diffpy.srfit 3.1.0rc0__tar.gz → 3.2.0__tar.gz

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/LICENSE.rst

@@ -1,18 +1,14 @@
 OPEN SOURCE LICENSE AGREEMENT
 =============================
 
-Copyright (c) 2009-2011, University of Tennessee
-Copyright (c) 1989, 1991 Free Software Foundation, Inc.
-Copyright (c) 2006, The Regents of the University of California through
-    Lawrence Berkeley National Laboratory
-Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
-Copyright (c) 2006-2007, Board of Trustees of Michigan State University
-Copyright (c) 2008-2012, The Trustees of Columbia University in the City
-    of New York
-Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National
-    Laboratory
-Copyright (c) 2020-2025, The Trustees of Columbia University in the City
-    of New York
+- Copyright (c) 2009-2011, University of Tennessee
+- Copyright (c) 1989, 1991 Free Software Foundation, Inc.
+- Copyright (c) 2006, The Regents of the University of California through Lawrence Berkeley National Laboratory
+- Copyright (c) 2014, Australian Synchrotron Research Program Inc., ("ASRP")
+- Copyright (c) 2006-2007, Board of Trustees of Michigan State University
+- Copyright (c) 2008-2012, The Trustees of Columbia University in the City of New York
+- Copyright (c) 2014-2019, Brookhaven Science Associates, Brookhaven National Laboratory
+- Copyright (c) 2020-2025, The Trustees of Columbia University in the City of New York
 
 
 The "DiffPy-CMI" is distributed subject to the following license conditions:
@@ -20,7 +16,7 @@ The "DiffPy-CMI" is distributed subject to the following license conditions:
 
 SOFTWARE LICENSE AGREEMENT
 
-    Software: DiffPy-CMI
+**Software:** DiffPy-CMI
 
 
 (1) The "Software", below, refers to the aforementioned DiffPy-CMI (in either

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffpy.srfit
-Version: 3.1.0rc0
+Version: 3.2.0
 Summary: Configurable code for solving atomic structures.
 Author-email: Simon Billinge <sb2896@columbia.edu>
 Maintainer-email: Simon Billinge <sb2896@columbia.edu>
@@ -11,7 +11,7 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
+Classifier: License :: Free To Use But Restricted
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
+        'License :: Free To Use But Restricted',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/requirements/docs.txt

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

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/builder.py

@@ -109,12 +109,17 @@ _builders = {}
 class EquationFactory(object):
     """A Factory for equations.
 
-    builders    --  A dictionary of BaseBuilders registered with the
-                    factory, indexed by name.
-    newargs     --  A set of new arguments created by makeEquation. This is
-                    redefined whenever makeEquation is called.
-    equations   --  Set of equations that have been built by the
-                    EquationFactory.
+    Attributes
+    ----------
+    builders
+        A dictionary of BaseBuilders registered with the
+        factory, indexed by name.
+    newargs
+        A set of new arguments created by makeEquation. This is
+        redefined whenever makeEquation is called.
+    equations
+        Set of equations that have been built by the
+        EquationFactory.
     """
 
     symbols = ("+", "-", "*", "/", "**", "%", "|")
@@ -137,21 +142,26 @@ class EquationFactory(object):
     ):
         """Make an equation from an equation string.
 
-        Arguments
-        eqstr       --  An equation in string form using standard python
-                        syntax.  The equation string can use any function
-                        registered literal or function, including numpy ufuncs
-                        that are automatically registered.
-        buildargs   --  A flag indicating whether missing arguments can be
-                        created by the Factory (default True). If False, then
-                        the a ValueError will be raised if there are undefined
-                        arguments in the eqstr. Built arguments will be of type
-                        argclass.
-        argclass    --  Class to use when creating new Arguments (default
-                        diffpy.srfit.equation.literals.Argument). The class
-                        constructor must accept the 'name' key word.
-        argkw       --  Key word dictionary to pass to the argclass constructor
-                        (default {}).
+        Parameters
+        ----------
+        eqstr
+            An equation in string form using standard python
+            syntax.  The equation string can use any function
+            registered literal or function, including numpy ufuncs
+            that are automatically registered.
+        buildargs
+            A flag indicating whether missing arguments can be
+            created by the Factory (default True). If False, then
+            the a ValueError will be raised if there are undefined
+            arguments in the eqstr. Built arguments will be of type
+            argclass.
+        argclass
+            Class to use when creating new Arguments (default
+            diffpy.srfit.equation.literals.Argument). The class
+            constructor must accept the 'name' key word.
+        argkw
+            Key word dictionary to pass to the argclass constructor
+            (default {}).
 
