[query] Move is.hail.check to test code

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

@@ -1,8 +1,5 @@
 package is.hail.types.physical
 
-import is.hail.annotations.Annotation
-import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.types.virtual.TArray
 
 trait PArrayIterator {
@@ -17,7 +14,4 @@ abstract class PArray extends PArrayBackedContainer {
   final protected[physical] val elementRequired = elementType.required
 
   def elementIterator(aoff: Long, length: Int): PArrayIterator
-
-  override def genNonmissingValue(sm: HailStateManager): Gen[IndexedSeq[Annotation]] =
-    Gen.buildableOf[Array](elementType.genValue(sm)).map(x => x: IndexedSeq[Annotation])
 }

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

@@ -1,9 +1,8 @@
 package is.hail.types.physical
 
 import is.hail.annotations._
-import is.hail.asm4s.{Code, _}
+import is.hail.asm4s._
 import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
 import is.hail.utils._
@@ -144,10 +143,4 @@ abstract class PBaseStruct extends PType {
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBaseStructValue
 
   override lazy val containsPointers: Boolean = types.exists(_.containsPointers)
-
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    if (types.isEmpty) {
-      Gen.const(Annotation.empty)
-    } else
-      Gen.uniformSequence(types.map(t => t.genValue(sm))).map(a => Annotation(a: _*))
 }

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

@@ -1,8 +1,5 @@
 package is.hail.types.physical
 
-import is.hail.annotations._
-import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.types.physical.stypes.interfaces.SContainer
 import is.hail.types.virtual.TDict
 
@@ -15,7 +12,4 @@ abstract class PDict extends PContainer {
   def sType: SContainer
 
   def elementType: PStruct
-
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    Gen.buildableOf2[Map](Gen.zip(keyType.genValue(sm), valueType.genValue(sm)))
 }

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

@@ -1,13 +1,7 @@
 package is.hail.types.physical
 
-import is.hail.annotations._
-import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.types.virtual.TSet
 
 abstract class PSet extends PContainer {
   lazy val virtualType: TSet = TSet(elementType.virtualType)
-
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    Gen.buildableOf[Set](elementType.genValue(sm))
 }

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

@@ -3,14 +3,12 @@ package is.hail.types.physical
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailStateManager}
-import is.hail.check.{Arbitrary, Gen}
 import is.hail.expr.ir._
 import is.hail.types.{tcoerce, Requiredness}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.SRNGState
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.variant.ReferenceGenome
 
 import org.apache.spark.sql.Row
 import org.json4s.CustomSerializer
@@ -31,108 +29,6 @@ class PStructSerializer extends CustomSerializer[PStruct](format =>
     )
 
