various updates for new scala version

benchmark/build.sbt

@@ -3,8 +3,6 @@ Common.commonSettings
 // lazy val breeze = project in file("core")
 name := "breeze-benchmark"
 
-addCompilerPlugin(("org.scalamacros" %% "paradise" % "2.1.0").cross(CrossVersion.full))
-
 libraryDependencies ++= Seq(
   "org.apfloat" % "apfloat" % "1.6.3",
   "org.jscience" % "jscience" % "4.3.1",

build.sbt

@@ -18,4 +18,3 @@ lazy val natives = project.in(file("natives")).dependsOn(math)
 lazy val viz = project.in(file("viz")).dependsOn(math)
 
 lazy val benchmark = project.in(file("benchmark")).dependsOn(math, natives)
-addCompilerPlugin(("org.scalamacros" %% "paradise" % "2.1.0").cross(CrossVersion.full))

macros/build.sbt

@@ -13,5 +13,3 @@ libraryDependencies := {
 }
 
 libraryDependencies += "org.scala-lang" % "scala-reflect" % s"${scalaVersion.value}"
-
-addCompilerPlugin(("org.scalamacros" %% "paradise" % "2.1.0").cross(CrossVersion.full))

math/build.sbt

@@ -2,45 +2,40 @@ name := "breeze"
 
 Common.commonSettings
 
-addCompilerPlugin(("org.scalamacros" %% "paradise" % "2.1.0").cross(CrossVersion.full))
-
 libraryDependencies ++= Seq(
   "com.github.fommil.netlib" % "core" % "1.1.2",
   "net.sourceforge.f2j" % "arpack_combined_all" % "0.1",
   "net.sf.opencsv" % "opencsv" % "2.3",
   "com.github.wendykierp" % "JTransforms" % "3.1",
   "org.apache.commons" % "commons-math3" % "3.2",
-  "org.spire-math" %% "spire" % "0.13.0",
-  "com.chuusai" %% "shapeless" % "2.3.2",
+  "com.chuusai" %% "shapeless" % "2.3.3",
   "org.slf4j" % "slf4j-api" % "1.7.5",
   "org.apache.logging.log4j" % "log4j-slf4j-impl" % "2.0-beta9" % "test",
   "org.apache.logging.log4j" % "log4j-core" % "2.0-beta9" % "test",
   "org.apache.logging.log4j" % "log4j-api" % "2.0-beta9" % "test"
 )
 
-libraryDependencies := {
-  val sv = scalaVersion.value
-  val deps = libraryDependencies.value
-  sv match {
-    case x if x.startsWith("2.10") =>
-      deps :+ compilerPlugin(("org.scalamacros" % "paradise" % "2.1.0").cross(CrossVersion.full))
-    case _ =>
-      deps
-  }
-}
-
-libraryDependencies := {
+libraryDependencies ++= {
   CrossVersion.partialVersion(scalaVersion.value) match {
-    case Some((2, scalaMajor)) if scalaMajor >= 12 =>
-      libraryDependencies.value ++ Seq(
+    case Some((2, 13)) =>
+      Seq(
+        "org.typelevel" % "spire_2.13.0-M5" % "0.16.1",
+        "org.scala-lang.modules" %% "scala-xml" % "1.0.6" % "test"
+      )
+    case Some((2, 12)) =>
+      Seq(
+        "org.typelevel" %% "spire" % "0.16.1",
         "org.scala-lang.modules" %% "scala-xml" % "1.0.6" % "test"
       )
-    case Some((2, scalaMajor)) if scalaMajor >= 11 =>
-      libraryDependencies.value ++ Seq(
+    case Some((2, 11)) =>
+      Seq(
+        "org.typelevel" %% "spire" % "0.16.1",
         "org.scala-lang.modules" %% "scala-xml" % "1.0.6" % "test"
       )
     case _ =>
-      libraryDependencies.value ++ Seq()
+      Seq(
+        "org.typelevel" %% "spire" % "0.16.1",
+      )
   }
 }
 

math/src/main/scala/breeze/linalg/Matrix.scala

@@ -243,10 +243,9 @@ trait MatrixConstructors[Mat[T] <: Matrix[T]] {
     fill(rows, cols)(rand.draw())
   }
 
-  // @specialized() R because of https://issues.scala-lang.org/browse/SI-8886
   /** Static constructor for a literal matrix. */
-  def apply[@specialized( /* Don't remove until SI-8886 is closed*/ ) R, @spec(Double, Int, Float, Long) V](
-      rows: R*)(implicit rl: LiteralRow[R, V], man: ClassTag[V], zero: Zero[V]) = {
+  def apply[R, @spec(Double, Int, Float, Long) V](
+      rows: R*)(implicit rl: LiteralRow[R, V], man: ClassTag[V], zero: Zero[V]): Mat[V] = {
     val nRows = rows.length
     val ns = rows.headOption match {
       case None => 0

math/src/test/scala/breeze/collection/immutable/BeamTest.scala

@@ -19,10 +19,10 @@ package breeze.collection.immutable
 import org.scalacheck._
 import org.scalatest._;
 import org.scalatest.junit._;
-import org.scalatest.prop._;
+import org.scalatestplus.scalacheck._;
 import org.junit.runner.RunWith
 
