fix: replace deprecated srfit pdf/structure API in examples

docs/examples/core/intensityfit/npintensity.py

@@ -47,14 +47,14 @@
 import numpy
 
 from diffpy.cmi.fit_tools import optimize_recipe
+from diffpy.cmistructure.diffpyparset import DiffpyStructureParSet
 from diffpy.srfit.fitbase import (
     FitContribution,
     FitRecipe,
     FitResults,
     Profile,
     ProfileGenerator,
 )
-from diffpy.srfit.structure.diffpyparset import DiffpyStructureParSet
 
 ######
 #  Example Code
@@ -103,7 +103,7 @@ def set_structure(self, strufile):
                         function whenever it is called.
 
         This will create the refinement Parameters using the
-        DiffpyStructureParSet adapter from diffpy.srfit.structure.diffpyparset.
+        DiffpyStructureParSet adapter from diffpy.cmistructure.diffpyparset.
         DiffpyStructureParSet is a ParameterSet object that organizes and gives
         attribute access to Parameters and ParameterSets adapted from a diffpy
         Structure object.  The Parameters embedded in the DiffpyStructureParSet
@@ -113,14 +113,14 @@ def set_structure(self, strufile):
         are organized hierarchically:
 
         phase
-          - lattice (retrieved with 'getLattice')
+          - lattice (retrieved with 'get_lattice')
             - a
             - b
             - c
             - alpha
             - beta
             - gamma
-          - scatterers (retrieved with 'getScatterers')
+          - scatterers (retrieved with 'get_scatterers')
             - atom1 (the name depends on the element)
               - x
               - y
@@ -136,7 +136,7 @@ def set_structure(self, strufile):
             - etc.
 
         The diffpy.structure.Structure instance is held within the
-        DiffpyStructureParSet as the 'stru' attribute.
+        DiffpyStructureParSet as the 'structure' attribute.
         """
         # Load the structure from file
         from diffpy.structure import Structure
@@ -170,7 +170,7 @@ def __call__(self, q):
         """
         self.count += 1
         print("iofq called", self.count)
-        return iofq(self.phase.stru, q)
+        return iofq(self.phase.structure, q)
 
 
 # End class IntensityGenerator
@@ -287,7 +287,7 @@ def gaussian(q, q0, width):
     # parameters to the same value (the lattice is cubic). Note that we
     # constrain to the "a" Parameter directly. In previous examples, we
     # constrained to a Variable by name. This has the same effect.
-    lattice = phase.getLattice()
+    lattice = phase.get_lattice()
     a = lattice.a
     recipe.add_variable(a)
     recipe.add_constraint(lattice.b, a)
@@ -297,7 +297,7 @@ def gaussian(q, q0, width):
     # this. Note that we don't give Uiso an initial value. The initial value
     # will be inferred from the following constraints.
     Uiso = recipe.create_new_variable("Uiso")
-    for atom in phase.getScatterers():
+    for atom in phase.get_scatterers():
         recipe.add_constraint(atom.Uiso, Uiso)
 
     # Give the recipe away so it can be used!

docs/examples/core/intensityfit/npintensityII.py

@@ -171,7 +171,7 @@ def gaussian(q, q0, width):
     # We can also refine structural parameters. We only have to do this once,
     # since each generator holds the same DiffpyStructureParSet.
     phase = generator1.phase
-    lattice = phase.getLattice()
+    lattice = phase.get_lattice()
     a = recipe.add_variable(lattice.a)
     # We want to allow for isotropic expansion, so we'll make constraints for
     # that.
@@ -182,7 +182,7 @@ def gaussian(q, q0, width):
     # this. Note that we don't give Uiso an initial value. The initial value
     # will be inferred from the subsequent constraints.
     Uiso = recipe.create_new_variable("Uiso")
-    for atom in phase.getScatterers():
+    for atom in phase.get_scatterers():
         recipe.add_constraint(atom.Uiso, Uiso)
 
