[pre-commit.ci] auto fixes from pre-commit hooks

Author: pre-commit-ci[bot]

devutils/makesdist

@@ -1,51 +1,57 @@
 #!/usr/bin/env python
 
-'''Create source distribution tar.gz archive, where each file belongs
+"""Create source distribution tar.gz archive, where each file belongs
 to a root user and modification time is set to the git commit time.
-'''
+"""
 
-import sys
+import glob
+import gzip
 import os
 import subprocess
-import glob
+import sys
 import tarfile
-import gzip
 
 BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 sys.path.insert(0, BASEDIR)
 
-from setup import versiondata, FALLBACK_VERSION
-timestamp = versiondata.getint('DEFAULT', 'timestamp')
+from setup import FALLBACK_VERSION, versiondata
 
-vfb = versiondata.get('DEFAULT', 'version').split('.post')[0] + '.post0'
+timestamp = versiondata.getint("DEFAULT", "timestamp")
+
+vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"
 emsg = "Invalid FALLBACK_VERSION. Expected %r got %r."
 assert vfb == FALLBACK_VERSION, emsg % (vfb, FALLBACK_VERSION)
 
+
 def inform(s):
     sys.stdout.write(s)
     sys.stdout.flush()
     return
 
+
 inform('Run "setup.py sdist --formats=tar" ')
-cmd_sdist = [sys.executable] + 'setup.py sdist --formats=tar'.split()
-ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
-if ec:  sys.exit(ec)
+cmd_sdist = [sys.executable] + "setup.py sdist --formats=tar".split()
+ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, "w"))
+if ec:
+    sys.exit(ec)
 inform("[done]\n")
 
-tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
+tarname = max(glob.glob(BASEDIR + "/dist/*.tar"), key=os.path.getmtime)
 
 tfin = tarfile.open(tarname)
-fpout = gzip.GzipFile(tarname + '.gz', 'w', mtime=0)
-tfout = tarfile.open(fileobj=fpout, mode='w')
+fpout = gzip.GzipFile(tarname + ".gz", "w", mtime=0)
+tfout = tarfile.open(fileobj=fpout, mode="w")
+
 
 def fixtarinfo(tinfo):
     tinfo.uid = tinfo.gid = 0
-    tinfo.uname = tinfo.gname = 'root'
+    tinfo.uname = tinfo.gname = "root"
     tinfo.mtime = timestamp
     tinfo.mode &= ~0o022
     return tinfo
 
-inform('Filter %s --> %s.gz ' % (2 * (os.path.basename(tarname),)))
+
+inform("Filter %s --> %s.gz " % (2 * (os.path.basename(tarname),)))
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 

doc/Makefile

@@ -31,4 +31,3 @@ clean:
 	rm -rf diffpy.srfitapi
 	rm -f srfit_examples.zip
 	$(MAKE) -C devmanual $@
-

doc/examples/coreshellnp.py

@@ -22,17 +22,15 @@
 """
 
 import numpy
-from scipy.optimize import leastsq
-
 from pyobjcryst import loadCrystal
+from scipy.optimize import leastsq
 
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
 
 ####### Example Code
 
+
 def makeRecipe(stru1, stru2, datname):
     """Create a fitting recipe for crystalline PDF data."""
 
@@ -43,7 +41,7 @@ def makeRecipe(stru1, stru2, datname):
     parser = PDFParser()
     parser.parseFile(datname)
     profile.loadParsedData(parser)
-    profile.setCalculationRange(xmin=1.5, xmax = 45, dx = 0.1)
+    profile.setCalculationRange(xmin=1.5, xmax=45, dx=0.1)
 
     ## The ProfileGenerator
     # In order to fit the core and shell phases simultaneously, we must use two
@@ -66,15 +64,16 @@ def makeRecipe(stru1, stru2, datname):
     contribution = FitContribution("cdszns")
     contribution.addProfileGenerator(generator_cds)
     contribution.addProfileGenerator(generator_zns)
-    contribution.setProfile(profile, xname = "r")
+    contribution.setProfile(profile, xname="r")
 
     # Set up the characteristic functions. We use a spherical CF for the core
     # and a spherical shell CF for the shell. Since this is set up as two
     # phases, we implicitly assume that the core-shell correlations contribute
     # very little to the PDF.
-    from diffpy.srfit.pdf.characteristicfunctions import sphericalCF, shellCF
-    contribution.registerFunction(sphericalCF, name = "f_CdS")
-    contribution.registerFunction(shellCF, name = "f_ZnS")
+    from diffpy.srfit.pdf.characteristicfunctions import shellCF, sphericalCF
+
+    contribution.registerFunction(sphericalCF, name="f_CdS")
+    contribution.registerFunction(shellCF, name="f_ZnS")
 
