Merge pull request #159 from cadenmyers13/fitrecipe2-dep

Deprecate: deprecate remaining functions of `Fitrecipe`

Author: sbillinge

docs/examples/debyemodelII.py

@@ -98,7 +98,7 @@ def plotResults(recipe):
 
     # The variable values are returned in the order in which the variables were
     # added to the FitRecipe.
-    lowToffset, highToffset, thetaD = recipe.getValues()
+    lowToffset, highToffset, thetaD = recipe.get_values()
 
     # We want to extend the fitting range to its full extent so we can get a
     # nice full plot.

docs/examples/gaussianrecipe.py

@@ -172,11 +172,11 @@ def scipyOptimize(recipe):
     # We're going to use the least-squares (Levenberg-Marquardt) optimizer from
     # scipy. We simply have to give it the function to minimize
     # (recipe.residual) and the starting values of the Variables
-    # (recipe.getValues()).
+    # (recipe.get_values()).
     from scipy.optimize.minpack import leastsq
 
     print("Fit using scipy's LM optimizer")
-    leastsq(recipe.residual, recipe.getValues())
+    leastsq(recipe.residual, recipe.get_values())
 
     return
 

docs/examples/nppdfobjcryst.py

@@ -143,7 +143,7 @@ def main():
     # Optimize
     from scipy.optimize import leastsq
 
-    leastsq(recipe.residual, recipe.getValues())
+    leastsq(recipe.residual, recipe.get_values())
 
     # Print results
     res = FitResults(recipe)

docs/examples/threedoublepeaks.py

@@ -179,11 +179,11 @@ def scipyOptimize(recipe):
     # We're going to use the least-squares (Levenberg-Marquardt) optimizer from
     # scipy. We simply have to give it the function to minimize
     # (recipe.residual) and the starting values of the Variables
-    # (recipe.getValues()).
+    # (recipe.get_values()).
     from scipy.optimize.minpack import leastsq
 
     print("Fit using scipy's LM optimizer")
-    leastsq(recipe.residual, recipe.getValues())
+    leastsq(recipe.residual, recipe.get_values())
 
     return
 

news/fitrecipe2-dep.rst

@@ -0,0 +1,33 @@
+**Added:**
+
+* Added ``convert_bounds_to_restraints`` method to ``FitRecipe``.
+* Added ``get_bounds_pairs`` method to ``FitRecipe``.
+* Added ``get_bounds_array`` method to ``FitRecipe``.
+* Added ``get_names`` method to ``FitRecipe`` and ``RecipeContainer``.
+* Added ``get_values`` method to ``FitRecipe`` and ``RecipeContainer``.
+* Added ``is_free`` method to ``FitRecipe``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated ``boundsToRestraints`` method for removal in 4.0.0.
+* Deprecated ``getBounds`` method for removal in 4.0.0.
+* Deprecated ``getBounds2`` method for removal in 4.0.0.
+* Deprecated ``getNames`` method for removal in 4.0.0.
+* Deprecated ``getValues`` method for removal in 4.0.0.
+* Deprecated ``isFree`` method for removal in 4.0.0.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/srfit/fitbase/calculator.py

@@ -77,9 +77,9 @@ class Calculator(Operator, ParameterSet):
     Properties
     ----------
     names
-        Variable names (read only). See getNames.
+        Variable names (read only). See get_names.
     values
-        Variable values (read only). See getValues.
+        Variable values (read only). See get_values.
     """
 
     # define abstract attributes from the Operator base.

src/diffpy/srfit/fitbase/fitcontribution.py

@@ -125,9 +125,9 @@ class FitContribution(ParameterSet):
     Properties
     ----------
     names
-        Variable names (read only). See getNames.
+        Variable names (read only). See get_names.
     values
-        Variable values (read only). See getValues.
+        Variable values (read only). See get_values.
     """
 
     def __init__(self, name):

src/diffpy/srfit/fitbase/fithook.py

@@ -164,8 +164,8 @@ def postcall(self, recipe, chiv):
 
         if self.verbose >= 3:
             print("Variables")
-            vnames = recipe.getNames()
-            vals = recipe.getValues()
+            vnames = recipe.get_names()
+            vals = recipe.get_values()
             # byname = _byname()
             items = sorted(zip(vnames, vals), key=_byname)
             for name, val in items:

src/diffpy/srfit/fitbase/fitrecipe.py

@@ -99,6 +99,30 @@
     base, "newVar", "create_new_variable", removal_version
 )
 
