Merge branch 'master' into release-0.1

CHANGELOG.md

@@ -1,5 +1,34 @@
 # Change Log
 
+## [v0.1.7](https://github.com/SeldonIO/seldon-core/tree/v0.1.7) (2018-06-04)
+[Full Changelog](https://github.com/SeldonIO/seldon-core/compare/v0.1.6...v0.1.7)
+
+**Closed issues:**
+
+- Quickstart problem [\#153](https://github.com/SeldonIO/seldon-core/issues/153)
+- NameError: global name 'ListValue' is not defined [\#148](https://github.com/SeldonIO/seldon-core/issues/148)
+- bad credentials error with get\_token function [\#144](https://github.com/SeldonIO/seldon-core/issues/144)
+- Make CRD Namespaced scoped [\#141](https://github.com/SeldonIO/seldon-core/issues/141)
+- Create wrappers for Java based models [\#137](https://github.com/SeldonIO/seldon-core/issues/137)
+- Update ksonnet prototypes for latest image version [\#130](https://github.com/SeldonIO/seldon-core/issues/130)
+- Create demo notebook for Azure [\#129](https://github.com/SeldonIO/seldon-core/issues/129)
+- Grafana Dashboard  [\#109](https://github.com/SeldonIO/seldon-core/issues/109)
+- Multiple helm seldon-core installs on separate namespaces fails [\#106](https://github.com/SeldonIO/seldon-core/issues/106)
+
+**Merged pull requests:**
+
+- Add install guide [\#156](https://github.com/SeldonIO/seldon-core/pull/156) ([cliveseldon](https://github.com/cliveseldon))
+- WIP : PySpark and PMML example [\#155](https://github.com/SeldonIO/seldon-core/pull/155) ([cliveseldon](https://github.com/cliveseldon))
+- Fix gRPC tests for wrappers and update sklearn iris example to show use [\#150](https://github.com/SeldonIO/seldon-core/pull/150) ([cliveseldon](https://github.com/cliveseldon))
+- Minikube RBAC updates and Notebooks for Model examples [\#147](https://github.com/SeldonIO/seldon-core/pull/147) ([cliveseldon](https://github.com/cliveseldon))
+- change ClusterRoleBinding to RoleBinding [\#146](https://github.com/SeldonIO/seldon-core/pull/146) ([gsunner](https://github.com/gsunner))
+- MNIST loadtest [\#143](https://github.com/SeldonIO/seldon-core/pull/143) ([cliveseldon](https://github.com/cliveseldon))
+- Openshift article on using s2i in seldon-core [\#140](https://github.com/SeldonIO/seldon-core/pull/140) ([cliveseldon](https://github.com/cliveseldon))
+- Java wrappers [\#138](https://github.com/SeldonIO/seldon-core/pull/138) ([cliveseldon](https://github.com/cliveseldon))
+- add notebook for azure demo [\#135](https://github.com/SeldonIO/seldon-core/pull/135) ([gsunner](https://github.com/gsunner))
+- update ksonnet defaults to 0.1.6 [\#131](https://github.com/SeldonIO/seldon-core/pull/131) ([cliveseldon](https://github.com/cliveseldon))
+- Typos fix [\#128](https://github.com/SeldonIO/seldon-core/pull/128) ([LevineHuang](https://github.com/LevineHuang))
+
 ## [v0.1.6](https://github.com/SeldonIO/seldon-core/tree/v0.1.6) (2018-03-29)
 [Full Changelog](https://github.com/SeldonIO/seldon-core/compare/v0.1.5...v0.1.6)
 

api-frontend/pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>io.seldon.apife</groupId>
 	<artifactId>seldon-apife</artifactId>
-	<version>0.1.7</version>
+	<version>0.1.8</version>
 	<packaging>jar</packaging>
 
