Merge pull request #159 from stevenhua0320/deprecate-getLastAtom

build: deprecate getLastAtom and add a test

Author: sbillinge

news/deprecate-getLastAtom.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Added `diffpy.structure.Structure.get_last_atom` in replace of `getLastAtom`
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated `diffpy.structure.Structure.getLastAtom` for removal in version 4.0.0
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/parsers/p_cif.py

@@ -498,7 +498,7 @@ def _parse_atom_site_label(self, block):
                 continue
             self.labelindex[curlabel] = len(self.stru)
             self.stru.add_new_atom()
-            a = self.stru.getLastAtom()
+            a = self.stru.get_last_atom()
             for fset, val in zip(prop_setters, values):
                 fset(a, val)
             if does_adp_type:

src/diffpy/structure/parsers/p_discus.py

@@ -265,7 +265,7 @@ def _parse_atom(self, words):
         xyz = [float(w) for w in words[1:4]]
         Biso = float(words[4])
         self.stru.add_new_atom(element, xyz)
-        a = self.stru.getLastAtom()
+        a = self.stru.get_last_atom()
         a.Bisoequiv = Biso
         return
 

src/diffpy/structure/parsers/p_pdb.py

@@ -198,7 +198,7 @@ def parseLines(self, lines):
                         element = line[12:14].strip()
                         element = element[0].upper() + element[1:].lower()
                     stru.add_new_atom(element, occupancy=occupancy, label=name)
-                    last_atom = stru.getLastAtom()
+                    last_atom = stru.get_last_atom()
                     last_atom.xyz_cartn = rc
                     last_atom.Uisoequiv = uiso
                 elif record == "SIGATM":

src/diffpy/structure/parsers/p_pdffit.py

@@ -133,7 +133,7 @@ def parseLines(self, lines):
                 xyz = [float(w) for w in wl1[1:4]]
                 occ = float(wl1[4])
                 stru.add_new_atom(element, xyz=xyz, occupancy=occ)
-                a = stru.getLastAtom()
+                a = stru.get_last_atom()
                 p_nl += 1
                 wl2 = next(ilines).split()
                 a.sigxyz = [float(w) for w in wl2[0:3]]

src/diffpy/structure/structure.py

@@ -34,6 +34,12 @@
     "add_new_atom",
     removal_version,
 )
+getLastAtom_deprecation_msg = build_deprecation_message(
+    base,
+    "getLastAtom",
+    "get_last_atom",
+    removal_version,
+)
 
 
 class Structure(list):
@@ -192,7 +198,16 @@ def add_new_atom(self, *args, **kwargs):
         self.append(atom, copy=False)
         return
 
+    @deprecated(getLastAtom_deprecation_msg)
     def getLastAtom(self):
+        """This function has been deprecated and will be removed in
+        version 4.0.0.
+
+        Please use diffpy.structure.Structure.get_last_atom instead.
+        """
+        return self.get_last_atom()
+
+    def get_last_atom(self):
         """Return Reference to the last `Atom` in this structure."""
         last_atom = self[-1]
         return last_atom

tests/test_structure.py

@@ -119,6 +119,23 @@ def test___copy__(self):
     # def test_getLastAtom(self):
     #     """check Structure.getLastAtom()"""
     #     return
+    def test_getLastAtom(self):
+        """Check Structure.getLastAtom()"""
+        s_lat = Lattice()
+        expected = Atom("C", [0, 0, 0])
+        structure = Structure(atoms=[Atom("C", [0, 0, 0])], lattice=s_lat)
+        actual = structure.getLastAtom()
+        assert actual.element == expected.element
+        assert numpy.allclose(expected.xyz, actual.xyz)
+
+    def test_get_last_atom(self):
+        """Check Structure.get_last_atom()"""
+        s_lat = Lattice()
+        expected = Atom("C", [0, 0, 0])
+        structure = Structure(atoms=[Atom("C", [0, 0, 0])], lattice=s_lat)
+        actual = structure.get_last_atom()
+        assert actual.element == expected.element
+        assert numpy.allclose(expected.xyz, actual.xyz)
 
     def test_addNewAtom(self):
         """Duplicate test for the deprecated addNewAtom method.