Port to Scala 3 (with newly released scalafmt)

* Port to Scala 3

* Refactor reference package object

* Convert package objects to toplevel

* Set Scala 3 rewrite rules

* Run scalafmt

* Update copyright

* Set version to 3.12.0-SNAPSHOT

* Update changelog

* Update GH actions

* Workaround for scalafmt issue

See scalameta/scalafmt#3787

.github/workflows/ci.yml

@@ -15,6 +15,8 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: jrouly/scalafmt-native-action@v3
+      with:
+        version: "3.8.0"
     - name: Set up JDK 8
       uses: actions/setup-java@v4
       with:

.github/workflows/release.yml

@@ -14,6 +14,8 @@ jobs:
     - run: git config --global user.email "[email protected]"
     - run: git config --global user.name "GPP Informatics"
     - uses: jrouly/scalafmt-native-action@v3
+      with:
+        version: "3.8.0"
     - name: Set up JDK 8
       uses: actions/setup-java@v4
       with:

.scalafix.conf

@@ -7,5 +7,5 @@ OrganizeImports {
   expandRelative = true
   groups = ["re:javax?\\.", "scala.", "*"]
   groupedImports = Merge
-  removeUnused = true
+  removeUnused = false
 }

.scalafmt.conf

@@ -1,5 +1,13 @@
 # PoolQ3 .scalafmt configuration
-version=3.7.17
+version=3.8.0
+runner.dialect = scala3
+
+# work around https://github.com/scalameta/scalafmt/issues/3787
+fileOverride {
+  "glob:**.sbt" {
+    runner.dialect = sbt1
+  }
+}
 style = IntelliJ
 
 maxColumn = 120
@@ -14,4 +22,6 @@ rewrite.redundantBraces.generalExpressions = false
 rewrite.redundantBraces.includeUnitMethods = false
 rewrite.redundantBraces.maxBreaks = 16
 rewrite.redundantBraces.stringInterpolation = true
-runner.dialect = scala213source3
+rewrite.scala3.convertToNewSyntax = true
+rewrite.scala3.removeOptionalBraces = oldSyntaxToo
+rewrite.scala3.insertEndMarkerMinLines = 8

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## 3.12.0
+* Update to Scala 3.3.1
+
 ## 3.11.0
 * Machine-parseable condition barcode summary file
 

build.sbt

@@ -2,41 +2,37 @@ val artifactId = "poolq"
 
 inThisBuild(
   List(
-    scalaVersion := "2.13.11",
+    scalaVersion := "3.3.1",
     semanticdbEnabled := true,
     semanticdbVersion := scalafixSemanticdb.revision,
     versionScheme := Some("early-semver")
   )
 )
 
 lazy val versions = new {
-  val acyclic = "0.2.1"
   val betterFiles = "3.9.2"
-  val betterMonadicFor = "0.3.1"
-  val catsEffect3 = "3.5.2"
+  val catsEffect3 = "3.5.3"
   val cats = "2.10.0"
   val commonsIo = "2.15.1"
   val commonsText = "1.11.0"
   val commonsMath3 = "3.6.1"
-  val fastutil = "8.5.12"
-  val fs2 = "3.9.3"
+  val fastutil = "8.5.13"
+  val fs2 = "3.9.4"
   val log4s = "1.10.0"
   val logback = "1.2.13"
   val munit = "0.7.29"
   val munitCatsEffect3 = "1.0.7"
   val samTools = "3.0.5"
   val scalaCheck = "1.17.0"
   val scalaCsv = "1.3.10"
-  val scalaTest = "3.2.17"
-  val scalaTestPlusScalaCheck = "3.2.2.0"
+  val scalaTest = "3.2.18"
+  val scalaTestPlusScalaCheck = "3.2.18.0"
   val scopt = "4.1.0"
   val slf4j = "1.7.36"
 }
 
