Merge pull request #147 from cadenmyers13/addcontrib-dep

sbillinge · web-flow · commit a1f1f49f884a · 2026-02-06T17:18:55.000-08:00
deprecate: `addContribution` deprecation
diff --git a/docs/examples/coreshellnp.py b/docs/examples/coreshellnp.py
@@ -85,7 +85,7 @@ def makeRecipe(stru1, stru2, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Vary the inner radius and thickness of the shell. Constrain the core
     # diameter to twice the shell radius.
diff --git a/docs/examples/crystalpdf.py b/docs/examples/crystalpdf.py
@@ -79,7 +79,7 @@ def makeRecipe(ciffile, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
 
diff --git a/docs/examples/crystalpdfall.py b/docs/examples/crystalpdfall.py
@@ -104,10 +104,10 @@ def makeRecipe(
 
     # Make the FitRecipe and add the FitContributions.
     recipe = FitRecipe()
-    recipe.addContribution(xcontribution_ni)
-    recipe.addContribution(xcontribution_si)
-    recipe.addContribution(ncontribution_ni)
-    recipe.addContribution(xcontribution_sini)
+    recipe.add_contribution(xcontribution_ni)
+    recipe.add_contribution(xcontribution_si)
+    recipe.add_contribution(ncontribution_ni)
+    recipe.add_contribution(xcontribution_sini)
 
     # Now we vary and constrain Parameters as before.
     for par in phase_ni.sgpars:
diff --git a/docs/examples/crystalpdfobjcryst.py b/docs/examples/crystalpdfobjcryst.py
@@ -67,7 +67,7 @@ def makeRecipe(ciffile, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
 
diff --git a/docs/examples/crystalpdftwodata.py b/docs/examples/crystalpdftwodata.py
@@ -110,8 +110,8 @@ def makeRecipe(ciffile, xdatname, ndatname):
 
     # Make the FitRecipe and add the FitContributions.
     recipe = FitRecipe()
-    recipe.addContribution(xcontribution)
-    recipe.addContribution(ncontribution)
+    recipe.add_contribution(xcontribution)
+    recipe.add_contribution(ncontribution)
 
     # Now we vary and constrain Parameters as before.
     recipe.addVar(xgenerator.scale, 1, "xscale")
diff --git a/docs/examples/crystalpdftwophase.py b/docs/examples/crystalpdftwophase.py
@@ -84,7 +84,7 @@ def makeRecipe(niciffile, siciffile, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
     # Start by configuring the scale factor and resolution factors.
diff --git a/docs/examples/debyemodel.py b/docs/examples/debyemodel.py
@@ -134,7 +134,7 @@ def makeRecipe():
     # to fit simultaneously, the contribution from each could be added to the
     # recipe.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Specify which Parameters we want to refine.
 
diff --git a/docs/examples/debyemodelII.py b/docs/examples/debyemodelII.py
@@ -71,8 +71,8 @@ def makeRecipeII():
     # Now create a fresh FitRecipe to work with and add to it the two
     # FitContributions.
     recipe = FitRecipe()
-    recipe.addContribution(lowT)
-    recipe.addContribution(highT)
+    recipe.add_contribution(lowT)
+    recipe.add_contribution(highT)
 
     # Change the fit ranges of the Profiles embedded within the
     # FitContributions. We want to fit one of the contributions at low
diff --git a/docs/examples/ellipsoidsas.py b/docs/examples/ellipsoidsas.py
@@ -68,7 +68,7 @@ def makeRecipe(datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
     # The SASGenerator uses the parameters from the params and dispersion
diff --git a/docs/examples/gaussiangenerator.py b/docs/examples/gaussiangenerator.py
@@ -150,7 +150,7 @@ def makeRecipe():
     # The FitRecipe
     # Now we create the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Specify which Parameters we want to vary in the fit.  This will add
     # Variables to the FitRecipe that directly modify the Parameters of the
diff --git a/docs/examples/gaussianrecipe.py b/docs/examples/gaussianrecipe.py
@@ -140,7 +140,7 @@ def makeRecipe():
     # Here we tell the FitRecipe to use our FitContribution. When the FitRecipe
     # calculates its residual function, it will call on the FitContribution to
     # do part of the work.
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Specify which Parameters we want to vary in the fit.  This will add
     # Variables to the FitRecipe that directly modify the Parameters of the
diff --git a/docs/examples/npintensity.py b/docs/examples/npintensity.py
@@ -260,7 +260,7 @@ def gaussian(q, q0, width):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Specify which parameters we want to refine.
     recipe.addVar(contribution.b0, 0)
diff --git a/docs/examples/npintensityII.py b/docs/examples/npintensityII.py
@@ -130,8 +130,8 @@ def gaussian(q, q0, width):
 
