dep & test: Replace deprecated functions and add tests for interface.py

docs/examples/coreshellnp.py

@@ -22,7 +22,7 @@
 
 from pathlib import Path
 
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 from scipy.optimize import leastsq
 
 from diffpy.srfit.fitbase import (
@@ -94,7 +94,7 @@ def makeRecipe(stru1, stru2, datname):
     # diameter to twice the shell radius.
     recipe.add_variable(contribution.radius, 15)
     recipe.add_variable(contribution.thickness, 11)
-    recipe.add_constraint(contribution.psize, "2 * radius")
+    recipe.add_constraint(contribution.particle_diameter, "2 * radius")
 
     # Configure the fit variables
     # Start by configuring the scale factor and resolution factors.
@@ -152,8 +152,8 @@ def main():
     data = Path(__file__).parent / "data/CdS_ZnS_nano.gr"
 
     # Make the recipe
-    stru1 = loadCrystal(cdsciffile)
-    stru2 = loadCrystal(znsciffile)
+    stru1 = create_crystal_from_cif(str(cdsciffile))
+    stru2 = create_crystal_from_cif(str(znsciffile))
     recipe = makeRecipe(stru1, stru2, data)
     from diffpy.srfit.fitbase.fithook import PlotFitHook
 

docs/examples/crystalpdfall.py

@@ -21,7 +21,7 @@
 from pathlib import Path
 
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -67,12 +67,12 @@ def makeRecipe(
     # The ProfileGenerators
     # We create one for each phase and share the phases.
     xgenerator_ni = PDFGenerator("xG_ni")
-    stru = loadCrystal(ciffile_ni)
+    stru = create_crystal_from_cif(str(ciffile_ni))
     xgenerator_ni.setStructure(stru)
     phase_ni = xgenerator_ni.phase
 
     xgenerator_si = PDFGenerator("xG_si")
-    stru = loadCrystal(ciffile_si)
+    stru = create_crystal_from_cif(str(ciffile_si))
     xgenerator_si.setStructure(stru)
     phase_si = xgenerator_si.phase
 

docs/examples/crystalpdfobjcryst.py

@@ -22,7 +22,7 @@
 from pathlib import Path
 
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -56,7 +56,7 @@ def makeRecipe(ciffile, datname):
     # create a Crystal object. That object is passed to the PDFGenerator as in
     # the previous example.
     generator = PDFGenerator("G")
-    stru = loadCrystal(ciffile)
+    stru = create_crystal_from_cif(str(ciffile))
     generator.setStructure(stru)
     generator.setQmax(40.0)
 

docs/examples/crystalpdftwodata.py

@@ -23,7 +23,7 @@
 from pathlib import Path
 
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -59,7 +59,7 @@ def makeRecipe(ciffile, xdatname, ndatname):
     # The ProfileGenerators
     # We need one of these for the x-ray data.
     xgenerator = PDFGenerator("G")
-    stru = loadCrystal(ciffile)
+    stru = create_crystal_from_cif(str(ciffile))
     xgenerator.setStructure(stru)
 
     # And we need one for the neutron data. We want to refine the same

docs/examples/crystalpdftwophase.py

@@ -23,7 +23,7 @@
 from pathlib import Path
 
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -61,11 +61,11 @@ def makeRecipe(niciffile, siciffile, datname):
     # The generator for the nickel phase. We call it "G_ni" and will use this
     # name later when we set the fitting equation in the FitContribution.
     generator_ni = PDFGenerator("G_ni")
-    stru = loadCrystal(niciffile)
+    stru = create_crystal_from_cif(str(niciffile))
     generator_ni.setStructure(stru)
     # The generator for the silicon phase. We call it "G_si".
     generator_si = PDFGenerator("G_si")
-    stru = loadCrystal(siciffile)
+    stru = create_crystal_from_cif(str(siciffile))
     generator_si.setStructure(stru)
 
     # The FitContribution

docs/examples/gaussianrecipe.py

@@ -172,7 +172,7 @@ def scipyOptimize(recipe):
     # scipy. We simply have to give it the function to minimize
     # (recipe.residual) and the starting values of the Variables
     # (recipe.get_values()).
-    from scipy.optimize.minpack import leastsq
+    from scipy.optimize import leastsq
 
     print("Fit using scipy's LM optimizer")
     leastsq(recipe.residual, recipe.get_values())

docs/examples/nppdfcrystal.py

@@ -27,7 +27,7 @@
 
 import matplotlib.pyplot as plt
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -53,7 +53,7 @@ def makeRecipe(ciffile, grdata):
 
     pdfgenerator = PDFGenerator("G")
     pdfgenerator.setQmax(30.0)
-    stru = loadCrystal(ciffile)
+    stru = create_crystal_from_cif(str(ciffile))
     pdfgenerator.setStructure(stru)
     pdfcontribution.add_profile_generator(pdfgenerator)
 
@@ -66,15 +66,15 @@ def makeRecipe(ciffile, grdata):
     pdfcontribution.set_equation("f * G")
 
