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@@ -783,3 +783,6 @@ openflamingo/lib/python3.10/site-packages/scipy/stats/__pycache__/_multivariate.
 openflamingo/lib/python3.10/site-packages/scipy/stats/_rcont/rcont.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
 openflamingo/lib/python3.10/site-packages/scipy/stats/__pycache__/_morestats.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
 phi4/lib/python3.10/site-packages/numpy/_core/lib/libnpymath.a filter=lfs diff=lfs merge=lfs -text
+phi4/lib/python3.10/site-packages/numpy/_core/__pycache__/fromnumeric.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
+openflamingo/lib/python3.10/site-packages/scipy/io/matlab/_streams.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
+openflamingo/lib/python3.10/site-packages/scipy/io/matlab/_mio5_utils.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text

openflamingo/lib/python3.10/site-packages/scipy/io/matlab/_mio5_utils.cpython-310-x86_64-linux-gnu.so

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openflamingo/lib/python3.10/site-packages/scipy/io/matlab/_streams.cpython-310-x86_64-linux-gnu.so

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openflamingo/lib/python3.10/site-packages/scipy/spatial/_ckdtree.pyi

@@ -0,0 +1,214 @@
+from __future__ import annotations
+from typing import (
+    Any,
+    Generic,
+    overload,
+    TypeVar,
+)
+
+import numpy as np
+import numpy.typing as npt
+from scipy.sparse import coo_matrix, dok_matrix
+
+from typing import Literal
+
+# TODO: Replace `ndarray` with a 1D float64 array when possible
+_BoxType = TypeVar("_BoxType", None, npt.NDArray[np.float64])
+
+# Copied from `numpy.typing._scalar_like._ScalarLike`
+# TODO: Expand with 0D arrays once we have shape support
+_ArrayLike0D = bool | int | float | complex | str | bytes | np.generic
+
+_WeightType = npt.ArrayLike | tuple[npt.ArrayLike | None, npt.ArrayLike | None]
+
+class cKDTreeNode:
+    @property
+    def data_points(self) -> npt.NDArray[np.float64]: ...
+    @property
+    def indices(self) -> npt.NDArray[np.intp]: ...
+
+    # These are read-only attributes in cython, which behave like properties
+    @property
+    def level(self) -> int: ...
+    @property
+    def split_dim(self) -> int: ...
+    @property
+    def children(self) -> int: ...
+    @property
+    def start_idx(self) -> int: ...
+    @property
+    def end_idx(self) -> int: ...
+    @property
+    def split(self) -> float: ...
+    @property
+    def lesser(self) -> cKDTreeNode | None: ...
+    @property
+    def greater(self) -> cKDTreeNode | None: ...
+
+class cKDTree(Generic[_BoxType]):
+    @property
+    def n(self) -> int: ...
+    @property
+    def m(self) -> int: ...
+    @property
+    def leafsize(self) -> int: ...
+    @property
+    def size(self) -> int: ...
+    @property
+    def tree(self) -> cKDTreeNode: ...
+
+    # These are read-only attributes in cython, which behave like properties
+    @property
+    def data(self) -> npt.NDArray[np.float64]: ...
+    @property
+    def maxes(self) -> npt.NDArray[np.float64]: ...
+    @property
+    def mins(self) -> npt.NDArray[np.float64]: ...
+    @property
+    def indices(self) -> npt.NDArray[np.float64]: ...
+    @property
+    def boxsize(self) -> _BoxType: ...
+
+    # NOTE: In practice `__init__` is used as constructor, not `__new__`.
+    # The latter gives us more flexibility in setting the generic parameter
+    # though.
+    @overload
+    def __new__(  # type: ignore[misc]
+        cls,
+        data: npt.ArrayLike,
+        leafsize: int = ...,
+        compact_nodes: bool = ...,
+        copy_data: bool = ...,
+        balanced_tree: bool = ...,
+        boxsize: None = ...,
+    ) -> cKDTree[None]: ...
+    @overload
+    def __new__(
+        cls,
+        data: npt.ArrayLike,
+        leafsize: int = ...,
+        compact_nodes: bool = ...,
+        copy_data: bool = ...,
+        balanced_tree: bool = ...,
+        boxsize: npt.ArrayLike = ...,
+    ) -> cKDTree[npt.NDArray[np.float64]]: ...
+
+    # TODO: returns a 2-tuple of scalars if `x.ndim == 1` and `k == 1`,
+    # returns a 2-tuple of arrays otherwise
+    def query(
+        self,
+        x: npt.ArrayLike,
+        k: npt.ArrayLike = ...,
+        eps: float = ...,
+        p: float = ...,
+        distance_upper_bound: float = ...,
+        workers: int | None = ...,
+    ) -> tuple[Any, Any]: ...
+
+    # TODO: returns a list scalars if `x.ndim <= 1`,
+    # returns an object array of lists otherwise
+    def query_ball_point(
+        self,
+        x: npt.ArrayLike,
+        r: npt.ArrayLike,
+        p: float,
+        eps: float = ...,
+        workers: int | None = ...,
+        return_sorted: bool | None = ...,
+        return_length: bool = ...
+    ) -> Any: ...
+
+    def query_ball_tree(
+        self,
+        other: cKDTree,
+        r: float,
+        p: float,
+        eps: float = ...,
+    ) -> list[list[int]]: ...
+
+    @overload
+    def query_pairs(  # type: ignore[misc]
+        self,
+        r: float,
+        p: float = ...,
+        eps: float = ...,
+        output_type: Literal["set"] = ...,
+    ) -> set[tuple[int, int]]: ...
+    @overload
+    def query_pairs(
+        self,
+        r: float,
+        p: float = ...,
+        eps: float = ...,
+        output_type: Literal["ndarray"] = ...,
+    ) -> npt.NDArray[np.intp]: ...
+
+    @overload
+    def count_neighbors(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        r: _ArrayLike0D,
+        p: float = ...,
+        weights: None | tuple[None, None] = ...,
+        cumulative: bool = ...,
+    ) -> int: ...
+    @overload
+    def count_neighbors(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        r: _ArrayLike0D,
+        p: float = ...,
+        weights: _WeightType = ...,
+        cumulative: bool = ...,
+    ) -> np.float64: ...
+    @overload
+    def count_neighbors(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        r: npt.ArrayLike,
+        p: float = ...,
+        weights: None | tuple[None, None] = ...,
+        cumulative: bool = ...,
+    ) -> npt.NDArray[np.intp]: ...
+    @overload
+    def count_neighbors(
+        self,
+        other: cKDTree,
+        r: npt.ArrayLike,
+        p: float = ...,
+        weights: _WeightType = ...,
+        cumulative: bool = ...,
+    ) -> npt.NDArray[np.float64]: ...
+
+    @overload
+    def sparse_distance_matrix(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        max_distance: float,
+        p: float = ...,
+        output_type: Literal["dok_matrix"] = ...,
+    ) -> dok_matrix: ...
+    @overload
+    def sparse_distance_matrix(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        max_distance: float,
+        p: float = ...,
+        output_type: Literal["coo_matrix"] = ...,
+    ) -> coo_matrix: ...
+    @overload
+    def sparse_distance_matrix(  # type: ignore[misc]
+        self,
+        other: cKDTree,
+        max_distance: float,
+        p: float = ...,
+        output_type: Literal["dict"] = ...,
+    ) -> dict[tuple[int, int], float]: ...
+    @overload
+    def sparse_distance_matrix(
+        self,
+        other: cKDTree,
+        max_distance: float,
+        p: float = ...,
+        output_type: Literal["ndarray"] = ...,
+    ) -> npt.NDArray[np.void]: ...

