diffpy.srfit 3.2.0rc0__tar.gz → 3.2.0rc2__tar.gz

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.srfit
-Version: 3.2.0rc0
+Version: 3.2.0rc2
 Summary: Configurable code for solving atomic structures.
 Author-email: Simon Billinge <sb2896@columbia.edu>
 Maintainer-email: Simon Billinge <sb2896@columbia.edu>

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/requirements/docs.txt

@@ -2,4 +2,4 @@ sphinx
 sphinx_rtd_theme
 sphinx-copybutton
 doctr
-m2r
+m2r2

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/fitcontribution.py

@@ -177,6 +177,7 @@ class FitContribution(ParameterSet):
             A name for the calculator. If name is None (default), then
             the ProfileGenerator's name attribute will be used.
 
+
         Raises ValueError if the ProfileGenerator has no name.
         Raises ValueError if the ProfileGenerator has the same name as some
         other managed object.
@@ -220,6 +221,7 @@ class FitContribution(ParameterSet):
             A dictionary of Parameters, indexed by name, that are used
             in the eqstr, but not registered (default {}).
 
+
         Raises ValueError if ns uses a name that is already used for a
         variable.
         """
@@ -266,6 +268,7 @@ class FitContribution(ParameterSet):
             used, or the chi2 residual will be used if that does not
             exist.
 
+
         Two residuals are preset for convenience, "chiv" and "resv".
         chiv is defined such that dot(chiv, chiv) = chi^2.
         resv is defined such that dot(resv, resv) = Rw^2.

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/fitrecipe.py

@@ -187,6 +187,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
         index
             Index of FitHook instance to remove (default -1).
 
+
         Raises ValueError if fithook is not None, but is not present in the
         sequence.
         Raises IndexError if the sequence is empty or index is out of range.
@@ -214,6 +215,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
         con
             The FitContribution to be stored.
 
+
         Raises ValueError if the FitContribution has no name
         Raises ValueError if the FitContribution has the same name as some
         other managed object.
@@ -236,6 +238,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
         parset
             The ParameterSet to be stored.
 
+
         Raises ValueError if the ParameterSet has no name.
         Raises ValueError if the ParameterSet has the same name as some other
         managed object.
@@ -506,7 +509,12 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
             A list of tags (default []). Both tag and tags can be
             applied.
 
-        Returns the ParameterProxy (variable) for the passed Parameter.
+
+        Returns
+        -------
+        vars
+            ParameterProxy (variable) for the passed Parameter.
+
 
         Raises ValueError if the name of the variable is already taken by
         another managed object.
@@ -549,6 +557,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
         var
             A variable of the FitRecipe.
 
+
         Raises ValueError if var is not part of the FitRecipe.
         """
 
@@ -592,6 +601,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
             A list of tags (default []). Both tag and tags can be
             applied.
 
+
         Returns the new variable (Parameter instance).
         """
         # This will fix the Parameter
@@ -798,6 +808,7 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
             A dictionary of Parameters, indexed by name, that are used
             in the eqstr, but not part of this object (default {}).
 
+
         Raises ValueError if ns uses a name that is already used for a
         variable.
         Raises ValueError if eqstr depends on a Parameter that is not part of

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/fitresults.py

@@ -90,6 +90,7 @@ class FitResults(object):
         The derivatives of the constraint equations with respect to
         the variables. This is used internally.
 
+
     Each of these attributes, except the recipe, are created or updated when
     the update method is called.
     """
@@ -338,7 +339,10 @@ class FitResults(object):
         update
             Flag indicating whether to call update() (default False).
 
-        Returns a string containing the formatted results.
+        Returns
+        -------
+        out
+            a string containing the formatted results.
         """
         if update:
             self.update()
@@ -515,7 +519,7 @@ class FitResults(object):
     def printResults(self, header="", footer="", update=False):
         """Format and print the results.
 
-        Attributes
+        Parameters
         ----------
         header
             A header to add to the output (default "")
@@ -533,8 +537,10 @@ class FitResults(object):
     def saveResults(self, filename, header="", footer="", update=False):
         """Format and save the results.
 
