build: change version number and refactor name of function.

Author: stevenhua0320

src/diffpy/structure/structure.py

@@ -25,14 +25,8 @@
 # ----------------------------------------------------------------------------
 
 base = "diffpy.structure.Structure"
-removal_version = "3.8.0"
+removal_version = "4.0.0"
 
-addNewAtom_deprecation_msg = build_deprecation_message(
-    base,
-    "addNewAtom",
-    "add_new_atom",
-    removal_version,
-)
 getLastAtom_deprecation_msg = build_deprecation_message(
     base,
     "getLastAtom",
@@ -208,17 +202,6 @@ def add_new_atom(self, *args, **kwargs):
         self.append(a, copy=False)
         return
 
-    @deprecated(addNewAtom_deprecation_msg)
-    def addNewAtom(self, *args, **kwargs):
-        """This function has been deprecated and will be removed in
-        version 3.8.0.
-
-        Please use diffpy.structure.Structure.add_new_atom instead.
-        """
-        kwargs["lattice"] = self.lattice
-        a = Atom(*args, **kwargs)
-        self.append(a, copy=False)
-        return
 
     def get_last_atom(self):
         """Return Reference to the last `Atom` in this structure."""
@@ -228,7 +211,7 @@ def get_last_atom(self):
     @deprecated(getLastAtom_deprecation_msg)
     def getLastAtom(self):
         """This function has been deprecated and will be removed in
-        version 3.8.0.
+        version 4.0.0.
 
         Please use diffpy.structure.Structure.get_last_atom instead.
         """
@@ -256,7 +239,7 @@ def assign_unique_labels(self):
     @deprecated(assignUniqueLabels_deprecation_msg)
     def assignUniqueLabels(self):
         """This function has been deprecated and will be removed in
-        version 3.8.0.
+        version 4.0.0.
 
         Please use diffpy.structure.Structure.assgin_unique_labels
         instead.
@@ -354,7 +337,7 @@ def place_in_lattice(self, new_lattice):
     @deprecated(placeInLattice_deprecation_msg)
     def placeInLattice(self, new_lattice):
         """This function has been deprecated and will be removed in
-        version 3.8.0.
+        version 4.0.0.
 
         Please use diffpy.structure.Structure.place_in_lattice instead.
         """
@@ -436,7 +419,7 @@ def read_str(self, s, format="auto"):
     @deprecated(readStr_deprecation_msg)
     def readStr(self, s, format="auto"):
         """This function has been deprecated and will be removed in
-        version 3.8.0.
+        version 4.0.0.
 
         Please use diffpy.structure.Structure.read_str instead.
         """
@@ -496,7 +479,7 @@ def write_str(self, format):
     @deprecated(writeStr_deprecation_msg)
     def writeStr(self, format):
         """This function has been deprecated and will be removed in
-        version 3.8.0.
+        version 4.0.0.
 
         Please use diffpy.structure.Structure.write_str instead.
         """

tests/test_p_cif.py

@@ -197,6 +197,33 @@ def test_parseFile(self):
     #       """
     #       return
 
+    def test_Write_and_Read(self):
+        """High-level check of P_cif.tostring()"""
+        # high-level check
+        stru_check = Structure()
+        stru_check.read(self.cdsebulkpdffitfile)
+        s_s = stru_check.writeStr("cif")
+        stru = Structure()
+        stru.readStr(s_s, "cif")
+        self.assertAlmostEqual(4.2352, stru.lattice.a, self.places)
+        self.assertAlmostEqual(4.2352, stru.lattice.b, self.places)
+        self.assertAlmostEqual(6.90603, stru.lattice.c, self.places)
+        self.assertEqual(4, len(stru))
+        a0 = stru[0]
+        self.assertEqual("Cd", a0.element)
+        self.assertTrue(numpy.allclose([0.3334, 0.6667, 0.0], a0.xyz))
+        self.assertTrue(a0.anisotropy)
+        self.assertAlmostEqual(0.01303, a0.U[0, 0])
+        self.assertAlmostEqual(0.01303, a0.U[1, 1])
+        self.assertAlmostEqual(0.01402, a0.U[2, 2])
+        a3 = stru[3]
+        self.assertEqual("Se", a3.element)
+        self.assertTrue(numpy.allclose([0.6666, 0.333300, 0.87667], a3.xyz))
+        self.assertAlmostEqual(0.015673, a3.U[0, 0])
+        self.assertAlmostEqual(0.015673, a3.U[1, 1])
+        self.assertAlmostEqual(0.046164, a3.U[2, 2])
+        return
+
     def test_write_and_read(self):
         """High-level check of P_cif.tostring()"""
         # high-level check