black applied

Author: pbashyal-nmdp

grim/conf/__init__.py

@@ -24,5 +24,5 @@
 
 
 __author__ = """Martin Maiers"""
-__email__ = '[email protected]'
-__version__ = '0.0.7'
+__email__ = "[email protected]"
+__version__ = "0.0.7"

grim/imputation/__init__.py

@@ -21,5 +21,5 @@
 
 
 __author__ = """Martin Maiers"""
-__email__ = '[email protected]'
-__version__ = '0.0.7'
+__email__ = "[email protected]"
+__version__ = "0.0.7"

grim/imputation/graph_generation/__init__.py

@@ -21,5 +21,5 @@
 
 
 __author__ = """Martin Maiers"""
-__email__ = '[email protected]'
-__version__ = '0.0.7'
+__email__ = "[email protected]"
+__version__ = "0.0.7"

grim/imputation/imputegl/__init__.py

@@ -23,5 +23,5 @@
 
 
 __author__ = """Martin Maiers"""
-__email__ = '[email protected]'
-__version__ = '0.0.7'
+__email__ = "[email protected]"
+__version__ = "0.0.7"

grim/imputation/imputegl/impute.py

@@ -119,10 +119,31 @@ def clean_up_gl(gl):
 
 
 class Imputation(object):
-    __slots__ = 'logger', 'verbose', 'populations', 'netGraph', 'priorMatrix', 'full_hapl', 'index_dict', 'full_loci', \
-                'factor', '_factor_missing_data', 'cypher', 'cypher_plan_b', 'matrix_planb', 'count_by_prob', \
-                'number_of_options_threshold', 'plan', 'option_1', 'option_2', \
-                'haplotypes_number_in_phase', 'save_space_mode', 'nodes_for_plan_A', 'unk_priors'    
+    __slots__ = (
+        "logger",
+        "verbose",
+        "populations",
+        "netGraph",
+        "priorMatrix",
+        "full_hapl",
+        "index_dict",
+        "full_loci",
+        "factor",
+        "_factor_missing_data",
+        "cypher",
+        "cypher_plan_b",
+        "matrix_planb",
+        "count_by_prob",
+        "number_of_options_threshold",
+        "plan",
+        "option_1",
+        "option_2",
+        "haplotypes_number_in_phase",
+        "save_space_mode",
+        "nodes_for_plan_A",
+        "unk_priors",
+    )
+
     def __init__(self, net=None, config=None, count_by_prob=None, verbose=False):
         """Constructor
         Intialize an instance of `Imputation` with a py2neo graph
@@ -394,7 +415,6 @@ def get_haplo_freqs(self, haplos, epsilon, n=25000):
         # haplos_joined = ["~".join(sorted(item)) for sublist in haplos for item in sublist]
         return self.netGraph.adjs_query(haplos_joined)
 
-
     # def get_haplo_freqs_miss(self, haplos, epsilon):
     #     haplo_probs = {}
     #     haplos_joined = ["~".join(sorted(item)) for sublist in haplos for item in sublist]

grim/imputation/imputegl/networkx_graph.py

@@ -9,7 +9,14 @@ def missing(labelA, labelB):
 
 
 class Graph(object):
-    __slots__ = 'graph', 'labelDict', 'whole_graph', 'full_loci', 'nodes_plan_a', 'nodes_plan_b'
+    __slots__ = (
+        "graph",
+        "labelDict",
+        "whole_graph",
+        "full_loci",
+        "nodes_plan_a",
+        "nodes_plan_b",
+    )
 
     def __init__(self, config):
         self.graph = nx.DiGraph()

grim/validation/__init__.py

@@ -21,5 +21,5 @@
 
 
 __author__ = """Martin Maiers"""
-__email__ = '[email protected]'
-__version__ = '0.0.7'
+__email__ = "[email protected]"
+__version__ = "0.0.7"