         Returns a callable Literal representing the equation string.
         """
@@ -202,11 +212,16 @@ class EquationFactory(object):
 
         This will register a builder for the function.
 
-        name    --  The name of the function
-        func    --  A callable python object
-        argnames--  The argument names for func. If these names do not
-                    correspond to builders, then new constants with value 0
-                    will be created for each name.
+        Attributes
+        ----------
+        name
+            The name of the function
+        func
+            A callable python object
+        argnames
+            The argument names for func. If these names do not
+            correspond to builders, then new constants with value 0
+            will be created for each name.
 
         Returns the registered builder.
         """
@@ -293,17 +308,22 @@ class EquationFactory(object):
         arguments, and creates new arguments if allowed. In the process it
         rebuilds the newargs attribute.
 
-        Arguments
-        eqstr       --  An equation in string as specified in the makeEquation
-                        method.
-        buildargs   --  A flag indicating whether missing arguments can be
-                        created by the factory. If False, then the a ValueError
-                        will be raised if there are undefined arguments in the
-                        eqstr.
-        argclass    --  Class to use when creating new Arguments. The class
-                        constructor must accept the 'name' key word.
-        argkw       --  Key word dictionary to pass to the argclass
-                        constructor.
+        Parameters
+        ----------
+        eqstr
+            An equation in string as specified in the makeEquation
+            method.
+        buildargs
+            A flag indicating whether missing arguments can be
+            created by the factory. If False, then the a ValueError
+            will be raised if there are undefined arguments in the
+            eqstr.
+        argclass
+            Class to use when creating new Arguments. The class
+            constructor must accept the 'name' key word.
+        argkw
+            Key word dictionary to pass to the argclass
+            constructor.
 
         Raises ValueError if new arguments must be created, but this is
         disallowed due to the buildargs flag.
@@ -392,7 +412,9 @@ class BaseBuilder(object):
     arguments can be other BaseBuilder instances or constants.
 
     Attributes
-    literal     --  The equation Literal being built by this instance.
+    ----------
+    literal
+        The equation Literal being built by this instance.
     """
 
     def __init__(self):
@@ -424,8 +446,11 @@ class BaseBuilder(object):
 
         Other can be an BaseBuilder or a constant.
 
-        onleft  --  Indicates that the operator was passed on the left side
-                    (default True).
+        Attributes
+        ----------
+        onleft
+            Indicates that the operator was passed on the left side
+            (default True).
         """
         # Create the Operator
         op = OperatorClass()
@@ -520,20 +545,27 @@ class ArgumentBuilder(BaseBuilder):
     arguments can be other BaseBuilder instances or constants.
 
     Attributes
-    literal     --  The Argument wrapped by this instance.
+    ----------
+    literal
+        The Argument wrapped by this instance.
     """
 
     def __init__(self, value=None, name=None, const=False, arg=None):
         """Create an ArgumentBuilder instance, containing a new Argument.
 
-        Arguments
-        value   --  The value of the wrapped Argument (float, default None)
-        name    --  The name of the wrapped Argument (string, default None)
-        const   --  Flag indicating whether the Argument is constant (bool,
-                    default False)
-        arg     --  A pre-defined Argument to use. If this is None (default),
-                    then a new Argument will be created from value, name and
-                    const.
+        Parameters
+        ----------
+        value
+            The value of the wrapped Argument (float, default None)
+        name
+            The name of the wrapped Argument (string, default None)
+        const
+            Flag indicating whether the Argument is constant (bool,
+            default False)
+        arg
+            A pre-defined Argument to use. If this is None (default),
+            then a new Argument will be created from value, name and
+            const.
         """
         BaseBuilder.__init__(self)
         if arg is None:
@@ -552,19 +584,25 @@ class OperatorBuilder(BaseBuilder):
     """BaseBuilder wrapper around an Operator literal.
 