     # Make a FitRecipe and associate the FitContributions.
     recipe = FitRecipe()
-    recipe.addContribution(contribution1)
-    recipe.addContribution(contribution2)
+    recipe.add_contribution(contribution1)
+    recipe.add_contribution(contribution2)
 
     # Specify which Parameters we want to refine. We want to refine the
     # background that we just defined in the FitContributions. We have to do
diff --git a/docs/examples/nppdfcrystal.py b/docs/examples/nppdfcrystal.py
@@ -67,7 +67,7 @@ def makeRecipe(ciffile, grdata):
     # Now make the recipe. Make sure we fit the characteristic function shape
     # parameters, in this case 'psize', which is the diameter of the particle.
     recipe = FitRecipe()
-    recipe.addContribution(pdfcontribution)
+    recipe.add_contribution(pdfcontribution)
 
     phase = pdfgenerator.phase
     for par in phase.sgpars:
diff --git a/docs/examples/nppdfobjcryst.py b/docs/examples/nppdfobjcryst.py
@@ -57,7 +57,7 @@ def makeRecipe(molecule, datname):
 
     # Make a FitRecipe.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Specify which parameters we want to refine. We'll be using the
     # MoleculeParSet within the generator, so let's get a handle to it. See the
diff --git a/docs/examples/nppdfsas.py b/docs/examples/nppdfsas.py
@@ -93,8 +93,8 @@ def makeRecipe(ciffile, grdata, iqdata):
 
     # Moving on
     recipe = FitRecipe()
-    recipe.addContribution(pdfcontribution)
-    recipe.addContribution(sascontribution)
+    recipe.add_contribution(pdfcontribution)
+    recipe.add_contribution(sascontribution)
 
     # PDF
     phase = pdfgenerator.phase
diff --git a/docs/examples/simplepdf.py b/docs/examples/simplepdf.py
@@ -44,7 +44,7 @@ def makeRecipe(ciffile, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
     phase = contribution.nickel.phase
diff --git a/docs/examples/simplepdftwophase.py b/docs/examples/simplepdftwophase.py
@@ -41,7 +41,7 @@ def makeRecipe(niciffile, siciffile, datname):
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
     # Start by configuring the scale factor and resolution factors.
diff --git a/docs/examples/threedoublepeaks.py b/docs/examples/threedoublepeaks.py
@@ -98,7 +98,7 @@ def delta(t, mu):
     # Here we tell the FitRecipe to use our FitContribution. When the FitRecipe
     # calculates its residual function, it will call on the FitContribution to
     # do part of the work.
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Vary the amplitudes for each double peak
     recipe.addVar(contribution.A1, 100)
diff --git a/news/addcontrib-dep.rst b/news/addcontrib-dep.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Added ``add_contribution`` in replace of ``addContribution``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``addContribution`` for removal in 4.0.0.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/diffpy/srfit/fitbase/fitrecipe.py b/src/diffpy/srfit/fitbase/fitrecipe.py
@@ -45,9 +45,16 @@
 from diffpy.srfit.fitbase.recipeorganizer import RecipeOrganizer
 from diffpy.srfit.interface import _fitrecipe_interface
 from diffpy.srfit.util.tagmanager import TagManager
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
 
 plt.style.use(all_styles["bg-style"])
 
+base = "diffpy.srfit.fitbase.FitRecipe"
+removal_version = "4.0.0"
+addcontrib_dep_msg = build_deprecation_message(
+    base, "addContribution", "add_contribution", removal_version
+)
+
 
 class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
     """FitRecipe class.
@@ -238,7 +245,7 @@ def clearFitHooks(self):
         del self.fithooks[:]
         return
 
-    def addContribution(self, con, weight=1.0):
+    def add_contribution(self, con, weight=1.0):
         """Add a FitContribution to the FitRecipe.
 
