Build updates incl. scala 2.12.12 and adoptopenjdk 11-hs BT-125 BT-126 (

broadinstitute#6194)

.circleci/config.yml

@@ -4,16 +4,6 @@ orbs:
   slack: circleci/[email protected]
   build-tools: circleci/[email protected]
 
-commands:
-  install_adoptopenjdk:
-    description: "Installing adoptopenjdk 8 and setting it as default Java"
-    steps:
-      - run: wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | sudo apt-key add -
-      - run: sudo add-apt-repository --yes https://adoptopenjdk.jfrog.io/adoptopenjdk/deb/
-      - run: sudo apt update
-      - run: sudo apt install adoptopenjdk-8-hotspot
-      - run: sudo update-java-alternatives --set adoptopenjdk-8-hotspot-amd64
-
 jobs:
   test:
     parameters:
@@ -41,7 +31,6 @@ jobs:
             if [[ -z "${CI_PULL_REQUEST}" ]] && [[ "${BUILD_TYPE}" != "sbt" ]] ; then
               circleci-agent step halt
             fi
-      - install_adoptopenjdk
       - checkout
       - run:
           name: Custom step - configure GIT identity

.gitignore

@@ -2,6 +2,7 @@
 *~
 .DS_Store
 .artifactory
+.bsp
 .idea/*
 **/.idea/*
 .ensime_cache/*

.sdkmanrc

@@ -0,0 +1,3 @@
+# Enable auto-env through the sdkman_auto_env config
+# Add key=value pairs of SDKs to use below
+java=11.0.10.hs-adpt

.travis.yml

@@ -1,14 +1,10 @@
-sudo: required
-dist: xenial
+os: linux
+dist: focal
 services:
   - docker
-language: scala
-scala:
-  - 2.12.9
+language: minimal
 git:
   depth: false
-jdk:
-  - openjdk8
 cache:
   directories:
     - $HOME/.ivy2/cache
@@ -21,10 +17,7 @@ before_cache:
   - find $HOME/.coursier/cache -name "ivydata-*.properties" -print -delete
   - find $HOME/.sbt -name "*.lock" -print -delete
 env:
-  global:
-    - PYTHON3_HOME=/opt/python/3.7.1
-    - PATH=$PYTHON3_HOME/bin\:$PATH
-  matrix:
+  jobs:
     # Setting this variable twice will cause the 'script' section to run twice with the respective env var invoked
     - >-
       BUILD_TYPE=centaurAws
@@ -101,6 +94,16 @@ env:
       BUILD_TYPE=dockerScripts
     - >-
       BUILD_TYPE=sbt
+      BUILD_SBT_INCLUDE=engine
+    - >-
+      BUILD_TYPE=sbt
+      BUILD_SBT_INCLUDE=server
+    - >-
+      BUILD_TYPE=sbt
+      BUILD_SBT_INCLUDE=services
+    - >-
+      BUILD_TYPE=sbt
+      BUILD_SBT_EXCLUDE='engine|server|services'
     - >-
       BUILD_TYPE=dbms
     - >-

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 ## 60 Release Notes
 
+### Java 11
+
+As of this version, a distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and
+containerized using [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
+
 ### Hybrid metadata storage ("carboniting") removed
 
 Carboniting functionality has been removed from Cromwell. 

centaur/test_cromwell.sh

@@ -111,7 +111,7 @@ if [[ -n ${CROMWELL_BRANCH} ]]; then
     git checkout "${CROMWELL_BRANCH}"
     git pull
     echo "Building Cromwell"
-    sbt --warn assembly >> "${ASSEMBLY_LOG}" 2>&1
+    sbt -Dsbt.supershell=false --warn assembly >> "${ASSEMBLY_LOG}" 2>&1
     cd ..
     # This is the "branch" logic but sets the CROMWELL_JAR to be used in either the "branch" or "jar" use cases.
     # Note that this may not be necessary in the docker-compose use case.
@@ -124,11 +124,11 @@ cd "${RUN_DIR}"
 TEST_STATUS="failed"
 
 if [[ "${CENTAUR_SBT_COVERAGE}" == "true" ]]; then
-    sbt --warn coverage centaur/it:compile
-    CP=$(sbt --warn coverage "export centaur/it:dependencyClasspath" -error)
+    sbt -Dsbt.supershell=false --warn coverage centaur/it:compile
+    CP=$(sbt -no-colors --error coverage "export centaur/it:dependencyClasspath")
 else
-    sbt --warn centaur/it:compile
-    CP=$(sbt --warn "export centaur/it:dependencyClasspath" -error)
+    sbt -Dsbt.supershell=false --warn centaur/it:compile
+    CP=$(sbt -no-colors --error "export centaur/it:dependencyClasspath")
 fi
 