     # Write the fitting equation. We want to sum the PDFs from each phase and
     # multiply it by a scaling factor.
@@ -106,27 +105,28 @@ def makeRecipe(stru1, stru2, datname):
     # subsequent refinement.
     phase_cds = generator_cds.phase
     for par in phase_cds.sgpars.latpars:
-        recipe.addVar(par, name = par.name + "_cds", tag = "lat")
+        recipe.addVar(par, name=par.name + "_cds", tag="lat")
     for par in phase_cds.sgpars.adppars:
-        recipe.addVar(par, 1, name = par.name + "_cds", tag = "adp")
-    recipe.addVar(phase_cds.sgpars.xyzpars.z_1, name = "z_1_cds", tag = "xyz")
+        recipe.addVar(par, 1, name=par.name + "_cds", tag="adp")
+    recipe.addVar(phase_cds.sgpars.xyzpars.z_1, name="z_1_cds", tag="xyz")
     # Since we know these have stacking disorder, constrain the B33 adps for
     # each atom type.
     recipe.constrain("B33_1_cds", "B33_0_cds")
-    recipe.addVar(generator_cds.delta2, name = "delta2_cds", value = 5)
+    recipe.addVar(generator_cds.delta2, name="delta2_cds", value=5)
 
     phase_zns = generator_zns.phase
     for par in phase_zns.sgpars.latpars:
-        recipe.addVar(par, name = par.name + "_zns", tag = "lat")
+        recipe.addVar(par, name=par.name + "_zns", tag="lat")
     for par in phase_zns.sgpars.adppars:
-        recipe.addVar(par, 1, name = par.name + "_zns", tag = "adp")
-    recipe.addVar(phase_zns.sgpars.xyzpars.z_1, name = "z_1_zns", tag = "xyz")
+        recipe.addVar(par, 1, name=par.name + "_zns", tag="adp")
+    recipe.addVar(phase_zns.sgpars.xyzpars.z_1, name="z_1_zns", tag="xyz")
     recipe.constrain("B33_1_zns", "B33_0_zns")
-    recipe.addVar(generator_zns.delta2, name = "delta2_zns", value = 2.5)
+    recipe.addVar(generator_zns.delta2, name="delta2_zns", value=2.5)
 
     # Give the recipe away so it can be used!
     return recipe
 
+
 def plotResults(recipe):
     """Plot the results contained within a refined FitRecipe."""
 
@@ -138,10 +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)
@@ -163,6 +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
 
@@ -172,23 +174,23 @@ def main():
     # Start with the lattice parameters. In makeRecipe, these were tagged with
     # "lat". Here is how we use that.
     recipe.free("lat")
-    leastsq(recipe.residual, recipe.values, maxfev = 50)
+    leastsq(recipe.residual, recipe.values, maxfev=50)
 
     # Now the scale and phase fraction.
     recipe.free("scale", "scale_CdS")
-    leastsq(recipe.residual, recipe.values, maxfev = 50)
+    leastsq(recipe.residual, recipe.values, maxfev=50)
 
     # The ADPs.
     recipe.free("adp")
-    leastsq(recipe.residual, recipe.values, maxfev = 100)
+    leastsq(recipe.residual, recipe.values, maxfev=100)
 
     # The delta2 parameters.
     recipe.free("delta2_cds", "delta2_zns")
-    leastsq(recipe.residual, recipe.values, maxfev = 50)
+    leastsq(recipe.residual, recipe.values, maxfev=50)
 
     # The shape parameters.
     recipe.free("radius", "thickness")
-    leastsq(recipe.residual, recipe.values, maxfev = 50)
+    leastsq(recipe.residual, recipe.values, maxfev=50)
 
     # The positional parameters.
     recipe.free("xyz")
@@ -202,6 +204,7 @@ def main():
     plotResults(recipe)
     return
 
+
 if __name__ == "__main__":
     main()
 

doc/examples/crystalpdf.py

@@ -26,17 +26,15 @@
 """
 
 import numpy
+from gaussianrecipe import scipyOptimize
 
-from diffpy.structure import Structure
+from diffpy.srfit.fitbase import FitContribution, FitRecipe, FitResults, Profile
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
-from diffpy.srfit.fitbase import Profile
-from diffpy.srfit.fitbase import FitContribution, FitRecipe
-from diffpy.srfit.fitbase import FitResults
-
-from gaussianrecipe import scipyOptimize
+from diffpy.structure import Structure
 
 ####### Example Code
 
+
 def makeRecipe(ciffile, datname):
     """Create a fitting recipe for crystalline PDF data."""
 
@@ -53,7 +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,
@@ -72,7 +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()
@@ -95,6 +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
@@ -124,6 +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."""
 
@@ -135,17 +135,19 @@ 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__":
 
     # Make the data and the recipe