         Attributes
@@ -255,6 +262,17 @@ def addContribution(self, con, weight=1.0):
         self._weights.append(weight)
         return
 
+    @deprecated(addcontrib_dep_msg)
+    def addContribution(self, con, weight=1.0):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.add_contribution
+        instead.
+        """
+        self.add_contribution(con, weight)
+        return
+
     def setWeight(self, con, weight):
         """Set the weight of a FitContribution."""
         idx = list(self._contributions.values()).index(con)
diff --git a/src/diffpy/srfit/fitbase/simplerecipe.py b/src/diffpy/srfit/fitbase/simplerecipe.py
@@ -94,7 +94,7 @@ def __init__(self, name="fit", conclass=FitContribution):
         contribution = conclass("contribution")
         self.profile = Profile()
         contribution.set_profile(self.profile)
-        self.addContribution(contribution)
+        self.add_contribution(contribution)
         self.results = FitResults(self, update=False)
 
         # Adopt all the FitContribution methods
diff --git a/src/diffpy/srfit/interface/interface.py b/src/diffpy/srfit/interface/interface.py
@@ -115,7 +115,7 @@ def __ior__(self, args):
 
         This accepts a single argument.
         """
-        self.addContribution(args)
+        self.add_contribution(args)
         return self
 
     def __iadd__(self, args):
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -157,7 +157,7 @@ def build_recipe_one_contribution():
     contribution.set_profile(profile)
     contribution.setEquation("A*sin(k*x + c)")
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
     recipe.addVar(contribution.A, 1)
     recipe.addVar(contribution.k, 1)
     recipe.addVar(contribution.c, 1)
@@ -182,8 +182,8 @@ def build_recipe_two_contributions():
     contribution2.set_profile(profile2)
     contribution2.setEquation("B*sin(m*x + d)")
     recipe = FitRecipe()
-    recipe.addContribution(contribution1)
-    recipe.addContribution(contribution2)
+    recipe.add_contribution(contribution1)
+    recipe.add_contribution(contribution2)
     recipe.addVar(contribution1.A, 1)
     recipe.addVar(contribution1.k, 1)
     recipe.addVar(contribution1.c, 1)
diff --git a/tests/test_fitrecipe.py b/tests/test_fitrecipe.py
@@ -51,7 +51,7 @@ def setUp(self):
         self.fitcontribution.k.setValue(1)
         self.fitcontribution.c.setValue(0)
 
-        self.recipe.addContribution(self.fitcontribution)
+        self.recipe.add_contribution(self.fitcontribution)
         return
 
     def testFixFree(self):
@@ -291,6 +291,54 @@ def testPrintFitHook(capturestdout):
     return
 
 
+def test_add_contribution(capturestdout):
+    """Duplicated test of PrintFitHooks except addContribution method has
+    changed to the new add_contribution method. This is because addContribution
+    is deprecated.
+
+    Remove this test after addContribution is removed and update
+    testPrintFitHook to use add_contribution instead of addContribution.
+    """
+    recipe = FitRecipe("recipe")
+    recipe.fithooks[0].verbose = 0
+
+    # Set up the Profile
+    profile = Profile()
+    x = linspace(0, pi, 10)
+    y = sin(x)
+    profile.setObservedProfile(x, y)
+
+    # Set up the FitContribution
+    fitcontribution = FitContribution("cont")
+    fitcontribution.set_profile(profile)
+    fitcontribution.setEquation("A*sin(k*x + c)")
+    fitcontribution.A.setValue(1)
+    fitcontribution.k.setValue(1)
+    fitcontribution.c.setValue(0)
+
+    recipe.add_contribution(fitcontribution)
+
+    recipe.addVar(fitcontribution.c)
+    recipe.restrain("c", lb=5)
+    (pfh,) = recipe.getFitHooks()
+    out = capturestdout(recipe.scalarResidual)
+    assert "" == out
+    pfh.verbose = 1
+    out = capturestdout(recipe.scalarResidual)
+    assert out.strip().isdigit()
+    assert "\nRestraints:" not in out
+    pfh.verbose = 2
+    out = capturestdout(recipe.scalarResidual)
+    assert "\nResidual:" in out
+    assert "\nRestraints:" in out
+    assert "\nVariables" not in out
+    pfh.verbose = 3
+    out = capturestdout(recipe.scalarResidual)
+    assert "\nVariables" in out
+    assert "c = " in out
+    return
+
+
 def optimize_recipe(recipe):
     recipe.fithooks[0].verbose = 0
     residuals = recipe.residual
@@ -327,7 +375,7 @@ def build_recipe_from_datafile(datafile):
     contribution.set_profile(profile)
     contribution.setEquation("m*x + b")
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
     recipe.addVar(contribution.m, 1)
     recipe.addVar(contribution.b, 0)
     return recipe