+isFree_dep_msg = build_deprecation_message(
+    base, "isFree", "is_free", removal_version
+)
+
+getValues_dep_msg = build_deprecation_message(
+    base, "getValues", "get_values", removal_version
+)
+
+getNames_dep_msg = build_deprecation_message(
+    base, "getNames", "get_names", removal_version
+)
+
+getBounds_dep_msg = build_deprecation_message(
+    base, "getBounds", "get_bounds_pairs", removal_version
+)
+
+getBounds2_dep_msg = build_deprecation_message(
+    base, "getBounds2", "get_bounds_array", removal_version
+)
+
+boundsToRestraints_dep_msg = build_deprecation_message(
+    base, "boundsToRestraints", "convert_bounds_to_restraints", removal_version
+)
+
 
 class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
     """FitRecipe class.
@@ -152,24 +176,24 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
     Properties
     ----------
     names
-        Variable names (read only). See getNames.
+        Variable names (read only). See get_names.
     values
-        Variable values (read only). See getValues.
+        Variable values (read only). See get_values.
     fixednames
         Names of the fixed refinable variables (read only).
     fixedvalues
         Values of the fixed refinable variables (read only).
     bounds
-        Bounds on parameters (read only). See getBounds.
+        Bounds on parameters (read only). See get_bounds_pairs.
     bounds2
-        Bounds on parameters (read only). See getBounds2.
+        Bounds on parameters (read only). See get_bounds_array.
     """
 
     fixednames = property(
         lambda self: [
             v.name
             for v in self._parameters.values()
-            if not (self.isFree(v) or self.isConstrained(v))
+            if not (self.is_free(v) or self.isConstrained(v))
         ],
         doc="names of the fixed refinable variables",
     )
@@ -178,13 +202,13 @@ class FitRecipe(_fitrecipe_interface, RecipeOrganizer):
             [
                 v.value
                 for v in self._parameters.values()
-                if not (self.isFree(v) or self.isConstrained(v))
+                if not (self.is_free(v) or self.isConstrained(v))
             ]
         ),
         doc="values of the fixed refinable variables",
     )
-    bounds = property(lambda self: self.getBounds())
-    bounds2 = property(lambda self: self.getBounds2())
+    bounds = property(lambda self: self.get_bounds_pairs())
+    bounds2 = property(lambda self: self.get_bounds_array())
 
     def __init__(self, name="fit"):
         """Initialization."""
@@ -935,10 +959,19 @@ def free(self, *args, **kw):
 
         return
 
-    def isFree(self, var):
+    def is_free(self, var):
         """Check if a variable is fixed."""
         return not self._tagmanager.hasTags(var, self._fixedtag)
 
+    @deprecated(isFree_dep_msg)
+    def isFree(self, var):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.is_free instead.
+        """
+        return self.is_free(var)
+
     def unconstrain(self, *pars):
         """Unconstrain a Parameter.
 
@@ -1034,33 +1067,78 @@ def constrain(self, par, con, ns={}):
         RecipeOrganizer.constrain(self, par, con, ns)
         return
 
-    def getValues(self):
+    def get_values(self):
         """Get the current values of the variables in a list."""
         return array(
-            [v.value for v in self._parameters.values() if self.isFree(v)]
+            [v.value for v in self._parameters.values() if self.is_free(v)]
         )
 
-    def getNames(self):
+    @deprecated(getValues_dep_msg)
+    def getValues(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.get_values instead."""
+        return self.get_values()
+
+    def get_names(self):
         """Get the names of the variables in a list."""
-        return [v.name for v in self._parameters.values() if self.isFree(v)]
+        return [v.name for v in self._parameters.values() if self.is_free(v)]
 
-    def getBounds(self):
+    @deprecated(getNames_dep_msg)
+    def getNames(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.get_names instead."""
+        return self.get_names()
+
+    def get_bounds_pairs(self):
         """Get the bounds on variables in a list.
 
