deprecate core.universe.as_Universe

- see #2920
- add deprecation note
- add test
- update CHANGELOG for 1.0.1

package/CHANGELOG

@@ -50,6 +50,7 @@ Deprecations
   * waterdynamics.HydrogenBondLifetimes will be removed in 2.0.0 and
     replaced with hydrogenbonds.HydrogenBondAnalysis.lifetime() (#2547)
   * lib.util.echo() will be removed in 2.0.0
+  * core.universe.as_Universe() will be removed in 2.0.0
 
 
 06/09/20 richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,

package/MDAnalysis/core/universe.py

@@ -102,6 +102,8 @@
 from .topologyattrs import AtomAttr, ResidueAttr, SegmentAttr
 from .topologyobjects import TopologyObject
 
+from ..lib.util import deprecate
+
 logger = logging.getLogger("MDAnalysis.core.universe")
 
 
@@ -1293,7 +1295,7 @@ def _fragdict(self):
         return fragdict
 
 
-# TODO: what is the point of this function???
+@deprecate(release="1.0.1", remove="2.0.0")
 def as_Universe(*args, **kwargs):
     """Return a universe from the input arguments.
 

testsuite/MDAnalysisTests/core/test_universe.py

@@ -601,7 +601,7 @@ def test_add_charges(self, universe, toadd, attrname, default):
 
         assert hasattr(universe.atoms, attrname)
         assert getattr(universe.atoms, attrname)[0] == default
-    
+
     @pytest.mark.parametrize(
         'attr,values', (
             ('bonds', [(1, 0), (1, 2)]),
@@ -636,7 +636,7 @@ def test_add_connection(self, universe, attr, values):
     def add_connection_error(self, universe, attr, values):
         with pytest.raises(ValueError):
             universe.add_TopologyAttr(attr, values)
-    
+
 
 def _a_or_reversed_in_b(a, b):
     """
@@ -694,7 +694,7 @@ def _check_invalid_addition(self, u, attr, to_add, err_msg):
         with pytest.raises(ValueError) as excinfo:
             _add_func(to_add)
         assert err_msg in str(excinfo.value)
-    
+
     @pytest.mark.parametrize(
         'attr,values', small_atom_indices
     )
@@ -752,23 +752,23 @@ def test_add_topologyobjects_wrong_universe_error(self, universe, empty, attr, v
         'attr,values', large_atom_indices
     )
     def test_add_topologygroups_to_populated(self, universe, attr, values):
-        topologygroup = mda.core.topologyobjects.TopologyGroup(np.array(values), 
+        topologygroup = mda.core.topologyobjects.TopologyGroup(np.array(values),
                                                                universe)
         self._check_valid_added_to_populated(universe, attr, values, topologygroup)
 
     @pytest.mark.parametrize(
         'attr,values', small_atom_indices
     )
     def test_add_topologygroup_wrong_universe_error(self, universe, empty, attr, values):
-        tg = mda.core.topologyobjects.TopologyGroup(np.array(values), 
+        tg = mda.core.topologyobjects.TopologyGroup(np.array(values),
                                                     universe)
         self._check_invalid_addition(empty, attr, tg, 'different Universes')
-    
+
     @pytest.mark.parametrize(
         'attr,values', small_atom_indices
     )
     def test_add_topologygroup_different_universe(self, universe, empty, attr, values):
-        tg = mda.core.topologyobjects.TopologyGroup(np.array(values), 
+        tg = mda.core.topologyobjects.TopologyGroup(np.array(values),
                                                                universe)
         self._check_valid_added_to_empty(empty, attr, values, tg.to_indices())
 
@@ -809,7 +809,7 @@ def test_add_wrong_number_of_atoms_error(self, universe, attr, n):
                   'tuples with {} atom indices').format(attr, n)
         idx = [(0, 1), (0, 1, 2), (8, 22, 1, 3), (5, 3, 4, 2)]
         self._check_invalid_addition(universe, attr, idx, errmsg)
-    
+
     def test_add_bonds_refresh_fragments(self, empty):
         with pytest.raises(NoDataError):
             getattr(empty.atoms, 'fragments')
@@ -833,7 +833,7 @@ def test_roundtrip(self, empty, attr, values):
         _delete_func(values)
         u_attr = getattr(empty, attr)
         assert len(u_attr) == 0
-    
+
 class TestDeleteTopologyObjects(object):
 
     TOP = {'bonds': [(0, 1), (2, 3), (3, 4), (4, 5), (7, 8)],
@@ -879,7 +879,7 @@ def _check_valid_deleted(self, u, attr, values, to_delete):
         assert len(u_attr) == original_length-len(values)
 
         not_deleted = [x for x in self.TOP[attr] if list(x) not in values]
-        assert all([x in u_attr.indices or x[::-1] in u_attr.indices 
+        assert all([x in u_attr.indices or x[::-1] in u_attr.indices
                    for x in not_deleted])
 
     def _check_invalid_deleted(self, u, attr, to_delete, err_msg):
@@ -923,7 +923,7 @@ def test_delete_atomgroup_wrong_universe_error(self, universe, universe2, attr,
     def test_delete_missing_atomgroup(self, universe, attr, values):
         ag = [universe.atoms[x] for x in values]
         self._check_invalid_deleted(universe, attr, ag, 'Cannot delete nonexistent')
-    
+
     @pytest.mark.parametrize(
         'attr,values', existing_atom_indices
     )
@@ -969,7 +969,7 @@ def test_delete_topologygroup_different_universe(self, universe, universe2, attr
         arr = np.array(values)
         tg = mda.core.topologyobjects.TopologyGroup(arr, universe2)
         self._check_valid_deleted(universe, attr, values, tg.to_indices())
-    
+
     @pytest.mark.parametrize(
         'attr,n', (
             ('bonds', 2),
@@ -982,8 +982,8 @@ def test_delete_wrong_number_of_atoms_error(self, universe, attr, n):
         idx = [(0, 1), (0, 1, 2), (8, 22, 1, 3), (5, 3, 4, 2)]
         errmsg = ('{} must be an iterable of '
                   'tuples with {} atom indices').format(attr, n)
-        self._check_invalid_deleted(universe, attr, idx, errmsg)  
-    
+        self._check_invalid_deleted(universe, attr, idx, errmsg)
+
     @pytest.mark.parametrize(
         'attr,values', existing_atom_indices
     )
@@ -1020,7 +1020,7 @@ def test_roundtrip(self, universe, attr, values):
 
         assert_array_equal(u_attr.indices, nu_attr.indices)
 
-    
+
 class TestAllCoordinatesKwarg(object):
     @pytest.fixture(scope='class')
     def u_GRO_TRR(self):
@@ -1131,3 +1131,7 @@ def test_empty_creation_raises_error(self):
         with pytest.raises(TypeError) as exc:
             u = mda.Universe()
         assert 'Universe.empty' in str(exc.value)
+
+def test_as_Universe_deprecation():
+    with pytest.deprecated_call():
+        _ = mda.core.universe.as_Universe(PSF, DCD)