Merge pull request #759 from viash-io/feature/scala3

WIP upgrade to scala 3

CHANGELOG.md

@@ -12,6 +12,11 @@ TODO add summary
 
 * `RRequirements`: Allow single quotes to be used again in the `.script` field (PR #771).
 
+* `scala`: Update Scala to Scala 3 (PR #759).
+  For most of the code, this was a minor update, so no breaking changes are expected.
+  The biggest change is how the exporting of the schema is done, but this has no impact on the user.
+  However, switching to Scala 3 allows for additional features and improvements in the future.
+
 ## BUG FIXES
 
 * `config build`: Fix a bug where a missing main script would cause a stack trace instead of a proper error message (PR #776).

build.sbt

@@ -2,31 +2,36 @@ name := "viash"
 
 version := "0.9.1-dev"
 
-scalaVersion := "2.13.14"
+scalaVersion := "3.3.4"
 
 libraryDependencies ++= Seq(
   "org.scalactic" %% "scalactic" % "3.2.15" % "test",
   "org.scalatest" %% "scalatest" % "3.2.15" % "test",
   "org.rogach" %% "scallop" % "5.0.0",
-  "org.scala-lang" % "scala-reflect" % scalaVersion.value,
   "org.scala-lang.modules" %% "scala-parser-combinators" % "2.1.1",
   "org.scala-lang.modules" %% "scala-parallel-collections" % "1.0.4",
-  "com.github.julien-truffaut" %% "monocle-core"  % "2.1.0",
-  "com.github.julien-truffaut" %% "monocle-macro" % "2.1.0"
+  "dev.optics" %% "monocle-core"  % "3.1.0",
+  "dev.optics" %% "monocle-macro" % "3.1.0"
 )
 
-val circeVersion = "0.14.1"
+val circeVersion = "0.14.7"
 
 libraryDependencies ++= Seq(
   "io.circe" %% "circe-core",
   "io.circe" %% "circe-generic",
   "io.circe" %% "circe-parser",
-  "io.circe" %% "circe-generic-extras",
-  "io.circe" %% "circe-optics",
-  "io.circe" %% "circe-yaml"
+  // "io.circe" %% "circe-generic-extras",
+  // "io.circe" %% "circe-optics",
+  // "io.circe" %% "circe-yaml"
 ).map(_ % circeVersion)
 
-scalacOptions ++= Seq("-unchecked", "-deprecation")
+libraryDependencies ++= Seq(
+  "io.circe" %% "circe-optics" % "0.15.0",
+  "io.circe" %% "circe-yaml" % "0.15.2",
+)
+
+scalacOptions ++= Seq("-unchecked", "-deprecation", "-explain")
+scalacOptions ++= Seq("-Xmax-inlines", "50")
 
 organization := "Data Intuitive"
 startYear := Some(2020)

src/main/scala/io/viash/Main.scala

@@ -34,6 +34,7 @@ import io.viash.helpers.LoggerLevel
 import io.viash.runners.Runner
 import io.viash.config.AppliedConfig
 import io.viash.engines.Engine
+import io.viash.helpers.data_structures.*
 
 object Main extends Logging {
   private val pkg = getClass.getPackage
@@ -551,7 +552,7 @@ object Main extends Logging {
         configs0
       }
 
-      configs1
+    configs1
   }
 
   // Handle dependencies operations for a single config

src/main/scala/io/viash/ViashBuild.scala

@@ -19,6 +19,7 @@ package io.viash
 
 import java.nio.file.{Files, Paths}
 import scala.sys.process.{Process, ProcessLogger}
+import io.viash.helpers.status
 import io.viash.helpers.status._
 
 import config._
@@ -31,7 +32,7 @@ object ViashBuild extends Logging {
     output: String,
     setup: Option[String] = None,
     push: Boolean = false
-  ): Status = {
+  ): status.Status = {
     val resources = appliedConfig.generateRunner(false)
 
     // create dir

src/main/scala/io/viash/ViashTest.scala

@@ -285,7 +285,7 @@ object ViashTest extends Logging {
         val configYaml = ConfigMeta.toMetaFile(appliedConfig, Some(dir))
 
         // assemble full resources list for test
-        val confFinal = resourcesLens.set(
+        val confFinal = resourcesLens.replace(
           testBash ::
           // the executable, wrapped with an executable runner,
           // to be run inside of the runner of the test

src/main/scala/io/viash/cli/DocumentedSubcommand.scala

@@ -21,7 +21,7 @@ import org.rogach.scallop.Subcommand
 import org.rogach.scallop.ScallopOptionGroup
 import org.rogach.scallop.ValueConverter
 import org.rogach.scallop.ScallopOption
-import scala.reflect.runtime.universe._
+import io.viash.helpers.typeOf
 
 /**
   * Wrapper class for Subcommand to expose protected members
@@ -76,7 +76,7 @@ class DocumentedSubcommand(commandNameAndAliases: String*) extends Subcommand(co
   // We need to get the TypeTag[A], which changes the interface of 'opt', however since we have default values we can't just overload the methods.
   // The same goes for 'trailArgs'. Not really for 'choice' but it's better to keep the same change in naming schema here too.
 