openflamingo/lib/python3.10/site-packages/scipy/spatial/_kdtree.py

@@ -0,0 +1,920 @@
+# Copyright Anne M. Archibald 2008
+# Released under the scipy license
+import numpy as np
+from ._ckdtree import cKDTree, cKDTreeNode
+
+__all__ = ['minkowski_distance_p', 'minkowski_distance',
+           'distance_matrix',
+           'Rectangle', 'KDTree']
+
+
+def minkowski_distance_p(x, y, p=2):
+    """Compute the pth power of the L**p distance between two arrays.
+
+    For efficiency, this function computes the L**p distance but does
+    not extract the pth root. If `p` is 1 or infinity, this is equal to
+    the actual L**p distance.
+
+    The last dimensions of `x` and `y` must be the same length.  Any
+    other dimensions must be compatible for broadcasting.
+
+    Parameters
+    ----------
+    x : (..., K) array_like
+        Input array.
+    y : (..., K) array_like
+        Input array.
+    p : float, 1 <= p <= infinity
+        Which Minkowski p-norm to use.
+
+    Returns
+    -------
+    dist : ndarray
+        pth power of the distance between the input arrays.
+
+    Examples
+    --------
+    >>> from scipy.spatial import minkowski_distance_p
+    >>> minkowski_distance_p([[0, 0], [0, 0]], [[1, 1], [0, 1]])
+    array([2, 1])
+
+    """
+    x = np.asarray(x)
+    y = np.asarray(y)
+
+    # Find smallest common datatype with float64 (return type of this
+    # function) - addresses #10262.
+    # Don't just cast to float64 for complex input case.
+    common_datatype = np.promote_types(np.promote_types(x.dtype, y.dtype),
+                                       'float64')
+
+    # Make sure x and y are NumPy arrays of correct datatype.
+    x = x.astype(common_datatype)
+    y = y.astype(common_datatype)
+
+    if p == np.inf:
+        return np.amax(np.abs(y-x), axis=-1)
+    elif p == 1:
+        return np.sum(np.abs(y-x), axis=-1)
+    else:
+        return np.sum(np.abs(y-x)**p, axis=-1)
+
+
+def minkowski_distance(x, y, p=2):
+    """Compute the L**p distance between two arrays.
+
+    The last dimensions of `x` and `y` must be the same length.  Any
+    other dimensions must be compatible for broadcasting.
+
+    Parameters
+    ----------
+    x : (..., K) array_like
+        Input array.
+    y : (..., K) array_like
+        Input array.
+    p : float, 1 <= p <= infinity
+        Which Minkowski p-norm to use.
+
+    Returns
+    -------
+    dist : ndarray
+        Distance between the input arrays.
+
+    Examples
+    --------
+    >>> from scipy.spatial import minkowski_distance
+    >>> minkowski_distance([[0, 0], [0, 0]], [[1, 1], [0, 1]])
+    array([ 1.41421356,  1.        ])
+
+    """
+    x = np.asarray(x)
+    y = np.asarray(y)
+    if p == np.inf or p == 1:
+        return minkowski_distance_p(x, y, p)
+    else:
+        return minkowski_distance_p(x, y, p)**(1./p)
+
+
+class Rectangle:
+    """Hyperrectangle class.
+
+    Represents a Cartesian product of intervals.
+    """
+    def __init__(self, maxes, mins):
+        """Construct a hyperrectangle."""
+        self.maxes = np.maximum(maxes,mins).astype(float)
+        self.mins = np.minimum(maxes,mins).astype(float)
+        self.m, = self.maxes.shape
+
+    def __repr__(self):
+        return "<Rectangle %s>" % list(zip(self.mins, self.maxes))
+
+    def volume(self):
+        """Total volume."""
+        return np.prod(self.maxes-self.mins)
+
+    def split(self, d, split):
+        """Produce two hyperrectangles by splitting.
+
+        In general, if you need to compute maximum and minimum
+        distances to the children, it can be done more efficiently
+        by updating the maximum and minimum distances to the parent.
+
+        Parameters
+        ----------
+        d : int
+            Axis to split hyperrectangle along.
+        split : float
+            Position along axis `d` to split at.
+
+        """
+        mid = np.copy(self.maxes)
+        mid[d] = split
+        less = Rectangle(self.mins, mid)
+        mid = np.copy(self.mins)
+        mid[d] = split
+        greater = Rectangle(mid, self.maxes)
+        return less, greater
+
+    def min_distance_point(self, x, p=2.):
+        """
+        Return the minimum distance between input and points in the
+        hyperrectangle.
+
+        Parameters
+        ----------
+        x : array_like
+            Input.
+        p : float, optional
+            Input.
+
+        """
+        return minkowski_distance(
+            0, np.maximum(0, np.maximum(self.mins-x, x-self.maxes)),
+            p
+        )
+
+    def max_distance_point(self, x, p=2.):
+        """
+        Return the maximum distance between input and points in the hyperrectangle.
+
+        Parameters
+        ----------
+        x : array_like
+            Input array.
+        p : float, optional
+            Input.
+
+        """
+        return minkowski_distance(0, np.maximum(self.maxes-x, x-self.mins), p)
+
+    def min_distance_rectangle(self, other, p=2.):
+        """
+        Compute the minimum distance between points in the two hyperrectangles.
+
+        Parameters
+        ----------
+        other : hyperrectangle
+            Input.
+        p : float
+            Input.
+
+        """
+        return minkowski_distance(
+            0,
+            np.maximum(0, np.maximum(self.mins-other.maxes,
+                                     other.mins-self.maxes)),
+            p
+        )
+
+    def max_distance_rectangle(self, other, p=2.):
+        """
+        Compute the maximum distance between points in the two hyperrectangles.
+
+        Parameters
+        ----------
+        other : hyperrectangle
+            Input.
+        p : float, optional
+            Input.
+
+        """
+        return minkowski_distance(
+            0, np.maximum(self.maxes-other.mins, other.maxes-self.mins), p)
+
+
+class KDTree(cKDTree):
+    """kd-tree for quick nearest-neighbor lookup.
+
+    This class provides an index into a set of k-dimensional points
+    which can be used to rapidly look up the nearest neighbors of any
+    point.
+
+    Parameters
+    ----------
+    data : array_like, shape (n,m)
+        The n data points of dimension m to be indexed. This array is
+        not copied unless this is necessary to produce a contiguous
+        array of doubles, and so modifying this data will result in
+        bogus results. The data are also copied if the kd-tree is built
+        with copy_data=True.
+    leafsize : positive int, optional
+        The number of points at which the algorithm switches over to
+        brute-force.  Default: 10.
+    compact_nodes : bool, optional
+        If True, the kd-tree is built to shrink the hyperrectangles to
+        the actual data range. This usually gives a more compact tree that
+        is robust against degenerated input data and gives faster queries
+        at the expense of longer build time. Default: True.
+    copy_data : bool, optional
+        If True the data is always copied to protect the kd-tree against
+        data corruption. Default: False.
+    balanced_tree : bool, optional
+        If True, the median is used to split the hyperrectangles instead of
+        the midpoint. This usually gives a more compact tree and
+        faster queries at the expense of longer build time. Default: True.
+    boxsize : array_like or scalar, optional
+        Apply a m-d toroidal topology to the KDTree.. The topology is generated
+        by :math:`x_i + n_i L_i` where :math:`n_i` are integers and :math:`L_i`
+        is the boxsize along i-th dimension. The input data shall be wrapped
+        into :math:`[0, L_i)`. A ValueError is raised if any of the data is
+        outside of this bound.
+
+    Notes
+    -----
+    The algorithm used is described in Maneewongvatana and Mount 1999.
+    The general idea is that the kd-tree is a binary tree, each of whose
+    nodes represents an axis-aligned hyperrectangle. Each node specifies
+    an axis and splits the set of points based on whether their coordinate
+    along that axis is greater than or less than a particular value.
+
+    During construction, the axis and splitting point are chosen by the
+    "sliding midpoint" rule, which ensures that the cells do not all
+    become long and thin.
+
+    The tree can be queried for the r closest neighbors of any given point
+    (optionally returning only those within some maximum distance of the
+    point). It can also be queried, with a substantial gain in efficiency,
+    for the r approximate closest neighbors.
+
