A] extends generic.Shrinkable[A] {
+  override def -=(elem: A): this.type = subtractOne(elem)
+  protected def subtractOne(elem: A): this.type
+}
diff --git a/hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala b/hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala
@@ -2,7 +2,5 @@ package is.hail.utils.compat
 
 package object immutable {
   type ArraySeq[+A] = scala.collection.immutable.ArraySeq[A]
-
-  val ArraySeq: scala.collection.compat.immutable.ArraySeq.type =
-    scala.collection.compat.immutable.ArraySeq
+  val ArraySeq = scala.collection.immutable.ArraySeq
 }
diff --git a/hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala b/hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala
@@ -0,0 +1,6 @@
+package is.hail.utils.compat
+
+package object mutable {
+  type Growable[-A] = scala.collection.mutable.Growable[A]
+  type Shrinkable[-A] = scala.collection.mutable.Shrinkable[A]
+}
diff --git a/hail/hail/src-2.13/is/hail/utils/compat/package.scala b/hail/hail/src-2.13/is/hail/utils/compat/package.scala
diff --git a/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala b/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala
@@ -4,8 +4,8 @@ import is.hail.backend.HailStateManager
 import is.hail.rvd.{RVDContext, RVDType}
 import is.hail.types.physical.PInterval
 import is.hail.utils._
+import is.hail.utils.compat.mutable.Growable
 
-import scala.collection.generic.Growable
 import scala.collection.mutable
 
 object OrderedRVIterator {

diff --git a/hail/hail/src/is/hail/annotations/WritableRegionValue.scala b/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.GrowableCompat
+import is.hail.utils.compat.mutable.Growable
 
 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 GrowableCompat[RegionValue] {
+    extends Iterable[RegionValue] with Growable[RegionValue] {
 
   val value = RegionValue(region, 0)
 

diff --git a/hail/hail/src/is/hail/backend/service/ServiceBackend.scala b/hail/hail/src/is/hail/backend/service/ServiceBackend.scala
@@ -259,7 +259,7 @@ class ServiceBackend(
                   val (failures, successes) =
                     Await.result(
                       Future
-                        .traverse(failedJobs.map(_.take(1)) append succeededJobs) { jobs =>
+                        .traverse(failedJobs.map(_.take(1)) lazyAppendedAll succeededJobs) { jobs =>
                           readPartitionOutputs(jobs.map(_.job_id - startJobId))
                         },
                       Duration.Inf,

diff --git a/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala
@@ -712,11 +712,11 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) {
   private def intervalsFromLiteral(lit: Any, ordering: Ordering[Any], wrapped: Boolean): KeySet =
     (lit: @unchecked) match {
       case x: Map[_, _] => intervalsFromCollection(x.keys, ordering, wrapped)
-      case x: Traversable[_] => intervalsFromCollection(x, ordering, wrapped)
+      case x: Iterable[_] => intervalsFromCollection(x, ordering, wrapped)
     }
 
   private def intervalsFromCollection(
-    lit: Traversable[Any],
+    lit: Iterable[Any],
     ordering: Ordering[Any],
     wrapped: Boolean,
   ): KeySet =
@@ -733,7 +733,7 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) {
             TInt32.ordering(null).toOrdering.asInstanceOf[Ordering[Integer]]
           )
           .flatMap(getIntervalFromContig(_, rg))
-      case x: Traversable[_] => x.asInstanceOf[Traversable[String]].toArray.toFastSeq
+      case x: Iterable[_] => x.asInstanceOf[Iterable[String]].toArray.toFastSeq
           .sortBy(rg.contigsIndex.get(_))(
             TInt32.ordering(null).toOrdering.asInstanceOf[Ordering[Integer]]
           )

diff --git a/hail/hail/src/is/hail/expr/ir/functions/Functions.scala b/hail/hail/src/is/hail/expr/ir/functions/Functions.scala
@@ -42,16 +42,15 @@ object IRFunctionRegistry {
   val irRegistry: mutable.Map[String, mutable.Map[IRFunctionSignature, IRFunctionImplementation]] =
     new mutable.HashMap()
 
