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build.sc
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build.sc
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import $ivy.`com.lihaoyi::mill-contrib-scoverage:$MILL_VERSION`
import coursier.maven.MavenRepository
import mill._
import mill.api.JarManifest
import mill.contrib.scoverage.ScoverageModule
import mill.define.{Target, Task}
import mill.scalalib._
import mill.scalalib.publish._
import os._
import java.util.jar.Attributes.Name.{IMPLEMENTATION_VERSION => ImplementationVersion}
/** The official package version. */
private val packageVersion = "1.0.0"
/** All the packages we will exclude that come bundled with HTSJDK and Picard. */
private val htsjdkAndPicardExcludes = Seq("org.apache.ant", "gov.nih.nlm.ncbi", "org.testng", "com.google.cloud.genomics")
/** A base trait for all test targets. */
trait ScalaTest extends TestModule {
override def ivyDeps = Agg(ivy"org.scalatest::scalatest::3.2.19".excludeOrg(organizations = "org.junit"))
override def testFramework: Target[String] = T { "org.scalatest.tools.Framework" }
}
/** The neodisambiguate Scala package package. */
object neodisambiguate extends ScalaModule with PublishModule with ScoverageModule {
object test extends ScalaTests with ScalaTest with ScoverageTests
def scalaVersion = "2.13.14"
def scoverageVersion = "2.1.1"
def publishVersion = T { packageVersion }
/** POM publishing settings for this package. */
def pomSettings: Target[PomSettings] = PomSettings(
description = "Disambiguate reads that were mapped to multiple references.",
organization = "io.cvbio",
url = "https://github.com/clintval/neodisambiguate",
licenses = Seq(License.MIT),
versionControl = VersionControl.github(owner = "clintval", repo = "neodisambiguate", tag = Some(packageVersion)),
developers = Seq(Developer(id = "clintval", name = "Clint Valentine", url = "https://github.com/clintval"))
)
/** The artifact name, fully resolved within the coordinate. */
override def artifactName: T[String] = T { "neodisambiguate" }
/** The JAR manifest. */
override def manifest: T[JarManifest] = super.manifest().add(ImplementationVersion.toString -> packageVersion)
/** Create a local JAR for this module. */
def executable = T {
val artifact = assembly()
makeDir.all(pwd / "bin")
println("Copying artifact to ./bin/neodisambiguate")
copy(artifact.path, pwd / "bin" / "neodisambiguate", replaceExisting = true)
}
override def ivyDeps = Agg(
ivy"com.fulcrumgenomics::commons::1.4.0",
ivy"com.fulcrumgenomics::fgbio::2.3.0".excludeOrg(htsjdkAndPicardExcludes: _*),
ivy"org.rogach::scallop::5.1.0",
ivy"org.slf4j:slf4j-nop:1.7.6", // For peace and quiet: https://www.slf4j.org/codes.html#StaticLoggerBinder
)
/** All the repositories we want to pull from. */
override def repositoriesTask: Task[Seq[coursier.Repository]] = 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://broadinstitute.jfrog.io/artifactory/libs-snapshot/"),
)
}
/** Inject a shell script into the header of the assembled JAR file to make it auto-executable.
*
* @see https://skife.org/java/unix/2011/06/20/really_executable_jars.html
*/
override def prependShellScript: T[String] = T {
finalMainClassOpt().map { cls =>
s"""#!/usr/bin/env sh
|set -e
|
|PROP_OPTS=()
|MEM_OPTS=()
|PASS_ARGS=()
|DEFAULT_MEM_OPTS=('-Xms512m' '-XX:+AggressiveHeap')
|
|for ARG in "$$@"; do
| case $$ARG in
| '-D'* | '-XX'*) PROP_OPTS+=("$$ARG");;
| '-Xm'*) MEM_OPTS+=("$$ARG");;
| *) PASS_ARGS+=("$$ARG");;
| esac
|done
|
|if [ -z "$${_JAVA_OPTIONS}" ] && [ -z "$${JAVA_OPTS}" ] && [ -z "$${MEM_OPTS}" ]; then
| MEM_OPTS=("$${DEFAULT_MEM_OPTS[*]}");
|fi
|
|# If not already set to some value, set MALLOC_ARENA_MAX to constrain the number of memory pools (arenas) used
|# by glibc to a reasonable number. The default behaviour is to scale with the number of CPUs, which can cause
|# VIRTUAL memory usage to be ~0.5GB per cpu core in the system, e.g. 32GB of a 64-core machine even when the
|# heap and resident memory are only 1-4GB! See the following link for more discussion:
|# https://www.ibm.com/developerworks/community/blogs/kevgrig/entry/linux_glibc_2_10_rhel_6_malloc_may_show_excessive_virtual_memory_usage?lang=en
|if [ -z "$${MALLOC_ARENA_MAX}" ]; then MALLOC_ARENA_MAX=4; fi
|
|exec java $$JAVA_OPTS $${MEM_OPTS[*]} $${PROP_OPTS[*]} -cp "$$0" "$cls" $${PASS_ARGS[*]}
|exit
""".trim.stripLineEnd.stripMargin
}.getOrElse("")
}
/** All Scala compiler options for this package. */
override def scalacOptions: T[Seq[String]] = T {
Seq(
"-opt:inline:io.cvbio.**", // Turn on the inliner.
"-opt-inline-from:io.cvbio.**", // Tells the inliner that it is allowed to inline things from these classes.
"-Yopt-log-inline", "_", // Optional, logs the inliner activity so you know it is doing something.
"-Yopt-inline-heuristics:at-inline-annotated", // Tells the inliner to use your `@inliner` tags.
"-opt-warnings:at-inline-failed", // Tells you if methods marked with `@inline` cannot be inlined, so you can remove the tag.
// The following are sourced from https://nathankleyn.com/2019/05/13/recommended-scalac-flags-for-2-13/
"-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.
"-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.
"-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 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-value-discard", // Warn when non-Unit expression results are unused.
"-Ywarn-unused:patvars", // Warn if a variable bound in a pattern is unused.
"-Ywarn-unused:privates", // Warn if a private member is unused.
"-Ybackend-parallelism", Math.min(Runtime.getRuntime.availableProcessors(), 8).toString, // Enable parallelization — scalac max is 16.
"-Ycache-plugin-class-loader:last-modified", // Enables caching of classloaders for compiler plugins
"-Ycache-macro-class-loader:last-modified", // and macro definitions. This can lead to performance improvements.
)
}
}