cleanup and update versions

Author: breandan

README.md

@@ -1,6 +1,6 @@
 # Kaliningraph
 
-[![Kotlin 1.5.0](https://img.shields.io/badge/Kotlin-1.5.0-blue.svg?style=flat&logo=kotlin)](http://kotlinlang.org)
+[![Kotlin 1.5.10](https://img.shields.io/badge/Kotlin-1.5.10-blue.svg?style=flat&logo=kotlin)](http://kotlinlang.org)
 [![](https://jitpack.io/v/breandan/kaliningraph.svg)](https://jitpack.io/#breandan/kaliningraph)
 [![CI](https://github.com/breandan/kaliningraph/workflows/CI/badge.svg)](https://github.com/breandan/kaliningraph/actions)
 
@@ -20,7 +20,7 @@ repositories {
 }
 
 dependencies {
-    implementation("com.github.breandan:kaliningraph:0.1.6")
+    implementation("com.github.breandan:kaliningraph:0.1.7")
 }
 ```
 
@@ -38,7 +38,7 @@ dependencies {
   <dependency>
     <groupId>com.github.breandan</groupId>
     <artifactId>kaliningraph</artifactId>
-    <version>0.1.6</version>
+    <version>0.1.7</version>
   </dependency>
 </project>
 ```
@@ -49,7 +49,7 @@ To access notebook support, use the following line magic:
 
 ```
 @file:Repository("https://jitpack.io")
-@file:DependsOn("com.github.breandan:kaliningraph:0.1.6")
+@file:DependsOn("com.github.breandan:kaliningraph:0.1.7")
 ```
 
 For more information, explore our tutorials:
@@ -67,7 +67,7 @@ What are neighbors? Neighbors are a graph.
 
 ## Getting Started
 
-Run [the demo](src/main/kotlin/edu/mcgill/kaliningraph/HelloKaliningraph.kt) via `./gradlew HelloKaliningraph` to get started.
+Run [the demo](src/test/kotlin/edu/mcgill/kaliningraph/HelloKaliningraph.kt) via `./gradlew HelloKaliningraph` to get started.
 
 ## Usage
 

build.gradle.kts

@@ -4,13 +4,13 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 
 plugins {
   `maven-publish`
-  kotlin("jvm") version "1.5.0"
-  kotlin("jupyter.api") version "0.10.0-17"
+  kotlin("jvm") version "1.5.10"
+  kotlin("jupyter.api") version "0.10.0-42"
   id("com.github.ben-manes.versions") version "0.38.0"
 }
 
 group = "com.github.breandan"
-version = "0.1.6"
+version = "0.1.7"
 
 repositories {
   mavenCentral()

notebooks/Hello Kaliningraph.ipynb

@@ -9,7 +9,7 @@
    "outputs": [],
    "source": [
     "@file:Repository(\"https://jitpack.io\")\n",
-    "@file:DependsOn(\"com.github.breandan:kaliningraph:0.1.6\")"
+    "@file:DependsOn(\"com.github.breandan:kaliningraph:0.1.7\")"
    ]
   },
   {

notebooks/Program Graphs.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "@file:Repository(\"https://jitpack.io\")\n",
-    "@file:DependsOn(\"com.github.breandan:kaliningraph:0.1.6\")"
+    "@file:DependsOn(\"com.github.breandan:kaliningraph:0.1.7\")"
    ]
   },
   {

src/main/kotlin/edu/mcgill/kaliningraph/Graph.kt

@@ -2,12 +2,9 @@ package edu.mcgill.kaliningraph
 
 import edu.mcgill.kaliningraph.matrix.*
 import edu.mcgill.kaliningraph.typefamily.*
-import guru.nidi.graphviz.attribute.Label
-import guru.nidi.graphviz.model.*
 import org.ejml.kotlin.*
-import kotlin.math.*
+import kotlin.math.sqrt
 import kotlin.random.Random
-import kotlin.reflect.KProperty
 
 abstract class Graph<G, E, V>(override val vertices: Set<V> = setOf()):
   IGraph<G, E, V>,
@@ -149,8 +146,6 @@ abstract class Graph<G, E, V>(override val vertices: Set<V> = setOf()):
 abstract class Edge<G, E, V>(override val source: V, override val target: V): IEdge<G, E, V>
   where G: Graph<G, E, V>, E: Edge<G, E, V>, V: Vertex<G, E, V> {
   override val graph by lazy { target.graph }
-  operator fun component1() = source
-  operator fun component2() = target
 }
 
 abstract class Vertex<G, E, V>(override val id: String): IVertex<G, E, V>
@@ -160,10 +155,6 @@ abstract class Vertex<G, E, V>(override val id: String): IVertex<G, E, V>
   override val neighbors by lazy { outgoing.map { it.target }.toSet() }
   override val outdegree by lazy { neighbors.size }
 
