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

MANIFEST.in

@@ -9,4 +9,3 @@ include doc/examples/README
 recursive-include doc/manual/source *.rst *.txt
 include doc/manual/source/conf.py
 include doc/manual/Makefile
-

devutils/prep.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env python
 # Run examples and other scripts that should be updated before release.
 
-import io, os, sys
+import io
+import os
 import re
+import sys
 
 __basedir__ = os.getcwdu()
 
@@ -25,15 +27,15 @@ def test(self, call, *args, **kwds):
         except Exception, e:
             self.messages.append("%s: error, details below.\n%s" %(testname, e))
         finally:
-            os.chdir(__basedir__)    
-        
+            os.chdir(__basedir__)
+
     def report(self):
         print '==== Results of Tests ===='
         print '\n'.join(self.messages)
-        
+
 def scrubeol(directory, filerestr):
     """Use unix-style endlines for files in directory matched by regex string.
-    
+
     Parameters
     ----------
     directory - A directory to scrub
@@ -42,22 +44,22 @@ def scrubeol(directory, filerestr):
     os.chdir(directory)
     files = [re.match(filerestr, f) for f in os.listdir(".")]
     files = [f.group(0) for f in files if f]
-    
+
     for f in files:
         original = open(f)
         text = unicode(original.read())
         original.close()
-        
+
         updated = io.open(f, 'w', newline='\n')
         updated.write(text)
         updated.close()
-        
+
         print "Updated %s to unix-style endlines." %f
 
 
 def rm(directory, filerestr):
     """Delete files in directory matched by regex string.
-    
+
     Parameters
     ----------
     directory - A directory to scrub
@@ -66,20 +68,20 @@ def rm(directory, filerestr):
     os.chdir(directory)
     files = [re.match(filerestr, f) for f in os.listdir(".")]
     files = [f.group(0) for f in files if f]
-    
+
     for f in files:
         os.remove(f)
-        
+
         print "Deleted %s." %f
-    
+
 
 
 if __name__ == "__main__":
 
     # Temporarily add examples to path
     lib_path = os.path.abspath(os.path.join('..','doc','examples'))
     sys.path.append(lib_path)
-    
+
     # Delete existing files that don't necessarily have a fixed name.
     rm("../doc/examples/output", r"known_dG.*\.pwa")
     rm("../doc/examples/output", r"unknown_dG.*\.pwa")
@@ -88,7 +90,7 @@ def rm(directory, filerestr):
     examples = Test()
     test_names = ["extract_single_peak",
                   "parameter_summary",
-                  "fit_initial", 
+                  "fit_initial",
                   "query_results",
                   "multimodel_known_dG1",
                   "multimodel_known_dG2",
@@ -103,11 +105,11 @@ def rm(directory, filerestr):
         examples.test(test.run, plot=False)
 
     examples.report()
-    
+
     ### Convert output of example files to Unix-style endlines for sdist.
     if os.linesep != '\n':
         print "==== Scrubbing Endlines ===="
         # All *.srmise and *.pwa files in examples directory.
         scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)")
 
-        
+

diffpy/__init__.py

@@ -20,7 +20,7 @@
 """
 
 
-__import__('pkg_resources').declare_namespace(__name__)
+__import__("pkg_resources").declare_namespace(__name__)
 
 
 # End of file

diffpy/srmise/__init__.py

@@ -13,18 +13,28 @@
 
 """Tools for peak extraction from PDF."""
 
-__all__ = ["basefunction", "srmiseerrors", "srmiselog", "dataclusters",
-           "modelcluster", "modelparts", "pdfdataset", "pdfpeakextraction",
-           "peakextraction", "peakstability", "multimodelselection"]
-
-from diffpy.srmise.version import __version__
+__all__ = [
+    "basefunction",
+    "srmiseerrors",
+    "srmiselog",
+    "dataclusters",
+    "modelcluster",
+    "modelparts",
+    "pdfdataset",
+    "pdfpeakextraction",
+    "peakextraction",
+    "peakstability",
+    "multimodelselection",
+]
 
 from basefunction import BaseFunction
 from dataclusters import DataClusters
 from modelcluster import ModelCluster, ModelCovariance
 from modelparts import ModelPart, ModelParts
+from multimodelselection import MultimodelSelection
 from pdfdataset import PDFDataSet
 from pdfpeakextraction import PDFPeakExtraction
 from peakextraction import PeakExtraction
 from peakstability import PeakStability
-from multimodelselection import MultimodelSelection
+
+from diffpy.srmise.version import __version__

diffpy/srmise/applications/extract.py

@@ -11,9 +11,11 @@
 #
 ##############################################################################
 