     # Now make the recipe. Make sure we fit the characteristic function shape
-    # parameters, in this case 'psize', which is the diameter of the particle.
+    # parameters, in this case 'particle_diameter'.
     recipe = FitRecipe()
     recipe.add_contribution(pdfcontribution)
 
     phase = pdfgenerator.phase
     for par in phase.sgpars:
         recipe.add_variable(par)
 
-    recipe.add_variable(pdfcontribution.psize, 20)
+    recipe.add_variable(pdfcontribution.particle_diameter, 20)
     recipe.add_variable(pdfgenerator.scale, 1)
     recipe.add_variable(pdfgenerator.delta2, 0)
     recipe.B11_0 = 0.1

docs/examples/nppdfsas.py

@@ -26,7 +26,7 @@
 
 import matplotlib.pyplot as plt
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import (
     FitContribution,
@@ -58,7 +58,7 @@ def makeRecipe(ciffile, grdata, iqdata):
 
     pdfgenerator = PDFGenerator("G")
     pdfgenerator.setQmax(30.0)
-    stru = loadCrystal(ciffile)
+    stru = create_crystal_from_cif(str(ciffile))
     pdfgenerator.setStructure(stru)
     pdfcontribution.add_profile_generator(pdfgenerator)
     pdfcontribution.set_residual_equation("resv")

docs/examples/simplepdftwophase.py

@@ -17,7 +17,7 @@
 from pathlib import Path
 
 from gaussianrecipe import scipyOptimize
-from pyobjcryst import loadCrystal
+from pyobjcryst.crystal import create_crystal_from_cif
 
 from diffpy.srfit.fitbase import FitRecipe, FitResults
 from diffpy.srfit.pdf import PDFContribution
@@ -33,10 +33,10 @@ def makeRecipe(niciffile, siciffile, datname):
     contribution.loadData(datname)
     contribution.set_calculation_range(xmax=20)
 
-    stru = loadCrystal(niciffile)
+    stru = create_crystal_from_cif(str(niciffile))
     contribution.addStructure("ni", stru)
 
-    stru = loadCrystal(siciffile)
+    stru = create_crystal_from_cif(str(siciffile))
     contribution.addStructure("si", stru)
 
     # Make the FitRecipe and add the FitContribution.

docs/examples/threedoublepeaks.py

@@ -184,7 +184,7 @@ def scipyOptimize(recipe):
     # scipy. We simply have to give it the function to minimize
     # (recipe.residual) and the starting values of the Variables
     # (recipe.get_values()).
-    from scipy.optimize.minpack import leastsq
+    from scipy.optimize import leastsq
 
     print("Fit using scipy's LM optimizer")
     leastsq(recipe.residual, recipe.get_values())

docs/source/api/diffpy.srfit.interface.rst

@@ -17,4 +17,5 @@ diffpy.srfit.interface.interface module
 .. automodule:: diffpy.srfit.interface.interface
     :members:
     :undoc-members:
+    :special-members: __lshift__, __imul__, __imod__, __iadd__, __ior__
     :show-inheritance:

news/fix-structure-deprecations.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* Document the ``*=``, ``%=``, ``+=``, ``|=``, and ``<<`` shorthand operators in the ``diffpy.srfit.interface`` API reference.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Use ``get_space_group``, ``position_formulas``, and ``u_formulas`` in place of the deprecated ``diffpy.structure`` functions ``GetSpaceGroup``, ``positionFormulas``, and ``UFormulas`` to silence deprecation warnings.
+* Use ``add_constraint`` and ``add_soft_bounds`` in the ``*=`` and ``%=`` operators of ``RecipeOrganizerInterface`` so they no longer raise deprecation warnings for ``constrain`` and ``restrain``.
+* Use ``pyobjcryst.crystal.create_crystal_from_cif``, ``scipy.optimize.leastsq``, and the ``particle_diameter`` argument of ``spherical_particle`` in the examples in place of deprecated or renamed APIs.
+
+**Security:**
+
+* <news item>

src/diffpy/srfit/interface/interface.py

@@ -72,14 +72,14 @@ def __imul__(self, args):
         Parameters
         ----------
         args : tuple
-            The arguments to pass to `constrain`.
+            The arguments to pass to `add_constraint`.
 
         Returns
         -------
         RecipeOrganizerInterface
             Return self after applying the constraint.
         """
-        _applyargs(args, self.constrain)
+        _applyargs(args, self.add_constraint)
         return self
 
     def __imod__(self, args):
@@ -91,14 +91,14 @@ def __imod__(self, args):
         Parameters
         ----------
         args : tuple
-            The arguments to pass to `restrain`.
+            The arguments to pass to `add_soft_bounds`.
 
