fix import module not used & string check

devutils/prep.py

@@ -8,6 +8,8 @@
 
 __basedir__ = os.getcwdu()
 
+from numpy.compat import unicode
+
 # Example imports
 
 
@@ -86,7 +88,7 @@ def rm(directory, filerestr):
     rm("../doc/examples/output", r"known_dG.*\.pwa")
     rm("../doc/examples/output", r"unknown_dG.*\.pwa")
 
-    ### Testing examples
+    # Testing examples
     examples = Test()
     test_names = [
         "extract_single_peak",
@@ -108,7 +110,7 @@ def rm(directory, filerestr):
 
     examples.report()
 
-    ### Convert output of example files to Unix-style endlines for sdist.
+    # 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.

diffpy/srmise/applications/extract.py

@@ -11,7 +11,8 @@
 #
 ##############################################################################
 
-from optparse import OptionGroup, OptionParser
+import textwrap
+from optparse import IndentedHelpFormatter, OptionGroup, OptionParser
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -539,7 +540,6 @@ def main():
         cov = None
         if options.performextraction:
             cov = ext.extract()
-        out = ext.extracted
 
         if options.savefile is not None:
             try:
@@ -591,13 +591,10 @@ def parsepars(mp, parseq):
     return mp.actualize(pars, "internal", free=free)
 
 
-### Class to preserve newlines in optparse
+# Class to preserve newlines in optparse
 # Borrowed, with minor changes, from
 # http://groups.google.com/group/comp.lang.python/browse_frm/thread/6df6e6b541a15bc2/09f28e26af0699b1
 
-import textwrap
-from optparse import IndentedHelpFormatter
-
 
 class IndentedHelpFormatterWithNL(IndentedHelpFormatter):
     def _format_text(self, text):
@@ -652,7 +649,7 @@ def format_option(self, option):
         return "".join(result)
 
 
-### End class
+# End class
 
 if __name__ == "__main__":
     main()

diffpy/srmise/applications/plot.py

@@ -19,7 +19,6 @@
 import mpl_toolkits.axisartist as AA
 import numpy as np
 from matplotlib.ticker import MultipleLocator
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 
 from diffpy.srmise import PDFPeakExtraction, PeakStability
@@ -107,7 +106,6 @@ def comparepositions(ppe, ip=None, **kwds):
     plt.plot(xe, ye, "g", lw=1.5, **ep_style)
 
     if ip is not None:
-        yb = (base, base)
         plt.axhline(base, linestyle=":", color="k")
         ax.yaxis.set_ticks([base + 0.5 * yideal, base + 0.5 * yext])
         ax.yaxis.set_ticklabels([yideal_label, yext_label])
@@ -134,7 +132,7 @@ def comparepositions(ppe, ip=None, **kwds):
 
 
 def dgseries(stability, **kwds):
-    ax = kwds.get("ax", plt.gca())
+    kwds.get("ax", plt.gca())
     dg_style = kwds.get("dg_style", default_dg_style)
 
     scale = kwds.get("scale", 1.0)
@@ -222,7 +220,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
     bottom_offset = kwds.get("bottom_offset", 3.0)
 
     # Style options
-    dg_style = kwds.get("dg_style", default_dg_style)
+    kwds.get("dg_style", default_dg_style)
     gobs_style = kwds.get("gobs_style", default_gobs_style)
     gfit_style = kwds.get("gfit_style", default_gfit_style)
     gind_style = kwds.get("gind_style", default_gind_style)
@@ -240,7 +238,7 @@ def makeplot(ppe_or_stability, ip=None, **kwds):
     # Other options
     datalabel = kwds.get("datalabel", None)
     dgformatstr = kwds.get("dgformatstr", r"$\delta$g=%f")
-    dgformatpost = kwds.get("dgformatpost", None)  # ->userfunction(string)
+    kwds.get("dgformatpost", None)  # ->userfunction(string)
     show_fit = kwds.get("show_fit", True)
     show_individual = kwds.get("show_individual", True)
     fill_individual = kwds.get("fill_individual", True)
@@ -532,7 +530,6 @@ def on_draw(event):
 
 def readcompare(filename):
     """Returns a list of distances read from filename, otherwise None."""
-    from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
     # TODO: Make this safer
     try:
@@ -551,7 +548,7 @@ def readcompare(filename):
     try:
         for line in datastring.split("\n"):
             distances.append(float(line))
-    except (ValueError, IndexError) as err:
+    except (ValueError, IndexError):
         print("Could not read distances from '%s'. Ignoring file." % filename)
 
     if len(distances) == 0:
@@ -620,7 +617,7 @@ def main():
         distances = readcompare(opts.compare)
 
     setfigformat(figsize=(6.0, 4.0))
-    figdict = makeplot(toplot, distances)
+    makeplot(toplot, distances)
     if opts.output:
         plt.savefig(opts.output, format=opts.format, dpi=600)
     if opts.show:

diffpy/srmise/basefunction.py

@@ -19,8 +19,7 @@
 import numpy as np
 from numpy.compat import unicode
 
-from diffpy.srmise.modelparts import ModelPart, ModelParts
-from diffpy.srmise.srmiseerrors import *
+from diffpy.srmise.srmiseerrors import SrMiseDataFormatError
 
 logger = logging.getLogger("diffpy.srmise")
 