 object PType {
-  def genScalar(required: Boolean): Gen[PType] =
-    Gen.oneOf(
-      PBoolean(required),
-      PInt32(required),
-      PInt64(required),
-      PFloat32(required),
-      PFloat64(required),
-      PCanonicalString(required),
-      PCanonicalCall(required),
-    )
-
-  val genOptionalScalar: Gen[PType] = genScalar(false)
-
-  val genRequiredScalar: Gen[PType] = genScalar(true)
-
-  def genComplexType(required: Boolean): Gen[PType] = {
-    val rgDependents = ReferenceGenome.hailReferences.toArray.map(PCanonicalLocus(_, required))
-    val others = Array(PCanonicalCall(required))
-    Gen.oneOfSeq(rgDependents ++ others)
-  }
-
-  def genFields(required: Boolean, genFieldType: Gen[PType]): Gen[Array[PField]] = {
-    Gen.buildableOf[Array](
-      Gen.zip(Gen.identifier, genFieldType)
-    )
-      .filter(fields => fields.map(_._1).areDistinct())
-      .map(fields =>
-        fields
-          .iterator
-          .zipWithIndex
-          .map { case ((k, t), i) => PField(k, t, i) }
-          .toArray
-      )
-  }
-
-  def preGenStruct(required: Boolean, genFieldType: Gen[PType]): Gen[PStruct] =
-    for (fields <- genFields(required, genFieldType)) yield PCanonicalStruct(fields, required)
-
-  def preGenTuple(required: Boolean, genFieldType: Gen[PType]): Gen[PTuple] =
-    for (fields <- genFields(required, genFieldType))
-      yield PCanonicalTuple(required, fields.map(_.typ): _*)
-
-  private val defaultRequiredGenRatio = 0.2
-
-  def genStruct: Gen[PStruct] = Gen.coin(defaultRequiredGenRatio).flatMap(preGenStruct(_, genArb))
-
-  val genOptionalStruct: Gen[PType] = preGenStruct(required = false, genArb)
-
-  val genRequiredStruct: Gen[PType] = preGenStruct(required = true, genArb)
-
-  val genInsertableStruct: Gen[PStruct] = Gen.coin(defaultRequiredGenRatio).flatMap(required =>
-    if (required)
-      preGenStruct(required = true, genArb)
-    else
-      preGenStruct(required = false, genOptional)
-  )
-
-  def genSized(size: Int, required: Boolean, genPStruct: Gen[PStruct]): Gen[PType] =
-    if (size < 1)
-      Gen.const(PCanonicalStruct.empty(required))
-    else if (size < 2)
-      genScalar(required)
-    else {
-      Gen.frequency(
-        (4, genScalar(required)),
-        (1, genComplexType(required)),
-        (
-          1,
-          genArb.map {
-            PCanonicalArray(_)
-          },
-        ),
-        (
-          1,
-          genArb.map {
-            PCanonicalSet(_)
-          },
-        ),
-        (
-          1,
-          genArb.map {
-            PCanonicalInterval(_)
-          },
-        ),
-        (1, preGenTuple(required, genArb)),
-        (1, Gen.zip(genRequired, genArb).map { case (k, v) => PCanonicalDict(k, v) }),
-        (1, genPStruct.resize(size)),
-      )
-    }
-
-  def preGenArb(required: Boolean, genStruct: Gen[PStruct] = genStruct): Gen[PType] =
-    Gen.sized(genSized(_, required, genStruct))
-
-  def genArb: Gen[PType] = Gen.coin(0.2).flatMap(preGenArb(_))
-
-  val genOptional: Gen[PType] = preGenArb(required = false)
-
-  val genRequired: Gen[PType] = preGenArb(required = true)
-
-  val genInsertable: Gen[PStruct] = genInsertableStruct
-
-  implicit def arbType = Arbitrary(genArb)
 
   def canonical(t: Type, required: Boolean, innerRequired: Boolean): PType = {
     t match {
@@ -397,15 +293,6 @@ object PType {
 }
 
 abstract class PType extends Serializable with Requiredness {
-  self =>
-
-  def genValue(sm: HailStateManager): Gen[Annotation] =
-    if (required) genNonmissingValue(sm)
-    else Gen.nextCoin(0.05).flatMap(isEmpty =>
-      if (isEmpty) Gen.const(null) else genNonmissingValue(sm)
-    )
-
-  def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = virtualType.genNonmissingValue(sm)
 
   def virtualType: Type
 

hail/hail/src/is/hail/types/virtual/TArray.scala

@@ -2,7 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations.{Annotation, ExtendedOrdering}
 import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 
 import org.json4s.jackson.JsonMethods
 
@@ -43,9 +42,6 @@ final case class TArray(elementType: Type) extends TContainer {
 
   override def str(a: Annotation): String = JsonMethods.compact(export(a))
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[IndexedSeq[Annotation]] =
-    Gen.buildableOf[Array](elementType.genValue(sm)).map(x => x: IndexedSeq[Annotation])
-
   def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.iterableOrdering(elementType.ordering(sm), missingEqual)
 

hail/hail/src/is/hail/types/virtual/TBaseStruct.scala

@@ -2,7 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.utils._
 
 import org.apache.spark.sql.Row
@@ -95,18 +94,6 @@ abstract class TBaseStruct extends Type {
 
   override def str(a: Annotation): String = JsonMethods.compact(export(a))
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = {
-    if (types.isEmpty) {
-      Gen.const(Annotation.empty)
-    } else
-      Gen.size.flatMap(fuel =>
-        if (types.length > fuel)
-          Gen.uniformSequence(types.map(t => Gen.const(null))).map(a => Annotation(a: _*))
-        else
-          Gen.uniformSequence(types.map(t => t.genValue(sm))).map(a => Annotation(a: _*))
-      )
-  }
-
   override def valuesSimilar(a1: Annotation, a2: Annotation, tolerance: Double, absolute: Boolean)
     : Boolean =
     a1 == a2 || (a1 != null && a2 != null

