[SPARK-5599] Check MLlib public APIs for 1.3

There are no break changes (against 1.2) in this PR. I hide the PythonMLLibAPI, which is only called by Py4J, and renamed `SparseMatrix.diag` to `SparseMatrix.spdiag`. All other changes are documentation and annotations. The `Experimental` tag is removed from `ALS.setAlpha` and `Rating`. One issue not addressed in this PR is the `setCheckpointDir` in `LDA` (https://issues.apache.org/jira/browse/SPARK-5604).

CC: srowen jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #4377 from mengxr/SPARK-5599 and squashes the following commits:

17975dc [Xiangrui Meng] fix tests
4487f20 [Xiangrui Meng] remove experimental tag from each stat method because Statistics is experimental already
3cd969a [Xiangrui Meng] remove freeman (sorry~) from StreamLA public doc
55900f5 [Xiangrui Meng] make IR experimental and update its doc
9b8eed3 [Xiangrui Meng] graduate Rating and setAlpha in ALS
b854d28 [Xiangrui Meng] correct iid doc in RandomRDDs
27f5bdd [Xiangrui Meng] update linalg docs and some new method signatures
371721b [Xiangrui Meng] mark fpg as experimental and update its doc
8aca7ee [Xiangrui Meng] change SLR to experimental and update the doc
ebbb2e9 [Xiangrui Meng] mark PIC experimental and update the doc
7830d3b [Xiangrui Meng] mark GMM experimental
a378496 [Xiangrui Meng] use the correct subscript syntax in PIC
c65c424 [Xiangrui Meng] update LDAModel doc
a213b0c [Xiangrui Meng] update GMM constructor
3993054 [Xiangrui Meng] hide algorithm in SLR
ad6b9ce [Xiangrui Meng] Revert "make ClassificatinModel.predict(JavaRDD) return JavaDoubleRDD"
0054684 [Xiangrui Meng] add doc to LRModel's constructor
a89763b [Xiangrui Meng] make ClassificatinModel.predict(JavaRDD) return JavaDoubleRDD
7c0946c [Xiangrui Meng] hide PythonMLLibAPI

2 files changed, 6 insertions, 6 deletions

diff --git a/mllib/src/test/java/org/apache/spark/mllib/linalg/JavaMatricesSuite.java b/mllib/src/test/java/org/apache/spark/mllib/linalg/JavaMatricesSuite.java
index 704d484d0b..3349c50224 100644
--- a/mllib/src/test/java/org/apache/spark/mllib/linalg/JavaMatricesSuite.java
+++ b/mllib/src/test/java/org/apache/spark/mllib/linalg/JavaMatricesSuite.java
@@ -71,8 +71,8 @@ public class JavaMatricesSuite implements Serializable {
         Matrix sm = Matrices.diag(sv);
         DenseMatrix d = DenseMatrix.diag(v);
         DenseMatrix sd = DenseMatrix.diag(sv);
-        SparseMatrix s = SparseMatrix.diag(v);
-        SparseMatrix ss = SparseMatrix.diag(sv);
+        SparseMatrix s = SparseMatrix.spdiag(v);
+        SparseMatrix ss = SparseMatrix.spdiag(sv);
 
         assertArrayEquals(m.toArray(), sm.toArray(), 0.0);
         assertArrayEquals(d.toArray(), sm.toArray(), 0.0);
diff --git a/mllib/src/test/scala/org/apache/spark/mllib/linalg/MatricesSuite.scala b/mllib/src/test/scala/org/apache/spark/mllib/linalg/MatricesSuite.scala
index b1ebfde0e5..c098b5458f 100644
--- a/mllib/src/test/scala/org/apache/spark/mllib/linalg/MatricesSuite.scala
+++ b/mllib/src/test/scala/org/apache/spark/mllib/linalg/MatricesSuite.scala
@@ -137,8 +137,8 @@ class MatricesSuite extends FunSuite {
     val spMat1 = new SparseMatrix(m, n, colPtrs, rowIndices, values)
     val deMat1 = new DenseMatrix(m, n, allValues)
 
-    val spMat2 = deMat1.toSparse()
-    val deMat2 = spMat1.toDense()
+    val spMat2 = deMat1.toSparse
+    val deMat2 = spMat1.toDense
 
     assert(spMat1.toBreeze === spMat2.toBreeze)
     assert(deMat1.toBreeze === deMat2.toBreeze)
@@ -185,8 +185,8 @@ class MatricesSuite extends FunSuite {
     assert(!dA.toArray.eq(dAT.toArray), "has to have a new array")
     assert(dA.values.eq(dAT.transpose.asInstanceOf[DenseMatrix].values), "should not copy array")
 
-    assert(dAT.toSparse().toBreeze === sATexpected.toBreeze)
-    assert(sAT.toDense().toBreeze === dATexpected.toBreeze)
+    assert(dAT.toSparse.toBreeze === sATexpected.toBreeze)
+    assert(sAT.toDense.toBreeze === dATexpected.toBreeze)
   }
 
   test("foreachActive") {