Merge branch 'master' of github.com:twosigma/beakerx into lukasz/7204…

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twosigma · May 23, 2018 · 91d4990 · 91d4990
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diff --git a/README.md b/README.md
@@ -24,14 +24,14 @@
 [![NPM version](https://badge.fury.io/js/beakerx.svg)](http://badge.fury.io/js/beakerx)
 [![PyPI Version](https://badge.fury.io/py/beakerx.svg)](http://badge.fury.io/py/beakerx)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/beakerx/badges/version.svg)](https://anaconda.org/conda-forge/beakerx)
-[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/twosigma/beakerx/0.17.0?filepath=StartHere.ipynb)
+[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/twosigma/beakerx/0.17.1?filepath=StartHere.ipynb)
 
 BeakerX is a collection of JVM kernels and interactive widgets for
 plotting, tables, autotranslation, and other extensions to Jupyter
 Notebook.  BeakerX is in beta and under active development.
 
 The [documentation](https://github.com/twosigma/beakerx/blob/master/StartHere.ipynb) consists of tutorial notebooks on GitHub.
-You can try it in the cloud for free with [Binder](https://mybinder.org/v2/gh/twosigma/beakerx/0.17.0?filepath=StartHere.ipynb).
+You can try it in the cloud for free with [Binder](https://mybinder.org/v2/gh/twosigma/beakerx/0.17.1?filepath=StartHere.ipynb).
 
 BeakerX is the successor to the [Beaker Notebook (source code
 archive)](https://github.com/twosigma/beaker-notebook-archive).  It

diff --git a/StartHere.ipynb b/StartHere.ipynb
@@ -25,7 +25,7 @@
     "[Python](doc/python/AutoTranslation.ipynb), [Groovy](doc/groovy/AutoTranslation.ipynb).\n",
     "\n",
     "### Groovy Plotting and Charting\n",
-    "[Example and Interaction](doc/groovy/Charting.ipynb), [Time Series and General APIs and Features](doc/groovy/PlotFeatures.ipynb), [Category Plots and Bar Charts](doc/groovy/CategoryPlot.ipynb), [Levels of Detail](doc/groovy/LevelsOfDetails.ipynb), [Histograms](doc/groovy/Histogram.ipynb), [Heatmaps](doc/groovy/Heatmap.ipynb), [Treemaps](doc/groovy/Treemap.ipynb), [Plot Actions](doc/groovy/PlotActions.ipynb), [Plot Seamless Updates](doc/groovy/PlotsPythonStyle.ipynb), [Second Y Axis](doc/groovy/2ndYaxis.ipynb).\n",
+    "[Example and Interaction](doc/groovy/Charting.ipynb), [Time Series and General APIs and Features](doc/groovy/PlotFeatures.ipynb), [Category Plots and Bar Charts](doc/groovy/CategoryPlot.ipynb), [Levels of Detail](doc/groovy/LevelsOfDetails.ipynb), [Histograms](doc/groovy/Histogram.ipynb), [Heatmaps](doc/groovy/Heatmap.ipynb), [Treemaps](doc/groovy/Treemap.ipynb), [Plot Actions](doc/groovy/PlotActions.ipynb), [Plot Seamless Updates](doc/groovy/PlotsPythonStyle.ipynb), [Second Y Axis](doc/groovy/2ndYaxis.ipynb), [3D Visualization and Maps](doc/groovy/3D.ipynb).\n",
     "\n",
     "### Table Display\n",
     "[Groovy API including Actions](doc/groovy/TableAPI.ipynb), [64-Bit Integers and BigNums](doc/groovy/BigInts.ipynb), [Automatic Display of Simple Data Structures](doc/groovy/MapLikeTable.ipynb), [Handling of Large Tables](doc/groovy/BigTable.ipynb).\n",

