deprecate bond guessing

package/CHANGELOG

@@ -112,6 +112,8 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * The `guess_bonds`, `vdwradii`, `fudge_factor`, and `lower_bound` kwargs
+   are deprecated for Universe creation.
  * Unknown masses are set to 0.0 for current version, this will be depracated
    in version 3.0.0 and replaced by :class:`Masses`' no_value_label attribute(np.nan)
    (PR #3753)

package/MDAnalysis/core/universe.py

@@ -407,6 +407,17 @@ def __init__(self, topology=None, *coordinates, all_coordinates=False,
             self._trajectory.add_transformations(*transformations)
 
         if guess_bonds:
+            warnings.warn(
+                "Bond guessing through the `guess_bonds` keyword is deprecated "
+                "and will be removed in MDAnalysis 3.0. "
+                "Instead, pass 'bonds', 'angles', and 'dihedrals' to "
+                "the `to_guess` keyword in Universe for guessing these. "
+                "The kwargs `fudge_factor`, `vdwradii`, and `lower_bound` "
+                "are also deprecated and will be removed in MDAnalysis 3.0, "
+                "where they should be passed into Context creation "
+                "or guess_TopologyAttrs instead.",
+                DeprecationWarning
+            )
             force_guess = list(force_guess) + ['bonds', 'angles', 'dihedrals']
 
         self.guess_TopologyAttrs(

testsuite/MDAnalysisTests/guesser/test_base.py

@@ -100,3 +100,8 @@ def test_partial_guess_attr_with_unknown_no_value_label(self):
         top = Topology(4, 1, 1, attrs=[names, types, ])
         u = mda.Universe(top, to_guess=['types'])
         assert_equal(u.atoms.types, ['', '', '', ''])
+
+
+def test_Universe_guess_bonds_deprecated():
+    with pytest.warns(DeprecationWarning, match='`guess_bonds` keyword is deprecated'):
+        u = mda.Universe(datafiles.PDB_full, guess_bonds=True)