Merge pull request #73 from bobleesj/cookie-black

Run black . without any manual modification

Author: sbillinge

doc/examples/coreshellnp.py

@@ -71,6 +71,7 @@ def makeRecipe(stru1, stru2, datname):
     # phases, we implicitly assume that the core-shell correlations contribute
     # very little to the PDF.
     from diffpy.srfit.pdf.characteristicfunctions import shellCF, sphericalCF
+
     contribution.registerFunction(sphericalCF, name="f_CdS")
     contribution.registerFunction(shellCF, name="f_ZnS")
 
@@ -137,10 +138,11 @@ def plotResults(recipe):
     diff = g - gcalc + diffzero
 
     import pylab
-    pylab.plot(r, g, 'bo', label="G(r) Data")
-    pylab.plot(r, gcalc, 'r-', label="G(r) Fit")
-    pylab.plot(r, diff, 'g-', label="G(r) diff")
-    pylab.plot(r, diffzero, 'k-')
+
+    pylab.plot(r, g, "bo", label="G(r) Data")
+    pylab.plot(r, gcalc, "r-", label="G(r) Fit")
+    pylab.plot(r, diff, "g-", label="G(r) diff")
+    pylab.plot(r, diffzero, "k-")
     pylab.xlabel(r"$r (\AA)$")
     pylab.ylabel(r"$G (\AA^{-2})$")
     pylab.legend(loc=1)
@@ -162,6 +164,7 @@ def main():
     stru2 = loadCrystal(znsciffile)
     recipe = makeRecipe(stru1, stru2, data)
     from diffpy.srfit.fitbase.fithook import PlotFitHook
+
     recipe.pushFitHook(PlotFitHook())
     recipe.fithooks[0].verbose = 3
 

doc/examples/crystalpdf.py

@@ -34,6 +34,7 @@
 
 ####### Example Code
 
+
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
 
@@ -50,7 +51,7 @@ def makeRecipe(ciffile, datname):
     parser = PDFParser()
     parser.parseFile(datname)
     profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax = 20)
+    profile.setCalculationRange(xmax=20)
 
     ## The ProfileGenerator
     # The PDFGenerator is for configuring and calculating a PDF profile. Here,
@@ -69,7 +70,7 @@ def makeRecipe(ciffile, datname):
     # before.
     contribution = FitContribution("nickel")
     contribution.addProfileGenerator(generator)
-    contribution.setProfile(profile, xname = "r")
+    contribution.setProfile(profile, xname="r")
 
     ## Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
@@ -92,6 +93,7 @@ def makeRecipe(ciffile, datname):
     # documentation for more details. The 'constrainAsSpaceGroup' method may
     # create new Parameters, which it returns in a SpaceGroupParameters object.
     from diffpy.srfit.structure import constrainAsSpaceGroup
+
     sgpars = constrainAsSpaceGroup(phase, "Fm-3m")
 
     # The SpaceGroupParameters object returned by 'constrainAsSpaceGroup' holds
@@ -121,6 +123,7 @@ def makeRecipe(ciffile, datname):
     # Give the recipe away so it can be used!
     return recipe
 
+
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
 
@@ -132,19 +135,20 @@ def plotResults(recipe):
     diff = g - gcalc + diffzero
 
     import pylab
-    pylab.plot(r,g,'bo',label="G(r) Data")
-    pylab.plot(r, gcalc,'r-',label="G(r) Fit")
-    pylab.plot(r,diff,'g-',label="G(r) diff")
-    pylab.plot(r,diffzero,'k-')
+
+    pylab.plot(r, g, "bo", label="G(r) Data")
+    pylab.plot(r, gcalc, "r-", label="G(r) Fit")
+    pylab.plot(r, diff, "g-", label="G(r) diff")
+    pylab.plot(r, diffzero, "k-")
     pylab.xlabel(r"$r (\AA)$")
     pylab.ylabel(r"$G (\AA^{-2})$")
     pylab.legend(loc=1)
 
     pylab.show()
     return
 
-if __name__ == "__main__":
 
