Bumped toolkit and dependency versions and resolved resulting issues.

build.sc

@@ -1,12 +1,8 @@
-import java.text.SimpleDateFormat
-import java.util.Date
-
 import mill._
 import mill.scalalib._
-import mill.scalalib.publish.{Developer, License, PomSettings, SCM}
+import mill.scalalib.publish._
 import java.util.jar.Attributes.Name.{IMPLEMENTATION_VERSION => ImplementationVersion}
 
-import ammonite.ops._
 import coursier.maven.MavenRepository
 
 import scala.sys.process.Process
@@ -15,23 +11,23 @@ import scala.util.{Failure, Success, Try}
 /** Base trait for build modules. */
 trait CommonModule extends SbtModule {
   def deployLocal(assembly: PathRef, jarName:String) = {
-    mkdir(pwd / 'jars)
+    os.makeDir.all(os.pwd / Symbol("jars"))
     println(s"Copying artifact ${assembly.path} to jars / $jarName")
-    cp.over(assembly.path, pwd / 'jars / jarName)
+    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/")
+    MavenRepository("https://broadinstitute.jfrog.io/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 = %%("git", args)(pwd).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")
@@ -73,21 +69,18 @@ trait ReleaseModule extends JavaModule {
 
 
 object tools extends CommonModule with PublishModule with ReleaseModule {
-  def scalaVersion = "2.13.3"
-  def millSourcePath = super.millSourcePath / ammonite.ops.up
-  def mainClass = Some("com.fulcrumgenomics.sv.cmdline.SvMain")
-  def artifactName = "fgsv"
+  def scalaVersion = "2.13.12"
+  override def millSourcePath = super.millSourcePath / os.up
+  override def mainClass = Some("com.fulcrumgenomics.sv.cmdline.SvMain")
+  override def artifactName = "fgsv"
   def gitHash = Process("git rev-parse --short HEAD").lineStream.head
-  def publishVersion = s"0.0.4-${gitHash}-SNAPSHOT"
+  def publishVersion = s"0.1.0-${gitHash}-SNAPSHOT"
   def pomSettings = PomSettings(
     description = artifactName(),
     organization = "com.fulcrumgenomics",
     url = "https://github.com/fulcrumgenomics/fgsv",
-    licenses = Seq(License("MIT License", "http://www.fulcrumgenomics.com")),
-    scm = SCM(
-      "git://github.com:fulcrumgenomics/fgsv.git",
-      "scm:git://github.com:fulcrumgenomics/fgsv.git"
-    ),
+    licenses = Seq(License.MIT),
+    versionControl = VersionControl.github("fulcrumgenomics","fgsv"),
     developers = Seq(
       Developer("tfenne", "Tim Fennell", "https://github.com/tfenne"),
       Developer("nh13", "Nils Homer", "https://github.com/nh13"),
@@ -101,23 +94,22 @@ 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"com.fulcrumgenomics:fgbio_2.13:1.5.0".excludeOrg(orgsToExclude:_*),
-    ivy"org.xerial.snappy:snappy-java:1.1.8.4"
+    ivy"com.fulcrumgenomics:fgbio_2.13:2.1.0".excludeOrg(orgsToExclude:_*)
   )
 
   object test extends Tests {
-    def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
-    def testFramework = "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.fulcrumgenomics.sv.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(), "fgsv.jar")  }
 }

mill

@@ -3,7 +3,7 @@
 # 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=0.9.12
+DEFAULT_MILL_VERSION=0.10.4
 
 set -e
 

src/main/scala/com/fulcrumgenomics/sv/internal/FgSvMetricsDoclet.scala

@@ -56,7 +56,7 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Locates the metrics documentation templates and turns them into simple case classes with comments as markdown. */
-  private lazy val metrics: Seq[MetricDescription] = {
+  override protected lazy val metrics: Seq[MetricDescription] = {
     def simplify(name: String) = if (name.indexOf('.') > 0) name.substring(name.lastIndexOf('.') + 1) else name
 
     findMetricsClasses.map{ template =>
@@ -89,7 +89,7 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Take the body of a scaladoc comment and renders it into MarkDown. */
-  private def renderBody(body: Body): String = {
+  override protected def renderBody(body: Body): String = {
     val buffer = new StringBuilder
 
     // Takes a block element and renders it into MarkDown and writes it into the buffer
@@ -125,6 +125,6 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
   }
 
   /** Turns the text from a heading into the text to use as a link target. */
-  private def toLinkTarget(heading: String): String = heading.toLowerCase.replace(' ', '-')
+  override protected def toLinkTarget(heading: String): String = heading.toLowerCase.replace(' ', '-')
 }