Merge pull request #165 from stevenhua0320/symmetryutilities-deprecate

chore: deprecate methods in `symmetryutilities.py`

Author: sbillinge

news/deprecate-symmetryutilities-1.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* Added ``is_space_group_latt_parms`` method in ``symmetryutilities.py``
+* Added ``is_constant_formula`` method in ``symmetryutilities.py``
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``isSpaceGroupLatPar`` method in ``symmetryutilities.py`` for removal in version 4.0.0
+* Deprecated ``isconstantFormula`` method in ``symmetryutilities.py`` for removal in version 4.0.0
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/pdffitstructure.py

@@ -16,6 +16,16 @@
 
 
 from diffpy.structure.structure import Structure
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+base = "diffpy.structure.PDFFitStructure"
+removal_version = "4.0.0"
+readStr_deprecation_msg = build_deprecation_message(
+    base,
+    "readStr",
+    "read_structure",
+    removal_version,
+)
 
 # ----------------------------------------------------------------------------
 
@@ -78,6 +88,7 @@ def read(self, filename, format="auto"):
             self.pdffit["spcgr"] = sg.short_name
         return p
 
+    @deprecated(readStr_deprecation_msg)
     def readStr(self, s, format="auto"):
         """'diffpy.structure.PDFFitStructure.readStr' is deprecated and
         will be removed in version 4.0.0.

src/diffpy/structure/symmetryutilities.py

@@ -32,6 +32,22 @@
 import numpy
 
 from diffpy.structure.structureerrors import SymmetryError
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+base = "diffpy.structure"
+removal_version = "4.0.0"
+isSpaceGroupLatPar_deprecation_msg = build_deprecation_message(
+    base,
+    "isSpaceGroupLatPar",
+    "is_space_group_latt_parms",
+    removal_version,
+)
+isconstantFormula_deprecation_msg = build_deprecation_message(
+    base,
+    "isconstantFormula",
+    "is_constant_formula",
+    removal_version,
+)
 
 # Constants ------------------------------------------------------------------
 
@@ -42,7 +58,17 @@
 # ----------------------------------------------------------------------------
 
 
+@deprecated(isSpaceGroupLatPar_deprecation_msg)
 def isSpaceGroupLatPar(spacegroup, a, b, c, alpha, beta, gamma):
+    """'diffpy.structure.isSpaceGroupLatPar' is deprecated and will be
+    removed in version 4.0.0.
+
+    Please use 'diffpy.structure.is_space_group_latt_parms' instead.
+    """
+    return is_space_group_latt_parms(spacegroup, a, b, c, alpha, beta, gamma)
+
+
+def is_space_group_latt_parms(spacegroup, a, b, c, alpha, beta, gamma):
     """Check if space group allows passed lattice parameters.
 
     Parameters
@@ -110,7 +136,17 @@ def check_cubic():
 _rx_constant_formula = re.compile(r"[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)??(/[-+]?\d+)?$")
 
 
+@deprecated(isconstantFormula_deprecation_msg)
 def isconstantFormula(s):
+    """'diffpy.structure.isconstantFormula' is deprecated and will be
+    removed in version 4.0.0.
+
+    Please use 'diffpy.structure.is_constant_formula' instead.
+    """
+    return is_constant_formula(s)
+
+
+def is_constant_formula(s):
     """Check if formula string is constant.
 
     Parameters
@@ -837,7 +873,7 @@ def pruneFormulaDictionary(eqdict):
     """
     pruned = {}
     for smb, eq in eqdict.items():
-        if not isconstantFormula(eq):
+        if not is_constant_formula(eq):
             pruned[smb] = eq
     return pruned
 

tests/test_symmetryutilities.py

@@ -27,6 +27,8 @@
     SymmetryConstraints,
     _Position2Tuple,
     expandPosition,
+    is_constant_formula,
+    is_space_group_latt_parms,
     isconstantFormula,
     isSpaceGroupLatPar,
     pruneFormulaDictionary,
@@ -67,6 +69,30 @@ def test_isSpaceGroupLatPar(self):
         self.assertTrue(isSpaceGroupLatPar(cubic, 3, 3, 3, 90, 90, 90))
         return
 
+    def test_is_space_group_lat_par(self):
+        """Check isSpaceGroupLatPar()"""
+        triclinic = GetSpaceGroup("P1")
+        monoclinic = GetSpaceGroup("P2")
+        orthorhombic = GetSpaceGroup("P222")
+        tetragonal = GetSpaceGroup("P4")
+        trigonal = GetSpaceGroup("P3")
+        hexagonal = GetSpaceGroup("P6")
+        cubic = GetSpaceGroup("P23")
+        self.assertTrue(is_space_group_latt_parms(triclinic, 1, 2, 3, 40, 50, 60))
+        self.assertFalse(is_space_group_latt_parms(monoclinic, 1, 2, 3, 40, 50, 60))
+        self.assertTrue(is_space_group_latt_parms(monoclinic, 1, 2, 3, 90, 50, 90))
+        self.assertFalse(is_space_group_latt_parms(orthorhombic, 1, 2, 3, 90, 50, 90))
+        self.assertTrue(is_space_group_latt_parms(orthorhombic, 1, 2, 3, 90, 90, 90))
+        self.assertFalse(is_space_group_latt_parms(tetragonal, 1, 2, 3, 90, 90, 90))
+        self.assertTrue(is_space_group_latt_parms(tetragonal, 2, 2, 3, 90, 90, 90))
+        self.assertFalse(is_space_group_latt_parms(trigonal, 2, 2, 3, 90, 90, 90))
+        self.assertTrue(is_space_group_latt_parms(trigonal, 2, 2, 2, 80, 80, 80))
+        self.assertFalse(is_space_group_latt_parms(hexagonal, 2, 2, 2, 80, 80, 80))
+        self.assertTrue(is_space_group_latt_parms(hexagonal, 2, 2, 3, 90, 90, 120))
+        self.assertFalse(is_space_group_latt_parms(cubic, 2, 2, 3, 90, 90, 120))
+        self.assertTrue(is_space_group_latt_parms(cubic, 3, 3, 3, 90, 90, 90))
+        return
+
     def test_sgtbx_spacegroup_aliases(self):
         """Check GetSpaceGroup for non-standard aliases from sgtbx."""
         self.assertIs(GetSpaceGroup("Fm3m"), GetSpaceGroup(225))
@@ -100,6 +126,15 @@ def test_isconstantFormula(self):
         self.assertTrue(isconstantFormula("+13/ 9"))
         return
 
+    def test_is_constant_formula(self):
+        """Check isconstantFormula()"""
+        self.assertFalse(is_constant_formula("x-y+z"))
+        self.assertTrue(is_constant_formula("6.023e23"))
+        self.assertTrue(is_constant_formula("22/7"))
+        self.assertTrue(is_constant_formula("- 22/7"))
+        self.assertTrue(is_constant_formula("+13/ 9"))
+        return
+
 
 # End of class TestRoutines