Initial reformatting

diffpy/pdfmorph/log.py

@@ -29,9 +29,9 @@
 def set_verbosity(vb):
     '''Set verbosity of the pdfmorph logger.
 
-    vb   -- integer or one of ('debug', 'info', 'warning', 'error') strings
+    :param vb: integer or one of ('debug', 'info', 'warning', 'error') strings.
 
-    No return value.
+    :return: No return value.
     '''
     try:
         if type(vb) is str:

diffpy/pdfmorph/pdfplot.py

@@ -26,19 +26,13 @@
 def plotPDFs(pairlist, labels=None, offset='auto', rmin=None, rmax=None):
     """Plots several PDFs on top of one another.
 
-    pairlist    --  iterable of (r, gr) pairs to plot
-    labels      --  iterable of names for the pairs. If this is not the same
-                    length as the pairlist, a legend will not be shown (default
-                    []).
-    offset      --  offset to place between plots. PDFs will be sequentially
-                    shifted in the y-direction by the offset. If offset is
-                    'auto' (default), the optimal offset will be determined
-                    automatically.
-    rmin        --  The minimum r-value to plot. If this is None (default), the
-                    lower bound of the PDF is not altered.
-    rmax        --  The maximum r-value to plot. If this is None (default), the
-                    upper bound of the PDF is not altered.
-
+    :param pairlist: iterable of (r, gr) pairs to plot
+    :param labels: iterable of names for the pairs. If this is not the same length as the pairlist, a legend will not
+        be shown (default []).
+    :param offset: offset to place between plots. PDFs will be sequentially shifted in the y-direction by the offset.
+        If offset is 'auto' (default), the optimal offset will be determined automatically.
+    :param rmin: The minimum r-value to plot. If this is None (default), the lower bound of the PDF is not altered.
+    :param rmax: The maximum r-value to plot. If this is None (default), the upper bound of the PDF is not altered.
     """
     if labels is None:
         labels = []
@@ -76,26 +70,22 @@ def comparePDFs(
     legend=True,
     l_width=1.5,
 ):
-    """Plot two PDFs on top of each other and difference curve.
-
-    pairlist    --  iterable of (r, gr) pairs to plot
-    labels      --  iterable of names for the pairs. If this is not the same
-                    length as the pairlist, a legend will not be shown (default
-                    []).
-    rmin        --  The minimum r-value to plot. If this is None (default), the
-                    lower bound of the PDF is not altered.
-    rmax        --  The maximum r-value to plot. If this is None (default), the
-                    upper bound of the PDF is not altered.
-    show        --  Show the plot (True)
-    maglim      --  Point after which to magnify the signal by mag. If None
-                    (default), no magnification will take place.
-    mag         --  Magnification factor (default 5)
-    rw          --  Rw value to display on the plot, if any.
-    legend      --  Display the legend (default True).
-
-    The second PDF will be shown as blue circles below and the first as a red
-    line.  The difference curve will be in green and offset for clarity.
-
+    """Plots two PDFs on top of each other and difference curve.
+
+    :param pairlist: iterable of (r, gr) pairs to plot.
+    :param labels: iterable of names for the pairs. If this is not the same length as the pairlist, a legend will not
+        be shown (default []).
+    :param rmin: The minimum r-value to plot. If this is None (default), the lower bound of the PDF is not altered.
+    :param rmax: The maximum r-value to plot. If this is None (default), the upper bound of the PDF is not altered.
+    :param show: Show the plot (default True).
+    :param maglim: Point after which to magnify the signal by mag. If None (default), no magnification will take
+        place.
+    :param mag: Magnification factor (default 5)
+    :param rw: Rw value to display on the plot, if any.
+    :param legend: Display the legend (default True).
+
+    The second PDF will be shown as blue circles below and the first as a red line. The difference curve will be in
+    green and offset for clarity.
     """
     if labels is None:
         labels = [2]
@@ -210,14 +200,12 @@ def comparePDFs(
 def truncatePDFs(r, gr, rmin=None, rmax=None):
     """Truncate a PDF to specified bounds.
 
-    r           --  r-values of the PDF
-    gr          --  PDF values.
-    rmin        --  The minimum r-value. If this is None (default), the lower
-                    bound of the PDF is not altered.
-    rmax        --  The maximum r-value. If this is None (default), the upper
-                    bound of the PDF is not altered.
+    :param r: r-values of the PDF
+    :param gr: PDF values.
+    :param rmin: The minimum r-value. If this is None (default), the lower bound of the PDF is not altered.
+    :param rmax: The maximum r-value. If this is None (default), the upper bound of the PDF is not altered.
 