-  override fun encode(): DoubleArray = id.vectorize()
-
-  override operator fun getValue(a: Any?, prop: KProperty<*>): V = V(prop.name)
-  override fun render(): MutableNode = Factory.mutNode(id).add(Label.of(toString()))
   override fun equals(other: Any?) =
     (other as? Vertex<*, *, *>)?.encode().contentEquals(encode())
   override fun hashCode() = id.hashCode()

src/main/kotlin/edu/mcgill/kaliningraph/LabeledGraph.kt

@@ -53,6 +53,11 @@ open class LabeledGraph(override val vertices: Set<LGVertex> = setOf()):
   companion object: LabeledGraph() {
     operator fun invoke(builder: LGBuilder.() -> Unit) =
       LGBuilder().also { it.builder() }.mutGraph
+
+    operator fun invoke(graph: String) =
+      graph.split(" ").fold(G()) { acc, it ->
+        acc + G(*it.toList().zipWithNext().toTypedArray())
+      }
   }
 
   var accumuator = mutableSetOf<String>()
@@ -63,7 +68,7 @@ open class LabeledGraph(override val vertices: Set<LGVertex> = setOf()):
   fun rewrite(substitution: Pair<String, String>) =
     randomWalk().take(200).toList().joinToString("")
       .replace(substitution.first, substitution.second)
-      .let { LabeledGraph.G(it) }
+      .let { LabeledGraph(it) }
 
   fun propagate() {
     val (previousStates, unoccupied) = vertices.partition { it.occupied }
@@ -96,8 +101,7 @@ open class LabeledEdge(
   override val source: LGVertex,
   override val target: LGVertex,
   val label: String? = null
-):
-  Edge<LabeledGraph, LabeledEdge, LGVertex>(source, target) {
+): Edge<LabeledGraph, LabeledEdge, LGVertex>(source, target) {
   constructor(source: LGVertex, target: LGVertex): this(source, target, null)
 
   override fun render() =

src/main/kotlin/edu/mcgill/kaliningraph/Utils.kt

@@ -63,7 +63,7 @@ fun BMat.show(filename: String = "temp") = matToImg().let { data ->
   }
 }.show()
 
-val browserCmd = System.getProperty("os.name").toLowerCase().let { os ->
+val browserCmd = System.getProperty("os.name").lowercase().let { os ->
   when {
     "win" in os -> "rundll32 url.dll,FileProtocolHandler"
     "mac" in os -> "open"
@@ -91,8 +91,6 @@ fun BMat.matToImg(f: Int = 20) = toEJMLSparse().matToImg(f)
 
 fun randomString() = UUID.randomUUID().toString().take(5)
 
-private operator fun <K, V> Pair<K, V>.component2(): V = second
-private operator fun <K, V> Pair<K, V>.component1(): K = first
 operator fun MutableNode.minus(target: LinkTarget): Link = addLink(target).links().last()!!
 
 fun randomMatrix(rows: Int, cols: Int = rows, rand: () -> Double = { Random.Default.nextDouble() }) =
@@ -101,7 +99,7 @@ fun randomMatrix(rows: Int, cols: Int = rows, rand: () -> Double = { Random.Defa
 fun randomVector(size: Int, rand: () -> Double = { Random.Default.nextDouble() }) =
   Array(size) { rand() }.toDoubleArray()
 
-fun Array<DoubleArray>.toEJMLSparse() = SpsMat(size, this[0].size, sumBy { it.count { it == 0.0 } })
+fun Array<DoubleArray>.toEJMLSparse() = SpsMat(size, this[0].size, sumOf { it.count { it == 0.0 } })
   .also { s -> for (i in indices) for (j in this[0].indices) this[i][j].let { if (0.0 < it) s[i, j] = it } }
 
 fun Array<DoubleArray>.toEJMLDense() = DMatrixRMaj(this)
@@ -115,7 +113,7 @@ fun <T> powBench(constructor: T, matmul: (T, T) -> T): Long =
   measureTimeMillis { constructor.power(100, matmul) }
 
 fun <T> T.power(exp: Int, matmul: (T, T) -> T) =
-  (0..exp).fold(this) { acc, i -> matmul(acc, this) }
+  generateSequence(this) { matmul(it, this) }.take(exp)
 
 const val DEFAULT_FEATURE_LEN = 20
 fun String.vectorize(len: Int = DEFAULT_FEATURE_LEN) =

src/main/kotlin/edu/mcgill/kaliningraph/typefamily/IGraph.kt

@@ -49,10 +49,6 @@ interface IGF<G: IGraph<G, E, V>, E: IEdge<G, E, V>, V: IVertex<G, E, V>> {
     }
   )
 