+if __name__ == "__main__":
     # Make the data and the recipe
     ciffile = "data/ni.cif"
     data = "data/ni-q27r100-neutron.gr"

doc/examples/crystalpdfall.py

@@ -28,24 +28,26 @@
 
 ####### Example Code
 
+
 def makeProfile(datafile):
     """Make an place data within a Profile."""
     profile = Profile()
     parser = PDFParser()
     parser.parseFile(datafile)
     profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax = 20)
+    profile.setCalculationRange(xmax=20)
     return profile
 
+
 def makeContribution(name, generator, profile):
     """Make a FitContribution and add a generator and profile."""
     contribution = FitContribution(name)
     contribution.addProfileGenerator(generator)
-    contribution.setProfile(profile, xname = "r")
+    contribution.setProfile(profile, xname="r")
     return contribution
 
-def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
-        xdata_sini):
+
+def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si, xdata_sini):
     """Create a fitting recipe for crystalline PDF data."""
 
     ## The Profiles
@@ -81,8 +83,7 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
     xcontribution_ni = makeContribution("xnickel", xgenerator_ni, xprofile_ni)
     xcontribution_si = makeContribution("xsilicon", xgenerator_si, xprofile_si)
     ncontribution_ni = makeContribution("nnickel", ngenerator_ni, nprofile_ni)
-    xcontribution_sini = makeContribution("xsini", xgenerator_sini_ni,
-            xprofile_sini)
+    xcontribution_sini = makeContribution("xsini", xgenerator_sini_ni, xprofile_sini)
     xcontribution_sini.addProfileGenerator(xgenerator_sini_si)
     xcontribution_sini.setEquation("scale * (xG_sini_ni +  xG_sini_si)")
 
@@ -101,22 +102,22 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
 
     # Now we vary and constrain Parameters as before.
     for par in phase_ni.sgpars:
-        recipe.addVar(par, name = par.name + "_ni")
+        recipe.addVar(par, name=par.name + "_ni")
     delta2_ni = recipe.newVar("delta2_ni", 2.5)
     recipe.constrain(xgenerator_ni.delta2, delta2_ni)
     recipe.constrain(ngenerator_ni.delta2, delta2_ni)
     recipe.constrain(xgenerator_sini_ni.delta2, delta2_ni)
 
     for par in phase_si.sgpars:
-        recipe.addVar(par, name = par.name + "_si")
+        recipe.addVar(par, name=par.name + "_si")
     delta2_si = recipe.newVar("delta2_si", 2.5)
     recipe.constrain(xgenerator_si.delta2, delta2_si)
     recipe.constrain(xgenerator_sini_si.delta2, delta2_si)
 
     # Now the experimental parameters
-    recipe.addVar(xgenerator_ni.scale, name = "xscale_ni")
-    recipe.addVar(xgenerator_si.scale, name = "xscale_si")
-    recipe.addVar(ngenerator_ni.scale, name = "nscale_ni")
+    recipe.addVar(xgenerator_ni.scale, name="xscale_ni")
+    recipe.addVar(xgenerator_si.scale, name="xscale_si")
+    recipe.addVar(ngenerator_ni.scale, name="nscale_ni")
     recipe.addVar(xcontribution_sini.scale, 1.0, "xscale_sini")
     recipe.newVar("pscale_sini_ni", 0.8)
     recipe.constrain(xgenerator_sini_ni.scale, "pscale_sini_ni")
@@ -133,6 +134,7 @@ def makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
     # Give the recipe away so it can be used!
     return recipe
 
