https://doi.org/10.5281/zenodo.10456900
build.sbt
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.
////////////////////////////////////////////////////////////////////////////////////////////////
assembly / assemblyJarName := "fgbio-" + version.value + ".jar"
////////////////////////////////////////////////////////////////////////////////////////////////
// Sonatype settings
////////////////////////////////////////////////////////////////////////////////////////////////
publishMavenStyle := true
publishTo := {
val centralSnapshots = "https://central.sonatype.com/repository/maven-snapshots/"
if (isSnapshot.value) Some("central-snapshots" at centralSnapshots)
else localStaging.value
}
Test / publishArtifact := false
pomIncludeRepository := { _ => false }
credentials ++= (for {
username <- Option(System.getenv().get("SONATYPE_USER"))
password <- Option(System.getenv().get("SONATYPE_PASS"))
} yield Credentials("Sonatype Nexus Repository Manager", "central.sonatype.com", 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 = "2.13.14"
lazy val commonSettings = Seq(
organization := "com.fulcrumgenomics",
organizationName := "Fulcrum Genomics LLC",
organizationHomepage := Some(url("https://fulcrumgenomics.com/")),
homepage := Some(url("http://github.com/fulcrumgenomics/fgbio")),
scmInfo := Some(ScmInfo(url("http://github.com/fulcrumgenomics/fgbio"), "scm:git@github.com:fulcrumgenomics/fgbio.git")),
startYear := Some(2015),
scalaVersion := primaryScalaVersion,
crossScalaVersions := Seq(primaryScalaVersion),
scalacOptions ++= Seq(
"-release:8", // Target the Java 1.8 release
"-deprecation", // Emit warning and location for usages of deprecated APIs.
"-explaintypes", // Explain type errors in more detail.
"-feature", // Emit warning and location for usages of features that should be imported explicitly.
"-opt-inline-from:com.fulcrumgenomics.**", // Tells the inliner that it is allowed to inline things from these classes.
"-opt-warnings:at-inline-failed", // Tells you if methods marked with `@inline` cannot be inlined, so you can remove the tag.
"-opt:inline:com.fulcrumgenomics.**", // Turn on the inliner.
"-unchecked", // Enable additional warnings where generated code depends on assumptions.
"-Xcheckinit", // Wrap field accessors to throw an exception on uninitialized access.
"-Xfatal-warnings", // Fail the compilation if there are any warnings.
"-Xlint:adapted-args", // Warn if an argument list is modified to match the receiver.
"-Xlint:constant", // Evaluation of a constant arithmetic expression results in an error.
"-Xlint:delayedinit-select", // Selecting member of DelayedInit.
"-Xlint:doc-detached", // A Scaladoc comment appears to be detached from its element.
"-Xlint:inaccessible", // Warn about inaccessible types in method signatures.
"-Xlint:infer-any", // Warn when a type argument is inferred to be `Any`.
"-Xlint:missing-interpolator", // A string literal appears to be missing an interpolator id.
"-Xlint:nullary-unit", // Warn when nullary methods return Unit.
"-Xlint:option-implicit", // Option.apply used implicit view.
"-Xlint:package-object-classes", // Class or object defined in package object.
"-Xlint:poly-implicit-overload", // Parameterized overloaded implicit methods are not visible as view bounds.
"-Xlint:private-shadow", // A private field (or class parameter) shadows a superclass field.
"-Xlint:stars-align", // Pattern sequence wildcard must align with sequence component.
"-Xlint:type-parameter-shadow", // A local type parameter shadows a type already in scope.
"-Xlint:unused", // Warn when anything is unused.
"-Ycache-macro-class-loader:last-modified", // and macro definitions. This can lead to performance improvements.
"-Ycache-plugin-class-loader:last-modified", // Enables caching of classloaders for compiler plugins
"-Yopt-inline-heuristics:at-inline-annotated", // Tells the inliner to use your `@inliner` tags.
"-Yopt-log-inline", "_", // Optional, logs the inliner activity so you know it is doing something.
"-Ywarn-dead-code", // Warn when dead code is identified.
"-Ywarn-extra-implicit", // Warn when more than one implicit parameter section is defined.
"-Ywarn-numeric-widen", // Warn on obsolete octal syntax.
"-Ywarn-numeric-widen", // Warn when numerics are widened.
"-Ywarn-unused:implicits", // Warn if an implicit parameter is unused.
"-Ywarn-unused:imports", // Warn if an import selector is not referenced.
"-Ywarn-unused:locals", // Warn if a local definition is unused.
"-Ywarn-unused:params", // Warn if a value parameter is unused.
"-Ywarn-unused:patvars", // Warn if a variable bound in a pattern is unused.
"-Ywarn-unused:privates", // Warn if a private member is unused.
"-Ywarn-value-discard", // Warn when non-Unit expression results are unused.
),
Compile / doc / scalacOptions ++= docScalacOptions,
Test / doc / scalacOptions ++= docScalacOptions,
useCoursier := false,
Test / testOptions += Tests.Argument(TestFrameworks.ScalaTest, "-h", Option(System.getenv("TEST_HTML_REPORTS")).getOrElse(htmlReportsDirectory)),
// uncomment for full stack traces
// Test / testOptions += Tests.Argument("-oDF"),
Test / fork := true,
resolvers += Resolver.sonatypeCentralSnapshots,
resolvers += Resolver.sonatypeCentralRepo("releases"),
resolvers += Resolver.mavenLocal,
resolvers += "broad-snapshots" at "https://broadinstitute.jfrog.io/artifactory/libs-snapshot/",
shellPrompt := { state => "%s| %s> ".format(GitCommand.prompt.apply(state), version.value) },
updateOptions := updateOptions.value.withCachedResolution(true),
pomExtra := <url>https://github.com/fulcrumgenomics/fgbio</url>
<licenses>
<license>
<name>MIT License</name>
<url>https://www.opensource.org/licenses/mit-license.html</url>
</license>
</licenses>
<developers>
<developer>
<id>nh13</id>
<name>Nils Homer</name>
<url>https://github.com/nh13</url>
<email>nils@fulcrumgenomics.com</email>
</developer>
<developer>
<id>tfenne</id>
<name>Tim Fennell</name>
<url>https://github.com/tfenne</url>
<email>tim@fulcrumgenomics.com</email>
</developer>
<developer>
<id>clintval</id>
<name>Clint Valentine</name>
<url>https://github.com/clintval</url>
<email>clint@fulcrumgenomics.com</email>
</developer>
</developers>
) ++ 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(
assembly / test := {},
assembly / logLevel := 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" % "2.1.0",
"com.fulcrumgenomics" %% "commons" % "1.6.0",
"com.fulcrumgenomics" %% "sopt" % "1.1.0",
"com.github.samtools" % "htsjdk" % "3.0.5" excludeAll(htsjdkExcludes: _*),
"org.apache.commons" % "commons-math3" % "3.6.1",
"com.beachape" %% "enumeratum" % "1.7.0",
"com.intel.gkl" % "gkl" % "0.8.10",
//---------- 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,)",
"org.xerial.snappy" % "snappy-java" % "[1.1.8.4,)"
))
////////////////////////////////////////////////////////////////////////////////////////////////
// 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
}
assembly / assemblyMergeStrategy := customMergeStrategy
