JavaConverters

Author: patrick-schultz

hail/build.mill

@@ -147,11 +147,6 @@ trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { o
     if (scalaVersion().startsWith("2.13")) {
       finalOptions ++
       Seq(
-      // collection types
-        // 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

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._

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
 

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}

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 = {

hail/hail/src/is/hail/io/vcf/LoadVCF.scala

@@ -28,8 +28,8 @@ import is.hail.variant._
 import scala.annotation.meta.param
 import scala.annotation.switch
 import scala.collection.BufferedIterator
-import scala.collection.JavaConverters._
 import scala.collection.compat._
+import scala.jdk.CollectionConverters._
 
 import htsjdk.variant.vcf._
 import org.apache.spark.{Partition, TaskContext}

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

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

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}

hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala

@@ -5,9 +5,8 @@ import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.virtual.{TStruct, Type}
 import is.hail.utils._
 
-import scala.collection.JavaConverters._
-import scala.collection.compat._
 import scala.collection.compat._
+import scala.jdk.CollectionConverters._
 
 object PCanonicalStruct {
   private val requiredEmpty = PCanonicalStruct(Array.empty[PField], true)