+    For large dimensions (20 is already large) do not expect this to run
+    significantly faster than brute force. High-dimensional nearest-neighbor
+    queries are a substantial open problem in computer science.
+
+    Attributes
+    ----------
+    data : ndarray, shape (n,m)
+        The n data points of dimension m to be indexed. This array is
+        not copied unless this is necessary to produce a contiguous
+        array of doubles. The data are also copied if the kd-tree is built
+        with `copy_data=True`.
+    leafsize : positive int
+        The number of points at which the algorithm switches over to
+        brute-force.
+    m : int
+        The dimension of a single data-point.
+    n : int
+        The number of data points.
+    maxes : ndarray, shape (m,)
+        The maximum value in each dimension of the n data points.
+    mins : ndarray, shape (m,)
+        The minimum value in each dimension of the n data points.
+    size : int
+        The number of nodes in the tree.
+
+    """
+
+    class node:
+        @staticmethod
+        def _create(ckdtree_node=None):
+            """Create either an inner or leaf node, wrapping a cKDTreeNode instance"""
+            if ckdtree_node is None:
+                return KDTree.node(ckdtree_node)
+            elif ckdtree_node.split_dim == -1:
+                return KDTree.leafnode(ckdtree_node)
+            else:
+                return KDTree.innernode(ckdtree_node)
+
+        def __init__(self, ckdtree_node=None):
+            if ckdtree_node is None:
+                ckdtree_node = cKDTreeNode()
+            self._node = ckdtree_node
+
+        def __lt__(self, other):
+            return id(self) < id(other)
+
+        def __gt__(self, other):
+            return id(self) > id(other)
+
+        def __le__(self, other):
+            return id(self) <= id(other)
+
+        def __ge__(self, other):
+            return id(self) >= id(other)
+
+        def __eq__(self, other):
+            return id(self) == id(other)
+
+    class leafnode(node):
+        @property
+        def idx(self):
+            return self._node.indices
+
+        @property
+        def children(self):
+            return self._node.children
+
+    class innernode(node):
+        def __init__(self, ckdtreenode):
+            assert isinstance(ckdtreenode, cKDTreeNode)
+            super().__init__(ckdtreenode)
+            self.less = KDTree.node._create(ckdtreenode.lesser)
+            self.greater = KDTree.node._create(ckdtreenode.greater)
+
+        @property
+        def split_dim(self):
+            return self._node.split_dim
+
+        @property
+        def split(self):
+            return self._node.split
+
+        @property
+        def children(self):
+            return self._node.children
+
+    @property
+    def tree(self):
+        if not hasattr(self, "_tree"):
+            self._tree = KDTree.node._create(super().tree)
+
+        return self._tree
+
+    def __init__(self, data, leafsize=10, compact_nodes=True, copy_data=False,
+                 balanced_tree=True, boxsize=None):
+        data = np.asarray(data)
+        if data.dtype.kind == 'c':
+            raise TypeError("KDTree does not work with complex data")
+
+        # Note KDTree has different default leafsize from cKDTree
+        super().__init__(data, leafsize, compact_nodes, copy_data,
+                         balanced_tree, boxsize)
+
+    def query(
+            self, x, k=1, eps=0, p=2, distance_upper_bound=np.inf, workers=1):
+        r"""Query the kd-tree for nearest neighbors.
+
+        Parameters
+        ----------
+        x : array_like, last dimension self.m
+            An array of points to query.
+        k : int or Sequence[int], optional
+            Either the number of nearest neighbors to return, or a list of the
+            k-th nearest neighbors to return, starting from 1.
+        eps : nonnegative float, optional
+            Return approximate nearest neighbors; the kth returned value
+            is guaranteed to be no further than (1+eps) times the
+            distance to the real kth nearest neighbor.
+        p : float, 1<=p<=infinity, optional
+            Which Minkowski p-norm to use.
+            1 is the sum-of-absolute-values distance ("Manhattan" distance).
+            2 is the usual Euclidean distance.
+            infinity is the maximum-coordinate-difference distance.
+            A large, finite p may cause a ValueError if overflow can occur.
+        distance_upper_bound : nonnegative float, optional
+            Return only neighbors within this distance. This is used to prune
+            tree searches, so if you are doing a series of nearest-neighbor
+            queries, it may help to supply the distance to the nearest neighbor
+            of the most recent point.
+        workers : int, optional
+            Number of workers to use for parallel processing. If -1 is given
+            all CPU threads are used. Default: 1.
+
+            .. versionadded:: 1.6.0
+
+        Returns
+        -------
+        d : float or array of floats
+            The distances to the nearest neighbors.
+            If ``x`` has shape ``tuple+(self.m,)``, then ``d`` has shape
+            ``tuple+(k,)``.
+            When k == 1, the last dimension of the output is squeezed.
+            Missing neighbors are indicated with infinite distances.
+            Hits are sorted by distance (nearest first).
+
+            .. versionchanged:: 1.9.0
+               Previously if ``k=None``, then `d` was an object array of
+               shape ``tuple``, containing lists of distances. This behavior
+               has been removed, use `query_ball_point` instead.
+
+        i : integer or array of integers
+            The index of each neighbor in ``self.data``.
+            ``i`` is the same shape as d.
+            Missing neighbors are indicated with ``self.n``.
+
+        Examples
+        --------
+
+        >>> import numpy as np
+        >>> from scipy.spatial import KDTree
+        >>> x, y = np.mgrid[0:5, 2:8]
+        >>> tree = KDTree(np.c_[x.ravel(), y.ravel()])
+
+        To query the nearest neighbours and return squeezed result, use
+
+        >>> dd, ii = tree.query([[0, 0], [2.2, 2.9]], k=1)
+        >>> print(dd, ii, sep='\n')
+        [2.         0.2236068]
+        [ 0 13]
+
+        To query the nearest neighbours and return unsqueezed result, use
+
+        >>> dd, ii = tree.query([[0, 0], [2.2, 2.9]], k=[1])
+        >>> print(dd, ii, sep='\n')
+        [[2.        ]
+         [0.2236068]]
+        [[ 0]
+         [13]]
+
+        To query the second nearest neighbours and return unsqueezed result,
+        use
+
+        >>> dd, ii = tree.query([[0, 0], [2.2, 2.9]], k=[2])
+        >>> print(dd, ii, sep='\n')
+        [[2.23606798]
+         [0.80622577]]
+        [[ 6]
+         [19]]
+
+        To query the first and second nearest neighbours, use
+
+        >>> dd, ii = tree.query([[0, 0], [2.2, 2.9]], k=2)
+        >>> print(dd, ii, sep='\n')
+        [[2.         2.23606798]
+         [0.2236068  0.80622577]]
+        [[ 0  6]
+         [13 19]]
+
+        or, be more specific
+
+        >>> dd, ii = tree.query([[0, 0], [2.2, 2.9]], k=[1, 2])
+        >>> print(dd, ii, sep='\n')
+        [[2.         2.23606798]
+         [0.2236068  0.80622577]]
+        [[ 0  6]
+         [13 19]]
+
+        """
+        x = np.asarray(x)
+        if x.dtype.kind == 'c':
+            raise TypeError("KDTree does not work with complex data")
+
+        if k is None:
+            raise ValueError("k must be an integer or a sequence of integers")
+
+        d, i = super().query(x, k, eps, p, distance_upper_bound, workers)
+        if isinstance(i, int):
+            i = np.intp(i)
+        return d, i
+
+    def query_ball_point(self, x, r, p=2., eps=0, workers=1,
+                         return_sorted=None, return_length=False):
+        """Find all points within distance r of point(s) x.
+
+        Parameters
+        ----------
+        x : array_like, shape tuple + (self.m,)
+            The point or points to search for neighbors of.
+        r : array_like, float
+            The radius of points to return, must broadcast to the length of x.
+        p : float, optional
+            Which Minkowski p-norm to use.  Should be in the range [1, inf].
+            A finite large p may cause a ValueError if overflow can occur.
+        eps : nonnegative float, optional
+            Approximate search. Branches of the tree are not explored if their
+            nearest points are further than ``r / (1 + eps)``, and branches are