diff --git a/beakerx/beakerx/_version.py b/beakerx/beakerx/_version.py
@@ -1,2 +1,2 @@
-version_info = (0, 17, 0)
+version_info = (0, 17, 1)
 __version__ = '.'.join(map(str, version_info))
diff --git a/doc/groovy/3D.ipynb b/doc/groovy/3D.ipynb
@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 3D Visualization and Maps\n",
+    "\n",
+    "There is an alpha Groovy API for [ipyvolume](https://github.com/maartenbreddels/ipyvolume). For this to work, the widget JS needs to be installed:\n",
+    "```\n",
+    "conda install -c conda-forge ipyvolume\n",
+    "```\n",
+    "\n",
+    "[Pythreejs](https://github.com/jupyter-widgets/pythreejs) and [ipyleaflet](https://github.com/jupyter-widgets/ipyleaflet) will be forthcoming, see [#6903](https://github.com/twosigma/beakerx/issues/6903). We hope these APIs will be included upstream in the original widget repositories."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%classpath config resolver jitpack.io https://jitpack.io\n",
+    "%classpath add mvn com.github.twosigma:ipyvolume:master-SNAPSHOT\n",
+    "import ipyvolume.PyLab;\n",
+    "\n",
+    "int size = 32;\n",
+    "int radius = 12;\n",
+    "float[][][] data = new float[size][size][size];\n",
+    "for (int x = 0; x<size; x++){\n",
+    "    for (int y = 0; y<size; y++){\n",
+    "        for (int z = 0; z<size; z++){\n",
+    "            if (Math.pow(x - size/2, 2) + Math.pow(y - size/2, 2) + Math.pow(z - size/2, 2) <= Math.pow(radius, 2)){\n",
+    "                data[x][y][z] = 1.0f;\n",
+    "            }\n",
+    "        }\n",
+    "    }\n",
+    "}\n",
+    "\n",
+    "figure = PyLab.volShow(data)"
+   ]
+  }
+ ],
+ "metadata": {
+  "anaconda-cloud": {},
+  "beakerx_kernel_parameters": {},
+  "kernelspec": {
+   "display_name": "Groovy",
+   "language": "groovy",
+   "name": "groovy"
+  },
+  "language_info": {
+   "codemirror_mode": "groovy",
+   "file_extension": ".groovy",
+   "mimetype": "",
+   "name": "Groovy",
+   "nbconverter_exporter": "",
+   "version": "2.4.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}
diff --git a/doc/groovy/LevelsOfDetails.ipynb b/doc/groovy/LevelsOfDetails.ipynb
@@ -1,12 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -23,9 +16,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "// generate a random walk\n",
@@ -44,15 +35,14 @@
     "}\n",
     "// now x is time for the x-axis, and y is the random variable\n",
     "beer = walk(10)\n",
-    "whiskey = walk(100)"
+    "whiskey = walk(100)\n",
+    "OutputCell.HIDDEN"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "p = new TimePlot(title: \"Drunken Sailor Walks\", showLegend: true, lodThreshold: 2000)\n",

diff --git a/doc/groovy/PolyglotMagic.ipynb b/doc/groovy/PolyglotMagic.ipynb
@@ -6,7 +6,14 @@
    "source": [
     "# Polyglot Magics\n",
     "\n",
-    "The BeakerX kernels have magics to run other kernels, including `%%python`.  There are magics for each BeakerX langage: `%%groovy`, `%%java`, `%%scala`, `%%sql`, `%%clojure`, and `%%kotlin`.  There is also a `%%kernel` magic to access any kernel available to Jupyter.  Widgets work through these magics.\n",
+    "The BeakerX kernels have magics to run other kernels, including `%%python`.  There are magics for each BeakerX langage: `%%groovy`, `%%java`, `%%scala`, `%%sql`, `%%clojure`, and `%%kotlin`.  There is also a `%%kernel` magic to access any kernel available to Jupyter.  Widgets work through these magics.  These magics give access to Python from the JVM.\n",
+    "\n",
+    "There are also [Groovy Magics](../python/KernelMagics.ipynb) magics for accessing the JVM from Python.\n",
+    "\n",
+    "Fleshing out the polyglot support in BeakerX with communication between languages ([#5039](https://github.com/twosigma/beakerx/issues/5039)) is on the agenda.\n",
+    "\n",
+    "\n",
+    "\n",
     "\n",
     "## Python Magic\n",
     "\n",

diff --git a/doc/kotlin/Kotlin.ipynb b/doc/kotlin/Kotlin.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "# Kotlin\n",
     "\n",
-    "[Kotlin](https://kotlinlang.org/) is a relative newcomer from [JetBrains](https://www.jetbrains.com/) and [Android](https://developer.android.com/kotlin/get-started.html).  It's intended to an improved version of Java, including [Null Safety](https://kotlinlang.org/docs/reference/null-safety.html)."
+    "[Kotlin](https://kotlinlang.org/) is a relative newcomer from [JetBrains](https://www.jetbrains.com/) and [Android](https://developer.android.com/kotlin/get-started.html).  It's intended to be an improved version of Java, including [Null Safety](https://kotlinlang.org/docs/reference/null-safety.html)."
    ]
   },
   {
@@ -58,7 +58,7 @@
    "mimetype": "",
    "name": "Kotlin",
    "nbconverter_exporter": "",
-   "version": "1.1.3"
+   "version": "1.2.21"
   }
  },
  "nbformat": 4,

diff --git a/doc/python/KernelMagics.ipynb b/doc/python/KernelMagics.ipynb
@@ -9,7 +9,9 @@
     "BeakerX has magics for Python so you can run cells in the other languages.\n",
     "The first few cells below show how complete the implementation is with Groovy, then we have just one cell in each other language.\n",
     "\n",
-    "Fleshing out the polyglot support in BeakerX with communication between languages ([#5039](https://github.com/twosigma/beakerx/issues/5039)) and the ability to access Python from the JVM kernels ([#6279](https://github.com/twosigma/beakerx/issues/6279)) are on the agenda.\n",
+    "There are also [Polyglot Magics](../groovy/PolyglotMagic.ipynb) magics for accessing Python from the JVM.\n",
+    "\n",
+    "Fleshing out the polyglot support in BeakerX with communication between languages ([#5039](https://github.com/twosigma/beakerx/issues/5039)) is on the agenda.\n",
     "\n",
     "## Groovy"
    ]
@@ -246,7 +248,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.6.5"
   }
  },
  "nbformat": 4,

diff --git a/doc/scala/SparkUI.ipynb b/doc/scala/SparkUI.ipynb
@@ -53,7 +53,6 @@
    "outputs": [],
    "source": [
     "%%spark\n",
-    "import org.apache.spark.sql.SparkSession\n",
     "SparkSession.builder()\n",
     "      .appName(\"BeakerX Demo\")\n",
     "      .master(\"local[4]\")"
@@ -73,7 +72,6 @@
    "outputs": [],
    "source": [
     "%%spark --connect\n",
-    "import org.apache.spark.sql.SparkSession\n",
     "SparkSession.builder().master(\"local[100]\")"
    ]
   },

diff --git a/js/lab/package-lock.json b/js/lab/package-lock.json
diff --git a/js/lab/package.json b/js/lab/package.json
@@ -1,6 +1,6 @@
 {
   "name": "beakerx-jupyterlab",
-  "version": "0.17.0",
+  "version": "0.17.1",
   "description": "BeakerX: Beaker Extensions for JupyterLab",
   "author": "Two Sigma Open Source, LLC",
   "main": "dist/index.js",

diff --git a/js/notebook/package.json b/js/notebook/package.json
@@ -1,6 +1,6 @@
 {
   "name": "beakerx",
-  "version": "0.17.0",
+  "version": "0.17.1",
   "description": "BeakerX: Beaker Extensions for Jupyter",
   "author": "Two Sigma Open Source, LLC",
   "main": "src/index.js",

diff --git a/js/notebook/src/SparkStateProgress.ts b/js/notebook/src/SparkStateProgress.ts
@@ -182,7 +182,7 @@ class SparkStateProgressView extends widgets.VBoxView {
     let valueActive = state.active;
     let valueWaiting = max - (valueDone + valueActive);
 
-    this.progressLabels = document.createElement('p');
+    this.progressLabels = document.createElement('div');
     this.progressLabels.classList.add('bx-spark-stageProgressLabels');
 
     this.progressLabels.innerHTML = `

diff --git a/js/notebook/src/shared/style/beakerx.scss b/js/notebook/src/shared/style/beakerx.scss
@@ -124,7 +124,6 @@ $focusColor: #66bb6a;
     font-size: 14px;
     line-height: 1.3em;
     flex-grow: 1;
-    max-width: 600px;
     text-indent: 0;
     transition: opacity 0.1s ease-in-out;
     padding: 0 15px;
@@ -134,6 +133,11 @@ $focusColor: #66bb6a;
       overflow: hidden;
       white-space: nowrap;
     }
+
+    p {
+      margin: 0;
+      padding: 0;
+    }
   }
 
   .foldout-content {

diff --git a/js/notebook/src/shared/style/spark.scss b/js/notebook/src/shared/style/spark.scss
@@ -20,6 +20,7 @@
   & > .bx-spark-stagePanel {
     padding: 0 15px;
     max-width: 600px;
+    margin: 0;
   }
 }
 
@@ -100,3 +101,16 @@
     width: 50%;
   }
 }
+
+.bx-spark-stageProgressLabels {
+  display: block;
+  line-height: 100%;
+  height: 18px;
+  align-items: center;
+
+  .label {
+    display: inline-block;
+    max-height: 100%;
+    line-height: 150%;
+  }
+}
diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/KernelInfoHandler.java b/kernel/base/src/main/java/com/twosigma/beakerx/KernelInfoHandler.java
@@ -49,9 +49,8 @@ public void handle(Message message) {
 
   private void handleMsg(Message message) {
     logger.debug("Processing kernel info request");
-    Message reply = new Message();
+    Message reply = new Message(new Header(KERNEL_INFO_REPLY, message.getHeader().getSession()));
     reply.setContent(content());
-    reply.setHeader(new Header(KERNEL_INFO_REPLY, message.getHeader().getSession()));
     reply.setParentHeader(message.getHeader());
     reply.setIdentities(message.getIdentities());
     send(reply);

