fixed automated_dihedral_tests that were order sensitive

- use set comparisons
- removed skipif for python < 3.8 and replaced with comment referencing
  issue #239

mdpow/tests/test_automated_dihedral_analysis.py

@@ -128,41 +128,30 @@ def test_build_universe(self, SM25_tmp_dir):
         solute_names = solute.atoms.names
         assert solute_names.all() == self.universe_solute_atom_names.all()
 
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Use set comparison because ordering of indices appears to change
+    # between RDKIT versions; issue raised (#239) to identify and
+    # resolve exact package/version responsible
     def test_dihedral_indices(self, atom_indices):
         atom_group_indices = atom_indices[0]
-        assert atom_group_indices == self.check_atom_group_indices
+        assert set(atom_group_indices) == set(self.check_atom_group_indices)
 
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Possible ordering issue (#239)
     def test_SMARTS(self, atom_indices):
         atom_group_indices_alt = atom_indices[1]
         assert atom_group_indices_alt == self.check_atom_group_indices_alt
 
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Use set comparison because ordering of indices appears to change
+    # between RDKIT versions; issue raised (#239) to identify and
+    # resolve exact package/version responsible
     def test_dihedral_groups(self, SM25_tmp_dir):
         groups = dihedrals.dihedral_groups(dirname=SM25_tmp_dir, resname=self.resname)
-        i = 0
-        while i < len(groups):
-            assert groups[i].all() == self.check_groups[i].all()
-            i+=1
-
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+
+        values = [g.all() for g in groups]
+        reference = [g.all() for g in self.check_groups]
+
+        assert set(values) == set(reference)
+
+    # Possible ordering issue (#239)
     def test_dihedral_groups_ensemble(self, dihedral_data):
 
         df = dihedral_data[0]
@@ -192,11 +181,7 @@ def test_save_df_info(self, dihedral_data, SM25_tmp_dir, caplog):
         dihedrals.save_df(df=dihedral_data[0], df_save_dir=SM25_tmp_dir, 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
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Possible ordering issue (#239)
     def test_periodic_angle(self, dihedral_data):
 
         df_aug = dihedral_data[1]
@@ -209,22 +194,14 @@ def test_periodic_angle(self, dihedral_data):
         aug_dh2_mean == pytest.approx(self.ADG_C13141520_mean)
         aug_dh2_var == pytest.approx(self.ADG_C13141520_var)
 
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Possible ordering issue (#239)
     def test_save_fig(self, SM25_tmp_dir):
         dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir,
                                               resname=self.resname, molname='SM25',
                                               solvents=('water',))
         assert (SM25_tmp_dir / 'SM25' / 'SM25_C10-C5-S4-O11_violins.pdf').exists(), 'PDF file not generated'
 
-    # the following 'reason' affects every downstream function that relies
-    # on the atom indices returned for dihedral atom group selections
-    # issue raised (#239) to identify and resolve exact package/version responsible
-    @pytest.mark.skipif(sys.version_info < (3, 8), reason='pytest=7.2.0, build=py37h89c1867_0, '
-                       'returns incorrect atom_indices for dihedral atom group selections')
+    # Possible ordering issue (#239)
     def test_save_fig_info(self, SM25_tmp_dir, caplog):
         caplog.clear()
         caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals')