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

diffpy/srmise/basefunction.py

@@ -15,14 +15,16 @@
 import logging
 import re
 import sys
-from fontTools.unicode import Unicode
+
 import numpy as np
+from fontTools.unicode import Unicode
 
 from diffpy.srmise.modelparts import ModelPart, ModelParts
 from diffpy.srmise.srmiseerrors import *
 
 logger = logging.getLogger("diffpy.srmise")
 
+
 class BaseFunction(object):
     """Base class for mathematical functions which model numeric sequences.
 
@@ -61,7 +63,15 @@ class BaseFunction(object):
     transform_parameters()
     """
 
-    def __init__(self, parameterdict, parformats, default_formats, metadict, base=None, Cache=None):
+    def __init__(
+        self,
+        parameterdict,
+        parformats,
+        default_formats,
+        metadict,
+        base=None,
+        Cache=None,
+    ):
         """Set parameterdict defined by subclass
 
         Parameters
@@ -96,23 +106,31 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No
         vals = self.parameterdict.values()
         vals.sort()
         if vals != range(self.npars):
-            emsg = "Argument parameterdict's values must uniquely specify "+\
-                   "the index of each parameter defined by its keys."
+            emsg = (
+                "Argument parameterdict's values must uniquely specify "
+                + "the index of each parameter defined by its keys."
+            )
             raise ValueError(emsg)
 
         self.parformats = parformats
 
         # Check validity of default_formats
         self.default_formats = default_formats
-        if not ("default_input" in self.default_formats and
-                "default_output" in self.default_formats):
-            emsg = "Argument default_formats must specify 'default_input' "+\
-                   "and 'default_output' as keys."
+        if not (
+            "default_input" in self.default_formats
+            and "default_output" in self.default_formats
+        ):
+            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:
-                emsg = "Keys of argument default_formats must map to a "+\
-                       "value within argument parformats."
+                emsg = (
+                    "Keys of argument default_formats must map to a "
+                    + "value within argument parformats."
+                )
                 raise ValueError()
 
         # Set metadictionary
@@ -126,12 +144,11 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No
         # of PeakFunction.
         # Object to cache: (basefunctioninstance, tuple of parameters)
         if Cache is not None:
-            #self.value = Cache(self.value, "value")
-            #self.jacobian = Cache(self.jacobian, "jacobian")
+            # self.value = Cache(self.value, "value")
+            # self.jacobian = Cache(self.jacobian, "jacobian")
             pass
         return
 
-
     #### "Virtual" class methods ####
 
     def actualize(self, *args, **kwds):
@@ -164,7 +181,6 @@ def _valueraw(self, *args, **kwds):
         emsg = "_valueraw must() be implemented in a BaseFunction subclass."
         raise NotImplementedError(emsg)
 
-
     #### Class methods ####
 
     def jacobian(self, p, r, rng=None):
@@ -179,8 +195,10 @@ def jacobian(self, p, r, rng=None):
               previously calculated values instead.
         """
         if self is not p._owner:
-            emsg = "Argument 'p' must be evaluated by the BaseFunction "+\
-                   "subclass which owns it."
+            emsg = (
+                "Argument 'p' must be evaluated by the BaseFunction "
+                + "subclass which owns it."
+            )
             raise ValueError(emsg)
 
         # normally r will be a sequence, but also allow single numeric values
@@ -192,7 +210,7 @@ def jacobian(self, p, r, rng=None):
             output = [None for j in jac]
             for idx in range(len(output)):
                 if jac[idx] is not None:
-                    output[idx] = r * 0.
+                    output[idx] = r * 0.0
                     output[idx][rng] = jac[idx]
             return output
         except TypeError:
@@ -201,10 +219,10 @@ def jacobian(self, p, r, rng=None):
     def transform_derivatives(self, pars, in_format=None, out_format=None):
         """Return gradient matrix for pars converted from in_format to out_format.
 
-           Parameters
-           pars - Sequence of parameters
-           in_format - A format defined for this class
-           out_format - A format defined for this class
+        Parameters
+        pars - Sequence of parameters
+        in_format - A format defined for this class
+        out_format - A format defined for this class
         """
         # Map unspecified formats to specific formats defined in default_formats
         if in_format is None:
@@ -223,25 +241,29 @@ def transform_derivatives(self, pars, in_format=None, out_format=None):
             out_format = self.default_formats["default_input"]
 
         if not in_format in self.parformats:
-            raise ValueError("Argument 'in_format' must be one of %s." \
-                              % self.parformats)
+            raise ValueError(
+                "Argument 'in_format' must be one of %s." % self.parformats
+            )
         if not out_format in self.parformats:
-             raise ValueError("Argument 'out_format' must be one of %s." \
-                              % self.parformats)
+            raise ValueError(
+                "Argument 'out_format' must be one of %s." % self.parformats
+            )
         if in_format == out_format:
             return np.identity(self.npars)
-        return self._transform_derivativesraw(pars, in_format=in_format, out_format=out_format)
+        return self._transform_derivativesraw(
+            pars, in_format=in_format, out_format=out_format
+        )
 
     def transform_parameters(self, pars, in_format=None, out_format=None):
         """Return new sequence with pars converted from in_format to out_format.
 