     # Give the recipe away so it can be used!

docs/examples/pdf/ch03NiModelling/exercises/diffpy-cmi/fitBulkNi.ipynb

@@ -63,9 +63,9 @@
     "from diffpy.srfit.fitbase import FitContribution, FitRecipe\n",
     "from diffpy.srfit.fitbase import FitResults\n",
     "from diffpy.srfit.fitbase import Profile\n",
-    "from diffpy.srfit.pdf import PDFParser, PDFGenerator\n",
+    "from diffpy.cmipdf import PDFParser, PDFGenerator\n",
     "from diffpy.structure.parsers import get_parser\n",
-    "from diffpy.srfit.structure import constrain_as_space_group"
+    "from diffpy.cmistructure import constrain_as_space_group"
    ]
   },
   {
@@ -311,7 +311,7 @@
     "    # This Generator will later compute the model PDF for the structure\n",
     "    # object we provide it here.\n",
     "    generator_crystal1 = PDFGenerator(\"G1\")\n",
-    "    generator_crystal1.setStructure(stru1, periodic=True)\n",
+    "    generator_crystal1.set_structure(stru1, periodic=True)\n",
     "\n",
     "    # 12: Create a Fit Contribution object, and arbitrarily name it 'crystal'.\n",
     "    # We then give the PDF Generator object we created just above\n",
@@ -363,8 +363,8 @@
     "    # below '.value = ' syntax.\n",
     "    recipe.crystal.G1.qdamp.value = QDAMP_I\n",
     "    recipe.crystal.G1.qbroad.value = QBROAD_I\n",
-    "    recipe.crystal.G1.setQmax(QMAX)\n",
-    "    recipe.crystal.G1.setQmin(QMIN)\n",
+    "    recipe.crystal.G1.set_qmax(QMAX)\n",
+    "    recipe.crystal.G1.set_qmin(QMIN)\n",
     "\n",
     "    # 17: Add a variable to the Fit Recipe object, initialize the variables\n",
     "    # with some value, and tag it with an arbitrary string. Here we add the scale\n",

docs/examples/pdf/ch03NiModelling/exercises/diffpy-cmi/fitNPPt.ipynb

@@ -47,10 +47,10 @@
    "outputs": [],
    "source": [
     "from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile\n",
-    "from diffpy.srfit.pdf import PDFParser, PDFGenerator\n",
+    "from diffpy.cmipdf import PDFParser, PDFGenerator\n",
     "from diffpy.structure.parsers import get_parser\n",
-    "from diffpy.srfit.pdf.characteristicfunctions import spherical_particle\n",
-    "from diffpy.srfit.structure import constrain_as_space_group"
+    "from diffpy.cmipdf.characteristicfunctions import spherical_particle\n",
+    "from diffpy.cmistructure import constrain_as_space_group"
    ]
   },
   {
@@ -273,7 +273,7 @@
     "\n",
     "    # 12: Create a PDF Generator object for a periodic structure model.\n",
     "    generator_crystal1 = PDFGenerator(\"G1\")\n",
-    "    generator_crystal1.setStructure(stru1, periodic=True)\n",
+    "    generator_crystal1.set_structure(stru1, periodic=True)\n",
     "\n",
     "    # 13: Create a Fit Contribution object.\n",
     "    contribution = FitContribution(\"crystal\")\n",
@@ -312,8 +312,8 @@
     "    # assign Q_max and Q_min.\n",
     "    generator_crystal1.qdamp.value = QDAMP_I\n",
     "    generator_crystal1.qbroad.value = QBROAD_I\n",
-    "    generator_crystal1.setQmax(QMAX)\n",
-    "    generator_crystal1.setQmin(QMIN)\n",
+    "    generator_crystal1.set_qmax(QMAX)\n",
+    "    generator_crystal1.set_qmin(QMIN)\n",
     "\n",
     "    # 18: Add, initialize, and tag variables in the Fit Recipe object.\n",
     "    # In this case we also add 'psize', which is the NP size.\n",

docs/examples/pdf/ch03NiModelling/solutions/diffpy-cmi/fitBulkNi.py

@@ -15,14 +15,14 @@
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
+from diffpy.cmipdf import PDFGenerator, PDFParser
+from diffpy.cmistructure import constrain_as_space_group
 from diffpy.srfit.fitbase import (
     FitContribution,
     FitRecipe,
     FitResults,
     Profile,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.structure import constrain_as_space_group
 from diffpy.structure.parsers import get_parser
 
 plt.style.use(all_styles["bg-style"])
@@ -116,7 +116,7 @@ def make_recipe(cif_path, dat_path):
     # This Generator will later compute the model PDF for the structure
     # object we provide it here.
     generator_crystal1 = PDFGenerator("G1")
-    generator_crystal1.setStructure(stru1, periodic=True)
+    generator_crystal1.set_structure(stru1, periodic=True)
 
