[SPARK-5477] refactor stat.py

There is only a single `stat.py` file for the `mllib.stat` package. We recently added `MultivariateGaussian` under `mllib.stat.distribution` in Scala/Java. It would be nice to refactor `stat.py` and make it easy to expand. Note that `ChiSqTestResult` is moved from `mllib.stat` to `mllib.stat.test`. The latter is used in Scala/Java. It is only used in the return value of `Statistics.chiSqTest`, so this should be an okay change.

davies

Author: Xiangrui Meng <meng@databricks.com>

Closes apache#4266 from mengxr/py-stat-refactor and squashes the following commits:

1a5e1db [Xiangrui Meng] refactor stat.py

mllib/pom.xml

@@ -125,6 +125,7 @@
         <directory>../python</directory>
         <includes>
           <include>pyspark/mllib/*.py</include>
+          <include>pyspark/mllib/stat/*.py</include>
           <include>pyspark/ml/*.py</include>
           <include>pyspark/ml/param/*.py</include>
         </includes>

python/pyspark/mllib/stat/__init__.py

@@ -0,0 +1,24 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""
+Python package for statistical functions in MLlib.
+"""
+
+from pyspark.mllib.stat._statistics import *
+
+__all__ = ["Statistics", "MultivariateStatisticalSummary"]

python/pyspark/mllib/stat.py → python/pyspark/mllib/stat/_statistics.py

@@ -15,17 +15,14 @@
 # limitations under the License.
 #
 
-"""
-Python package for statistical functions in MLlib.
-"""
-
 from pyspark import RDD
 from pyspark.mllib.common import callMLlibFunc, JavaModelWrapper
 from pyspark.mllib.linalg import Matrix, _convert_to_vector
 from pyspark.mllib.regression import LabeledPoint
+from pyspark.mllib.stat.test import ChiSqTestResult
 
 
-__all__ = ['MultivariateStatisticalSummary', 'ChiSqTestResult', 'Statistics']
+__all__ = ['MultivariateStatisticalSummary', 'Statistics']
 
 
 class MultivariateStatisticalSummary(JavaModelWrapper):
@@ -53,54 +50,6 @@ def min(self):
         return self.call("min").toArray()
 
 
-class ChiSqTestResult(JavaModelWrapper):
-    """
-    .. note:: Experimental
-
-    Object containing the test results for the chi-squared hypothesis test.
-    """
-    @property
-    def method(self):
-        """
-        Name of the test method
-        """
-        return self._java_model.method()
-
-    @property
-    def pValue(self):
-        """
-        The probability of obtaining a test statistic result at least as
-        extreme as the one that was actually observed, assuming that the
-        null hypothesis is true.
-        """
-        return self._java_model.pValue()
-
-    @property
-    def degreesOfFreedom(self):
-        """
-        Returns the degree(s) of freedom of the hypothesis test.
-        Return type should be Number(e.g. Int, Double) or tuples of Numbers.
-        """
-        return self._java_model.degreesOfFreedom()
-
-    @property
-    def statistic(self):
-        """
-        Test statistic.
-        """
-        return self._java_model.statistic()
-
-    @property
-    def nullHypothesis(self):
-        """
-        Null hypothesis of the test.
-        """
-        return self._java_model.nullHypothesis()
-
-    def __str__(self):
-        return self._java_model.toString()
-
-
 class Statistics(object):
 
     @staticmethod

python/pyspark/mllib/stat/test.py

@@ -0,0 +1,69 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from pyspark.mllib.common import JavaModelWrapper
+
+
+__all__ = ["ChiSqTestResult"]
+
+
+class ChiSqTestResult(JavaModelWrapper):
+    """
+    .. note:: Experimental
+
+    Object containing the test results for the chi-squared hypothesis test.
+    """
+    @property
+    def method(self):
+        """
+        Name of the test method
+        """
+        return self._java_model.method()
+
+    @property
+    def pValue(self):
+        """
+        The probability of obtaining a test statistic result at least as
+        extreme as the one that was actually observed, assuming that the
+        null hypothesis is true.
+        """
+        return self._java_model.pValue()
+
+    @property
+    def degreesOfFreedom(self):
+        """
+        Returns the degree(s) of freedom of the hypothesis test.
+        Return type should be Number(e.g. Int, Double) or tuples of Numbers.
+        """
+        return self._java_model.degreesOfFreedom()
+
+    @property
+    def statistic(self):
+        """
+        Test statistic.
+        """
+        return self._java_model.statistic()
+
+    @property
+    def nullHypothesis(self):
+        """
+        Null hypothesis of the test.
+        """
+        return self._java_model.nullHypothesis()
+
+    def __str__(self):
+        return self._java_model.toString()

python/run-tests

@@ -76,7 +76,7 @@ function run_mllib_tests() {
     run_test "pyspark/mllib/rand.py"
     run_test "pyspark/mllib/recommendation.py"
     run_test "pyspark/mllib/regression.py"
-    run_test "pyspark/mllib/stat.py"
+    run_test "pyspark/mllib/stat/_statistics.py"
     run_test "pyspark/mllib/tree.py"
     run_test "pyspark/mllib/util.py"
     run_test "pyspark/mllib/tests.py"