Merge branch 'Cookie' of github.com:diffpy/diffpy.srmise into Cookie

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__))

diffpy/srmise/baselines/arbitrary.py

@@ -13,10 +13,8 @@
 
 import logging
 
-import matplotlib.pyplot as plt
 import numpy as np
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.baselines import Polynomial
 from diffpy.srmise.baselines.base import BaselineFunction
 from diffpy.srmise.srmiseerrors import SrMiseEstimationError
@@ -97,7 +95,7 @@ def __init__(self, npars, valuef, jacobianf=None, estimatef=None, Cache=None):
         metadict["estimatef"] = (estimatef, repr)
         BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache)
 
-    #### Methods required by BaselineFunction ####
+    # Methods required by BaselineFunction ####
 
     def estimate_parameters(self, r, y):
         """Estimate parameters for data baseline.
@@ -133,7 +131,7 @@ def _jacobianraw(self, pars, r, free):
               needed.  True for evaluation, False for no evaluation."""
         nfree = None
         if self.jacobianf is None:
-            nfree = (pars == True).sum()
+            nfree = (pars is True).sum()
             if nfree != 0:
                 emsg = "No jacobian routine provided to Arbitrary."
                 raise NotImplementedError(emsg)

diffpy/srmise/baselines/base.py

@@ -15,10 +15,9 @@
 
 import numpy as np
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.basefunction import BaseFunction
 from diffpy.srmise.modelparts import ModelPart
-from diffpy.srmise.srmiseerrors import *
+from diffpy.srmise.srmiseerrors import SrMiseDataFormatError
 
 logger = logging.getLogger("diffpy.srmise")
 
@@ -85,9 +84,9 @@ def __init__(
                evaluations."""
         BaseFunction.__init__(self, parameterdict, parformats, default_formats, metadict, base, Cache)
 
-    #### "Virtual" class methods ####
+    # "Virtual" class methods ####
 
-    #### Methods required by BaseFunction ####
+    # Methods required by BaseFunction ####
 
     def actualize(
         self,
@@ -136,17 +135,16 @@ def factory(baselinestr, ownerlist):
         baselinestr: string representing Baseline
         ownerlist: List of BaseFunctions that owner is in
         """
-        from numpy import array
 
         data = baselinestr.strip().splitlines()
 
         # dictionary of parameters
         pdict = {}
         for d in data:
-            l = d.split("=", 1)
-            if len(l) == 2:
+            result = d.split("=", 1)
+            if len(result) == 2:
                 try:
-                    pdict[l[0]] = eval(l[1])
+                    pdict[result[0]] = eval(result[1])
                 except Exception:
                     emsg = "Invalid parameter: %s" % d
                     raise SrMiseDataFormatError(emsg)
@@ -169,10 +167,8 @@ def factory(baselinestr, ownerlist):
 # simple test code
 if __name__ == "__main__":
 
-    import matplotlib.pyplot as plt
     from numpy.random import randn
 
-    from diffpy.srmise.modelcluster import ModelCluster
     from diffpy.srmise.modelevaluators import AICc
     from diffpy.srmise.peaks import GaussianOverR, Peaks
 

diffpy/srmise/baselines/fromsequence.py

@@ -13,11 +13,9 @@
 
 import logging
 
-import matplotlib.pyplot as plt
 import numpy as np
 import scipy.interpolate as spi
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.baselines.base import BaselineFunction
 
 logger = logging.getLogger("diffpy.srmise")
@@ -80,7 +78,7 @@ def __init__(self, *args, **kwds):
         metadict["y"] = (y, self.xyrepr)
         BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache=None)
 
-    #### Methods required by BaselineFunction ####
+    # Methods required by BaselineFunction ####
 
     def estimate_parameters(self, r, y):
         """Return empty numpy array.
@@ -151,7 +149,7 @@ def _valueraw(self, pars, r):
                     [r[0], r[-1]],
                     [self.minx, self.maxx],
                 )
-        except (IndexError, TypeError) as e:
+        except (IndexError, TypeError):
             if r < self.minx or r > self.maxx:
                 logger.warn(
                     "Warning: Evaluating interpolating function at %s, outside safe range of %s.",
@@ -169,7 +167,7 @@ def xyrepr(self, var):
 
     def readxy(self, filename):
         """ """
-        from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
+        from diffpy.srmise.srmiseerrors import SrMiseDataFormatError
 
         # TODO: Make this safer
         try:

diffpy/srmise/baselines/nanospherical.py

@@ -13,12 +13,9 @@
 
 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
 
 logger = logging.getLogger("diffpy.srmise")
 
@@ -54,7 +51,7 @@ def __init__(self, Cache=None):
         metadict = {}
         BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache)
 
-    #### Methods required by BaselineFunction ####
+    # Methods required by BaselineFunction ####
 
     #    def estimate_parameters(self, r, y):
     #        """Estimate parameters for spherical baseline. (Not implemented!)
@@ -90,7 +87,7 @@ def _jacobianraw(self, pars, r, free):
             emsg = "Argument free must have " + str(self.npars) + " elements."
             raise ValueError(emsg)
         jacobian = [None for p in range(self.npars)]
-        if (free == False).sum() == self.npars:
+        if (free is False).sum() == self.npars:
             return jacobian
 
         if np.isscalar(r):
@@ -123,7 +120,7 @@ def _jacobianrawscale(self, pars, r):
                pars[1] = radius
         r - sequence or scalar over which pars is evaluated.
         """
-        s = np.abs(pars[0])
+        np.abs(pars[0])
         R = np.abs(pars[1])
         rdivR = r / R
         # From abs'(s) in derivative, which is equivalent to sign(s) except at 0 where it