import fixes

trinity-xai · Sep 21, 2024 · cb3f00e · cb3f00e
1 parent 2c5bc6a
commit cb3f00e
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diff --git a/src/main/java/com/clust4j/Clust4j.java b/src/main/java/com/clust4j/Clust4j.java
@@ -20,14 +20,15 @@
 import java.io.IOException;
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
+import java.io.Serializable;
 
 /**
  * The absolute super type for all clust4j objects (models and datasets)
  * that should be able to commonly serialize their data.
  *
  * @author Taylor G Smith
  */
-public abstract class Clust4j implements java.io.Serializable {
+public abstract class Clust4j implements Serializable {
     private static final long serialVersionUID = -4522135376738501625L;
 
     /**

diff --git a/src/main/java/com/clust4j/algo/AbstractCentroidClusterer.java b/src/main/java/com/clust4j/algo/AbstractCentroidClusterer.java
@@ -27,6 +27,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Random;
@@ -95,7 +96,7 @@ static interface Initializer {
         int[] getInitialCentroidSeeds(AbstractCentroidClusterer model, double[][] X, int k, final Random seed);
     }
 
-    public static enum InitializationStrategy implements java.io.Serializable, Initializer, NamedEntity {
+    public static enum InitializationStrategy implements Serializable, Initializer, NamedEntity {
         AUTO {
             @Override
             public int[] getInitialCentroidSeeds(AbstractCentroidClusterer model, double[][] X, int k, final Random seed) {

diff --git a/src/main/java/com/clust4j/algo/AbstractClusterer.java b/src/main/java/com/clust4j/algo/AbstractClusterer.java
@@ -35,6 +35,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -50,7 +51,7 @@
  */
 public abstract class AbstractClusterer
     extends BaseModel
-    implements Loggable, NamedEntity, java.io.Serializable, MetricValidator {
+    implements Loggable, NamedEntity, Serializable, MetricValidator {
 
     private static final long serialVersionUID = -3623527903903305017L;
 

diff --git a/src/main/java/com/clust4j/algo/AffinityPropagation.java b/src/main/java/com/clust4j/algo/AffinityPropagation.java
@@ -17,6 +17,7 @@
 
 import com.clust4j.GlobalState;
 import com.clust4j.except.ModelNotFitException;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.metrics.pairwise.GeometricallySeparable;
@@ -291,7 +292,7 @@ public String getName() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.AFFINITY_PROP;
+        return Log.Tag.Algo.AFFINITY_PROP;
     }
 
     /**

diff --git a/src/main/java/com/clust4j/algo/BaseClassifier.java b/src/main/java/com/clust4j/algo/BaseClassifier.java
@@ -19,14 +19,16 @@
 import com.clust4j.metrics.scoring.UnsupervisedMetric;
 import org.apache.commons.math3.linear.RealMatrix;
 
+import java.io.Serializable;
+
 import static com.clust4j.metrics.scoring.UnsupervisedMetric.SILHOUETTE;
 
 /**
  * An interface for classifiers, both supervised and unsupervised.
  *
  * @author Taylor G Smith
  */
-public interface BaseClassifier extends java.io.Serializable {
+public interface BaseClassifier extends Serializable {
     public final static SupervisedMetric DEF_SUPERVISED_METRIC = SupervisedMetric.BINOMIAL_ACCURACY;
     public final static UnsupervisedMetric DEF_UNSUPERVISED_METRIC = SILHOUETTE;
 

diff --git a/src/main/java/com/clust4j/algo/BaseModel.java b/src/main/java/com/clust4j/algo/BaseModel.java
@@ -19,9 +19,10 @@
 import com.clust4j.utils.SynchronicityLock;
 import com.clust4j.utils.TableFormatter;
 
+import java.io.Serializable;
 import java.text.NumberFormat;
 
