fix a few warnings

Author: tribbloid

module/core/src/main/scala/com/tribbloids/spookystuff/agent/Agent.scala

@@ -17,7 +17,7 @@ import scala.util.Try
 /**
   * the only implementation should be manually cleaned By ActionLike, so don't set lifespan unless absolutely necessary
   */
-class Agent(
+class Agent( // TODO: this is actually the harness, not the agent
     val spooky: SpookyContext,
     override val _lifespan: Lifespan = Lifespan.TaskOrJVM().forShipping
 ) extends LocalCleanable {

module/core/src/main/scala/com/tribbloids/spookystuff/agent/PythonDriver.scala

@@ -9,7 +9,7 @@ import com.tribbloids.spookystuff.commons.lifespan.Cleanable.Lifespan
 import com.tribbloids.spookystuff.commons.{CommonUtils, DSLUtils}
 import com.tribbloids.spookystuff.io.{LocalResolver, WriteMode}
 import com.tribbloids.spookystuff.utils.SpookyUtils
-import com.tribbloids.spookystuff.{CommonConst, PyException, PyInterpretationException, SpookyContext}
+import com.tribbloids.spookystuff.{CommonConst, PyInterpretationException, PythonException, SpookyContext}
 import org.apache.commons.io.FileUtils
 import org.slf4j.LoggerFactory
 
@@ -151,7 +151,7 @@ class PythonDriver(
               try {
                 this._interpret("exit()")
               } catch {
-                case _: PyException =>
+                case _: PythonException =>
               }
             }
             Thread.sleep(1000)
@@ -221,7 +221,7 @@ class PythonDriver(
               )
             return Array.empty[String]
           } else {
-            val ee = new PyException(
+            val ee = new PyInterpretationException(
               indentedCode,
               this.outputBuffer,
               cause,
@@ -258,9 +258,9 @@ class PythonDriver(
   }
 
   private def _interpretCaptureError(
-      preamble: String = "",
-      code: String = "",
-      spookyOpt: Option[SpookyContext] = None
+      preamble: String,
+      code: String,
+      spookyOpt: Option[SpookyContext]
   ): Array[String] = {
 
     val codeTryExcept =

module/core/src/main/scala/com/tribbloids/spookystuff/doc/Observation.scala

@@ -52,6 +52,10 @@ object Observation {
 }
 
 // all subclasses should be small, will be shipped around by Spark
+
+/**
+  * always indexed by its UID
+  */
 @SQLUserDefinedType(udt = classOf[FetchedUDT])
 sealed trait Observation extends Serializable {
 

module/core/src/main/scala/com/tribbloids/spookystuff/exceptions.scala

@@ -31,12 +31,14 @@ class ActionExceptionWithCoreDump(
 ) extends ActionException(getMessage_simple, getCause)
     with HasCoreDump
 
-class PyException(
-    val code: String,
-    val output: String,
+trait PythonException extends SpookyException {}
+
+case class PyInterpretationException(
+    code: String,
+    output: String,
     override val getCause: Throwable = null,
-    val historyCodeOpt: Option[String] = None
-) extends SpookyException {
+    historyCodeOpt: Option[String] = None
+) extends PythonException {
 
   override def getMessage_simple: String =
     s"""
@@ -50,18 +52,11 @@ class PyException(
      """.stripMargin.trim
 }
 
-case class PyInterpretationException(
-    override val code: String,
-    override val output: String,
-    override val getCause: Throwable = null,
-    override val historyCodeOpt: Option[String] = None
-) extends PyException(code, output, getCause, historyCodeOpt)
-
 class DFSReadException(
     override val getMessage_simple: String = "",
     override val getCause: Throwable = null
 ) extends IOException(getMessage_simple, getCause)
-    with SpookyException
+    with SpookyException {}
 
 class DFSWriteException(
     override val getMessage_simple: String = "",

module/core/src/main/scala/com/tribbloids/spookystuff/execution/ExploreRunner.scala

@@ -98,7 +98,6 @@ case class ExploreRunner[I, O](
       val newVs = reducer(effective, oldVs)
       open += group -> newVs
 
-      open
     }
 
     def intoVisited(
@@ -125,7 +124,6 @@ case class ExploreRunner[I, O](
 
 //      val __DEBUG = newVs.map(v => v._1.depth)
 
-      visited
     }
   }
 

module/core/src/test/scala/com/tribbloids/spookystuff/execution/ExploreRunnerSpec.scala

@@ -39,7 +39,7 @@ class ExploreRunnerSpec extends SpookyBaseSpec {
           dirs.findFirst("path").flatMap(_.text)
         }
 
-      val plan = Option(ds.plan).collect {
+      val plan: ExplorePlan[Data.Exploring[Unit], Option[String]] = Option(ds.plan).collect {
         case v: ExplorePlan[Data.Exploring[Unit], Option[String]] => v
       }.get
 
@@ -104,7 +104,7 @@ class ExploreRunnerSpec extends SpookyBaseSpec {
           action
         }
 
-      val plan = Option(ds.plan).collect {
+      val plan: ExplorePlan[Data.Exploring[Unit], Data.Exploring[Option[String]]] = Option(ds.plan).collect {
         case v: ExplorePlan[Data.Exploring[Unit], Data.Exploring[Option[String]]] => v
       }.get