fix: use diffpy.cmistructure

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

@@ -19,6 +19,6 @@ jobs:
       headless: false
       run: |
         set -Eeuo pipefail
-        python -m pip install --no-deps diffpy.srfit==3.4.0rc0
+        python -m pip install --no-deps diffpy.cmistructure
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tests-on-pr.yml

@@ -13,6 +13,6 @@ jobs:
       headless: false
       run: |
         set -Eeuo pipefail
-        python -m pip install --no-deps diffpy.srfit==3.4.0rc0
+        python -m pip install --no-deps diffpy.cmistructure
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

news/rm-srfit-rc-pin.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Require ``diffpy.srfit`` 3.4.0 or later. Older versions lack the methods diffpy.cmipdf calls, so installing it next to ``diffpy.srfit`` 3.3.1 failed at run time.
+
+**Security:**
+
+* <news item>

news/use-cmistructure.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* ``diffpy.cmistructure`` as a dependency.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Build ``diffpy.cmistructure`` parameter sets in ``set_structure`` and ``add_structure``, and accept them in ``set_structure_from_parset`` and ``add_structure_from_parset``. These used ``diffpy.srfit.structure`` and raised ``AttributeError: stru`` for a ``diffpy.cmistructure`` parameter set.
+
+**Security:**
+
+* <news item>

requirements/conda.txt

@@ -1,4 +1,4 @@
 numpy
 diffpy.srreal
-diffpy.srfit
+diffpy.srfit>=3.4.0
 diffpy.structure

requirements/pip.txt

@@ -1,4 +1,5 @@
 numpy
 diffpy.srreal
-diffpy.srfit
+diffpy.srfit>=3.4.0
 diffpy.structure
+diffpy.cmistructure

src/diffpy/cmipdf/basepdfgenerator.py

@@ -23,10 +23,10 @@
 
 import numpy
 
+from diffpy.cmistructure import structure_to_parameter_set
 from diffpy.srfit.exceptions import SrFitError
 from diffpy.srfit.fitbase import ProfileGenerator
 from diffpy.srfit.fitbase.parameter import ParameterAdapter
-from diffpy.srfit.structure import struToParameterSet
 
 # FIXME - Parameter creation will have to be smarter once deeper calculator
 # configuration is enabled.
@@ -257,7 +257,7 @@ def set_structure(self, structure, name="phase", periodic=True):
         This creates a DiffpyStructureParSet, ObjCrystCrystalParSet or
         ObjCrystMoleculeParSet that adapts structure to a ParameterSet
         interface.
-        See those classes (located in diffpy.srfit.structure) for how they are
+        See those classes (located in diffpy.cmistructure) for how they are
         used. The resulting ParameterSet will be managed by this generator.
 
         Parameters
@@ -276,7 +276,7 @@ def set_structure(self, structure, name="phase", periodic=True):
         """
 
         # Create the ParameterSet
-        parset = struToParameterSet(name, structure)
+        parset = structure_to_parameter_set(name, structure)
 
         # Set the phase
         self.set_structure_from_parset(parset, periodic)
@@ -304,13 +304,13 @@ def set_structure_from_parset(self, parset, periodic=True):
         """
         # Store the ParameterSet for easy access
         self._phase = parset
-        self.structure = self._phase.stru
+        self.structure = self._phase.structure
 
         # Put this ParameterSet in the ProfileGenerator.
         self.add_parameter_set(parset)
 
         # Set periodicity
-        self._phase.useSymmetry(periodic)
+        self._phase.use_symmetry(periodic)
         return
 
     def _prepare(self, r):

src/diffpy/cmipdf/debyepdfgenerator.py

@@ -93,7 +93,7 @@ def set_structure(self, structure, name="phase", periodic=False):
         This creates a DiffpyStructureParSet, ObjCrystCrystalParSet or
         ObjCrystMoleculeParSet that adapts structure to a ParameterSet
         interface.
-        See those classes (located in diffpy.srfit.structure) for how they are
+        See those classes (located in diffpy.cmistructure) for how they are
         used. The resulting ParameterSet will be managed by this generator.
 