-abstract public class BaseModel extends Clust4j implements java.io.Serializable {
+abstract public class BaseModel extends Clust4j implements Serializable {
     private static final long serialVersionUID = 4707757741169405063L;
     public final static TableFormatter formatter;
 

diff --git a/src/main/java/com/clust4j/algo/BoruvkaAlgorithm.java b/src/main/java/com/clust4j/algo/BoruvkaAlgorithm.java
@@ -24,6 +24,8 @@
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
+
 /**
  * A graph traversal algorithm used in identifying the minimum spanning tree
  * in a graph for which all edge weights are distinct. Used in conjunction with
@@ -32,7 +34,7 @@
  * @author Taylor G Smith
  * @see <a href="https://en.wikipedia.org/wiki/Bor%C5%AFvka%27s_algorithm">Boruvka's algorithm</a>
  */
-class BoruvkaAlgorithm implements java.io.Serializable {
+class BoruvkaAlgorithm implements Serializable {
     private static final long serialVersionUID = 3935595821188876442L;
 
     // the initialization reorganizes the trees

diff --git a/src/main/java/com/clust4j/algo/CentroidLearner.java b/src/main/java/com/clust4j/algo/CentroidLearner.java
@@ -19,10 +19,11 @@
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.linear.RealMatrix;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 
-public interface CentroidLearner extends java.io.Serializable {
+public interface CentroidLearner extends Serializable {
     /**
      * A standalone mixin class to handle predictions from {@link CentroidLearner}
      * classes that are also a {@link BaseClassifier} and a subclass of {@link AbstractClusterer}.

diff --git a/src/main/java/com/clust4j/algo/ConvergeablePlanner.java b/src/main/java/com/clust4j/algo/ConvergeablePlanner.java
@@ -15,7 +15,9 @@
  *******************************************************************************/
 package com.clust4j.algo;
 
-interface ConvergeablePlanner extends java.io.Serializable {
+import java.io.Serializable;
+
+interface ConvergeablePlanner extends Serializable {
     /**
      * The maximum number of iterations the algorithm
      * is permitted before aborting without converging

diff --git a/src/main/java/com/clust4j/algo/DBSCAN.java b/src/main/java/com/clust4j/algo/DBSCAN.java
@@ -15,6 +15,7 @@
  *******************************************************************************/
 package com.clust4j.algo;
 
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.metrics.pairwise.GeometricallySeparable;
@@ -297,7 +298,7 @@ protected DBSCAN fit() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.DBSCAN;
+        return Log.Tag.Algo.DBSCAN;
     }
 
     @Override

diff --git a/src/main/java/com/clust4j/algo/HDBSCAN.java b/src/main/java/com/clust4j/algo/HDBSCAN.java
@@ -16,6 +16,7 @@
 package com.clust4j.algo;
 
 import com.clust4j.GlobalState;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.log.Loggable;
@@ -1457,7 +1458,7 @@ public int[] getLabels() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.HDBSCAN;
+        return Log.Tag.Algo.HDBSCAN;
     }
 
     @Override

diff --git a/src/main/java/com/clust4j/algo/HierarchicalAgglomerative.java b/src/main/java/com/clust4j/algo/HierarchicalAgglomerative.java
@@ -18,6 +18,7 @@
 import com.clust4j.NamedEntity;
 import com.clust4j.kernel.CircularKernel;
 import com.clust4j.kernel.LogKernel;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.metrics.pairwise.Distance;
@@ -30,6 +31,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashSet;
 
@@ -79,7 +81,7 @@ interface LinkageTreeBuilder extends MetricValidator {
      *
      * @author Taylor G Smith
      */
-    public enum Linkage implements java.io.Serializable, LinkageTreeBuilder {
+    public enum Linkage implements Serializable, LinkageTreeBuilder {
         AVERAGE {
             @Override
             public AverageLinkageTree buildTree(HierarchicalAgglomerative h) {
@@ -185,7 +187,7 @@ final protected ModelSummary modelSummary() {
      *
      * @author Taylor G Smith
      */
-    protected static class EfficientDistanceMatrix implements java.io.Serializable {
+    protected static class EfficientDistanceMatrix implements Serializable {
         private static final long serialVersionUID = -7329893729526766664L;
         final protected double[] dists;
 
