Update the version of Mill and fixup all compiler warnings (#36)

* Update the version of Mill and fixup all compiler warnings * Generate docs files --------- Co-authored-by: Nobody <[email protected]>
fulcrumgenomics · Apr 10, 2024 · e4f968b · e4f968b
1 parent 3994076
commit e4f968b
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 .idea
 .idea_modules
+.java-version
 out
 jars
 project
@@ -8,3 +9,4 @@ target
 .metals
 .vscode
 .bsp
+*.iml
diff --git a/build.sc b/build.sc
@@ -16,12 +16,58 @@ trait CommonModule extends SbtModule {
     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://broadinstitute.jfrog.io/artifactory/libs-snapshot/")
-  )
+  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/")
+    )
+  }
+
+  /** All Scala compiler options for this package. */
+  override def scalacOptions: T[Seq[String]] = T {
+    Seq(
+      "-opt:inline:com.fulcrumgenomics.**", // Turn on the inliner.
+      "-opt-inline-from:com.fulcrumgenomics.**", // 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-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.
+    )
+  }
 }
 
 /** A base trait for versioning modules. */
@@ -69,11 +115,11 @@ trait ReleaseModule extends JavaModule {
 
 
 object tools extends CommonModule with PublishModule with ReleaseModule {
-  def scalaVersion = "2.13.8"
+  def scalaVersion = "2.13.11"
   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 gitHash = Process("git rev-parse --short HEAD").lazyLines.head
   def publishVersion = s"0.1.0-${gitHash}-SNAPSHOT"
   def pomSettings = PomSettings(
     description = artifactName(),
@@ -96,12 +142,12 @@ object tools extends CommonModule with PublishModule with ReleaseModule {
 
   override def ivyDeps = Agg(
     ivy"org.scala-lang:scala-compiler:${scalaVersion()}",
-    ivy"com.fulcrumgenomics:fgbio_2.13:2.1.0".excludeOrg(orgsToExclude:_*)
+    ivy"com.fulcrumgenomics:fgbio_2.13:2.2.1".excludeOrg(orgsToExclude:_*)
   )
 
-  object test extends Tests {
-    override def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
-    override def testFramework = "org.scalatest.tools.Framework"
+  object test extends SbtModuleTests {
+    override def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.2.17")
+    override def testFramework: Target[String] = T { "org.scalatest.tools.Framework" }
 
     // run mill tools.test.singleTest com.fulcrumgenomics.sv.x.y.x.TestClassName
     def singleTest(args: String*) = T.command {

diff --git a/docs/tools/FilterAndMerge.md b/docs/tools/FilterAndMerge.md
@@ -15,7 +15,6 @@ Filters and merges SVPileup output.
 |----|----|----|-----------|---------|---------------|----------------|
 |input|i|FilePath|The input pileup file from SvPileup|Required|1||
 |output|o|FilePath|The output filtered and merged SvPileup file|Required|1||
-|dict|d|PathToSequenceDictionary|The path to the reference sequence dictionary.|Required|1||
 |min-pre|m|Int|The minimum # of observations to examine an input site|Optional|1|1|
 |min-post|M|Int|The minimum # of observations to output a site|Optional|1|1|
 |slop|s|Int|The maximum # bases between a breakend across adjacent sites|Optional|1|0|

diff --git a/docs/tools/index.md b/docs/tools/index.md
@@ -4,7 +4,7 @@ title: fgsv tools
 
 # fgsv tools
 
-The following tools are available in fgsv version 0.1.1-b1923e1.
+The following tools are available in fgsv version 0.1.1-836bce0.
 ## All tools
 
 All tools.

diff --git a/mill b/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=0.10.4
+DEFAULT_MILL_VERSION=0.11.7
 
 set -e
 

diff --git a/src/main/scala/com/fulcrumgenomics/sv/internal/FgSvMetricsDoclet.scala b/src/main/scala/com/fulcrumgenomics/sv/internal/FgSvMetricsDoclet.scala
@@ -85,22 +85,22 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
 
     find(universe.rootPackage)
       .filter(d => d.isClass && !d.isAbstract)
-      .filter(d => d.parentTypes.exists { case (template, typ) => template.toString == classOf[Metric].getName })
+      .filter(d => d.parentTypes.exists { case (template, _) => template.toString == classOf[Metric].getName })
   }
 