+            added in bulk if their furthest points are nearer than
+            ``r * (1 + eps)``.
+        workers : int, optional
+            Number of jobs to schedule for parallel processing. If -1 is given
+            all processors are used. Default: 1.
+
+            .. versionadded:: 1.6.0
+        return_sorted : bool, optional
+            Sorts returned indices if True and does not sort them if False. If
+            None, does not sort single point queries, but does sort
+            multi-point queries which was the behavior before this option
+            was added.
+
+            .. versionadded:: 1.6.0
+        return_length : bool, optional
+            Return the number of points inside the radius instead of a list
+            of the indices.
+
+            .. versionadded:: 1.6.0
+
+        Returns
+        -------
+        results : list or array of lists
+            If `x` is a single point, returns a list of the indices of the
+            neighbors of `x`. If `x` is an array of points, returns an object
+            array of shape tuple containing lists of neighbors.
+
+        Notes
+        -----
+        If you have many points whose neighbors you want to find, you may save
+        substantial amounts of time by putting them in a KDTree and using
+        query_ball_tree.
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> from scipy import spatial
+        >>> x, y = np.mgrid[0:5, 0:5]
+        >>> points = np.c_[x.ravel(), y.ravel()]
+        >>> tree = spatial.KDTree(points)
+        >>> sorted(tree.query_ball_point([2, 0], 1))
+        [5, 10, 11, 15]
+
+        Query multiple points and plot the results:
+
+        >>> import matplotlib.pyplot as plt
+        >>> points = np.asarray(points)
+        >>> plt.plot(points[:,0], points[:,1], '.')
+        >>> for results in tree.query_ball_point(([2, 0], [3, 3]), 1):
+        ...     nearby_points = points[results]
+        ...     plt.plot(nearby_points[:,0], nearby_points[:,1], 'o')
+        >>> plt.margins(0.1, 0.1)
+        >>> plt.show()
+
+        """
+        x = np.asarray(x)
+        if x.dtype.kind == 'c':
+            raise TypeError("KDTree does not work with complex data")
+        return super().query_ball_point(
+            x, r, p, eps, workers, return_sorted, return_length)
+
+    def query_ball_tree(self, other, r, p=2., eps=0):
+        """
+        Find all pairs of points between `self` and `other` whose distance is
+        at most r.
+
+        Parameters
+        ----------
+        other : KDTree instance
+            The tree containing points to search against.
+        r : float
+            The maximum distance, has to be positive.
+        p : float, optional
+            Which Minkowski norm to use.  `p` has to meet the condition
+            ``1 <= p <= infinity``.
+        eps : float, optional
+            Approximate search.  Branches of the tree are not explored
+            if their nearest points are further than ``r/(1+eps)``, and
+            branches are added in bulk if their furthest points are nearer
+            than ``r * (1+eps)``.  `eps` has to be non-negative.
+
+        Returns
+        -------
+        results : list of lists
+            For each element ``self.data[i]`` of this tree, ``results[i]`` is a
+            list of the indices of its neighbors in ``other.data``.
+
+        Examples
+        --------
+        You can search all pairs of points between two kd-trees within a distance:
+
+        >>> import matplotlib.pyplot as plt
+        >>> import numpy as np
+        >>> from scipy.spatial import KDTree
+        >>> rng = np.random.default_rng()
+        >>> points1 = rng.random((15, 2))
+        >>> points2 = rng.random((15, 2))
+        >>> plt.figure(figsize=(6, 6))
+        >>> plt.plot(points1[:, 0], points1[:, 1], "xk", markersize=14)
+        >>> plt.plot(points2[:, 0], points2[:, 1], "og", markersize=14)
+        >>> kd_tree1 = KDTree(points1)
+        >>> kd_tree2 = KDTree(points2)
+        >>> indexes = kd_tree1.query_ball_tree(kd_tree2, r=0.2)
+        >>> for i in range(len(indexes)):
+        ...     for j in indexes[i]:
+        ...         plt.plot([points1[i, 0], points2[j, 0]],
+        ...             [points1[i, 1], points2[j, 1]], "-r")
+        >>> plt.show()
+
+        """
+        return super().query_ball_tree(other, r, p, eps)
+
+    def query_pairs(self, r, p=2., eps=0, output_type='set'):
+        """Find all pairs of points in `self` whose distance is at most r.
+
+        Parameters
+        ----------
+        r : positive float
+            The maximum distance.
+        p : float, optional
+            Which Minkowski norm to use.  `p` has to meet the condition
+            ``1 <= p <= infinity``.
+        eps : float, optional
+            Approximate search.  Branches of the tree are not explored
+            if their nearest points are further than ``r/(1+eps)``, and
+            branches are added in bulk if their furthest points are nearer
+            than ``r * (1+eps)``.  `eps` has to be non-negative.
+        output_type : string, optional
+            Choose the output container, 'set' or 'ndarray'. Default: 'set'
+
+            .. versionadded:: 1.6.0
+
+        Returns
+        -------
+        results : set or ndarray
+            Set of pairs ``(i,j)``, with ``i < j``, for which the corresponding
+            positions are close. If output_type is 'ndarray', an ndarry is
+            returned instead of a set.
+
+        Examples
+        --------
+        You can search all pairs of points in a kd-tree within a distance:
+
+        >>> import matplotlib.pyplot as plt
+        >>> import numpy as np
+        >>> from scipy.spatial import KDTree
+        >>> rng = np.random.default_rng()
+        >>> points = rng.random((20, 2))
+        >>> plt.figure(figsize=(6, 6))
+        >>> plt.plot(points[:, 0], points[:, 1], "xk", markersize=14)
+        >>> kd_tree = KDTree(points)
+        >>> pairs = kd_tree.query_pairs(r=0.2)
+        >>> for (i, j) in pairs:
+        ...     plt.plot([points[i, 0], points[j, 0]],
+        ...             [points[i, 1], points[j, 1]], "-r")
+        >>> plt.show()
+
+        """
+        return super().query_pairs(r, p, eps, output_type)
+
+    def count_neighbors(self, other, r, p=2., weights=None, cumulative=True):
+        """Count how many nearby pairs can be formed.
+
+        Count the number of pairs ``(x1,x2)`` can be formed, with ``x1`` drawn
+        from ``self`` and ``x2`` drawn from ``other``, and where
+        ``distance(x1, x2, p) <= r``.
+
+        Data points on ``self`` and ``other`` are optionally weighted by the
+        ``weights`` argument. (See below)
+
+        This is adapted from the "two-point correlation" algorithm described by
+        Gray and Moore [1]_.  See notes for further discussion.
+
+        Parameters
+        ----------
+        other : KDTree
+            The other tree to draw points from, can be the same tree as self.
+        r : float or one-dimensional array of floats
+            The radius to produce a count for. Multiple radii are searched with
+            a single tree traversal.
+            If the count is non-cumulative(``cumulative=False``), ``r`` defines
+            the edges of the bins, and must be non-decreasing.
+        p : float, optional
+            1<=p<=infinity.
+            Which Minkowski p-norm to use.
+            Default 2.0.
+            A finite large p may cause a ValueError if overflow can occur.
+        weights : tuple, array_like, or None, optional
+            If None, the pair-counting is unweighted.
+            If given as a tuple, weights[0] is the weights of points in
+            ``self``, and weights[1] is the weights of points in ``other``;
+            either can be None to indicate the points are unweighted.
+            If given as an array_like, weights is the weights of points in
+            ``self`` and ``other``. For this to make sense, ``self`` and
+            ``other`` must be the same tree. If ``self`` and ``other`` are two
+            different trees, a ``ValueError`` is raised.
+            Default: None
+
+            .. versionadded:: 1.6.0
+        cumulative : bool, optional
+            Whether the returned counts are cumulative. When cumulative is set
+            to ``False`` the algorithm is optimized to work with a large number
+            of bins (>10) specified by ``r``. When ``cumulative`` is set to
+            True, the algorithm is optimized to work with a small number of