@@ -295,7 +297,7 @@ else if (i > j)
         }
     }
 
-    abstract class HierarchicalDendrogram implements java.io.Serializable, NamedEntity {
+    abstract class HierarchicalDendrogram implements Serializable, NamedEntity {
         private static final long serialVersionUID = 5295537901834851676L;
         public final HierarchicalAgglomerative ref;
         public final GeometricallySeparable dist;
@@ -598,7 +600,7 @@ public int[] getLabels() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.AGGLOMERATIVE;
+        return Log.Tag.Algo.AGGLOMERATIVE;
     }
 
     @Override

diff --git a/src/main/java/com/clust4j/algo/KMeans.java b/src/main/java/com/clust4j/algo/KMeans.java
@@ -16,6 +16,7 @@
 package com.clust4j.algo;
 
 import com.clust4j.except.NaNException;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.metrics.pairwise.Distance;
@@ -213,7 +214,7 @@ protected KMeans fit() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.KMEANS;
+        return Log.Tag.Algo.KMEANS;
     }
 
     @Override

diff --git a/src/main/java/com/clust4j/algo/LabelEncoder.java b/src/main/java/com/clust4j/algo/LabelEncoder.java
@@ -18,10 +18,11 @@
 import com.clust4j.except.ModelNotFitException;
 import com.clust4j.utils.VecUtils;
 
+import java.io.Serializable;
 import java.util.LinkedHashSet;
 import java.util.TreeMap;
 
-public class LabelEncoder extends BaseModel implements java.io.Serializable {
+public class LabelEncoder extends BaseModel implements Serializable {
     private static final long serialVersionUID = 6618077714920820376L;
 
     final int[] rawLabels;

diff --git a/src/main/java/com/clust4j/algo/MeanShift.java b/src/main/java/com/clust4j/algo/MeanShift.java
@@ -19,6 +19,7 @@
 import com.clust4j.except.ModelNotFitException;
 import com.clust4j.kernel.GaussianKernel;
 import com.clust4j.kernel.RadialBasisKernel;
+import com.clust4j.log.Log;
 import com.clust4j.log.Log.Tag.Algo;
 import com.clust4j.log.LogTimer;
 import com.clust4j.log.Loggable;
@@ -32,6 +33,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -343,7 +345,7 @@ final protected static double autoEstimateBW(NearestNeighbors nn, double[][] dat
      */
     static class ParallelBandwidthEstimator
         extends ParallelChunkingTask<Double>
-        implements java.io.Serializable {
+        implements Serializable {
 
         private static final long serialVersionUID = 1171269106158790138L;
         final NearestNeighbors nn;
@@ -577,7 +579,7 @@ else if (!seen_k)
      *
      * @author Taylor G Smith
      */
-    static abstract class CenterIntensity implements java.io.Serializable, Iterable<MeanShiftSeed> {
+    static abstract class CenterIntensity implements Serializable, Iterable<MeanShiftSeed> {
         private static final long serialVersionUID = -6535787295158719610L;
 
         abstract int getIters();
@@ -860,7 +862,7 @@ public String getName() {
 
     @Override
     public Algo getLoggerTag() {
-        return com.clust4j.log.Log.Tag.Algo.MEANSHIFT;
+        return Log.Tag.Algo.MEANSHIFT;
     }
 
