build: deprecate CamelCase function for structure.py

news/deprecate-camel-case-1.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: deprecate CamelCase function for structure.py
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

requirements/conda.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

requirements/pip.txt

@@ -1,2 +1,3 @@
 numpy
 pycifrw
+diffpy.utils

src/diffpy/structure/apps/transtru.py

@@ -109,10 +109,10 @@ def main():
         strufile = args[1]
         stru = Structure()
         if args[1] == "-":
-            stru.readStr(sys.stdin.read(), infmt)
+            stru.read_str(sys.stdin.read(), infmt)
         else:
             stru.read(strufile, infmt)
-        sys.stdout.write(stru.writeStr(outfmt))
+        sys.stdout.write(stru.write_str(outfmt))
     except IndexError:
         print("strufile not specified", file=sys.stderr)
         sys.exit(2)

src/diffpy/structure/parsers/p_cif.py

@@ -497,8 +497,8 @@ def _parse_atom_site_label(self, block):
             if curlabel == "?":
                 continue
             self.labelindex[curlabel] = len(self.stru)
-            self.stru.addNewAtom()
-            a = self.stru.getLastAtom()
+            self.stru.add_new_atom()
+            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

@@ -264,8 +264,8 @@ def _parse_atom(self, words):
         element = words[0][0:1].upper() + words[0][1:].lower()
         xyz = [float(w) for w in words[1:4]]
         Biso = float(words[4])
-        self.stru.addNewAtom(element, xyz)
-        a = self.stru.getLastAtom()
+        self.stru.add_new_atom(element, xyz)
+        a = self.stru.get_last_atom()
         a.Bisoequiv = Biso
         return
 

src/diffpy/structure/parsers/p_pdb.py

@@ -197,8 +197,8 @@ def parseLines(self, lines):
                         # get element from the first 2 characters of name
                         element = line[12:14].strip()
                         element = element[0].upper() + element[1:].lower()
-                    stru.addNewAtom(element, occupancy=occupancy, label=name)
-                    last_atom = stru.getLastAtom()
+                    stru.add_new_atom(element, occupancy=occupancy, label=name)
+                    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

@@ -132,8 +132,8 @@ def parseLines(self, lines):
                 element = wl1[0][0].upper() + wl1[0][1:].lower()
                 xyz = [float(w) for w in wl1[1:4]]
                 occ = float(wl1[4])
-                stru.addNewAtom(element, xyz=xyz, occupancy=occ)
-                a = stru.getLastAtom()
+                stru.add_new_atom(element, xyz=xyz, occupancy=occ)
+                a = stru.get_last_atom()
                 p_nl += 1
                 wl2 = next(ilines).split()
                 a.sigxyz = [float(w) for w in wl2[0:3]]
@@ -169,7 +169,7 @@ def parseLines(self, lines):
             if stru.pdffit["ncell"][:3] != [1, 1, 1]:
                 superlatpars = [latpars[i] * stru.pdffit["ncell"][i] for i in range(3)] + latpars[3:]
                 superlattice = Lattice(*superlatpars)
-                stru.placeInLattice(superlattice)
+                stru.place_in_lattice(superlattice)
                 stru.pdffit["ncell"] = [1, 1, 1, p_natoms]
         except (ValueError, IndexError):
             emsg = "%d: file is not in PDFfit format" % p_nl

src/diffpy/structure/parsers/p_rawxyz.py

@@ -103,7 +103,7 @@ def parseLines(self, lines):
                 xyz = [float(f) for f in fields[x_idx : x_idx + 3]]
                 if len(xyz) == 2:
                     xyz.append(0.0)
-                stru.addNewAtom(element, xyz=xyz)
+                stru.add_new_atom(element, xyz=xyz)
         except ValueError:
             emsg = "%d: invalid number" % p_nl
             exc_type, exc_value, exc_traceback = sys.exc_info()

src/diffpy/structure/parsers/p_xcfg.py

@@ -269,7 +269,7 @@ def parseLines(self, lines):
                 elif len(words) == xcfg_entry_count and p_element is not None:
                     fields = [float(w) for w in words]
                     xyz = [xcfg_A * xi for xi in fields[:3]]
-                    stru.addNewAtom(p_element, xyz=xyz)
+                    stru.add_new_atom(p_element, xyz=xyz)
                     a = stru[-1]
                     _assign_auxiliaries(
                         a,

src/diffpy/structure/parsers/p_xyz.py

@@ -109,7 +109,7 @@ def parseLines(self, lines):
                 element = fields[0]
                 element = element[0].upper() + element[1:].lower()
                 xyz = [float(f) for f in fields[1:4]]
-                stru.addNewAtom(element, xyz=xyz)
+                stru.add_new_atom(element, xyz=xyz)
         except ValueError:
             exc_type, exc_value, exc_traceback = sys.exc_info()
             emsg = "%d: invalid number format" % p_nl

src/diffpy/structure/pdffitstructure.py

@@ -97,7 +97,7 @@ def readStr(self, s, format="auto"):
         StructureParser
             Instance of `StructureParser` used to load the data.
         """
-        p = Structure.readStr(self, s, format)
+        p = Structure.read_str(self, s, format)
         sg = getattr(p, "spacegroup", None)
         if sg:
             self.pdffit["spcgr"] = sg.short_name