Merge pull request #146 from cadenmyers13/addprofilegenerator-dep

sbillinge · web-flow · commit d3c210eb3b8f · 2026-02-06T17:16:26.000-08:00
deprecate: `addProfileGenerator` deprecation
diff --git a/docs/examples/coreshellnp.py b/docs/examples/coreshellnp.py
@@ -66,8 +66,8 @@ def makeRecipe(stru1, stru2, datname):
     # The FitContribution
     # Add both generators and the profile to the FitContribution.
     contribution = FitContribution("cdszns")
-    contribution.addProfileGenerator(generator_cds)
-    contribution.addProfileGenerator(generator_zns)
+    contribution.add_profile_generator(generator_cds)
+    contribution.add_profile_generator(generator_zns)
     contribution.set_profile(profile, xname="r")
 
     # Set up the characteristic functions. We use a spherical CF for the core
diff --git a/docs/examples/crystalpdf.py b/docs/examples/crystalpdf.py
@@ -74,7 +74,7 @@ def makeRecipe(ciffile, datname):
     # Here we associate the Profile and ProfileGenerator, as has been done
     # before.
     contribution = FitContribution("nickel")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="r")
 
     # Make the FitRecipe and add the FitContribution.
diff --git a/docs/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py
@@ -47,7 +47,7 @@ def makeProfile(datafile):
 def makeContribution(name, generator, profile):
     """Make a FitContribution and add a generator and profile."""
     contribution = FitContribution(name)
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="r")
     return contribution
 
@@ -93,7 +93,7 @@ def makeRecipe(
     xcontribution_sini = makeContribution(
         "xsini", xgenerator_sini_ni, xprofile_sini
     )
-    xcontribution_sini.addProfileGenerator(xgenerator_sini_si)
+    xcontribution_sini.add_profile_generator(xgenerator_sini_si)
     xcontribution_sini.setEquation("scale * (xG_sini_ni +  xG_sini_si)")
 
     # As explained in another example, we want to minimize using Rw^2.
diff --git a/docs/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py
@@ -62,7 +62,7 @@ def makeRecipe(ciffile, datname):
 
     # The FitContribution
     contribution = FitContribution("nickel")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="r")
 
     # Make the FitRecipe and add the FitContribution.
diff --git a/docs/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py
@@ -84,11 +84,11 @@ def makeRecipe(ciffile, xdatname, ndatname):
     # The FitContributions
     # We associate the x-ray PDFGenerator and Profile in one FitContribution...
     xcontribution = FitContribution("xnickel")
-    xcontribution.addProfileGenerator(xgenerator)
+    xcontribution.add_profile_generator(xgenerator)
     xcontribution.set_profile(xprofile, xname="r")
     # and the neutron objects in another.
     ncontribution = FitContribution("nnickel")
-    ncontribution.addProfileGenerator(ngenerator)
+    ncontribution.add_profile_generator(ngenerator)
     ncontribution.set_profile(nprofile, xname="r")
 
     # This example is different than the previous ones in that we are composing
diff --git a/docs/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py
@@ -72,8 +72,8 @@ def makeRecipe(niciffile, siciffile, datname):
     # Add both generators to the FitContribution. Add the Profile. This will
     # send the metadata to the generators.
     contribution = FitContribution("nisi")
-    contribution.addProfileGenerator(generator_ni)
-    contribution.addProfileGenerator(generator_si)
+    contribution.add_profile_generator(generator_ni)
+    contribution.add_profile_generator(generator_si)
     contribution.set_profile(profile, xname="r")
 
     # Write the fitting equation. We want to sum the PDFs from each phase and
diff --git a/docs/examples/ellipsoidsas.py b/docs/examples/ellipsoidsas.py
@@ -57,7 +57,7 @@ def makeRecipe(datname):
     # Here we associate the Profile and ProfileGenerator, as has been done
     # before.
     contribution = FitContribution("ellipsoid")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="q")
 
     # We want to fit the log of the signal to the log of the data so that the
diff --git a/docs/examples/gaussiangenerator.py b/docs/examples/gaussiangenerator.py
@@ -144,7 +144,7 @@ def makeRecipe():
     # attribute of the FitContribution by its name ("g"). Note that this will
     # set the fitting equation to "g", which calls the GaussianGenerator.
     contribution = FitContribution("g1")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile)
 
     # The FitRecipe
diff --git a/docs/examples/npintensity.py b/docs/examples/npintensity.py
@@ -203,7 +203,7 @@ def makeRecipe(strufile, datname):
     # the FitContribution to name the x-variable of the profile "q", so we can
     # use it in equations with this name.
     contribution = FitContribution("bucky")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="q")
 
     # Now we're ready to define the fitting equation for the FitContribution.
diff --git a/docs/examples/npintensityII.py b/docs/examples/npintensityII.py
@@ -88,10 +88,10 @@ def makeRecipe(strufile, datname1, datname2):
     # The FitContributions
     # Create the FitContributions.
     contribution1 = FitContribution("bucky1")
-    contribution1.addProfileGenerator(generator1)
+    contribution1.add_profile_generator(generator1)
     contribution1.set_profile(profile1, xname="q")
     contribution2 = FitContribution("bucky2")
-    contribution2.addProfileGenerator(generator2)
+    contribution2.add_profile_generator(generator2)
     contribution2.set_profile(profile2, xname="q")
 