@@ -120,7 +119,7 @@ def __init__(
             emsg = "Argument default_formats must specify 'default_input' " + "and 'default_output' as keys."
             raise ValueError(emsg)
         for f in self.default_formats.values():
-            if not f in self.parformats:
+            if f not in self.parformats:
                 emsg = "Keys of argument default_formats must map to a " + "value within argument parformats."
                 raise ValueError()
 
@@ -140,7 +139,7 @@ def __init__(
             pass
         return
 
-    #### "Virtual" class methods ####
+    # "Virtual" class methods ####
 
     def actualize(self, *args, **kwds):
         """Create ModelPart instance of self with given parameters.  ("Virtual" method)"""
@@ -172,7 +171,7 @@ def _valueraw(self, *args, **kwds):
         emsg = "_valueraw must() be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
-    #### Class methods ####
+    # Class methods ####
 
     def jacobian(self, p, r, rng=None):
         """Calculate jacobian of p, possibly restricted by range.
@@ -228,9 +227,9 @@ def transform_derivatives(self, pars, in_format=None, out_format=None):
         elif out_format == "default_input":
             out_format = self.default_formats["default_input"]
 
-        if not in_format in self.parformats:
+        if in_format not in self.parformats:
             raise ValueError("Argument 'in_format' must be one of %s." % self.parformats)
-        if not out_format in self.parformats:
+        if out_format not in self.parformats:
             raise ValueError("Argument 'out_format' must be one of %s." % self.parformats)
         if in_format == out_format:
             return np.identity(self.npars)
@@ -263,9 +262,9 @@ def transform_parameters(self, pars, in_format=None, out_format=None):
         elif out_format == "default_input":
             out_format = self.default_formats["default_input"]
 
-        if not in_format in self.parformats:
+        if in_format not in self.parformats:
             raise ValueError("Argument 'in_format' must be one of %s." % self.parformats)
-        if not out_format in self.parformats:
+        if out_format not in self.parformats:
             raise ValueError("Argument 'out_format' must be one of %s." % self.parformats)
         # if in_format == out_format:
         #    return pars
@@ -335,7 +334,7 @@ def writestr(self, baselist):
         """
         if self.base is not None and self.base not in baselist:
             emsg = "baselist does not include this BaseFunction's base function."
-            raise ValueError("emsg")
+            raise ValueError(emsg)
         lines = []
         # Write function type
         lines.append("function=%s" % repr(self.__class__.__name__))

doc/examples/parameter_summary.py

@@ -37,25 +37,25 @@
 
 def run(plot=True):
 
-    ## Initialize peak extraction
+    # Initialize peak extraction
     # Create peak extraction object
     ppe = PDFPeakExtraction()
 
     # Load the PDF from a file
     ppe.loadpdf("data/TiO2_fine_qmax26.gr")
 
-    ###### Set up extraction parameters.
+    # Set up extraction parameters.
     # In this section we'll examine the major extraction parameters in detail.
     # diffpy.srmise strives to provide reasonable default values for these
     # parameters.  For normal use setting the range, baseline, and uncertainty
     # should be sufficient.
     kwds = {}
 
-    ## Range
+    # Range
     # Range defaults to the entire PDF if not specified.
     kwds["rng"] = [1.5, 10.0]
 
-    ## dg
+    # dg
     # diffpy.srmise selects model complexity based primarily on the uncertainty
     # of the PDF.  Note that very small uncertainties (<1%) can make peak
     # extraction excessively slow.  In general, the smaller the uncertainty the
@@ -80,7 +80,7 @@ def run(plot=True):
     #     1273-1283. doi:10.1107/S1600576714010516
     kwds["dg"] = 0.35  # Play with this value!
 
