Update dependencies (#39)

* Use sbt 1.10.7 * Update plugins * Update dependencies and fix errors * Updated scalafmt and scalafix * Formatting carnage * Require sbt and Update scalafmt in GitHub actions * Set version to 3.13.0-SNAPSHOT * Require Java 11 * Roll back to samtools 3.0.5 Any versions beyond 3.0.5 will require JDK 17 or higher * Update documentation
broadinstitute · Feb 11, 2025 · 1afbf72 · 1afbf72
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,12 +16,14 @@ jobs:
     - uses: actions/checkout@v4
     - uses: jrouly/scalafmt-native-action@v3
       with:
-        version: "3.8.1"
-    - name: Set up JDK 8
+        version: "3.8.3"
+    - name: Set up JDK 11
       uses: actions/setup-java@v4
       with:
-        java-version: '8'
         distribution: 'temurin'
+        java-version: '11'
+    - name: Setup sbt launcher
+      uses: sbt/setup-sbt@v1
     - run: sbt "scalafixAll --check"
     - name: Run tests
       run: make test-all
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -15,12 +15,14 @@ jobs:
     - run: git config --global user.name "GPP Informatics"
     - uses: jrouly/scalafmt-native-action@v3
       with:
-        version: "3.8.1"
-    - name: Set up JDK 8
+        version: "3.8.3"
+    - name: Set up JDK 11
       uses: actions/setup-java@v4
       with:
-        java-version: '8'
         distribution: 'temurin'
+        java-version: '11'
+    - name: Setup sbt launcher
+      uses: sbt/setup-sbt@v1
     - run: sbt "scalafixAll --check"
     - name: Run tests
       run: make test-all

diff --git a/.scalafix.conf b/.scalafix.conf
@@ -7,5 +7,6 @@ OrganizeImports {
   expandRelative = true
   groups = ["re:javax?\\.", "scala.", "*"]
   groupedImports = Merge
-  removeUnused = false
+  removeUnused = true
+  targetDialect = Scala3
 }
diff --git a/.scalafmt.conf b/.scalafmt.conf
@@ -1,16 +1,29 @@
-# PoolQ3 .scalafmt configuration
-version=3.8.1
+# PoolQ .scalafmt configuration
+version=3.8.3
 runner.dialect = scala3
+fileOverride {
+  "glob:**.sbt" {
+    runner.dialect = sbt1
+  }
+}
 
-style = IntelliJ
+# start with basic IntelliJ configuration
+preset = IntelliJ
 
+# customizations
+align.preset=none
+importSelectors = singleLine
 maxColumn = 120
-newlines.afterCurlyLambdaParams=squash
+continuationIndent.defnSite = 4
+newlines.afterCurlyLambdaParams = squash
 newlines.topLevelStatementBlankLines = [
   { blanks = 1 }
 ]
 project.git = true
-rewrite.rules = [AvoidInfix, RedundantBraces, RedundantParens, Imports, SortModifiers]
+
+# rewrite rules
+rewrite.rules = [AvoidInfix, Imports, RedundantBraces, RedundantParens, SortModifiers]
+rewrite.imports.expand = false
 rewrite.imports.sort = ascii
 rewrite.redundantBraces.generalExpressions = false
 rewrite.redundantBraces.includeUnitMethods = false

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # PoolQ 3.0
 
-Copyright (c) 2024 Genetic Perturbation Platform, The Broad Institute of Harvard and MIT.
+Copyright (c) 2025 Genetic Perturbation Platform, The Broad Institute of Harvard and MIT.
 
 [![Build Status](/~https://github.com/broadinstitute/poolq/actions/workflows/ci.yml/badge.svg)](/~https://github.com/broadinstitute/poolq/actions/workflows/ci.yml)
 

diff --git a/build.sbt b/build.sbt
@@ -2,7 +2,7 @@ val artifactId = "poolq"
 
 inThisBuild(
   List(
-    scalaVersion := "3.3.3",
+    scalaVersion := "3.6.3",
     semanticdbEnabled := true,
     semanticdbVersion := scalafixSemanticdb.revision,
     versionScheme := Some("early-semver")
@@ -11,21 +11,21 @@ inThisBuild(
 
