Merge pull request #1 from fulcrumgenomics/update_skeleton_fix_deprec…

…ations

Update mill and fix up all deprecations.

.gitignore

@@ -2,3 +2,4 @@
 .idea_modules
 out
 jars
+.bsp

build.sc

@@ -1,31 +1,35 @@
+import coursier.maven.MavenRepository
+import mill._
+import mill.scalalib._
+import mill.scalalib.publish._
+
 import java.text.SimpleDateFormat
 import java.util.Date
 import java.util.jar.Attributes.Name.{IMPLEMENTATION_VERSION => ImplementationVersion}
 import scala.sys.process.Process
-import scala.util.{Failure, Success, Try}
-import mill._, scalalib._, publish._
-import coursier.maven.MavenRepository
 
 /** Base trait for build modules. */
 trait CommonModule extends SbtModule {
- def deployLocal(assembly: PathRef, jarName:String) = {
- os.makeDir.all(os.pwd / 'jars)
+ def deployLocal(assembly: PathRef, jarName: String): Unit = {
+ os.makeDir.all(os.pwd / Symbol("jars"))
  println(s"Copying artifact ${assembly.path} to jars / $jarName")
- os.copy(assembly.path, os.pwd / 'jars / jarName, replaceExisting=true)
+ os.copy(assembly.path, os.pwd / Symbol("jars") / jarName, replaceExisting=true)
  }
 
- override def repositories: Seq[coursier.Repository] = super.repositories ++ Seq(
- MavenRepository("https://oss.sonatype.org/content/repositories/public"),
- MavenRepository("https://oss.sonatype.org/content/repositories/snapshots"),
- MavenRepository("https://jcenter.bintray.com/"),
- MavenRepository("https://artifactory.broadinstitute.org/artifactory/libs-snapshot/")
- )
+ override def repositoriesTask = T.task {
+ super.repositoriesTask() ++ Seq(
+ MavenRepository("https://oss.sonatype.org/content/repositories/public"),
+ MavenRepository("https://oss.sonatype.org/content/repositories/snapshots"),
+ MavenRepository("https://jcenter.bintray.com/"),
+ MavenRepository("https://artifactory.broadinstitute.org/artifactory/libs-snapshot/")
+ )
+ }
 }
 
 /** A base trait for versioning modules. */
 trait ReleaseModule extends JavaModule {
  /** Execute Git arguments and return the standard output. */
- private def git(args: String*): String = os.proc("git", args).call().out.string.trim
+ private def git(args: String*): String = os.proc("git", args).call().out.text().trim
 
  /** Get the commit hash at the HEAD of this branch. */
  private def gitHead: String = git("rev-parse", "HEAD")
@@ -40,8 +44,8 @@ trait ReleaseModule extends JavaModule {
 
  /** The implementation version. */
  private def implementationVersion = T input {
- val prefix = s"${today}-${shortHash}"
- if (dirty) s"${prefix}-dirty" else prefix
+ val prefix = s"$today-$shortHash"
+ if (dirty) s"$prefix-dirty" else prefix
  }
 
  /** The version string `Target`. */
@@ -54,10 +58,10 @@ trait ReleaseModule extends JavaModule {
 
 object tools extends CommonModule with PublishModule with ReleaseModule {
  def scalaVersion = "2.13.8"
- def mainClass = Some("com.client.cmdline.ClientMain")
- def artifactName = "client-tools"
- def gitHash = Process("git rev-parse --short HEAD").lineStream.head
- def publishVersion = s"0.0.1-${gitHash}-SNAPSHOT"
+ override def mainClass = Some("com.client.cmdline.ClientMain")
+ override def artifactName = "client-tools"
+ def gitHash = Process("git rev-parse --short HEAD").lazyLines.head
+ def publishVersion = s"0.0.1-$gitHash-SNAPSHOT"
  def pomSettings = PomSettings(
  description = artifactName(),
  organization = "com.client",
@@ -77,25 +81,24 @@ object tools extends CommonModule with PublishModule with ReleaseModule {
  "com.google.cloud.genomics"
  )
 