+
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
 
@@ -141,67 +143,67 @@ def plotResults(recipe):
     xr_ni = xnickel.profile.x
     xg_ni = xnickel.profile.y
     xgcalc_ni = xnickel.profile.ycalc
-    xdiffzero_ni =  -0.8 * max(xg_ni) * numpy.ones_like(xg_ni)
+    xdiffzero_ni = -0.8 * max(xg_ni) * numpy.ones_like(xg_ni)
     xdiff_ni = xg_ni - xgcalc_ni + xdiffzero_ni
 
     xsilicon = recipe.xsilicon
     xr_si = xsilicon.profile.x
     xg_si = xsilicon.profile.y
     xgcalc_si = xsilicon.profile.ycalc
-    xdiffzero_si =  -0.8 * max(xg_si) * numpy.ones_like(xg_si)
+    xdiffzero_si = -0.8 * max(xg_si) * numpy.ones_like(xg_si)
     xdiff_si = xg_si - xgcalc_si + xdiffzero_si
 
     nnickel = recipe.nnickel
     nr_ni = nnickel.profile.x
     ng_ni = nnickel.profile.y
     ngcalc_ni = nnickel.profile.ycalc
-    ndiffzero_ni =  -0.8 * max(ng_ni) * numpy.ones_like(ng_ni)
+    ndiffzero_ni = -0.8 * max(ng_ni) * numpy.ones_like(ng_ni)
     ndiff_ni = ng_ni - ngcalc_ni + ndiffzero_ni
 
     xsini = recipe.xsini
     xr_sini = xsini.profile.x
     xg_sini = xsini.profile.y
     xgcalc_sini = xsini.profile.ycalc
-    xdiffzero_sini =  -0.8 * max(xg_sini) * numpy.ones_like(xg_sini)
+    xdiffzero_sini = -0.8 * max(xg_sini) * numpy.ones_like(xg_sini)
     xdiff_sini = xg_sini - xgcalc_sini + xdiffzero_sini
 
-
     import pylab
+
     pylab.subplot(2, 2, 1)
-    pylab.plot(xr_ni,xg_ni,'bo',label="G(r) x-ray nickel Data")
-    pylab.plot(xr_ni,xgcalc_ni,'r-',label="G(r) x-ray nickel Fit")
-    pylab.plot(xr_ni,xdiff_ni,'g-',label="G(r) x-ray nickel diff")
-    pylab.plot(xr_ni,xdiffzero_ni,'k-')
+    pylab.plot(xr_ni, xg_ni, "bo", label="G(r) x-ray nickel Data")
+    pylab.plot(xr_ni, xgcalc_ni, "r-", label="G(r) x-ray nickel Fit")
+    pylab.plot(xr_ni, xdiff_ni, "g-", label="G(r) x-ray nickel diff")
+    pylab.plot(xr_ni, xdiffzero_ni, "k-")
     pylab.xlabel(r"$r (\AA)$")
     pylab.ylabel(r"$G (\AA^{-2})$")
     pylab.legend(loc=1)
 
     pylab.subplot(2, 2, 2)
-    pylab.plot(xr_si,xg_si,'bo',label="G(r) x-ray silicon Data")
-    pylab.plot(xr_si,xgcalc_si,'r-',label="G(r) x-ray silicon Fit")
-    pylab.plot(xr_si,xdiff_si,'g-',label="G(r) x-ray silicon diff")
-    pylab.plot(xr_si,xdiffzero_si,'k-')
+    pylab.plot(xr_si, xg_si, "bo", label="G(r) x-ray silicon Data")
+    pylab.plot(xr_si, xgcalc_si, "r-", label="G(r) x-ray silicon Fit")
+    pylab.plot(xr_si, xdiff_si, "g-", label="G(r) x-ray silicon diff")
+    pylab.plot(xr_si, xdiffzero_si, "k-")
     pylab.legend(loc=1)
 
