Scala 2.12 and sbt updates

centaur/test_cromwell.sh

@@ -124,11 +124,11 @@ cd "${RUN_DIR}"
 TEST_STATUS="failed"
 
 if [[ "${CENTAUR_SBT_COVERAGE}" == "true" ]]; then
-    sbt -Dsbt.supershell=false --warn coverage centaur/it:compile
-    CP=$(sbt -no-colors --error coverage "export centaur/it:dependencyClasspath")
+    sbt -Dsbt.supershell=false --warn coverage centaur/IntegrationTest/compile
+    CP=$(sbt -no-colors --error coverage "export centaur/IntegrationTest/dependencyClasspath")
 else
-    sbt -Dsbt.supershell=false --warn centaur/it:compile
-    CP=$(sbt -no-colors --error "export centaur/it:dependencyClasspath")
+    sbt -Dsbt.supershell=false --warn centaur/IntegrationTest/compile
+    CP=$(sbt -no-colors --error "export centaur/IntegrationTest/dependencyClasspath")
 fi
 
 # Add the it-classes folder to the classpath to ensure logback configuration files are picked up.

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", // scala-steward:off (CROM-6777) - 2.12.13 blocked by duplicate import of nowarn
+    scalaVersion := "2.12.14",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,

codegen_java/project/build.properties

@@ -1 +1 @@
-sbt.version=1.4.9
+sbt.version=1.5.5

project/Publishing.scala

@@ -47,7 +47,7 @@ object Publishing {
       val artifact: File = assembly.value
       val artifactTargetPath = s"/app/${artifact.name}"
       val projectName = name.value
-      val additionalDockerInstr: Seq[Instruction] = dockerCustomSettings.value
+      val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
         from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
@@ -100,8 +100,7 @@ object Publishing {
     docker / buildOptions := BuildOptions(
       cache = false,
       removeIntermediateContainers = BuildOptions.Remove.Always
-    ),
-    ThisBuild / dockerCustomSettings := Nil // setting the default value
+    )
   )
 
   def dockerPushSettings(pushEnabled: Boolean): Seq[Setting[_]] = {

project/Settings.scala

@@ -81,14 +81,12 @@ object Settings {
   lazy val assemblySettings = Seq(
     assembly / assemblyJarName := name.value + "-" + version.value + ".jar",
     assembly / test := {},
-    assembly / assemblyMergeStrategy := customMergeStrategy.value,
-    assembly / logLevel :=
-      sys.env.get("CROMWELL_SBT_ASSEMBLY_LOG_LEVEL").flatMap(Level.apply).getOrElse((assembly / logLevel).value)
+    assembly / assemblyMergeStrategy := customMergeStrategy.value
   )
 
-  val Scala2_12Version = "2.12.12" // scala-steward:off (CROM-6777) - 2.12.13 blocked by duplicate import of nowarn
-  val ScalaVersion: String = Scala2_12Version
-  val sharedSettings: Seq[Setting[_]] =
+  val Scala2_12Version = "2.12.14"
+  private val ScalaVersion: String = Scala2_12Version
+  private val sharedSettings: Seq[Setting[_]] =
     cromwellVersionWithGit ++ publishingSettings ++ List(
     organization := "org.broadinstitute",
     scalaVersion := ScalaVersion,

project/Testing.scala

@@ -64,7 +64,7 @@ object Testing {
       spanScaleFactor,
       "-W",
       "300",
-      "300",
+      "300"
     )
 
   /** Run minnie-kenny only once per sbt invocation. */
@@ -101,7 +101,11 @@ object Testing {
     CromwellBenchmarkTest / testFrameworks += new TestFramework("org.scalameter.ScalaMeterFramework"),
     // Don't execute benchmarks in parallel
     CromwellBenchmarkTest / parallelExecution := false,
-    // Make sure no secrets are commited to git
+    // Until we move away from Travis do not execute ANY tests in parallel (see also Settings.sharedSettings)
+    Test / parallelExecution := false,
+    // Since parallelExecution is off do not buffer test results
+    Test / logBuffered := false,
+    // Make sure no secrets are committed to git
     minnieKenny := {
       val log = streams.value.log
       val args = spaceDelimited("<arg>").parsed
@@ -110,10 +114,10 @@ object Testing {
     Test / test := {
       minnieKenny.toTask("").value
       (Test / test).value
-    },
+    }
   )
 
-  val integrationTestSettings = List(
+  private val integrationTestSettings = List(
     libraryDependencies ++= testDependencies.map(_ % IntegrationTest)
   ) ++ itSettings
 

project/build.properties

@@ -1,2 +1,2 @@
 # scala-steward:off
-sbt.version=1.4.9
+sbt.version=1.5.5

project/plugins.sbt

@@ -1,4 +1,4 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.8.2")
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.15.0")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.0.0")
 addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "1.0.0")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.8.2")

project/project/build.properties

@@ -1,2 +1,2 @@
 # scala-steward:off
-sbt.version=1.4.9
+sbt.version=1.5.5

publish/docker-setup.sh

@@ -33,7 +33,7 @@ apt-get install \
 # sbt launcher non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.4.9/sbt-1.4.9.tgz" |
+curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 

scripts/docker-develop/Dockerfile

@@ -17,8 +17,8 @@ RUN apt-get update -q && \
 #   Git
 
 # Env variables
-ENV SCALA_VERSION 2.12.12
-ENV SBT_VERSION 1.4.9
+ENV SCALA_VERSION 2.12.14
+ENV SBT_VERSION 1.5.3
 
 #
 ## AdoptOpenJDK Hotspot

src/ci/bin/test.inc.sh

@@ -813,7 +813,7 @@ cromwell::private::install_sbt_launcher() {
     # Non-deb package installation instructions adapted from
     # - https://github.com/sbt/sbt/releases/tag/v1.4.9
     # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-    curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.4.9/sbt-1.4.9.tgz" |
+    curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
         sudo tar zxf - -C /usr/share
     sudo update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
 }
@@ -1147,9 +1147,9 @@ cromwell::private::assemble_jars() {
     # CROMWELL_BUILD_SBT_ASSEMBLY_COMMAND allows for an override of the default `assembly` command for assembly.
     # This can be useful to reduce time and memory that might otherwise be spent assembling unused subprojects.
     # shellcheck disable=SC2086
-    CROMWELL_SBT_ASSEMBLY_LOG_LEVEL=error \
-        sbt \
+    sbt \
         -Dsbt.supershell=false \
+        'set ThisBuild / assembly / logLevel := Level.Error' \
         --warn \
         ${CROMWELL_BUILD_SBT_COVERAGE_COMMAND} \
         --error \
@@ -1198,11 +1198,11 @@ cromwell::private::generate_code_coverage() {
 }
 
 cromwell::private::publish_artifacts_only() {
-    CROMWELL_SBT_ASSEMBLY_LOG_LEVEL=warn sbt -Dsbt.supershell=false --warn "$@" publish
+    sbt 'set ThisBuild / assembly / logLevel := Level.Warn' -Dsbt.supershell=false --warn "$@" publish
 }
 
 cromwell::private::publish_artifacts_and_docker() {
-    CROMWELL_SBT_ASSEMBLY_LOG_LEVEL=warn sbt -Dsbt.supershell=false --warn "$@" publish dockerBuildAndPush
+    sbt 'set ThisBuild / assembly / logLevel := Level.Warn' -Dsbt.supershell=false --warn "$@" publish dockerBuildAndPush
 }
 
 cromwell::private::publish_artifacts_check() {
@@ -1510,7 +1510,7 @@ cromwell:build::run_sbt_test() {
     sbt \
         -Dsbt.supershell=false \
         ${CROMWELL_BUILD_SBT_COVERAGE_COMMAND} \
-        test:compile
+        Test/compile
 
     local sbt_tests
 

src/ci/docker-compose/cromwell-test/docker-setup.sh

@@ -66,7 +66,7 @@ apt-get clean
 # non-deb package installation instructions adapted from
 # - https://github.com/sbt/sbt/releases/tag/v1.4.9
 # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.4.9/sbt-1.4.9.tgz" |
+curl -L --silent "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
     tar zxf - -C /usr/share
 update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1