Code syntax to Scala 3 and Typelevel SBT plugin migration

gvonness · Aug 13, 2023 · bad35ec · bad35ec
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -9,111 +9,171 @@ name: Continuous Integration
 
 on:
   pull_request:
-    branches: ['**']
+    branches: ['**', '!update/**', '!pr/**']
   push:
-    branches: ['**']
+    branches: ['**', '!update/**', '!pr/**']
     tags: [v*]
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  SONATYPE_USERNAME: ${{ secrets.SONATYPE_USERNAME }}
-  SONATYPE_PASSWORD: ${{ secrets.SONATYPE_PASSWORD }}
-  PGP_SECRET: ${{ secrets.PGP_SECRET }}
+
+
+concurrency:
+  group: ${{ github.workflow }} @ ${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build:
     name: Build and Test
     strategy:
       matrix:
         os: [ubuntu-latest]
-        scala: [2.13.11]
-        java: [temurin@11]
+        scala: [2.13]
+        java: [temurin@8]
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
     steps:
       - name: Checkout current branch (full)
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Setup Java (temurin@11)
-        if: matrix.java == 'temurin@11'
-        uses: actions/setup-java@v2
+      - name: Setup Java (temurin@8)
+        id: setup-java-temurin-8
+        if: matrix.java == 'temurin@8'
+        uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 11
+          java-version: 8
+          cache: sbt
 
-      - name: Cache sbt
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.sbt
-            ~/.ivy2/cache
-            ~/.coursier/cache/v1
-            ~/.cache/coursier/v1
-            ~/AppData/Local/Coursier/Cache/v1
-            ~/Library/Caches/Coursier/v1
-          key: ${{ runner.os }}-sbt-cache-v2-${{ hashFiles('**/*.sbt') }}-${{ hashFiles('project/build.properties') }}
+      - name: sbt update
+        if: matrix.java == 'temurin@8' && steps.setup-java-temurin-8.outputs.cache-hit == 'false'
+        run: sbt +update
 
       - name: Check that workflows are up to date
-        run: sbt ++${{ matrix.scala }} githubWorkflowCheck
+        run: sbt githubWorkflowCheck
+
+      - name: Check headers and formatting
+        if: matrix.java == 'temurin@8' && matrix.os == 'ubuntu-latest'
+        run: sbt '++ ${{ matrix.scala }}' headerCheckAll scalafmtCheckAll 'project /' scalafmtSbtCheck
+
+      - name: Test
+        run: sbt '++ ${{ matrix.scala }}' test
+
+      - name: Check binary compatibility
+        if: matrix.java == 'temurin@8' && matrix.os == 'ubuntu-latest'
+        run: sbt '++ ${{ matrix.scala }}' mimaReportBinaryIssues
 
-      - run: sbt ++${{ matrix.scala }} ci
+      - name: Generate API documentation
+        if: matrix.java == 'temurin@8' && matrix.os == 'ubuntu-latest'
+        run: sbt '++ ${{ matrix.scala }}' doc
+
+      - name: Make target directories
+        if: github.event_name != 'pull_request' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main')
+        run: mkdir -p target project/target
 
       - name: Compress target directories
+        if: github.event_name != 'pull_request' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main')
         run: tar cf targets.tar target project/target
 
       - name: Upload target directories
-        uses: actions/upload-artifact@v2
+        if: github.event_name != 'pull_request' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main')
+        uses: actions/upload-artifact@v3
         with:
-          name: target-${{ matrix.os }}-${{ matrix.scala }}-${{ matrix.java }}
+          name: target-${{ matrix.os }}-${{ matrix.java }}-${{ matrix.scala }}
           path: targets.tar
 
   publish:
     name: Publish Artifacts
     needs: [build]
-    if: github.event_name != 'pull_request' && (startsWith(github.ref, 'refs/tags/v'))
+    if: github.event_name != 'pull_request' && (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main')
     strategy:
       matrix:
         os: [ubuntu-latest]
-        scala: [2.13.11]
-        java: [temurin@11]
+        java: [temurin@8]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout current branch (full)
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Setup Java (temurin@11)
-        if: matrix.java == 'temurin@11'
-        uses: actions/setup-java@v2
+      - name: Setup Java (temurin@8)
+        id: setup-java-temurin-8
+        if: matrix.java == 'temurin@8'
+        uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 11
+          java-version: 8
+          cache: sbt
 
