scipy 1.16.2__cp311-cp311-win_arm64.whl

scipy/_lib/deprecation.py

@@ -0,0 +1,274 @@
+from inspect import Parameter, signature
+import functools
+import warnings
+from importlib import import_module
+from scipy._lib._docscrape import FunctionDoc
+
+
+__all__ = ["_deprecated"]
+
+
+# Object to use as default value for arguments to be deprecated. This should
+# be used over 'None' as the user could parse 'None' as a positional argument
+_NoValue = object()
+
+def _sub_module_deprecation(*, sub_package, module, private_modules, all,
+                            attribute, correct_module=None, dep_version="1.16.0"):
+    """Helper function for deprecating modules that are public but were
+    intended to be private.
+
+    Parameters
+    ----------
+    sub_package : str
+        Subpackage the module belongs to eg. stats
+    module : str
+        Public but intended private module to deprecate
+    private_modules : list
+        Private replacement(s) for `module`; should contain the
+        content of ``all``, possibly spread over several modules.
+    all : list
+        ``__all__`` belonging to `module`
+    attribute : str
+        The attribute in `module` being accessed
+    correct_module : str, optional
+        Module in `sub_package` that `attribute` should be imported from.
+        Default is that `attribute` should be imported from ``scipy.sub_package``.
+    dep_version : str, optional
+        Version in which deprecated attributes will be removed.
+    """
+    if correct_module is not None:
+        correct_import = f"scipy.{sub_package}.{correct_module}"
+    else:
+        correct_import = f"scipy.{sub_package}"
+
+    if attribute not in all:
+        raise AttributeError(
+            f"`scipy.{sub_package}.{module}` has no attribute `{attribute}`; "
+            f"furthermore, `scipy.{sub_package}.{module}` is deprecated "
+            f"and will be removed in SciPy 2.0.0."
+        )
+
+    attr = getattr(import_module(correct_import), attribute, None)
+
+    if attr is not None:
+        message = (
+            f"Please import `{attribute}` from the `{correct_import}` namespace; "
+            f"the `scipy.{sub_package}.{module}` namespace is deprecated "
+            f"and will be removed in SciPy 2.0.0."
+        )
+    else:
+        message = (
+            f"`scipy.{sub_package}.{module}.{attribute}` is deprecated along with "
+            f"the `scipy.{sub_package}.{module}` namespace. "
+            f"`scipy.{sub_package}.{module}.{attribute}` will be removed "
+            f"in SciPy {dep_version}, and the `scipy.{sub_package}.{module}` namespace "
+            f"will be removed in SciPy 2.0.0."
+        )
+
+    warnings.warn(message, category=DeprecationWarning, stacklevel=3)
+
+    for module in private_modules:
+        try:
+            return getattr(import_module(f"scipy.{sub_package}.{module}"), attribute)
+        except AttributeError as e:
+            # still raise an error if the attribute isn't in any of the expected
+            # private modules
+            if module == private_modules[-1]:
+                raise e
+            continue
+    
+
+def _deprecated(msg, stacklevel=2):
+    """Deprecate a function by emitting a warning on use."""
+    def wrap(fun):
+        if isinstance(fun, type):
+            warnings.warn(
+                f"Trying to deprecate class {fun!r}",
+                category=RuntimeWarning, stacklevel=2)
+            return fun
+
+        @functools.wraps(fun)
+        def call(*args, **kwargs):
+            warnings.warn(msg, category=DeprecationWarning,
+                          stacklevel=stacklevel)
+            return fun(*args, **kwargs)
+        call.__doc__ = fun.__doc__
+        return call
+
+    return wrap
+
+
+class _DeprecationHelperStr:
+    """
+    Helper class used by deprecate_cython_api
+    """
+    def __init__(self, content, message):
+        self._content = content
+        self._message = message
+
+    def __hash__(self):
+        return hash(self._content)
+
+    def __eq__(self, other):
+        res = (self._content == other)
+        if res:
+            warnings.warn(self._message, category=DeprecationWarning,
+                          stacklevel=2)
+        return res
+
+
+def deprecate_cython_api(module, routine_name, new_name=None, message=None):
+    """
+    Deprecate an exported cdef function in a public Cython API module.
