dep: deprecate diffpy.srfit.structure in favor of diffpy.cmistructure

news/structure-dep.rst

@@ -0,0 +1,26 @@
+**Added:**
+
+* ``diffpy.srfit.structure.structure_to_parameter_set`` and ``SrRealParSet.restrain_bvs``, which take the names they have in ``diffpy.cmistructure``.
+
+**Changed:**
+
+* The deprecation messages of ``constrainAsSpaceGroup`` and of ``setConst`` on the ObjCrystParSet bond length, bond angle and dihedral angle parameters now point to ``diffpy.cmistructure`` instead of ``diffpy.srfit.structure``.
+
+**Deprecated:**
+
+* ``diffpy.srfit.structure``, which moved to ``diffpy.cmistructure``. Importing it now raises a ``DeprecationWarning``.
+* ``diffpy.srfit.structure.struToParameterSet``. Please use ``diffpy.cmistructure.structure_to_parameter_set`` instead.
+* ``SrRealParSet.restrainBVS``. Please use ``diffpy.cmistructure.srrealparset.SrRealParSet.restrain_bvs`` instead.
+* The ``.stru`` attribute of the structure parameter sets and of ``ObjCrystMoleculeParSet``. Please use ``.structure`` in ``diffpy.cmistructure`` instead.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -62,6 +62,7 @@ dependencies = {file = ["requirements/pip.txt"]}
 # Fail when srfit source calls one of srfit's own deprecated names.
 filterwarnings = [
     "error:'diffpy\\.srfit\\.:DeprecationWarning:diffpy\\.srfit",
+    "ignore:'diffpy\\.srfit\\.(pdf|sas|structure)' is deprecated:DeprecationWarning",
 ]
 
 [tool.codespell]

src/diffpy/srfit/pdf/basepdfgenerator.py

@@ -25,7 +25,7 @@
 from diffpy.srfit.exceptions import SrFitError
 from diffpy.srfit.fitbase import ProfileGenerator
 from diffpy.srfit.fitbase.parameter import ParameterAdapter
-from diffpy.srfit.structure import struToParameterSet
+from diffpy.srfit.structure import structure_to_parameter_set
 
 # FIXME - Parameter creation will have to be smarter once deeper calculator
 # configuration is enabled.
@@ -282,7 +282,7 @@ def setStructure(self, stru, name="phase", periodic=True):
             PDF calculation.
         """
         # Create the ParameterSet
-        parset = struToParameterSet(name, stru)
+        parset = structure_to_parameter_set(name, stru)
 
         # Set the phase
         self.setPhase(parset, periodic)
@@ -310,7 +310,7 @@ def setPhase(self, parset, periodic=True):
         """
         # Store the ParameterSet for easy access
         self._phase = parset
-        self.stru = self._phase.stru
+        self.stru = self._phase.structure
 
         # Put this ParameterSet in the ProfileGenerator.
         self.add_parameter_set(parset)

src/diffpy/srfit/structure/__init__.py

@@ -16,50 +16,95 @@
 ParameterSet interface and automatic structure constraint generation
 from space group information."""
 
+import warnings
+
 from diffpy.srfit.structure.sgconstraints import (
     constrain_as_space_group,
     constrainAsSpaceGroup,
 )
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+removal_version = "4.0.0"
+
+warnings.warn(
+    build_deprecation_message(
+        "diffpy.srfit",
+        "structure",
+        "cmistructure",
+        removal_version,
+        new_base="diffpy",
+    ),
+    DeprecationWarning,
+    stacklevel=2,
+)
+
+struToParameterSet_dep_msg = build_deprecation_message(
+    "diffpy.srfit.structure",
+    "struToParameterSet",
+    "structure_to_parameter_set",
+    removal_version,
+    new_base="diffpy.cmistructure",
+)
 
 
-def struToParameterSet(name, stru):
-    """Creates a ParameterSet from an structure.
+def structure_to_parameter_set(name, structure):
+    """Create a ParameterSet adapted to a structure object.
 
-    This returns a ParameterSet adapted for the structure depending on its
-    type.
+    The adapter is chosen from the type of `structure`. Supported types
+    are diffpy.structure.Structure, pyobjcryst.crystal.Crystal,
+    pyobjcryst.molecule.Molecule and
+    cctbx.crystal.special_position_settings.
 
     Parameters
     ----------
-    stru
-        a structure object known by this module
-    name
-        A name to give the structure.
-
-    Raises TypeError if stru cannot be adapted
+    name : str
+        The name to give the structure.
+    structure : object
+        The structure object to adapt.
+
+    Returns
+    -------
+    BaseStructureParSet
+        The ParameterSet adapting `structure`.
+
+    Raises
+    ------
+    TypeError
+        If `structure` is not one of the supported structure types.
     """
     from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
 
-    if DiffpyStructureParSet.canAdapt(stru):
-        return DiffpyStructureParSet(name, stru)
+    if DiffpyStructureParSet.canAdapt(structure):
+        return DiffpyStructureParSet(name, structure)
 
     from diffpy.srfit.structure.objcrystparset import ObjCrystCrystalParSet
 
-    if ObjCrystCrystalParSet.canAdapt(stru):
-        return ObjCrystCrystalParSet(name, stru)
+    if ObjCrystCrystalParSet.canAdapt(structure):
+        return ObjCrystCrystalParSet(name, structure)
 
     from diffpy.srfit.structure.objcrystparset import ObjCrystMoleculeParSet
 
-    if ObjCrystMoleculeParSet.canAdapt(stru):
-        return ObjCrystMoleculeParSet(name, stru)
+    if ObjCrystMoleculeParSet.canAdapt(structure):
+        return ObjCrystMoleculeParSet(name, structure)
 
     from diffpy.srfit.structure.cctbxparset import CCTBXCrystalParSet
 
-    if CCTBXCrystalParSet.canAdapt(stru):
-        return CCTBXCrystalParSet(name, stru)
+    if CCTBXCrystalParSet.canAdapt(structure):
+        return CCTBXCrystalParSet(name, structure)
 
     raise TypeError("Unadaptable structure format")
 