-        filename -  Name of the save file.
+        Parameters
         ----------------------------------
+        filename
+            Name of the save file.
         header
             A header to add to the output (default "")
         footer

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/parameter.py

@@ -72,6 +72,7 @@ class Parameter(_parameter_interface, Argument, Validatable):
             A flag inticating whether the Parameter is a constant (like
             pi).
 
+
         Raises ValueError if the name is not a valid attribute identifier
         """
         self.constrained = False
@@ -94,7 +95,10 @@ class Parameter(_parameter_interface, Argument, Validatable):
             The upper bounds for the bounds list. If this is None
             (default), then the upper bound will not be alterered.
 
-        Returns self so that mutators can be chained.
+        Returns
+        -------
+        self
+            Returns self so that mutators can be chained.
         """
         Argument.setValue(self, val)
         return self
@@ -112,7 +116,10 @@ class Parameter(_parameter_interface, Argument, Validatable):
             is not None, then the parameter will get a new value,
             constant or otherwise.
 
-        Returns self so that mutators can be chained.
+        Returns
+        -------
+        self
+            Returns self so that mutators can be chained.
         """
         self.const = bool(const)
         if value is not None:
@@ -129,7 +136,10 @@ class Parameter(_parameter_interface, Argument, Validatable):
         ub
             The upper bound for the bounds list.
 
-        Returns self so that mutators can be chained.
+        Returns
+        -------
+        self
+            Returns self so that mutators can be chained.
         """
         if lb is not None:
             self.bounds[0] = lb
@@ -150,7 +160,10 @@ class Parameter(_parameter_interface, Argument, Validatable):
             value + ur. If this is None (default), then the value of the
             lower radius is used.
 
-        Returns self so that mutators can be chained.
+        Returns
+        -------
+        self
+            Returns self so that mutators can be chained.
         """
         val = self.getValue()
         lb = val - lr
@@ -199,6 +212,7 @@ class ParameterProxy(Parameter):
         par
             The Parameter this is a proxy for.
 
+
         Raises ValueError if the name is not a valid attribute identifier
         """
         validateName(name)
@@ -312,6 +326,7 @@ class ParameterAdapter(Parameter):
             parameter. If attr is None (default), then both getter and
             setter must be specified.
 
+
         Raises ValueError if exactly one of getter or setter is not None, or if
         getter, setter and attr are all None.
         """

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/parameterset.py

@@ -95,6 +95,7 @@ class ParameterSet(RecipeOrganizer):
         parset
             The ParameterSet to be stored.
 
+
         Raises ValueError if the ParameterSet has no name.
         Raises ValueError if the ParameterSet has the same name as some other
         managed object.

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/profile.py

@@ -319,7 +319,14 @@ class Profile(Observable, Validatable):
         Raises ValueError if the call to numpy.loadtxt returns fewer
         than 2 arrays.
 
-        Returns the x, y and dy arrays loaded from the file
+        Returns
+        -------
+        x
+            x array loaded from the file.
+        y
+            y array loaded from the file.
+        dy
+            dy array loaded from the file.
         """
         if len(args) == 8 and not args[-1]:
             args = list(args)
@@ -423,9 +430,13 @@ def rebinArray(A, xold, xnew):
     xnew
         New sampling array
 
+
     This uses cubic spline interpolation.
 
-    Returns: A new array over the new sampling array.
+    Returns
+    -------
+    array
+        A new array over the new sampling array.
     """
     if numpy.array_equal(xold, xnew):
         return A

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/profilegenerator.py

@@ -20,14 +20,23 @@ be associated with a FitContribution to help calculate a profile.
 
