fix too many leading #, import modules, and unused var (#29)

Author: stevenhua0320

Diff for: diffpy/srmise/peaks/gaussian.py

@@ -13,10 +13,8 @@
 
 import logging
 
-import matplotlib.pyplot as plt
 import numpy as np
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.peaks.base import PeakFunction
 from diffpy.srmise.srmiseerrors import SrMiseEstimationError, SrMiseScalingError, SrMiseTransformationError
 
@@ -59,7 +57,7 @@ def __init__(self, maxwidth, Cache=None):
             raise ValueError(emsg)
         self.maxwidth = maxwidth
 
-        ### Useful constants ###
+        # Useful constants ###
         # c1 and c2 help with function values
         self.c1 = self.maxwidth * np.sqrt(np.pi / (8 * np.log(2)))
         self.c2 = self.maxwidth**2 / (8 * np.log(2))
@@ -73,7 +71,7 @@ def __init__(self, maxwidth, Cache=None):
 
         return
 
-    #### Methods required by PeakFunction ####
+    # Methods required by PeakFunction ####
 
     def estimate_parameters(self, r, y):
         """Estimate parameters for single peak from data provided.
@@ -102,11 +100,10 @@ def estimate_parameters(self, r, y):
             emsg = "Not enough data for successful estimation."
             raise SrMiseEstimationError(emsg)
 
-        #### Estimation ####
+        # Estimation ####
         guesspars = np.array([0.0, 0.0, 0.0], dtype=float)
         min_y = use_y.min()
         max_y = use_y.max()
-        center = use_r[use_y.argmax()]
 
         if min_y != max_y:
             weights = (use_y - min_y) ** 2
@@ -204,7 +201,7 @@ def _jacobianraw(self, pars, r, free):
               needed.  True for evaluation, False for no evaluation.
         """
         jacobian = [None, None, None]
-        if (free == False).sum() == self.npars:
+        if (free is False).sum() == self.npars:
             return jacobian
 
         # Optimization
@@ -228,8 +225,8 @@ def _jacobianraw(self, pars, r, free):
             # derivative with respect to peak area
             # abs'(x)=sign(x) for real x except at 0 where it is undetermined.  Since any real peak necessarily has
             # non-zero area and the function is paramaterized such that values of either sign represent equivalent
-            # curves I arbitrarily choose positive sign for pars[2]==0 in order to push the system back into a realistic
-            # parameter space should this improbable scenario occur.
+            # curves I arbitrarily choose positive sign for pars[2]==0 in order to
+            # push the system back into a realistic parameter space should this improbable scenario occur.
             #   jacobian[2] = sign(pars[2])*exp_p
             if pars[2] >= 0:
                 jacobian[2] = exp_p
@@ -321,7 +318,7 @@ def _valueraw(self, pars, r):
     def getmodule(self):
         return __name__
 
-    #### Other methods ####
+    # Other methods ####
 
     def max(self, pars):
         """Return position and height of the peak maximum."""

Diff for: diffpy/srmise/peaks/gaussianoverr.py

@@ -13,10 +13,8 @@
 
 import logging
 
-import matplotlib.pyplot as plt
 import numpy as np
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.peaks.base import PeakFunction
 from diffpy.srmise.srmiseerrors import SrMiseEstimationError, SrMiseScalingError, SrMiseTransformationError
 
@@ -59,7 +57,7 @@ def __init__(self, maxwidth, Cache=None):
             raise ValueError(emsg)
         self.maxwidth = maxwidth
 
-        ### Useful constants ###
+        # Useful constants ###
         # c1 and c2 help with function values
         self.c1 = self.maxwidth * np.sqrt(np.pi / (8 * np.log(2)))
         self.c2 = self.maxwidth**2 / (8 * np.log(2))
@@ -73,7 +71,7 @@ def __init__(self, maxwidth, Cache=None):
 
         return
 
-    #### Methods required by PeakFunction ####
+    # Methods required by PeakFunction ####
 
     def estimate_parameters(self, r, y):
         """Estimate parameters for single peak from data provided.
@@ -102,11 +100,10 @@ def estimate_parameters(self, r, y):
             emsg = "Not enough data for successful estimation."
             raise SrMiseEstimationError(emsg)
 
-        #### Estimation ####
+        # Estimation ####
         guesspars = np.array([0.0, 0.0, 0.0], dtype=float)
         min_y = use_y.min()
         max_y = use_y.max()
-        center = use_r[use_y.argmax()]
 
         if min_y != max_y:
             weights = (use_y - min_y) ** 2
@@ -218,7 +215,7 @@ def _jacobianraw(self, pars, r, free):
               needed.  True for evaluation, False for no evaluation.
         """
         jacobian = [None, None, None]
-        if (free == False).sum() == self.npars:
+        if (free is False).sum() == self.npars:
             return jacobian
 
