Merge pull request #153 from cadenmyers13/fitrecipe2-dep

deprecate: `addParameterSet` deprecation in `FitRecipe` and `ParameterSet`

Author: sbillinge

docs/examples/npintensity.py

@@ -32,9 +32,9 @@
 
 Extensions
 
-- The IntensityGenerator class uses the 'addParameterSet' method to associate
+- The IntensityGenerator class uses the 'add_parameter_set' method to associate
   the structure adapter (DiffpyStructureParSet) with the generator. Most SrFit
-  classes have an 'addParameterSet' class and can store ParameterSet objects.
+  classes have an 'add_parameter_set' class and can store ParameterSet objects.
   Grab the phase object from the IntensityGenerator and try to add it to other
   objects used in the fit recipe. Create variables from the moved Parameters
   rather than from the 'phase' that lives in the IntensityGenerator and see if
@@ -153,7 +153,7 @@ def setStructure(self, strufile):
         parset = DiffpyStructureParSet("phase", stru)
 
         # Put this ParameterSet in the ProfileGenerator.
-        self.addParameterSet(parset)
+        self.add_parameter_set(parset)
 
         return
 

docs/examples/npintensityII.py

@@ -83,7 +83,7 @@ def makeRecipe(strufile, datname1, datname2):
     generator1 = IntensityGenerator("I")
     generator1.setStructure(strufile)
     generator2 = IntensityGenerator("I")
-    generator2.addParameterSet(generator1.phase)
+    generator2.add_parameter_set(generator1.phase)
 
     # The FitContributions
     # Create the FitContributions.
@@ -99,7 +99,8 @@ def makeRecipe(strufile, datname1, datname2):
     # the same form and use the same Parameter names.  By default, Parameters
     # in different contributions are different Parameters even if they have the
     # same names.  FitContributions are isolated namespaces than only share
-    # information if you tell them to by using addParameter or addParameterSet.
+    # information if you tell them to by using addParameter or
+    # add_parameter_set.
     bkgdstr = "b0 + b1*q + b2*q**2 + b3*q**3 + b4*q**4 + b5*q**5 + b6*q**6 +\
                b7*q**7 +b8*q**8 + b9*q**9"
 

news/addparameterset-dep.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* Added ``add_parameter_set`` method to replace deprecated ``FitRecipe.addParameterSet``.
+* Added ``add_parameter_set`` method to replace deprecated ``ParameterSet.addParameterSet``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``addParameterSet`` method in ``FitRecipe``.
+* Deprecate ``addParameterSet`` method in ``ParameterSet``.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/srfit/fitbase/fitrecipe.py

@@ -75,6 +75,10 @@
     base, "setWeight", "set_weight", removal_version
 )
 
+addparset_dep_msg = build_deprecation_message(
+    base, "addParameterSet", "add_parameter_set", removal_version
+)
+
 
 class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
     """FitRecipe class.
@@ -345,7 +349,7 @@ def setWeight(self, con, weight):
         self.set_weight(con, weight)
         return
 
-    def addParameterSet(self, parset):
+    def add_parameter_set(self, parset):
         """Add a ParameterSet to the hierarchy.
 
         Attributes
@@ -361,6 +365,16 @@ def addParameterSet(self, parset):
         self._add_object(parset, self._parsets, True)
         return
 
+    @deprecated(addparset_dep_msg)
+    def addParameterSet(self, parset):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.add_parameter_set instead.
+        """
+        self.add_parameter_set(parset)
+        return
+
     def removeParameterSet(self, parset):
         """Remove a ParameterSet from the hierarchy.
 

src/diffpy/srfit/fitbase/parameterset.py

@@ -25,6 +25,14 @@
 from collections import OrderedDict
 
 from diffpy.srfit.fitbase.recipeorganizer import RecipeOrganizer
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
+
+base = "diffpy.srfit.fitbase.parameterset.ParameterSet"
+removal_version = "4.0.0"
+
+addparset_dep_msg = build_deprecation_message(
+    base, "addParameterSet", "add_parameter_set", removal_version
+)
 
 
 class ParameterSet(RecipeOrganizer):
@@ -87,7 +95,7 @@ def __init__(self, name):
     newParameter = RecipeOrganizer._new_parameter
     removeParameter = RecipeOrganizer._remove_parameter
 
-    def addParameterSet(self, parset):
+    def add_parameter_set(self, parset):
         """Add a ParameterSet to the hierarchy.
 