     # Now we're ready to define the fitting equation for each FitContribution.
diff --git a/docs/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py
@@ -54,7 +54,7 @@ def makeRecipe(ciffile, grdata):
     pdfgenerator.setQmax(30.0)
     stru = loadCrystal(ciffile)
     pdfgenerator.setStructure(stru)
-    pdfcontribution.addProfileGenerator(pdfgenerator)
+    pdfcontribution.add_profile_generator(pdfgenerator)
 
     # Register the nanoparticle shape factor.
     from diffpy.srfit.pdf.characteristicfunctions import sphericalCF
diff --git a/docs/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py
@@ -52,7 +52,7 @@ def makeRecipe(molecule, datname):
 
     # The FitContribution
     contribution = FitContribution("bucky")
-    contribution.addProfileGenerator(generator)
+    contribution.add_profile_generator(generator)
     contribution.set_profile(profile, xname="r")
 
     # Make a FitRecipe.
diff --git a/docs/examples/nppdfsas.py b/docs/examples/nppdfsas.py
@@ -58,7 +58,7 @@ def makeRecipe(ciffile, grdata, iqdata):
     pdfgenerator.setQmax(30.0)
     stru = loadCrystal(ciffile)
     pdfgenerator.setStructure(stru)
-    pdfcontribution.addProfileGenerator(pdfgenerator)
+    pdfcontribution.add_profile_generator(pdfgenerator)
     pdfcontribution.setResidualEquation("resv")
 
     # Create a SAS contribution as well. We assume the nanoparticle is roughly
@@ -77,7 +77,7 @@ def makeRecipe(ciffile, grdata, iqdata):
 
     model = EllipsoidModel()
     sasgenerator = SASGenerator("generator", model)
-    sascontribution.addProfileGenerator(sasgenerator)
+    sascontribution.add_profile_generator(sasgenerator)
     sascontribution.setResidualEquation("resv")
 
     # Now we set up a characteristic function calculator that depends on the
diff --git a/news/addprofilegenerator-dep.rst b/news/addprofilegenerator-dep.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Added ``add_profile_generator`` to replace deprecated function.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``addProfileGenerator`` for removal in 4.0.0.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/srfit/fitbase/fitcontribution.py b/src/diffpy/srfit/fitbase/fitcontribution.py
@@ -41,6 +41,13 @@
     removal_version,
 )
 
+addprofilegenerator_dep_msg = build_deprecation_message(
+    base,
+    "addProfileGenerator",
+    "add_profile_generator",
+    removal_version,
+)
+
 
 class FitContribution(ParameterSet):
     """FitContribution class.
@@ -179,7 +186,7 @@ def setProfile(self, profile, xname=None, yname=None, dyname=None):
             profile, xname=xname, yname=yname, dyname=dyname
         )
 
-    def addProfileGenerator(self, gen, name=None):
+    def add_profile_generator(self, gen, name=None):
         """Add a ProfileGenerator to be used by this FitContribution.
 
         The ProfileGenerator is given a name so that it can be used as part of
@@ -223,6 +230,18 @@ def addProfileGenerator(self, gen, name=None):
 
         return
 
+    @deprecated(addprofilegenerator_dep_msg)
+    def addProfileGenerator(self, gen, name=None):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use
+        diffpy.srfit.fitbase.FitContribution.add_profile_generator
+        instead.
+        """
+        self.add_profile_generator(gen, name=name)
+        return
+
     def setEquation(self, eqstr, ns={}):
         """Set the profile equation for the FitContribution.
 
diff --git a/src/diffpy/srfit/pdf/pdfcontribution.py b/src/diffpy/srfit/pdf/pdfcontribution.py
@@ -273,7 +273,7 @@ def _setup_generator(self, gen):
         with setStructure or setPhase.
         """
         # Add the generator to this FitContribution
-        self.addProfileGenerator(gen)
+        self.add_profile_generator(gen)
 
         # Set the proper equation for the fit, depending on the number of
         # phases we have.
diff --git a/tests/test_contribution.py b/tests/test_contribution.py
@@ -67,6 +67,18 @@ def testAddProfileGenerator(self):
         self.assertTrue(fc._eq is not None)
         return
 
+    def test_add_profile_generator(self):
+        fc = self.fitcontribution
+        gen = self.gen
+        fc.add_profile_generator(gen, "gen")
+
+        xobs = arange(0, 10, 0.5)
+        self.assertTrue(array_equal(xobs, gen(xobs)))
+
+        self.assertTrue(gen.profile is None)
+        self.assertTrue(fc._eq is not None)
+        return
+
     def testInteraction(self):
         """Test the interaction between the profile and profile generator."""
         fc = self.fitcontribution
@@ -75,7 +87,7 @@ def testInteraction(self):
 
         # Add the calculator and profile
         fc.set_profile(profile)
-        fc.addProfileGenerator(gen, "I")
+        fc.add_profile_generator(gen, "I")
 
         # Check attributes are created
         self.assertTrue(fc.profile is profile)
@@ -120,7 +132,7 @@ def testReplacements(self):
 
         # Validate equations
         fc.set_profile(profile)
-        fc.addProfileGenerator(gen, "I")
+        fc.add_profile_generator(gen, "I")
         self.assertTrue(array_equal(gen.value, xobs))
         self.assertTrue(array_equal(fc._eq(), xobs))
         self.assertAlmostEqual(0, sum(fc._reseq()))
@@ -196,7 +208,7 @@ def testResidual(noObserversInGlobalBuilders):
     # Add the calculator and profile
     fc.set_profile(profile)
     assert fc.profile is profile
-    fc.addProfileGenerator(gen, "I")
+    fc.add_profile_generator(gen, "I")
     assert fc._eq._value is None
     assert fc._reseq._value is None
     assert 1 == len(fc._generators)