-      - name: Cache sbt
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.sbt
-            ~/.ivy2/cache
-            ~/.coursier/cache/v1
-            ~/.cache/coursier/v1
-            ~/AppData/Local/Coursier/Cache/v1
-            ~/Library/Caches/Coursier/v1
-          key: ${{ runner.os }}-sbt-cache-v2-${{ hashFiles('**/*.sbt') }}-${{ hashFiles('project/build.properties') }}
-
-      - name: Download target directories (2.13.11)
-        uses: actions/download-artifact@v2
+      - name: sbt update
+        if: matrix.java == 'temurin@8' && steps.setup-java-temurin-8.outputs.cache-hit == 'false'
+        run: sbt +update
+
+      - name: Download target directories (2.13)
+        uses: actions/download-artifact@v3
         with:
-          name: target-${{ matrix.os }}-2.13.11-${{ matrix.java }}
+          name: target-${{ matrix.os }}-${{ matrix.java }}-2.13
 
-      - name: Inflate target directories (2.13.11)
+      - name: Inflate target directories (2.13)
         run: |
           tar xf targets.tar
           rm targets.tar
 
       - name: Import signing key
-        run: echo $PGP_SECRET | base64 -d | gpg --import
+        if: env.PGP_SECRET != '' && env.PGP_PASSPHRASE == ''
+        env:
+          PGP_SECRET: ${{ secrets.PGP_SECRET }}
+          PGP_PASSPHRASE: ${{ secrets.PGP_PASSPHRASE }}
+        run: echo $PGP_SECRET | base64 -di | gpg --import
+
+      - name: Import signing key and strip passphrase
+        if: env.PGP_SECRET != '' && env.PGP_PASSPHRASE != ''
+        env:
+          PGP_SECRET: ${{ secrets.PGP_SECRET }}
+          PGP_PASSPHRASE: ${{ secrets.PGP_PASSPHRASE }}
+        run: |
+          echo "$PGP_SECRET" | base64 -di > /tmp/signing-key.gpg
+          echo "$PGP_PASSPHRASE" | gpg --pinentry-mode loopback --passphrase-fd 0 --import /tmp/signing-key.gpg
+          (echo "$PGP_PASSPHRASE"; echo; echo) | gpg --command-fd 0 --pinentry-mode loopback --change-passphrase $(gpg --list-secret-keys --with-colons 2> /dev/null | grep '^sec:' | cut --delimiter ':' --fields 5 | tail -n 1)
+
+      - name: Publish
+        env:
+          SONATYPE_USERNAME: ${{ secrets.SONATYPE_USERNAME }}
+          SONATYPE_PASSWORD: ${{ secrets.SONATYPE_PASSWORD }}
+          SONATYPE_CREDENTIAL_HOST: ${{ secrets.SONATYPE_CREDENTIAL_HOST }}
+        run: sbt tlCiRelease
+
+  dependency-submission:
+    name: Submit Dependencies
+    if: github.event_name != 'pull_request'
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        java: [temurin@8]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout current branch (full)
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
-      - run: sbt ++${{ matrix.scala }} release
+      - name: Setup Java (temurin@8)
+        id: setup-java-temurin-8
+        if: matrix.java == 'temurin@8'
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 8
+          cache: sbt
+
+      - name: sbt update
+        if: matrix.java == 'temurin@8' && steps.setup-java-temurin-8.outputs.cache-hit == 'false'
+        run: sbt +update
+
+      - name: Submit Dependencies
+        uses: scalacenter/sbt-dependency-submission@v2
+        with:
+          configs-ignore: test scala-tool scala-doc-tool test-internal
diff --git a/.scalafmt.conf b/.scalafmt.conf
@@ -22,4 +22,4 @@ spaces {
 }
 
 project.git = true
-runner.dialect = scala213
+runner.dialect = scala3
diff --git a/build.sbt b/build.sbt
@@ -1,24 +1,13 @@
-ThisBuild / baseVersion := "0.9.0"
-
-ThisBuild / organization      := "ai.entrolution"
-ThisBuild / organizationName  := "Greg von Nessi"
-ThisBuild / publishGithubUser := "gvonness"
-ThisBuild / publishFullName   := "Greg von Nessi"
-
-ThisBuild / homepage := Some(url("https://github.com/gvonness/thylacine"))
-ThisBuild / scmInfo := Some(
-  ScmInfo(url("https://github.com/gvonness/thylacine"), "git@github.com:gvonness/thylacine.git")
+ThisBuild / tlBaseVersion := "0.10"
+
+ThisBuild / organization     := "ai.entrolution"
+ThisBuild / organizationName := "Greg von Nessi"
+ThisBuild / startYear        := Some(2023)
+ThisBuild / licenses         := Seq(License.Apache2)
+ThisBuild / developers ++= List(
+  tlGitHubDev("gvonness", "Greg von Nessi")
 )
 