   /** Take the body of a scaladoc comment and renders it into MarkDown. */
   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
-    def renderBlock(block: Block, indent: String): Unit = {
+    def renderBlock(block: Block): Unit = {
       (block: @unchecked) match {
-        case para:  Paragraph      => render(para.text)
-        case dlist: DefinitionList => () // TODO
-        case hr:    HorizontalRule => () // TODO
-        case olist: OrderedList    => () // TODO
-        case title: Title          => buffer.append("#" * title.level).append(" "); render(title.text); buffer.append("\n\n")
-        case ulist: UnorderedList  => () // TODO
+        case para:  Paragraph     => render(para.text)
+        case _: DefinitionList    => () // TODO
+        case _:    HorizontalRule => () // TODO
+        case _: OrderedList       => () // TODO
+        case title: Title         => buffer.append("#" * title.level).append(" "); render(title.text); buffer.append("\n\n")
+        case _: UnorderedList     => () // TODO
       }
     }
 
@@ -120,7 +120,7 @@ class FgSvMetricsDoclet extends FgMetricsDoclet {
       case under:   Underline   => buffer.append("__"); render(under.text); buffer.append("__")
     }
 
-    body.blocks.foreach(renderBlock(_, ""))
+    body.blocks.foreach(renderBlock)
     buffer.toString()
   }
 

diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala
@@ -358,7 +358,7 @@ case class AggregatedBreakpointPileup(id: String,
         )
         numOverlap match {
           case None => None
-          case Some(n) => Some(total.toDouble / n, n)
+          case Some(n) => Some((total.toDouble / n, n))
         }
     }
     val leftResult  = frequency_and_count(left_contig, left_pileups, left_min_pos, left_max_pos)
@@ -457,10 +457,6 @@ case class AggregatedBreakpointPileup(id: String,
       right_targets         = if (rightOverlapNames.isEmpty) None else Some(rightOverlapNames.mkString(",")),
     )
   }
-
-  private def overlapsTarget(contig: String, start: Int, end: Int, targets: OverlapDetector[BEDFeature]): Boolean = {
-    targets.overlapsAny(new Interval(contig, start, end))
-  }
 }
 
 
@@ -512,5 +508,5 @@ class PositionList(val positions: Seq[Int]) {
 
 object PositionList {
   def apply(positions: Int*): PositionList = new PositionList(positions)
-  def apply(s: String): PositionList = new PositionList(s.split(",").map(_.toInt))
+  def apply(s: String): PositionList = new PositionList(s.split(",").map(_.toInt).toIndexedSeq)
 }
diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala
@@ -2,11 +2,10 @@ package com.fulcrumgenomics.sv.tools
 
 import com.fulcrumgenomics.FgBioDef._
 import com.fulcrumgenomics.commons.collection.BetterBufferedIterator
-import com.fulcrumgenomics.commons.util.{NumericCounter, SimpleCounter}
-import com.fulcrumgenomics.fasta.SequenceDictionary
+import com.fulcrumgenomics.commons.util.NumericCounter
 import com.fulcrumgenomics.sopt.{arg, clp}
 import com.fulcrumgenomics.sv.cmdline.{ClpGroups, SvTool}
-import com.fulcrumgenomics.sv.{BreakpointPileup, EvidenceType}
+import com.fulcrumgenomics.sv.BreakpointPileup
 import com.fulcrumgenomics.util.{Io, Metric}
 