-@RunWith(classOf[JUnitRunner])
+
 class BeamTest extends FunSuite with Checkers {
   test("creation doesn't go over size") {
     check(Prop.forAll { (size: Int, cl: List[Int]) =>

math/src/test/scala/breeze/collection/mutable/BeamTest.scala

@@ -18,11 +18,8 @@ package breeze.collection.mutable
 
 import org.scalacheck._
 import org.scalatest._;
-import org.scalatest.junit._;
-import org.scalatest.prop._;
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 
-@RunWith(classOf[JUnitRunner])
 class BeamTest extends FunSuite with Checkers {
   test("creation doesn't go over size") {
     check(Prop.forAll { (size: Int, cl: List[Int]) =>

math/src/test/scala/breeze/collection/mutable/OpenAddressHashArrayTest.scala

@@ -15,18 +15,14 @@ package breeze.collection.mutable
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-import org.scalatest.prop.Checkers
+import org.scalatestplus.scalacheck.Checkers
 import org.scalatest.FunSuite
-import org.scalatest.junit.JUnitRunner
-import org.junit.runner.RunWith
 import org.scalacheck.{Arbitrary, Prop}
 
 /**
  *
  * @author dlwh
  */
-
-@RunWith(classOf[JUnitRunner])
 class OpenAddressHashArrayTest extends FunSuite with Checkers {
   test("add stuff, make sure it and only it is there") {
     implicit val arbInt: Arbitrary[Int] = Arbitrary { Arbitrary.arbInt.arbitrary.map(_.abs % 1000) }

math/src/test/scala/breeze/collection/mutable/SparseArrayTest.scala

@@ -18,11 +18,8 @@ package breeze.collection.mutable
 
 import breeze.linalg.SparseVector
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 
-@RunWith(classOf[JUnitRunner])
 class SparseArrayTest extends FunSuite with Checkers {
   test("Map") {
     val x = SparseArray(1, 0, 2, 0, 3, 0, -1, -2, -3)

math/src/test/scala/breeze/generic/MultimethodTest.scala

@@ -15,11 +15,8 @@ package breeze.generic
  limitations under the License.
  */
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 
-@RunWith(classOf[JUnitRunner])
 class MultimethodTest extends FunSuite with Checkers {
   trait T
   trait V extends T

math/src/test/scala/breeze/linalg/CSCMatrixTest.scala

@@ -15,20 +15,15 @@ package breeze.linalg
  limitations under the License.
  */
 
-import breeze.generic.UFunc
-import breeze.linalg.operators.{OpAdd, OpType}
 import breeze.math.MutableOptimizationSpace.SparseFieldOptimizationSpace
 import breeze.math.{Complex, Field}
 import breeze.numerics.{abs, inf}
 import breeze.storage.Zero
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck.Checkers
 
 import scala.reflect.ClassTag
 
-@RunWith(classOf[JUnitRunner])
 class CSCMatrixTest extends FunSuite with Checkers with MatrixTestUtils {
   test("Multiply") {
     val a = CSCMatrix((1.0, 2.0, 3.0), (4.0, 5.0, 6.0))

math/src/test/scala/breeze/linalg/Counter2Test.scala

@@ -15,11 +15,8 @@ package breeze.linalg
  limitations under the License.
  */
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 
-@RunWith(classOf[JUnitRunner])
 class Counter2Test extends FunSuite with Checkers {
   test("Getting and setting") {
     val x = Counter2[String, Int, Double]()

math/src/test/scala/breeze/linalg/CounterTest.scala

@@ -16,16 +16,13 @@ package breeze.linalg
  */
 import breeze.math.TensorSpaceTestBase
 import breeze.stats.mean
-import org.junit.runner.RunWith
 import org.scalacheck.Arbitrary
 import org.scalatest.FunSuite
-import org.scalatest.junit.JUnitRunner
-import org.scalatest.prop.Checkers
+import org.scalatestplus.scalacheck.Checkers
 
 /**
  * @author dlwh
  */
-@RunWith(classOf[JUnitRunner])
 class CounterTest extends FunSuite with Checkers {
   val TOLERANCE = 1e-4
   def assertClose(a: Double, b: Double) =
@@ -84,7 +81,7 @@ class CounterTest extends FunSuite with Checkers {
     assert(x === Counter(1 -> log(1.0), 2 -> log(2.0)))
   }
 }
-@RunWith(classOf[JUnitRunner])
+
 class CounterOps_IntTest extends TensorSpaceTestBase[Counter[Int, Int], Int, Int] {
   val space = Counter.space[Int, Int]
 

math/src/test/scala/breeze/linalg/DenseMatrixTest.scala

@@ -17,15 +17,12 @@ package breeze.linalg
  */
 
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 import breeze.math.Complex
 import breeze.numerics._
 import breeze.stats.distributions.Rand
 import breeze.util.DoubleImplicits
 