     Attributes
-    literal     --  The Operator wrapped by this instance.
-    name        --  The name of the operator to be wrapped
+    ----------
+    literal
+        The Operator wrapped by this instance.
+    name
+        The name of the operator to be wrapped
     """
 
     def __init__(self, name, op=None):
         """Wrap an Operator or a function by name.
 
-        Arguments
-        name    --  The name of the wrapped Operator
-        op      --  If specified, this sets the literal attribute as this
-                    operator (default None). Otherwise, the name is assumed to
-                    be that of a numpy ufunc, which is used to specify the
-                    Operator.
+        Parameters
+        ----------
+        name
+            The name of the wrapped Operator
+        op
+            If specified, this sets the literal attribute as this
+            operator (default None). Otherwise, the name is assumed to
+            be that of a numpy ufunc, which is used to specify the
+            Operator.
         """
         BaseBuilder.__init__(self)
         self.name = name
@@ -576,7 +614,10 @@ class OperatorBuilder(BaseBuilder):
 
         This creates a new builder that encapsulates the operation.
 
-        args    --  Arguments of the operation.
+        Attributes
+        ----------
+        args
+            Arguments of the operation.
 
         Raises ValueError if self.literal.nin >= 0 and len(args) != op.nin
         """
@@ -637,10 +678,16 @@ def wrapOperator(name, op):
 def wrapFunction(name, func, nin=2, nout=1):
     """Wrap a function in an OperatorBuilder instance.
 
-    name    --  The name of the function
-    func    --  A callable python object
-    nin     --  The number of input arguments (default 2)
-    nout    --  The number of return values (default 1)
+    Attributes
+    ----------
+    name
+        The name of the function
+    func
+        A callable python object
+    nin
+        The number of input arguments (default 2)
+    nout
+        The number of return values (default 1)
 
     Returns the OperatorBuilder instance that wraps the function.
     """

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/equationmod.py

@@ -56,19 +56,32 @@ class Equation(Operator):
     accepts new argument values for the literal tree.
 
     Attributes
-    root    --  The root Literal of the equation tree
-    argdict --  An OrderedDict of Arguments from the root.
-    args    --  Property that gets the values of argdict.
+    ----------
+    root
+        The root Literal of the equation tree
+    argdict
+        An OrderedDict of Arguments from the root.
+    args
+        Property that gets the values of argdict.
 
     Operator Attributes
-    args    --  List of Literal arguments, set with 'addLiteral'
-    name    --  A name for this operator. e.g. "add" or "sin"
-    nin     --  Number of inputs (<1 means this is variable)
-    nout    --  Number of outputs
-    operation   --  Function that performs the operation. e.g. numpy.add.
-    symbol  --  The symbolic representation. e.g. "+" or "sin".
-    _value  --  The value of the Operator.
-    value   --  Property for 'getValue'.
+    -------------------
+    args
+        List of Literal arguments, set with 'addLiteral'
+    name
+        A name for this operator. e.g. "add" or "sin"
+    nin
+        Number of inputs (<1 means this is variable)
+    nout
+        Number of outputs
+    operation
+        Function that performs the operation. e.g. numpy.add.
+    symbol
+        The symbolic representation. e.g. "+" or "sin".
+    _value
+        The value of the Operator.
+    value
+        Property for 'getValue'.
     """
 
     # define abstract attributes from the Operator base.
@@ -78,10 +91,14 @@ class Equation(Operator):
     def __init__(self, name=None, root=None):
         """Initialize.
 
-        name    --  A name for this Equation.
-        root    --  The root node of the Literal tree (default None). If root
-                    is not passed here, you must call the 'setRoot' method to
-                    set or change the root node.
+        Attributes
+        ----------
+        name
+            A name for this Equation.
+        root
+            The root node of the Literal tree (default None). If root
+            is not passed here, you must call the 'setRoot' method to
+            set or change the root node.
         """
         # Operator stuff. We circumvent Operator.__init__ since we're using
         # args as a property. We cannot set it, as the Operator tries to do.
@@ -127,7 +144,7 @@ class Equation(Operator):
     )
 
     def __dir__(self):
-        "Return sorted list of attributes for this object."
+        """Return sorted list of attributes for this object."""
         rv = set(dir(type(self)))
         rv.update(self.__dict__, self.argdict)
         rv = sorted(rv)

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/literals/argument.py

@@ -30,11 +30,16 @@ class Argument(Literal, ArgumentABC):
     """Argument class.
 
