Stream-based runner (#269)

* Stream-based runner

Additionally, restricted the possible Monad instances that can be
used with the `repeat` function and also generalized `repeat` to work
for both `Step` and `StepS` structures.

* Allow for custom measurements

Measurements that are collected from a collection and then saved
as a case class, will automatically have a parquet schema derived
and as a result will be able to be saved to disk in parquet format.

* Force string identifiers for algorithm and problem

The user is now forced to define a name for the algorithm and the
problem so that they can be identified in the result output. It's not
the best strategy, but it is a valid one until a better scheme is
devised.

* Disallow empty algorithm and problem names

Move empty literals for algorithm and problem names to compile time
errors.

* Adjust the collection after environment changes

Missed acutally using the `onChange` handler in the interpretter.

build.sbt

@@ -3,9 +3,11 @@ import sbt.Keys._
 import sbtrelease.ReleaseStateTransformations._
 
 val scalazVersion     = "7.2.7"
+val scalazStreamVersion = "0.8.6a"
 val spireVersion      = "0.13.0"
 val monocleVersion    = "1.3.2"
 val scalacheckVersion = "1.12.6"
+val avro4sVersion = "1.8.3"
 
 lazy val buildSettings = Seq(
   organization := "net.cilib"
@@ -161,27 +163,35 @@ lazy val core = project
         "eu.timepit" %% "refined" % "0.8.5"
       ),
       wartremoverErrors in (Compile, compile) ++= Seq(
+        //Wart.Any,
+        //Wart.Nothing,
+        Wart.AnyVal,
         Wart.ArrayEquals,
-        Wart.JavaSerializable,
-        //      Wart.Any,
-        Wart.ExplicitImplicitTypes,
-        Wart.LeakingSealed,
-        Wart.StringPlusAny,
         Wart.AsInstanceOf,
-        Wart.IsInstanceOf,
+        Wart.DefaultArguments,
+        Wart.ExplicitImplicitTypes,
+        Wart.FinalCaseClass,
+        Wart.FinalVal,
         Wart.ImplicitConversion,
         Wart.ImplicitParameter,
-        Wart.DefaultArguments,
-        //Wart.ListOps,
+        Wart.IsInstanceOf,
+        Wart.JavaConversions,
+        Wart.JavaSerializable,
+        Wart.LeakingSealed,
+        Wart.MutableDataStructures,
         Wart.NonUnitStatements,
         Wart.Null,
         Wart.Option2Iterable,
         Wart.OptionPartial,
-        //Wart.Overloading,
+        Wart.Overloading,
         Wart.Product,
+        //Wart.PublicInference,
         Wart.Return,
         Wart.Serializable,
+        Wart.StringPlusAny,
+        Wart.Throw,
         Wart.TraversableOps,
+        Wart.TryPartial,
         Wart.Var
       )
     ))
@@ -267,16 +277,20 @@ lazy val example = project
       moduleName := "cilib-example",
       libraryDependencies ++= Seq(
         "net.cilib" %% "benchmarks" % "0.1.1",
-        "org.scalaz" %% "scalaz-core" % scalazVersion,
-        "org.scalaz" %% "scalaz-concurrent" % scalazVersion,
-        "org.scalaz" %% "scalaz-effect" % scalazVersion,
-        "org.scalaz.stream" %% "scalaz-stream" % "0.8.6a"
+        "org.scalaz" %% "scalaz-effect" % scalazVersion
       )
     ))
 
 lazy val exec = project
   .dependsOn(core)
-  .settings(Seq(moduleName := "cilib-exec") ++ cilibSettings)
+  .settings(cilibSettings ++ Seq(
+    moduleName := "cilib-exec",
+    libraryDependencies ++= Seq(
+      "org.scalaz" %% "scalaz-concurrent" % scalazVersion,
+      "org.scalaz.stream" %% "scalaz-stream" % scalazStreamVersion,
+      "com.sksamuel.avro4s" %% "avro4s-core" % avro4sVersion
+    )
+  ))
 
 lazy val moo = project
   .dependsOn(core)
@@ -308,15 +322,15 @@ lazy val tests = project
     ))
 
 lazy val io = project
-  .dependsOn(core)
+  .dependsOn(core, exec)
   .settings(
     cilibSettings ++ noPublishSettings ++ Seq(
       moduleName := "cilib-io",
       libraryDependencies ++= Seq(
         "com.chuusai" %% "shapeless" % "2.3.2",
-        "org.apache.orc" % "orc-core" % "1.3.3",
-        "com.sksamuel.avro4s" %% "avro4s-core" % "1.8.0",
-        "org.apache.parquet" % "parquet-avro" % "1.8.2",
-        "org.scalaz.stream" %% "scalaz-stream" % "0.8.6a"
+        "com.sksamuel.avro4s" %% "avro4s-core" % avro4sVersion,
+        "org.apache.parquet" % "parquet-avro" % "1.9.0",
+        "org.apache.hadoop" % "hadoop-client" % "2.7.3",
+        "org.scalaz.stream" %% "scalaz-stream" % scalazStreamVersion
       )
     ))

core/src/main/scala/cilib/Constraint.scala

@@ -30,7 +30,7 @@ object ViolationCount {
     }
 }
 
-case class ConstraintFunction[A](f: NonEmptyList[A] => Double) {
+final case class ConstraintFunction[A](f: NonEmptyList[A] => Double) {
   def apply(a: NonEmptyList[A]): Double =
     f(a)
 }

core/src/main/scala/cilib/Lenses.scala

@@ -2,7 +2,7 @@ package cilib
 
 import monocle._
 
-case class Mem[A](b: Position[A], v: Position[A])
+final case class Mem[A](b: Position[A], v: Position[A])
 