 

diff --git a/src/main/java/com/clust4j/algo/NearestNeighborHeapSearch.java b/src/main/java/com/clust4j/algo/NearestNeighborHeapSearch.java
@@ -29,6 +29,7 @@
 import org.apache.commons.math3.linear.RealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import static com.clust4j.GlobalState.Mathematics.*;
@@ -41,7 +42,7 @@
  * @author Taylor G Smith
  * @see <a href="https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/neighbors/binary_tree.pxi">sklearn BinaryTree</a>
  */
-abstract class NearestNeighborHeapSearch implements java.io.Serializable {
+abstract class NearestNeighborHeapSearch implements Serializable {
     private static final long serialVersionUID = -5617532034886067210L;
 
     final static public int DEF_LEAF_SIZE = 40;
@@ -202,7 +203,7 @@ interface Density {
      *
      * @author Taylor G Smith
      */
-    public static enum PartialKernelDensity implements Density, java.io.Serializable {
+    public static enum PartialKernelDensity implements Density, Serializable {
         LOG_COSINE {
             @Override
             public double getDensity(double dist, double h) {
@@ -295,7 +296,7 @@ public double getNorm(double h, int d) {
      * @author Taylor G Smith
      */
     // Tested: passing
-    public static class MutableDouble implements Comparable<Double>, java.io.Serializable {
+    public static class MutableDouble implements Comparable<Double>, Serializable {
         private static final long serialVersionUID = -4636023903600763877L;
         public Double value = 0.0;
 
@@ -318,7 +319,7 @@ public int compareTo(final Double n) {
      * @author Taylor G Smith
      */
     // Tested: passing
-    public static class NodeData implements DeepCloneable, java.io.Serializable {
+    public static class NodeData implements DeepCloneable, Serializable {
         private static final long serialVersionUID = -2469826821608908612L;
         int idx_start, idx_end;
         boolean is_leaf;
@@ -383,7 +384,7 @@ public int start() {
      *
      * @author Taylor G Smith
      */
-    abstract static class Heap implements java.io.Serializable {
+    abstract static class Heap implements Serializable {
         private static final long serialVersionUID = 8073174366388667577L;
 
         abstract static class Node {

diff --git a/src/main/java/com/clust4j/algo/Neighborhood.java b/src/main/java/com/clust4j/algo/Neighborhood.java
@@ -5,9 +5,11 @@
 import com.clust4j.utils.MatUtils;
 import com.clust4j.utils.MatrixFormatter;
 
+import java.io.Serializable;
+
 public class Neighborhood
     extends EntryPair<double[][], int[][]>
-    implements DeepCloneable, java.io.Serializable {
+    implements DeepCloneable, Serializable {
 
     private static final long serialVersionUID = 2016176782694689004L;
     private static final MatrixFormatter fmt = new MatrixFormatter();

diff --git a/src/main/java/com/clust4j/algo/NoiseyClusterer.java b/src/main/java/com/clust4j/algo/NoiseyClusterer.java
@@ -15,6 +15,8 @@
  *******************************************************************************/
 package com.clust4j.algo;
 
+import java.io.Serializable;
+
 /**
  * Any cluster that does not force a prediction for every
  * single point is considered a "noisey clusterer." This interface
@@ -26,7 +28,7 @@
  * @see {@link DBSCAN}
  * @see {@link MeanShift}
  */
-public interface NoiseyClusterer extends java.io.Serializable {
+public interface NoiseyClusterer extends Serializable {
     final public static int NOISE_CLASS = -1;
 
     /**

diff --git a/src/main/java/com/clust4j/algo/ParallelChunkingTask.java b/src/main/java/com/clust4j/algo/ParallelChunkingTask.java
@@ -22,6 +22,7 @@
 import com.clust4j.utils.MatrixFormatter;
 import org.apache.commons.math3.util.FastMath;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.concurrent.ForkJoinPool;
 import java.util.concurrent.RecursiveTask;
@@ -38,7 +39,7 @@ public abstract class ParallelChunkingTask<T> extends RecursiveTask<T> implement
      *
      * @author Taylor G Smith
      */
-    public static class Chunk implements java.io.Serializable {
+    public static class Chunk implements Serializable {
         private static final long serialVersionUID = -4981036399670388292L;
         final double[][] chunk;
         final public int start;