[refactor] move java package to namespace java

jvm-packages/checkstyle-suppressions.xml

@@ -29,5 +29,5 @@
 
 <suppressions>
 <suppress checks=".*"
-	files="xgboost4j/src/main/java/ml/dmlc/xgboost4j/XgboostJNI.java"/>
+	files="xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/XgboostJNI.java"/>
 </suppressions>

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/BasicWalkThrough.java

@@ -13,18 +13,18 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
-import ml.dmlc.xgboost4j.demo.util.DataLoader;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
+import ml.dmlc.xgboost4j.java.demo.util.DataLoader;
 
 /**
  * a simple example of java wrapper for xgboost

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/BoostFromPrediction.java

@@ -13,14 +13,14 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 
 /**
  * example for start from a initial base prediction

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/CrossValidation.java

@@ -13,14 +13,14 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.io.IOException;
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 
 /**
  * an example of cross validation

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/CustomObjective.java

@@ -13,17 +13,16 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
+import ml.dmlc.xgboost4j.java.*;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import ml.dmlc.xgboost4j.*;
-
 /**
  * an example user define objective and eval
  * NOTE: when you do customized loss function, the default prediction value is margin

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/DistTrain.java

@@ -1,14 +1,13 @@
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
+import ml.dmlc.xgboost4j.java.*;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import ml.dmlc.xgboost4j.*;
-
 
 /**
  * Distributed training example, used to quick test distributed training.

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/ExternalMemory.java

@@ -13,14 +13,14 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 
 /**
  * simple example for using external memory version

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/GeneralizedLinearModel.java

@@ -13,15 +13,15 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
-import ml.dmlc.xgboost4j.demo.util.CustomEval;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
+import ml.dmlc.xgboost4j.java.demo.util.CustomEval;
 
 /**
  * this is an example of fit generalized linear model in xgboost

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/PredictFirstNtree.java

@@ -13,15 +13,15 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
-import ml.dmlc.xgboost4j.demo.util.CustomEval;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
+import ml.dmlc.xgboost4j.java.demo.util.CustomEval;
 
 /**
  * predict first ntree

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/PredictLeafIndices.java

@@ -13,15 +13,15 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo;
+package ml.dmlc.xgboost4j.java.demo;
 
 import java.util.Arrays;
 import java.util.HashMap;
 
-import ml.dmlc.xgboost4j.Booster;
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.XGBoost;
-import ml.dmlc.xgboost4j.XGBoostError;
+import ml.dmlc.xgboost4j.java.Booster;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.XGBoost;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 
 /**
  * predict leaf indices

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/util/CustomEval.java

@@ -13,14 +13,14 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo.util;
+package ml.dmlc.xgboost4j.java.demo.util;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-import ml.dmlc.xgboost4j.DMatrix;
-import ml.dmlc.xgboost4j.IEvaluation;
-import ml.dmlc.xgboost4j.XGBoostError;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.IEvaluation;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 
 /**
  * a util evaluation class for examples

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/java/demo/util/DataLoader.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j.demo.util;
+package ml.dmlc.xgboost4j.java.demo.util;
 
 import java.io.*;
 import java.util.ArrayList;

jvm-packages/xgboost4j-flink/src/main/scala/ml/dmlc/xgboost4j/flink/Test.scala

@@ -16,8 +16,7 @@
 
 package ml.dmlc.xgboost4j.flink
 
-import ml.dmlc.xgboost4j.Rabit
-import ml.dmlc.xgboost4j.RabitTracker
+import ml.dmlc.xgboost4j.java.{RabitTracker, Rabit}
 import ml.dmlc.xgboost4j.scala.Booster
 import ml.dmlc.xgboost4j.scala.DMatrix
 import ml.dmlc.xgboost4j.scala.XGBoost

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/Booster.java

@@ -1,4 +1,4 @@
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.IOException;
 import java.io.Serializable;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/DMatrix.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.IOException;
 import java.util.Iterator;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/DataBatch.java

@@ -1,4 +1,4 @@
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 /**
  * A mini-batch of data that can be converted to DMatrix.

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/IEvaluation.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 /**
  * interface for customized evaluation

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/IObjective.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.Serializable;
 import java.util.List;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/JNIErrorHandle.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.IOException;
 

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/JavaBoosterImpl.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.*;
 import java.util.HashMap;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/NativeLibLoader.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.*;
 import java.lang.reflect.Field;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/Rabit.java

@@ -1,4 +1,4 @@
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.io.IOException;
 import java.util.Map;

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/RabitTracker.java

@@ -1,4 +1,4 @@
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 
 

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/XGBoost.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.util.*;
 

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/XGBoostError.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 /**
  * custom error class for xgboost

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/XgboostJNI.java

@@ -13,7 +13,7 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 
 /**

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/Booster.scala

@@ -18,11 +18,9 @@ package ml.dmlc.xgboost4j.scala
 
 import java.io.IOException
 
+import ml.dmlc.xgboost4j.java.XGBoostError
 import scala.collection.mutable
 
-import ml.dmlc.xgboost4j.XGBoostError
-
-
 trait Booster extends Serializable {
 
 