 	<name>api-frontend</name>

cluster-manager/pom.xml

@@ -4,7 +4,7 @@
   <groupId>io.seldon.clustermanager</groupId>
   <artifactId>seldon-cluster-manager</artifactId>
   <packaging>jar</packaging>
-  <version>0.1.7</version>
+  <version>0.1.8</version>
   <name>seldon-cluster-manager</name>
   <url>http://maven.apache.org</url>
 

core-builder/Dockerfile

@@ -27,9 +27,10 @@ RUN \
 
 # dependencies for release script
 RUN \
+    # install env for python3
     apt-get update -y && \
-    apt-get install -y python-pip && \
-    pip install pyyaml && \
+    apt-get install -y python3-pip && \
+    pip3 install pyyaml && \
     apt-get remove -y --auto-remove && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 WORKDIR /work

core-builder/Makefile

@@ -1,5 +1,5 @@
 DOCKER_IMAGE_NAME=seldonio/core-builder
-DOCKER_IMAGE_VERSION=0.2
+DOCKER_IMAGE_VERSION=0.3
 
 build_docker_image:
 	docker build --force-rm=true -t $(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_VERSION) .

docs/getting_started/minikube.md

@@ -213,12 +213,4 @@ The response contains:
     * "names": The names of your classes.
     * "ndarray": The predicted  probabilities for each class.
 
-## Next Steps
-
- * You can run several notebooks that show various examples on minikube and Google cloud platform
-   *  [Jupyter Notebook showing deployment of prebuilt model using Minikube](https://github.com/SeldonIO/seldon-core/blob/master/notebooks/kubectl_demo_minikube.ipynb)
-   * [Jupyter Notebook showing deployment of prebuilt model using GCP cluster](https://github.com/SeldonIO/seldon-core/blob/master/notebooks/kubectl_demo_gcp.ipynb)
-   * [Epsilon-greedy multi-armed bandits for real time optimization of models](https://github.com/SeldonIO/seldon-core/blob/master/notebooks/epsilon_greedy_gcp.ipynb)
-   * [Advanced graphs showing the various types of runtime prediction graphs that can be built](https://github.com/cliveseldon/seldon-core/blob/master/notebooks/advanced_graphs.ipynb) 
-   * [Jupyter notebook to create seldon-core with ksonnet and expose APIs using Ambassador.](https://github.com/SeldonIO/seldon-core/blob/master/notebooks/ksonnet_ambassador_minikube.ipynb)
 

docs/readme.md

@@ -1,10 +1,5 @@
 # Seldon Documentation
 
-## Quick Start
-
- - [Quick Start using Minikube](./getting_started/minikube.md)
- - [Jupyter Notebook showing deployment of prebuilt model](https://github.com/SeldonIO/seldon-core/blob/master/notebooks/kubectl_demo_minikube.ipynb)
-
 ## Deployment Guide
 
 ![API](./deploy.png)

