removed TopologyGroup reshaping and added tests

package/CHANGELOG

@@ -24,6 +24,8 @@ Fixes
   * Chainreader and continuous option work correctly when readers work for more 
     than one format (Issue #2353)
   * PDBQTParser now gives icode TopologyAttrs (Issue #2361)
+  * TopologyGroup no longer reshapes the type, guessed, and order properties
+    (Issue #2392)
 
 Enhancements
   * Uniforms exception handling between Python 2.7 and Python 3: raised exceptions

package/MDAnalysis/core/topologyobjects.py

@@ -539,18 +539,19 @@ def __init__(self, bondidx, universe, btype=None, type=None, guessed=None,
             raise ValueError("Unsupported btype, use one of '{}'"
                              "".format(', '.join(_BTYPE_TO_SHAPE)))
 
+        bondidx = np.asarray(bondidx)
         nbonds = len(bondidx)
         # remove duplicate bonds
         if type is None:
-            type = np.repeat(None, nbonds).reshape(nbonds, 1)
+            type = np.repeat(None, nbonds)
         if guessed is None:
-            guessed = np.repeat(True, nbonds).reshape(nbonds, 1)
+            guessed = np.repeat(True, nbonds)
         elif guessed is True or guessed is False:
-            guessed = np.repeat(guessed, nbonds).reshape(nbonds, 1)
+            guessed = np.repeat(guessed, nbonds)
         else:
-            guessed = np.asarray(guessed, dtype=np.bool).reshape(nbonds, 1)
+            guessed = np.asarray(guessed, dtype=np.bool)
         if order is None:
-            order = np.repeat(None, nbonds).reshape(nbonds, 1)
+            order = np.repeat(None, nbonds)
 
         if nbonds > 0:
             uniq, uniq_idx = util.unique_rows(bondidx, return_index=True)
@@ -736,7 +737,7 @@ def __add__(self, other):
                     type=np.concatenate([self._bondtypes,
                                          np.array([other._bondtype])]),
                     guessed=np.concatenate([self._guessed,
-                                            np.array([[other.is_guessed]])]),
+                                            np.array([other.is_guessed])]),
                     order=np.concatenate([self._order,
                                           np.array([other.order])]),
                 )

package/MDAnalysis/core/universe.py

@@ -1013,17 +1013,20 @@ def _add_TopologyObjects(self, object_type, values, types=None, guessed=False,
         order : int (optional)
             Bond order
         """
-        values = [x.indices if isinstance(x, (AtomGroup, TopologyObject)) 
-                  else x for x in values]
         if all(isinstance(x, TopologyObject) for x in values):
             first = values[0]
             try:
-                types = value.type
+                types = first.type
             except AttributeError:
                 types = None
             guessed = first.is_guessed
             order = first.order
 
+        print(types, guessed, order)
+
+        values = [x.indices if isinstance(x, (AtomGroup, TopologyObject)) 
+                  else x for x in values]
+
         try:
             attr = getattr(self._topology, object_type)
         except AttributeError:

testsuite/MDAnalysisTests/core/test_topologyobjects.py

@@ -360,14 +360,12 @@ def test_dihedral_tg_creation_notype(self, PSFDCD):
     def test_create_guessed_tg(self, PSFDCD):
         vals = np.array([[0, 10], [5, 15]])
         tg = TopologyGroup(vals, PSFDCD, guessed=True)
-
-        assert_equal(tg._guessed, np.array([[True], [True]]))
+        assert_equal(tg._guessed, np.array([True, True]))
 
     def test_create_guessed_tg_2(self, PSFDCD):
         vals = np.array([[0, 10], [5, 15]])
         tg = TopologyGroup(vals, PSFDCD, guessed=False)
-
-        assert_equal(tg._guessed, np.array([[False], [False]]))
+        assert_equal(tg._guessed, np.array([False, False]))
 
     def test_TG_equality(self, PSFDCD):
         """Make two identical TGs,

testsuite/MDAnalysisTests/core/test_universe.py

@@ -59,6 +59,7 @@
 from MDAnalysis.topology.base import TopologyReaderBase
 from MDAnalysis.transformations import translate
 from MDAnalysisTests import assert_nowarns
+from MDAnalysis.exceptions import NoDataError
 
