From 7ab6d814e10fdc2038ba4ce237e1636cbb751e97 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:30:02 -0700 Subject: [PATCH 01/12] Use sbt 1.9.9 --- project/build.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project/build.properties b/project/build.properties index abbbce5..04267b1 100644 --- a/project/build.properties +++ b/project/build.properties @@ -1 +1 @@ -sbt.version=1.9.8 +sbt.version=1.9.9 From af2354c20c048f7b1693bc3b3a4b00261514272d Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:30:08 -0700 Subject: [PATCH 02/12] Update dependencies --- build.sbt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/build.sbt b/build.sbt index 8568f98..090eeb0 100644 --- a/build.sbt +++ b/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") @@ -11,18 +11,18 @@ 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 commonsIo = "2.16.0" val commonsText = "1.11.0" 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 samTools = "4.1.0" val scalaCheck = "1.17.0" val scalaCsv = "1.3.10" val scalaTest = "3.2.18" From 7ac96283794b62adc7059d14293ab8322bc02cc5 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:30:13 -0700 Subject: [PATCH 03/12] Update plugins --- project/plugins.sbt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/project/plugins.sbt b/project/plugins.sbt index b686cc6..eace698 100644 --- 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" % "0.12.0") 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.scalameta" % "sbt-scalafmt" % "2.5.2") +addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.11") From 693d6e4e839e5dc44c669eb8f171641807b7c9a8 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:30:18 -0700 Subject: [PATCH 04/12] Update changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 25ce629..da1b7eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,8 @@ # Changelog +## 3.12.1 +No user-facing changes + ## 3.12.0 * Update to Scala 3.3.1 From 9d570eed2d6f65da7fb12082fcd9ef1131a0a3a0 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:38:40 -0700 Subject: [PATCH 05/12] Use scalafmt 3.8.1 --- .scalafmt.conf | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.scalafmt.conf b/.scalafmt.conf index afac328..a2746b5 100644 --- a/.scalafmt.conf +++ b/.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 From a46b13b98349f4184df046f1141e431cdc01465d Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Tue, 2 Apr 2024 13:38:46 -0700 Subject: [PATCH 06/12] Update scalafmt in github actions --- .github/workflows/ci.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3b60555..2692984 100644 --- a/.github/workflows/ci.yml +++ b/.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: diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index a7a1759..b90a9c2 100644 --- a/.github/workflows/release.yml +++ b/.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: From 2c264ce993503220b44e5513177942586feb435f Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:08:30 -0700 Subject: [PATCH 07/12] =?UTF-8?q?Improved=20error=20messaging=20=E2=80=A2?= =?UTF-8?q?=20quote=20with=20`=20=E2=80=A2=20use=20mkString=20to=20avoid?= =?UTF-8?q?=20showing=20`List()`?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../org/broadinstitute/gpp/poolq3/parser/BarcodeSet.scala | 2 +- .../org/broadinstitute/gpp/poolq3/parser/ReferenceData.scala | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/scala/org/broadinstitute/gpp/poolq3/parser/BarcodeSet.scala b/src/main/scala/org/broadinstitute/gpp/poolq3/parser/BarcodeSet.scala index d5345e1..9f6f9ad 100644 --- a/src/main/scala/org/broadinstitute/gpp/poolq3/parser/BarcodeSet.scala +++ b/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 diff --git a/src/main/scala/org/broadinstitute/gpp/poolq3/parser/ReferenceData.scala b/src/main/scala/org/broadinstitute/gpp/poolq3/parser/ReferenceData.scala index 9b1ded7..16f8327 100644 --- a/src/main/scala/org/broadinstitute/gpp/poolq3/parser/ReferenceData.scala +++ b/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("`", "`, `", "`")}" ) } From e291cf754818443cf9f2d6193e0450599b7df924 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:22:12 -0700 Subject: [PATCH 08/12] Update dependencies --- build.sbt | 6 +++--- project/plugins.sbt | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/build.sbt b/build.sbt index 090eeb0..9d58150 100644 --- a/build.sbt +++ b/build.sbt @@ -13,8 +13,8 @@ lazy val versions = new { val betterFiles = "3.9.2" val catsEffect3 = "3.5.4" val cats = "2.10.0" - val commonsIo = "2.16.0" - 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 = "3.10.2" @@ -23,7 +23,7 @@ lazy val versions = new { val munit = "0.7.29" val munitCatsEffect3 = "1.0.7" val samTools = "4.1.0" - 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" diff --git a/project/plugins.sbt b/project/plugins.sbt index eace698..a91299b 100644 --- a/project/plugins.sbt +++ b/project/plugins.sbt @@ -6,6 +6,6 @@ addSbtPlugin("com.eed3si9n" % "sbt-buildinfo" % "0.12.0") addSbtPlugin("com.github.cb372" % "sbt-explicit-dependencies" % "0.3.1") addSbtPlugin("com.github.sbt" % "sbt-release" % "1.4.0") addSbtPlugin("de.heikoseeberger" % "sbt-header" % "5.10.0") -addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.0") +addSbtPlugin("org.typelevel" % "sbt-tpolecat" % "0.5.1") addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.2") addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.11") From 46755c006dd0da382a340ac9c63788f0455eab0d Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:22:21 -0700 Subject: [PATCH 09/12] Try jdk11 --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2692984..54ab373 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,10 +17,10 @@ jobs: - uses: jrouly/scalafmt-native-action@v3 with: version: "3.8.1" - - name: Set up JDK 8 + - name: Set up JDK 11 uses: actions/setup-java@v4 with: - java-version: '8' + java-version: '11' distribution: 'temurin' - run: sbt "scalafixAll --check" - name: Run tests From c9f2b983c060f87ad519e6bc62ff05b407cdce48 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:24:57 -0700 Subject: [PATCH 10/12] Back off jdk update --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 54ab373..2692984 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,10 +17,10 @@ jobs: - uses: jrouly/scalafmt-native-action@v3 with: version: "3.8.1" - - name: Set up JDK 11 + - name: Set up JDK 8 uses: actions/setup-java@v4 with: - java-version: '11' + java-version: '8' distribution: 'temurin' - run: sbt "scalafixAll --check" - name: Run tests From 47c94f59e929f2d2389efbd7319970a647605c24 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:25:03 -0700 Subject: [PATCH 11/12] Back off scalafix update --- project/plugins.sbt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project/plugins.sbt b/project/plugins.sbt index a91299b..7774e97 100644 --- a/project/plugins.sbt +++ b/project/plugins.sbt @@ -1,5 +1,5 @@ addSbtPlugin("ch.epfl.scala" % "sbt-missinglink" % "0.3.6") -addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.12.0") +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" % "0.12.0") From 8c97e87b85a143a6cf53fbfea1af64c288b0b9d9 Mon Sep 17 00:00:00 2001 From: Mark Tomko Date: Thu, 18 Apr 2024 09:41:58 -0700 Subject: [PATCH 12/12] Stick with JDK8 for now --- build.sbt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sbt b/build.sbt index 9d58150..eab08e3 100644 --- a/build.sbt +++ b/build.sbt @@ -22,7 +22,7 @@ lazy val versions = new { val logback = "1.2.13" val munit = "0.7.29" val munitCatsEffect3 = "1.0.7" - val samTools = "4.1.0" + val samTools = "3.0.5" val scalaCheck = "1.18.0" val scalaCsv = "1.3.10" val scalaTest = "3.2.18"