Merge pull request #44 from ycexiao/update-version

chore: update python version requirements

Author: sbillinge

cookiecutter.json

@@ -13,8 +13,8 @@
   "package_dir_name": "diffpy.apps",
   "project_short_description": "User applications to help with tasks using diffpy packages",
   "project_keywords": "diffraction, PDF, X-ray, neutron",
-  "minimum_supported_python_version": "3.11",
-  "maximum_supported_python_version": "3.13",
+  "minimum_supported_python_version": "3.12",
+  "maximum_supported_python_version": "3.14",
   "project_needs_c_code_compiled": "No",
   "project_has_gui_tests": "No"
 }

news/update-version.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Support python>=3.12, <3.14; Replace deprecated methods.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -15,7 +15,7 @@ maintainers = [
 description = "User applications to help with tasks using diffpy packages"
 keywords = ['diffraction', 'PDF', 'X-ray', 'neutron']
 readme = "README.rst"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.15"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,9 +25,9 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
+        'Programming Language :: Python :: 3.14',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]

src/diffpy/apps/pdfadapter.py

@@ -12,8 +12,8 @@
     Profile,
 )
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.structure import constrainAsSpaceGroup
-from diffpy.structure.parsers import getParser
+from diffpy.srfit.structure import constrain_as_space_group
+from diffpy.structure.parsers import get_parser
 
 
 class PDFAdapter:
@@ -147,7 +147,7 @@ def initialize_structures(
                 run_parallel = False
         for i, structure_path in enumerate(structure_paths):
             name = names[i] if names and i < len(names) else f"G{i+1}"
-            stru_parser = getParser("cif")
+            stru_parser = get_parser("cif")
             structure = stru_parser.parse(Path(structure_path).read_text())
             sg = getattr(stru_parser, "spacegroup", None)
             spacegroup = sg.short_name if sg is not None else "P1"
@@ -176,7 +176,7 @@ def initialize_contribution(self, equation=None):
         ----------
         equation : list of str, optional
             The list of a single equation passed to
-            FitContribution.setEquation.
+            FitContribution.set_equation
 
         Returns
         -------
@@ -220,7 +220,9 @@ def initialize_recipe(
             recipe.add_constraint(pdfgenerator.qdamp, qdamp)
             recipe.add_constraint(pdfgenerator.qbroad, qbroad)
             stru_parset = pdfgenerator.phase
-            spacegroupparams = constrainAsSpaceGroup(stru_parset, spacegroup)
+            spacegroupparams = constrain_as_space_group(
+                stru_parset, spacegroup
+            )
             for par in spacegroupparams.xyzpars:
                 recipe.add_variable(
                     par, name=f"{pdfgenerator.name}_{par.name}", fixed=False

src/diffpy/apps/refinebase/parametric_model.py

@@ -644,8 +644,8 @@ def create_pdf_model_from_code(
             if hasattr(structure, "GetCrystal")
             else structure
         )
-        if hasattr(crystal, "GetSpaceGroup"):
-            spacegroup_symbol = crystal.GetSpaceGroup().GetName()
+        if hasattr(crystal, "get_space_group"):
+            spacegroup_symbol = crystal.get_space_group().get_name()
         else:
             logging.warning(
                 "Could not determine a space group for the structure named "

src/diffpy/apps/refinebase/refinement_session.py

@@ -67,7 +67,7 @@ def add_profile_from_arrays(
         if profile_name is None:
             profile_name = str(uuid.uuid4())
         profile = Profile()
-        profile.setObservedProfile(xobs=xarray, yobs=yarray, dyobs=dy)
+        profile.set_observed_profile(xobs=xarray, yobs=yarray, dyobs=dy)
         profile.xpar.name = xname
         profile._xname = xname
         profile.ypar.name = yname
@@ -531,7 +531,7 @@ def _solve(
                 par = self.get_variable(eq_or_var_name)["obj"]
                 par.bound_range(lb, ub)
         recipe.free("all")
-        leastsq(recipe.residual, recipe.getValues())
+        leastsq(recipe.residual, recipe.get_values())
         # NOTE: non-scalar value will raise error in `get_results_string`
         try:
             result_string = FitResults(recipe).get_results_string()

tests/conftest.py

@@ -39,5 +39,5 @@ def sine_profile():
     xobs = numpy.linspace(-numpy.pi, numpy.pi, 100)
     yobs = numpy.sin(xobs) + 1e-3 * numpy.random.normal(size=xobs.shape)
     sine_profile = Profile()
-    sine_profile.setObservedProfile(xobs, yobs)
+    sine_profile.set_observed_profile(xobs, yobs)
     return sine_profile

tests/helper.py

@@ -10,8 +10,8 @@
     Profile,
 )
 from diffpy.srfit.pdf import DebyePDFGenerator, PDFGenerator, PDFParser
-from diffpy.srfit.structure import constrainAsSpaceGroup
-from diffpy.structure.parsers import getParser
+from diffpy.srfit.structure import constrain_as_space_group
+from diffpy.structure.parsers import get_parser
 