-  // TODO: generify, only works for labeled graphs
-  fun G(graph: String): G =
-    graph.split(" ").fold(G()) { acc, it -> acc + G(it.toCharArray().toList()) }
-
   // Gafter's gadget! http://gafter.blogspot.com/2006/12/super-type-tokens.html
   private fun gev(): Array<Class<*>> =
     (generateSequence(javaClass) { it.superclass as Class<IGF<G, E, V>> }
@@ -83,11 +79,16 @@ interface IGraph<G, E, V>: IGF<G, E, V>, Set<V>, (V) -> Set<V>
  *   - Pros: Useful for describing many algebraic path problems
  *   - Cons: Esoteric API / unsuitable as an abstract interface
  *
- * Algebraic perspective    : https://github.com/snowleopard/alga-paper/releases/download/final/algebraic-graphs.pdf
- * Type-family perspective  : https://www.cs.cornell.edu/~ross/publications/shapes/shapes-pldi14-tr.pdf#page=3
- * Inductive perspective    : https://web.engr.oregonstate.edu/~erwig/papers/InductiveGraphs_JFP01.pdf
- * Mathematical perspective : https://doi.org/10.1007/978-0-387-75450-5
- * Semiring perspective     : http://stedolan.net/research/semirings.pdf
+ * Algebraic perspective   : https://github.com/snowleopard/alga-paper/releases/download/final/algebraic-graphs.pdf
+ *                         : https://arxiv.org/pdf/1909.04881.pdf
+ * Type-family perspective : https://www.cs.cornell.edu/~ross/publications/shapes/shapes-pldi14-tr.pdf#page=3
+ *                         : https://www.cs.cornell.edu/andru/papers/familia/familia.pdf#page=8
+ * Inductive perspective   : https://web.engr.oregonstate.edu/~erwig/papers/InductiveGraphs_JFP01.pdf
+ *                         : https://doi.org/10.1145/258949.258955
+ *                         : https://www.cs.utexas.edu/~wcook/Drafts/2012/graphs.pdf
+ * Semiring perspective    : http://stedolan.net/research/semirings.pdf
+ *                         : https://doi.org/10.1007/978-0-387-75450-5
+ *                         : https://doi.org/10.2200/S00245ED1V01Y201001CNT003
  */
 
   where G: IGraph<G, E, V>, E: IEdge<G, E, V>, V: IVertex<G, E, V> {
@@ -134,6 +135,9 @@ interface IEdge<G, E, V>: IGF<G, E, V>
   val source: V
   val target: V
 
+  operator fun component1() = source
+  operator fun component2() = target
+
   fun render(): Link = (source.render() - target.render()).add(Label.of(""))
 }
 
@@ -146,8 +150,8 @@ interface IVertex<G, E, V>: IGF<G, E, V>, Encodable
   val outgoing: Set<E> get() = edgeMap(this as V).toSet()
   val edgeMap: (V) -> Set<E> // Make a self-loop by passing this
 
-  open val neighbors get() = outgoing.map { it.target }.toSet()
-  open val outdegree get() = neighbors.size
+  val neighbors get() = outgoing.map { it.target }.toSet()
+  val outdegree get() = neighbors.size
 
   // tailrec prohibited on open members? may be possible with deep recursion
   // https://kotlinlang.org/api/latest/jvm/stdlib/kotlin/-deep-recursive-function/
@@ -181,6 +185,6 @@ infix fun Collection<Any>.allAre(that: Any) = all { it isA that }
 infix fun Collection<Any>.anyAre(that: Any) = any { it isA that }
 
 // https://github.com/amodeus-science/amod
-//abstract class Map : IGraph<Map, Road, City>
-//abstract class Road : IEdge<Map, Road, City>
-//abstract class City : IVertex<Map, Road, City>
+abstract class TMap  : IGraph<TMap, TRoad, TCity>
+abstract class TRoad : IEdge<TMap, TRoad, TCity>
+abstract class TCity : IVertex<TMap, TRoad, TCity>

src/test/kotlin/edu/mcgill/kaliningraph/LabeledGraphTest.kt

@@ -20,5 +20,5 @@ class LabeledGraphTest {
   )
 
   @Test
-  fun testStringConstructor() = assertEquals(graph, LabeledGraph.G("abcde ace"))
+  fun testStringConstructor() = assertEquals(graph, LabeledGraph("abcde ace"))
 }

src/test/kotlin/edu/mcgill/kaliningraph/Rewriter.kt

@@ -8,7 +8,7 @@ import kotlin.random.Random
 @ExperimentalStdlibApi
 fun main() {
   animate(
-    LabeledGraph.G("abcdecfghia").also { println(it) }
+    LabeledGraph("abcdecfghia").also { println(it) }
   ) { _: Document, it: KeyboardEvent, graphs: MutableList<LabeledGraph> ->
     when {
       "Left" in it.key -> {