dep & test: Replace deprecated functions and add tests for interface.py (#230)

* chore: replace deprecated functions

* replace deprecated function in test

* fix deprecated functions in examples and add tests for interface

* fix file header

* trigger ci

* doc: add short hand operators to docs

Author: cadenmyers13

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())