Revert import paths

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