[SPARK-2478] [mllib] DecisionTree Python API

Added experimental Python API for Decision Trees.

API:
* class DecisionTreeModel
** predict() for single examples and RDDs, taking both feature vectors and LabeledPoints
** numNodes()
** depth()
** __str__()
* class DecisionTree
** trainClassifier()
** trainRegressor()
** train()

Examples and testing:
* Added example testing classification and regression with batch prediction: examples/src/main/python/mllib/tree.py
* Have also tested example usage in doc of python/pyspark/mllib/tree.py which tests single-example prediction with dense and sparse vectors

Also: Small bug fix in python/pyspark/mllib/_common.py: In _linear_predictor_typecheck, changed check for RDD to use isinstance() instead of type() in order to catch RDD subclasses.

CC mengxr manishamde

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #1727 from jkbradley/decisiontree-python-new and squashes the following commits:

3744488 [Joseph K. Bradley] Renamed test tree.py to decision_tree_runner.py Small updates based on github review.
6b86a9d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
affceb9 [Joseph K. Bradley] * Fixed bug in doc tests in pyspark/mllib/util.py caused by change in loadLibSVMFile behavior.  (It used to threshold labels at 0 to make them 0/1, but it now leaves them as they are.) * Fixed small bug in loadLibSVMFile: If a data file had no features, then loadLibSVMFile would create a single all-zero feature.
67a29bc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
cf46ad7 [Joseph K. Bradley] Python DecisionTreeModel * predict(empty RDD) returns an empty RDD instead of an error. * Removed support for calling predict() on LabeledPoint and RDD[LabeledPoint] * predict() does not cache serialized RDD any more.
aa29873 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
bf21be4 [Joseph K. Bradley] removed old run() func from DecisionTree
fa10ea7 [Joseph K. Bradley] Small style update
7968692 [Joseph K. Bradley] small braces typo fix
e34c263 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4801b40 [Joseph K. Bradley] Small style update to DecisionTreeSuite
db0eab2 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix2' into decisiontree-python-new
6873fa9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
225822f [Joseph K. Bradley] Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature.
93953f1 [Joseph K. Bradley] Likely done with Python API.
6df89a9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
4562c08 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
665ba78 [Joseph K. Bradley] Small updates towards Python DecisionTree API
188cb0d [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
6622247 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
b8fac57 [Joseph K. Bradley] Finished Python DecisionTree API and example but need to test a bit more.
2b20c61 [Joseph K. Bradley] Small doc and style updates
1b29c13 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
584449a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals
8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type.
376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1
e06e423 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
bab3f19 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them.
52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
f5a036c [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification.  Caused problems in past, but fixed now.
8e227ea [Joseph K. Bradley] Changed Strategy so it only requires numClassesForClassification >= 2 for classification
cd1d933 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features.
8a758db [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new
5fe44ed [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new
2283df8 [Joseph K. Bradley] 2 bug fixes.
73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix
5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail.  Will describe bug in next commit.
f825352 [Joseph K. Bradley] Wrote Python API and example for DecisionTree.  Also added toString, depth, and numNodes methods to DecisionTreeModel.

1 files changed, 1 insertions, 0 deletions

diff --git a/python/run-tests b/python/run-tests
index 5049e15ce5..48feba2f5b 100755
--- a/python/run-tests
+++ b/python/run-tests
@@ -71,6 +71,7 @@ run_test "pyspark/mllib/random.py"
 run_test "pyspark/mllib/recommendation.py"
 run_test "pyspark/mllib/regression.py"
 run_test "pyspark/mllib/tests.py"
+run_test "pyspark/mllib/util.py"
 
 if [[ $FAILED == 0 ]]; then
     echo -en "\033[32m"  # Green