 
 class IOErrorParser(TopologyReaderBase):
@@ -683,22 +684,46 @@ def test_add_dihedrals(self, universe):
         assert not hasattr(universe, 'dihedrals')
         universe.add_Dihedrals(dih)
         assert len(universe.dihedrals) == len(idx)
-    
+
     def test_add_atomgroups(self, universe):
         idx = [[1, 2, 3, 1], [3, 1, 5, 2], [3, 1, 5, 2]]
         imp = [universe.atoms[i] for i in idx]
 
         assert not hasattr(universe, 'impropers')
         universe.add_Impropers(imp)
         assert len(universe.impropers) == 2
+
+    def test_add_topologygroups(self, universe):
+        arr = np.array([[1, 0, 2], [1, 2, 3]])
+        tg = mda.core.topologyobjects.TopologyGroup(arr, universe)
+
+        assert not hasattr(universe, 'angles')
+        assert len(tg) == 2
+        universe.add_Angles(tg)
+        assert len(universe.angles) == 2
+
+        ua = universe.angles[-1]
+        tga = tg[0]
+        assert ua.is_guessed == tga.is_guessed
+        assert ua.order == tga.order
+
+        assert list(ua.indices) == list(arr[-1])
+
+    def test_add_topologygroup_error(self, universe):
+        arr = np.array([(1, 0), (1, 2)])
+        tg = mda.core.topologyobjects.TopologyGroup(arr, universe)
+
+        with pytest.raises(ValueError):
+            universe.add_Angles(tg)
 
-    def add_angles_wrong_number_of_atoms_error(self, universe):
+    def test_add_angles_wrong_number_of_atoms_error(self, universe):
         indices = [(0, 1, 2), (2, 3, 0), (4, 1)]
         with pytest.raises(ValueError):
             universe.add_Angles(indices)
 
-    def add_bonds_refresh_fragments(self, universe):
-        assert not hasattr(universe.atoms, 'fragments')
+    def test_add_bonds_refresh_fragments(self, universe):
+        with pytest.raises(NoDataError):
+            assert not hasattr(universe.atoms, 'fragments')
 
         universe.add_Bonds([universe.atoms[:2]])
         assert len(universe.atoms.fragments) == len(universe.atoms)-1
@@ -739,27 +764,34 @@ def test_delete_atomgroups(self, universe):
         universe.delete_Dihedrals([ag])
         assert len(universe.dihedrals) == 1
 
-    def delete_mixed_topologyobjects_type(self, universe):
-        mixed = [universe.atoms[[0, 1, 2]].angle, (3, 4, 5)]
-        universe.delete_Angles(mixed)
-        assert len(universe.angles) == 1
+    def test_delete_mixed_topologyobjects_type(self, universe):
+        mixed = [universe.atoms[[1, 3, 5, 2]].improper, (5, 3, 4, 2)]
+        universe.delete_Impropers(mixed)
+        assert len(universe.impropers) == 1
 
-    def delete_angles_wrong_number_of_atoms_error(self, universe):
+    def test_delete_angles_wrong_number_of_atoms_error(self, universe):
         indices = [(0, 1, 2), (2, 3, 0), (4, 1)]
         with pytest.raises(ValueError):
             universe.delete_Angles(indices)
 
-    def ignore_topologyobjects_not_in_universe(self, universe):
+    def test_ignore_topologyobjects_not_in_universe(self, universe):
         n_bonds = len(universe.bonds)
         bonds = [(0, 1), (99, 100), (22, 2)]
         universe.delete_Bonds(bonds)
         assert len(universe.bonds) == n_bonds-1
 
-    def delete_bonds_refresh_fragments(self, universe):
+    def test_delete_bonds_refresh_fragments(self, universe):
         n_fragments = len(universe.atoms.fragments)
         universe.delete_Bonds([universe.atoms[[2, 3]]])
         assert len(universe.atoms.fragments) == n_fragments + 1
 
+    def test_delete_bonds_empty_universe(self):
+        u = make_Universe()
+        assert not hasattr(u, 'bonds')
+        bonds = [(0, 1), (99, 100), (22, 2)]
+        with pytest.raises(ValueError):
+            u.delete_Bonds(bonds)
+
 class TestAllCoordinatesKwarg(object):
     @pytest.fixture(scope='class')
     def u_GRO_TRR(self):