Merge pull request #70 from astrolabsoftware/0.1.4

Bump version to v0.1.4
astrolabsoftware · Jul 13, 2018 · cd1e68c · cd1e68c
2 parents 02c8ef6 + c2d249b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,8 @@
+## 0.1.4
+
+- Unify the IO: One constructor to rule them all! ([PR](https://github.com/astrolabsoftware/spark3D/pull/69))
+- Octree and Geometry Objects Bug Fixes ([PR](https://github.com/astrolabsoftware/spark3D/pull/67))
+
 ## 0.1.3
 
 - Add KNN routines ([KNN](https://github.com/astrolabsoftware/spark3D/pull/59), [KNN](https://github.com/astrolabsoftware/spark3D/pull/60), [KNN](https://github.com/astrolabsoftware/spark3D/pull/62))

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 - [05/2018] **GSoC 2018**: spark3D has been selected to the Google Summer of Code (GSoC) 2018. Congratulation to [@mayurdb](https://github.com/mayurdb) who will work on the project this year!
 - [06/2018] **Release**: version 0.1.0, 0.1.1
 - [07/2018] **New location**: spark3D is an official project of [AstroLab Software](https://astrolabsoftware.github.io/)!
-- [07/2018] **Release**: version 0.1.3
+- [07/2018] **Release**: version 0.1.3, 0.1.4
 
 ## Installation and tutorials
 

diff --git a/build.sbt b/build.sbt
@@ -19,7 +19,7 @@ import xerial.sbt.Sonatype._
 lazy val root = (project in file(".")).
  settings(
    inThisBuild(List(
-     version      := "0.1.3"
+     version      := "0.1.4"
    )),
    // Name of the application
    name := "spark3D",

diff --git a/docs/01_installation.md b/docs/01_installation.md
@@ -20,7 +20,7 @@ another version, feel free to contact us. In addition to Spark, the library has
 You can link spark3D to your project (either `spark-shell` or `spark-submit`) by specifying the coordinates:
 
 ```bash
-toto:~$ spark-submit --packages "com.github.astrolabsoftware:spark3d_2.11:0.1.3" <...>
+toto:~$ spark-submit --packages "com.github.astrolabsoftware:spark3d_2.11:0.1.4" <...>
 ```
 
 It might not contain the latest features though (see *Building from source*).
@@ -69,7 +69,7 @@ result on the screen, plus details of the coverage at
 First produce a jar of the spark3D library, and then launch a spark-shell by specifying the external dependencies:
 
 ```bash
-toto:~$ JARS="target/scala-2.11/spark3d_2.11-0.1.3.jar,lib/jhealpix.jar"
+toto:~$ JARS="target/scala-2.11/spark3d_2.11-0.1.4.jar,lib/jhealpix.jar"
 toto:~$ PACKAGES="com.github.astrolabsoftware:spark-fits_2.11:0.6.0"
 toto:~$ spark-shell --jars $JARS --packages $PACKAGES
 ```
@@ -83,7 +83,7 @@ scala> // etc...
 Note that if you make a fat jar (that is building with `sbt assembly` and not `sbt package`), you do not need to specify external dependencies as they are already included in the resulting jar:
 
 ```bash
-toto:~$ FATJARS="target/scala-2.11/spark3D-assembly-0.1.3.jar"
+toto:~$ FATJARS="target/scala-2.11/spark3D-assembly-0.1.4.jar"
 toto:~$ spark-shell --jars $FATJARS
 ```
 

diff --git a/docs/02_introduction.md b/docs/02_introduction.md
@@ -73,7 +73,8 @@ import com.astrolabsoftware.spark3d.spatial3DRDD.Point3DRDD
 // We assume filename contains at least 3 columns whose names are `colnames`
 // Order of columns in the file does not matter, as they will be re-aranged
 // according to `colnames`.
-val pointRDD = new Point3DRDD(spark: SparkSession, filename: String, colnames: String, isSpherical: Boolean, format: String, options: Map[String, String])
+val pointRDD = new Point3DRDD(spark: SparkSession, filename: String, colnames: String,
+  isSpherical: Boolean, format: String, options: Map[String, String])
 ```
 
 `format` and `options` control the correct reading of your data.
@@ -134,7 +135,8 @@ import com.astrolabsoftware.spark3d.spatial3DRDD.SphereRDD
 // We assume filename contains at least 4 columns whose names are `colnames`.
 // Order of columns in the file does not matter, as they will be re-aranged
 // according to `colnames`.
-val sphereRDD = new SphereRDD(spark: SparkSession, filename: String, colnames: String, isSpherical: Boolean, format: String, options: Map[String, String])
+val sphereRDD = new SphereRDD(spark: SparkSession, filename: String, colnames: String,
+  isSpherical: Boolean, format: String, options: Map[String, String])
 ```
 
 The resulting RDD is a `RDD[ShellEnvelope]`.

diff --git a/docs/04_query.md b/docs/04_query.md
@@ -155,7 +155,20 @@ For more details on the cross-match, see the following [notebook](https://github
 
 ## Neighbour search
 
-TBD
+Brute force KNN:
+
+```scala
+// Load the data
+val pRDD = new Point3DRDD(spark, fn, columns, isSpherical, "csv", options)
+
+// Centre object for the query
+val queryObject = new Point3D(0.0, 0.0, 0.0, false)
+
+// Find the `nNeighbours` closest neighbours
+val knn = SpatialQuery.KNN(queryObject, pRDD.rawRDD, nNeighbours)
+```
+
+To come: partitioning + indexing!
 
 ## Benchmarks
 

diff --git a/docs/_pages/home.md b/docs/_pages/home.md
@@ -8,7 +8,7 @@ header:
   cta_url: "/docs/installation/"
   caption:
 intro:
-  - excerpt: '<p><font size="6">Spark extension for processing large-scale 3D data sets: Astrophysics, High Energy Physics, Meteorology, ...</font></p><br /><a href="https://github.com/astrolabsoftware/spark3D/releases/tag/0.1.3">Latest release v0.1.3</a>'
+  - excerpt: '<p><font size="6">Spark extension for processing large-scale 3D data sets: Astrophysics, High Energy Physics, Meteorology, ...</font></p><br /><a href="https://github.com/astrolabsoftware/spark3D/releases/tag/0.1.4">Latest release v0.1.4</a>'
 excerpt: '{::nomarkdown}<iframe style="display: inline-block;" src="https://ghbtns.com/github-btn.html?user=astrolabsoftware&repo=spark3D&type=star&count=true&size=large" frameborder="0" scrolling="0" width="160px" height="30px"></iframe> <iframe style="display: inline-block;" src="https://ghbtns.com/github-btn.html?user=astrolabsoftware&repo=spark3D&type=fork&count=true&size=large" frameborder="0" scrolling="0" width="158px" height="30px"></iframe>{:/nomarkdown}'
 feature_row:
   - image_path:

diff --git a/docs/about.md b/docs/about.md
@@ -38,7 +38,7 @@ Several goals have to be undertaken in this project:
   + indexing mechanisms
   + ways to define a metric (ie. distance between objects)
   + selection capability of objects or objects within a region
-- work with as many input file format as possible (CSV, JSON, FITS, and so on)
+- work with as many input file format as possible (CSV, ROOT, FITS, HDF5 and so on)
 - package the developments into an open-source library.
 
 ## Support

diff --git a/examples/jupyter/CrossMatch.ipynb b/examples/jupyter/CrossMatch.ipynb
@@ -75,11 +75,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Marking com.github.astrolabsoftware:spark-fits_2.11:0.4.0 for download\n",
+      "Marking com.github.astrolabsoftware:spark-fits_2.11:0.6.0 for download\n",
       "Preparing to fetch from:\n",
       "-> file:/var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps7614799531666607290/\n",
       "-> https://repo1.maven.org/maven2\n",
-      "-> New file at /var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps7614799531666607290/https/repo1.maven.org/maven2/com/github/astrolabsoftware/spark-fits_2.11/0.4.0/spark-fits_2.11-0.4.0.jar\n",
+      "-> New file at /var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps7614799531666607290/https/repo1.maven.org/maven2/com/github/astrolabsoftware/spark-fits_2.11/0.6.0/spark-fits_2.11-0.6.0.jar\n",
       "Marking com.github.haifengl:smile-plot:1.5.1 for download\n",
       "Preparing to fetch from:\n",
       "-> file:/var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps7614799531666607290/\n",
@@ -113,7 +113,7 @@
    ],
    "source": [
     "// Package to read data from FITS file\n",
-    "%AddDeps com.github.astrolabsoftware spark-fits_2.11 0.4.0\n",
+    "%AddDeps com.github.astrolabsoftware spark-fits_2.11 0.6.0\n",
     "\n",
     "// Smile provides visualisation tools\n",
     "%AddDeps com.github.haifengl smile-plot 1.5.1\n",

diff --git a/examples/jupyter/onion_partitioning.ipynb b/examples/jupyter/onion_partitioning.ipynb
@@ -24,11 +24,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Marking com.github.astrolabsoftware:spark-fits_2.11:0.3.0 for download\n",
+      "Marking com.github.astrolabsoftware:spark-fits_2.11:0.6.0 for download\n",
       "Preparing to fetch from:\n",
       "-> file:/var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps3353854346753658887/\n",
       "-> https://repo1.maven.org/maven2\n",
-      "-> New file at /var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps3353854346753658887/https/repo1.maven.org/maven2/com/github/astrolabsoftware/spark-fits_2.11/0.3.0/spark-fits_2.11-0.3.0.jar\n",
+      "-> New file at /var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps3353854346753658887/https/repo1.maven.org/maven2/com/github/astrolabsoftware/spark-fits_2.11/0.6.0/spark-fits_2.11-0.6.0.jar\n",
       "Marking com.github.haifengl:smile-plot:1.5.1 for download\n",
       "Preparing to fetch from:\n",
       "-> file:/var/folders/my/lfvl285927q2hzk545f39sy40000gn/T/toree_add_deps3353854346753658887/\n",
@@ -62,7 +62,7 @@
    ],
    "source": [
     "// Package to read data from FITS file\n",
-    "%AddDeps com.github.astrolabsoftware spark-fits_2.11 0.3.0\n",
+    "%AddDeps com.github.astrolabsoftware spark-fits_2.11 0.6.0\n",
     "\n",
     "// Smile provides visualisation tools\n",
     "%AddDeps com.github.haifengl smile-plot 1.5.1\n",

diff --git a/run_scala.sh b/run_scala.sh
@@ -18,7 +18,7 @@ SBT_VERSION=2.11.8
 SBT_VERSION_SPARK=2.11
 
 ## Package version
-VERSION=0.1.3
+VERSION=0.1.4
 
 # Package it
 sbt ++${SBT_VERSION} package
@@ -31,7 +31,7 @@ display="show"
 
 ## Dependencies
 jars="lib/jhealpix.jar,lib/swingx-0.9.1.jar"
-packages="com.github.astrolabsoftware:spark-fits_2.11:0.4.0,com.github.haifengl:smile-core:1.5.1,com.github.haifengl:smile-plot:1.5.1,com.github.haifengl:smile-math:1.5.1,com.github.haifengl:smile-scala_2.11:1.5.1"
+packages="com.github.astrolabsoftware:spark-fits_2.11:0.6.0,com.github.haifengl:smile-core:1.5.1,com.github.haifengl:smile-plot:1.5.1,com.github.haifengl:smile-math:1.5.1,com.github.haifengl:smile-scala_2.11:1.5.1"
 
 # Run it!
 spark-submit \

diff --git a/run_xmatch_cluster.sh b/run_xmatch_cluster.sh
@@ -18,7 +18,7 @@ SBT_VERSION=2.11.8
 SBT_VERSION_SPARK=2.11
 
 ## Package version
-VERSION=0.1.3
+VERSION=0.1.4
 
 # Package it
 sbt ++${SBT_VERSION} package
@@ -36,7 +36,7 @@ kind="healpix"
 
 ## Dependencies
 jars="lib/jhealpix.jar"
-packages="com.github.astrolabsoftware:spark-fits_2.11:0.4.0"
+packages="com.github.astrolabsoftware:spark-fits_2.11:0.6.0"
 
 # Run it!
 spark-submit \