Updated build and dependencies: (#402)

- Scala 2.13 only (and updated to 2.13.8)
- Updated to sbt 1.6.2
- Updated sbt plugins to match
- Updated various dependencies

build.sbt

@@ -44,7 +44,7 @@ releaseProcess := Seq[ReleaseStep](
 // For the aggregate (root) jar, override the name.  For the sub-projects,
 // see the build.sbt in each project folder.
 ////////////////////////////////////////////////////////////////////////////////////////////////
-assemblyJarName in assembly := "dagr-" + version.value + ".jar"
+assembly / assemblyJarName := "dagr-" + version.value + ".jar"
 
 ////////////////////////////////////////////////////////////////////////////////////////////////
 // Sonatype settings
@@ -58,7 +58,7 @@ lazy val sonatypeSettings = Seq(
       else
         Some("releases"  at nexus + "service/local/staging/deploy/maven2")
     },
-    publishArtifact in Test := false,
+    Test / publishArtifact := false,
     pomIncludeRepository := { _ => false },
     // For Travis CI - see http://www.cakesolutions.net/teamblogs/publishing-artefacts-to-oss-sonatype-nexus-using-sbt-and-travis-ci
     credentials ++= (for {
@@ -88,31 +88,32 @@ lazy val commonSettings = Seq(
   organizationHomepage := Some(url("http://www.fulcrumgenomics.com")),
   homepage             := Some(url("http://github.com/fulcrumgenomics/dagr")),
   startYear            := Some(2015),
-  scalaVersion         := "2.13.0",
-  crossScalaVersions   := Seq("2.12.8", "2.13.0"),
+  scalaVersion         := "2.13.8",
+  crossScalaVersions   := Seq("2.13.8"),
   scalacOptions        ++= Seq("-target:jvm-1.8", "-deprecation"),
-  scalacOptions in (Compile, doc) ++= docScalacOptions,
-  scalacOptions in (Test, doc) ++= docScalacOptions,
+  Compile / doc / scalacOptions ++= docScalacOptions,
+  Test / doc/ scalacOptions  ++= docScalacOptions,
+  useCoursier          := false,
   autoAPIMappings := true,
-  testOptions in Test  += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
-  testOptions in Test  += Tests.Argument("-l", "LongRunningTest"), // ignores long running tests
+  Test / testOptions  += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
+  Test / testOptions  += Tests.Argument("-l", "LongRunningTest"), // ignores long running tests
   // uncomment for full stack traces
   //testOptions in Test  += Tests.Argument("-oD"),
-  fork in Test         := true,
+  Test / fork          := true,
   resolvers            += Resolver.jcenterRepo,
   resolvers            += Resolver.sonatypeRepo("public"),
   resolvers            += Resolver.mavenLocal,
   shellPrompt          := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
   coverageExcludedPackages := "<empty>;dagr\\.tasks.*;dagr\\.pipelines.*",
   updateOptions        := updateOptions.value.withCachedResolution(true),
-  javaOptions in Test += "-Ddagr.color-status=false",
+  Test / javaOptions   += "-Ddagr.color-status=false",
   // Needed to avoid "sbt.ForkMain failed with exit code 137"
   //in Travis with `sudo: false`.
   // See https://github.com/sbt/sbt/issues/653
   // and https://github.com/travis-ci/travis-ci/issues/3775
-  javaOptions in Test += "-Xmx1G",
+  Test / javaOptions += "-Xmx1G",
   libraryDependencies += "org.scalatest" %% "scalatest" % "3.0.8" % "test->*" excludeAll ExclusionRule(organization="org.junit", name="junit"),
-  assemblyJarName in assembly := s"${name.value}-${version.value}.jar"
+  assembly / assemblyJarName  := s"${name.value}-${version.value}.jar"
 ) ++ Defaults.coreDefaultSettings ++ sonatypeSettings
 