 _DATA_DIR = Path(__file__).parent / "data"
 
@@ -49,21 +49,21 @@ def run_ni_example():
     QBROAD_I = 0.02
     RUN_PARALLEL = True
 
-    p_cif = getParser("cif")
-    stru1 = p_cif.parseFile(structure_path)
+    p_cif = get_parser("cif")
+    stru1 = p_cif.parse_file(structure_path)
     sg = p_cif.spacegroup.short_name
     profile = Profile()
     parser = PDFParser()
-    parser.parseFile(profile_path)
-    profile.loadParsedData(parser)
-    profile.setCalculationRange(xmin=PDF_RMIN, xmax=PDF_RMAX, dx=PDF_RSTEP)
+    parser.parse_file(profile_path)
+    profile.load_parsed_data(parser)
+    profile.set_calculation_range(xmin=PDF_RMIN, xmax=PDF_RMAX, dx=PDF_RSTEP)
     generator_crystal1 = PDFGenerator("G1")
     generator_crystal1.setStructure(stru1, periodic=True)
     generator_crystal1.setQmax(QMAX)
     generator_crystal1.setQmin(QMIN)
     generator_crystal1.delta2.value = DELTA2_I
     contribution = FitContribution("crystal")
-    contribution.addProfileGenerator(generator_crystal1)
+    contribution.add_profile_generator(generator_crystal1)
     if RUN_PARALLEL:
         try:
             import multiprocessing
@@ -82,28 +82,28 @@ def run_ni_example():
                 "\nYou don't appear to have the necessary packages for "
                 "parallelization"
             )
-    contribution.setProfile(profile, xname="r")
-    contribution.setEquation("s0*G1")
+    contribution.set_profile(profile, xname="r")
+    contribution.set_equation("s0*G1")
     recipe = FitRecipe()
-    recipe.addContribution(contribution)
+    recipe.add_contribution(contribution)
     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.addVar(contribution.s0, SCALE_I, name="s0")
-    spacegroupparams = constrainAsSpaceGroup(generator_crystal1.phase, sg)
+    recipe.add_variable(contribution.s0, SCALE_I, name="s0")
+    spacegroupparams = constrain_as_space_group(generator_crystal1.phase, sg)
     for par in spacegroupparams.latpars:
-        recipe.addVar(par, value=CUBICLAT_I, fixed=False, name="G1_a")
+        recipe.add_variable(par, value=CUBICLAT_I, fixed=False, name="G1_a")
     for par in spacegroupparams.adppars:
-        recipe.addVar(par, value=UISO_I, fixed=False, name="G1_Uiso_0")
-    recipe.addVar(generator_crystal1.delta2, name="G1_delta2")
-    recipe.addVar(
+        recipe.add_variable(par, value=UISO_I, fixed=False, name="G1_Uiso_0")
+    recipe.add_variable(generator_crystal1.delta2, name="G1_delta2")
+    recipe.add_variable(
         generator_crystal1.qdamp,
         fixed=False,
         name="qdamp",
         value=QDAMP_I,
     )
-    recipe.addVar(
+    recipe.add_variable(
         generator_crystal1.qbroad,
         fixed=False,
         name="qbroad",

tests/test_pdfadapter.py

@@ -37,7 +37,9 @@ def test_pdfadapter():
     adapter.initialize_structures([str(structure_path)])
     adapter.initialize_contribution(equation=["s0*G1"])
     adapter.initialize_recipe()
-    adapter.recipe.addVar(list(adapter.recipe._contributions.values())[0].s0)
+    adapter.recipe.add_variable(
+        list(adapter.recipe._contributions.values())[0].s0
+    )
     adapter.set_initial_variable_values(initial_pv_dict)
     adapter.recipe.fix("all")
     for var in variables_to_refine: