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Updates #36

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merged 12 commits into from
Apr 18, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion .github/workflows/release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
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8 changes: 1 addition & 7 deletions .scalafmt.conf
Original file line number Diff line number Diff line change
@@ -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
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3 changes: 3 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
# Changelog

## 3.12.1
No user-facing changes

## 3.12.0
* Update to Scala 3.3.1

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12 changes: 6 additions & 6 deletions build.sbt
Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand All @@ -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"
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2 changes: 1 addition & 1 deletion project/build.properties
Original file line number Diff line number Diff line change
@@ -1 +1 @@
sbt.version=1.9.8
sbt.version=1.9.9
10 changes: 5 additions & 5 deletions project/plugins.sbt
Original file line number Diff line number Diff line change
Expand Up @@ -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")
Original file line number Diff line number Diff line change
Expand Up @@ -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`")))
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question: why is this an improvement?

.map(bcs => new BarcodeSet(bcs.toSet))
.flatTap(checkSet(file, _))
.get // throws if an error was encountered
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Original file line number Diff line number Diff line change
Expand Up @@ -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("`", "`, `", "`")}"
)
}

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