 
+@deprecated(struToParameterSet_dep_msg)
+def struToParameterSet(name, stru):
+    """This function has been deprecated and will be removed in version
+    4.0.0.
+
+    Please use diffpy.cmistructure.structure_to_parameter_set instead.
+    """
+    return structure_to_parameter_set(name, stru)
+
+
 # silence pyflakes checker
 assert constrain_as_space_group
 assert constrainAsSpaceGroup

src/diffpy/srfit/structure/basestructureparset.py

@@ -21,6 +21,17 @@
 __all__ = ["BaseStructureParSet"]
 
 from diffpy.srfit.fitbase.parameterset import ParameterSet
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+removal_version = "4.0.0"
+
+stru_dep_msg = build_deprecation_message(
+    "diffpy.srfit.structure.basestructureparset.BaseStructureParSet",
+    "stru",
+    "structure",
+    removal_version,
+    new_base="diffpy.cmistructure.basestructureparset.BaseStructureParSet",
+)
 
 
 class BaseStructureParSet(ParameterSet):
@@ -32,10 +43,27 @@ class BaseStructureParSet(ParameterSet):
 
     Attributes
     ----------
-    stru
+    structure
         The adapted object
     """
 
+    @property
+    @deprecated(stru_dep_msg)
+    def stru(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.cmistructure.basestructureparset.BaseStructureParSet.structure
+        instead.
+        """
+        return self.structure
+
+    @stru.setter
+    @deprecated(stru_dep_msg)
+    def stru(self, value):
+        self.structure = value
+
     @classmethod
     def canAdapt(self, stru):
         """Return whether the structure can be adapted by this class."""

src/diffpy/srfit/structure/cctbxparset.py

@@ -92,32 +92,32 @@ def __init__(self, name, strups, idx):
     def _xyzgetter(self, i):
 
         def f(dummy):
-            return self.strups.stru.scatterers()[self.idx].site[i]
+            return self.strups.structure.scatterers()[self.idx].site[i]
 
         return f
 
     def _xyzsetter(self, i):
 
         def f(dummy, value):
-            xyz = list(self.strups.stru.scatterers()[self.idx].site)
+            xyz = list(self.strups.structure.scatterers()[self.idx].site)
             xyz[i] = value
-            self.strups.stru.scatterers()[self.idx].site = tuple(xyz)
+            self.strups.structure.scatterers()[self.idx].site = tuple(xyz)
             return
 
         return f
 
     def _getocc(self, dummy):
-        return self.strups.stru.scatterers()[self.idx].occupancy
+        return self.strups.structure.scatterers()[self.idx].occupancy
 
     def _setocc(self, dummy, value):
-        self.strups.stru.scatterers()[self.idx].occupancy = value
+        self.strups.structure.scatterers()[self.idx].occupancy = value
         return
 
     def _getuiso(self, dummy):
-        return self.strups.stru.scatterers()[self.idx].u_iso
+        return self.strups.structure.scatterers()[self.idx].u_iso
 
     def _setuiso(self, dummy, value):
-        self.strups.stru.scatterers()[self.idx].u_iso = value
+        self.strups.structure.scatterers()[self.idx].u_iso = value
         return
 
     def _getelem(self):
@@ -161,7 +161,7 @@ def __init__(self, strups):
         """
         ParameterSet.__init__(self, "unitcell")
         self.strups = strups
-        self._latpars = list(self.strups.stru.unit_cell().parameters())
+        self._latpars = list(self.strups.structure.unit_cell().parameters())
 
         self.add_parameter(
             ParameterAdapter("a", None, self._latgetter(0), self._latsetter(0))
@@ -236,7 +236,7 @@ def __init__(self, name, stru):
             A CCTBX structure instance.
         """
         ParameterSet.__init__(self, name)
-        self.stru = stru
+        self.structure = stru
         self.add_parameter_set(CCTBXUnitCellParSet(self))
         self.scatterers = []
 
@@ -272,7 +272,7 @@ def update(self):
             return
 
         self._update = False
-        stru = self.stru
+        stru = self.structure
         sgn = stru.space_group().match_tabulated_settings().number()
 
         # Create the symmetry object
@@ -289,7 +289,7 @@ def update(self):
 
         self.unitcell._latpars = list(newstru.unit_cell().parameters())
 
-        self.stru = newstru
+        self.structure = newstru
         return
 
     @classmethod
@@ -317,7 +317,7 @@ def getScatterers(self):
 
     def getSpaceGroup(self):
         """Get the HM space group symbol for the structure."""
-        sg = self.stru.space_group()
+        sg = self.structure.space_group()
         t = sg.type()
         return t.lookup_symbol()
 

src/diffpy/srfit/structure/diffpyparset.py

@@ -285,7 +285,7 @@ def __init__(self, name, stru):
             A diffpy.structure.Structure instance
         """
         SrRealParSet.__init__(self, name)
-        self.stru = stru
+        self.structure = stru
         self.add_parameter_set(DiffpyLatticeParSet(stru.lattice))
         self.atoms = []
 
@@ -305,7 +305,7 @@ def __init__(self, name, stru):
         return
 
     def __repr__(self):
-        return repr(self.stru)
+        return repr(self.structure)
 
     def getLattice(self):
         """Get the ParameterSet containing the lattice Parameters."""