     pylab.subplot(2, 2, 3)
-    pylab.plot(nr_ni,ng_ni,'bo',label="G(r) neutron nickel Data")
-    pylab.plot(nr_ni,ngcalc_ni,'r-',label="G(r) neutron nickel Fit")
-    pylab.plot(nr_ni,ndiff_ni,'g-',label="G(r) neutron nickel diff")
-    pylab.plot(nr_ni,ndiffzero_ni,'k-')
+    pylab.plot(nr_ni, ng_ni, "bo", label="G(r) neutron nickel Data")
+    pylab.plot(nr_ni, ngcalc_ni, "r-", label="G(r) neutron nickel Fit")
+    pylab.plot(nr_ni, ndiff_ni, "g-", label="G(r) neutron nickel diff")
+    pylab.plot(nr_ni, ndiffzero_ni, "k-")
     pylab.legend(loc=1)
 
     pylab.subplot(2, 2, 4)
-    pylab.plot(xr_sini,xg_sini,'bo',label="G(r) x-ray sini Data")
-    pylab.plot(xr_sini,xgcalc_sini,'r-',label="G(r) x-ray sini Fit")
-    pylab.plot(xr_sini,xdiff_sini,'g-',label="G(r) x-ray sini diff")
-    pylab.plot(xr_sini,xdiffzero_sini,'k-')
+    pylab.plot(xr_sini, xg_sini, "bo", label="G(r) x-ray sini Data")
+    pylab.plot(xr_sini, xgcalc_sini, "r-", label="G(r) x-ray sini Fit")
+    pylab.plot(xr_sini, xdiff_sini, "g-", label="G(r) x-ray sini diff")
+    pylab.plot(xr_sini, xdiffzero_sini, "k-")
     pylab.legend(loc=1)
 
     pylab.show()
     return
 
-if __name__ == "__main__":
 
+if __name__ == "__main__":
     # Make the data and the recipe
     ciffile_ni = "data/ni.cif"
     ciffile_si = "data/si.cif"
@@ -211,8 +213,7 @@ def plotResults(recipe):
     xdata_sini = "data/si90ni10-q27r60-xray.gr"
 
     # Make the recipe
-    recipe =  makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si,
-            xdata_sini)
+    recipe = makeRecipe(ciffile_ni, ciffile_si, xdata_ni, ndata_ni, xdata_si, xdata_sini)
 
     # Optimize
     scipyOptimize(recipe)

doc/examples/crystalpdfobjcryst.py

@@ -29,6 +29,7 @@
 
 ####### Example Code
 
+
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
 
@@ -43,7 +44,7 @@ def makeRecipe(ciffile, datname):
     parser = PDFParser()
     parser.parseFile(datname)
     profile.loadParsedData(parser)
-    profile.setCalculationRange(xmax = 20)
+    profile.setCalculationRange(xmax=20)
 
     ## The ProfileGenerator
     # This time we use the CreateCrystalFromCIF method of pyobjcryst.crystal to
@@ -57,7 +58,7 @@ def makeRecipe(ciffile, datname):
     ## The FitContribution
     contribution = FitContribution("nickel")
     contribution.addProfileGenerator(generator)
-    contribution.setProfile(profile, xname = "r")
+    contribution.setProfile(profile, xname="r")
 
     # Make the FitRecipe and add the FitContribution.
     recipe = FitRecipe()
@@ -86,7 +87,7 @@ def makeRecipe(ciffile, datname):
     for par in phase.sgpars:
         recipe.addVar(par)
     # set the initial thermal factor to a non-zero value
-    assert hasattr(recipe, 'B11_0')
+    assert hasattr(recipe, "B11_0")
     recipe.B11_0 = 0.1
 
     # We now select non-structural parameters to refine.
@@ -100,8 +101,8 @@ def makeRecipe(ciffile, datname):
     # Give the recipe away so it can be used!
     return recipe
 
-if __name__ == "__main__":
 
+if __name__ == "__main__":
     # Make the data and the recipe
     ciffile = "data/si.cif"
     data = "data/si-q27r60-xray.gr"