Modify the tests to run from the main app

src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala

@@ -1,7 +1,6 @@
 package eu.neverblink.jelly.cli
 
 import caseapp.*
-import eu.neverblink.jelly.cli.JellyCommand.emptyRemainingArgs
 
 import java.io.{ByteArrayOutputStream, OutputStream, PrintStream}
 import scala.compiletime.uninitialized
@@ -51,23 +50,10 @@ abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
       s
     else throw new IllegalStateException("Not in test mode")
 
-  /** Run the command in test mode, capturing stdout and stderr.
-    * @param options
-    *   the command options
-    * @param remainingArgs
-    *   the remaining arguments
-    * @throws ExitError
-    *   if the command exits
-    * @return
-    *   (stdout, stderr)
-    */
-  @throws[ExitError]
-  def runTest(options: T, remainingArgs: RemainingArgs = emptyRemainingArgs): (String, String) =
+  def setUpTest(): Unit =
     if !isTest then testMode(true)
     osOut.reset()
     osErr.reset()
-    run(options, remainingArgs)
-    (getOut, getErr)
 
   @throws[ExitError]
   override def exit(code: Int): Nothing =

src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala

@@ -1,6 +1,5 @@
 package eu.neverblink.jelly.cli.command
 
-import caseapp.core.{Indexed, RemainingArgs}
 import eu.neverblink.jelly.cli.command.helpers.*
 import eu.neverblink.jelly.cli.command.rdf.*
 import org.apache.jena.riot.RDFLanguages
@@ -11,37 +10,35 @@ import scala.io.Source
 import scala.util.Using
 
 class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
+
   "rdf from-jelly command" should {
     "be able to convert a Jelly file to NTriples output stream" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = None)
-      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
       val (out, err) =
-        RdfFromJelly.runTest(
-          options,
-          args,
-        )
+        TestAppRunner.runCommand(RdfFromJelly, List("rdf", "from-jelly", jellyFile))
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
+
     "be able to convert a Jelly stream to NTriples output stream" in {
       DataGenHelper.generateJellyInputStream(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = None)
-      val (out, err) = RdfFromJelly.runTest(options)
+      val (out, err) = TestAppRunner.runCommand(RdfFromJelly, List("rdf", "from-jelly"))
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
     "be able to convert a Jelly file to NTriples file" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
-      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
       val nQuadString = DataGenHelper.generateNQuadString(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
-      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
-      val (out, err) = RdfFromJelly.runTest(options, args)
+      val (out, err) =
+        TestAppRunner.runCommand(
+          RdfFromJelly,
+          List("rdf", "from-jelly", jellyFile, "--to", outputFile),
+        )
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted
       }
@@ -53,8 +50,8 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
       DataGenHelper.generateJellyInputStream(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
-      val (out, err) = RdfFromJelly.runTest(options)
+      val (out, err) =
+        TestAppRunner.runCommand(RdfFromJelly, List("rdf", "from-jelly", "--to", outputFile))
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted
       }

src/test/scala/eu/neverblink/jelly/cli/command/VersionSpec.scala

@@ -1,12 +1,13 @@
 package eu.neverblink.jelly.cli.command
 
+import eu.neverblink.jelly.cli.command.helpers.TestAppRunner
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpec
 
 class VersionSpec extends AnyWordSpec, Matchers:
   "version command" should {
     "print something" in {
-      val (out, err) = Version.runTest(VersionOptions())
+      val (out, err) = TestAppRunner.runCommand(Version, List("version"))
       out should startWith("jelly-cli")
       out should include("Jelly-JVM")
       out should include("Apache Jena")

src/test/scala/eu/neverblink/jelly/cli/command/helpers/TestAppRunner.scala

@@ -0,0 +1,15 @@
+package eu.neverblink.jelly.cli.command.helpers
+import eu.neverblink.jelly.cli.{App, JellyCommand}
+
+object TestAppRunner:
+  /*
+   * Runs a command in test mode from the outside app parsing level
+   * @param command
+   *  the command to run
+   * @param args
+   * the command line arguments
+   */
+  def runCommand(command: JellyCommand[?], args: List[String]): (String, String) =
+    command.setUpTest()
+    App.main(args.toArray)
+    (command.getOut, command.getErr)