Changing to the mill build system

.coveragerc

@@ -0,0 +1,2 @@
+[html]
+directory = out/commons/scoverage/htmlReport

.gitignore

@@ -1,2 +1,2 @@
 .idea
-target
+out

.travis.yml

@@ -1,24 +1,24 @@
 sudo: required
 language: scala
 scala:
-- 2.12.2
+  - 2.12.2
 jdk:
-- oraclejdk8
+  - oraclejdk8
 script:
-- sbt +clean coverage +test && sbt coverageReport coverageAggregate
-- find $HOME/.sbt -name "*.lock" | xargs rm
-- find $HOME/.ivy2 -name "ivydata-*.properties" | xargs rm
+  - curl -L -o ~/bin/mill https://github.com/lihaoyi/mill/releases/download/0.4.0/0.4.0-9-1db2ee && chmod +x ~/bin/mill
+  - export PATH=~/bin/mill:$PATH
+  - mill __.clean && mill __.test && mill __.scoverage.xmlReport 
 cache:
   directories:
-  - "$HOME/.ivy2/cache"
-  - "$HOME/.sbt/boot/"
+    - "$HOME/.ivy2/cache"
+    - "$HOME/.coursier"
+
 before_install:
-- pip install --user codecov
-- sudo chmod +x /usr/local/bin/sbt
+  - pip install --user codecov
 after_success:
 - codecov
 - test "$TRAVIS_REPO_SLUG" == 'fulcrumgenomics/commons' && test "$TRAVIS_PULL_REQUEST"
-  == 'false' && test "$TRAVIS_BRANCH" == 'master' && sbt +publish
+  == 'false' && test "$TRAVIS_BRANCH" == 'master' && mill mill.scalalib.PublishModule/publishAll "${SONATYPE_USERNAME}:${SONATYPE_PASSWORD}" __.publishArtifacts --release true
 env:
   global:
   - secure: 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

README.md

@@ -3,7 +3,6 @@
 [![Code Review](https://api.codacy.com/project/badge/grade/52e1d786d9784c7192fae2f8e853fa34)](https://www.codacy.com/app/contact_32/commons)
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/com.fulcrumgenomics/commons_2.11/badge.svg)](https://maven-badges.herokuapp.com/maven-central/com.fulcrumgenomics/commons_2.11)
 [![Javadocs](http://javadoc.io/badge/com.fulcrumgenomics/commons_2.12.svg)](http://javadoc.io/doc/com.fulcrumgenomics/commons_2.12)
-[![Dependency Status](https://www.versioneye.com/user/projects/56b2d2d593b95a003c714340/badge.svg)](https://www.versioneye.com/user/projects/56b2d2d593b95a003c714340#dialog_dependency_badge)
 [![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/fulcrumgenomics/commons/blob/master/LICENSE)
 [![Language](http://img.shields.io/badge/language-scala-brightgreen.svg)](http://www.scala-lang.org/)
 

build.sc

@@ -0,0 +1,56 @@
+// IMPORTANT: the version of the contrib modules must be 0.4.0-9-1db2ee or later.
+// IMPORTANT: if you change this version to a release, please update the .travis.yml
+// FIXME: change to a release version after 0.4.0-9-1db2ee
+import $ivy.`com.lihaoyi::mill-contrib-buildinfo:0.4.0-9-1db2ee`
+import mill.contrib.scoverage.ScoverageModule
+
+import mill.scalalib.{PublishModule, Dep, DepSyntax, ScalaModule}
+import mill.scalalib.publish.{PomSettings, License, Developer, SCM}
+import ammonite.ops._
+
+import scala.sys.process.Process
+
+object commons extends ScalaModule with ScoverageModule with PublishModule {
+  def artifactName = "commons"
+  def gitHash = Process("git rev-parse --short HEAD").lineStream.head
+  def publishVersion = s"0.6.0-${gitHash}-SNAPSHOT"
+  def scalaVersion = "2.12.8"
+  def scoverageVersion = "1.3.1"
+  def scalacOptions = Seq("-target:jvm-1.8", "-deprecation", "-unchecked")
+
+  // TODO: start year (2015)
+  // TODO: organization homepage ("http://www.fulcrumgenomics.com")
+  def pomSettings = PomSettings(
+    description = artifactName(),
+    organization = "com.fulcrumgenomics",
+    url = "https://github.com/fulcrumgenomics/commons",
+    licenses = Seq(License("MIT license", "http://www.opensource.org/licenses/mit-license.php")),
+    scm = SCM(
+      "git://github.com/fulcrumgenomics/commons.git",
+      "scm:git://github.com/fulcrumgenomics/commons.git"
+    ),
+    developers = Seq(
+      Developer("nh13", "Nils Homer", "https://github.com/nh13"),
+      Developer("tfenne", "Tim Fennell", "https://github.com/tfenne")
+    )
+  )
+
+  def ivyDeps = Agg(
+    ivy"org.scala-lang:scala-compiler:${scalaVersion()}",
+    ivy"com.typesafe:config:1.3.2"
+  )
+
+  // TODO: ignore long running tests with "-l LongRunningTest"
+  object test extends ScoverageTests {
+    def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.0.5")
+    def testFrameworks = Seq("org.scalatest.tools.Framework")
+  }
+
+  private def deployJar(assembly: PathRef, jarName:String) = {
+    mkdir(pwd / 'jars)
+    println(s"Copying artifact ${assembly.path} to jars / $jarName")
+    cp.over(assembly.path, pwd / 'jars / jarName)
+  }
+
+  def assemblyJar = T { deployJar(assembly(), s"commons-${publishVersion()}.jar") }
+}

src/test/scala/com/fulcrumgenomics/commons/io/AsyncStreamSinkTest.scala → commons/test/src/com/fulcrumgenomics/commons/io/AsyncStreamSinkTest.scala

@@ -35,7 +35,7 @@ import scala.collection.mutable
   */
 class AsyncStreamSinkTest extends UnitSpec {
   "AsyncStreamSink" should "capture all the output" in {
-    val file = Paths.get("src/test/resources/com/fulcrumgenomics/commons/io/async-stream-sink-test.txt")
+    val file = Paths.get("commons/test/resources/com/fulcrumgenomics/commons/io/async-stream-sink-test.txt")
     val expected = Io.toSource(file).getLines().toList
 
     val proc = new ProcessBuilder("cat", file.toString).start()

src/test/scala/com/fulcrumgenomics/commons/io/IoTest.scala → commons/test/src/com/fulcrumgenomics/commons/io/IoTest.scala

@@ -166,7 +166,7 @@ class IoTest extends UnitSpec {
   }
 
   // The expected lines from the file loaded as a resource
-  private val ResourceLines = Io.readLines(Paths.get("src/test/resources/com/fulcrumgenomics/commons/io/to-lines-from-resource-test.txt")).toList
+  private val ResourceLines = Io.readLines(Paths.get("commons/test/resources/com/fulcrumgenomics/commons/io/to-lines-from-resource-test.txt")).toList
 
   "Io.readLinesFromResource" should "read lines from a resource" in {
     val actual = Io.readLinesFromResource("/com/fulcrumgenomics/commons/io/to-lines-from-resource-test.txt").toList