revert import changes

hail-is · Nov 15, 2023 · 6d24d95 · 6d24d95
1 parent 39d2e4c
commit 6d24d95
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diff --git a/hail/src/main/scala/is/hail/backend/Backend.scala b/hail/src/main/scala/is/hail/backend/Backend.scala
@@ -1,27 +1,31 @@
 package is.hail.backend
 
+import java.io._
+import java.nio.charset.StandardCharsets
+
+import org.json4s._
+import org.json4s.jackson.{JsonMethods, Serialization}
+
 import is.hail.asm4s._
 import is.hail.backend.spark.SparkBackend
 import is.hail.expr.ir.lowering.{TableStage, TableStageDependency}
-import is.hail.expr.ir.{BaseIR, CodeCacheKey, CompiledFunction, IRParser, IRParserEnvironment, LoweringAnalyses, SortField, TableIR, TableReader}
+import is.hail.expr.ir.{CodeCacheKey, CompiledFunction, LoweringAnalyses, SortField, TableIR, TableReader}
+import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.io.fs._
 import is.hail.io.plink.LoadPlink
 import is.hail.io.vcf.LoadVCF
-import is.hail.io.{BufferSpec, TypedCodecSpec}
+import is.hail.expr.ir.{IRParser, BaseIR}
 import is.hail.linalg.BlockMatrix
 import is.hail.types._
 import is.hail.types.encoded.EType
-import is.hail.types.physical.PTuple
 import is.hail.types.virtual.TFloat64
+import is.hail.types.physical.PTuple
 import is.hail.utils._
 import is.hail.variant.ReferenceGenome
-import org.json4s._
-import org.json4s.jackson.{JsonMethods, Serialization}
 
-import java.io._
-import java.nio.charset.StandardCharsets
 import scala.collection.mutable
 import scala.reflect.ClassTag
+import is.hail.expr.ir.IRParserEnvironment
 
 
 object Backend {

diff --git a/hail/src/main/scala/is/hail/backend/local/LocalBackend.scala b/hail/src/main/scala/is/hail/backend/local/LocalBackend.scala
@@ -1,29 +1,31 @@
 package is.hail.backend.local
 
-import is.hail.annotations.{Region, SafeRow}
+import is.hail.annotations.{Region, SafeRow, UnsafeRow}
 import is.hail.asm4s._
 import is.hail.backend._
-import is.hail.expr.Validate
 import is.hail.expr.ir.analyses.SemanticHash
 import is.hail.expr.ir.lowering._
 import is.hail.expr.ir.{IRParser, _}
+import is.hail.expr.{JSONAnnotationImpex, Validate}
 import is.hail.io.fs._
+import is.hail.io.plink.LoadPlink
 import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.linalg.BlockMatrix
 import is.hail.types._
 import is.hail.types.encoded.EType
 import is.hail.types.physical.PTuple
-import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
+import is.hail.types.physical.stypes.{PTypeReferenceSingleCodeType, SingleCodeType}
 import is.hail.types.virtual.TVoid
 import is.hail.utils._
 import is.hail.variant.ReferenceGenome
 import is.hail.{HailContext, HailFeatureFlags}
 import org.apache.hadoop
 import org.json4s._
-import org.json4s.jackson.Serialization
+import org.json4s.jackson.{JsonMethods, Serialization}
 import org.sparkproject.guava.util.concurrent.MoreExecutors
 
 import java.io.PrintWriter
+import java.nio.charset.StandardCharsets
 import scala.collection.JavaConverters._
 import scala.reflect.ClassTag
 

diff --git a/hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala b/hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala
@@ -9,6 +9,7 @@ import is.hail.expr.ir.lowering._
 import is.hail.expr.ir.{IRParser, _}
 import is.hail.expr.{JSONAnnotationImpex, SparkAnnotationImpex, Validate}
 import is.hail.io.fs._
+import is.hail.io.plink.LoadPlink
 import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.linalg.{BlockMatrix, RowMatrix}
 import is.hail.rvd.RVD
@@ -28,10 +29,11 @@ import org.apache.spark.broadcast.Broadcast
 import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.{DataFrame, SparkSession}
 import org.json4s
-import org.json4s.DefaultFormats
 import org.json4s.jackson.{JsonMethods, Serialization}
+import org.json4s.{DefaultFormats, Formats}
 
-import java.io.{Closeable, PrintWriter}
+import com.sun.net.httpserver.{HttpExchange}
+import java.io.{Closeable, PrintWriter, OutputStream}
 import scala.collection.JavaConverters._
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer

diff --git a/hail/src/main/scala/is/hail/expr/ir/AggOp.scala b/hail/src/main/scala/is/hail/expr/ir/AggOp.scala
@@ -1,6 +1,8 @@
 package is.hail.expr.ir
 
 import is.hail.expr.ir.agg._
+import is.hail.types.TypeWithRequiredness
+import is.hail.types.physical._
 import is.hail.types.virtual._
 import is.hail.utils.FastSeq
 

diff --git a/hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala b/hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala
@@ -1,10 +1,12 @@
 package is.hail.expr.ir
 
-import is.hail.expr.ir.orderings.CodeOrdering
+import is.hail.asm4s.Code
+import is.hail.expr.ir.orderings.{CodeOrdering, StructOrdering}
 import is.hail.expr.ir.orderings.CodeOrdering.F
+import is.hail.types.physical.PType
 import is.hail.types.physical.stypes.SType
 import is.hail.types.physical.stypes.interfaces.SBaseStruct
-import is.hail.types.virtual.Type
+import is.hail.types.virtual.{TStruct, Type}
 
 object ComparisonOp {
 

diff --git a/hail/src/main/scala/is/hail/variant/ReferenceGenome.scala b/hail/src/main/scala/is/hail/variant/ReferenceGenome.scala
@@ -1,25 +1,29 @@
 package is.hail.variant
 
+import java.io.InputStream
 import htsjdk.samtools.reference.FastaSequenceIndex
 import is.hail.HailContext
-import is.hail.annotations.ExtendedOrdering
-import is.hail.backend.{BroadcastValue, ExecuteContext}
+import is.hail.asm4s.Code
+import is.hail.backend.{BroadcastValue, ExecuteContext, HailStateManager}
 import is.hail.check.Gen
-import is.hail.expr.ir.RelationalSpec
+import is.hail.expr.ir.{EmitClassBuilder, RelationalSpec}
 import is.hail.expr.{JSONExtractContig, JSONExtractIntervalLocus, JSONExtractReferenceGenome, Parser}
 import is.hail.io.fs.FS
-import is.hail.io.reference.{FASTAReader, FASTAReaderConfig, LiftOver}
+import is.hail.io.reference.LiftOver
+import is.hail.io.reference.{FASTAReader, FASTAReaderConfig}
 import is.hail.types._
-import is.hail.types.virtual.{TLocus, Type}
+import is.hail.types.virtual.{TInt64, TLocus, Type}
 import is.hail.utils._
-import org.apache.spark.TaskContext
-import org.json4s._
-import org.json4s.jackson.{JsonMethods, Serialization}
 
-import java.io.InputStream
 import scala.collection.JavaConverters._
 import scala.collection.mutable
 import scala.language.implicitConversions
+import org.apache.spark.TaskContext
+import org.json4s._
+import org.json4s.jackson.{JsonMethods, Serialization}
+
+import java.lang.ThreadLocal
+import is.hail.annotations.ExtendedOrdering
 
 
 class BroadcastRG(rgParam: ReferenceGenome) extends Serializable {