Add HDBScanBenchmark

And some small cosmetic changes

Co-Authored-By: Ioannis Panagiotas <ioannis.panagiotas@neo4j.com>

Author: vnickolov

algo/src/main/java/org/neo4j/gds/hdbscan/BoruvkaMST.java

@@ -114,7 +114,7 @@ public GeometricMSTResult compute() {
     }
 
     private void performIteration() {
-        if (!closestDistanceTracker.isUpdated()) {
+        if (closestDistanceTracker.isNotUpdated()) {
 
             ParallelUtil.parallelForEachNode(
                 nodeCount, concurrency, terminationFlag,

algo/src/main/java/org/neo4j/gds/hdbscan/ClosestDistanceInformationTracker.java

@@ -65,25 +65,29 @@ static ClosestDistanceInformationTracker create(long size, HugeDoubleArray cores
                 tracker.tryToAssign(u, u, neighbor, adaptedDistance);
             }
         }
-        tracker.setUpdated(true);
+        tracker.updated();
 
         return tracker;
 
     }
 
-    private void setUpdated(boolean updated) {
-        this.updated = updated;
+    private void updated() {
+        this.updated = true;
     }
 
-    boolean isUpdated() {
-        return updated;
+    private void notUpdated() {
+        this.updated = false;
+    }
+
+    boolean isNotUpdated() {
+        return !updated;
     }
 
     void reset(long upTo) {
         for (long u = 0; u < upTo; ++u) {
             resetComponent(u);
         }
-        setUpdated(false);
+        notUpdated();
     }
 
     void resetComponent(long u) {

algo/src/main/java/org/neo4j/gds/hdbscan/DualTreeMSTAlgorithm.java

@@ -136,7 +136,7 @@ void resetNodeBounds() {
     }
 
     private void performIteration() {
-        if (!closestDistanceTracker.isUpdated()) {
+        if (closestDistanceTracker.isNotUpdated()) {
             resetNodeBounds();
             traversalStep(kdTree.root(), kdTree.root());
         }

algo/src/main/java/org/neo4j/gds/hdbscan/HDBScan.java

@@ -40,7 +40,7 @@ public class HDBScan extends Algorithm<HugeLongArray> {
     private final int samples;
     private final long minClusterSize;
 
-    protected HDBScan(
+    public HDBScan(
         IdMap nodes,
         NodePropertyValues nodePropertyValues,
         Concurrency concurrency,

algo/src/test/java/org/neo4j/gds/hdbscan/BoruvkaMSTTest.java

@@ -24,6 +24,7 @@
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 import org.neo4j.gds.core.concurrency.Concurrency;
+import org.neo4j.gds.core.utils.progress.tasks.ProgressTracker;
 import org.neo4j.gds.extension.GdlExtension;
 import org.neo4j.gds.extension.GdlGraph;
 import org.neo4j.gds.extension.Inject;
@@ -61,7 +62,7 @@ class Case1 {
         @ValueSource(ints={1,4})
         void shouldReturnEuclideanMSTWithZeroCoreValues(int concurrency) {
             var nodePropertyValues = graph.nodeProperties("point");
-            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1).build();
+            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1, ProgressTracker.NULL_TRACKER).build();
 
             var dualTree =  BoruvkaMST.createWithZeroCores(
                 nodePropertyValues,
@@ -118,7 +119,7 @@ class Case2 {
         @ValueSource(ints={1,4})
         void shouldReturnEuclideanMSTWithZeroCoreValues(int concurrency) {
             var nodePropertyValues = graph.nodeProperties("point");
-            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1).build();
+            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1, ProgressTracker.NULL_TRACKER).build();
 
             var dualTree =  BoruvkaMST.createWithZeroCores(
                 nodePropertyValues,
@@ -175,7 +176,7 @@ class Case3 {
         @ValueSource(ints={1,4})
         void shouldReturnEuclideanMSTWithZeroCoreValues(int concurrency) {
             var nodePropertyValues = graph.nodeProperties("point");
-            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1).build();
+            var kdTree = new KdTreeBuilder(graph, nodePropertyValues, 1, 1, ProgressTracker.NULL_TRACKER).build();
 
             var dualTree =  BoruvkaMST.createWithZeroCores(
                 nodePropertyValues,