Merge branch 'v3.3.0' of github.com:diffpy/diffpy.srfit into setequation-dep

Author: cadenmyers13

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -1,9 +1,6 @@
 name: CI
 
 on:
-  push:
-    branches:
-      - main
   release:
     types:
       - prereleased

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
@@ -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.

docs/examples/crystalpdf.py

@@ -74,12 +74,12 @@ 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.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
 

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.set_equation("scale * (xG_sini_ni +  xG_sini_si)")
 
     # As explained in another example, we want to minimize using Rw^2.
@@ -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:

docs/examples/crystalpdfobjcryst.py

@@ -62,12 +62,12 @@ 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.
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
 
     # Configure the fit variables
 

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
@@ -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")

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
@@ -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.

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.
 

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

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
@@ -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