+
+    Only functions can be deprecated; typedefs etc. cannot.
+
+    Parameters
+    ----------
+    module : module
+        Public Cython API module (e.g. scipy.linalg.cython_blas).
+    routine_name : str
+        Name of the routine to deprecate. May also be a fused-type
+        routine (in which case its all specializations are deprecated).
+    new_name : str
+        New name to include in the deprecation warning message
+    message : str
+        Additional text in the deprecation warning message
+
+    Examples
+    --------
+    Usually, this function would be used in the top-level of the
+    module ``.pyx`` file:
+
+    >>> from scipy._lib.deprecation import deprecate_cython_api
+    >>> import scipy.linalg.cython_blas as mod
+    >>> deprecate_cython_api(mod, "dgemm", "dgemm_new",
+    ...                      message="Deprecated in Scipy 1.5.0")
+    >>> del deprecate_cython_api, mod
+
+    After this, Cython modules that use the deprecated function emit a
+    deprecation warning when they are imported.
+
+    """
+    old_name = f"{module.__name__}.{routine_name}"
+
+    if new_name is None:
+        depdoc = f"`{old_name}` is deprecated!"
+    else:
+        depdoc = f"`{old_name}` is deprecated, use `{new_name}` instead!"
+
+    if message is not None:
+        depdoc += "\n" + message
+
+    d = module.__pyx_capi__
+
+    # Check if the function is a fused-type function with a mangled name
+    j = 0
+    has_fused = False
+    while True:
+        fused_name = f"__pyx_fuse_{j}{routine_name}"
+        if fused_name in d:
+            has_fused = True
+            d[_DeprecationHelperStr(fused_name, depdoc)] = d.pop(fused_name)
+            j += 1
+        else:
+            break
+
+    # If not, apply deprecation to the named routine
+    if not has_fused:
+        d[_DeprecationHelperStr(routine_name, depdoc)] = d.pop(routine_name)
+
+
+# taken from scikit-learn, see
+# https://github.com/scikit-learn/scikit-learn/blob/1.3.0/sklearn/utils/validation.py#L38
+def _deprecate_positional_args(func=None, *, version=None,
+                               deprecated_args=None, custom_message=""):
+    """Decorator for methods that issues warnings for positional arguments.
+
+    Using the keyword-only argument syntax in pep 3102, arguments after the
+    * will issue a warning when passed as a positional argument.
+
+    Parameters
+    ----------
+    func : callable, default=None
+        Function to check arguments on.
+    version : callable, default=None
+        The version when positional arguments will result in error.
+    deprecated_args : set of str, optional
+        Arguments to deprecate - whether passed by position or keyword.
+    custom_message : str, optional
+        Custom message to add to deprecation warning and documentation.
+    """
+    if version is None:
+        msg = "Need to specify a version where signature will be changed"
+        raise ValueError(msg)
+
+    deprecated_args = set() if deprecated_args is None else set(deprecated_args)
+
+    def _inner_deprecate_positional_args(f):
+        sig = signature(f)
+        kwonly_args = []
+        all_args = []
+
+        for name, param in sig.parameters.items():
+            if param.kind == Parameter.POSITIONAL_OR_KEYWORD:
+                all_args.append(name)
+            elif param.kind == Parameter.KEYWORD_ONLY:
+                kwonly_args.append(name)
+
+        def warn_deprecated_args(kwargs):
+            intersection = deprecated_args.intersection(kwargs)
+            if intersection:
+                message = (f"Arguments {intersection} are deprecated, whether passed "
+                           "by position or keyword. They will be removed in SciPy "
+                           f"{version}. ")
+                message += custom_message
+                warnings.warn(message, category=DeprecationWarning, stacklevel=3)
+
+        @functools.wraps(f)
+        def inner_f(*args, **kwargs):
+
+            extra_args = len(args) - len(all_args)
+            if extra_args <= 0:
+                warn_deprecated_args(kwargs)
+                return f(*args, **kwargs)
+
+            # extra_args > 0
+            kwonly_extra_args = set(kwonly_args[:extra_args]) - deprecated_args
+            args_msg = ", ".join(kwonly_extra_args)
+            warnings.warn(
+                (
+                    f"You are passing as positional arguments: {args_msg}. "
+                    "Please change your invocation to use keyword arguments. "
+                    f"From SciPy {version}, passing these as positional "
+                    "arguments will result in an error."