 To define a ProfileGenerator, one must implement the required Parameters
 and ParameterSets as well as overload the __call__ method with the
-calculation. A very simple example is > class
-Gaussian(ProfileGenerator): > >    def __init__(self): >        #
-Initialize and give this a name >        ProfileGenerator.__init__(self,
-"g") >        # Add amplitude, center and width parameters >
-self.newParameter("amp", 0) >        self.newParameter("center", 0) >
-self.newParameter("width", 0) > >    def __call__(self, x): >        a =
-self.amp.getValue() >        x0 = self.center.getValue() >        w =
-self.width.getValue() >        return a * exp(-0.5*((x-x0)/w)**2)
+calculation. A very simple example is
+
+.. code:: python
+
+    class Gaussian(ProfileGenerator):
+        def __init__(self):
+            # Initialize and give this a name
+            ProfileGenerator.__init__(self, "g")
+            # Add amplitude, center and width parameters
+            self.newParameter("amp", 0)
+            self.newParameter("center", 0)
+            self.newParameter("width", 0)
+        def __call__(self, x):
+            a = self.amp.getValue()
+            x0 = self.center.getValue()
+            w = self.width.getValue()
+            return a * exp(-0.5*((x-x0)/w)**2)
 
 More examples can be found in the example directory of the
 documentation.

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/profileparser.py

@@ -29,8 +29,6 @@ from diffpy.srfit.exceptions import ParseError
 class ProfileParser(object):
     """Class for parsing data from a or string.
 
-    Attributes
-
     Attributes
     ----------
     _format
@@ -41,20 +39,20 @@ class ProfileParser(object):
         The data from each bank. Each bank contains a (x, y, dx,
         dy)
         tuple:
-                    x
-        A numpy array containing the independent
-        variable read from the file.
-                    y
-        A numpy array containing the profile
-        from the file.
-                    dx
-        A numpy array containing the uncertainty in x
-        read from the file. This is None if the
-        uncertainty cannot be read.
-                    dy
-        A numpy array containing the uncertainty read
-        from the file. This is None if the uncertainty
-        cannot be read.
+        x
+            A numpy array containing the independent
+            variable read from the file.
+        y
+            A numpy array containing the profile
+            from the file.
+        dx
+            A numpy array containing the uncertainty in x
+            read from the file. This is None if the
+            uncertainty cannot be read.
+        dy
+            A numpy array containing the uncertainty read
+            from the file. This is None if the uncertainty
+            cannot be read.
     _x
         Independent variable from the chosen bank
     _y
@@ -66,10 +64,9 @@ class ProfileParser(object):
     _meta
         A dictionary containing metadata read from the file.
 
-    General Metadata
 
-    Attributes
-    ----------
+    General Metadata
+    ----------------
     filename
         The name of the file from which data was parsed. This key
         will not exist if data was not read from file.

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/recipeorganizer.py

@@ -250,6 +250,7 @@ class RecipeContainer(Observable, Configurable, Validatable):
             If True (default), a ValueError is raised an object of the
             given name already exists.
 
+
         Raises ValueError if the object has no name.
         Raises ValueError if the object has the same name as some other managed
         object.
@@ -313,6 +314,7 @@ class RecipeContainer(Observable, Configurable, Validatable):
         obj
             The object to find.
 
+
         Returns a list of objects. The first member of the list is this object,
         and each subsequent member is a sub-object of the previous one.  The
         last entry in the list is obj. If obj cannot be found, the list is
@@ -402,6 +404,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
     values
         Variable values (read only). See getValues.
 
+
     Raises ValueError if the name is not a valid attribute identifier
     """
 
@@ -442,6 +445,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             If True (default), a ValueError is raised a Parameter of
             the specified name has already been inserted.
 
+
         Raises ValueError if the Parameter has no name.
         Raises ValueError if the Parameter has the same name as a contained
         RecipeContainer.
@@ -527,10 +531,12 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             If this is None (default), then the argument names will
             be extracted from the function.
 
+
         Note that name and argnames can be extracted from regular python
         functions (of type 'function'), bound class methods and callable
         classes.
 
+
         Raises TypeError if name or argnames cannot be automatically
         extracted.
         Raises TypeError if an automatically extracted name is '<lambda>'.
@@ -628,6 +634,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             used in fstr, but not part of the FitRecipe (default
             {}).
 
+
         Raises ValueError if ns uses a name that is already used for another
         managed object.
         Raises ValueError if the function name is the name of another managed
@@ -660,6 +667,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             A dictionary of Parameters, indexed by name, that are
             used in fstr, but not part of the FitRecipe (default {}).
 
