Black lint changes to match version used by CI

Author: akutuva21

bionetgen/atomizer/atomizeTool.py

@@ -4,7 +4,6 @@
 
 from bionetgen.core.utils.logging import BNGLogger, log_level
 
-
 d = BNGDefaults()
 
 

bionetgen/atomizer/atomizer/detectOntology.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 import pprint
 import difflib
 from collections import Counter

bionetgen/atomizer/contactMap.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 # import sys
 # sys.path.insert(0, '../utils/')
 import utils.consoleCommands as console

bionetgen/atomizer/libsbml2bngl.py

@@ -1651,7 +1651,7 @@ def main():
         metavar="FILE",
     )
 
-    (options, _) = parser.parse_args()
+    options, _ = parser.parse_args()
     # 144
     rdfArray = []
     # classificationArray = []

bionetgen/atomizer/rulifier/stdgraph.py

@@ -130,13 +130,13 @@ def createBitNode(graph, molecule, nodeList, simplifiedText):
                 if simplifiedText:
                     nodeName += "o"
                 else:
-                    nodeName += "\u25CF "
+                    nodeName += "\u25cf "
                 nodeId.append(bit[0])
             else:
                 if simplifiedText:
                     nodeName += "x"
                 else:
-                    nodeName += "\u25CB "
+                    nodeName += "\u25cb "
                 # nodeName += u"\u00B7 "
             if (idx + 1) % gridDict[len(node)] == 0 and idx + 1 != len(node):
                 nodeName.strip(" ")

bionetgen/atomizer/sbml2bngl.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 from copy import deepcopy, copy
 from bionetgen.atomizer.writer import bnglWriter as writer
 
@@ -1453,7 +1454,7 @@ def reduceComponentSymmetryFactors(self, reaction, translator, functions):
                 for molecule in translator[element[0]].molecules:
                     for component in molecule.components:
                         molecule.sort()
-                        componentList = Counter([(molecule.signature(freactionCenter))])
+                        componentList = Counter([molecule.signature(freactionCenter)])
                         for _ in range(0, int(element[1])):
                             rcomponent[
                                 (
@@ -1469,7 +1470,7 @@ def reduceComponentSymmetryFactors(self, reaction, translator, functions):
                 for molecule in translator[element[0]].molecules:
                     molecule.sort()
                     for component in molecule.components:
-                        componentList = Counter([(molecule.signature(breactionCenter))])
+                        componentList = Counter([molecule.signature(breactionCenter)])
                         for _ in range(0, int(element[1])):
                             pcomponent[
                                 (

bionetgen/atomizer/sbml2json.py

@@ -405,7 +405,7 @@ def main():
         help="the output JSON file. Default = <input>.py",
         metavar="FILE",
     )
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     reader = libsbml.SBMLReader()
     nameStr = options.input
     if options.output == None:

bionetgen/atomizer/utils/consoleCommands.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 import bionetgen
 
 

bionetgen/atomizer/utils/extractAtomic.py

@@ -5,6 +5,7 @@
 
 @author: proto
 """
+
 from collections import Counter
 
 

bionetgen/atomizer/utils/readBNGXML.py

@@ -4,6 +4,7 @@
 
 @author: proto
 """
+
 from lxml import etree
 from . import smallStructures as st
 from io import StringIO