+                ),
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            kwargs.update(zip(sig.parameters, args))
+            warn_deprecated_args(kwargs)
+            return f(**kwargs)
+
+        doc = FunctionDoc(inner_f)
+        kwonly_extra_args = set(kwonly_args) - deprecated_args
+        admonition = f"""
+.. deprecated:: {version}
+    Use of argument(s) ``{kwonly_extra_args}`` by position is deprecated; beginning in 
+    SciPy {version}, these will be keyword-only. """
+        if deprecated_args:
+            admonition += (f"Argument(s) ``{deprecated_args}`` are deprecated, whether "
+                           "passed by position or keyword; they will be removed in "
+                           f"SciPy {version}. ")
+        admonition += custom_message
+        doc['Extended Summary'] += [admonition]
+
+        doc = str(doc).split("\n", 1)[1]  # remove signature
+        inner_f.__doc__ = str(doc)
+
+        return inner_f
+
+    if func is not None:
+        return _inner_deprecate_positional_args(func)
+
+    return _inner_deprecate_positional_args

scipy/_lib/doccer.py

@@ -0,0 +1,366 @@
+"""Utilities to allow inserting docstring fragments for common
+parameters into function and method docstrings."""
+
+from collections.abc import Callable, Iterable, Mapping
+from typing import Protocol, TypeVar
+import sys
+
+__all__ = [
+    "docformat",
+    "inherit_docstring_from",
+    "indentcount_lines",
+    "filldoc",
+    "unindent_dict",
+    "unindent_string",
+    "extend_notes_in_docstring",
+    "replace_notes_in_docstring",
+    "doc_replace",
+]
+
+_F = TypeVar("_F", bound=Callable[..., object])
+
+
+class Decorator(Protocol):
+    """A decorator of a function."""
+
+    def __call__(self, func: _F, /) -> _F: ...
+
+
+def docformat(docstring: str, docdict: Mapping[str, str] | None = None) -> str:
+    """Fill a function docstring from variables in dictionary.
+
+    Adapt the indent of the inserted docs
+
+    Parameters
+    ----------
+    docstring : str
+        A docstring from a function, possibly with dict formatting strings.
+    docdict : dict[str, str], optional
+        A dictionary with keys that match the dict formatting strings
+        and values that are docstring fragments to be inserted. The
+        indentation of the inserted docstrings is set to match the
+        minimum indentation of the ``docstring`` by adding this
+        indentation to all lines of the inserted string, except the
+        first.
+
+    Returns
+    -------
+    docstring : str
+        string with requested ``docdict`` strings inserted.
+
+    Examples
+    --------
+    >>> docformat(' Test string with %(value)s', {'value':'inserted value'})
+    ' Test string with inserted value'
+    >>> docstring = 'First line\\n    Second line\\n    %(value)s'
+    >>> inserted_string = "indented\\nstring"
+    >>> docdict = {'value': inserted_string}
+    >>> docformat(docstring, docdict)
+    'First line\\n    Second line\\n    indented\\n    string'
+    """
+    if not docstring:
+        return docstring
+    if docdict is None:
+        docdict = {}
+    if not docdict:
+        return docstring
+    lines = docstring.expandtabs().splitlines()
+    # Find the minimum indent of the main docstring, after first line
+    if len(lines) < 2:
+        icount = 0
+    else:
+        icount = indentcount_lines(lines[1:])
+    indent = " " * icount
+    # Insert this indent to dictionary docstrings
+    indented = {}
+    for name, dstr in docdict.items():
+        lines = dstr.expandtabs().splitlines()
+        indented[name] = ("\n" + indent).join(lines)
+    return docstring % indented
+
+
+def inherit_docstring_from(cls: object) -> Decorator:
+    """This decorator modifies the decorated function's docstring by
+    replacing occurrences of '%(super)s' with the docstring of the
+    method of the same name from the class `cls`.