 lazy val versions = new {
   val betterFiles = "3.9.2"
-  val catsEffect3 = "3.5.4"
-  val cats = "2.10.0"
-  val commonsIo = "2.16.1"
-  val commonsText = "1.12.0"
+  val catsEffect3 = "3.5.7"
+  val cats = "2.13.0"
+  val commonsIo = "2.18.0"
+  val commonsText = "1.13.0"
   val commonsMath3 = "3.6.1"
-  val fastutil = "8.5.13"
-  val fs2 = "3.10.2"
+  val fastutil = "8.5.15"
+  val fs2 = "3.11.0"
   val log4s = "1.10.0"
   val logback = "1.2.13"
-  val munit = "0.7.29"
-  val munitCatsEffect3 = "1.0.7"
+  val munit = "1.1.0"
+  val munitCatsEffect3 = "2.0.0"
   val samTools = "3.0.5"
-  val scalaCheck = "1.18.0"
-  val scalaCsv = "1.3.10"
-  val scalaTest = "3.2.18"
+  val scalaCheck = "1.18.1"
+  val scalaCsv = "2.0.0"
+  val scalaTest = "3.2.19"
   val scalaTestPlusScalaCheck = "3.2.18.0"
   val scopt = "4.1.0"
   val slf4j = "1.7.36"
@@ -52,7 +52,7 @@ lazy val libraries = new {
   val commonsText = "org.apache.commons" % "commons-text" % versions.commonsText
   val munit = "org.scalameta" %% "munit" % versions.munit
   val munitScalacheck = "org.scalameta" %% "munit-scalacheck" % versions.munit
-  val munitCatsEffect3 = "org.typelevel" %% "munit-cats-effect-3" % versions.munitCatsEffect3
+  val munitCatsEffect = "org.typelevel" %% "munit-cats-effect" % versions.munitCatsEffect3
   val scalaTest = "org.scalatest" %% "scalatest" % versions.scalaTest
   val scalaCheck = "org.scalacheck" %% "scalacheck" % versions.scalaCheck
   val scalaTestPlusScalaCheck = "org.scalatestplus" %% "scalacheck-1-17" % versions.scalaTestPlusScalaCheck
@@ -77,7 +77,7 @@ lazy val dependencies =
     libraries.fs2Core % Test,
     libraries.fs2Io % Test,
     libraries.munit % Test,
-    libraries.munitCatsEffect3 % Test,
+    libraries.munitCatsEffect % Test,
     libraries.munitScalacheck % Test,
     libraries.scalaCheck % Test,
     libraries.scalaTest % Test,
@@ -99,11 +99,11 @@ lazy val headerSettings = List(
 lazy val assemblySettings = List(
   assembly / assemblyJarName := "../bin/poolq3.jar",
   assembly / assemblyMergeStrategy := {
-    case "logback.xml"                                                 => MergeStrategy.first
-    case "logback-test.xml"                                            => MergeStrategy.discard
-    case PathList("module-info.class")                                 => MergeStrategy.discard
+    case "logback.xml" => MergeStrategy.first
+    case "logback-test.xml" => MergeStrategy.discard
+    case PathList("module-info.class") => MergeStrategy.discard
     case PathList("META-INF", "versions", xs @ _, "module-info.class") => MergeStrategy.discard
-    case "module-info.class"                                           => MergeStrategy.first
+    case "module-info.class" => MergeStrategy.first
     case x =>
       val old = (assembly / assemblyMergeStrategy).value
       old(x)

diff --git a/docs/MANUAL.md b/docs/MANUAL.md
@@ -2,7 +2,7 @@
 
 PoolQ is a counter for indexed samples from next-gen sequencing of pooled DNA.
 
-_This documentation covers PoolQ version 3.11.0 (last updated 02/13/2024)._
+_This documentation covers PoolQ version 3.13.0 (last updated 02/11/2025)._
 
 ## Background
 
@@ -550,8 +550,8 @@ it, you need to download the zip file and unzip it.
 