docs/wrappers/java.md

@@ -38,7 +38,7 @@ Create a Spring Boot Maven project and include the dependency:
 <dependency>
 	<groupId>io.seldon.wrapper</groupId>
 	<artifactId>seldon-core-wrapper</artifactId>
-	<version>0.1.0</version>
+	<version>0.1.1</version>
 </dependency>
 ```
 

engine/pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>io.seldon.engine</groupId>
 	<artifactId>seldon-engine</artifactId>
-	<version>0.1.7</version>
+	<version>0.1.8</version>
 	<packaging>jar</packaging>
 
 	<name>engine</name>
@@ -76,9 +76,9 @@
 	<dependencies>
 		<!-- https://mvnrepository.com/artifact/org.nd4j/nd4j-native -->
 		<dependency>
-		    <groupId>org.nd4j</groupId>
-		    <artifactId>nd4j-native-platform</artifactId>
-		    <version>0.9.1</version>
+   			<groupId>org.ojalgo</groupId>
+    		<artifactId>ojalgo</artifactId>
+    		<version>45.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.springframework.boot</groupId>

engine/src/main/java/io/seldon/engine/predictors/AverageCombinerUnit.java

@@ -18,16 +18,14 @@
 import java.util.Iterator;
 import java.util.List;
 
-import org.nd4j.linalg.api.ndarray.INDArray;
-import org.nd4j.linalg.factory.Nd4j;
+import org.ojalgo.matrix.BasicMatrix;
+import org.ojalgo.matrix.PrimitiveMatrix;
 import org.springframework.stereotype.Component;
 
 import io.seldon.engine.exception.APIException;
 import io.seldon.protos.PredictionProtos.DefaultData;
 import io.seldon.protos.PredictionProtos.SeldonMessage;
 
-import io.seldon.engine.predictors.PredictorUtils;
-
 @Component
 public class AverageCombinerUnit extends PredictiveUnitImpl {
 
@@ -49,8 +47,8 @@ public SeldonMessage aggregate(List<SeldonMessage> outputs, PredictiveUnitState
 		if (shape.length!=2){
 			throw new APIException(APIException.ApiExceptionType.ENGINE_INVALID_COMBINER_RESPONSE, String.format("Combiner received data that is not 2 dimensional"));
 		}
-
-		INDArray currentSum = Nd4j.zeros(shape[0],shape[1]);
+		BasicMatrix.Factory<PrimitiveMatrix> matrixFactory = PrimitiveMatrix.FACTORY;
+		PrimitiveMatrix currentSum = matrixFactory.makeZero(shape[0], shape[1]);
 		SeldonMessage.Builder respBuilder = SeldonMessage.newBuilder();
 
 		for (Iterator<SeldonMessage> i = outputs.iterator(); i.hasNext();)
@@ -69,10 +67,10 @@ public SeldonMessage aggregate(List<SeldonMessage> outputs, PredictiveUnitState
 			if (inputShape[1] != shape[1]){
 				throw new APIException(APIException.ApiExceptionType.ENGINE_INVALID_COMBINER_RESPONSE, String.format("Expected batch length %d but found %d",shape[1],inputShape[1]));
 			}
-			INDArray inputArr = PredictorUtils.getINDArray(inputData);
+			PrimitiveMatrix inputArr = PredictorUtils.getOJMatrix(inputData);
 			currentSum = currentSum.add(inputArr);
 		}
-		currentSum = currentSum.div((float)outputs.size());
+		currentSum = currentSum.divide((float)outputs.size());
 
 		DefaultData newData = PredictorUtils.updateData(outputs.get(0).getData(), currentSum);
 		respBuilder.setData(newData);

engine/src/main/java/io/seldon/engine/predictors/PredictiveUnitBean.java

@@ -22,7 +22,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.Future;
 
-import org.nd4j.linalg.api.ndarray.INDArray;
+import org.ojalgo.matrix.PrimitiveMatrix;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Async;
 import org.springframework.scheduling.annotation.AsyncResult;
@@ -37,8 +37,8 @@
 import io.seldon.engine.service.InternalPredictionService;
 import io.seldon.protos.DeploymentProtos.PredictiveUnit.PredictiveUnitMethod;
 import io.seldon.protos.PredictionProtos.Feedback;