 lazy val libraries = new {
-  val acyclic = "com.lihaoyi" %% "acyclic" % versions.acyclic
   val betterFiles = "com.github.pathikrit" %% "better-files" % versions.betterFiles
-  val betterMonadicFor = "com.olegpy" %% "better-monadic-for" % versions.betterMonadicFor
   val cats = "org.typelevel" %% "cats-core" % versions.cats
   val catsEffect3 = "org.typelevel" %% "cats-effect" % versions.catsEffect3
   val commonsIo = "commons-io" % "commons-io" % versions.commonsIo
@@ -59,12 +55,11 @@ lazy val libraries = new {
   val munitCatsEffect3 = "org.typelevel" %% "munit-cats-effect-3" % versions.munitCatsEffect3
   val scalaTest = "org.scalatest" %% "scalatest" % versions.scalaTest
   val scalaCheck = "org.scalacheck" %% "scalacheck" % versions.scalaCheck
-  val scalaTestPlusScalaCheck = "org.scalatestplus" %% "scalacheck-1-14" % versions.scalaTestPlusScalaCheck
+  val scalaTestPlusScalaCheck = "org.scalatestplus" %% "scalacheck-1-17" % versions.scalaTestPlusScalaCheck
 }
 
 lazy val dependencies =
   List(
-    libraries.acyclic % "provided",
     libraries.cats,
     libraries.commonsIo,
     libraries.commonsMath3,
@@ -90,7 +85,7 @@ lazy val dependencies =
   )
 
 lazy val headerLicenseText =
-  """|Copyright (c) 2022 The Broad Institute, Inc. All rights reserved.
+  """|Copyright (c) 2024 The Broad Institute, Inc. All rights reserved.
      |
      |SPDX-License-Identifier: BSD-3-Clause
      |""".stripMargin
@@ -130,13 +125,9 @@ lazy val poolq = project
     name := "poolq3",
     organization := "org.broadinstitute.gpp",
     libraryDependencies := dependencies,
-    scalacOptions ++= List("-P:acyclic:force", "-Xsource:3"),
     buildInfoKeys := Seq[BuildInfoKey](name, version),
     buildInfoPackage := "org.broadinstitute.gpp.poolq3",
-    addCompilerPlugin(libraries.acyclic),
-    addCompilerPlugin(libraries.betterMonadicFor),
     testFrameworks += new TestFramework("munit.Framework"),
-    scalacOptions += "-Yrangepos", // ensure munit clues work
     // Tests pass in parallel, but SLF4J logging behaves weirdly. Disable this flag to examine test
     // log output; leave this enabled for very fast test execution.
     Test / parallelExecution := true

src/main/scala/org/broadinstitute/gpp/poolq3/PoolQ.scala

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 The Broad Institute, Inc. All rights reserved.
+ * Copyright (c) 2024 The Broad Institute, Inc. All rights reserved.
  *
  * SPDX-License-Identifier: BSD-3-Clause
  */
@@ -9,7 +9,7 @@ import java.nio.file.{Files, Path}
 
 import scala.util.{Failure, Success, Try, Using}
 
-import cats.syntax.all._
+import cats.syntax.all.*
 import org.broadinstitute.gpp.poolq3.PoolQConfig.synthesizeArgs
 import org.broadinstitute.gpp.poolq3.barcode.{BarcodePolicy, Barcodes, barcodeSource}
 import org.broadinstitute.gpp.poolq3.parser.{BarcodeSet, CloseableIterable, ReferenceData}
@@ -20,7 +20,7 @@ import org.broadinstitute.gpp.poolq3.process.{
   ScoringConsumer,
   UnexpectedSequenceTracker
 }
-import org.broadinstitute.gpp.poolq3.reference.{ExactReference, Reference, referenceFor}
+import org.broadinstitute.gpp.poolq3.reference.{ExactReference, Reference}
 import org.broadinstitute.gpp.poolq3.reports.{
   BarcodeCountsWriter,
   CorrelationFileWriter,
@@ -45,7 +45,7 @@ import org.broadinstitute.gpp.poolq3.types.{
 }
 import org.log4s.{Logger, getLogger}
 
-object PoolQ {
+object PoolQ:
 
   private[this] val log: Logger = getLogger
 
@@ -60,19 +60,17 @@ object PoolQ {
     )
 
   final def main(args: Array[String]): Unit =
-    PoolQConfig.parse(args) match {
+    PoolQConfig.parse(args) match
       case None => System.exit(-1)
       case Some(config) =>
-        run(config) match {
+        run(config) match
           case Success(_) => // do nothing
           case Failure(t) =>
             log.error(t)("PoolQ failed")
             System.exit(-1)
-        }
-    }
 