+            ``r``. Default: True
+
+            .. versionadded:: 1.6.0
+
+        Returns
+        -------
+        result : scalar or 1-D array
+            The number of pairs. For unweighted counts, the result is integer.
+            For weighted counts, the result is float.
+            If cumulative is False, ``result[i]`` contains the counts with
+            ``(-inf if i == 0 else r[i-1]) < R <= r[i]``
+
+        Notes
+        -----
+        Pair-counting is the basic operation used to calculate the two point
+        correlation functions from a data set composed of position of objects.
+
+        Two point correlation function measures the clustering of objects and
+        is widely used in cosmology to quantify the large scale structure
+        in our Universe, but it may be useful for data analysis in other fields
+        where self-similar assembly of objects also occur.
+
+        The Landy-Szalay estimator for the two point correlation function of
+        ``D`` measures the clustering signal in ``D``. [2]_
+
+        For example, given the position of two sets of objects,
+
+        - objects ``D`` (data) contains the clustering signal, and
+
+        - objects ``R`` (random) that contains no signal,
+
+        .. math::
+
+             \\xi(r) = \\frac{<D, D> - 2 f <D, R> + f^2<R, R>}{f^2<R, R>},
+
+        where the brackets represents counting pairs between two data sets
+        in a finite bin around ``r`` (distance), corresponding to setting
+        `cumulative=False`, and ``f = float(len(D)) / float(len(R))`` is the
+        ratio between number of objects from data and random.
+
+        The algorithm implemented here is loosely based on the dual-tree
+        algorithm described in [1]_. We switch between two different
+        pair-cumulation scheme depending on the setting of ``cumulative``.
+        The computing time of the method we use when for
+        ``cumulative == False`` does not scale with the total number of bins.
+        The algorithm for ``cumulative == True`` scales linearly with the
+        number of bins, though it is slightly faster when only
+        1 or 2 bins are used. [5]_.
+
+        As an extension to the naive pair-counting,
+        weighted pair-counting counts the product of weights instead
+        of number of pairs.
+        Weighted pair-counting is used to estimate marked correlation functions
+        ([3]_, section 2.2),
+        or to properly calculate the average of data per distance bin
+        (e.g. [4]_, section 2.1 on redshift).
+
+        .. [1] Gray and Moore,
+               "N-body problems in statistical learning",
+               Mining the sky, 2000,
+               https://arxiv.org/abs/astro-ph/0012333
+
+        .. [2] Landy and Szalay,
+               "Bias and variance of angular correlation functions",
+               The Astrophysical Journal, 1993,
+               http://adsabs.harvard.edu/abs/1993ApJ...412...64L
+
+        .. [3] Sheth, Connolly and Skibba,
+               "Marked correlations in galaxy formation models",
+               Arxiv e-print, 2005,
+               https://arxiv.org/abs/astro-ph/0511773
+
+        .. [4] Hawkins, et al.,
+               "The 2dF Galaxy Redshift Survey: correlation functions,
+               peculiar velocities and the matter density of the Universe",
+               Monthly Notices of the Royal Astronomical Society, 2002,
+               http://adsabs.harvard.edu/abs/2003MNRAS.346...78H
+
+        .. [5] https://github.com/scipy/scipy/pull/5647#issuecomment-168474926
+
+        Examples
+        --------
+        You can count neighbors number between two kd-trees within a distance:
+
+        >>> import numpy as np
+        >>> from scipy.spatial import KDTree
+        >>> rng = np.random.default_rng()
+        >>> points1 = rng.random((5, 2))
+        >>> points2 = rng.random((5, 2))
+        >>> kd_tree1 = KDTree(points1)
+        >>> kd_tree2 = KDTree(points2)
+        >>> kd_tree1.count_neighbors(kd_tree2, 0.2)
+        1
+
+        This number is same as the total pair number calculated by
+        `query_ball_tree`:
+
+        >>> indexes = kd_tree1.query_ball_tree(kd_tree2, r=0.2)
+        >>> sum([len(i) for i in indexes])
+        1
+
+        """
+        return super().count_neighbors(other, r, p, weights, cumulative)
+
+    def sparse_distance_matrix(
+            self, other, max_distance, p=2., output_type='dok_matrix'):
+        """Compute a sparse distance matrix.
+
+        Computes a distance matrix between two KDTrees, leaving as zero
+        any distance greater than max_distance.
+
+        Parameters
+        ----------
+        other : KDTree
+
+        max_distance : positive float
+
+        p : float, 1<=p<=infinity
+            Which Minkowski p-norm to use.
+            A finite large p may cause a ValueError if overflow can occur.
+
+        output_type : string, optional
+            Which container to use for output data. Options: 'dok_matrix',
+            'coo_matrix', 'dict', or 'ndarray'. Default: 'dok_matrix'.
+
+            .. versionadded:: 1.6.0
+
+        Returns
+        -------
+        result : dok_matrix, coo_matrix, dict or ndarray
+            Sparse matrix representing the results in "dictionary of keys"
+            format. If a dict is returned the keys are (i,j) tuples of indices.
+            If output_type is 'ndarray' a record array with fields 'i', 'j',
+            and 'v' is returned,
+
+        Examples
+        --------
+        You can compute a sparse distance matrix between two kd-trees:
+
+        >>> import numpy as np
+        >>> from scipy.spatial import KDTree
+        >>> rng = np.random.default_rng()
+        >>> points1 = rng.random((5, 2))
+        >>> points2 = rng.random((5, 2))
+        >>> kd_tree1 = KDTree(points1)
+        >>> kd_tree2 = KDTree(points2)
+        >>> sdm = kd_tree1.sparse_distance_matrix(kd_tree2, 0.3)
+        >>> sdm.toarray()
+        array([[0.        , 0.        , 0.12295571, 0.        , 0.        ],
+           [0.        , 0.        , 0.        , 0.        , 0.        ],
+           [0.28942611, 0.        , 0.        , 0.2333084 , 0.        ],
+           [0.        , 0.        , 0.        , 0.        , 0.        ],
+           [0.24617575, 0.29571802, 0.26836782, 0.        , 0.        ]])
+
+        You can check distances above the `max_distance` are zeros:
+
+        >>> from scipy.spatial import distance_matrix
+        >>> distance_matrix(points1, points2)
+        array([[0.56906522, 0.39923701, 0.12295571, 0.8658745 , 0.79428925],
+           [0.37327919, 0.7225693 , 0.87665969, 0.32580855, 0.75679479],
+           [0.28942611, 0.30088013, 0.6395831 , 0.2333084 , 0.33630734],
+           [0.31994999, 0.72658602, 0.71124834, 0.55396483, 0.90785663],
+           [0.24617575, 0.29571802, 0.26836782, 0.57714465, 0.6473269 ]])
+
+        """
+        return super().sparse_distance_matrix(
+            other, max_distance, p, output_type)
+
+
+def distance_matrix(x, y, p=2, threshold=1000000):
+    """Compute the distance matrix.
+
+    Returns the matrix of all pair-wise distances.
+
+    Parameters
+    ----------
+    x : (M, K) array_like
+        Matrix of M vectors in K dimensions.
+    y : (N, K) array_like
+        Matrix of N vectors in K dimensions.
+    p : float, 1 <= p <= infinity
+        Which Minkowski p-norm to use.
+    threshold : positive int
+        If ``M * N * K`` > `threshold`, algorithm uses a Python loop instead
+        of large temporary arrays.
+
+    Returns
+    -------
+    result : (M, N) ndarray
+        Matrix containing the distance from every vector in `x` to every vector
+        in `y`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance_matrix
+    >>> distance_matrix([[0,0],[0,1]], [[1,0],[1,1]])
+    array([[ 1.        ,  1.41421356],
+           [ 1.41421356,  1.        ]])
+
+    """
+
+    x = np.asarray(x)
+    m, k = x.shape
+    y = np.asarray(y)
+    n, kk = y.shape
+
+    if k != kk:
+        raise ValueError(f"x contains {k}-dimensional vectors but y contains "
+                         f"{kk}-dimensional vectors")
+
+    if m*n*k <= threshold:
+        return minkowski_distance(x[:,np.newaxis,:],y[np.newaxis,:,:],p)
+    else:
+        result = np.empty((m,n),dtype=float)  # FIXME: figure out the best dtype
+        if m < n:
+            for i in range(m):
+                result[i,:] = minkowski_distance(x[i],y,p)
+        else:
+            for j in range(n):
+                result[:,j] = minkowski_distance(x,y[j],p)
+        return result