- def ivyDeps = Agg(
+ override def ivyDeps = Agg(
  ivy"org.scala-lang:scala-compiler:${scalaVersion()}",
- ivy"mysql:mysql-connector-java:5.1.24",
  ivy"com.fulcrumgenomics:commons_2.13:1.1.0",
  ivy"com.fulcrumgenomics:sopt_2.13:1.1.0",
  ivy"com.fulcrumgenomics:fgbio_2.13:1.4.0-61dde53-SNAPSHOT".excludeOrg(orgsToExclude:_*),
  )
 
  object test extends Tests {
- def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
- def testFrameworks = Seq("org.scalatest.tools.Framework")
+ override def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
+ override def testFramework = "org.scalatest.tools.Framework"
 
  // run mill tools.test.singleTest com.client.x.y.x.TestClassName
  def singleTest(args: String*) = T.command {
  super.runMain("org.scalatest.run", args: _*)
  }
  }
 
- def javacOptions = Seq("-source", "1.8", "-target", "1.8")
+ override def javacOptions = Seq("-source", "1.8", "-target", "1.8")
 
  def deployLocal = T { super.deployLocal(assembly(), "client-tools.jar") }
 }

mill

@@ -3,14 +3,14 @@
 # This is a wrapper script, that automatically download mill from GitHub release pages
 # You can give the required mill version with MILL_VERSION env variable
 # If no version is given, it falls back to the value of DEFAULT_MILL_VERSION
-DEFAULT_MILL_VERSION=0.10.1
+DEFAULT_MILL_VERSION=0.10.4
 
 set -e
 
 if [ -z "$MILL_VERSION" ] ; then
  if [ -f ".mill-version" ] ; then
  MILL_VERSION="$(head -n 1 .mill-version 2> /dev/null)"
- elif [ -f "mill" ] && [ "$BASH_SOURCE" != "mill" ] ; then
+ elif [ -f "mill" ] && [ "$0" != "mill" ] ; then
  MILL_VERSION=$(grep -F "DEFAULT_MILL_VERSION=" "mill" | head -n 1 | cut -d= -f2)
  else
  MILL_VERSION=$DEFAULT_MILL_VERSION
@@ -28,13 +28,14 @@ version_remainder="$MILL_VERSION"
 MILL_MAJOR_VERSION="${version_remainder%%.*}"; version_remainder="${version_remainder#*.}"
 MILL_MINOR_VERSION="${version_remainder%%.*}"; version_remainder="${version_remainder#*.}"
 
-if [ ! -x "$MILL_EXEC_PATH" ] ; then
- mkdir -p $MILL_DOWNLOAD_PATH
+if [ ! -s "$MILL_EXEC_PATH" ] ; then
+ mkdir -p "$MILL_DOWNLOAD_PATH"
  if [ "$MILL_MAJOR_VERSION" -gt 0 ] || [ "$MILL_MINOR_VERSION" -ge 5 ] ; then
  ASSEMBLY="-assembly"
  fi
  DOWNLOAD_FILE=$MILL_EXEC_PATH-tmp-download
- MILL_DOWNLOAD_URL="https:/lihaoyi/mill/releases/download/${MILL_VERSION%%-*}/$MILL_VERSION${ASSEMBLY}"
+ MILL_VERSION_TAG=$(echo $MILL_VERSION | sed -E 's/([^-]+)(-M[0-9]+)?(-.*)?/\1\2/')
+ MILL_DOWNLOAD_URL="https:/lihaoyi/mill/releases/download/${MILL_VERSION_TAG}/$MILL_VERSION${ASSEMBLY}"
  curl --fail -L -o "$DOWNLOAD_FILE" "$MILL_DOWNLOAD_URL"
  chmod +x "$DOWNLOAD_FILE"
  mv "$DOWNLOAD_FILE" "$MILL_EXEC_PATH"