   /** The main entry point for PoolQ3 as an API */
-  final def run(config: PoolQConfig): Try[PoolQSummary] = {
+  final def run(config: PoolQConfig): Try[PoolQSummary] =
     log.info(s"PoolQ version: ${BuildInfo.version}")
     logCli(config)
 
@@ -108,7 +106,7 @@ object PoolQ {
 
     log.info("Building row reference")
     val rowReference: Reference =
-      referenceFor(
+      Reference(
         config.rowMatchFn,
         ReferenceData.truncator(rowBarcodeLength),
         config.countAmbiguous,
@@ -118,7 +116,7 @@ object PoolQ {
     log.info("Building column reference")
     val colBarcodeLength = colBarcodePolicyOpt.map(_.length).getOrElse(colReferenceData.barcodeLength)
     val colReference: Reference =
-      referenceFor(
+      Reference(
         config.colMatchFn,
         ReferenceData.truncator(colBarcodeLength),
         config.countAmbiguous,
@@ -136,21 +134,20 @@ object PoolQ {
       barcodeSource(config.input, rowBarcodePolicy, revRowBarcodePolicyOpt, colBarcodePolicyOrLength, umiInfo.map(_._2))
 
     lazy val unexpectedSequenceCacheDirOpt: Option[Path] =
-      if (config.skipUnexpectedSequenceReport) None
-      else {
+      if config.skipUnexpectedSequenceReport then None
+      else
         val ret = config.unexpectedSequenceCacheDir.map(Files.createDirectories(_)).orElse {
           val ret: Path = Files.createTempDirectory("unexpected-sequence-cache")
           Some(ret)
         }
         ret.foreach(path => log.info(s"Writing unexpected sequence cache files to $path"))
         ret
-      }
 
     lazy val unexpectedSequenceTrackerOpt: Option[UnexpectedSequenceTracker] =
       unexpectedSequenceCacheDirOpt.map(new UnexpectedSequenceTracker(_, colReference))
 
     val consumer =
-      if (config.noopConsumer) new NoOpConsumer
+      if config.noopConsumer then new NoOpConsumer
       else
         new ScoringConsumer(
           rowReference,
@@ -162,7 +159,7 @@ object PoolQ {
           config.isPairedEnd
         )
 
-    for {
+    for
       runSummary <- runProcess(barcodes, consumer)
       state = runSummary.state
       counts = state.known
@@ -220,17 +217,19 @@ object PoolQ {
               config.unexpectedSequenceMaxSampleSize
             )
             .as(UnexpectedSequencesFileType.some)
-        if (config.removeUnexpectedSequenceCache) {
+        if config.removeUnexpectedSequenceCache then
           log.info(s"Removing unexpected sequence cache ${config.unexpectedSequenceCacheDir}")
           UnexpectedSequenceWriter.removeCache(dir)
-        }
         ret
       }
       _ = log.info(s"Writing run info ${config.output.unexpectedSequencesFile}")
       _ <- RunInfoWriter.write(config.output.runInfoFile, config)
       _ = log.info("PoolQ complete")
-    } yield PoolQSummary(runSummary, AlwaysWrittenFiles ++ Set(cfto, usfto).flatten)
-  }
+    yield PoolQSummary(runSummary, AlwaysWrittenFiles ++ Set(cfto, usfto).flatten)
+
+    end for
+
+  end run
 
   def runProcess(barcodes: CloseableIterable[Barcodes], consumer: Consumer): Try[PoolQRunSummary] =
     Using(barcodes.iterator) { iterator =>
@@ -257,7 +256,7 @@ object PoolQ {
         (rowBarcodePolicy, None, rowBarcodePolicy.length)
       }
 
-  private[this] def logCli(config: PoolQConfig): Unit = {
+  private[this] def logCli(config: PoolQConfig): Unit =
     val logStr =
       synthesizeArgs(config)
         .map {
@@ -266,6 +265,7 @@ object PoolQ {
         }
         .mkString(" \\\n")
     log.info(s"PoolQ command-line settings:\n$logStr")
-  }
 
-}
+  end logCli
+
+end PoolQ