-ThisBuild / startYear := Some(2020)
-ThisBuild / endYear   := Some(2022)
-
-ThisBuild / spiewakCiReleaseSnapshots := false
-ThisBuild / spiewakMainBranches       := Seq("main")
-
-ThisBuild / sonatypeCredentialHost := "s01.oss.sonatype.org"
-ThisBuild / sonatypeRepository     := "https://s01.oss.sonatype.org/service/local"
-
 scalaVersion                   := DependencyVersions.scala2p13Version
 ThisBuild / crossScalaVersions := Seq(DependencyVersions.scala2p13Version)
 
@@ -41,7 +30,6 @@ lazy val commonSettings = Seq(
 )
 
 lazy val thylacine = (project in file("."))
-  .enablePlugins(SonatypeCiReleasePlugin)
   .settings(
     commonSettings,
     name := "thylacine",

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -3,7 +3,7 @@ import sbt.*
 object DependencyVersions {
   val scala2p13Version = "2.13.11"
 
-  val bengalStmVersion           = "0.9.4"
+  val bengalStmVersion           = "0.9.5"
   val bigMathVersion             = "2.3.2"
   val breezeVersion              = "2.1.0"
   val catsEffectVersion          = "3.4.8"

diff --git a/project/plugins.sbt b/project/plugins.sbt
@@ -1,5 +1,2 @@
-addSbtPlugin("org.jetbrains"    % "sbt-ide-settings"     % "1.1.0")
-addSbtPlugin("org.scalameta"    % "sbt-scalafmt"         % "2.4.6")
-addSbtPlugin("ch.epfl.scala"    % "sbt-scalafix"         % "0.9.34")
-addSbtPlugin("com.codecommit"   % "sbt-spiewak-sonatype" % "0.23.0")
-addCompilerPlugin("com.olegpy" %% "better-monadic-for"   % "0.3.1" % "test")
+addSbtPlugin("org.jetbrains" % "sbt-ide-settings" % "1.1.0")
+addSbtPlugin("org.typelevel" % "sbt-typelevel"    % "0.5.0-RC11")
diff --git a/src/main/scala/thylacine/config/ConjugateGradientConfig.scala b/src/main/scala/thylacine/config/ConjugateGradientConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/CoordinateSlideConfig.scala b/src/main/scala/thylacine/config/CoordinateSlideConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/HmcmcConfig.scala b/src/main/scala/thylacine/config/HmcmcConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/HookeAndJeevesConfig.scala b/src/main/scala/thylacine/config/HookeAndJeevesConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/LeapfrogMcmcConfig.scala b/src/main/scala/thylacine/config/LeapfrogMcmcConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/MdsConfig.scala b/src/main/scala/thylacine/config/MdsConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/config/SlqConfig.scala b/src/main/scala/thylacine/config/SlqConfig.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/model/components/forwardmodel/ForwardModel.scala b/src/main/scala/thylacine/model/components/forwardmodel/ForwardModel.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -17,12 +17,12 @@
 package ai.entrolution
 package thylacine.model.components.forwardmodel
 
-import thylacine.model.core._
-import thylacine.model.core.values._
+import thylacine.model.core.*
+import thylacine.model.core.values.*
 
-import cats.syntax.all._
+import cats.syntax.all.*
 
-private[thylacine] trait ForwardModel[F[_]] extends GenericMapping with CanValidate[ForwardModel[F]] {
+trait ForwardModel[F[_]] extends GenericMapping with CanValidate[ForwardModel[F]] {
   this: AsyncImplicits[F] =>
 
   // Note that input validation should be done within

diff --git a/src/main/scala/thylacine/model/components/forwardmodel/InMemoryMemoizedForwardModel.scala b/src/main/scala/thylacine/model/components/forwardmodel/InMemoryMemoizedForwardModel.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/src/main/scala/thylacine/model/components/forwardmodel/LinearForwardModel.scala b/src/main/scala/thylacine/model/components/forwardmodel/LinearForwardModel.scala
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2022 Greg von Nessi
+ * Copyright 2023 Greg von Nessi
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -18,15 +18,15 @@ package ai.entrolution
 package thylacine.model.components.forwardmodel
 
 import bengal.stm.STM
-import thylacine.model.core.GenericIdentifier._
-import thylacine.model.core._
+import thylacine.model.core.GenericIdentifier.*
+import thylacine.model.core.*
 import thylacine.model.core.computation.CachedComputation
-import thylacine.model.core.values._
+import thylacine.model.core.values.*
 import thylacine.model.core.values.modelparameters.ModelParameterContext
 
 import breeze.linalg.{ DenseMatrix, DenseVector }
 import cats.effect.kernel.Async
-import cats.syntax.all._
+import cats.syntax.all.*
 
 import scala.annotation.unused