fix linting

Author: ajfriedman22

ensemble_md/replica_exchange_EE.py

@@ -164,7 +164,7 @@ def set_params(self, analysis):
             "resname_transform": None,
             "resname_list": None,
             "swap_rep_pattern": None,
-            "allow_virtual_V": False, # Allow use of V to indicate virtual atoms in topology
+            "allow_virtual_V": False,  # Allow use of V to indicate virtual atoms in topology
             "nst_sim": None,
             "proposal": 'exhaustive',
             "w_combine": False,

ensemble_md/tests/test_coordinate_swap.py

@@ -61,10 +61,10 @@ def test_fix_break():
     test_fix = coordinate_swap.fix_break(broken_mol, 'C2D', [2.74964, 2.74964, 2.74964], df_connect_res, False, 1)
 
     broken_mol_3D = md.load(f'{input_path}/coord_swap/broken_mol_3D.gro')
-    test_fix_3D = coordinate_swap.fix_break(broken_mol_3D, 'C2D', [2.74964, 2.74964, 2.74964], df_connect_res, False, 1)
+    test_fix_3D = coordinate_swap.fix_break(broken_mol_3D, 'C2D', [2.74964, 2.74964, 2.74964], df_connect_res, False, 1)  # noqa: E501
 
     already_fixed = md.load(f'{input_path}/coord_swap/fixed_mol.gro')
-    still_fixed = coordinate_swap.fix_break(already_fixed, 'C2D', [2.74964, 2.74964, 2.74964], df_connect_res, False, 1)
+    still_fixed = coordinate_swap.fix_break(already_fixed, 'C2D', [2.74964, 2.74964, 2.74964], df_connect_res, False, 1)  # noqa: E501
 
     fixed_mol = md.load(f'{input_path}/coord_swap/fixed_mol.gro')
 
@@ -139,8 +139,8 @@ def test_get_miss_coord():
 
     A_dimensions = coordinate_swap.get_dimensions(open(molA_file, 'r').readlines())
     B_dimensions = coordinate_swap.get_dimensions(open(molB_file, 'r').readlines())
-    molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA], False)
-    molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB], False)
+    molA = coordinate_swap.fix_break(molA, nameA, A_dimensions, connection_map[connection_map['Resname'] == nameA], False)  # noqa: E501
+    molB = coordinate_swap.fix_break(molB, nameB, B_dimensions, connection_map[connection_map['Resname'] == nameB], False)  # noqa: E501
 
     df_no_coords = pd.read_csv(f'{input_path}/coord_swap/extract_missing.csv')
     df = pd.read_csv(f'{input_path}/coord_swap/df_atom_swap.csv')