Merge pull request #170 from stevenhua0320/deprecate-symmetryutilities-6

chore: deprecate SymmetryConstraints class method

Author: sbillinge

news/deprecate-symmetryutilities-6.rst

@@ -0,0 +1,32 @@
+**Added:**
+
+* Added ``_find_constraints`` method in ``SymmetryConstraints`` class
+* Added ``pos_parm_symbols`` method in ``SymmetryConstraints`` class
+* Added ``pos_parm_values`` method in ``SymmetryConstraints`` class
+* Added ``u_parm_symbols`` method in ``SymmetryConstraints`` class
+* Added ``u_parm_values`` method in ``SymmetryConstraints`` class
+* Added ``u_formulas`` method in ``SymmetryConstraints`` class
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``posparSymbols`` method in ``SymmetryConstraints`` class for removal in version 4.0.0
+* Deprecated ``posparValues`` method in ``SymmetryConstraints`` class for removal in version 4.0.0
+* Deprecated ``UparSymbols`` method in ``SymmetryConstraints`` class for removal in version 4.0.0
+* Deprecated ``UparValues`` method in ``SymmetryConstraints`` class for removal in version 4.0.0
+* Deprecated ``UFormulas`` method in ``SymmetryConstraints`` class for removal in version 4.0.0
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/symmetryutilities.py

@@ -1043,6 +1043,39 @@ def prune_formula_dictionary(eqdict):
     return pruned
 
 
+symmetry_constraints = "diffpy.symmetryutilities.SymmetryConstraints"
+posparSymbols_deprecation_msg = build_deprecation_message(
+    symmetry_constraints,
+    "posparSymbols",
+    "pospar_symbols",
+    removal_version,
+)
+posparValues_deprecation_msg = build_deprecation_message(
+    symmetry_constraints,
+    "posparValues",
+    "pospar_values",
+    removal_version,
+)
+UparSymbols_deprecation_msg = build_deprecation_message(
+    symmetry_constraints,
+    "UparSymbols",
+    "upar_symbols",
+    removal_version,
+)
+UparValues_deprecation_msg = build_deprecation_message(
+    symmetry_constraints,
+    "UparValues",
+    "upar_values",
+    removal_version,
+)
+UFormulas_deprecation_msg = build_deprecation_message(
+    symmetry_constraints,
+    "UFormulas",
+    "u_formulas",
+    removal_version,
+)
+
+
 class SymmetryConstraints(object):
     """Generate symmetry constraints for specified positions.
 
@@ -1132,10 +1165,10 @@ def __init__(self, spacegroup, positions, Uijs=None, sgoffset=[0, 0, 0], eps=Non
         self.Ueqns = numpos * [None]
         self.Uisotropy = numpos * [False]
         # all members should be initialized here
-        self._findConstraints()
+        self._find_constraints()
         return
 
-    def _findConstraints(self):
+    def _find_constraints(self):
         """Find constraints for positions and anisotropic displacements
         `Uij`."""
         numpos = len(self.positions)
@@ -1184,11 +1217,29 @@ def _findConstraints(self):
         self.corepos = [self.positions[i] for i in coreidx]
         return
 
+    @deprecated(posparSymbols_deprecation_msg)
     def posparSymbols(self):
+        """'diffpy.structure.SymmetryConstraints.posparSymbols' is
+        deprecated and will be removed in version 4.0.0.
+
+        Please use 'diffpy.structure.SymmetryConstraints.pos_parm_symbols' instead.
+        """
+        return self.pos_parm_symbols()
+
+    def pos_parm_symbols(self):
         """Return list of standard position parameter symbols."""
         return [n for n, v in self.pospars]
 
+    @deprecated(posparValues_deprecation_msg)
     def posparValues(self):
+        """'diffpy.structure.SymmetryConstraints.posparValues' is
+        deprecated and will be removed in version 4.0.0.
+
+        Please use 'diffpy.structure.SymmetryConstraints.pos_parm_values' instead.
+        """
+        return self.pos_parm_values()
+
+    def pos_parm_values(self):
         """Return list of position parameters values."""
         return [v for n, v in self.pospars]
 
@@ -1214,7 +1265,7 @@ def positionFormulas(self, xyzsymbols=None):
             emsg = "Not enough symbols for %i position parameters" % len(self.pospars)
             raise SymmetryError(emsg)
         # build translation dictionary
-        trsmbl = dict(zip(self.posparSymbols(), xyzsymbols))
+        trsmbl = dict(zip(self.pos_parm_symbols(), xyzsymbols))
 
         def translatesymbol(matchobj):
             return trsmbl[matchobj.group(0)]
@@ -1249,16 +1300,45 @@ def positionFormulasPruned(self, xyzsymbols=None):
         rv = [prune_formula_dictionary(eqns) for eqns in self.positionFormulas(xyzsymbols)]
         return rv
 
+    @deprecated(UparSymbols_deprecation_msg)
     def UparSymbols(self):
+        """'diffpy.structure.SymmetryConstraints.UparSymbols' is
+        deprecated and will be removed in version 4.0.0.
+
+        Please use 'diffpy.structure.SymmetryConstraints.u_parm_symbols' instead.
+        """
+        return self.u_parm_symbols()
+
+    def u_parm_symbols(self):
         """Return list of standard atom displacement parameter
         symbols."""
         return [n for n, v in self.Upars]
 
+    @deprecated(UparValues_deprecation_msg)
     def UparValues(self):
+        """'diffpy.structure.SymmetryConstraints.UparValues' is
+        deprecated and will be removed in version 4.0.0.
+
+        Please use 'diffpy.structure.SymmetryConstraints.u_parm_values'
+        instead.
+        """
+        return [v for n, v in self.Upars]
+
+    def u_parm_values(self):
         """Return list of atom displacement parameters values."""
         return [v for n, v in self.Upars]
 
+    @deprecated(UFormula_deprecation_msg)
     def UFormulas(self, Usymbols=None):
+        """'diffpy.structure.SymmetryConstraints.UFormulas' is
+        deprecated and will be removed in version 4.0.0.
+
+        Please use 'diffpy.structure.SymmetryConstraints.u_formulas'
+        instead.
+        """
+        return self.u_formulas(Usymbols)
+
+    def u_formulas(self, Usymbols=None):
         """List of atom displacement formulas with custom parameter
         symbols.
 