-import io.seldon.protos.PredictionProtos.SeldonMessage;
 import io.seldon.protos.PredictionProtos.Meta;
+import io.seldon.protos.PredictionProtos.SeldonMessage;
 
 @Component
 public class PredictiveUnitBean extends PredictiveUnitImpl {
@@ -227,8 +227,8 @@ public void doSendFeedback(Feedback feedback, PredictiveUnitState state) throws
 	private int getBranchIndex(SeldonMessage routerReturn, PredictiveUnitState state){
 		int branchIndex = 0;
 		try {
-			INDArray dataArray = PredictorUtils.getINDArray(routerReturn.getData());
-			branchIndex = (int) dataArray.getInt(0);
+			PrimitiveMatrix dataArray = PredictorUtils.getOJMatrix(routerReturn.getData());
+			branchIndex = dataArray.get(0).intValue();
 		}
 		catch (IndexOutOfBoundsException e) {
 			throw new APIException(APIException.ApiExceptionType.ENGINE_INVALID_ROUTING,"Router that caused the exception: id="+state.name+" name="+state.name);

engine/src/main/java/io/seldon/engine/predictors/PredictorUtils.java

@@ -15,56 +15,22 @@
  *******************************************************************************/
 package io.seldon.engine.predictors;
 
-import io.seldon.protos.PredictionProtos.Tensor;
-import io.seldon.protos.PredictionProtos.DefaultData.DataOneofCase;
-import io.seldon.protos.PredictionProtos.DefaultData;
-
-import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
-import java.util.stream.Collectors;
 
-import org.nd4j.linalg.api.ndarray.INDArray;
-import org.nd4j.linalg.factory.Nd4j;
+import org.ojalgo.matrix.BasicMatrix;
+import org.ojalgo.matrix.PrimitiveMatrix;
 
 import com.google.protobuf.ListValue;
 import com.google.protobuf.Value;
 
+import io.seldon.protos.PredictionProtos.DefaultData;
+import io.seldon.protos.PredictionProtos.DefaultData.DataOneofCase;
+import io.seldon.protos.PredictionProtos.Tensor;
+
 public class PredictorUtils {
 
-	public static DefaultData tensorToNDArray(DefaultData data){
-		if (data.getDataOneofCase() == DataOneofCase.TENSOR)
-		{
-			List<Double> valuesList = data.getTensor().getValuesList();
-			List<Integer> shapeList = data.getTensor().getShapeList();
-
-			DefaultData.Builder dataBuilder = DefaultData.newBuilder();
-
-			int index=0;
-			for (Iterator<String> i = data.getNamesList().iterator(); i.hasNext();){
-				dataBuilder.setNames(index, i.next());
-				index++;
-			}
-
-			ListValue.Builder b1 = ListValue.newBuilder();
-			for (int i = 0; i < shapeList.get(0); ++i) {
-				ListValue.Builder b2 = ListValue.newBuilder();
-				for (int j = 0; j < shapeList.get(1); j++){
-					b2.addValues(Value.newBuilder().setNumberValue(valuesList.get(i*shapeList.get(1))+j));
-				}
-				b1.addValues(Value.newBuilder().setListValue(b2.build()));
-			}
-			dataBuilder.setNdarray(b1.build());
-
-			return dataBuilder.build();
-
-		}
-		else if (data.getDataOneofCase() == DataOneofCase.NDARRAY)
-		{
-			return data;
-		}
-		return null;
-	}
+
 
 	public static DefaultData nDArrayToTensor(DefaultData data){
 		if (data.getDataOneofCase() == DataOneofCase.TENSOR)
@@ -98,49 +64,45 @@ else if (data.getDataOneofCase() == DataOneofCase.NDARRAY)
 		}
 		return null;
 	}
-	
-	public static INDArray getINDArray(DefaultData data){
-
+
+	public static PrimitiveMatrix getOJMatrix(DefaultData data){
+		BasicMatrix.Factory<PrimitiveMatrix> matrixFactory = PrimitiveMatrix.FACTORY;
 		if (data.getDataOneofCase() == DataOneofCase.TENSOR)
 		{
 
 			List<Double> valuesList = data.getTensor().getValuesList();
 			List<Integer> shapeList = data.getTensor().getShapeList();
 
-			double[] values = new double[valuesList.size()];