+
         Raises ValueError if ns uses a name that is already used for a
         variable.
         """
@@ -689,6 +697,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             A dictionary of Parameters, indexed by name, that are used
             in the parameter, but not part of this object (default {}).
 
+
         Raises ValueError if ns uses a name that is already used for a
         variable.
         Raises ValueError if par is a string but not part of this object or in
@@ -800,6 +809,7 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             Recurse into managed objects and clear all constraints
             found there as well.
 
+
         This removes constraints that are held in this organizer, no matter
         where the constrained parameters are from.
         """
@@ -833,11 +843,13 @@ class RecipeOrganizer(_recipeorganizer_interface, RecipeContainer):
             in the equation string, but not part of the RecipeOrganizer
             (default {}).
 
+
         The penalty is calculated as
         (max(0, lb - val, val - ub)/sig)**2
         and val is the value of the calculated equation.  This is multiplied by
         the average chi^2 if scaled is True.
 
+
         Raises ValueError if ns uses a name that is already used for a
         Parameter.
         Raises ValueError if res depends on a Parameter that is not part of
@@ -1120,6 +1132,7 @@ def equationFromString(
         Key word dictionary to pass to the argclass constructor
         (default {}).
 
+
     Raises ValueError if ns uses a name that is already defined in the factory.
     Raises ValueError if the equation has undefined parameters.
     """

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/restraint.py

@@ -47,6 +47,7 @@ class Restraint(Validatable):
         the unrestrained point-average chi^2 (chi^2/numpoints)
         (default False).
 
+
     The penalty is calculated as
     (max(0, lb - val, val - ub)/sig)**2
     and val is the value of the calculated equation.  This is multiplied by the
@@ -90,7 +91,10 @@ class Restraint(Validatable):
             The point-average chi^2 which is optionally used to scale the
             penalty (default 1.0).
 
-        Returns the penalty as a float
+        Returns
+        -------
+        penalty
+            Returns the penalty as a float
         """
         val = self.eq()
         penalty = (max(0, self.lb - val, val - self.ub) / self.sig) ** 2

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/fitbase/simplerecipe.py

@@ -130,6 +130,7 @@ class SimpleRecipe(FitRecipe):
             dyobs is None (default), it will be set to 1 at each
             observed xobs.
 
+
         Raises ValueError if len(yobs) != len(xobs)
         Raises ValueError if dyobs != None and len(dyobs) != len(xobs)
         """
@@ -192,7 +193,7 @@ class SimpleRecipe(FitRecipe):
         to by dy. Any other arrays are ignored. These are passed to
         setObservedProfile.
 
-        Raises ValueError if the call to numpy.loadtxt returns fewer
+         Raises ValueError if the call to numpy.loadtxt returns fewer
         than 2 arrays.
 
         Returns the x, y and dy arrays loaded from the file
@@ -217,6 +218,7 @@ class SimpleRecipe(FitRecipe):
             A dictionary of Parameters, indexed by name, that are used
             in the eqstr, but not registered (default {}).
 
+
         Raises ValueError if ns uses a name that is already used for a
         variable.
         """
@@ -254,8 +256,10 @@ class SimpleRecipe(FitRecipe):
     def saveResults(self, filename, header="", footer=""):
         """Format and save the results.
 
-        filename -  Name of the save file.
-        ----------------------------------
+        Parameters
+        ----------
+        filename
+            Name of the save file.
         header
             A header to add to the output (default "")
         footer

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/pdf/basepdfgenerator.py

@@ -65,10 +65,9 @@ class BasePDFGenerator(ProfileGenerator):
         Resolution peak broadening term
     qdamp
         Resolution peak dampening term
-
-    Managed ParameterSets:
-    The structure ParameterSet (SrRealParSet instance) used to calculate the
-    profile is named by the user.
+    Managed ParameterSets
+        The structure ParameterSet (SrRealParSet instance) used to
+        calculate the profile is named by the user.
 