-           Also restores parameters to a preferred range if it permits multiple
-           values that correspond to the same physical result.
+        Also restores parameters to a preferred range if it permits multiple
+        values that correspond to the same physical result.
 
-           Parameters
-           pars - Sequence of parameters
-           in_format - A format defined for this class
-           out_format - A format defined for this class
+        Parameters
+        pars - Sequence of parameters
+        in_format - A format defined for this class
+        out_format - A format defined for this class
         """
         # Map unspecified formats to specific formats defined in default_formats
         if in_format is None:
@@ -260,15 +282,18 @@ def transform_parameters(self, pars, in_format=None, out_format=None):
             out_format = self.default_formats["default_input"]
 
         if not in_format in self.parformats:
-            raise ValueError("Argument 'in_format' must be one of %s." \
-                              % self.parformats)
+            raise ValueError(
+                "Argument 'in_format' must be one of %s." % self.parformats
+            )
         if not out_format in self.parformats:
-             raise ValueError("Argument 'out_format' must be one of %s." \
-                              % self.parformats)
-        #if in_format == out_format:
+            raise ValueError(
+                "Argument 'out_format' must be one of %s." % self.parformats
+            )
+        # if in_format == out_format:
         #    return pars
-        return self._transform_parametersraw(pars, in_format=in_format, out_format=out_format)
-
+        return self._transform_parametersraw(
+            pars, in_format=in_format, out_format=out_format
+        )
 
     def value(self, p, r, rng=None):
         """Calculate value of ModelPart over r, possibly restricted by range.
@@ -282,16 +307,18 @@ def value(self, p, r, rng=None):
               previously calculated values instead.
         """
         if self is not p._owner:
-            emsg = "Argument 'p' must be evaluated by the BaseFunction "+\
-                   "subclass which owns it."
+            emsg = (
+                "Argument 'p' must be evaluated by the BaseFunction "
+                + "subclass which owns it."
+            )
             raise ValueError(emsg)
 
         # normally r will be a sequence, but also allow single numeric values
         try:
             if rng is None:
                 rng = slice(0, len(r))
             rpart = r[rng]
-            output = r * 0.
+            output = r * 0.0
             output[rng] = self._valueraw(p.pars, rpart)
             return output
         except TypeError:
@@ -338,17 +365,17 @@ def writestr(self, baselist):
             raise ValueError("emsg")
         lines = []
         # Write function type
-        lines.append("function=%s" %repr(self.__class__.__name__))
-        lines.append("module=%s" %repr(self.getmodule()))
+        lines.append("function=%s" % repr(self.__class__.__name__))
+        lines.append("module=%s" % repr(self.getmodule()))
         # Write base
         if self.base is not None:
-            lines.append("base=%s" %repr(baselist.index(self.base)))
+            lines.append("base=%s" % repr(baselist.index(self.base)))
         else:
-            lines.append("base=%s" %repr(None))
+            lines.append("base=%s" % repr(None))
         # Write all other metadata
         for k, (v, f) in self.metadict.iteritems():
-            lines.append("%s=%s" %(k, f(v)))
-        datastring = "\n".join(lines)+"\n"
+            lines.append("%s=%s" % (k, f(v)))
+        datastring = "\n".join(lines) + "\n"
         return datastring
 
     @staticmethod
@@ -367,19 +394,19 @@ def factory(functionstr, baselist):
 
         # populate dictionary with parameter definition
         # "key=value"->{"key":"value"}
-        data = re.split(r'(?:[\r\n]+|\A)(\S+)=', data)
+        data = re.split(r"(?:[\r\n]+|\A)(\S+)=", data)
         ddict = {}
-        for i in range(len(data)/2):
-            ddict[data[2*i+1]] = data[2*i+2]
+        for i in range(len(data) / 2):
+            ddict[data[2 * i + 1]] = data[2 * i + 2]
 
         # dictionary of parameters
         pdict = {}
-        for (k, v) in ddict.items():
+        for k, v in ddict.items():
             try:
                 pdict[k] = eval(v)
             except Exception as e:
                 logger.exception(e)
-                emsg = ("Invalid parameter: %s=%s" %(k,v))
+                emsg = "Invalid parameter: %s=%s" % (k, v)
                 raise SrMiseDataFormatError(emsg)
 
         function_name = pdict["function"]
@@ -438,9 +465,9 @@ def safefunction(f, fsafe):
         return
 
 
-#end of class BaseFunction
+# end of class BaseFunction
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
     from diffpy.srmise.peaks import GaussianOverR, TerminationRipples