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build.sbt
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build.sbt
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import com.typesafe.sbt.SbtGit.GitCommand
import sbt._
import sbtassembly.AssemblyKeys.assembly
import sbtassembly.MergeStrategy
import sbtrelease.ReleasePlugin.autoImport.ReleaseTransformations._
import scoverage.ScoverageKeys._
////////////////////////////////////////////////////////////////////////////////////////////////
// We have the following "settings" in this build.sbt:
// - versioning with sbt-release
// - custom JAR name for the root project
// - settings to publish to Sonatype
// - scaladoc settings
// - custom merge strategy for assembly
////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////
// Use sbt-release to bupm the version numbers.
//
// see: http://blog.byjean.eu/2015/07/10/painless-release-with-sbt.html
////////////////////////////////////////////////////////////////////////////////////////////////
// Release settings
releaseVersionBump := sbtrelease.Version.Bump.Next
releasePublishArtifactsAction := PgpKeys.publishSigned.value
releaseProcess := Seq[ReleaseStep](
checkSnapshotDependencies,
inquireVersions,
runClean,
runTest,
setReleaseVersion,
commitReleaseVersion,
tagRelease,
releaseStepCommand("publishSigned"),
setNextVersion,
commitNextVersion,
releaseStepCommand("sonatypeReleaseAll"),
pushChanges
)
////////////////////////////////////////////////////////////////////////////////////////////////
// For the aggregate (root) jar, override the name. For the sub-projects,
// see the build.sbt in each project folder.
////////////////////////////////////////////////////////////////////////////////////////////////
assemblyJarName in assembly := "fgbio-" + version.value + ".jar"
////////////////////////////////////////////////////////////////////////////////////////////////
// Sonatype settings
////////////////////////////////////////////////////////////////////////////////////////////////
publishMavenStyle := true
publishTo := {
val nexus = "https://oss.sonatype.org/"
if (isSnapshot.value)
Some("snapshots" at nexus + "content/repositories/snapshots")
else
Some("releases" at nexus + "service/local/staging/deploy/maven2")
}
publishArtifact in Test := false
pomIncludeRepository := { _ => false }
// For Travis CI - see http://www.cakesolutions.net/teamblogs/publishing-artefacts-to-oss-sonatype-nexus-using-sbt-and-travis-ci
credentials ++= (for {
username <- Option(System.getenv().get("SONATYPE_USER"))
password <- Option(System.getenv().get("SONATYPE_PASS"))
} yield Credentials("Sonatype Nexus Repository Manager", "oss.sonatype.org", username, password)).toSeq
////////////////////////////////////////////////////////////////////////////////////////////////
// Coverage settings: don't include personal packages in coverage counts
////////////////////////////////////////////////////////////////////////////////////////////////
coverageExcludedPackages := "com.fulcrumgenomics.personal.*;com.fulcrumgenomics.internal.*"
val htmlReportsDirectory: String = "target/test-reports"
////////////////////////////////////////////////////////////////////////////////////////////////
// scaladoc options
////////////////////////////////////////////////////////////////////////////////////////////////
val docScalacOptions = Seq("-groups", "-implicits")
////////////////////////////////////////////////////////////////////////////////////////////////
// Common settings
////////////////////////////////////////////////////////////////////////////////////////////////
val primaryScalaVersion = "2.13.3"
lazy val commonSettings = Seq(
organization := "com.fulcrumgenomics",
organizationName := "Fulcrum Genomics LLC",
homepage := Some(url("http://github.com/fulcrumgenomics/fgbio")),
startYear := Some(2015),
scalaVersion := primaryScalaVersion,
crossScalaVersions := Seq(primaryScalaVersion),
scalacOptions ++= Seq("-target:jvm-1.8", "-deprecation", "-unchecked"),
scalacOptions in (Compile, doc) ++= docScalacOptions,
scalacOptions in (Test, doc) ++= docScalacOptions,
useCoursier := false,
autoAPIMappings := true,
testOptions in Test += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
// uncomment for full stack traces
//testOptions in Test += Tests.Argument("-oDF"),
fork in Test := true,
resolvers += Resolver.sonatypeRepo("public"),
resolvers += Resolver.mavenLocal,
resolvers += "broad-snapshots" at "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/",
shellPrompt := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
updateOptions := updateOptions.value.withCachedResolution(true)
) ++ Defaults.coreDefaultSettings
////////////////////////////////////////////////////////////////////////////////////////////////
// root project
////////////////////////////////////////////////////////////////////////////////////////////////
lazy val htsjdkExcludes = Seq(
ExclusionRule(organization="org.apache.ant"),
ExclusionRule(organization="gov.nih.nlm.ncbi"),
ExclusionRule(organization="org.testng"),
ExclusionRule(organization="com.google.cloud.genomics")
)
lazy val assemblySettings = Seq(
test in assembly := {},
logLevel in assembly := Level.Info
)
lazy val root = Project(id="fgbio", base=file("."))