 ////////////////////////////////////////////////////////////////////////////////////////////////
@@ -123,15 +124,15 @@ lazy val core = Project(id="dagr-core", base=file("core"))
   .settings(description := "Core methods and classes to execute tasks in dagr.")
   .settings(
     libraryDependencies ++= Seq(
-      "com.fulcrumgenomics" %%  "commons"           %  "1.2.0",
-      "com.fulcrumgenomics" %%  "sopt"              %  "1.0.0",
-      "com.github.dblock"   %   "oshi-core"         %  "3.3",
+      "com.fulcrumgenomics" %%  "commons"           %  "1.4.0",
+      "com.fulcrumgenomics" %%  "sopt"              %  "1.1.0",
+      "com.github.oshi"     %   "oshi-core"         % "6.1.4",
       "org.scala-lang"      %   "scala-reflect"     %  scalaVersion.value,
       "org.scala-lang"      %   "scala-compiler"    %  scalaVersion.value,
       "org.reflections"     %   "reflections"       %  "0.9.10",
-      "com.typesafe"        %   "config"            %  "1.3.2",
+      "com.typesafe"        %   "config"            %  "1.4.2",
       "javax.servlet"       %   "javax.servlet-api" %  "3.1.0",
-      "jline"               %   "jline"             %  "2.14.2"
+      "jline"               %   "jline"             %  "2.14.6"
     )
   )
   .disablePlugins(sbtassembly.AssemblyPlugin)
@@ -151,8 +152,8 @@ lazy val tasks = Project(id="dagr-tasks", base=file("tasks"))
   .settings(commonSettings: _*)
   .settings(
     libraryDependencies ++= Seq(
-      "com.github.samtools"       % "htsjdk"     % "2.16.1" excludeAll(htsjdkAndPicardExcludes: _*),
-      "com.github.broadinstitute" % "picard"     % "2.18.16" excludeAll(htsjdkAndPicardExcludes: _*)
+      "com.github.samtools"       % "htsjdk"     % "2.24.1" excludeAll(htsjdkAndPicardExcludes: _*),
+      "com.github.broadinstitute" % "picard"     % "2.26.11" excludeAll(htsjdkAndPicardExcludes: _*)
     )
   )
   .disablePlugins(sbtassembly.AssemblyPlugin)
@@ -171,8 +172,8 @@ lazy val pipelines = Project(id="dagr-pipelines", base=file("pipelines"))
 // root (dagr) project
 ////////////////////////////////////////////////////////////////////////////////////////////////
 lazy val assemblySettings = Seq(
-  test in assembly     := {},
-  logLevel in assembly := Level.Info
+  assembly / test     := {},
+  assembly / logLevel := Level.Info
 )
 lazy val root = Project(id="dagr", base=file("."))
   .settings(commonSettings: _*)
@@ -216,4 +217,5 @@ val customMergeStrategy: String => MergeStrategy = {
     MergeStrategy.first
   case _ => MergeStrategy.deduplicate
 }
-assemblyMergeStrategy in assembly := customMergeStrategy
+
+assembly / assemblyMergeStrategy := customMergeStrategy

core/src/main/scala/dagr/core/cmdline/DagrCoreMain.scala

@@ -279,8 +279,7 @@ class DagrCoreMain extends LazyLogging {
         }
         new DagrScriptManager().loadScripts(
           scripts,
-          Files.createTempDirectory(PathUtil.pathTo(System.getProperty("java.io.tmpdir")), "dagrScripts"),
-          quiet = false
+          Files.createTempDirectory(PathUtil.pathTo(System.getProperty("java.io.tmpdir")), "dagrScripts")
         )
       case _ => false
     }

core/src/main/scala/dagr/core/cmdline/DagrScriptManager.scala

@@ -26,17 +26,17 @@
 
 package dagr.core.cmdline
 
-import java.net.{URL, URLClassLoader}
-import java.nio.file.Path
-
-import com.fulcrumgenomics.commons.io.Io
-import com.fulcrumgenomics.commons.util.{LazyLogging, LogLevel}
 import com.fulcrumgenomics.commons.CommonsDef._
+import com.fulcrumgenomics.commons.io.Io
+import com.fulcrumgenomics.commons.util.LazyLogging
 import org.reflections.util.ClasspathHelper
 