     # 12: Create a Fit Contribution object, and arbitrarily name it 'crystal'.
     # We then give the PDF Generator object we created just above
@@ -173,8 +173,8 @@ def make_recipe(cif_path, dat_path):
     # below '.value = ' syntax.
     recipe.crystal.G1.qdamp.value = QDAMP_I
     recipe.crystal.G1.qbroad.value = QBROAD_I
-    recipe.crystal.G1.setQmax(QMAX)
-    recipe.crystal.G1.setQmin(QMIN)
+    recipe.crystal.G1.set_qmax(QMAX)
+    recipe.crystal.G1.set_qmin(QMIN)
 
     # 17: Add a variable to the Fit Recipe object, initialize the variables
     # with some value, and tag it with an arbitrary string. Here we add the

docs/examples/pdf/ch03NiModelling/solutions/diffpy-cmi/fitBulkNi_NPPt_soln2.ipynb

@@ -55,14 +55,14 @@
     "\n",
     "from diffpy.utils.parsers.loaddata import loadData\n",
     "from diffpy.srfit.fitbase import FitRecipe, FitContribution, Profile, FitResults\n",
-    "from diffpy.srfit.pdf import PDFGenerator, PDFParser\n",
+    "from diffpy.cmipdf import PDFGenerator, PDFParser\n",
     "from diffpy.srfit.fitbase.parameterset import ParameterSet\n",
     "from pyobjcryst import loadCrystal\n",
     "from pyobjcryst.crystal import Crystal\n",
     "\n",
     "#We import the form factors. We will use this to fit the Pt nanoparticles as spherical particles.\n",
-    "import diffpy.srfit.pdf.characteristicfunctions\n",
-    "F = diffpy.srfit.pdf.characteristicfunctions"
+    "import diffpy.cmipdf.characteristicfunctions\n",
+    "F = diffpy.cmipdf.characteristicfunctions"
    ]
   },
   {
@@ -123,7 +123,7 @@
     "    fc = FitContribution(fc_name)\n",
     "    for name, crystal in crystals.items():\n",
     "        pg = PDFGenerator(name)\n",
-    "        pg.setStructure(crystal, periodic=True)\n",
+    "        pg.set_structure(crystal, periodic=True)\n",
     "        fc.add_profile_generator(pg)\n",
     "    for name, (f, argnames) in functions.items():\n",
     "        fc.register_function(f, name=name, argnames=argnames)\n",
@@ -236,7 +236,7 @@
     "            fixed=True,\n",
     "            tags=_get_tags(name, \"lat\")\n",
     "        ).bound_range(0.)\n",
-    "    atoms: typing.List[ParameterSet] = pg.phase.getScatterers()\n",
+    "    atoms: typing.List[ParameterSet] = pg.phase.get_scatterers()\n",
     "    for atom in atoms:\n",
     "        par = atom.Biso\n",
     "        recipe.add_variable(\n",
@@ -537,7 +537,7 @@
     "    if pg_names is not None:\n",
     "        for pg_name in pg_names:\n",
     "            pg: PDFGenerator = getattr(fc, pg_name)\n",
-    "            stru: Crystal = pg.stru\n",
+    "            stru: Crystal = pg.structure\n",
     "            cif_path = f_path.with_name(\n",
     "                \"{}_{}\".format(f_path.stem, pg_name)\n",
     "            ).with_suffix(\".cif\")\n",

docs/examples/pdf/ch03NiModelling/solutions/diffpy-cmi/fitNPPt.py

@@ -19,15 +19,15 @@
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
+from diffpy.cmipdf import PDFGenerator, PDFParser
+from diffpy.cmipdf.characteristicfunctions import spherical_particle
+from diffpy.cmistructure import constrain_as_space_group
 from diffpy.srfit.fitbase import (
     FitContribution,
     FitRecipe,
     FitResults,
     Profile,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.pdf.characteristicfunctions import spherical_particle
-from diffpy.srfit.structure import constrain_as_space_group
 from diffpy.structure.parsers import get_parser
 
 plt.style.use(all_styles["bg-style"])
@@ -126,7 +126,7 @@ def make_recipe(cif_path, dat_path):
 
     # 12: Create a PDF Generator object for a periodic structure model.
     generator_crystal1 = PDFGenerator("G1")
-    generator_crystal1.setStructure(stru1, periodic=True)
+    generator_crystal1.set_structure(stru1, periodic=True)
 