-  val jvmRegistry: mutable.MultiMap[String, JVMFunction] =
-    new mutable.HashMap[String, mutable.Set[JVMFunction]] with mutable.MultiMap[String, JVMFunction]
+  val jvmRegistry: mutable.Map[String, mutable.Set[JVMFunction]] = mutable.HashMap.empty
 
   private[this] def requireJavaIdentifier(name: String): Unit =
     if (!isJavaIdentifier(name))
       throw new IllegalArgumentException(s"Illegal function name, not Java identifier: $name")
 
   def addJVMFunction(f: JVMFunction): Unit = {
     requireJavaIdentifier(f.name)
-    jvmRegistry.addBinding(f.name, f)
+    jvmRegistry.getOrElseUpdate(f.name, mutable.Set.empty) += f
   }
 
   def addIR(

diff --git a/hail/hail/src/is/hail/expr/ir/package.scala b/hail/hail/src/is/hail/expr/ir/package.scala
@@ -11,6 +11,8 @@ import is.hail.types.virtual._
 import is.hail.types.virtual.TIterable.elementType
 import is.hail.utils._
 
+import scala.collection.BufferedIterator
+
 import java.util.UUID
 
 package object ir {

diff --git a/hail/hail/src/is/hail/io/ElasticsearchConnector.scala b/hail/hail/src/is/hail/io/ElasticsearchConnector.scala
@@ -1,7 +1,7 @@
 package is.hail.io
 
-import scala.collection.JavaConverters._
 import scala.collection.Map
+import scala.jdk.CollectionConverters._
 
 import org.apache.spark
 import org.elasticsearch.spark.sql._

diff --git a/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala b/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala
@@ -14,7 +14,7 @@ import is.hail.types.virtual._
 import is.hail.utils.compat._
 import is.hail.utils.compat.immutable.ArraySeq
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 import java.io.InputStream
 

diff --git a/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala b/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala
@@ -14,9 +14,9 @@ import is.hail.shadedazure.com.azure.storage.blob.models.{
 import is.hail.shadedazure.com.azure.storage.blob.specialized.BlockBlobClient
 import is.hail.utils.FastSeq
 
-import scala.collection.JavaConverters._
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer
+import scala.jdk.CollectionConverters._
 
 import java.io.{ByteArrayOutputStream, FileNotFoundException, OutputStream}
 import java.nio.file.{Path, Paths}

diff --git a/hail/hail/src/is/hail/io/fs/FS.scala b/hail/hail/src/is/hail/io/fs/FS.scala
@@ -630,8 +630,7 @@ trait FS extends Serializable with Logging {
     }
   }
 
-  def writeTable(filename: String, lines: Traversable[String], header: Option[String] = None)
-    : Unit = {
+  def writeTable(filename: String, lines: Iterable[String], header: Option[String] = None): Unit = {
     using(new OutputStreamWriter(create(filename))) { fw =>
       header.foreach { h =>
         fw.write(h)

diff --git a/hail/hail/src/is/hail/io/reference/LiftOver.scala b/hail/hail/src/is/hail/io/reference/LiftOver.scala
@@ -5,7 +5,7 @@ import is.hail.io.reference.LiftOver.MinMatchDefault
 import is.hail.utils.{fatal, using, Interval}
 import is.hail.variant.{Locus, ReferenceGenome}
 
-import scala.collection.convert.ImplicitConversions.{`collection AsScalaIterable`, `map AsScala`}
+import scala.jdk.CollectionConverters._
 
 object LiftOver {
   def apply(fs: FS, chainFile: String): LiftOver = {
@@ -65,9 +65,9 @@ class LiftOver private (chainFile: String) extends Serializable {
   }
 
   def checkChainFile(srcRG: ReferenceGenome, destRG: ReferenceGenome): Unit =
-    asJava.getContigMap.foreach { case (srcContig, destContigs) =>
+    asJava.getContigMap.asScala.foreach { case (srcContig, destContigs) =>
       srcRG.checkContig(srcContig)
-      destContigs.foreach(destRG.checkContig)
+      destContigs.asScala.foreach(destRG.checkContig)
     }
 
