[query] extract utils into new module

Author: ehigham

hail/build.mill

@@ -126,7 +126,7 @@ trait HailScalaModule extends ScalaModule, HailJavaModule, ScalafmtModule, Scala
           "-Wconf:cat=deprecation&msg=symbol literal is deprecated:s",
           raw"-Wconf:cat=unused-imports&origin=scala\.collection\.compat\._:s",
           raw"-Wconf:cat=unused-imports&origin=scala\.Option\.option2Iterable:s",
-          raw"-Wconf:cat=unused-imports&origin=is\.hail\.utils\.compat\._:s",
+          raw"-Wconf:cat=unused-imports&origin=is\.hail\.collection\.compat\._:s",
           raw"-Wconf:msg=unused value of type org\.scalatest\..*Assertion:s",
           raw"-Wconf:msg=unused value of type org\.mockito\.stubbing\.ScalaOngoingStubbing:s",
         )

hail/hail/ir-gen/src/Main.scala

@@ -1213,9 +1213,10 @@ object Main {
     val pack = "package is.hail.expr.ir.defs"
     val imports = Seq(
       "is.hail.annotations.Annotation",
+      "is.hail.collection.FastSeq",
       "is.hail.io.{AbstractTypedCodecSpec, BufferSpec}",
       "is.hail.types.virtual.{Type, TArray, TStream, TVoid, TStruct, TTuple}",
-      "is.hail.utils.{FastSeq, StringEscapeUtils}",
+      "is.hail.utils.StringEscapeUtils",
       "is.hail.expr.ir.{AggOp, BaseIR, IR, TableIR, MatrixIR, BlockMatrixIR, Name, UnaryOp, BinaryOp, " +
         "ComparisonOp, CanEmit, EmitParamType, TableWriter, " +
         "WrappedMatrixNativeMultiWriter, MatrixWriter, MatrixNativeMultiWriter, BlockMatrixWriter, " +

hail/hail/package.mill

@@ -25,6 +25,7 @@ trait RootHailModule extends CrossScalaModule, HailScalaModule:
 
   override def moduleDeps: Seq[JavaModule] =
     Seq(
+      build.hail.utils(crossValue),
       build.hail.memory(if buildMode == CI then "debug" else "release"),
     )
 

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

@@ -2,10 +2,10 @@ package is.hail
 
 import is.hail.backend.ExecutionCache
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{agg, Optimize}
 import is.hail.io.fs.RequesterPaysConfig
 import is.hail.types.encoded.EType
-import is.hail.utils._
 
 import scala.collection.mutable
 

hail/hail/src/is/hail/HailFeatureFlags.scala

@@ -1,5 +1,6 @@
 package is.hail.annotations
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.types.virtual._
 import is.hail.utils._
 

hail/hail/src/is/hail/annotations/Annotation.scala

@@ -6,8 +6,9 @@ import is.hail.expr.ir.defs.EncodedLiteral
 import is.hail.io.{BufferSpec, Decoder, TypedCodecSpec}
 import is.hail.types.physical.{PArray, PStruct, PType}
 import is.hail.types.virtual.{TBaseStruct, TStruct}
-import is.hail.utils.{formatSpace, ArrayOfByteArrayOutputStream, Logging}
-import is.hail.utils.prettyPrint.ArrayOfByteArrayInputStream
+import is.hail.utils.{
+  formatSpace, ArrayOfByteArrayInputStream, ArrayOfByteArrayOutputStream, Logging,
+}
 
 import java.io.InputStream
 

hail/hail/src/is/hail/annotations/BroadcastValue.scala

@@ -1,6 +1,6 @@
 package is.hail.annotations
 
-import is.hail.expr.ir.LongArrayBuilder
+import is.hail.collection.LongArrayBuilder
 
 import scala.collection.mutable
 

hail/hail/src/is/hail/annotations/ChunkCache.scala

@@ -1,5 +1,6 @@
 package is.hail.annotations
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.utils._
 
 import org.apache.spark.sql.Row

hail/hail/src/is/hail/annotations/ExtendedOrdering.scala

@@ -1,10 +1,12 @@
 package is.hail.annotations
 
 import is.hail.backend.HailStateManager
+import is.hail.collection.{FlipbookIterator, StagingIterator, StateMachine}
+import is.hail.collection.compat.mutable.Growable
+import is.hail.collection.implicits.toRichIterator
 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.mutable