         Returns
         -------
         RecipeOrganizerInterface
             Return self after applying the restraint.
         """
-        _applyargs(args, self.restrain)
+        _applyargs(args, self.add_soft_bounds)
         return self
 
     def __iadd__(self, args):

src/diffpy/srfit/structure/objcrystparset.py

@@ -1911,17 +1911,17 @@ def _create_space_group(sgobjcryst):
         """
         import copy
 
-        from diffpy.structure.spacegroups import GetSpaceGroup, SymOp
+        from diffpy.structure.spacegroups import SymOp, get_space_group
 
         name = sgobjcryst.GetName()
         extnstr = ":%s" % sgobjcryst.GetExtension()
         if name.endswith(extnstr):
             name = name[: -len(extnstr)]
 
         # Get whatever spacegroup we can get by name. This will set the proper
-        # crystal system.  Creating a copy of the singleton from GetSpaceGroup,
-        # as this function messes with sg.symop_list.
-        sg = copy.copy(GetSpaceGroup(name))
+        # crystal system.  Creating a copy of the singleton from
+        # get_space_group, as this function messes with sg.symop_list.
+        sg = copy.copy(get_space_group(name))
 
         # Replace the symmetry operations to guarantee that we get it right.
         symops = sgobjcryst.GetSymmetryOperations()

src/diffpy/srfit/structure/sgconstraints.py

@@ -112,11 +112,11 @@ def constrain_as_space_group(
             b and c are constrained to a, and alpha, beta and
             gamma are fixed to 90.
     """
-    from diffpy.structure.spacegroups import GetSpaceGroup, SpaceGroup
+    from diffpy.structure.spacegroups import SpaceGroup, get_space_group
 
     sg = spacegroup
     if not isinstance(spacegroup, SpaceGroup):
-        sg = GetSpaceGroup(spacegroup)
+        sg = get_space_group(spacegroup)
     sgp = _constrain_as_space_group(
         phase,
         sg,
@@ -309,7 +309,7 @@ def __init__(
             A BaseStructure object to be constrained.
         sg
             The space group number or symbol (compatible with
-            diffpy.structure.spacegroups.GetSpaceGroup.
+            diffpy.structure.spacegroups.get_space_group.
         sgoffset
             Optional offset for sg origin.
         scatterers
@@ -533,7 +533,7 @@ def _constrain_xyzs(self, positions):
             self._xyzpars.addParameter(newpar)
 
         # Constrain non-free xyz parameters
-        fpos = g.positionFormulas(xyznames)
+        fpos = g.position_formulas(xyznames)
         for idx, tmp in enumerate(zip(scatterers, fpos)):
             scatterer, fp = tmp
 
@@ -634,7 +634,7 @@ def _constrain_adps(self, positions):
                     isosymbol, isoname, params=self._parameters
                 )
 
-        fadp = g.UFormulas(adpnames)
+        fadp = g.u_formulas(adpnames)
 
         # Constrain dependent anisotropics. We use the fact that an
         # anisotropic cannot be dependent on an isotropic.

tests/test_interface.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2026-present The DiffPy Team. All rights reserved.
+#
+# File coded by: Caden Myers
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.srfit/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Tests for the interface module."""
+
+from diffpy.srfit.fitbase import FitRecipe
+
+
+def _make_recipe_with_variables():
+    """Return a recipe with the variables p1 = 1 and p2 = 2."""
+    recipe = FitRecipe("recipe")
+    p1 = recipe.create_new_variable("p1", 1)
+    p2 = recipe.create_new_variable("p2", 2)
+    return recipe, p1, p2
+
+
+# Test that "*=" constrains a Parameter to an equation.
+# C1: p1 is constrained to "2*p2" with "*=", and p2 is then set to 3.
+# Expected: p1 is constrained and its value is 6.
+def test_constrain_operator():
+    recipe, p1, p2 = _make_recipe_with_variables()
+    recipe *= "p1", "2*p2"
+    p2.set_value(3)
+    recipe._constraints[p1].update()
+    assert recipe.is_constrained(p1)
+    actual_p1_value = p1.get_value()
+    expected_p1_value = 6
+    assert actual_p1_value == expected_p1_value
+
+
+# Test that "%=" restrains an equation between soft bounds.
+# C1: "p1+p2" is restrained between 0 and 10 with "%=", and p2 is then set
+# to 10.
+# Expected: The recipe has one restraint with a penalty of 1.
+def test_restrain_operator():
+    recipe, _, p2 = _make_recipe_with_variables()
+    recipe %= "p1+p2", 0, 10
+    p2.set_value(10)
+    actual_number_of_restraints = len(recipe._restraints)
+    expected_number_of_restraints = 1
+    assert actual_number_of_restraints == expected_number_of_restraints
+    (restraint,) = recipe._restraints
+    actual_penalty = restraint.penalty()
+    expected_penalty = 1
+    assert actual_penalty == expected_penalty

tests/test_objcrystparset.py

@@ -723,7 +723,7 @@ def xtestCreateSpaceGroup(self):
             shn = smbls.hermann_mauguin()
             short_name = shn.replace(" ", "")
             if spacegroups.IsSpaceGroupIdentifier(short_name):
-                sg = spacegroups.GetSpaceGroup(shn)
+                sg = spacegroups.get_space_group(shn)
                 sgnew = self.getObjCrystParSetSpaceGroup(sg)
                 # print("dbsg: " + repr(self.sgsEquivalent(sg, sgnew)))
                 assert self.sgsEquivalent(sg, sgnew)