-import scala.reflect.internal.util.{FakePos, NoPosition, Position, StringOps}
+import java.net.{URL, URLClassLoader}
+import java.nio.file.Path
+import scala.reflect.internal.util.Position
 import scala.tools.nsc.io.PlainFile
-import scala.tools.nsc.reporters.AbstractReporter
+import scala.reflect.internal.Reporter
+import scala.tools.nsc.reporters.{FilteringReporter}
 import scala.tools.nsc.{Global, Settings}
 
 object DagrScriptManager {
@@ -60,89 +60,22 @@ object DagrScriptManager {
     * NSC (New Scala Compiler) reporter which logs to Log4J.
     * Heavily based on scala/src/compiler/scala/tools/nsc/reporters/ConsoleReporter.scala
     */
-  private class DagrReporter(val settings: Settings, val quiet: Boolean = false) extends AbstractReporter with LazyLogging {
-    def displayPrompt(): Unit = {
-      throw new UnsupportedOperationException("Unable to prompt the user.  Prompting should be off.")
-    }
-
-    /**
-      * Displays the message at position with severity.
-      * @param posIn Position of the event in the file that generated the message.
-      * @param msg Message to display.
-      * @param severity Severity of the event.
-      */
-    def display(posIn: Position, msg: String, severity: Severity): Unit = {
-      severity.count += 1
-      val level = severity match {
-        case INFO => LogLevel.Info
-        case WARNING => LogLevel.Warning
-        case ERROR => LogLevel.Error
-      }
-
-      val p2 = Option(posIn) match {
-        case None => NoPosition
-        case Some(p) if p.isDefined => p.finalPosition //posIn.inUltimateSource(posIn.source)
-        case Some(p) => p
-      }
-
-      p2 match {
-        case FakePos(fmsg) =>
-          printMessage(level, s"$fmsg $msg")
-        case NoPosition =>
-          printMessage(level, msg)
-        case pos: Position =>
-          val file = pos.source.file
-          printMessage(level, file.name + ":" + pos.line + ": " + msg)
-          printSourceLine(level, pos)
-      }
-    }
-
-    /**
-      * Prints the source code line of an event followed by a pointer within the line to the error.
-      * @param level Severity level.
-      * @param pos Position in the file of the event.
-      */
-    private def printSourceLine(level: LogLevel, pos: Position): Unit = {
-      printMessage(level, pos.lineContent.stripLineEnd)
-      printColumnMarker(level, pos)
-    }
-
-    /**
-      * Prints the column marker of the given position.
-      * @param level Severity level.
-      * @param pos Position in the file of the event.
-      */
-    private def printColumnMarker(level: LogLevel, pos: Position): Unit = {
-      if (pos.isDefined) {
-        printMessage(level, " " * (pos.column - 1) + "^")
-      }
-    }
-
-    /**
-      * Prints a summary count of warnings and errors.
-      */
-    def printSummary(): Unit = {
-      if (WARNING.count > 0)
-        printMessage(LogLevel.Warning, StringOps.countElementsAsString(WARNING.count, "warning") + " found")
-      if (ERROR.count > 0)
-        printMessage(LogLevel.Error, StringOps.countElementsAsString(ERROR.count, "error") + " found")
-    }
-
-    /**
-      * Prints the message at the severity level.
-      * @param level Severity level.
-      * @param message Message content.
-      */
-    private def printMessage(level: LogLevel, message: String): Unit = {
-      if (!quiet) {
-        level match {
-          case LogLevel.Debug   => logger.debug(message)
-          case LogLevel.Info    => logger.info(message)
-          case LogLevel.Warning => logger.warning(message)
-          case LogLevel.Error   => logger.error(message)
-          case LogLevel.Fatal   => logger.fatal(message)
-          case _ => throw new DagrScriptManagerException(s"Could not determine log level: $level")
-        }
+  private class DagrReporter(val settings: Settings) extends FilteringReporter with LazyLogging {
+    var errors: Int = 0
+    var warnings: Int = 0
+    var infos: Int = 0
+
+    override def doReport(pos: Position, msg: String, severity: Severity): Unit = {
+      severity match {
+        case Reporter.INFO    =>
+          infos += 1
+          logger.info(msg)
+        case Reporter.WARNING =>
+          warnings += 1
+          logger.warning(msg)
+        case Reporter.ERROR   =>
+          errors += 1
+          logger.error(msg)
       }
     }
   }
@@ -156,7 +89,7 @@ private[core] class DagrScriptManager extends LazyLogging {
     * Compiles and loads the scripts in the files into the current classloader.
     * Heavily based on scala/src/compiler/scala/tools/ant/Scalac.scala
     */
-  def loadScripts(scripts: Iterable[Path], tempDir: Path, quiet: Boolean = true): Unit = {
+  def loadScripts(scripts: Iterable[Path], tempDir: Path): Unit = {
     // Make sure the scripts actually exist and we can write to the tempDir
     Io.assertReadable(scripts)
     Io.assertWritableDirectory(tempDir)
@@ -173,29 +106,26 @@ private[core] class DagrScriptManager extends LazyLogging {
         settings.classpath.append(url.getPath)
       })
 