-  def registerOpt[A](
+  inline def registerOpt[A](
     name: String,
     short: Option[Char] = None,
     descr: String = "",
@@ -86,9 +86,8 @@ class DocumentedSubcommand(commandNameAndAliases: String*) extends Subcommand(co
     argName: String = "arg",
     hidden: Boolean = false,
     group: ScallopOptionGroup = null
-  )(implicit conv:ValueConverter[A], tag: TypeTag[A]): ScallopOption[A] = {
+  )(implicit conv:ValueConverter[A]): ScallopOption[A] = {
 
-    val `type` = tag.tpe
     val cleanName = name match {
       case null => ""
       case _ => name
@@ -103,14 +102,14 @@ class DocumentedSubcommand(commandNameAndAliases: String*) extends Subcommand(co
       argName = Some(argName), 
       hidden = hidden, 
       choices = None, 
-      `type` = `type`.toString(), 
+      `type` = typeOf[A],
       optType = "opt"
     )
     registeredOpts = registeredOpts :+ registeredOpt
     opt(name, short.getOrElse('\u0000'), removeMarkup(descr), default, validate, required, argName, hidden, short.isEmpty, group)
   }
 
-  def registerChoice(
+  inline def registerChoice(
     choices: Seq[String],
     name: String,
     short: Option[Char],
@@ -143,17 +142,16 @@ class DocumentedSubcommand(commandNameAndAliases: String*) extends Subcommand(co
     choice(choices, name, short.getOrElse('\u0000'), removeMarkup(descr), default, required, argName, hidden, short.isEmpty, group)
   }
 
-  def registerTrailArg[A](
+  inline def registerTrailArg[A](
     name: String,
     descr: String = "",
     validate: A => Boolean = (_:A) => true,
     required: Boolean = true,
     default: => Option[A] = None,
     hidden: Boolean = false,
     group: ScallopOptionGroup = null
-  )(implicit conv:ValueConverter[A], tag: TypeTag[A]) = {
+  )(implicit conv:ValueConverter[A]) = {
 
-    val `type` = tag.tpe
     val cleanName = name match {
       case null => ""
       case _ => name
@@ -168,7 +166,7 @@ class DocumentedSubcommand(commandNameAndAliases: String*) extends Subcommand(co
       argName = None, 
       hidden = hidden, 
       choices = None, 
-      `type` = `type`.toString, 
+      `type` = typeOf[A],
       optType = "trailArgs"
     )
     registeredOpts = registeredOpts :+ registeredOpt

src/main/scala/io/viash/cli/package.scala

@@ -18,7 +18,6 @@
 package io.viash
 
 import io.circe.Encoder
-import io.circe.generic.extras.semiauto.deriveConfiguredEncoder
 import org.rogach.scallop.CliOption
 
 package object cli {

src/main/scala/io/viash/config/ArgumentGroup.scala

@@ -40,7 +40,7 @@ import io.viash.schemas._
     |      - name: "--output_optional"
     |        type: file
     |        direction: output
-    |""".stripMargin,
+    |""",
     "yaml")
 case class ArgumentGroup(
   @description("The name of the argument group.")
@@ -62,7 +62,7 @@ case class ArgumentGroup(
   @example(
     """description: |
       |  A (multiline) description of the purpose of the arguments
-      |  in this argument group.""".stripMargin, "yaml")
+      |  in this argument group.""", "yaml")
   @default("Empty")
   description: Option[String] = None,
 
@@ -76,7 +76,7 @@ case class ArgumentGroup(
       | - @[boolean](arg_boolean)
       | - @[boolean_true](arg_boolean_true)
       | - @[boolean_false](arg_boolean_false)
-      |""".stripMargin)
+      |""")
   @example(
     """arguments:
       |  - name: --foo
@@ -91,7 +91,7 @@ case class ArgumentGroup(
       |    multiple_sep: ";"
       |  - name: --bar
       |    type: string
-      |""".stripMargin,
+      |""",
       "yaml")
   @default("Empty")
   arguments: List[Argument[_]] = Nil

src/main/scala/io/viash/config/Author.scala

@@ -34,7 +34,7 @@ import io.viash.schemas._
     |    twitter: janedoe
     |    orcid: XXAABBCCXX
     |    groups: [ one, two, three ]
-    |""".stripMargin, "yaml")
+    |""", "yaml")
 case class Author(
   @description("Full name of the author, usually in the name of FirstName MiddleName LastName.")
   name: String,
@@ -48,7 +48,7 @@ case class Author(
       |* `"author"`: Authors who have made substantial contributions to the component.
       |* `"maintainer"`: The maintainer of the component.
       |* `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
-      |""".stripMargin)
+      |""")
   @default("Empty")
   roles: OneOrMore[String] = Nil,
 

src/main/scala/io/viash/config/ComputationalRequirements.scala

@@ -24,7 +24,7 @@ import io.viash.schemas._
   """requirements:
     |  cpus: 5
     |  memory: 10GB
-    |""".stripMargin,
+    |""",
     "yaml")
 @since("Viash 0.6.0")
 case class ComputationalRequirements(