Merge pull request #9 from biopet/BIOPET-927

Update plugin to sbt 1.0.2

.travis.yml

@@ -4,7 +4,7 @@ scala:
   - 2.11.11
 
 script:
-  - sbt clean scripted headerCheck
+  - sbt clean scripted scalafmt headerCheck
   - "git diff --exit-code || (echo ERROR: Git changes detected, please regenerate the readme and run scalafmt with: sbt headerCreate scalafmt && exit 1)"
 #after_success:
 #  - sbt coveralls

build.sbt

@@ -21,7 +21,7 @@ publishMavenStyle := true
 
 sbtPlugin := true
 
-scalaVersion := "2.10.6"
+scalaVersion := "2.12.3"
 
 resolvers += Resolver.sonatypeRepo("snapshots")
 
@@ -34,7 +34,6 @@ publishTo := {
     Some(Opts.resolver.sonatypeStaging)
 }
 
-ScriptedPlugin.scriptedSettings
 scriptedLaunchOpts := { scriptedLaunchOpts.value ++
   Seq("-Xmx1024M",
     "-Dplugin.version=" + version.value)
@@ -72,32 +71,32 @@ libraryDependencies ++= Seq(
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "org.planet42" % "laika-sbt" % "0.7.0",
+    "org.planet42" % "laika-sbt" % "0.7.5",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "com.eed3si9n" % "sbt-assembly" % "0.14.5",
+    "com.eed3si9n" % "sbt-assembly" % "0.14.6",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "com.jsuereth" % "sbt-pgp" % "1.0.0",
+    "com.jsuereth" % "sbt-pgp" % "1.1.0",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "org.xerial.sbt" % "sbt-sonatype" % "1.1",
+    "org.xerial.sbt" % "sbt-sonatype" % "2.0",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "com.typesafe.sbt" % "sbt-site" % "1.3.1",
+    "com.typesafe.sbt" % "sbt-site" % "1.3.2",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "com.github.gseitz" % "sbt-release" % "1.0.6",
+    "com.github.gseitz" % "sbt-release" % "1.0.7",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
@@ -112,12 +111,12 @@ libraryDependencies ++= Seq(
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "de.heikoseeberger" % "sbt-header" % "4.0.0",
+    "de.heikoseeberger" % "sbt-header" % "4.1.0",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   ),
   Defaults.sbtPluginExtra(
-    "com.lucidchart" % "sbt-scalafmt" % "1.10",
+    "com.lucidchart" % "sbt-scalafmt" % "1.15",
     (sbtBinaryVersion in pluginCrossBuild).value,
     (scalaBinaryVersion in pluginCrossBuild).value
   )

project/build.properties

@@ -1 +1 @@
-sbt.version=0.13.16
+sbt.version=1.0.2

project/plugins.sbt

@@ -1,12 +1,9 @@
-addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.5")
-addSbtPlugin("com.lucidchart" % "sbt-scalafmt" % "1.10")
+addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "0.14.6")
+addSbtPlugin("com.lucidchart" % "sbt-scalafmt" % "1.15")
 addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.5.1")
-addSbtPlugin("com.github.gseitz" % "sbt-release" % "1.0.6")
-addSbtPlugin("com.jsuereth" % "sbt-pgp" % "1.0.0")
-addSbtPlugin("org.xerial.sbt" % "sbt-sonatype" % "1.1")
+addSbtPlugin("com.github.gseitz" % "sbt-release" % "1.0.7")
+addSbtPlugin("com.jsuereth" % "sbt-pgp" % "1.1.0")
+addSbtPlugin("org.xerial.sbt" % "sbt-sonatype" % "2.0")
 addSbtPlugin("org.scoverage" % "sbt-coveralls" % "1.2.2")
 addSbtPlugin("com.typesafe.sbt" % "sbt-git" % "0.9.3")
-addSbtPlugin("org.planet42" % "laika-sbt" % "0.7.0")
-addSbtPlugin("com.typesafe.sbt" % "sbt-site" % "1.3.1")
-addSbtPlugin("com.typesafe.sbt" % "sbt-ghpages" % "0.6.2")
-addSbtPlugin("de.heikoseeberger" % "sbt-header" % "4.0.0")
+addSbtPlugin("de.heikoseeberger" % "sbt-header" % "4.1.0")

project/scripted.sbt

@@ -1 +1 @@
-libraryDependencies += { "org.scala-sbt" % "scripted-plugin" % sbtVersion.value }
+libraryDependencies += { "org.scala-sbt" %% "scripted-plugin" % sbtVersion.value }