     # 13: Create a Fit Contribution object.
     contribution = FitContribution("crystal")
@@ -172,8 +172,8 @@ def make_recipe(cif_path, dat_path):
     # assign Q_max and Q_min.
     generator_crystal1.qdamp.value = QDAMP_I
     generator_crystal1.qbroad.value = QBROAD_I
-    generator_crystal1.setQmax(QMAX)
-    generator_crystal1.setQmin(QMIN)
+    generator_crystal1.set_qmax(QMAX)
+    generator_crystal1.set_qmin(QMIN)
 
     # 18: Add, initialize, and tag variables in the Fit Recipe object.
     # In this case we also add 'psize', which is the NP size.

docs/examples/pdf/ch03NiModelling/solutions/diffpy-cmi/helper_functions.py

@@ -5,14 +5,14 @@
 from pyobjcryst.crystal import Crystal
 from scipy.optimize import least_squares
 
+from diffpy.cmipdf import PDFGenerator, PDFParser
 from diffpy.srfit.fitbase import (
     FitContribution,
     FitRecipe,
     FitResults,
     Profile,
 )
 from diffpy.srfit.fitbase.parameterset import ParameterSet
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
 
 
 # Recipe functions
@@ -51,7 +51,7 @@ def _create_recipe(
     fc = FitContribution(fc_name)
     for name, crystal in crystals.items():
         pg = PDFGenerator(name)
-        pg.setStructure(crystal, periodic=True)
+        pg.set_structure(crystal, periodic=True)
         fc.add_profile_generator(pg)
     for name, (f, argnames) in functions.items():
         fc.register_function(f, name=name, argnames=argnames)
@@ -162,7 +162,7 @@ def _add_params_in_pg(recipe: FitRecipe, pg: PDFGenerator) -> None:
             fixed=True,
             tags=_get_tags(name, "lat"),
         ).bound_range(0.0)
-    atoms: typing.List[ParameterSet] = pg.phase.getScatterers()
+    atoms: typing.List[ParameterSet] = pg.phase.get_scatterers()
     for atom in atoms:
         par = atom.Biso
         recipe.add_variable(
@@ -435,7 +435,7 @@ def save_results(
     if pg_names is not None:
         for pg_name in pg_names:
             pg: PDFGenerator = getattr(fc, pg_name)
-            stru: Crystal = pg.stru
+            stru: Crystal = pg.structure
             cif_path = f_path.with_name(
                 "{}_{}".format(f_path.stem, pg_name)
             ).with_suffix(".cif")

docs/examples/pdf/ch05Fit2Phase/solutions/diffpy-cmi/fit2P.py

@@ -16,14 +16,14 @@
 from scipy.optimize import least_squares
 
 # ... and the relevant CMI packages
+from diffpy.cmipdf import PDFGenerator, PDFParser
+from diffpy.cmistructure import constrain_as_space_group
 from diffpy.srfit.fitbase import (
     FitContribution,
     FitRecipe,
     FitResults,
     Profile,
 )
-from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.structure import constrain_as_space_group
 from diffpy.structure.parsers import get_parser
 
 plt.style.use(all_styles["bg-style"])
@@ -109,12 +109,12 @@ def make_recipe(cif_path1, cif_path2, dat_path):
     # 11a: Create a PDF Generator object for a periodic structure model
     # of phase 1.
     generator_crystal1 = PDFGenerator("G_Si")
-    generator_crystal1.setStructure(stru1, periodic=True)
+    generator_crystal1.set_structure(stru1, periodic=True)
 
     # 11b: Create a PDF Generator object for a periodic structure model
     # of phase 2.
     generator_crystal2 = PDFGenerator("G_Ni")
-    generator_crystal2.setStructure(stru2, periodic=True)
+    generator_crystal2.set_structure(stru2, periodic=True)
 
     # 12: Create a Fit Contribution object. This is new, as we
     # need to tell the Fit Contribution about BOTH the phase
@@ -192,8 +192,8 @@ def make_recipe(cif_path1, cif_path2, dat_path):
         # assign Q_max and Q_min for each phase.
         generator.qdamp.value = QDAMP_I
         generator.qbroad.value = QBROAD_I
-        generator.setQmax(QMAX)
-        generator.setQmin(QMIN)
+        generator.set_qmax(QMAX)
+        generator.set_qmin(QMIN)
 
         # 18c: Get the symmetry equivalent parameters for each phase.
         spacegroupparams = constrain_as_space_group(