openflamingo/lib/python3.10/site-packages/scipy/spatial/_procrustes.py

@@ -0,0 +1,132 @@
+"""
+This module provides functions to perform full Procrustes analysis.
+
+This code was originally written by Justin Kucynski and ported over from
+scikit-bio by Yoshiki Vazquez-Baeza.
+"""
+
+import numpy as np
+from scipy.linalg import orthogonal_procrustes
+
+
+__all__ = ['procrustes']
+
+
+def procrustes(data1, data2):
+    r"""Procrustes analysis, a similarity test for two data sets.
+
+    Each input matrix is a set of points or vectors (the rows of the matrix).
+    The dimension of the space is the number of columns of each matrix. Given
+    two identically sized matrices, procrustes standardizes both such that:
+
+    - :math:`tr(AA^{T}) = 1`.
+
+    - Both sets of points are centered around the origin.
+
+    Procrustes ([1]_, [2]_) then applies the optimal transform to the second
+    matrix (including scaling/dilation, rotations, and reflections) to minimize
+    :math:`M^{2}=\sum(data1-data2)^{2}`, or the sum of the squares of the
+    pointwise differences between the two input datasets.
+
+    This function was not designed to handle datasets with different numbers of
+    datapoints (rows).  If two data sets have different dimensionality
+    (different number of columns), simply add columns of zeros to the smaller
+    of the two.
+
+    Parameters
+    ----------
+    data1 : array_like
+        Matrix, n rows represent points in k (columns) space `data1` is the
+        reference data, after it is standardised, the data from `data2` will be
+        transformed to fit the pattern in `data1` (must have >1 unique points).
+    data2 : array_like
+        n rows of data in k space to be fit to `data1`.  Must be the  same
+        shape ``(numrows, numcols)`` as data1 (must have >1 unique points).
+
+    Returns
+    -------
+    mtx1 : array_like
+        A standardized version of `data1`.
+    mtx2 : array_like
+        The orientation of `data2` that best fits `data1`. Centered, but not
+        necessarily :math:`tr(AA^{T}) = 1`.
+    disparity : float
+        :math:`M^{2}` as defined above.
+
+    Raises
+    ------
+    ValueError
+        If the input arrays are not two-dimensional.
+        If the shape of the input arrays is different.
+        If the input arrays have zero columns or zero rows.
+
+    See Also
+    --------
+    scipy.linalg.orthogonal_procrustes
+    scipy.spatial.distance.directed_hausdorff : Another similarity test
+      for two data sets
+
+    Notes
+    -----
+    - The disparity should not depend on the order of the input matrices, but
+      the output matrices will, as only the first output matrix is guaranteed
+      to be scaled such that :math:`tr(AA^{T}) = 1`.
+
+    - Duplicate data points are generally ok, duplicating a data point will
+      increase its effect on the procrustes fit.
+
+    - The disparity scales as the number of points per input matrix.
+
+    References
+    ----------
+    .. [1] Krzanowski, W. J. (2000). "Principles of Multivariate analysis".
+    .. [2] Gower, J. C. (1975). "Generalized procrustes analysis".
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.spatial import procrustes
+
+    The matrix ``b`` is a rotated, shifted, scaled and mirrored version of
+    ``a`` here:
+
+    >>> a = np.array([[1, 3], [1, 2], [1, 1], [2, 1]], 'd')
+    >>> b = np.array([[4, -2], [4, -4], [4, -6], [2, -6]], 'd')
+    >>> mtx1, mtx2, disparity = procrustes(a, b)
+    >>> round(disparity)
+    0.0
+
+    """
+    mtx1 = np.array(data1, dtype=np.float64, copy=True)
+    mtx2 = np.array(data2, dtype=np.float64, copy=True)
+
+    if mtx1.ndim != 2 or mtx2.ndim != 2:
+        raise ValueError("Input matrices must be two-dimensional")
+    if mtx1.shape != mtx2.shape:
+        raise ValueError("Input matrices must be of same shape")
+    if mtx1.size == 0:
+        raise ValueError("Input matrices must be >0 rows and >0 cols")
+
+    # translate all the data to the origin
+    mtx1 -= np.mean(mtx1, 0)
+    mtx2 -= np.mean(mtx2, 0)
+
+    norm1 = np.linalg.norm(mtx1)
+    norm2 = np.linalg.norm(mtx2)
+
+    if norm1 == 0 or norm2 == 0:
+        raise ValueError("Input matrices must contain >1 unique points")
+
+    # change scaling of data (in rows) such that trace(mtx*mtx') = 1
+    mtx1 /= norm1
+    mtx2 /= norm2
+
+    # transform mtx2 to minimize disparity
+    R, s = orthogonal_procrustes(mtx1, mtx2)
+    mtx2 = np.dot(mtx2, R.T) * s
+
+    # measure the dissimilarity between the two datasets
+    disparity = np.sum(np.square(mtx1 - mtx2))
+
+    return mtx1, mtx2, disparity
+