.settings(commonSettings: _*)
.settings(assemblySettings: _*)
.settings(description := "fgbio")
.settings(mainClass := Some("com.fulcrumgenomics.cmdline.FgBioMain"))
.settings(
libraryDependencies ++= Seq(
"org.scala-lang" % "scala-reflect" % scalaVersion.value,
"org.scala-lang" % "scala-compiler" % scalaVersion.value,
"org.scala-lang.modules" %% "scala-xml" % "1.2.0",
"org.scala-lang.modules" %% "scala-collection-compat" % "2.1.1",
"com.fulcrumgenomics" %% "commons" % "1.3.0",
"com.fulcrumgenomics" %% "sopt" % "1.1.0",
"com.github.samtools" % "htsjdk" % "2.23.0" excludeAll(htsjdkExcludes: _*),
"org.apache.commons" % "commons-math3" % "3.6.1",
"com.beachape" %% "enumeratum" % "1.6.1",
"com.intel.gkl" % "gkl" % "0.8.8",
//---------- Test libraries -------------------//
"org.scalatest" %% "scalatest" % "3.1.3" % "test->*" excludeAll ExclusionRule(organization="org.junit", name="junit")
))
.settings(dependencyOverrides ++= Seq(
"org.apache.logging.log4j" % "log4j-api" % "[2.17.0,)",
"org.apache.logging.log4j" % "log4j-core" % "[2.17.0,)",
))
////////////////////////////////////////////////////////////////////////////////////////////////
// Merge strategy for assembly
////////////////////////////////////////////////////////////////////////////////////////////////
val customMergeStrategy: String => MergeStrategy = {
case x if Assembly.isConfigFile(x) =>
MergeStrategy.concat
case PathList(ps@_*) if Assembly.isReadme(ps.last) || Assembly.isLicenseFile(ps.last) =>
MergeStrategy.rename
case PathList("META-INF", xs@_*) =>
xs map {
_.toLowerCase
} match {
case ("manifest.mf" :: Nil) | ("index.list" :: Nil) | ("dependencies" :: Nil) =>
MergeStrategy.discard
case ps@(x :: xt) if ps.last.endsWith(".sf") || ps.last.endsWith(".dsa") =>
MergeStrategy.discard
case "plexus" :: xt =>
MergeStrategy.discard
case "spring.tooling" :: xt =>
MergeStrategy.discard
case "com.google.guava" :: xt =>
MergeStrategy.discard
case "services" :: xt =>
MergeStrategy.filterDistinctLines
case ("spring.schemas" :: Nil) | ("spring.handlers" :: Nil) =>
MergeStrategy.filterDistinctLines
case _ => MergeStrategy.deduplicate
}
case "asm-license.txt" | "overview.html" =>
MergeStrategy.discard
case "logback.xml" =>
MergeStrategy.first
case _ => MergeStrategy.deduplicate
}
assemblyMergeStrategy in assembly := customMergeStrategy