Merge branch 'develop'

.gitignore

@@ -1,5 +1,12 @@
-tags
-.idea/
-target
-.artifactory
+# common scala config
 *~
+.DS_Store
+.artifactory
+.idea/*
+!/.idea/inspectionProfiles/
+.idea/inspectionProfiles/*
+!/.idea/inspectionProfiles/Project_Default.xml
+target
+
+# custom config
+tags

.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="TypeAnnotation" enabled="false" level="WARNING" enabled_by_default="false" />
+  </profile>
+</component>

.pullapprove.yml

@@ -5,10 +5,11 @@ author_approval: ignored
 reviewers:
     required: 2
     members:
-        - cjllanwarne
         - Horneth
-        - mcovarr
+        - cjllanwarne
         - geoffjentry
-        - kshakir
+        - katevoss
         - kcibul
+        - kshakir
+        - mcovarr
         - ruchim

build.sbt

@@ -10,7 +10,7 @@ scalaVersion := "2.11.8"
 
 lazy val versionSettings = Seq(
   // Upcoming release, or current if we're on the master branch
-  git.baseVersion := "0.8",
+  git.baseVersion := "0.9",
 
   // Shorten the git commit hash
   git.gitHeadCommit := git.gitHeadCommit.value map { _.take(7) },
@@ -34,7 +34,7 @@ resolvers ++= Seq(
 )
 
 libraryDependencies ++= Seq(
-  "org.broadinstitute" %% "wdl4s" % "0.8",
+  "org.broadinstitute" %% "wdl4s" % "0.10",
   //---------- Test libraries -------------------//
   "org.scalatest" %% "scalatest" % "2.2.5" % Test
 )

src/main/scala/wdltool/GraphPrint.scala

@@ -10,7 +10,8 @@ object GraphPrint {
   case class WorkflowDigraph(workflowName: String, digraph: Set[String])
 
   def generateWorkflowDigraph(file: String, allNodesMode: Boolean): WorkflowDigraph = {
-    val namespace = WdlNamespaceWithWorkflow.load(Files.readAllLines(Paths.get(file)).asScala.mkString(System.lineSeparator()), Seq(WdlNamespace.fileResolver _))
+    // It's ok to use .get here, we're happy to throw an exception and crash the program!
+    val namespace = WdlNamespaceWithWorkflow.load(Files.readAllLines(Paths.get(file)).asScala.mkString(System.lineSeparator()), Seq(WdlNamespace.fileResolver _)).get
 
     val digraph = if (allNodesMode) {
       listAllGraphNodes(namespace)

src/main/scala/wdltool/Main.scala

@@ -94,7 +94,7 @@ object Main extends App {
   private[this] def continueIf(valid: => Boolean)(block: => Termination): Termination = if (valid) block else BadUsageTermination
 
   private[this] def loadWdl(path: String)(f: WdlNamespace => Termination): Termination = {
-    Try(WdlNamespace.loadUsingPath(Paths.get(path), None, None)) match {
+    WdlNamespace.loadUsingPath(Paths.get(path), None, None) match {
       case Success(namespace) => f(namespace)
       case Failure(t) => UnsuccessfulTermination(t.getMessage)
     }