 import scala.collection.immutable.IndexedSeq
@@ -18,7 +17,6 @@ import scala.collection.immutable.IndexedSeq
 class FilterAndMerge
 ( @arg(flag='i', doc="The input pileup file from SvPileup") input: FilePath,
   @arg(flag='o', doc="The output filtered and merged SvPileup file") output: FilePath,
-  @arg(flag='d', doc="The path to the reference sequence dictionary.") dict: PathToSequenceDictionary,
   @arg(flag='m', doc="The minimum # of observations to examine an input site") minPre: Int = 1,
   @arg(flag='M', doc="The minimum # of observations to output a site") minPost: Int = 1,
   @arg(flag='s', doc="The maximum # bases between a breakend across adjacent sites") slop: Int = 0,
@@ -28,8 +26,6 @@ class FilterAndMerge
   Io.assertCanWriteFile(output)
 
   override def execute(): Unit = {
-    val dict = SequenceDictionary(this.dict)
-
     // Read in the pileups
     val iter   = Metric.iterator[BreakpointPileup](input)
       .filter(_.total >= minPre)
@@ -117,12 +113,12 @@ object MergedPileup {
       left_contig    = pileups.head.left_contig,
       left_start     = pileups.map(_.left_pos).min,
       left_end       = pileups.map(_.left_pos).max,
-      left_mean      = Math.round(leftMean),
+      left_mean      = Math.round(leftMean.toFloat),
       left_strand    = pileups.head.left_strand,
       right_contig   = pileups.head.right_contig,
       right_start    = pileups.map(_.right_pos).min,
       right_end      = pileups.map(_.right_pos).max,
-      right_mean     = Math.round(rightMean),
+      right_mean     = Math.round(rightMean.toFloat),
       right_strand   = pileups.head.right_strand,
       mean_count     = meanCount,
       stddev_count   = counts.stddev(meanCount),

diff --git a/src/test/scala/com/fulcrumgenomics/sv/UnitSpec.scala b/src/test/scala/com/fulcrumgenomics/sv/UnitSpec.scala
@@ -3,7 +3,8 @@ package com.fulcrumgenomics.sv
 import com.fulcrumgenomics.FgBioDef.PathToBam
 import com.fulcrumgenomics.bam.api.{SamRecord, SamSource}
 import org.scalatest.flatspec.AnyFlatSpec
-import org.scalatest.{Matchers, OptionValues}
+import org.scalatest.OptionValues
+import org.scalatest.matchers.should._
 
 import java.nio.file.{Files, Path}
 

diff --git a/src/test/scala/com/fulcrumgenomics/sv/tools/SvPileupTest.scala b/src/test/scala/com/fulcrumgenomics/sv/tools/SvPileupTest.scala
@@ -111,7 +111,7 @@ class SvPileupTest extends UnitSpec {
   // Objects and functions used in testing findBreakpoint()
   //////////////////////////////////////////////////////////////////////////////
   private val builder = {
-    val seqs = (Range.inclusive(1, 22) ++ Seq("X", "Y")).map { chr =>
+    val seqs = (Range.inclusive(1, 22).map(_.toString) ++ Seq("X", "Y")).map { chr =>
       SequenceMetadata(name="chr" + chr, length=200e6.toInt)
     } ++ Seq(SequenceMetadata(name="chrM", length=16000, topology = Some(Topology.Circular)))
     new SamBuilder(readLength=100, sd=Some(SequenceDictionary(seqs:_*)))
@@ -435,8 +435,8 @@ class SvPileupTest extends UnitSpec {
       val prefix = makeTempFile("output", "")
       Outputs(
         prefix = prefix,
-        bam    = PathUtil.pathTo(prefix + ".bam"),
-        txt    = PathUtil.pathTo(prefix + ".txt")
+        bam    = PathUtil.pathTo(prefix.toString + ".bam"),
+        txt    = PathUtil.pathTo(prefix.toString + ".txt")
       )
     }
   }
@@ -473,8 +473,6 @@ class SvPileupTest extends UnitSpec {
     }
 
     val leftFromTag  = s"0;left;from;${SplitRead.snakeName}"
-    val rightFromTag = s"0;right;from;${SplitRead.snakeName}"
-    val leftIntoTag  = f"0;left;into;${SplitRead.snakeName}"
     val rightIntoTag = f"0;right;into;${SplitRead.snakeName}"
 
     // r1Half2 is not annotated, since it is superseded by r1Half1 -> fullR2