   def restore(fs: FS): Unit = {

diff --git a/hail/hail/src/is/hail/io/vcf/LoadVCF.scala b/hail/hail/src/is/hail/io/vcf/LoadVCF.scala
@@ -27,8 +27,9 @@ import is.hail.variant._
 
 import scala.annotation.meta.param
 import scala.annotation.switch
-import scala.collection.JavaConverters._
+import scala.collection.BufferedIterator
 import scala.collection.compat._
+import scala.jdk.CollectionConverters._
 
 import htsjdk.variant.vcf._
 import org.apache.spark.{Partition, TaskContext}

diff --git a/hail/hail/src/is/hail/methods/Nirvana.scala b/hail/hail/src/is/hail/methods/Nirvana.scala
@@ -12,8 +12,8 @@ import is.hail.types.virtual._
 import is.hail.utils._
 import is.hail.variant.{Locus, RegionValueVariant}
 
-import scala.collection.JavaConverters._
 import scala.collection.mutable
+import scala.jdk.CollectionConverters._
 
 import java.io.{FileInputStream, IOException}
 import java.util.Properties

diff --git a/hail/hail/src/is/hail/methods/VEP.scala b/hail/hail/src/is/hail/methods/VEP.scala
@@ -14,8 +14,8 @@ import is.hail.types.virtual._
 import is.hail.utils._
 import is.hail.variant.{Locus, RegionValueVariant, VariantMethods}
 
-import scala.collection.JavaConverters._
 import scala.collection.mutable
+import scala.jdk.CollectionConverters._
 
 import com.fasterxml.jackson.core.JsonParseException
 import org.apache.spark.sql.Row

diff --git a/hail/hail/src/is/hail/rvd/KeyedRVD.scala b/hail/hail/src/is/hail/rvd/KeyedRVD.scala
@@ -6,8 +6,7 @@ import is.hail.sparkextras._
 import is.hail.types.physical.PStruct
 import is.hail.types.virtual.TInterval
 import is.hail.utils._
-
-import scala.collection.generic.Growable
+import is.hail.utils.compat.mutable.Growable
 
 class KeyedRVD(val rvd: RVD, val key: Int) {
   require(key <= rvd.typ.key.length && key >= 0)

diff --git a/hail/hail/src/is/hail/services/BatchClient.scala b/hail/hail/src/is/hail/services/BatchClient.scala
@@ -10,7 +10,7 @@ import is.hail.services.oauth2.CloudCredentials
 import is.hail.services.requests.Requester
 import is.hail.utils._
 
-import scala.collection.immutable.Stream.cons
+import scala.collection.compat.immutable.LazyList
 import scala.util.Random
 
 import java.net.{URL, URLEncoder}
@@ -252,9 +252,9 @@ case class BatchClient private (req: Requester) extends Logging with AutoCloseab
       JobStateDeserializer +
       JobListEntryDeserializer
 
-  private[this] def paginated[S, A](s0: S)(f: S => (A, S)): Stream[A] = {
+  private[this] def paginated[S, A](s0: S)(f: S => (A, S)): LazyList[A] = {
     val (a, s1) = f(s0)
-    cons(a, paginated(s1)(f))
+    LazyList.cons(a, paginated(s1)(f))
   }
 
   def newBatch(createRequest: BatchRequest): Int = {
@@ -287,7 +287,7 @@ case class BatchClient private (req: Requester) extends Logging with AutoCloseab
       .extract[JobGroupResponse]
 
   def getJobGroupJobs(batchId: Int, jobGroupId: Int, status: Option[JobState] = None)
-    : Stream[IndexedSeq[JobListEntry]] = {
+    : LazyList[IndexedSeq[JobListEntry]] = {
     val q = status.map(s => s"state=${s.toString.toLowerCase}").getOrElse("")
     paginated(Some(0): Option[Int]) {
       case Some(jobId) =>

diff --git a/hail/hail/src/is/hail/services/oauth2.scala b/hail/hail/src/is/hail/services/oauth2.scala
@@ -11,7 +11,7 @@ import is.hail.shadedazure.com.azure.identity.{
 }
 import is.hail.utils.{defaultJSONFormats, using}
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 import java.io.Serializable
 import java.nio.file.{Files, Path}

diff --git a/hail/hail/src/is/hail/sparkextras/ContextRDD.scala b/hail/hail/src/is/hail/sparkextras/ContextRDD.scala
@@ -5,6 +5,7 @@ import is.hail.backend.spark.{SparkBackend, SparkTaskContext}
 import is.hail.rvd.RVDContext
 import is.hail.utils._
 