openflamingo/lib/python3.10/site-packages/scipy/spatial/_qhull.pyi

@@ -0,0 +1,213 @@
+'''
+Static type checking stub file for scipy/spatial/qhull.pyx
+'''
+
+
+import numpy as np
+from numpy.typing import ArrayLike, NDArray
+from typing_extensions import final
+
+class QhullError(RuntimeError):
+    ...
+    
+@final
+class _Qhull:
+    # Read-only cython attribute that behaves, more or less, like a property
+    @property
+    def ndim(self) -> int: ...
+    mode_option: bytes
+    options: bytes
+    furthest_site: bool
+
+    def __init__(
+        self,
+        mode_option: bytes,
+        points: NDArray[np.float64],
+        options: None | bytes = ...,
+        required_options: None | bytes = ...,
+        furthest_site: bool = ...,
+        incremental: bool = ...,
+        interior_point: None | NDArray[np.float64] = ...,
+    ) -> None: ...
+    def check_active(self) -> None: ...
+    def close(self) -> None: ...
+    def get_points(self) -> NDArray[np.float64]: ...
+    def add_points(
+        self,
+        points: ArrayLike,
+        interior_point: ArrayLike = ...
+    ) -> None: ...
+    def get_paraboloid_shift_scale(self) -> tuple[float, float]: ...
+    def volume_area(self) -> tuple[float, float]: ...
+    def triangulate(self) -> None: ...
+    def get_simplex_facet_array(self) -> tuple[
+        NDArray[np.intc],
+        NDArray[np.intc],
+        NDArray[np.float64],
+        NDArray[np.intc],
+        NDArray[np.intc],
+    ]: ...
+    def get_hull_points(self) -> NDArray[np.float64]: ...
+    def get_hull_facets(self) -> tuple[
+        list[list[int]],
+        NDArray[np.float64],
+    ]: ...
+    def get_voronoi_diagram(self) -> tuple[
+        NDArray[np.float64],
+        NDArray[np.intc],
+        list[list[int]],
+        list[list[int]],
+        NDArray[np.intp],
+    ]: ...
+    def get_extremes_2d(self) -> NDArray[np.intc]: ...
+
+def _get_barycentric_transforms(
+    points: NDArray[np.float64],
+    simplices: NDArray[np.intc],
+    eps: float
+) -> NDArray[np.float64]: ...
+
+class _QhullUser:
+    ndim: int
+    npoints: int
+    min_bound: NDArray[np.float64]
+    max_bound: NDArray[np.float64]
+
+    def __init__(self, qhull: _Qhull, incremental: bool = ...) -> None: ...
+    def close(self) -> None: ...
+    def _update(self, qhull: _Qhull) -> None: ...
+    def _add_points(
+        self,
+        points: ArrayLike,
+        restart: bool = ...,
+        interior_point: ArrayLike = ...
+    ) -> None: ...
+
+class Delaunay(_QhullUser):
+    furthest_site: bool
+    paraboloid_scale: float
+    paraboloid_shift: float
+    simplices: NDArray[np.intc]
+    neighbors: NDArray[np.intc]
+    equations: NDArray[np.float64]
+    coplanar: NDArray[np.intc]
+    good: NDArray[np.intc]
+    nsimplex: int
+    vertices: NDArray[np.intc]
+
+    def __init__(
+        self,
+        points: ArrayLike,
+        furthest_site: bool = ...,
+        incremental: bool = ...,
+        qhull_options: None | str = ...
+    ) -> None: ...
+    def _update(self, qhull: _Qhull) -> None: ...
+    def add_points(
+        self,
+        points: ArrayLike,
+        restart: bool = ...
+    ) -> None: ...
+    @property
+    def points(self) -> NDArray[np.float64]: ...
+    @property
+    def transform(self) -> NDArray[np.float64]: ...
+    @property
+    def vertex_to_simplex(self) -> NDArray[np.intc]: ...
+    @property
+    def vertex_neighbor_vertices(self) -> tuple[
+        NDArray[np.intc],
+        NDArray[np.intc],
+    ]: ...
+    @property
+    def convex_hull(self) -> NDArray[np.intc]: ...
+    def find_simplex(
+        self,
+        xi: ArrayLike,
+        bruteforce: bool = ...,
+        tol: float = ...
+    ) -> NDArray[np.intc]: ...
+    def plane_distance(self, xi: ArrayLike) -> NDArray[np.float64]: ...
+    def lift_points(self, x: ArrayLike) -> NDArray[np.float64]: ...
+
+def tsearch(tri: Delaunay, xi: ArrayLike) -> NDArray[np.intc]: ...
+def _copy_docstr(dst: object, src: object) -> None: ...
+
+class ConvexHull(_QhullUser):
+    simplices: NDArray[np.intc]
+    neighbors: NDArray[np.intc]
+    equations: NDArray[np.float64]
+    coplanar: NDArray[np.intc]
+    good: None | NDArray[np.bool_]
+    volume: float
+    area: float
+    nsimplex: int
+
+    def __init__(
+        self,
+        points: ArrayLike,
+        incremental: bool = ...,
+        qhull_options: None | str = ...
+    ) -> None: ...
+    def _update(self, qhull: _Qhull) -> None: ...
+    def add_points(self, points: ArrayLike,
+                   restart: bool = ...) -> None: ...
+    @property
+    def points(self) -> NDArray[np.float64]: ...
+    @property
+    def vertices(self) -> NDArray[np.intc]: ...
+
+class Voronoi(_QhullUser):
+    vertices: NDArray[np.float64]
+    ridge_points: NDArray[np.intc]
+    ridge_vertices: list[list[int]]
+    regions: list[list[int]]
+    point_region: NDArray[np.intp]
+    furthest_site: bool
+
+    def __init__(
+        self,
+        points: ArrayLike,
+        furthest_site: bool = ...,
+        incremental: bool = ...,
+        qhull_options: None | str = ...
+    ) -> None: ...
+    def _update(self, qhull: _Qhull) -> None: ...
+    def add_points(
+        self,
+        points: ArrayLike,
+        restart: bool = ...
+    ) -> None: ...
+    @property
+    def points(self) -> NDArray[np.float64]: ...
+    @property
+    def ridge_dict(self) -> dict[tuple[int, int], list[int]]: ...
+
+class HalfspaceIntersection(_QhullUser):
+    interior_point: NDArray[np.float64]
+    dual_facets: list[list[int]]
+    dual_equations: NDArray[np.float64]
+    dual_points: NDArray[np.float64]
+    dual_volume: float
+    dual_area: float
+    intersections: NDArray[np.float64]
+    ndim: int
+    nineq: int
+
+    def __init__(
+        self,
+        halfspaces: ArrayLike,
+        interior_point: ArrayLike,
+        incremental: bool = ...,
+        qhull_options: None | str = ...
+    ) -> None: ...
+    def _update(self, qhull: _Qhull) -> None: ...
+    def add_halfspaces(
+        self,
+        halfspaces: ArrayLike,
+        restart: bool = ...
+    ) -> None: ...
+    @property
+    def halfspaces(self) -> NDArray[np.float64]: ...
+    @property
+    def dual_vertices(self) -> NDArray[np.integer]: ...

openflamingo/lib/python3.10/site-packages/scipy/spatial/_voronoi.pyi

@@ -0,0 +1,4 @@
+
+import numpy as np
+
+def sort_vertices_of_regions(simplices: np.ndarray, regions: list[list[int]]) -> None: ...  # noqa: E501