src/main/scala/nl/biopet/sbtbiopet/BiopetPlugin.scala

@@ -40,7 +40,7 @@ import com.typesafe.sbt.site.laika.LaikaSitePlugin
 import com.typesafe.sbt.site.laika.LaikaSitePlugin.autoImport.LaikaSite
 import com.typesafe.sbt.site.{SitePlugin, SiteScaladocPlugin}
 import de.heikoseeberger.sbtheader.HeaderPlugin
-import laika.sbt.LaikaSbtPlugin.LaikaKeys.{Laika, rawContent}
+import laika.sbt.LaikaPlugin.autoImport.{Laika, laikaRawContent}
 import org.scoverage.coveralls.CoverallsPlugin
 import sbt.Keys._
 import sbt.{Def, _}
@@ -188,7 +188,7 @@ object BiopetPlugin extends AutoPlugin {
     siteSubdirName in SiteScaladoc := {
       if (isSnapshot.value) { "develop/api" } else s"${version.value}/api"
     },
-    rawContent in Laika := true, //Laika use raw HTML content in markdown.
+    laikaRawContent in Laika := true, //Laika use raw HTML content in markdown.
     includeFilter in ghpagesCleanSite := biopetCleanSiteFilter.value,
     biopetGenerateDocs := biopetGenerateDocsFunction().value,
     biopetGenerateReadme := biopetGenerateReadmeFunction().value,
@@ -201,16 +201,16 @@ object BiopetPlugin extends AutoPlugin {
    * The merge strategy that is used in biopet projects
    */
   protected def biopetMergeStrategy: String => MergeStrategy = {
-    case PathList(ps @ _ *) if ps.last endsWith "pom.properties" =>
+    case PathList(ps @ _*) if ps.last endsWith "pom.properties" =>
       MergeStrategy.first
-    case PathList(ps @ _ *) if ps.last endsWith "pom.xml" =>
+    case PathList(ps @ _*) if ps.last endsWith "pom.xml" =>
       MergeStrategy.first
     case x if Assembly.isConfigFile(x) =>
       MergeStrategy.concat
-    case PathList(ps @ _ *)
+    case PathList(ps @ _*)
         if Assembly.isReadme(ps.last) || Assembly.isLicenseFile(ps.last) =>
       MergeStrategy.rename
-    case PathList("META-INF", xs @ _ *) =>
+    case PathList("META-INF", xs @ _*) =>
       xs map {
         _.toLowerCase
       } match {
@@ -284,8 +284,7 @@ object BiopetPlugin extends AutoPlugin {
             f.getPath.contains("develop")
           } else {
             f.getPath.contains(s"${version.value}") ||
-            f.getPath == new java.io.File(ghpagesRepository.value,
-                                          "index.html").getPath
+            f.getPath == new java.io.File(ghpagesRepository.value, "index.html").getPath
           }
         }
       }
@@ -295,45 +294,71 @@ object BiopetPlugin extends AutoPlugin {
    * Accesses the tools main method to generate documentation using our custom built-in documentation function
    */
   protected def biopetGenerateDocsFunction(): Def.Initialize[Task[Unit]] =
-    Def.task[Unit] {
+    Def.taskDyn {
       if (biopetIsTool.value) {
-        import Attributed.data
-        val r = (runner in Compile).value
-        val args = Seq("--generateDocs",
-                       s"outputDir=${biopetDocsDir.value.toString}," +
-                         s"version=${version.value}," +
-                         s"release=${!isSnapshot.value}",
-                       version.value)
-        val classPath = (fullClasspath in Compile).value
-        r.run(
-            s"${(mainClass in assembly).value.get}",
-            data(classPath),
-            args,
-            streams.value.log
-          )
-          .foreach(sys.error)
-      }
+        Def
+          .task[Unit] {
+            val r = (runner in Compile).value
+            val classPath = (fullClasspath in Runtime).value
+
+            val streamsLogValue = streams.value.log
+
+            val args = Seq("--generateDocs",
+                           s"outputDir=${biopetDocsDir.value.toString}," +
+                             s"version=${version.value}," +
+                             s"release=${!isSnapshot.value}",
+                           version.value)
+
+            val mainClassString = (mainClass in assembly).value match {
+              case Some(x) => x
+              case _ =>
+                throw new IllegalStateException(
+                  "Mainclass should be defined for a tool.")
+            }
+            import Attributed.data
+            r.run(
+              mainClassString,
+              data(classPath),
+              args,
+              streamsLogValue
+            )
+
+          }
+          .dependsOn(compile in Compile)
+      } else Def.task[Unit] {}
     }
 
   /*
    * Accesses the tools main method to generate a README using our custom built-in documentation function
    */
   protected def biopetGenerateReadmeFunction(): Def.Initialize[Task[Unit]] =
-    Def
-      .task[Unit] {
-        if (biopetIsTool.value) {
-          import sbt.Attributed.data
-          val r: ScalaRun = (runner in Compile).value
-          val args = Seq("--generateReadme", biopetReadmePath.value.toString)
-          val classPath = (fullClasspath in Compile).value
-          r.run(
-              s"${(mainClass in assembly).value.get}",
+    Def.taskDyn {
+      if (biopetIsTool.value) {
+        Def
+          .task[Unit] {
+            val r = (runner in Compile).value
+            val classPath = (fullClasspath in Runtime).value
+
+            val args = Seq("--generateReadme", biopetReadmePath.value.toString)
+
+            val streamsLogValue = streams.value.log
+
+            val mainClassString = (mainClass in assembly).value match {
+              case Some(x) => x
+              case _ =>
+                throw new IllegalStateException(
+                  "Mainclass should be defined for a tool.")
+            }
+            import Attributed.data
+            r.run(
+              mainClassString,
               data(classPath),
               args,
-              streams.value.log
+              streamsLogValue
             )
-            .foreach(sys.error)
-        }
-      }
-      .dependsOn(compile in Compile)
+
+          }
+          .dependsOn(compile in Compile)
+      } else Def.task[Unit] {}
+    }
 }

src/sbt-test/sbtbiopet/developtool/project/plugins.sbt

@@ -1,7 +1,5 @@
 sys.props.get("plugin.version") match {
   case Some(x) => addSbtPlugin("com.github.biopet" % "sbt-biopet" % x)
-  case _ => addSbtPlugin("com.github.biopet" % "sbt-biopet" % "0.2-SNAPSHOT")
-  /* case _ => sys.error("""|The system property 'plugin.version' is not defined.
+  case _ => sys.error("""|The system property 'plugin.version' is not defined.
                          |Specify this property using the scriptedLaunchOpts -D.""".stripMargin)
- */
 }