Scala 2.12 and sbt updates

codegen_java/build.sbt

@@ -6,7 +6,7 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.12.12",
+    scalaVersion := "2.12.13",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,

project/Merging.scala

@@ -3,6 +3,20 @@ import sbtassembly.AssemblyPlugin.autoImport._
 import sbtassembly.{MergeStrategy, PathList}
 
 object Merging {
+  //noinspection SameParameterValue
+  // Based on https://stackoverflow.com/questions/24363363/how-can-a-duplicate-class-be-excluded-from-sbt-assembly#57759013
+  private def excludeFromJar(jarName: String): sbtassembly.MergeStrategy = new sbtassembly.MergeStrategy {
+    override def name: String = "excludeFromJar"
+
+    override def apply(tempDir: File, path: String, files: Seq[File]): Either[String, Seq[(File, String)]] = {
+      val filteredFiles = files flatMap { file =>
+        val (source, _, _, isFromJar) = sbtassembly.AssemblyUtils.sourceOfFileForMerge(tempDir, file)
+        if (isFromJar && source.getName != jarName) Option(file -> path) else None
+      }
+      Right(filteredFiles)
+    }
+  }
+
   val customMergeStrategy: Def.Initialize[String => MergeStrategy] = Def.setting {
     case PathList(ps@_*) if ps.last == "project.properties" =>
       // Merge/Filter project.properties files from Google jars that otherwise collide at merge time.
@@ -16,11 +30,11 @@ object Merging {
       path map {
         _.toLowerCase
       } match {
-        case "spring.tooling" :: xs =>
+        case "spring.tooling" :: _ =>
           MergeStrategy.discard
         case "io.netty.versions.properties" :: Nil =>
           MergeStrategy.first
-        case "maven" :: "com.google.guava" :: xs =>
+        case "maven" :: "com.google.guava" :: _ =>
           MergeStrategy.first
         case _ =>
           val oldStrategy = (assembly / assemblyMergeStrategy).value
@@ -40,6 +54,9 @@ object Merging {
       MergeStrategy.discard
     case PathList("mime.types") =>
       MergeStrategy.last
+    case PathList("scala", "annotation", "nowarn.class" | "nowarn$.class") =>
+      // scala-collection-compat shading bug: https://github.com/scala/scala-collection-compat/issues/426
+      excludeFromJar("scala-collection-compat_2.12-2.4.2.jar")
     case x =>
       val oldStrategy = (assembly / assemblyMergeStrategy).value
       oldStrategy(x)

project/Settings.scala

@@ -93,8 +93,7 @@ object Settings {
       sys.env.get("CROMWELL_SBT_ASSEMBLY_LOG_LEVEL").flatMap(Level.apply).getOrElse((assembly / logLevel).value)
   )
 
-  // 2.12.13 blocked on the release of sbt-scoverage 1.6.2 https://github.com/scoverage/sbt-scoverage/issues/319
-  val Scala2_12Version = "2.12.12"
+  val Scala2_12Version = "2.12.13"
   val ScalaVersion = Scala2_12Version
   val sharedSettings =
     cromwellVersionWithGit ++ artifactorySettings ++ List(

project/plugins.sbt

@@ -1,4 +1,4 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.8.0")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.15.0")
 addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "1.0.0")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.6.1")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.7.2")

scripts/docker-develop/Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update -q && \
 #   Git
 
 # Env variables
-ENV SCALA_VERSION 2.12.12
+ENV SCALA_VERSION 2.12.13
 ENV SBT_VERSION 1.4.9
 
 #