     Attributes
-    name    --  A name for this Argument.
-    const   --  A flag indicating whether this is considered a constant.
-                Constants may be given special treatment by the Visitors.
-    _value  --  The value of the Argument. Modified with 'setValue'.
-    value   --  Property for 'getValue' and 'setValue'.
+    ----------
+    name
+        A name for this Argument.
+    const
+        A flag indicating whether this is considered a constant.
+        Constants may be given special treatment by the Visitors.
+    _value
+        The value of the Argument. Modified with 'setValue'.
+    value
+        Property for 'getValue' and 'setValue'.
     """
 
     const = None
@@ -57,7 +62,10 @@ class Argument(Literal, ArgumentABC):
     def setValue(self, val):
         """Set the value of the Literal.
 
-        val --  The value to assign
+        Attributes
+        ----------
+        val
+            The value to assign
         """
         if isinstance(self._value, ndarray) or isinstance(val, ndarray):
             notequiv = not array_equal(self._value, val)

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/literals/literal.py

@@ -31,8 +31,11 @@ class Literal(Observable, LiteralABC):
     Literal derives from Observable. See diffpy.srfit.util.observable.
 
     Attributes
-    name    --  A name for this Literal (default None).
-    _value  --  The value of the Literal.
+    ----------
+    name
+        A name for this Literal (default None).
+    _value
+        The value of the Literal.
     """
 
     name = None

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/literals/operators.py

@@ -345,7 +345,10 @@ class UFuncOperator(Operator):
 
         Arguments
 
-        op  --  A numpy ufunc
+        Attributes
+        ----------
+        op
+            A numpy ufunc
         """
         Operator.__init__(self, name=op.__name__)
         self.symbol = op.__name__

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/visitors/__init__.py

@@ -35,8 +35,11 @@ from diffpy.srfit.equation.visitors.validator import Validator
 def getArgs(literal, getconsts=True):
     """Get the Arguments of a Literal tree.
 
-    getconsts   --  If True (default), then Arguments designated as constant
-                    are also retrieved.
+    Attributes
+    ----------
+    getconsts
+        If True (default), then Arguments designated as constant
+        are also retrieved.
 
     Returns a list of Arguments searched for depth-first.
     """
@@ -47,9 +50,12 @@ def getArgs(literal, getconsts=True):
 def getExpression(literal, eqskip=None):
     """Get math expression string from the Literal tree object.
 
-    eqskip  --  regular expression pattern for Equation objects that should
-                be printed under their own name.  Expand all Equation objects
-                when None.
+    Attributes
+    ----------
+    eqskip
+        regular expression pattern for Equation objects that should
+        be printed under their own name.  Expand all Equation objects
+        when None.
 
     Return string.
     """

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/visitors/argfinder.py

@@ -26,16 +26,21 @@ class ArgFinder(Visitor):
     """ArgFinder extracts Arguments from a Literal tree.
 
     Attributes
-    args    --  The list of collected Arguments
-    getconsts  --  Flag indicating whether to grab constant arguments.
+    ----------
+    args
+        The list of collected Arguments
+    getconsts
+        Flag indicating whether to grab constant arguments.
     """
 
     def __init__(self, getconsts=True):
         """Initialize.
 
-        Arguments
-        getconsts   --  Flag indicating whether to parse constant arguments
-                        (default True).
+        Parameters
+        ----------
+        getconsts
+            Flag indicating whether to parse constant arguments
+            (default True).
         """
         self.args = []
         self.getconsts = getconsts

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/visitors/printer.py

@@ -30,10 +30,14 @@ class Printer(Visitor):
 
     Attributes:
 
-    eqskip  --  regular expression pattern for Equation objects that should
-                not be expanded, but printed under their own name.  Expand
-                all equations when None.
-    output  --  The output generated by the printer.
+    Attributes
+    ----------
+    eqskip
+        regular expression pattern for Equation objects that should
+        not be expanded, but printed under their own name.  Expand
+        all equations when None.
+    output
+        The output generated by the printer.
     """
 
     # store compiled RE pattern for eqskip or None when none.

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/visitors/swapper.py

@@ -25,17 +25,24 @@ class Swapper(Visitor):
     Note that this cannot swap out a root node of a literal tree. This case
     must be tested for explicitly.
 