+import scala.collection.compat._
 import scala.reflect.ClassTag
 
 import org.apache.spark._
@@ -182,7 +183,7 @@ class ContextRDD[T: ClassTag](
   def filter(f: T => Boolean): ContextRDD[T] =
     mapPartitions(_.filter(f), preservesPartitioning = true)
 
-  def flatMap[U: ClassTag](f: T => TraversableOnce[U]): ContextRDD[U] =
+  def flatMap[U: ClassTag](f: T => IterableOnce[U]): ContextRDD[U] =
     mapPartitions(_.flatMap(f))
 
   def mapPartitions[U: ClassTag](
@@ -203,7 +204,7 @@ class ContextRDD[T: ClassTag](
   def cfilter(f: (RVDContext, T) => Boolean): ContextRDD[T] =
     cmapPartitions((c, it) => it.filter(f(c, _)), true)
 
-  def cflatMap[U: ClassTag](f: (RVDContext, T) => TraversableOnce[U]): ContextRDD[U] =
+  def cflatMap[U: ClassTag](f: (RVDContext, T) => IterableOnce[U]): ContextRDD[U] =
     cmapPartitions((c, it) => it.flatMap(f(c, _)))
 
   def cmapPartitions[U: ClassTag](

diff --git a/hail/hail/src/is/hail/stats/LeveneHaldane.scala b/hail/hail/src/is/hail/stats/LeveneHaldane.scala
@@ -2,6 +2,8 @@ package is.hail.stats
 
 import is.hail.utils._
 
+import scala.collection.compat.immutable.LazyList
+
 import org.apache.commons.math3.distribution.AbstractIntegerDistribution
 import org.apache.commons.math3.random.RandomGenerator
 
@@ -12,8 +14,8 @@ class LeveneHaldane(
   val n: Int,
   val nA: Int,
   val mode: Int,
-  pRU: Stream[Double],
-  pLU: Stream[Double],
+  pRU: LazyList[Double],
+  pLU: LazyList[Double],
   pN: Double,
   rng: RandomGenerator,
 ) extends AbstractIntegerDistribution(rng) {
@@ -69,7 +71,7 @@ class LeveneHaldane(
       0.0
     else {
       val cutoff = p0U * 0.5e-16
-      def mpU(s: Stream[Double]): Double = {
+      def mpU(s: LazyList[Double]): Double = {
         val (sEq, sLess) =
           s.dropWhile(D_>(_, p0U, tolerance = 1.0e-12)).span(D_==(_, p0U, tolerance = 1.0e-12))
         0.5 * sEq.sum + sLess.takeWhile(_ > cutoff).sum
@@ -100,9 +102,9 @@ object LeveneHaldane {
       (nA + 1.0) * (nB + 1) / (2 * n + 3)
     ).toInt
 
-    def pRUfrom(nAB: Int, p: Double): Stream[Double] =
+    def pRUfrom(nAB: Int, p: Double): LazyList[Double] =
       p #:: pRUfrom(nAB + 2, p * (nA - nAB) * (nB - nAB) / ((nAB + 2.0) * (nAB + 1)))
-    def pLUfrom(nAB: Int, p: Double): Stream[Double] =
+    def pLUfrom(nAB: Int, p: Double): LazyList[Double] =
       p #:: pLUfrom(nAB - 2, p * nAB * (nAB - 1) / ((nA - nAB + 2.0) * (nB - nAB + 2)))
 
     // Unnormalized probability mass function going right, respectively left, from the mode by 2s