PEP 8

package/MDAnalysis/topology/base.py

@@ -144,11 +144,11 @@ def squash_by(child_parent_ids, *attributes):
 
 def squash_by_attributes(squash_attributes, *other_attributes):
     """Squash a child-parent relationship using combinations of attributes
-    parents will retain their order of appearance 
+    parents will retain their order of appearance
 
     Arguments
     ---------
-    squash_attributes - list of attribute arrays (attributes used to 
+    squash_attributes - list of attribute arrays (attributes used to
                         identify the parent)
     *other_attributes - other arrays that need to follow the sorting of ids
 
@@ -164,18 +164,17 @@ def squash_by_attributes(squash_attributes, *other_attributes):
     unique_combos, sort_mask, atom_idx = np.unique(
         squash_array, return_index=True, return_inverse=True, axis=0)
 
-
     appearance_order = np.argsort(sort_mask)
-    new_index = np.arange(0,len(appearance_order))
+    new_index = np.arange(0, len(appearance_order))
     resort_pairs = np.column_stack((appearance_order, new_index))
     atom_idx_mapping = dict(resort_pairs)
 
     sorted_atom_idx = np.vectorize(atom_idx_mapping.get)(atom_idx).astype(int)
     sorted_mask = np.sort(sort_mask)
-    
+
     squashed_attrs = [attr[sorted_mask] for attr in squash_attributes]
     other_attrs = [attr[sorted_mask] for attr in other_attributes]
-    
+
     return sorted_atom_idx, squashed_attrs, other_attrs
 
 

testsuite/MDAnalysisTests/topology/test_mol2.py

@@ -317,6 +317,7 @@ def test_unformat():
                        match='Some atoms in the mol2 file'):
         u = mda.Universe(StringIO(mol2_resname_unformat), format='MOL2')
 
+
 def test_repeat_resid():
     u = mda.Universe(StringIO(mol2_repeat_resid), format='MOL2')
 

testsuite/MDAnalysisTests/topology/test_pdb.py

@@ -330,11 +330,12 @@ def test_nobonds_error():
 
 pdb_repeat_resid = """\
 ATOM      1  CA  LYS A   1      65.978  40.866  -0.183  1.00  0.00           C
-ATOM      2  CA  SER A   2      64.324  40.006   3.164  1.00  0.00           C  
-ATOM      3  CA  LEU A   1      64.000  39.236   8.648  1.00  0.00           C  
-ATOM      4  N   LYS A   1      66.135  42.099  -1.007  1.00  0.00           N1+
+ATOM      2  CA  SER A   2      64.324  40.006   3.164  1.00  0.00           C
+ATOM      3  CA  LEU A   1      64.000  39.236   8.648  1.00  0.00           C
+ATOM      4  N   LYS A   1      66.135  42.099  -1.007  1.00  0.00           N
 """
 
+
 def test_repeat_resid():
     u = mda.Universe(StringIO(pdb_repeat_resid), format='PDB')