fix tests to accommodate kwarg updates in dihedrals module

mdpow/tests/test_automated_dihedral_analysis.py

@@ -52,14 +52,13 @@ def mol_sol_data(self, SM25_tmp_dir):
         return mol, solute
 
     @pytest.fixture(scope="function")
-    def atom_indices(self, SM25_tmp_dir, mol_sol_data):
+    def atom_indices(self, mol_sol_data):
         mol, _ = mol_sol_data
-        atom_group_indices = dihedrals.get_atom_indices(dirname=SM25_tmp_dir, mol=mol)
+        atom_group_indices = dihedrals.get_atom_indices(mol=mol)
 
         # testing optional user input of alternate SMARTS string
         # for automated dihedral atom group selection
-        atom_group_indices_alt = dihedrals.get_atom_indices(dirname=SM25_tmp_dir, mol=mol,
-                                                            SMARTS='[!$(*#*)&!D1]-!@[!$(*#*)&!D1]')
+        atom_group_indices_alt = dihedrals.get_atom_indices(mol=mol, SMARTS='[!$(*#*)&!D1]-!@[!$(*#*)&!D1]')
         return atom_group_indices, atom_group_indices_alt
         # fixture output, tuple:
         # atom_indices[0]=atom_group_indices
@@ -252,14 +251,14 @@ def test_dihedral_groups_ensemble(self, dihedral_data):
 
     def test_save_df(self, dihedral_data, SM25_tmp_dir):
         df, _ = dihedral_data
-        dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, molname='SM25')
+        dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, resname='UNK', molname='SM25')
         assert (SM25_tmp_dir / 'SM25' / 'SM25_full_df.csv.bz2').exists(), 'Compressed csv file not saved'
 
     def test_save_df_info(self, dihedral_data, SM25_tmp_dir, caplog):
         df, _ = dihedral_data
         caplog.clear()
         caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals')
-        dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, molname='SM25')
+        dihedrals.save_df(df=df, df_save_dir=SM25_tmp_dir, resname='UNK', molname='SM25')
         assert f'Results DataFrame saved as {SM25_tmp_dir}/SM25/SM25_full_df.csv.bz2' in caplog.text, 'Save location not logged or returned'
 
     # the following 'reason' affects every downstream function that relies

mdpow/workflows/dihedrals.py

@@ -808,7 +808,7 @@ def automated_dihedral_analysis(dirname, figdir, resname,
 
     u = build_universe(dirname=dirname)
     mol, solute = rdkit_conversion(u=u, resname=resname)
-    atom_indices = get_atom_indices(dirname=dirname, mol=mol, SMARTS=SMARTS)
+    atom_indices = get_atom_indices(mol=mol, SMARTS=SMARTS)
     bond_indices = get_bond_indices(mol=mol, atom_indices=atom_indices)
     dihedral_groups = get_dihedral_groups(solute=solute, atom_indices=atom_indices)
     ab_pairs = get_paired_indices(atom_indices=atom_indices, bond_indices=bond_indices,
@@ -821,7 +821,7 @@ def automated_dihedral_analysis(dirname, figdir, resname,
 
     else:
 
-        df = dihedral_groups_ensemble(atom_indices=atom_indices, dirname=dirname,
+        df = dihedral_groups_ensemble(dirname=dirname, atom_indices=atom_indices,
                                       solvents=solvents, interactions=interactions,
                                       start=start, stop=stop, step=step)
 
@@ -830,6 +830,7 @@ def automated_dihedral_analysis(dirname, figdir, resname,
 
     df_aug = periodic_angle_padding(df, padding=padding)
 
+    #kwargs in weird order
     plot_dihedral_violins(df_aug, resname=resname, molname=molname, mol=mol, plot_pdf_width=plot_pdf_width,
                  ab_pairs=ab_pairs, figdir=figdir, width=width, solvents=solvents)