Updates (#36)

* Use sbt 1.9.9

* Update dependencies

* Update plugins

* Update changelog

* Use scalafmt 3.8.1

* Update scalafmt in github actions

* Improved error messaging
• quote with `
• use mkString to avoid showing `List()`

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: jrouly/scalafmt-native-action@v3
       with:
-        version: "3.8.0"
+        version: "3.8.1"
     - name: Set up JDK 8
       uses: actions/setup-java@v4
       with:

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
     - run: git config --global user.name "GPP Informatics"
     - uses: jrouly/scalafmt-native-action@v3
       with:
-        version: "3.8.0"
+        version: "3.8.1"
     - name: Set up JDK 8
       uses: actions/setup-java@v4
       with:

.scalafmt.conf

@@ -1,13 +1,7 @@
 # PoolQ3 .scalafmt configuration
-version=3.8.0
+version=3.8.1
 runner.dialect = scala3
 
-# work around https://github.com/scalameta/scalafmt/issues/3787
-fileOverride {
-  "glob:**.sbt" {
-    runner.dialect = sbt1
-  }
-}
 style = IntelliJ
 
 maxColumn = 120

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## 3.12.1
+No user-facing changes
+
 ## 3.12.0
 * Update to Scala 3.3.1
 

build.sbt

@@ -2,7 +2,7 @@ val artifactId = "poolq"
 
 inThisBuild(
   List(
-    scalaVersion := "3.3.1",
+    scalaVersion := "3.3.3",
     semanticdbEnabled := true,
     semanticdbVersion := scalafixSemanticdb.revision,
     versionScheme := Some("early-semver")
@@ -11,19 +11,19 @@ inThisBuild(
 
 lazy val versions = new {
   val betterFiles = "3.9.2"
-  val catsEffect3 = "3.5.3"
+  val catsEffect3 = "3.5.4"
   val cats = "2.10.0"
-  val commonsIo = "2.15.1"
-  val commonsText = "1.11.0"
+  val commonsIo = "2.16.1"
+  val commonsText = "1.12.0"
   val commonsMath3 = "3.6.1"
   val fastutil = "8.5.13"
-  val fs2 = "3.9.4"
+  val fs2 = "3.10.2"
   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 scalaCheck = "1.18.0"
   val scalaCsv = "1.3.10"
   val scalaTest = "3.2.18"
   val scalaTestPlusScalaCheck = "3.2.18.0"

project/build.properties

@@ -1 +1 @@
-sbt.version=1.9.8
+sbt.version=1.9.9

project/plugins.sbt

@@ -2,10 +2,10 @@ addSbtPlugin("ch.epfl.scala" % "sbt-missinglink" % "0.3.6")
 addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.11.0")
 addSbtPlugin("com.codecommit" % "sbt-github-packages" % "0.5.3")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.2.0")
-addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.11.0")
+addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.12.0")
 addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.3.1")
-addSbtPlugin("com.github.sbt" % "sbt-release" % "1.1.0")
+addSbtPlugin("com.github.sbt" % "sbt-release" % "1.4.0")
 addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.10.0")
-addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.0")
-addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.0")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.8")
+addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.1")
+addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.2")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.11")

src/main/scala/org/broadinstitute/gpp/poolq3/parser/BarcodeSet.scala

@@ -46,7 +46,7 @@ object BarcodeSet:
         .asScala
         .toList
         .map(_.trim)
-        .traverse(parseBarcode(s => InvalidFileException(file, s"Invalid DNA barcode '$s'")))
+        .traverse(parseBarcode(s => InvalidFileException(file, s"Invalid DNA barcode `$s`")))
         .map(bcs => new BarcodeSet(bcs.toSet))
         .flatTap(checkSet(file, _))
         .get // throws if an error was encountered

src/main/scala/org/broadinstitute/gpp/poolq3/parser/ReferenceData.scala

@@ -93,11 +93,11 @@ object ReferenceData:
             // and reject cases where the barcode is empty but the ID is non-empty
             if barcode.isEmpty && id.isEmpty then None
             else if isReferenceBarcode(barcode) then Some(ReferenceEntry(barcode, id))
-            else throw InvalidFileException(file, s"Invalid DNA barcode '$barcode' for ID '$id'")
+            else throw InvalidFileException(file, s"Invalid DNA barcode '$barcode' for ID `$id`")
           case _ =>
             throw InvalidFileException(
               file,
-              s"Incorrect number of columns. At least 2 required, got: ${xs.length}: $xs"
+              s"Incorrect number of columns. At least 2 required, got: ${xs.length}: ${xs.mkString("`", "`, `", "`")}"
             )
       }