Code style standardization

ccinput/calculation.py

@@ -106,7 +106,7 @@ def __init__(
             raise InvalidParameter(
                 f"Multiplicity must at least 1 (received '{multiplicity}')"
             )
-            
+
         if parse_name:
             if not file:
                 raise InvalidParameter(

ccinput/packages/gaussian.py

@@ -11,7 +11,7 @@
     get_dihedral,
     get_npxyz,
     check_fragments,
-    add_fragments_xyz
+    add_fragments_xyz,
 )
 from ccinput.constants import CalcType, ATOMIC_NUMBER, LOWERCASE_ATOMIC_SYMBOLS
 from ccinput.exceptions import InvalidParameter, ImpossibleCalculation
@@ -201,9 +201,11 @@ def handle_command(self):
                     self.command_line += f"{method}/{gen_keyword} "
         else:
             self.command_line += f"{method} "
-        #Counterpoise related commands processing
-        if 'counterpoise' in self.commands.keys() :
-            check_fragments(self.commands['counterpoise'][0],self.calc.fragments,self.calc.xyz)
+        # Counterpoise related commands processing
+        if "counterpoise" in self.commands.keys():
+            check_fragments(
+                self.commands["counterpoise"][0], self.calc.fragments, self.calc.xyz
+            )
 
     def parse_custom_basis_set(self, base_bs):
         custom_basis_sets = self.calc.parameters.custom_basis_sets
@@ -287,11 +289,11 @@ def parse_custom_basis_set(self, base_bs):
 
     def handle_xyz(self):
         lines = [i + "\n" for i in clean_xyz(self.calc.xyz).split("\n") if i != ""]
-        #If counterpoise correction is the option, modify xyz corresponding to fragments
-        if self.calc.fragments != None :
+        # If counterpoise correction is the option, modify xyz corresponding to fragments
+        if self.calc.fragments != None:
             print(self.calc.fragments)
             print(type(self.calc.fragments))
-            lines = add_fragments_xyz(lines,self.calc.fragments)
+            lines = add_fragments_xyz(lines, self.calc.fragments)
         self.xyz_structure = "".join(lines)
 
     def parse_custom_solvation_radii(self):

ccinput/tests/test_gaussian.py

@@ -3793,13 +3793,13 @@ def test_sp_HF_CP_wrong_fragments(self):
             "method": "HF",
             "basis_set": "3-21G",
             "charge": "0",
-            "specifications" : "counterpoise=2",
-            "fragments" : "1,1,1,1,2,2,2,2,2,5"
+            "specifications": "counterpoise=2",
+            "fragments": "1,1,1,1,2,2,2,2,2,5",
         }
 
         with self.assertRaises(InvalidParameter):
             self.generate_calculation(**params)
-    
+
     def test_sp_HF_CP_1(self):
         params = {
             "nproc": 8,
@@ -3810,8 +3810,8 @@ def test_sp_HF_CP_1(self):
             "method": "HF",
             "basis_set": "3-21G",
             "charge": "0",
-            "specifications" : "counterpoise=4 ",
-            "fragments" : "1,1,2,2,2,3,4,4,4"
+            "specifications": "counterpoise=4 ",
+            "fragments": "1,1,2,2,2,3,4,4,4",
         }
 
         inp = self.generate_calculation(**params)
@@ -3838,7 +3838,7 @@ def test_sp_HF_CP_1(self):
         """
 
         self.assertTrue(self.is_equivalent(REF, inp.input_file))
-    
+
     def test_sp_HF_CP_2(self):
         params = {
             "nproc": 8,
@@ -3849,8 +3849,8 @@ def test_sp_HF_CP_2(self):
             "method": "HF",
             "basis_set": "3-21G",
             "charge": "0",
-            "specifications" : "counterpoise=2",
-            "fragments" : "1,1,1,1,2,2,2,2,2"
+            "specifications": "counterpoise=2",
+            "fragments": "1,1,1,1,2,2,2,2,2",
         }
 
         inp = self.generate_calculation(**params)
@@ -3889,8 +3889,8 @@ def test_sp_HF_CP_wrong_num_frag(self):
             "method": "HF",
             "basis_set": "3-21G",
             "charge": "0",
-            "specifications" : "counterpoise=3",
-             "fragments" : "1,2,3,3,3,4,5,5,5",
+            "specifications": "counterpoise=3",
+            "fragments": "1,2,3,3,3,4,5,5,5",
         }
 
         with self.assertRaises(InvalidParameter):
@@ -3906,8 +3906,8 @@ def test_sp_HF_CP_wrong_start_num(self):
             "method": "HF",
             "basis_set": "3-21G",
             "charge": "0",
-            "specifications" : "counterpoise=3 ",
-            "fragments" : "2,2,2,2,2,3,3,3,4"
+            "specifications": "counterpoise=3 ",
+            "fragments": "2,2,2,2,2,3,3,3,4",
         }
 
         with self.assertRaises(InvalidParameter):

ccinput/utilities.py

@@ -421,25 +421,33 @@ def get_charge_mult_from_name(name):
         mult = 1
 
     return charge, mult
-def add_fragments_xyz(xyz,frag):
+
+
+def add_fragments_xyz(xyz, frag):
     "Add fragment information to xyz"
     xyz_frag = []
-    frag = frag.split(',')
-    for i,line in enumerate(xyz):
+    frag = frag.split(",")
+    for i, line in enumerate(xyz):
         line_splitted = line.split()
-        xyz_frag.append(f"{line_splitted[0]}(Fragment={frag[i]}) {line_splitted[1]} {line_splitted[2]} {line_splitted[3]} \n")
+        xyz_frag.append(
+            f"{line_splitted[0]}(Fragment={frag[i]}) {line_splitted[1]} {line_splitted[2]} {line_splitted[3]} \n"
+        )
     return xyz_frag
-def check_fragments(counterpoise,fragments,xyz):
+
+
+def check_fragments(counterpoise, fragments, xyz):
     """Checks if the fragments are reasonably defined"""
-    fragments = fragments.split(',')
+    fragments = fragments.split(",")
     try:
         fragments = [int(i) for i in fragments]
     except:
         raise InvalidParameter("Fragment numbers must be integers")
     unique_fragments = list(set(fragments))
-    if len([i + "\n" for i in clean_xyz(xyz).split("\n") if i != ""]) != len(fragments) :
+    if len([i + "\n" for i in clean_xyz(xyz).split("\n") if i != ""]) != len(fragments):
         raise InvalidParameter("You must assign exactly one fragment to each atom")
-    elif (sorted(unique_fragments) != list(range(1,max(unique_fragments)+1))):
+    elif sorted(unique_fragments) != list(range(1, max(unique_fragments) + 1)):
         raise InvalidParameter("Fragment numbers must start from 1")
-    elif ( len(unique_fragments) != int(counterpoise) ) :
-        raise InvalidParameter("Counterpoise keyword must be equal to the total number of fragments")
+    elif len(unique_fragments) != int(counterpoise):
+        raise InvalidParameter(
+            "Counterpoise keyword must be equal to the total number of fragments"
+        )

ccinput/wrapper.py

@@ -149,7 +149,7 @@ def generate_calculation(
         file=file,
         driver=driver,
         **kwargs,
-        fragments=fragments
+        fragments=fragments,
     )
 
     return process_calculation(calc)