hail/hail/src/is/hail/types/virtual/TBinary.scala

@@ -2,17 +2,12 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 
 case object TBinary extends Type {
   def _toPretty = "Binary"
 
   def _typeCheck(a: Any): Boolean = a.isInstanceOf[Array[Byte]]
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    Gen.buildableOf(arbitrary[Byte])
-
   def mkOrdering(sm: HailStateManager, _missingEqual: Boolean = true): ExtendedOrdering =
     ExtendedOrdering.iterableOrdering(new ExtendedOrdering {
       val missingEqual = _missingEqual

hail/hail/src/is/hail/types/virtual/TBoolean.scala

@@ -2,8 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 
 case object TBoolean extends Type {
   def _toPretty = "Boolean"
@@ -17,8 +15,6 @@ case object TBoolean extends Type {
 
   def parse(s: String): Annotation = s.toBoolean
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = arbitrary[Boolean]
-
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[Boolean]], missingEqual)
 

hail/hail/src/is/hail/types/virtual/TCall.scala

@@ -2,7 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.variant.Call
 
 case object TCall extends Type {
@@ -15,8 +14,6 @@ case object TCall extends Type {
 
   def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = Call.genNonmissingValue
-
   override def str(a: Annotation): String =
     if (a == null) "NA" else Call.toString(a.asInstanceOf[Call])
 

hail/hail/src/is/hail/types/virtual/TDict.scala

@@ -2,7 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations.{Annotation, ExtendedOrdering}
 import is.hail.backend.HailStateManager
-import is.hail.check.Gen
 import is.hail.utils._
 
 import org.json4s.jackson.JsonMethods
@@ -59,9 +58,6 @@ final case class TDict(keyType: Type, valueType: Type) extends TContainer {
 
   override def str(a: Annotation): String = JsonMethods.compact(export(a))
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    Gen.buildableOf2[Map](Gen.zip(keyType.genValue(sm), valueType.genValue(sm)))
-
   override def valuesSimilar(a1: Annotation, a2: Annotation, tolerance: Double, absolute: Boolean)
     : Boolean =
     a1 == a2 || (a1 != null && a2 != null &&

hail/hail/src/is/hail/types/virtual/TFloat32.scala

@@ -2,8 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 import is.hail.utils._
 
 case object TFloat32 extends TNumeric {
@@ -19,9 +17,6 @@ case object TFloat32 extends TNumeric {
   override def str(a: Annotation): String =
     if (a == null) "NA" else "%.5e".format(a.asInstanceOf[Float])
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] =
-    arbitrary[Double].map(_.toFloat)
-
   override def valuesSimilar(a1: Annotation, a2: Annotation, tolerance: Double, absolute: Boolean)
     : Boolean =
     a1 == a2 || (a1 != null && a2 != null && {

hail/hail/src/is/hail/types/virtual/TFloat64.scala

@@ -2,8 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 import is.hail.utils._
 
 case object TFloat64 extends TNumeric {
@@ -19,8 +17,6 @@ case object TFloat64 extends TNumeric {
   override def str(a: Annotation): String =
     if (a == null) "NA" else "%.5e".format(a.asInstanceOf[Double])
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = arbitrary[Double]
-
   override def valuesSimilar(a1: Annotation, a2: Annotation, tolerance: Double, absolute: Boolean)
     : Boolean =
     a1 == a2 || (a1 != null && a2 != null && {

hail/hail/src/is/hail/types/virtual/TInt32.scala

@@ -2,8 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 
 case object TInt32 extends TIntegral {
   def _toPretty = "Int32"
@@ -13,8 +11,6 @@ case object TInt32 extends TIntegral {
 
   def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = arbitrary[Int]
-
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[Int]], missingEqual)
 

hail/hail/src/is/hail/types/virtual/TInt64.scala

@@ -2,8 +2,6 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.check.Arbitrary._
-import is.hail.check.Gen
 
 case object TInt64 extends TIntegral {
   def _toPretty = "Int64"
@@ -13,8 +11,6 @@ case object TInt64 extends TIntegral {
 
   def _typeCheck(a: Any): Boolean = a.isInstanceOf[Long]
 
-  override def genNonmissingValue(sm: HailStateManager): Gen[Annotation] = arbitrary[Long]
-
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[Long]], missingEqual)