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/DMatrix.scala

@@ -18,7 +18,7 @@ package ml.dmlc.xgboost4j.scala
 
 import _root_.scala.collection.JavaConverters._
 
-import ml.dmlc.xgboost4j.{DMatrix => JDMatrix, DataBatch, XGBoostError}
+import ml.dmlc.xgboost4j.java.{DMatrix => JDMatrix, DataBatch, XGBoostError}
 
 class DMatrix private[scala](private[scala] val jDMatrix: JDMatrix) {
 
@@ -45,8 +45,8 @@ class DMatrix private[scala](private[scala] val jDMatrix: JDMatrix) {
     this(new JDMatrix(headers, indices, data, st))
   }
 
-  private[xgboost4j] def this(dataBatch: DataBatch) {
-    this(new JDMatrix(List(dataBatch).asJava.iterator, null))
+  private[xgboost4j] def this(dataBatches: Iterator[DataBatch]) {
+    this(new JDMatrix(dataBatches.asJava, null))
   }
 
   /**

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/EvalTrait.scala

@@ -16,7 +16,8 @@
 
 package ml.dmlc.xgboost4j.scala
 
-import ml.dmlc.xgboost4j.{DMatrix => JDMatrix, IEvaluation}
+import ml.dmlc.xgboost4j.java
+import ml.dmlc.xgboost4j.java.IEvaluation
 
 trait EvalTrait extends IEvaluation {
 
@@ -36,7 +37,7 @@ trait EvalTrait extends IEvaluation {
    */
   def eval(predicts: Array[Array[Float]], dmat: DMatrix): Float
 
-  private[scala] def eval(predicts: Array[Array[Float]], jdmat: JDMatrix): Float = {
+  private[scala] def eval(predicts: Array[Array[Float]], jdmat: java.DMatrix): Float = {
     eval(predicts, new DMatrix(jdmat))
   }
 }

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/ObjectiveTrait.scala

@@ -16,10 +16,10 @@
 
 package ml.dmlc.xgboost4j.scala
 
+import ml.dmlc.xgboost4j.java
+import ml.dmlc.xgboost4j.java.IObjective
 import scala.collection.JavaConverters._
 
-import ml.dmlc.xgboost4j.{DMatrix => JDMatrix, IObjective}
-
 trait ObjectiveTrait extends IObjective {
   /**
    * user define objective function, return gradient and second order gradient
@@ -30,7 +30,7 @@ trait ObjectiveTrait extends IObjective {
    */
   def getGradient(predicts: Array[Array[Float]], dtrain: DMatrix): List[Array[Float]]
 
-  private[scala] def getGradient(predicts: Array[Array[Float]], dtrain: JDMatrix):
+  private[scala] def getGradient(predicts: Array[Array[Float]], dtrain: java.DMatrix):
     java.util.List[Array[Float]] = {
     getGradient(predicts, new DMatrix(dtrain)).asJava
   }

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/ScalaBoosterImpl.scala

@@ -16,12 +16,11 @@
 
 package ml.dmlc.xgboost4j.scala
 
+import ml.dmlc.xgboost4j.java
 import scala.collection.JavaConverters._
 import scala.collection.mutable
 
-import ml.dmlc.xgboost4j.{Booster => JBooster}
-
-private[scala] class ScalaBoosterImpl private[xgboost4j](booster: JBooster) extends Booster {
+private[scala] class ScalaBoosterImpl private[xgboost4j](booster: java.Booster) extends Booster {
 
   override def setParam(key: String, value: String): Unit = {
     booster.setParam(key, value)

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/XGBoost.scala

@@ -18,8 +18,6 @@ package ml.dmlc.xgboost4j.scala
 
 import scala.collection.JavaConverters._
 
-import ml.dmlc.xgboost4j.{XGBoost => JXGBoost}
-
 object XGBoost {
 
   def train(

jvm-packages/xgboost4j/src/test/java/ml/dmlc/xgboost4j/java/BoosterImplTest.java

@@ -13,12 +13,13 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.util.HashMap;
 import java.util.Map;
 
 import junit.framework.TestCase;
+import ml.dmlc.xgboost4j.java.*;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.junit.Test;

jvm-packages/xgboost4j/src/test/java/ml/dmlc/xgboost4j/java/DMatrixTest.java

@@ -13,12 +13,15 @@
  See the License for the specific language governing permissions and
  limitations under the License.
  */
-package ml.dmlc.xgboost4j;
+package ml.dmlc.xgboost4j.java;
 
 import java.util.Arrays;
 import java.util.Random;
 
 import junit.framework.TestCase;
+import ml.dmlc.xgboost4j.java.DMatrix;
+import ml.dmlc.xgboost4j.java.DataBatch;
+import ml.dmlc.xgboost4j.java.XGBoostError;
 import org.junit.Test;
 
 /**

jvm-packages/xgboost4j/src/test/scala/ml/dmlc/xgboost4j/scala/DMatrixSuite.scala

@@ -20,7 +20,6 @@ import java.util.Arrays
 
 import scala.util.Random
 
-import ml.dmlc.xgboost4j.{DMatrix => JDMatrix}
 import org.scalatest.FunSuite
 
 class DMatrixSuite extends FunSuite {

jvm-packages/xgboost4j/src/test/scala/ml/dmlc/xgboost4j/scala/ScalaBoosterImplSuite.scala

@@ -16,7 +16,7 @@
 
 package ml.dmlc.xgboost4j.scala
 
-import ml.dmlc.xgboost4j.XGBoostError
+import ml.dmlc.xgboost4j.java.XGBoostError
 import org.apache.commons.logging.LogFactory
 import org.scalatest.FunSuite