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/evaluator/BaseEvaluator.java b/kernel/base/src/main/java/com/twosigma/beakerx/evaluator/BaseEvaluator.java
@@ -74,6 +74,7 @@ public BaseEvaluator(String id, String sId, CellExecutor cellExecutor, TempFolde
   }
 
   protected TryResult evaluate(SimpleEvaluationObject seo, Callable<TryResult> callable) {
+    InternalVariable.setValue(seo);
     Future<TryResult> submit = executorService.submit(callable);
     TryResult either = null;
     try {

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/handler/CompleteHandler.java b/kernel/base/src/main/java/com/twosigma/beakerx/handler/CompleteHandler.java
@@ -57,8 +57,7 @@ private void handleMsg(Message message) {
   }
 
   private Message createMsg(Message message, int cursorPos, AutocompleteResult autocomplete) {
-    Message reply = new Message();
-    reply.setHeader(new Header(COMPLETE_REPLY, message.getHeader().getSession()));
+    Message reply = new Message(new Header(COMPLETE_REPLY, message.getHeader().getSession()));
     reply.setIdentities(message.getIdentities());
     reply.setParentHeader(message.getHeader());
     Map<String, Serializable> content = new HashMap<>();

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/handler/InspectHandler.java b/kernel/base/src/main/java/com/twosigma/beakerx/handler/InspectHandler.java
@@ -58,8 +58,7 @@ private void handleMsg(Message message) {
     }
 
     private Message createMsg(Message message, InspectResult inspectResult) {
-        Message reply = new Message();
-        reply.setHeader(new Header(INSPECT_REPLY, message.getHeader().getSession()));
+        Message reply = new Message(new Header(INSPECT_REPLY, message.getHeader().getSession()));
         reply.setIdentities(message.getIdentities());
         reply.setParentHeader(message.getHeader());
         Map<String, Serializable> content = new HashMap<>();

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/handler/IsCompleteRequestHandler.java b/kernel/base/src/main/java/com/twosigma/beakerx/handler/IsCompleteRequestHandler.java
@@ -45,11 +45,10 @@ public void handle(Message message) {
 
   private void handleMsg(Message message) {
     logger.debug("Processing is complete request");
-    Message reply = new Message();
+    Message reply = new Message(new Header(IS_COMPLETE_REPLY, message.getHeader().getSession()));
     HashMap<String, Serializable> map = new HashMap<>();
     map.put("status", "complete");
     reply.setContent(map);
-    reply.setHeader(new Header(IS_COMPLETE_REPLY, message.getHeader().getSession()));
     reply.setParentHeader(message.getHeader());
     reply.setIdentities(message.getIdentities());
     send(reply);

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/kernel/MagicKernelManager.java b/kernel/base/src/main/java/com/twosigma/beakerx/kernel/MagicKernelManager.java
@@ -135,14 +135,13 @@ private List<Message> getIopubMessages() throws IOException {
 
     private Message parseMessage(String stringJson) throws IOException {
         ObjectMapper mapper = new ObjectMapper();
-        Message msg = new Message();
         JsonNode json = mapper.readTree(stringJson);
+        Message msg = new Message(mapper.convertValue(json.get("header"), Header.class));
         msg.setContent(mapper.convertValue(json.get("content"), Map.class));
         msg.setMetadata(mapper.convertValue(json.get("metadata"), Map.class));
         msg.setBuffers(mapper.convertValue(json.get("buffers"), List.class));
         List<byte[]> identities = mapper.convertValue(json.get("comm_id"), List.class);
         msg.setIdentities(identities == null ? new ArrayList<>() : identities);
-        msg.setHeader(mapper.convertValue(json.get("header"), Header.class));
         return msg;
     }
 

diff --git a/kernel/base/src/main/java/com/twosigma/beakerx/kernel/comm/BaseHandler.java b/kernel/base/src/main/java/com/twosigma/beakerx/kernel/comm/BaseHandler.java
@@ -63,9 +63,8 @@ protected T getValueFromData(Message message, String key) {
   protected Message createReplyMessage(Message message, Serializable responceData) {
     Message ret = null;
     if (message != null) {
-      ret = new Message();
+      ret = new Message(new Header(COMM_MSG, message.getHeader().getSession()));
       Map<String, Serializable> commMap = message.getContent();
-      ret.setHeader(new Header(COMM_MSG, message.getHeader().getSession()));
       HashMap<String, Serializable> map = new HashMap<>();
       map.put(COMM_ID, getString(commMap, COMM_ID));
       map.put(DATA, responceData);