-      val reporter = new DagrReporter(settings, quiet)
+      val reporter = new DagrReporter(settings)
       val compiler: Global = new Global(settings, reporter)
       val run = new compiler.Run
 
-      if (!quiet) {
-        logger.info("Compiling %s Dagr Script%s".format(scripts.size, plural(scripts.size)))
-        logger.debug("Compilation directory: " + settings.outdir.value)
-      }
+      logger.info("Compiling %s Dagr Script%s".format(scripts.size, plural(scripts.size)))
+      logger.debug("Compilation directory: " + settings.outdir.value)
       run.compileFiles(scripts.toList.map(script => new PlainFile(script.toFile)))
 
       // add `tempDir` to the classpath
       if (!reporter.hasErrors) addToClasspath(urls = Seq(tempDir.toUri.toURL))
 
-      reporter.printSummary()
       if (reporter.hasErrors) {
-        val msg = "Compile of %s failed with %d error%s".format(scripts.mkString(", "), reporter.ERROR.count, plural(reporter.ERROR.count))
+        val msg = "Compile of %s failed with %d error%s".format(scripts.mkString(", "), reporter.errors, plural(reporter.errors))
         throw new DagrScriptManagerException(msg)
       }
-      else if (reporter.WARNING.count > 0) {
-        if (!quiet) logger.warning("Compile succeeded with %d warning%s".format(reporter.WARNING.count, plural(reporter.WARNING.count)))
+      else if (reporter.warnings > 0) {
+        logger.warning("Compile succeeded with %d warning%s".format(reporter.warnings, plural(reporter.warnings)))
       }
       else {
-        if (!quiet) logger.info("Compilation complete")
+        logger.info("Compilation complete")
       }
     }
   }

project/build.properties

@@ -1 +1 @@
-sbt.version=1.1.6
+sbt.version=1.6.2

project/plugins.sbt

@@ -1,9 +1,10 @@
-resolvers += Resolver.url("fix-sbt-plugin-releases", url("http://dl.bintray.com/sbt/sbt-plugin-releases"))(Resolver.ivyStylePatterns)
+resolvers += Resolver.url("fix-sbt-plugin-releases", url("https://dl.bintray.com/sbt/sbt-plugin-releases"))(Resolver.ivyStylePatterns)
 
-addSbtPlugin("com.typesafe.sbt"  % "sbt-git"       % "0.9.3")
-addSbtPlugin("com.github.gseitz" % "sbt-release"   % "1.0.6")
-addSbtPlugin("com.eed3si9n"      % "sbt-assembly"  % "0.14.6")
-addSbtPlugin("org.scoverage"     % "sbt-scoverage" % "1.6.0")
-addSbtPlugin("org.xerial.sbt"    % "sbt-sonatype"  % "2.2")
-addSbtPlugin("com.jsuereth"      % "sbt-pgp"       % "1.1.0")
-addSbtPlugin("net.virtual-void"  % "sbt-dependency-graph" % "0.9.0")
+addDependencyTreePlugin
+
+addSbtPlugin("com.typesafe.sbt"  % "sbt-git"       % "1.0.0")
+addSbtPlugin("com.github.gseitz" % "sbt-release"   % "1.0.10")
+addSbtPlugin("com.eed3si9n"      % "sbt-assembly"  % "1.2.0")
+addSbtPlugin("org.scoverage"     % "sbt-scoverage" % "1.6.1")
+addSbtPlugin("org.xerial.sbt"    % "sbt-sonatype"  % "3.9.4")
+addSbtPlugin("com.jsuereth"      % "sbt-pgp"       % "2.0.1")