+
+    If the decorated method has no docstring, it is simply given the
+    docstring of `cls`s method.
+
+    Parameters
+    ----------
+    cls : type or object
+        A class with a method with the same name as the decorated method.
+        The docstring of the method in this class replaces '%(super)s' in the
+        docstring of the decorated method.
+
+    Returns
+    -------
+    decfunc : function
+        The decorator function that modifies the __doc__ attribute
+        of its argument.
+
+    Examples
+    --------
+    In the following, the docstring for Bar.func created using the
+    docstring of `Foo.func`.
+
+    >>> class Foo:
+    ...     def func(self):
+    ...         '''Do something useful.'''
+    ...         return
+    ...
+    >>> class Bar(Foo):
+    ...     @inherit_docstring_from(Foo)
+    ...     def func(self):
+    ...         '''%(super)s
+    ...         Do it fast.
+    ...         '''
+    ...         return
+    ...
+    >>> b = Bar()
+    >>> b.func.__doc__
+    'Do something useful.\n        Do it fast.\n        '
+    """
+
+    def _doc(func: _F) -> _F:
+        cls_docstring = getattr(cls, func.__name__).__doc__
+        func_docstring = func.__doc__
+        if func_docstring is None:
+            func.__doc__ = cls_docstring
+        else:
+            new_docstring = func_docstring % dict(super=cls_docstring)
+            func.__doc__ = new_docstring
+        return func
+
+    return _doc
+
+
+def extend_notes_in_docstring(cls: object, notes: str) -> Decorator:
+    """This decorator replaces the decorated function's docstring
+    with the docstring from corresponding method in `cls`.
+    It extends the 'Notes' section of that docstring to include
+    the given `notes`.
+
+    Parameters
+    ----------
+    cls : type or object
+        A class with a method with the same name as the decorated method.
+        The docstring of the method in this class replaces the docstring of the
+        decorated method.
+    notes : str
+        Additional notes to append to the 'Notes' section of the docstring.
+
+    Returns
+    -------
+    decfunc : function
+        The decorator function that modifies the __doc__ attribute
+        of its argument.
+    """
+
+    def _doc(func: _F) -> _F:
+        cls_docstring = getattr(cls, func.__name__).__doc__
+        # If python is called with -OO option,
+        # there is no docstring
+        if cls_docstring is None:
+            return func
+        end_of_notes = cls_docstring.find("        References\n")
+        if end_of_notes == -1:
+            end_of_notes = cls_docstring.find("        Examples\n")
+            if end_of_notes == -1:
+                end_of_notes = len(cls_docstring)
+        func.__doc__ = (
+            cls_docstring[:end_of_notes] + notes + cls_docstring[end_of_notes:]
+        )
+        return func
+
+    return _doc
+
+
+def replace_notes_in_docstring(cls: object, notes: str) -> Decorator:
+    """This decorator replaces the decorated function's docstring
+    with the docstring from corresponding method in `cls`.
+    It replaces the 'Notes' section of that docstring with
+    the given `notes`.
+
+    Parameters
+    ----------
+    cls : type or object
+        A class with a method with the same name as the decorated method.
+        The docstring of the method in this class replaces the docstring of the
+        decorated method.
+    notes : str
+        The notes to replace the existing 'Notes' section with.
+
+    Returns
+    -------
+    decfunc : function
+        The decorator function that modifies the __doc__ attribute
+        of its argument.
+    """
+
+    def _doc(func: _F) -> _F:
+        cls_docstring = getattr(cls, func.__name__).__doc__
+        notes_header = "        Notes\n        -----\n"
+        # If python is called with -OO option,
+        # there is no docstring
+        if cls_docstring is None:
+            return func
+        start_of_notes = cls_docstring.find(notes_header)
+        end_of_notes = cls_docstring.find("        References\n")
+        if end_of_notes == -1:
+            end_of_notes = cls_docstring.find("        Examples\n")
+            if end_of_notes == -1:
+                end_of_notes = len(cls_docstring)
+        func.__doc__ = (
+            cls_docstring[: start_of_notes + len(notes_header)]
+            + notes
+            + cls_docstring[end_of_notes:]
+        )
+        return func
+
+    return _doc
+
+
+def indentcount_lines(lines: Iterable[str]) -> int:
+    """Minimum indent for all lines in line list
+
+    Parameters
+    ----------
+    lines : Iterable[str]
+        The lines to find the minimum indent of.