     Usable Metadata
     ---------------

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/pdf/characteristicfunctions.py

@@ -54,6 +54,7 @@ def sphericalCF(r, psize):
     psize
         The particle diameter
 
+
     From Kodama et al., Acta Cryst. A, 62, 444-453
     (converted from radius to diameter)
     """
@@ -78,6 +79,7 @@ def spheroidalCF(r, erad, prad):
     erad
         equatorial radius
 
+
     erad < prad equates to a prolate spheroid
     erad > prad equates to a oblate spheroid
     erad == prad is a sphere
@@ -101,6 +103,7 @@ def spheroidalCF2(r, psize, axrat):
     axrat
         The ratio of axis lengths
 
+
     From Lei et al., Phys. Rev. B, 80, 024118 (2009)
     """
     pelpt = 1.0 * axrat
@@ -211,6 +214,7 @@ def lognormalSphericalCF(r, psize, psig):
     psig
         The log-normal width of the particle diameter
 
+
     Here, r is the independent variable, mu is the mean of the distribution
     (not of the particle size), and s is the width of the distribution. This is
     the characteristic function for the lognormal distribution of particle
@@ -265,6 +269,7 @@ def sheetCF(r, sthick):
     sthick
         Thickness of nanosheet
 
+
     From Kodama et al., Acta Cryst. A, 62, 444-453
     """
     # handle zero or negative sthick.  make it work for scalars and arrays.
@@ -294,6 +299,7 @@ def shellCF(r, radius, thickness):
     thickness
         Thickness of shell
 
+
     outer radius = radius + thickness
 
     From Lei et al., Phys. Rev. B, 80, 024118 (2009)
@@ -315,6 +321,7 @@ def shellCF2(r, a, delta):
 
     outer radius = a + thickness/2
 
+
     From Lei et al., Phys. Rev. B, 80, 024118 (2009)
     """
     a = 1.0 * a
@@ -359,13 +366,12 @@ class SASCF(Calculator):
     ----------
     _model
         BaseModel object this adapts.
-
-    Managed Parameters:
-    These depend on the parameters of the BaseModel object held by _model. They
-    are created from the 'params' attribute of the BaseModel. If a dispersion
-    is set for the BaseModel, the dispersion "width" will be accessible under
-    "<parname>_width", where <parname> is the name a parameter adjusted by
-    dispersion.
+    Managed Parameters
+        These depend on the parameters of the BaseModel object held by _model.
+        They are created from the 'params' attribute of the BaseModel. If a
+        dispersion is set for the BaseModel, the dispersion "width" will be
+        accessible under "<parname>_width", where <parname> is the name a
+        parameter adjusted by dispersion.
     """
 
     def __init__(self, name, model):

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/pdf/debyepdfgenerator.py

@@ -57,9 +57,9 @@ class DebyePDFGenerator(BasePDFGenerator):
     qdamp
         Resolution peak dampening term
 
-    Managed ParameterSets:
-    The structure ParameterSet (SrRealStructure instance) used to calculate the
-    profile is named by the user.
+    Managed ParameterSets
+        The structure ParameterSet (SrRealStructure instance) used to calculate
+        the profile is named by the user.
 
     Usable Metadata
     ---------------

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/pdf/pdfcontribution.py

@@ -201,6 +201,7 @@ class PDFContribution(FitContribution):
             do not support periodicity, in which case this may be
             ignored.
 
+
         Returns the new phase (ParameterSet appropriate for what was passed in
         stru.)
         """
@@ -245,6 +246,7 @@ class PDFContribution(FitContribution):
             do not support periodicity, in which case this may be
             ignored.
 
+
         Returns the new phase (ParameterSet appropriate for what was passed in
         stru.)
         """

{diffpy_srfit-3.2.0rc0 → diffpy_srfit-3.2.0rc2}/src/diffpy/srfit/pdf/pdfgenerator.py

@@ -56,10 +56,9 @@ class PDFGenerator(BasePDFGenerator):
         Resolution peak broadening term
     qdamp
         Resolution peak dampening term
-
-    Managed ParameterSets:
-    The structure ParameterSet (SrRealStructure instance) used to calculate the
-    profile is named by the user.
+    Managed ParameterSets
+        The structure ParameterSet (SrRealStructure instance) used to
+        calculate the profile is named by the user.
 
     Usable Metadata
     ---------------