-from optparse import OptionParser, OptionGroup
-import numpy as np
+from optparse import OptionGroup, OptionParser
+
 import matplotlib.pyplot as plt
+import numpy as np
+
 
 def main():
     """Default SrMise entry-point."""
@@ -78,7 +80,7 @@ def main():
                           version=version,
                           formatter=IndentedHelpFormatterWithNL())
 
-    parser.set_defaults(plot=False, liveplot=False, wait=False, 
+    parser.set_defaults(plot=False, liveplot=False, wait=False,
                         performextraction=True, verbosity="warning")
     dg_defaults = {'absolute':None, 'data':None, 'max-fraction':.05,
                    'ptp-fraction':.05, 'dG-fraction':1.}
@@ -203,7 +205,7 @@ def main():
                           "'absolute'=%s\n"
                           "'max-fraction'=%s\n"
                           "'ptp-fraction'=%s\n"
-                          "'dG-fraction'=%s" %(dg_defaults['absolute'], 
+                          "'dG-fraction'=%s" %(dg_defaults['absolute'],
                                                dg_defaults['max-fraction'],
                                                dg_defaults['ptp-fraction'],
                                                dg_defaults['dG-fraction']))
@@ -269,8 +271,7 @@ def main():
     srmiselog.setlevel(options.verbosity)
 
     from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction
-    from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, \
-                                           SrMiseFileError
+    from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
     if options.peakfunction is not None:
         from diffpy.srmise import peaks
@@ -364,7 +365,7 @@ def main():
         elif options.dg_mode == "ptp-fraction":
             pdict["effective_dy"] = options.dg*ext.y.ptp()*np.ones(len(ext.y))
         elif options.dg_mode == "dG-fraction":
-            pdict["effective_dy"] = options.dg*ext.dy            
+            pdict["effective_dy"] = options.dg*ext.dy
         if options.rng is not None:
             pdict["rng"] = list(options.rng)
         if options.qmax is not None:
@@ -403,7 +404,7 @@ def main():
                 print err
                 print "Could not save pwa summary to '%s'." %options.pwafile
 
-        
+
         print ext
         if cov is not None:
             print cov
@@ -442,8 +443,9 @@ def parsepars(mp, parseq):
 # Borrowed, with minor changes, from
 # http://groups.google.com/group/comp.lang.python/browse_frm/thread/6df6e6b541a15bc2/09f28e26af0699b1
 
-from optparse import IndentedHelpFormatter
 import textwrap
+from optparse import IndentedHelpFormatter
+
 
 class IndentedHelpFormatterWithNL(IndentedHelpFormatter):
   def _format_text(self, text):

diffpy/srmise/applications/plot.py

@@ -12,18 +12,17 @@
 ##############################################################################
 """plot extracted peaks and comparison to ideal distances (if given)"""
 
-import sys
 import optparse
-
-from diffpy.srmise import PDFPeakExtraction, PeakStability
-from diffpy.srmise.pdfpeakextraction import resample
+import sys
 
 import matplotlib.pyplot as plt
+import mpl_toolkits.axisartist as AA
 import numpy as np
-
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
-import mpl_toolkits.axisartist as AA
+
+from diffpy.srmise import PDFPeakExtraction, PeakStability
+from diffpy.srmise.pdfpeakextraction import resample
 
 # For a given figure, returns a label of interest
 labeldict = {}

diffpy/srmise/basefunction.py

@@ -12,14 +12,15 @@
 ##############################################################################
 """Defines BaseFunction, the base class for mathematical functions in srmise."""
 
-import sys
+import logging
 import re
+import sys
 
 import numpy as np
+
+from diffpy.srmise.modelparts import ModelPart, ModelParts
 from diffpy.srmise.srmiseerrors import *
-from diffpy.srmise.modelparts import ModelParts, ModelPart
 
-import logging
 logger = logging.getLogger("diffpy.srmise")
 
 class BaseFunction(object):

diffpy/srmise/baselines/__init__.py

@@ -13,8 +13,8 @@
 
 __all__ = ["base", "arbitrary", "fromsequence", "nanospherical", "polynomial"]
 
-from base import Baseline
 from arbitrary import Arbitrary
+from base import Baseline
 from fromsequence import FromSequence
 from nanospherical import NanoSpherical
 from polynomial import Polynomial

diffpy/srmise/baselines/arbitrary.py

@@ -11,13 +11,15 @@
 #
 ##############################################################################
 
+import logging
+
+import matplotlib.pyplot as plt
 import numpy as np
+
+import diffpy.srmise.srmiselog
 from diffpy.srmise.baselines.base import BaselineFunction
 from diffpy.srmise.srmiseerrors import SrMiseEstimationError
 
-import matplotlib.pyplot as plt
-
-import logging, diffpy.srmise.srmiselog
 logger = logging.getLogger("diffpy.srmise")
 
 class Arbitrary (BaselineFunction):