+
+    Returns
+    -------
+    indent : int
+        The minimum indent.
+
+
+    Examples
+    --------
+    >>> lines = [' one', '  two', '   three']
+    >>> indentcount_lines(lines)
+    1
+    >>> lines = []
+    >>> indentcount_lines(lines)
+    0
+    >>> lines = [' one']
+    >>> indentcount_lines(lines)
+    1
+    >>> indentcount_lines(['    '])
+    0
+    """
+    indentno = sys.maxsize
+    for line in lines:
+        stripped = line.lstrip()
+        if stripped:
+            indentno = min(indentno, len(line) - len(stripped))
+    if indentno == sys.maxsize:
+        return 0
+    return indentno
+
+
+def filldoc(docdict: Mapping[str, str], unindent_params: bool = True) -> Decorator:
+    """Return docstring decorator using docdict variable dictionary.
+
+    Parameters
+    ----------
+    docdict : dict[str, str]
+        A dictionary containing name, docstring fragment pairs.
+    unindent_params : bool, optional
+        If True, strip common indentation from all parameters in docdict.
+        Default is False.
+
+    Returns
+    -------
+    decfunc : function
+        The decorator function that applies dictionary to its
+        argument's __doc__ attribute.
+    """
+    if unindent_params:
+        docdict = unindent_dict(docdict)
+
+    def decorate(func: _F) -> _F:
+        # __doc__ may be None for optimized Python (-OO)
+        doc = func.__doc__ or ""
+        func.__doc__ = docformat(doc, docdict)
+        return func
+
+    return decorate
+
+
+def unindent_dict(docdict: Mapping[str, str]) -> dict[str, str]:
+    """Unindent all strings in a docdict.
+
+    Parameters
+    ----------
+    docdict : dict[str, str]
+        A dictionary with string values to unindent.
+
+    Returns
+    -------
+    docdict : dict[str, str]
+        The `docdict` dictionary but each of its string values are unindented.
+    """
+    can_dict: dict[str, str] = {}
+    for name, dstr in docdict.items():
+        can_dict[name] = unindent_string(dstr)
+    return can_dict
+
+
+def unindent_string(docstring: str) -> str:
+    """Set docstring to minimum indent for all lines, including first.
+
+    Parameters
+    ----------
+    docstring : str
+        The input docstring to unindent.
+
+    Returns
+    -------
+    docstring : str
+        The unindented docstring.
+
+    Examples
+    --------
+    >>> unindent_string(' two')
+    'two'
+    >>> unindent_string('  two\\n   three')
+    'two\\n three'
+    """
+    lines = docstring.expandtabs().splitlines()
+    icount = indentcount_lines(lines)
+    if icount == 0:
+        return docstring
+    return "\n".join([line[icount:] for line in lines])
+
+
+def doc_replace(obj: object, oldval: str, newval: str) -> Decorator:
+    """Decorator to take the docstring from obj, with oldval replaced by newval
+
+    Equivalent to ``func.__doc__ = obj.__doc__.replace(oldval, newval)``
+
+    Parameters
+    ----------
+    obj : object
+        A class or object whose docstring will be used as the basis for the
+        replacement operation.
+    oldval : str
+        The string to search for in the docstring.
+    newval : str
+        The string to replace `oldval` with in the docstring.
+
+    Returns
+    -------
+    decfunc : function
+        A decorator function that replaces occurrences of `oldval` with `newval`
+        in the docstring of the decorated function.
+    """
+    # __doc__ may be None for optimized Python (-OO)
+    doc = (obj.__doc__ or "").replace(oldval, newval)
+
+    def inner(func: _F) -> _F:
+        func.__doc__ = doc
+        return func
+
+    return inner