         Parameters

tests/test_generators.py

@@ -3,7 +3,9 @@
 import numpy as np
 import pytest
 
-from diffpy.cmipdf import PDFGenerator
+from diffpy.cmipdf import DebyePDFGenerator, PDFGenerator
+from diffpy.cmistructure import constrain_as_space_group
+from diffpy.cmistructure.diffpyparset import DiffpyStructureParSet
 from diffpy.srreal.pdfcalculator import PDFCalculator
 
 
@@ -51,6 +53,70 @@ def test_set_qmin():
     assert actual_qmins == expected_qmins
 
 
+# set_structure adapts the structure with a diffpy.cmistructure parameter
+# set, which the generator then manages as its phase.
+@pytest.mark.parametrize(
+    "input_generator_class",
+    [
+        # C1: A diffpy.structure Structure is set on a generator,
+        # 1. PDFGenerator, 2. DebyePDFGenerator.
+        # Expected: The phase is a diffpy.cmistructure DiffpyStructureParSet
+        # that adapts the structure.
+        PDFGenerator,
+        DebyePDFGenerator,
+    ],
+)
+def test_set_structure(ni_pdffit_structure, input_generator_class):
+    generator = input_generator_class()
+    generator.set_structure(ni_pdffit_structure)
+    actual_phase = (type(generator.phase), generator.phase.structure)
+    expected_phase = (DiffpyStructureParSet, ni_pdffit_structure)
+    assert actual_phase == expected_phase
+
+
+# set_structure_from_parset manages the given diffpy.cmistructure parameter
+# set as the phase, and periodic sets whether it uses symmetry.
+@pytest.mark.parametrize(
+    "input_periodic, expected_using_symmetry",
+    [
+        # C1: The parameter set is set as periodic.
+        # Expected: The generator manages that parameter set, its structure
+        # is the adapted structure, and the parameter set uses symmetry.
+        (True, True),
+        # C2: The parameter set is set as not periodic.
+        # Expected: The same, except that it does not use symmetry.
+        (False, False),
+    ],
+)
+def test_set_structure_from_parset(
+    ni_pdffit_structure, input_periodic, expected_using_symmetry
+):
+    parameter_set = DiffpyStructureParSet("phase", ni_pdffit_structure)
+    generator = PDFGenerator()
+    generator.set_structure_from_parset(parameter_set, periodic=input_periodic)
+    actual_state = (
+        generator.phase is parameter_set,
+        generator.structure is ni_pdffit_structure,
+        parameter_set.using_symmetry(),
+    )
+    expected_state = (True, True, expected_using_symmetry)
+    assert actual_state == expected_state
+
+
+def test_constrain_as_space_group_accepts_generator(ni_pdffit_structure):
+    # C1: A PDFGenerator holding face-centered cubic Ni is passed to
+    # diffpy.cmistructure's constrain_as_space_group with Fm-3m.
+    # Expected: Only the lattice length a of its phase is left free.
+    generator = PDFGenerator()
+    generator.set_structure(ni_pdffit_structure)
+    space_group_parameters = constrain_as_space_group(generator, "Fm-3m")
+    actual_free_lattice_names = [
+        parameter.name for parameter in space_group_parameters.latpars
+    ]
+    expected_free_lattice_names = ["a"]
+    assert actual_free_lattice_names == expected_free_lattice_names
+
+
 def test_parameter_names(ni_pdffit_structure):
     # C1: A structure is set on the generator.
     # Expected: The generator holds one Parameter for each calculator

tests/test_pdfcontribution.py

@@ -8,6 +8,7 @@
 import pytest
 
 from diffpy.cmipdf import PDFContribution
+from diffpy.cmistructure.diffpyparset import DiffpyStructureParSet
 from diffpy.srfit.exceptions import SrFitError
 from diffpy.structure import Structure, load_structure
 
@@ -126,3 +127,31 @@ def test_pickling(datafile):
     actual_residual = unpickled_contribution.residual()
     expected_residual = _make_ni_contribution(datafile, uiso=0.004).residual()
     assert np.allclose(actual_residual, expected_residual)
+
+
+def test_add_structure(datafile):
+    # C1: A diffpy.structure Structure is added to the contribution.
+    # Expected: The new generator's phase is a diffpy.cmistructure
+    # DiffpyStructureParSet that adapts the structure.
+    contribution = PDFContribution("pdf")
+    ni = load_structure(str(datafile("ni.cif")))
+    contribution.add_structure(ni, name="ni")
+    actual_phase = (
+        type(contribution.ni.phase),
+        contribution.ni.phase.structure,
+    )
+    expected_phase = (DiffpyStructureParSet, ni)
+    assert actual_phase == expected_phase
+
+
+def test_add_structure_from_parset(datafile):
+    # C1: A diffpy.cmistructure DiffpyStructureParSet is added to the
+    # contribution.
+    # Expected: The new generator manages that parameter set as its phase.
+    contribution = PDFContribution("pdf")
+    ni = load_structure(str(datafile("ni.cif")))
+    parameter_set = DiffpyStructureParSet("phase", ni)
+    contribution.add_structure_from_parset(parameter_set, name="ni")
+    actual_phase = contribution.ni.phase
+    expected_phase = parameter_set
+    assert actual_phase is expected_phase