 ## Prerequisites
 
-PoolQ is built for Java 8. To run PoolQ, you will need a JRE for version 8 or later. To compile
-PoolQ you will need a Java 8 JDK. You can download an appropriate JRE or JDK from Oracle at:
+PoolQ is built for Java 11. To run PoolQ, you will need a JRE for version 11 or later. To compile
+PoolQ you will need a Java 11 JDK. You can download an appropriate JRE or JDK from Oracle at:
 
 > [http://www.oracle.com/technetwork/java/javase/downloads/index.html](http://www.oracle.com/technetwork/java/javase/downloads/index.html)
 

diff --git a/project/build.properties b/project/build.properties
@@ -1 +1 @@
-sbt.version=1.9.9
+sbt.version=1.10.7
diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1,11 +1,11 @@
 addSbtPlugin("ch.epfl.scala" % "sbt-missinglink" % "0.3.6")
-addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.11.0")
+addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.14.0")
 addSbtPlugin("com.codecommit" % "sbt-github-packages" % "0.5.3")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.2.0")
-addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.12.0")
+addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.13.1")
 addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.3.1")
 addSbtPlugin("com.github.sbt" % "sbt-release" % "1.4.0")
 addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.10.0")
-addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.1")
-addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.2")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.11")
+addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.2")
+addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.4")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.3.0")
diff --git a/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQ.scala b/src/main/scala/org/broadinstitute/gpp/poolq3/PoolQ.scala
@@ -13,43 +13,17 @@ 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}
-import org.broadinstitute.gpp.poolq3.process.{
-  Consumer,
-  NoOpConsumer,
-  PoolQProcess,
-  ScoringConsumer,
-  UnexpectedSequenceTracker
-}
+import org.broadinstitute.gpp.poolq3.process.{Consumer, NoOpConsumer, PoolQProcess, ScoringConsumer, UnexpectedSequenceTracker}
 import org.broadinstitute.gpp.poolq3.reference.{ExactReference, Reference}
-import org.broadinstitute.gpp.poolq3.reports.{
-  BarcodeCountsWriter,
-  CorrelationFileWriter,
-  CountsWriter,
-  LogNormalizedCountsWriter,
-  QualityWriter,
-  RunInfoWriter,
-  UmiQualityWriter,
-  UnexpectedSequenceWriter
-}
-import org.broadinstitute.gpp.poolq3.types.{
-  BarcodeCountsFileType,
-  ConditionBarcodeCountsSummaryFileType,
-  CountsFileType,
-  LogNormalizedCountsFileType,
-  OutputFileType,
-  PoolQRunSummary,
-  PoolQSummary,
-  QualityFileType,
-  RunInfoFileType,
-  UnexpectedSequencesFileType
-}
+import org.broadinstitute.gpp.poolq3.reports.{BarcodeCountsWriter, CorrelationFileWriter, CountsWriter, LogNormalizedCountsWriter, QualityWriter, RunInfoWriter, UmiQualityWriter, UnexpectedSequenceWriter}
+import org.broadinstitute.gpp.poolq3.types.{BarcodeCountsFileType, ConditionBarcodeCountsSummaryFileType, CountsFileType, LogNormalizedCountsFileType, OutputFileType, PoolQRunSummary, PoolQSummary, QualityFileType, RunInfoFileType, UnexpectedSequencesFileType}
 import org.log4s.{Logger, getLogger}
 
 object PoolQ:
 
-  private[this] val log: Logger = getLogger
+  private val log: Logger = getLogger
 
-  private[this] val AlwaysWrittenFiles: Set[OutputFileType] =
+  private val AlwaysWrittenFiles: Set[OutputFileType] =
     Set(
       CountsFileType,
       QualityFileType,
@@ -238,11 +212,11 @@ object PoolQ:
     }
 
   private[poolq3] def makeRowBarcodePolicy(
-    rowReferenceData: ReferenceData,
-    rowBarcodePolicyStr: String,
-    reverseRowBarcodePolicyStr: Option[String],
-    reverseRowReads: Option[(Option[String], Path)],
-    skipShortReads: Boolean
+      rowReferenceData: ReferenceData,
+      rowBarcodePolicyStr: String,
+      reverseRowBarcodePolicyStr: Option[String],
+      reverseRowReads: Option[(Option[String], Path)],
+      skipShortReads: Boolean
   ): (BarcodePolicy, Option[BarcodePolicy], Int) =
     (reverseRowBarcodePolicyStr, reverseRowReads)
       .mapN { (revPolicy, _) =>
@@ -256,11 +230,11 @@ object PoolQ:
         (rowBarcodePolicy, None, rowBarcodePolicy.length)
       }
 
-  private[this] def logCli(config: PoolQConfig): Unit =
+  private def logCli(config: PoolQConfig): Unit =
     val logStr =
       synthesizeArgs(config)
         .map {
-          case (param, "")  => s"--$param"
+          case (param, "") => s"--$param"
           case (param, arg) => s"--$param $arg"
         }
         .mkString(" \\\n")