feat: deprecate the camelCase methods and short attribute names in diffpy.srfit.structure

docs/source/api/diffpy.srfit.structure.rst

@@ -3,6 +3,10 @@
 diffpy.srfit.structure package
 ==============================
 
+.. deprecated:: 3.5.0
+    ``diffpy.srfit.structure`` has moved to ``diffpy.cmistructure`` and will
+    be removed in version 4.0.0. Please use ``diffpy.cmistructure`` instead.
+
 .. automodule:: diffpy.srfit.structure
     :members:
     :undoc-members:

news/structure-names-dep.rst

@@ -0,0 +1,26 @@
+**Added:**
+
+* The snake_case names of the structure adapter methods, which they have in ``diffpy.cmistructure``: ``can_adapt``, ``get_lattice``, ``get_scatterers``, ``get_space_group``, ``use_symmetry``, ``using_symmetry``, ``is_dummy``, ``has_scatterers``, ``wrap_restraints``, ``wrap_stretch_mode_parameters``, ``restrain_bond_length``, ``restrain_bond_angle``, ``restrain_dihedral_angle`` and their ``*_parameter`` forms, ``add_bond_length_parameter``, ``add_bond_angle_parameter``, ``add_dihedral_angle_parameter``, ``StretchModeParameter.add_atoms`` and ``BaseSpaceGroupParameters.add_parameter``.
+* The attributes ``.angle_units``, ``.scatterer``, ``.restraint``, ``.mutated_atoms``, ``.space_group``, ``.structure_parameter_set`` and ``.index``, which they are called in ``diffpy.cmistructure``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* The camelCase methods of the ``diffpy.srfit.structure`` adapters (``canAdapt``, ``getLattice``, ``getScatterers``, ``getSpaceGroup``, ``useSymmetry``, ``usingSymmetry``, ``isDummy``, ``hasScatterers``, ``wrapRestraints``, ``wrapStretchModeParameters``, the ``restrainBond*`` and ``restrainDihedral*`` methods, the ``add*Parameter`` methods of ``ObjCrystMoleculeParSet``, ``StretchModeParameter.addAtoms`` and ``BaseSpaceGroupParameters.addParameter``). Please use their snake_case names in ``diffpy.cmistructure`` instead.
+* The attributes ``.angunits``, ``.scat``, ``.res``, ``.matoms``, ``.sg``, ``.strups`` and ``.idx``. Please use ``.angle_units``, ``.scatterer``, ``.restraint``, ``.mutated_atoms``, ``.space_group``, ``.structure_parameter_set`` and ``.index`` in ``diffpy.cmistructure`` instead.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* ``ObjCrystMoleculeParSet.get_lattice`` no longer raises ``AttributeError``. It called ``newPar``, which ``ParameterSet`` doesn't have.
+* ``ObjCrystMoleculeParSet.wrap_stretch_mode_parameters`` no longer raises ``AttributeError`` for a molecule with stretch modes. It called ``AddAtoms``, which ``StretchModeParameter`` doesn't have.
+
+**Security:**
+
+* <news item>

src/diffpy/srfit/pdf/basepdfgenerator.py

@@ -430,7 +430,7 @@ def set_structure_from_parset(self, parset, periodic=True):
         self.add_parameter_set(parset)
 
         # Set periodicity
-        self._phase.useSymmetry(periodic)
+        self._phase.use_symmetry(periodic)
         return
 
     @deprecated(setPhase_dep_msg)

src/diffpy/srfit/structure/__init__.py

@@ -74,22 +74,22 @@ def structure_to_parameter_set(name, structure):
     """
     from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
 
-    if DiffpyStructureParSet.canAdapt(structure):
+    if DiffpyStructureParSet.can_adapt(structure):
         return DiffpyStructureParSet(name, structure)
 
     from diffpy.srfit.structure.objcrystparset import ObjCrystCrystalParSet
 
-    if ObjCrystCrystalParSet.canAdapt(structure):
+    if ObjCrystCrystalParSet.can_adapt(structure):
         return ObjCrystCrystalParSet(name, structure)
 
     from diffpy.srfit.structure.objcrystparset import ObjCrystMoleculeParSet
 
-    if ObjCrystMoleculeParSet.canAdapt(structure):
+    if ObjCrystMoleculeParSet.can_adapt(structure):
         return ObjCrystMoleculeParSet(name, structure)
 
     from diffpy.srfit.structure.cctbxparset import CCTBXCrystalParSet
 
-    if CCTBXCrystalParSet.canAdapt(structure):
+    if CCTBXCrystalParSet.can_adapt(structure):
         return CCTBXCrystalParSet(name, structure)
 
     raise TypeError("Unadaptable structure format")

src/diffpy/srfit/structure/basestructureparset.py

@@ -34,6 +34,34 @@
 )
 
 
+parset_base = "diffpy.srfit.structure.basestructureparset.BaseStructureParSet"
+parset_new_base = "diffpy.cmistructure.basestructureparset.BaseStructureParSet"
+
+parset_canAdapt_dep_msg = build_deprecation_message(
+    parset_base,
+    "canAdapt",
+    "can_adapt",
+    removal_version,
+    new_base=parset_new_base,
+)
+
+parset_getLattice_dep_msg = build_deprecation_message(
+    parset_base,
+    "getLattice",
+    "get_lattice",
+    removal_version,
+    new_base=parset_new_base,
+)
+
+parset_getScatterers_dep_msg = build_deprecation_message(
+    parset_base,
+    "getScatterers",
+    "get_scatterers",
+    removal_version,
+    new_base=parset_new_base,
+)
+
+
 class BaseStructureParSet(ParameterSet):
     """Base class for structure adapters.
 
@@ -65,23 +93,46 @@ def stru(self, value):
         self.structure = value
 
     @classmethod
-    def canAdapt(self, stru):
+    def can_adapt(self, stru):
         """Return whether the structure can be adapted by this class."""
         return False
 
-    def getLattice(self):
+    @classmethod
+    @deprecated(parset_canAdapt_dep_msg)
+    def canAdapt(self, stru):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.cmistructure.basestructureparset.BaseStructureParSet.can_adapt
+        instead.
+        """
+        return self.can_adapt(stru)
+
+    def get_lattice(self):
         """Get a ParameterSet containing the lattice Parameters.
 
         The returned ParameterSet may contain other Parameters than the
         lattice Parameters. It is assumed that the lattice parameters
         are named "a", "b", "c", "alpha", "beta", "gamma".
 
-        Lattice must also have the "angunits" attribute, which is either
-        "deg" or "rad", to signify degrees or radians.
+        Lattice must also have the "angle_units" attribute, which is
+        either "deg" or "rad", to signify degrees or radians.
         """
         raise NotImplementedError("The must be overloaded")
 
-    def getScatterers(self):
+    @deprecated(parset_getLattice_dep_msg)
+    def getLattice(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.cmistructure.basestructureparset.BaseStructureParSet.get_lattice
+        instead.
+        """
+        return self.get_lattice()
+
+    def get_scatterers(self):
         """Get a list of ParameterSets that represents the scatterers.
 
         The site positions must be accessible from the list entries via
@@ -90,3 +141,14 @@ def getScatterers(self):
         isotropic, anisotropic) depends on the adapted structure.
         """
         raise NotImplementedError("The must be overloaded")
+
+    @deprecated(parset_getScatterers_dep_msg)
+    def getScatterers(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.cmistructure.basestructureparset.BaseStructureParSet.get_scatterers
+        instead.
+        """
+        return self.get_scatterers()