-    ## baseline
+    # baseline
     # As a crystal PDF, a linear baseline crossing the origin is appropriate.
     # Here we define the linear baseline B(r) = -.5*r + 0, and explicitly set
     # the y-intercept as a fixed parameter which will not be fit.  For
@@ -91,7 +91,7 @@ def run(plot=True):
     slope = -0.65  # Play with this value!
     y_intercept = 0.0
     kwds["baseline"] = blfunc.actualize([slope, y_intercept], free=[True, False])
-    ## pf
+    # pf
     # The pf (peakfunction) parameter allows setting the shape of peaks to be
     # extracted.  Termination effects are added automatically to the peak
     # function during extraction.  In the harmonic approximation of atomic
@@ -109,7 +109,7 @@ def run(plot=True):
     pf = GaussianOverR(0.7)
     kwds["pf"] = [pf]  # Despite the list, only one entry is currently supported.
 
-    ## qmax
+    # qmax
     # PDFs typically report the value of qmax (i.e. the maximum momentum
     # transfer q in the measurement), but it can be specified explicitly also.
     # If the PDF does not report qmax, diffpy.srmise attempts to estimate it
@@ -119,7 +119,7 @@ def run(plot=True):
     # diffpy.srmise does not consider Nyquist sampling or termination effects.
     kwds["qmax"] = 26.0
 
-    ## nyquist
+    # nyquist
     # This parameter governs whether diffpy.srmise attempts to find a model
     # on a Nyquist-sampled grid with dr=pi/qmax, which is a grid where data
     # uncertainties are least correlated without loss of information.  By
@@ -132,7 +132,7 @@ def run(plot=True):
     #     doi:10.1103/PhysRevB.84.134105
     kwds["nyquist"] = True
 
-    ## supersample
+    # supersample
     # This parameter dictates the data be oversampled by at least this factor
     # (relative to the Nyquist rate) during the early stages of peak
     # extraction. If the input PDF is even more finely sampled, that level of
@@ -141,7 +141,7 @@ def run(plot=True):
     # finding and clustering process, but reduces speed.
     kwds["supersample"] = 4.0
 
-    ## cres
+    # cres
     # The cres (clustering resolution) parameter governs the sensitivity of the
     # clustering method used by diffpy.srmise.  In short, when the data are
     # being clustered, data which are further than the clustering resolution
@@ -156,7 +156,7 @@ def run(plot=True):
     # Apply peak extraction parameters.
     ppe.setvars(**kwds)
 
-    ## initial_peaks
+    # initial_peaks
     # Initial peaks are peaks which are kept fixed during the early stages of
     # peak extraction, effectively condition results upon their values.  Since
     # initial peaks are sometimes dependent on other SrMise parameters (e.g.
@@ -168,7 +168,7 @@ def run(plot=True):
     # diffpy.srmise estimate the peak parameters.
     # 2) Explicit specification of peak parameters.
 
-    ## Initial peaks from approximate positions.
+    # Initial peaks from approximate positions.
     # This routine estimates peak parameters by finding the peak-like cluster
     # containing the specified point.  It does not search for occluded peaks,
     # so works best on well-separated peaks.  It does, however, take any
@@ -177,7 +177,7 @@ def run(plot=True):
     for p in positions:
         ppe.estimate_peak(p)  # adds to initial_peaks
 
-    ## Initial peaks from explicit parameters.
+    # Initial peaks from explicit parameters.
     # Adding initial peaks explicitly is similar to defining a baseline.
     # Namely, choosing a peak function and then actualizing it with given
     # parameters. For this example peaks are created from the same GaussianOverR
@@ -194,22 +194,22 @@ def run(plot=True):
         peaks.append(pf.actualize(p, free=[True, False, True], in_format="pwa"))
     ppe.add_peaks(peaks)  # adds to initial_peaks
 
-    ## Initial peaks and pruning
+    # Initial peaks and pruning
     # While initial peaks condition what other peaks can be extracted, by
     # default they can also be pruned if a simpler model appears better.  To
     # prevent this, they can be set as non-removable.
     for ip in ppe.initial_peaks:
         ip.removable = False
 
-    ## Plot initial parameters
+    # Plot initial parameters
     if plot:
         makeplot(ppe)
         plt.title("Initial Peaks")
 
-    ###### Perform peak extraction
+    # Perform peak extraction
     ppe.extract()
 
-    ## Save output
+    # Save output
     # The write() method saves a file which preserves all aspects of peak
     # extraction and its results, by convention using the .srmise extension,
     # and which can later be read by diffpy.srmise.
@@ -222,7 +222,7 @@ def run(plot=True):
     ppe.write("output/parameter_summary.srmise")
     ppe.writepwa("output/parameter_summary.pwa")
 
-    ## Plot results.
+    # Plot results.
     # Display plot of extracted peak.  It is also possible to plot an existing
     # .srmise file from the command line using
     #     srmise output/TiO2_parameterdetail.srmise --no-extract --plot