-    Returns the truncated r, gr
+    :return: Returns the truncated r, gr.
     """
 
     if rmin is not None:

diffpy/pdfmorph/refine.py

@@ -13,8 +13,7 @@
 #
 ##############################################################################
 
-"""refine -- Refine a morph or morph chain
-"""
+"""Refine a morph or morph chain."""
 
 from scipy.optimize import leastsq
 from scipy.stats import pearsonr
@@ -35,17 +34,16 @@ class Refiner(object):
     x_morph, y_morph  --  Morphed arrays.
     x_target, y_target  --  Target arrays.
     pars        --  List of names of parameters to be refined.
-    residual    --  The residual function to optimize. Default _residual. Can
-                    be assigned to other functions.
+    residual    --  The residual function to optimize. Default _residual. Can be assigned to other functions.
 
     """
 
     def __init__(self, chain, x_morph, y_morph, x_target, y_target):
         """Initialize the arrays.
 
-        chain       --  The Morph or MorphChain to refine
-        x_morph, y_morph  --  Morphed arrays.
-        x_target, y_target  --  Target arrays.
+        :param chain: The Morph or MorphChain to refine.
+        :param x_morph, y_morph: Morphed arrays.
+        :param x_target, y_target: Target arrays.
         """
         self.chain = chain
         self.x_morph = x_morph
@@ -74,9 +72,8 @@ def _residual(self, pvals):
     def _pearson(self, pvals):
         """Pearson correlation function.
 
-        This gives e**-p (vector), where p is the pearson correlation function.
-        We seek to minimize this, which occurrs when the correlation is the
-        largest.
+        This gives e**-p (vector), where p is the pearson correlation function. We seek to minimize this, which
+        occurs when the correlation is the largest.
         """
         self._update_chain(pvals)
         _x_morph, _y_morph, _x_target, _y_target = self.chain(
@@ -95,19 +92,16 @@ def _add_pearson(self, pvals):
     def refine(self, *args, **kw):
         """Refine the chain.
 
-        Additional arguments are used to specify which parameters are to be
-        refined. If no arguments are passed, then all parameters will be
-        refined.  Keywords pass initial values to the parameters, whether or
-        not they are refined.
+        Additional arguments are used to specify which parameters are to be refined. If no arguments are passed, then
+        all parameters will be refined. Keywords pass initial values to the parameters, whether or not they are
+        refined.
 
         This uses the leastsq algorithm from scipy.optimize.
 
-        This returns the final scalar residual value. The parameters from the
-        fit can be retrieved from the config dictionary of the morph or morph
-        chain.
-
-        Raises ValueError if a minimum cannot be found.
+        :return: This returns the final scalar residual value. The parameters from the fit can be retrieved from the
+            config dictionary of the morph or morph chain.
 
+        :raise ValueError: if a minimum cannot be found.
         """
 
         self.pars = args or self.chain.config.keys()
@@ -133,5 +127,4 @@ def refine(self, *args, **kw):
 
         return dot(fvec, fvec)
 
-
 # End class Refiner

diffpy/pdfmorph/tools.py

@@ -14,8 +14,7 @@
 ##############################################################################
 
 
-"""Tools used in morphs and morph chains.
-"""
+"""Tools used in morphs and morph chains."""
 
 
 import numpy
@@ -31,18 +30,14 @@ def estimateScale(y_morph_in, y_target_in):
 def estimateBaselineSlope(r, gr, rmin=None, rmax=None):
     """Estimate the slope of the linear baseline of a PDF.
 
-    This fits a the equation slope*r through the bottom of the PDF.
+    This fits an equation of the form slope*r through the bottom of the PDF.
 
-    r       --  The r-grid used for the PDF.
-    gr      --  The PDF over the r-grid.
-    rmin    --  The minimum r-value to consider. If this is None (default)
-                is None, then the minimum of r is used.
-    rmax    --  The maximum r-value to consider. If this is None (default)
-                is None, then the maximum of r is used.
-
-    Returns the slope of baseline. If the PDF is scaled properly, this is equal
-    to -4*pi*rho0.
+    :param r: The r-grid used for the PDF.
+    :param gr: The PDF over the r-grid.
+    :param rmin: The minimum r-value to consider. If this is None (default) is None, then the minimum of r is used.
+    :param rmax: The maximum r-value to consider. If this is None (default) is None, then the maximum of r is used.
 
+    :return: Returns the slope of baseline. If the PDF is scaled properly, this is equal to -4*pi*rho0.
     """
     from scipy.optimize import leastsq
     from numpy import dot
@@ -99,10 +94,9 @@ def get_pearson(chain):
 def readPDF(fname):
     """Reads an .gr file, loads r and G(r) vectors.
 
-    fname -- name of the file we want to read.
-
-    Returns r and gr arrays.
+    :param fname: name of the file we want to read.
 
+    :return: Returns r and gr arrays.
     """
     from diffpy.utils.parsers import loadData
 

diffpy/pdfmorph/version.py

@@ -13,8 +13,7 @@
 #
 ##############################################################################
 
-"""Definition of __version__ and __date__ for diffpy.pdfmorph.
-"""
+"""Definition of __version__ and __date__ for diffpy.pdfmorph."""
 
 
 # obtain version information