-        Returns a list of (lb, ub) pairs, where lb is the lower bound
-        and ub is the upper bound.
+        Returns
+        -------
+        bounds_pair_list : list of tuple of float
+            A list of ``(lower, upper)`` bounds on the variables, in the same
+            order as ``get_names`` and ``get_values``.
         """
-        return [v.bounds for v in self._parameters.values() if self.isFree(v)]
+        return [v.bounds for v in self._parameters.values() if self.is_free(v)]
+
+    @deprecated(getBounds_dep_msg)
+    def getBounds(self):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
 
+        Please use diffpy.srfit.fitbase.FitRecipe.get_bounds_pairs
+        instead.
+        """
+        return self.get_bounds_pairs()
+
+    def get_bounds_array(self):
+        """Get the bounds on variables in two numpy arrays.
+
+        Returns
+        -------
+        lower_bounds : numpy.ndarray
+            A numpy array of lower bounds on the variables, in the same order
+            as ``get_names`` and ``get_values``.
+        upper_bounds : numpy.ndarray
+            A numpy array of upper bounds on the variables, in the same order
+            as ``get_names`` and ``get_values``.
+        """
+        bounds = self.get_bounds_pairs()
+        lower_bounds = array([b[0] for b in bounds])
+        upper_bounds = array([b[1] for b in bounds])
+        return lower_bounds, upper_bounds
+
+    @deprecated(getBounds2_dep_msg)
     def getBounds2(self):
-        """Get the bounds on variables in two lists.
+        """This function has been deprecated and will be removed in version
+        4.0.0.
 
-        Returns lower- and upper-bound lists of variable bounds.
+        Please use diffpy.srfit.fitbase.FitRecipe.get_bounds_array instead.
         """
-        bounds = self.getBounds()
-        lb = array([b[0] for b in bounds])
-        ub = array([b[1] for b in bounds])
-        return lb, ub
+        return self.get_bounds_array()
 
     def set_plot_defaults(self, **kwargs):
         """Set default plotting options for all future plots.
@@ -1346,18 +1424,23 @@ def plot_recipe(self, ax=None, return_fig=False, **kwargs):
             else:
                 return figures, axes_list
 
-    def boundsToRestraints(self, sig=1, scaled=False):
+    def convert_bounds_to_restraints(self, sig=1, scaled=False):
         """Turn all bounded parameters into restraints.
 
         The bounds become limits on the restraint.
 
-        Attributes
+        Parameters
         ----------
-        sig
-            The uncertainty on the bounds (scalar or iterable,
-            default 1).
-        scaled
-            Scale the restraints, see restrain.
+        sig : float or iterable of float, optional
+            The number of standard deviations associated with each bound.
+            Smaller values produce stronger restraints. If a scalar is given,
+            the same value is applied to all parameters. If an iterable is
+            provided, it must match the number of parameters. Default is 1.
+
+        scaled : bool, optional
+            If True, scale each restraint by the magnitude of the corresponding
+            parameter, consistent with the behavior of :meth:`restrain`.
+            Default is False.
         """
         pars = self._parameters.values()
         if not hasattr(sig, "__iter__"):
@@ -1368,11 +1451,22 @@ def boundsToRestraints(self, sig=1, scaled=False):
             )
         return
 
+    @deprecated(boundsToRestraints_dep_msg)
+    def boundsToRestraints(self, sig=1, scaled=False):
+        """This function has been deprecated and will be removed in version
+        4.0.0.
+
+        Please use diffpy.srfit.fitbase.FitRecipe.convert_bounds_to_restraints
+        instead.
+        """
+        self.convert_bounds_to_restraints(sig, scaled)
+        return
+
     def _apply_values(self, p):
         """Apply variable values to the variables."""
         if len(p) == 0:
             return
-        vargen = (v for v in self._parameters.values() if self.isFree(v))
+        vargen = (v for v in self._parameters.values() if self.is_free(v))
         for var, pval in zip(vargen, p):
             var.setValue(pval)
         return

src/diffpy/srfit/fitbase/fitresults.py

@@ -152,8 +152,8 @@ def update(self):
         recipe._prepare()
 
         # Store the variable names and values
-        self.varnames = recipe.getNames()
-        self.varvals = recipe.getValues()
+        self.varnames = recipe.get_names()
+        self.varvals = recipe.get_values()
         fixedpars = recipe._tagmanager.union(recipe._fixedtag)
         fixedpars = [p for p in fixedpars if not p.constrained]
         self.fixednames = [p.name for p in fixedpars]