Expose MDAnalysis.topology.guessers and MDAnalysis.guesser.tables under MDAnalysis.topology.core

package/MDAnalysis/topology/core.py

@@ -38,4 +38,12 @@
 from ..core._get_readers import get_parser_for
 from ..lib.util import cached
 
+# Deprecated local imports
+from MDAnalysis.guesser import tables
+from .guessers import (
+    guess_atom_element, guess_atom_type,
+    get_atom_mass, guess_atom_mass, guess_atom_charge,
+    guess_bonds, guess_angles, guess_dihedrals, guess_improper_dihedrals,
+)
+
 #tumbleweed

package/MDAnalysis/topology/guessers.py

@@ -107,19 +107,17 @@
 
 from ..lib import distances
 from MDAnalysis.guesser import tables
+from MDAnalysis.lib.util import deprecate
 
 
-wmsg = (
-    "Deprecated in version 2.8.0\n"
+deprecation_msg = (
     "MDAnalysis.topology.guessers is deprecated in favour of "
-    "the new Guessers API and will be removed in MDAnalysis version 3.0.0. "
+    "the new Guessers API. "
     "See MDAnalysis.guesser.default_guesser for more details."
 )
 
 
-warnings.warn(wmsg, category=DeprecationWarning)
-
-
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_masses(atom_types):
     """Guess the mass of many atoms based upon their type
 
@@ -137,6 +135,7 @@ def guess_masses(atom_types):
     return masses
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def validate_atom_types(atom_types):
     """Vaildates the atom types based on whether they are available in our tables
 
@@ -162,6 +161,7 @@ def validate_atom_types(atom_types):
                 warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_types(atom_names):
     """Guess the atom type of many atoms based on atom name
 
@@ -177,6 +177,7 @@ def guess_types(atom_names):
     return np.array([guess_atom_element(name) for name in atom_names], dtype=object)
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_atom_type(atomname):
     """Guess atom type from the name.
 
@@ -197,6 +198,8 @@ def guess_atom_type(atomname):
 NUMBERS = re.compile(r'[0-9]') # match numbers
 SYMBOLS = re.compile(r'[*+-]')  # match *, +, -
 
+
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_atom_element(atomname):
     """Guess the element of the atom from the name.
 
@@ -246,6 +249,7 @@ def guess_atom_element(atomname):
         return no_symbols
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_bonds(atoms, coords, box=None, **kwargs):
     r"""Guess if bonds exist between two atoms based on their distance.
 
@@ -354,6 +358,7 @@ def guess_bonds(atoms, coords, box=None, **kwargs):
     return tuple(bonds)
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_angles(bonds):
     """Given a list of Bonds, find all angles that exist between atoms.
 
@@ -390,6 +395,7 @@ def guess_angles(bonds):
     return tuple(angles_found)
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_dihedrals(angles):
     """Given a list of Angles, find all dihedrals that exist between atoms.
 
@@ -423,6 +429,7 @@ def guess_dihedrals(angles):
     return tuple(dihedrals_found)
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_improper_dihedrals(angles):
     """Given a list of Angles, find all improper dihedrals that exist between
     atoms.
@@ -459,6 +466,7 @@ def guess_improper_dihedrals(angles):
     return tuple(dihedrals_found)
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def get_atom_mass(element):
     """Return the atomic mass in u for *element*.
 
@@ -478,6 +486,7 @@ def get_atom_mass(element):
             return 0.0
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_atom_mass(atomname):
     """Guess a mass based on the atom name.
 
@@ -489,6 +498,7 @@ def guess_atom_mass(atomname):
     return get_atom_mass(guess_atom_element(atomname))
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_atom_charge(atomname):
     """Guess atom charge from the name.
 
@@ -498,6 +508,7 @@ def guess_atom_charge(atomname):
     return 0.0
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_aromaticities(atomgroup):
     """Guess aromaticity of atoms using RDKit
 
@@ -518,6 +529,7 @@ def guess_aromaticities(atomgroup):
     return np.array([atom.GetIsAromatic() for atom in mol.GetAtoms()])
 
 
+@deprecate(release="2.8.0", remove="3.0.0", message=deprecation_msg)
 def guess_gasteiger_charges(atomgroup):
     """Guess Gasteiger partial charges using RDKit
 

testsuite/MDAnalysisTests/topology/test_guessers.py

@@ -46,12 +46,6 @@
                                     reason="requires RDKit")
 
 
-def test_moved_to_guessers_warning():
-    wmsg = "deprecated in favour of the new Guessers API"
-    with pytest.warns(DeprecationWarning, match=wmsg):
-        reload(guessers)
-
-
 class TestGuessMasses(object):
     def test_guess_masses(self):
         out = guessers.guess_masses(['C', 'C', 'H'])
@@ -60,7 +54,7 @@ def test_guess_masses(self):
         assert_equal(out, np.array([12.011, 12.011, 1.008]))
 
     def test_guess_masses_warn(self):
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match='Failed to guess the mass'):
             guessers.guess_masses(['X'])
 
     def test_guess_masses_miss(self):
@@ -210,3 +204,59 @@ def test_guess_gasteiger_charges(smi):
     u = mda.Universe(mol)
     values = guessers.guess_gasteiger_charges(u.atoms)
     assert_equal(values, expected)
+
+
+class TestDeprecationWarning:
+    wmsg = (
+    "MDAnalysis.topology.guessers is deprecated in favour of "
+    "the new Guessers API. "
+    "See MDAnalysis.guesser.default_guesser for more details."
+    )
+
+    @pytest.mark.parametrize('func, arg', [
+        [guessers.guess_masses, ['C']],
+        [guessers.validate_atom_types, ['C']],
+        [guessers.guess_types, ['CA']],
+        [guessers.guess_atom_type, 'CA'],
+        [guessers.guess_atom_element, 'CA'],
+        [guessers.get_atom_mass, 'C'],
+        [guessers.guess_atom_mass, 'CA'],
+        [guessers.guess_atom_charge, 'CA'],
+    ])
+    def test_mass_type_elements_deprecations(self, func, arg):
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            func(arg)
+
+    def test_bonds_deprecations(self):
+        u = mda.Universe(datafiles.two_water_gro)
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            guessers.guess_bonds(u.atoms, u.atoms.positions)
+
+    def test_angles_dihedral_deprecations(self):
+        u = make_starshape()
+        ag = u.atoms[:5]
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            angles = guessers.guess_angles(ag.bonds)
+
+        # add angles back to the Universe
+        u.add_TopologyAttr(Angles(angles))
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            guessers.guess_dihedrals(ag.angles)
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            guessers.guess_improper_dihedrals(ag.angles)
+
+    @requires_rdkit
+    def test_rdkit_guessers_deprecations(self):
+        mol = Chem.MolFromSmiles('c1ccccc1')
+        mol = Chem.AddHs(mol)
+        u = mda.Universe(mol)
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            guessers.guess_aromaticities(u.atoms)
+
+        with pytest.warns(DeprecationWarning, match=self.wmsg):
+            guessers.guess_gasteiger_charges(u.atoms)