 # Add the it-classes folder to the classpath to ensure logback configuration files are picked up.

codegen_java/build.sbt

@@ -6,10 +6,10 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.12.8",
+    scalaVersion := "2.12.12",
     scalacOptions ++= Seq("-feature"),
-    javacOptions in compile ++= Seq("-Xlint:deprecation"),
-    publishArtifact in (Compile, packageDoc) := false,
+    compile / javacOptions ++= Seq("-Xlint:deprecation"),
+    Compile / packageDoc / publishArtifact := false,
     resolvers += Resolver.mavenLocal,
     updateOptions := updateOptions.value.withGigahorse(false),
     libraryDependencies ++= Seq(
@@ -25,4 +25,3 @@ lazy val root = (project in file(".")).
       "com.novocode" % "junit-interface" % "0.10" % "test"
     )) ++ publishSettings:_*
   )
-

codegen_java/project/Publishing.scala

@@ -24,8 +24,8 @@ import Artifactory._
   //priority over the local package cache. see here: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
     Seq(
       publishTo := Option(artifactoryResolver(false)),
-      publishArtifact in Compile := true,
-      publishArtifact in Test := true,
+      Compile / publishArtifact := true,
+      Test / publishArtifact := true,
       credentials += artifactoryCredentials
     )
 

codegen_java/project/build.properties

@@ -1 +1 @@
-sbt.version=1.2.6
+sbt.version=1.4.9

docs/Releases.md

@@ -18,7 +18,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-[Java 8](http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html) is required to run Cromwell.
+A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 

docs/WOMtool.md

@@ -6,7 +6,7 @@ The following is the toolchain used for development of womtool.  Other versions
 
 * [Scala 2.12](http://www.scala-lang.org/)
 * [SBT 1.x](https://www.scala-sbt.org/)
-* [Java 8](http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html)
+* [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/)
 * [Git](https://git-scm.com/)
 
 ## Building

docs/developers/Building.md

@@ -5,7 +5,7 @@ features or fixes, the following are required to build Cromwell from source:
 
 * [Scala 2.12](http://www.scala-lang.org/)
 * [SBT 1.x](https://www.scala-sbt.org/)
-* [Java 8](http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html)
+* [AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/)
 * [Git](https://git-scm.com/)
 
 You can also use the [development image](https://github.com/broadinstitute/cromwell/tree/develop/scripts/docker-develop), and build a development container to work inside:
@@ -47,4 +47,3 @@ $ sbt server/docker
 ```
 
 This will build and tag a Docker image with a name like `broadinstitute/cromwell:<VERSION>-SNAP`.
-

docs/developers/Centaur.md

@@ -16,7 +16,7 @@ There are two ways to invoke the integration tests:
 
 * `sbt "centaur/it:test"` - compiles and run via sbt directly, simple but also has the problem of running 2x cores tests in parallel which can overwhelm your Cromwell server if running in a development environment
 
-* `run_tests_parallel.sh [THREADS]` - runs the same tests with an enforced parallelism limit.  Defaults to `3` if not specified
+* `src/ci/bin/testCentaurLocal.sh` - runs the same tests using the continuous integration pipeline configuration
 
 ### Tags
 

project/ContinuousIntegration.scala

@@ -50,10 +50,10 @@ object ContinuousIntegration {
 
   def aggregateSettings(rootProject: Project): Seq[Setting[_]] = List(
     // Before compiling, check if the expected projects are aggregated so that they will be compiled-and-tested too.
-    compile in Compile := {
+    Compile / compile := {
       streams.value.log // make sure logger is loaded
       validateAggregatedProjects(rootProject, state.value)
-      (compile in Compile).value
+      (Compile / compile).value
     },
   )
 

project/Merging.scala

@@ -23,7 +23,7 @@ object Merging {
         case "maven" :: "com.google.guava" :: xs =>
           MergeStrategy.first
         case _ =>
-          val oldStrategy = (assemblyMergeStrategy in assembly).value
+          val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
       }
     case x@PathList("OSGI-INF", path@_*) =>
@@ -33,15 +33,15 @@ object Merging {
         case "l10n" :: "bundle.properties" :: Nil =>
           MergeStrategy.concat
         case _ =>
-          val oldStrategy = (assemblyMergeStrategy in assembly).value
+          val oldStrategy = (assembly / assemblyMergeStrategy).value
           oldStrategy(x)
       }
     case "asm-license.txt" | "module-info.class" | "overview.html" | "cobertura.properties" =>
       MergeStrategy.discard
     case PathList("mime.types") =>
       MergeStrategy.last
     case x =>
-      val oldStrategy = (assemblyMergeStrategy in assembly).value
+      val oldStrategy = (assembly / assemblyMergeStrategy).value
       oldStrategy(x)
   }
 }