@@ -1282,7 +1362,7 @@ def UFormulas(self, Usymbols=None):
             emsg = "Not enough symbols for %i U parameters" % len(self.Upars)
             raise SymmetryError(emsg)
         # build translation dictionary
-        trsmbl = dict(zip(self.UparSymbols(), Usymbols))
+        trsmbl = dict(zip(self.u_parm_symbols(), Usymbols))
 
         def translatesymbol(matchobj):
             return trsmbl[matchobj.group(0)]
@@ -1315,7 +1395,7 @@ def UFormulasPruned(self, Usymbols=None):
             List of atom displacement formulas in tuples of
             ``(U11, U22, U33, U12, U13, U23)``.
         """
-        rv = [prune_formula_dictionary(eqns) for eqns in self.UFormulas(Usymbols)]
+        rv = [prune_formula_dictionary(eqns) for eqns in self.u_formulas(Usymbols)]
         return rv
 
 

tests/test_symmetryutilities.py

@@ -758,7 +758,7 @@ def test_u_formula_g186c_eqxyz(self):
             "U13": 0.0,
             "U23": 0.0,
         }
-        for ufms in symcon.UFormulas():
+        for ufms in symcon.u_formulas():
             for n, fm in ufms.items():
                 self.assertEqual(uisod[n], eval(fm, upd))
         return
@@ -905,6 +905,18 @@ def test_UparSymbols(self):
         self.assertEqual(["U110"], sc225.UparSymbols())
         return
 
+    def test_upar_symbols(self):
+        """Check SymmetryConstraints.UparSymbols()"""
+        sg1 = GetSpaceGroup(1)
+        sg225 = GetSpaceGroup(225)
+        pos = [[0, 0, 0]]
+        Uijs = numpy.zeros((1, 3, 3))
+        sc1 = SymmetryConstraints(sg1, pos, Uijs)
+        self.assertEqual(6, len(sc1.u_parm_symbols()))
+        sc225 = SymmetryConstraints(sg225, pos, Uijs)
+        self.assertEqual(["U110"], sc225.u_parm_symbols())
+        return
+
     def test_UparValues(self):
         """Check SymmetryConstraints.UparValues()"""
         places = 12
@@ -920,6 +932,34 @@ def test_UparValues(self):
         self.assertAlmostEqual(0.2, sc225.UparValues()[0], places)
         return
 
+    def test_upar_values(self):
+        """Check SymmetryConstraints.UparValues()"""
+        places = 12
+        sg1 = GetSpaceGroup(1)
+        sg225 = GetSpaceGroup(225)
+        pos = [[0, 0, 0]]
+        Uijs = [[[0.1, 0.4, 0.5], [0.4, 0.2, 0.6], [0.5, 0.6, 0.3]]]
+        sc1 = SymmetryConstraints(sg1, pos, Uijs)
+        duv = 0.1 * numpy.arange(1, 7) - sc1.u_parm_values()
+        self.assertAlmostEqual(0, max(numpy.fabs(duv)), places)
+        sc225 = SymmetryConstraints(sg225, pos, Uijs)
+        self.assertEqual(1, len(sc225.u_parm_values()))
+        self.assertAlmostEqual(0.2, sc225.u_parm_values()[0], places)
+        return
+
+    def test_posparSymbols_and_posparValues(self):
+        """Check SymmetryConstraints.posparSymbols and_posparValues()"""
+        sg225 = GetSpaceGroup(225)
+        eau = ExpandAsymmetricUnit(sg225, [[0, 0, 0]])
+        sc = SymmetryConstraints(sg225, eau.expandedpos)
+        sc.pospars = [("x", 0.12), ("y", 0.34), ("z", 0.56)]
+        actual_symbols = sc.posparSymbols()
+        actual_values = sc.posparValues()
+        expected_symbols = ["x", "y", "z"]
+        expected_values = [0.12, 0.34, 0.56]
+        assert expected_symbols == actual_symbols
+        assert expected_values == actual_values
+
 
 #   def test_UFormulas(self):
 #       """check SymmetryConstraints.UFormulas()
@@ -1056,5 +1096,22 @@ def test_null_space(A, expected_dim):
     assert numpy.allclose(actual @ actual.T, numpy.eye(expected_dim), atol=1e-12)
 
 
+@pytest.mark.parametrize(
+    "params, expected_symbols, expected_values",
+    [
+        pytest.param([("x", 0.12), ("y", 0.34), ("z", 0.56)], ["x", "y", "z"], [0.12, 0.34, 0.56]),
+    ],
+)
+def test_pospar_symbols_and_pospar_values(params, expected_symbols, expected_values):
+    """Check SymmetryConstraints.pospar_symbols and_pospar_values()"""
+    sg225 = GetSpaceGroup(225)
+    eau = ExpandAsymmetricUnit(sg225, [[0, 0, 0]])
+    sc = SymmetryConstraints(sg225, eau.expandedpos)
+    sc.pospars = params
+    actual_symbols, actual_values = sc.pos_parm_symbols(), sc.pos_parm_values()
+    assert actual_symbols == expected_symbols
+    assert actual_values == expected_values
+
+
 if __name__ == "__main__":
     unittest.main()