-@RunWith(classOf[JUnitRunner])
 class DenseMatrixTest extends FunSuite with Checkers with Matchers with DoubleImplicits with MatrixTestUtils {
 
   test("Slicing") {

math/src/test/scala/breeze/linalg/DenseVectorTest.scala

@@ -4,9 +4,7 @@ import breeze.numerics.isNonfinite
 import org.netlib.blas.Ddot
 import org.scalacheck._
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 import breeze.math._
 import breeze.stats.mean
 import java.util
@@ -19,7 +17,6 @@ import scala.reflect.ClassTag
  *
  * @author dlwh
  */
-@RunWith(classOf[JUnitRunner])
 class DenseVectorTest extends FunSuite with Checkers {
 
   val TOLERANCE = 1e-4
@@ -593,22 +590,22 @@ abstract class DenseVectorPropertyTestBase[T: ClassTag] extends TensorSpaceTestB
  *
  * @author dlwh
  */
-@RunWith(classOf[JUnitRunner])
+
 class DenseVectorOps_DoubleTest
     extends DenseVectorPropertyTestBase[Double]
     with DoubleValuedTensorSpaceTestBase[DenseVector[Double], Int] {
   val space = DenseVector.space[Double]
   def genScalar: Arbitrary[Double] = RandomInstanceSupport.genReasonableDouble
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class DenseVectorOps_IntTest extends DenseVectorPropertyTestBase[Int] {
   val space = DenseVector.space[Int]
 
   def genScalar: Arbitrary[Int] = Arbitrary { Gen.Choose.chooseInt.choose(-1000, 1000) }
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class DenseVectorOps_ComplexTest extends DenseVectorPropertyTestBase[Complex] {
   val space = DenseVector.space[Complex]
   def genScalar: Arbitrary[Complex] = Arbitrary {
@@ -619,7 +616,7 @@ class DenseVectorOps_ComplexTest extends DenseVectorPropertyTestBase[Complex] {
   }
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class DenseVectorOps_FloatTest extends DenseVectorPropertyTestBase[Float] {
   val space = DenseVector.space[Float]
 

math/src/test/scala/breeze/linalg/HashVectorTest.scala

@@ -1,8 +1,6 @@
 package breeze.linalg
 
 import org.scalatest._
-import org.scalatest.junit._
-import org.junit.runner.RunWith
 import breeze.math._
 import breeze.stats.mean
 import breeze.storage.Zero
@@ -13,7 +11,6 @@ import scala.reflect.ClassTag
  *
  * @author dlwh
  */
-@RunWith(classOf[JUnitRunner])
 class HashVectorTest extends FunSuite {
 
   val TOLERANCE = 1e-4
@@ -258,23 +255,23 @@ abstract class HashVectorPropertyTestBase[T: ClassTag: Zero] extends TensorSpace
   }
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class HashVectorOps_DoubleTest
     extends HashVectorPropertyTestBase[Double]
     with DoubleValuedTensorSpaceTestBase[HashVector[Double], Int] {
   val space = HashVector.space[Double]
   def genScalar: Arbitrary[Double] = RandomInstanceSupport.genReasonableDouble
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class HashVectorOps_FloatTest extends HashVectorPropertyTestBase[Float] {
   val space = HashVector.space[Float]
 
   override val TOL: Double = 1E-2
   def genScalar: Arbitrary[Float] = Arbitrary { RandomInstanceSupport.genReasonableDouble.arbitrary.map(_.toFloat) }
 }
 
-@RunWith(classOf[JUnitRunner])
+
 class HashVectorOps_IntTest extends HashVectorPropertyTestBase[Int] {
   val space = HashVector.space[Int]
   def genScalar: Arbitrary[Int] = Arbitrary { Gen.Choose.chooseInt.choose(-1000, 1000) }

math/src/test/scala/breeze/linalg/LinearAlgebraTest.scala

@@ -24,9 +24,7 @@ import breeze.linalg.svd.SVD
 import breeze.stats.distributions.{RandBasis, MultivariateGaussian}
 import org.scalacheck.{Arbitrary, Gen, Prop}
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 import breeze.util.DoubleImplicits
 import breeze.numerics._
 import breeze.stats.{mean, median, meanAndVariance}
@@ -36,8 +34,6 @@ import breeze.{math => bmath}
  *
  * @author dlwh
  */
-
-@RunWith(classOf[JUnitRunner])
 class LinearAlgebraTest extends FunSuite with Checkers with Matchers with DoubleImplicits {
   test("kron") {
     val a = DenseMatrix((1, 2), (3, 4))

math/src/test/scala/breeze/linalg/MatrixTest.scala

@@ -16,12 +16,10 @@ package breeze.linalg
  limitations under the License.
  */
 import org.scalatest._
-import org.scalatest.junit._
-import org.scalatest.prop._
-import org.junit.runner.RunWith
+import org.scalatestplus.scalacheck._
 import breeze.math.Complex
 
-@RunWith(classOf[JUnitRunner])
+
 class MatrixTest extends FunSuite with Checkers {
   test("Multiply") {
     val a = Matrix((1.0, 2.0, 3.0), (4.0, 5.0, 6.0))