         Attributes
@@ -103,6 +111,18 @@ def addParameterSet(self, parset):
         self._add_object(parset, self._parsets, True)
         return
 
+    @deprecated(addparset_dep_msg)
+    def addParameterSet(self, parset):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.srfit.fitbase.parameterset.ParameterSet.add_parameter_set
+        instead.
+        """
+        self.add_parameter_set(parset)
+        return
+
     def removeParameterSet(self, parset):
         """Remove a ParameterSet from the hierarchy.
 

src/diffpy/srfit/pdf/basepdfgenerator.py

@@ -277,7 +277,7 @@ def setPhase(self, parset, periodic=True):
         self.stru = self._phase.stru
 
         # Put this ParameterSet in the ProfileGenerator.
-        self.addParameterSet(parset)
+        self.add_parameter_set(parset)
 
         # Set periodicity
         self._phase.useSymmetry(periodic)

src/diffpy/srfit/structure/cctbxparset.py

@@ -237,7 +237,7 @@ def __init__(self, name, stru):
         """
         ParameterSet.__init__(self, name)
         self.stru = stru
-        self.addParameterSet(CCTBXUnitCellParSet(self))
+        self.add_parameter_set(CCTBXUnitCellParSet(self))
         self.scatterers = []
 
         self._update = False
@@ -249,7 +249,7 @@ def __init__(self, name, stru):
             sname = "%s%i" % (el, i)
             cdict[el] = i + 1
             scatterer = CCTBXScattererParSet(sname, self, i)
-            self.addParameterSet(scatterer)
+            self.add_parameter_set(scatterer)
             self.scatterers.append(scatterer)
 
         # Constrain the lattice

src/diffpy/srfit/structure/diffpyparset.py

@@ -284,7 +284,7 @@ def __init__(self, name, stru):
         """
         SrRealParSet.__init__(self, name)
         self.stru = stru
-        self.addParameterSet(DiffpyLatticeParSet(stru.lattice))
+        self.add_parameter_set(DiffpyLatticeParSet(stru.lattice))
         self.atoms = []
 
         cdict = {}
@@ -297,7 +297,7 @@ def __init__(self, name, stru):
             aname = "%s%i" % (el, i)
             cdict[el] = i + 1
             atom = DiffpyAtomParSet(aname, a)
-            self.addParameterSet(atom)
+            self.add_parameter_set(atom)
             self.atoms.append(atom)
 
         return

src/diffpy/srfit/structure/objcrystparset.py

@@ -252,7 +252,7 @@ def __init__(self, name, molecule, parent=None):
 
             atom = ObjCrystMolAtomParSet(name, a, self)
             atom.molecule = self
-            self.addParameterSet(atom)
+            self.add_parameter_set(atom)
             self.atoms.append(atom)
             anames.append(name)
 
@@ -1760,7 +1760,7 @@ def __init__(self, name, cryst):
             else:
                 raise TypeError("Unrecognized scatterer '%s'" % cname)
 
-            self.addParameterSet(parset)
+            self.add_parameter_set(parset)
             self.scatterers.append(parset)
             snames.append(name)
 

tests/test_parameterset.py

@@ -27,14 +27,35 @@ def setUp(self):
         return
 
     def testAddParameterSet(self):
-        """Test the addParameterSet method."""
+        """Test the deprecated addParameterSet method.
+
+        Remove this test after the addParameterSet is removed in version
+        4.0.0.
+        """
         parset2 = ParameterSet("parset2")
         p1 = Parameter("parset2", 1)
 
         self.parset.addParameterSet(parset2)
         self.assertTrue(self.parset.parset2 is parset2)
 
-        self.assertRaises(ValueError, self.parset.addParameterSet, p1)
+        self.assertRaises(ValueError, self.parset.add_parameter_set, p1)
+
+        p1.name = "p1"
+        parset2.addParameter(p1)
+
+        self.assertTrue(self.parset.parset2.p1 is p1)
+
+        return
+
+    def test_add_parameter_set(self):
+        """Test the add_parameter_set method."""
+        parset2 = ParameterSet("parset2")
+        p1 = Parameter("parset2", 1)
+
+        self.parset.add_parameter_set(parset2)
+        self.assertTrue(self.parset.parset2 is parset2)
+
+        self.assertRaises(ValueError, self.parset.add_parameter_set, p1)
 
         p1.name = "p1"
         parset2.addParameter(p1)