STYLE: Format with black (#237)

Author: NickEdwards7502

python/varspark/rfmodel.py

@@ -4,80 +4,109 @@
 from typedecorator import params, Nullable
 
 from varspark import java
+from varspark.core import VarsparkContext
 from varspark.importanceanalysis import ImportanceAnalysis
 from varspark.lfdrvsnohail import LocalFdrVs
 
+
 class RandomForestModel(object):
-    @params(self=object, ss=SparkSession,
-                 mtry_fraction=Nullable(float), oob=Nullable(bool),
-                 seed=Nullable(int), var_ordinal_levels=Nullable(int),
-                 max_depth=int, min_node_size=int)
-    def __init__(self, ss, mtry_fraction=None,
-                 oob=True, seed=None, var_ordinal_levels=3,
-                 max_depth=java.MAX_INT, min_node_size=1):
-        self.ss = ss
-        self.sc = ss.sparkContext
-        self._jvm = self.sc._jvm
-        self._vs_api = getattr(self._jvm, 'au.csiro.variantspark.api')
-        self.sql = SQLContext.getOrCreate(self.sc)
-        self._jsql = self.sql._jsqlContext
-        self.mtry_fraction=mtry_fraction
+    @params(
+        self=object,
+        vc=VarsparkContext,
+        mtry_fraction=Nullable(float),
+        oob=Nullable(bool),
+        seed=Nullable(int),
+        var_ordinal_levels=Nullable(int),
+        max_depth=Nullable(int),
+        min_node_size=Nullable(int),
+    )
+    def __init__(
+        self,
+        vc,
+        mtry_fraction=None,
+        oob=True,
+        seed=None,
+        var_ordinal_levels=3,
+        max_depth=java.MAX_INT,
+        min_node_size=1,
+    ):
+        self.sc = vc.sc
+        self.sql = vc.sql
+        self._jsql = vc._jsql
+        self._jvm = vc._jvm
+        self._vs_api = vc._vs_api
+        self._jvsc = vc._jvsc
+        self.mtry_fraction = mtry_fraction
         self.oob = oob
         self.seed = seed
         self.var_ordinal_levels = var_ordinal_levels
         self.max_depth = max_depth
         self.min_node_size = min_node_size
         self.vs_algo = self._jvm.au.csiro.variantspark.algo
-        self.jrf_params = self.vs_algo.RandomForestParams(bool(oob),
-                                                java.jfloat_or(
-                                                    mtry_fraction),
-                                                True, java.NAN, True,
-                                                java.jlong_or(seed,
-                                                              randint(
-                                                                  java.MIN_LONG,
-                                                                  java.MAX_LONG)),
-                                                max_depth,
-                                                min_node_size, False,
-                                                0)
+        self.jrf_params = self.vs_algo.RandomForestParams(
+            bool(oob),
+            java.jfloat_or(mtry_fraction),
+            True,
+            java.NAN,
+            True,
+            java.jlong_or(seed, randint(java.MIN_LONG, java.MAX_LONG)),
+            max_depth,
+            min_node_size,
+            False,
+            0,
+        )
         self._jrf_model = None
 
-    @params(self=object, X=object, y=object, n_trees=Nullable(int), batch_size=Nullable(int))
+    @params(
+        self=object,
+        X=object,
+        y=object,
+        n_trees=Nullable(int),
+        batch_size=Nullable(int),
+    )
     def fit_trees(self, X, y, n_trees=1000, batch_size=100):
-        """ Fits random forest model on provided input features and labels
+        """Fits random forest model on provided input features and labels
         :param (int) n_trees: Number of trees in the forest
         :param (int) batch_size:
         """
         self.n_trees = n_trees
         self.batch_size = batch_size
         self._jfs = X._jfs
-        self._jrf_model = self._vs_api.RFModelTrainer.trainModel(X._jfs, y, self.jrf_params, self.n_trees, self.batch_size)
+        self._jrf_model = self._vs_api.RFModelTrainer.trainModel(
+            X._jfs, y, self.jrf_params, self.n_trees, self.batch_size
+        )
 
     @params(self=object)
     def importance_analysis(self):
-        """ Returns gini variable importances for a fitted random forest model
+        """Returns gini variable importances for a fitted random forest model
         :return ImportanceAnalysis: Class containing importances and associated methods
         """
         jia = self._vs_api.ImportanceAnalysis(self._jsql, self._jfs, self._jrf_model)
         return ImportanceAnalysis(jia, self.sql)
 
     @params(self=object)
     def oob_error(self):
-        """ Returns the overall out-of-bag error associated with a fitted random forest model
+        """Returns the overall out-of-bag error associated with a fitted random forest model
         :return oob_error (float): Out of bag error associated with the fitted model
         """
         oob_error = self._jrf_model.oobError()
         return oob_error
 
     @params(self=object)
     def get_lfdr(self):
-        """ Returns the class with the information preloaded to compute the local FDR
+        """Returns the class with the information preloaded to compute the local FDR
         :return: class LocalFdrVs with the importances loaded
         """
         return LocalFdrVs.from_imp_df(self.importance_analysis().variable_importance())
 
-    @params(self=object, file_name=str, resolve_variable_names=Nullable(bool), batch_size=Nullable(int))
+    @params(
+        self=object,
+        file_name=str,
+        resolve_variable_names=Nullable(bool),
+        batch_size=Nullable(int),
+    )
     def export_to_json(self, file_name, resolve_variable_names=True, batch_size=1000):
-        """ Exports the random forest model to Json format
+        """Exports the random forest model to Json format
 
         :param (string) file_name: File name to export
         :param (bool) resolve_variable_names: Indicates whether to associate variant ids with exported nodes
@@ -86,5 +115,6 @@ def export_to_json(self, file_name, resolve_variable_names=True, batch_size=1000
         jexp = self._vs_api.ExportModel(self._jrf_model, self._jfs)
         jexp.toJson(file_name, resolve_variable_names, batch_size)
 
+
 # Deprecated
 RFModelContext = RandomForestModel