-    Attributes:
-    newlit  --  The literal to be placed into the literal tree.
-    oldlit  --  The literal to be replaced.
+    Attributes
+    ----------
+    newlit
+        The literal to be placed into the literal tree.
+    oldlit
+        The literal to be replaced.
     """
 
     def __init__(self, oldlit, newlit):
         """Initialize.
 
-        oldlit  --  The literal to be replaced.
-        newlit  --  The literal to be placed into the literal tree. See the
-                    class for how the replacement takes place.
+        Attributes
+        ----------
+        oldlit
+            The literal to be replaced.
+        newlit
+            The literal to be placed into the literal tree. See the
+            class for how the replacement takes place.
         """
 
         self.newlit = newlit

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/equation/visitors/validator.py

@@ -34,10 +34,13 @@ msg = "'%s' does not have the interface required by '%s'"
 class Validator(Visitor):
     """Validator error for checking validity of an equation tree.
 
-    Attributes:
-    errors  --  List of strings describing errors.
-    _nin    --  Variable for counting the number input arguments for an
-                operator.
+    Attributes
+    ----------
+    errors
+        List of strings describing errors.
+    _nin
+        Variable for counting the number input arguments for an
+        operator.
     """
 
     def __init__(self):

{diffpy_srfit-3.1.0rc0 → diffpy_srfit-3.2.0}/src/diffpy/srfit/fitbase/calculator.py

@@ -36,30 +36,50 @@ class Calculator(Operator, ParameterSet):
     calculate a generic signal.
 
     Attributes
-    name            --  A name for this organizer.
-    meta            --  A dictionary of metadata needed by the calculator.
-    _calculators    --  A managed dictionary of Calculators, indexed by name.
-    _constraints    --  A set of constrained Parameters. Constraints can be
-                        added using the 'constrain' methods.
-    _parameters     --  A managed OrderedDict of contained Parameters.
-    _parsets        --  A managed dictionary of ParameterSets.
-    _restraints     --  A set of Restraints. Restraints can be added using the
-                        'restrain' or 'confine' methods.
-    _eqfactory      --  A diffpy.srfit.equation.builder.EquationFactory
-                        instance that is used create Equations from string.
+    ----------
+    name
+        A name for this organizer.
+    meta
+        A dictionary of metadata needed by the calculator.
+    _calculators
+        A managed dictionary of Calculators, indexed by name.
+    _constraints
+        A set of constrained Parameters. Constraints can be
+        added using the 'constrain' methods.
+    _parameters
+        A managed OrderedDict of contained Parameters.
+    _parsets
+        A managed dictionary of ParameterSets.
+    _restraints
+        A set of Restraints. Restraints can be added using the
+        'restrain' or 'confine' methods.
+    _eqfactory
+        A diffpy.srfit.equation.builder.EquationFactory
+        instance that is used create Equations from string.
 
     Operator Attributes
-    args    --  List of Literal arguments
-    nin     --  Number of inputs (<1 means this is variable)
-    nout    --  Number of outputs (1)
-    operation   --  Function that performs the operation, self.__call__
-    symbol  --  Same as name
-    _value  --  The value of the Operator.
-    value   --  Property for 'getValue'.
+    -------------------
+    args
+        List of Literal arguments
+    nin
+        Number of inputs (<1 means this is variable)
+    nout
+        Number of outputs (1)
+    operation
+        Function that performs the operation, self.__call__
+    symbol
+        Same as name
+    _value
+        The value of the Operator.
+    value
+        Property for 'getValue'.
 
     Properties
-    names           --  Variable names (read only). See getNames.
-    values          --  Variable values (read only). See getValues.
+    ----------
+    names
+        Variable names (read only). See getNames.
+    values
+        Variable values (read only). See getValues.
     """
 
     # define abstract attributes from the Operator base.