 @annotation.implicitNotFound(
   "A HasMemory instance cannot be found for the provided state type ${S}")

core/src/main/scala/cilib/Step.scala

@@ -140,9 +140,6 @@ object StepS {
         StepS(M.put(s))
     }
 
-  def apply[A, S, B](f: S => Step[A, (S, B)]): StepS[A, S, B] =
-    StepS(StateT[Step[A, ?], S, B](f))
-
   def pointR[A, S, B](a: RVar[B]): StepS[A, S, B] =
     StepS(StateT[Step[A, ?], S, B]((s: S) => Step.pointR(a).map((s, _))))
 

docs/src/main/tut/usage/gbestpso.md

@@ -28,6 +28,7 @@ As the very first step, we need to get the needed imports in scope:
 ```tut:silent
 import cilib._
 import cilib.pso._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 

eda/src/main/scala/EDA.scala

@@ -4,8 +4,6 @@ package eda
 import scalaz._
 import Scalaz._
 
-import spire.implicits._
-
 object EDA {
 
   def eda[M, S, A](

example/src/main/scala/cilib/example/GA.scala

@@ -67,5 +67,5 @@ object GAExample extends SafeApp {
 
   // Our IO[Unit] that runs at the end of the world
   override val runc: IO[Unit] =
-    putStrLn(Runner.repeat(1000, cullingGA, swarm).run(env).run(RNG.fromTime).toString)
+    putStrLn(exec.Runner.repeat(1000, cullingGA, swarm).run(env).run(RNG.fromTime).toString)
 }

example/src/main/scala/cilib/example/GBestPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 
@@ -30,17 +31,17 @@ object GBestPSO extends SafeApp {
     Position.createCollection(PSO.createParticle(x => Entity(Mem(x, x.zeroed), x)))(env.bounds, 20)
   val iter = Iteration.sync(gbestPSO)
 
+  val problemStream = Runner.staticProblem("spherical", env.eval, RNG.init(123L)).take(1000)
+
   // Our IO[Unit] that runs the algorithm, at the end of the world
   override val runc: IO[Unit] = {
-    val result = Runner.repeat(1000, iter, swarm).run(env).run(RNG.fromTime)
-
-    result._2 match {
-      case -\/(error) =>
-        throw error
-
-      case \/-(value) =>
-        val positions = value.map(x => Lenses._position.get(x))
-        putStrLn(positions.toString)
-    }
+    val t = Runner.foldStep(env,
+                            RNG.fromTime,
+                            swarm,
+                            Algorithm("gbestPSO", iter),
+                            problemStream,
+                            (x: NonEmptyList[Particle[Mem[Double], Double]]) => RVar.point(x))
+
+    putStrLn(t.runLast.unsafePerformSync.toString)
   }
 }

example/src/main/scala/cilib/example/GCPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 
@@ -45,7 +46,7 @@ object GCPSO extends SafeApp {
 
     val result =
       Runner
-        .repeatS(1000, iter, swarm)
+        .repeat(1000, iter, swarm)
         .run(algParams)
         .run(env)
         .run(RNG.fromTime)

example/src/main/scala/cilib/example/LBestPSO.scala

@@ -11,6 +11,7 @@ import spire.math.Interval
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 object LBestPSO extends SafeApp {
   val env =

example/src/main/scala/cilib/example/Mixed.scala

@@ -13,6 +13,7 @@ import spire.implicits._
 
 import cilib.de._
 import cilib.pso._
+import cilib.exec._
 
 object Mixed extends SafeApp {
 

example/src/main/scala/cilib/example/NMPCPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 

example/src/main/scala/cilib/example/PCXPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 

example/src/main/scala/cilib/example/RandomSearchGA.scala

@@ -11,6 +11,7 @@ import eu.timepit.refined.auto._
 import spire.implicits._
 import spire.math.Interval
 import cilib.ga._
+import cilib.exec._
 
 object RandomSearchGA extends SafeApp {
   type Ind = Individual[Unit]

example/src/main/scala/cilib/example/UNDXPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 

example/src/main/scala/cilib/example/VonNeumannPSO.scala

@@ -3,6 +3,7 @@ package example
 
 import cilib.pso._
 import cilib.pso.Defaults._
+import cilib.exec._
 
 import eu.timepit.refined.auto._
 

exec/src/main/scala/cilib/Environment.scala

@@ -0,0 +1,18 @@
+package cilib
+package exec
+
+import eu.timepit.refined.api.Refined
+import eu.timepit.refined.auto._
+import eu.timepit.refined.numeric._
+
+sealed abstract class Env
+final case object Unchanged extends Env
+final case object Change extends Env
+
+object Env {
+  def constant: Stream[Env] =
+    Stream(Unchanged) #::: constant
+
+  def frequency[A](n: Int Refined Positive): Stream[Env] =
+    (constant.take(n - 1) #::: Stream[Env](Change)) #::: frequency(n)
+}

exec/src/main/scala/cilib/Measurement.scala

@@ -0,0 +1,11 @@
+package cilib
+package exec
+
+import com.sksamuel.avro4s._
+
+final case class Measurement[A: SchemaFor](alg: String,
+                                           prob: String,
+                                           iteration: Int,
+                                           env: Env,
+                                           seed: Long,
+                                           data: A)

exec/src/main/scala/cilib/MonadStep.scala

@@ -0,0 +1,8 @@
+package cilib
+package exec
+
+import scalaz.Monad
+
+abstract class MonadStep[M[_]: Monad] {
+  def pointR[A](r: RVar[A]): M[A]
+}