         # Optimization
@@ -242,8 +239,8 @@ def _jacobianraw(self, pars, r, free):
             # derivative with respect to peak area
             # abs'(x)=sign(x) for real x except at 0 where it is undetermined.  Since any real peak necessarily has
             # non-zero area and the function is paramaterized such that values of either sign represent equivalent
-            # curves I arbitrarily choose positive sign for pars[2]==0 in order to push the system back into a realistic
-            # parameter space should this improbable scenario occur.
+            # curves I arbitrarily choose positive sign for pars[2]==0 in order to
+            # push the system back into a realistic parameter space should this improbable scenario occur.
             #   jacobian[2] = sign(pars[2])*exp_p
             if pars[2] >= 0:
                 jacobian[2] = exp_p
@@ -387,7 +384,7 @@ def _valueraw(self, pars, r):
     def getmodule(self):
         return __name__
 
-    #### Other methods ####
+    # Other methods ####
 
     def max(self, pars):
         """Return position and height of the peak maximum."""

Diff for: diffpy/srmise/peaks/terminationripples.py

@@ -16,7 +16,6 @@
 import numpy as np
 import scipy.fftpack as fp
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.peaks.base import PeakFunction
 
 logger = logging.getLogger("diffpy.srmise")
@@ -55,7 +54,7 @@ def __init__(self, base, qmax, extension=4.0, supersample=5.0, Cache=None):
         PeakFunction.__init__(self, parameterdict, formats, default_formats, metadict, base, Cache)
         return
 
-    #### Methods required by PeakFunction ####
+    # Methods required by PeakFunction ####
 
     # TODO: A smart way to convert from the basefunctions estimate to an
     # appropriate one when ripples are considered.  This may not be necessary,
@@ -122,7 +121,7 @@ def _valueraw(self, pars, r):
         r: sequence or scalar over which pars is evaluated"""
         return self.base._valueraw(pars, r)
 
-    #### Overridden PeakFunction functions ####
+    # Overridden PeakFunction functions ####
     # jacobian() and value() are not normally overridden by PeakFunction
     # subclasses, but are here to minimize the effect of edge-effects while
     # introducing termination ripples.
@@ -236,7 +235,7 @@ def value(self, peak, r, rng=None):
     def getmodule(self):
         return __name__
 
-    #### Other methods ####
+    # Other methods ####
 
     def cut_freq(self, sequence, delta):
         """Remove high-frequency components from sequence.
@@ -278,10 +277,10 @@ def extend_grid(self, r, dr):
     from numpy.random import randn
 
     from diffpy.srmise.modelcluster import ModelCluster
-    from diffpy.srmise.modelevaluator import AICc
-    from diffpy.srmise.peakfunctions.gaussianoverr import GaussianOverR
-    from diffpy.srmise.peakfunctions.peaks import Peaks
-    from diffpy.srmise.peakfunctions.terminationripples import TerminationRipples
+    from diffpy.srmise.modelevaluators import AICc
+    from diffpy.srmise.peaks import Peaks
+    from diffpy.srmise.peaks.gaussianoverr import GaussianOverR
+    from diffpy.srmise.peaks.terminationripples import TerminationRipples
 
     res = 0.01
     r = np.arange(2, 4, res)

Diff for: diffpy/srmise/peakstability.py

@@ -40,7 +40,7 @@ def setppe(self, ppe):
     def load(self, filename):
         try:
             import cPickle as pickle
-        except:
+        except ImportError:
             import pickle
 
         in_s = open(filename, "rb")
@@ -68,7 +68,7 @@ def load(self, filename):
     def save(self, filename):
         try:
             import cPickle as pickle
-        except:
+        except ImportError:
             import pickle
         out_s = open(filename, "wb")
         try:
@@ -150,7 +150,7 @@ def animate(self, results=None, step=False, **kwds):
         self.setcurrent(0)
         plt.ion()
         plt.plot(*self.ppe.extracted.plottable())
-        a = plt.axis()
+        plt.axis()
         for i in results:
             self.setcurrent(i)
             plt.ioff()

Diff for: diffpy/srmise/srmiseerrors.py

@@ -28,7 +28,7 @@
    """
 
 
-### Superclass class for diffpy.srmise.mise
+# Superclass class for diffpy.srmise.mise
 class SrMiseError(Exception):
     """Superclass of all diffpy.srmise exceptions."""
 
@@ -43,7 +43,7 @@ def __str__(self):
         return self.info
 
 
-### SrMiseError subclasses ###
+# SrMiseError subclasses ###
 
 
 class SrMiseDataFormatError(SrMiseError):