-			int[] shape = new int[shapeList.size()];
-			for (int i = 0; i < values.length; i++) {
-				values[i] = valuesList.get(i);
-			 }
-			for (int i = 0; i < shape.length; i++) {
-				shape[i] = shapeList.get(i);
+			int rows = shapeList.get(0);
+			int columns = shapeList.get(1);
+
+			double[][] values = new double[rows][columns];
+			for (int i = 0; i < rows*columns; i++) {
+				values[i/columns][i%columns] = valuesList.get(i);
 			 }
-
-			INDArray newArr = Nd4j.create(values,shape,'c');
 
-			return newArr;
+			return matrixFactory.rows(values);
 		}
 		else if (data.getDataOneofCase() == DataOneofCase.NDARRAY)
 		{
 			ListValue list = data.getNdarray();
-			int bLength = list.getValuesCount();
-			int vLength = list.getValues(0).getListValue().getValuesCount();
-
-			double[] values = new double[bLength*vLength];
-			int[] shape = {bLength,vLength};
+			int rows = list.getValuesCount();
+			int cols = list.getValues(0).getListValue().getValuesCount();
 
-			for (int i = 0; i < bLength; ++i) {
-				for (int j = 0; j < vLength; j++){
-					values[i*bLength+j] = list.getValues(i).getListValue().getValues(j).getNumberValue();
+			double[][] values = new double[rows][cols];
+			for (int i = 0; i < rows; ++i) {
+				for (int j = 0; j < cols; j++){
+					values[i][j] = list.getValues(i).getListValue().getValues(j).getNumberValue();
 				}
 			}
 
-			INDArray newArr = Nd4j.create(values,shape,'c');
-
-			return newArr;
+			return matrixFactory.rows(values);
 		}
 		return null;
 	}
+
+
+
 
 	public static int[] getShape(DefaultData data){
 		if (data.getDataOneofCase() == DataOneofCase.TENSOR){
@@ -162,7 +124,7 @@ else if(data.getDataOneofCase() == DataOneofCase.NDARRAY){
 		return null;
 	}
 
-	public static DefaultData updateData(DefaultData oldData, INDArray newData){
+	public static DefaultData updateData(DefaultData oldData, PrimitiveMatrix newData){
 		DefaultData.Builder dataBuilder = DefaultData.newBuilder();
 
 		dataBuilder.addAllNames(oldData.getNamesList());
@@ -175,23 +137,24 @@ public static DefaultData updateData(DefaultData oldData, INDArray newData){
 
 		if (oldData.getDataOneofCase() == DataOneofCase.TENSOR){
 			Tensor.Builder tBuilder = Tensor.newBuilder();
-			List<Integer> shapeList = Arrays.stream(newData.shape()).boxed().collect(Collectors.toList());
-			tBuilder.addAllShape(shapeList);
+
+			tBuilder.addShape((int)newData.countRows());
+			tBuilder.addShape((int)newData.countColumns());
 
-			for (int i=0; i<shapeList.get(0); ++i){
-				for (int j=0; j<shapeList.get(1); ++j){
-					tBuilder.addValues(newData.getDouble(i,j));
+			for (int i=0; i<newData.countRows(); ++i){
+				for (int j=0; j<newData.countColumns(); ++j){
+					tBuilder.addValues(newData.get(i,j));
 				}
 			}
 			dataBuilder.setTensor(tBuilder);
 			return dataBuilder.build();
 		}
 		else if (oldData.getDataOneofCase() == DataOneofCase.NDARRAY){
 			ListValue.Builder b1 = ListValue.newBuilder();
-			for (int i = 0; i < newData.shape()[0]; ++i) {
+			for (int i = 0; i < newData.countRows(); ++i) {
 				ListValue.Builder b2 = ListValue.newBuilder();
-				for (int j = 0; j < newData.shape()[1]; j++){
-					b2.addValues(Value.newBuilder().setNumberValue(newData.getDouble(i,j)));
+				for (int j = 0; j < newData.countColumns(); j++){
+					b2.addValues(Value.newBuilder().setNumberValue(newData.get(i,j)));
 				}
 				b1.addValues(Value.newBuilder().setListValue(b2.build()));
 			}
@@ -202,5 +165,6 @@ else if (oldData.getDataOneofCase() == DataOneofCase.NDARRAY){
 
 	}
 
+
 }