openflamingo/lib/python3.10/site-packages/scipy/spatial/distance.pyi

@@ -0,0 +1,211 @@
+from __future__ import annotations
+from typing import (overload, Any, SupportsFloat, Literal, Protocol, SupportsIndex)
+
+import numpy as np
+from numpy.typing import ArrayLike, NDArray
+
+# Anything that can be parsed by `np.float64.__init__` and is thus
+# compatible with `ndarray.__setitem__` (for a float64 array)
+_FloatValue = None | str | bytes | SupportsFloat | SupportsIndex
+
+class _MetricCallback1(Protocol):
+    def __call__(
+        self, __XA: NDArray[Any], __XB: NDArray[Any]
+    ) -> _FloatValue: ...
+
+class _MetricCallback2(Protocol):
+    def __call__(
+        self, __XA: NDArray[Any], __XB: NDArray[Any], **kwargs: Any
+    ) -> _FloatValue: ...
+
+# TODO: Use a single protocol with a parameter specification variable
+# once available (PEP 612)
+_MetricCallback = _MetricCallback1 | _MetricCallback2
+
+_MetricKind = Literal[
+    'braycurtis',
+    'canberra',
+    'chebychev', 'chebyshev', 'cheby', 'cheb', 'ch',
+    'cityblock', 'cblock', 'cb', 'c',
+    'correlation', 'co',
+    'cosine', 'cos',
+    'dice',
+    'euclidean', 'euclid', 'eu', 'e',
+    'hamming', 'hamm', 'ha', 'h',
+    'minkowski', 'mi', 'm', 'pnorm',
+    'jaccard', 'jacc', 'ja', 'j',
+    'jensenshannon', 'js',
+    'kulczynski1',
+    'mahalanobis', 'mahal', 'mah',
+    'rogerstanimoto',
+    'russellrao',
+    'seuclidean', 'se', 's',
+    'sokalmichener',
+    'sokalsneath',
+    'sqeuclidean', 'sqe', 'sqeuclid',
+    'yule',
+]
+
+# Function annotations
+
+def braycurtis(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def canberra(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+# TODO: Add `metric`-specific overloads
+# Returns a float64 or float128 array, depending on the input dtype
+@overload
+def cdist(
+    XA: ArrayLike,
+    XB: ArrayLike,
+    metric: _MetricKind = ...,
+    *,
+    out: None | NDArray[np.floating[Any]] = ...,
+    p: float = ...,
+    w: ArrayLike | None = ...,
+    V: ArrayLike | None = ...,
+    VI: ArrayLike | None = ...,
+) -> NDArray[np.floating[Any]]: ...
+@overload
+def cdist(
+    XA: ArrayLike,
+    XB: ArrayLike,
+    metric: _MetricCallback,
+    *,
+    out: None | NDArray[np.floating[Any]] = ...,
+    **kwargs: Any,
+) -> NDArray[np.floating[Any]]: ...
+
+# TODO: Wait for dtype support; the return type is
+# dependent on the input arrays dtype
+def chebyshev(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> Any: ...
+
+# TODO: Wait for dtype support; the return type is
+# dependent on the input arrays dtype
+def cityblock(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> Any: ...
+
+def correlation(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ..., centered: bool = ...
+) -> np.float64: ...
+
+def cosine(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def dice(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...
+
+def directed_hausdorff(
+    u: ArrayLike, v: ArrayLike, seed: int | None = ...
+) -> tuple[float, int, int]: ...
+
+def euclidean(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...
+
+def hamming(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def is_valid_dm(
+    D: ArrayLike,
+    tol: float = ...,
+    throw: bool = ...,
+    name: str | None = ...,
+    warning: bool = ...,
+) -> bool: ...
+
+def is_valid_y(
+    y: ArrayLike,
+    warning: bool = ...,
+    throw: bool = ...,
+    name: str | None = ...,
+) -> bool: ...
+
+def jaccard(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def jensenshannon(
+    p: ArrayLike, q: ArrayLike, base: float | None = ...
+) -> np.float64: ...
+
+def kulczynski1(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def mahalanobis(
+    u: ArrayLike, v: ArrayLike, VI: ArrayLike
+) -> np.float64: ...
+
+def minkowski(
+    u: ArrayLike, v: ArrayLike, p: float = ..., w: ArrayLike | None = ...
+) -> float: ...
+
+def num_obs_dm(d: ArrayLike) -> int: ...
+
+def num_obs_y(Y: ArrayLike) -> int: ...
+
+# TODO: Add `metric`-specific overloads
+@overload
+def pdist(
+    X: ArrayLike,
+    metric: _MetricKind = ...,
+    *,
+    out: None | NDArray[np.floating[Any]] = ...,
+    p: float = ...,
+    w: ArrayLike | None = ...,
+    V: ArrayLike | None = ...,
+    VI: ArrayLike | None = ...,
+) -> NDArray[np.floating[Any]]: ...
+@overload
+def pdist(
+    X: ArrayLike,
+    metric: _MetricCallback,
+    *,
+    out: None | NDArray[np.floating[Any]] = ...,
+    **kwargs: Any,
+) -> NDArray[np.floating[Any]]: ...
+
+def seuclidean(
+    u: ArrayLike, v: ArrayLike, V: ArrayLike
+) -> float: ...
+
+def sokalmichener(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...
+
+def sokalsneath(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def sqeuclidean(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> np.float64: ...
+
+def squareform(
+    X: ArrayLike,
+    force: Literal["no", "tomatrix", "tovector"] = ...,
+    checks: bool = ...,
+) -> NDArray[Any]: ...
+
+def rogerstanimoto(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...
+
+def russellrao(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...
+
+def yule(
+    u: ArrayLike, v: ArrayLike, w: ArrayLike | None = ...
+) -> float: ...

openflamingo/lib/python3.10/site-packages/scipy/spatial/qhull.py

@@ -0,0 +1,25 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.spatial` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'ConvexHull',
+    'Delaunay',
+    'HalfspaceIntersection',
+    'QhullError',
+    'Voronoi',
+    'tsearch',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="spatial", module="qhull",
+                                   private_modules=["_qhull"], all=__all__,
+                                   attribute=name)

openflamingo/lib/python3.10/site-packages/scipy/spatial/tests/data/cdist-X2.txt

@@ -0,0 +1,20 @@
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+5.015172758330755931e-01 5.569527971282052237e-01 1.122406928736449094e-01 8.960352822124777461e-01 6.049568585854003810e-02 1.202196001338627918e-01 1.870314295763603196e-01 9.017590029396971296e-01 3.597904628087450485e-01 2.130941062746317671e-01 2.556281834629479111e-01 5.123669364829196438e-01 4.754061129282013409e-01 9.764470380372083369e-01 8.038663983900646848e-01 6.960491266420890666e-01 2.940135977911654264e-01 2.857282759910040326e-03 4.599343225832352999e-02 5.597554495210212977e-01 7.445266674304001908e-01 3.387528030535971180e-01 6.429542922125383031e-01 2.123331785532429627e-01 5.302332654117811739e-01 7.262555377662539557e-01 3.982425859900724507e-01 3.243388301740235402e-01 6.191064123738921898e-01 8.988047781373914580e-01 7.819700328765150088e-01 7.664269102804815992e-01 6.734095355422575757e-03 2.904762329148526945e-01 5.097537644843168625e-01 9.524734606001823423e-01 4.812869576591960463e-01 6.236868013640477493e-01 1.459170943214320726e-01 9.874505139403206844e-01 7.561708982837871407e-01 3.798591332432484924e-01 6.056633451375117438e-01 7.935708170258731764e-01 1.458141583518740569e-01 7.082511296391911237e-01 1.098798009731616343e-02 3.655618484905173160e-01 9.551862303858617009e-01 8.148959351152762487e-02 4.739306219219985294e-02 7.963357515359494876e-01 6.208332695202813944e-01 3.884182264923189409e-01 4.589167647950288531e-01 6.496652974138312775e-01 2.467528128074852889e-01 5.309593064844935206e-01 5.364606369543487574e-01 2.421352989851309756e-01 3.776834556696828660e-02 1.564861233558080267e-01 5.197231021782636740e-01 8.725375120634637494e-01 2.441225493455024820e-01 2.320363366041028330e-01 5.026358683423555185e-01 7.035766000474735771e-01 8.347805591467084563e-01 2.303229841813967393e-01 6.908373419683054850e-01 2.646662377366995056e-01 1.259467197942290007e-01 9.372770922994989595e-01 6.674216272867254940e-01 1.027944489143072238e-01 5.686267290346079806e-01 3.948222804451942958e-01 4.689706944496729868e-01 4.446117700449114807e-02 6.817992275557515081e-01 9.084821829413957106e-01 9.184021015315092518e-01 3.045815734169987632e-01 2.204958624923980537e-03 7.542672057172502553e-01 9.460844786545006269e-01 3.373139094575949848e-02 9.059565314915285494e-01 9.938525461318854504e-01 2.542072661725306437e-01 9.685734112479216229e-02 8.223629541824816203e-01 1.057429056898460118e-01 8.080679390260248063e-01 5.823014244609205914e-01 6.413551528031806725e-01 1.787341975438894170e-01 1.250471413912357388e-01 8.390281297596062782e-01

openflamingo/lib/python3.10/site-packages/scipy/spatial/tests/data/pdist-hamming-ml.txt

@@ -0,0 +1 @@
+   4.6000000e-01   4.3000000e-01   4.3000000e-01   5.4000000e-01   4.1000000e-01   5.3000000e-01   4.3000000e-01   5.9000000e-01   4.8000000e-01   4.7000000e-01   4.6000000e-01   4.9000000e-01   4.5000000e-01   5.5000000e-01   5.3000000e-01   4.5000000e-01   4.8000000e-01   4.7000000e-01   4.8000000e-01   5.1000000e-01   4.9000000e-01   4.4000000e-01   4.9000000e-01   4.7000000e-01   4.9000000e-01   4.7000000e-01   5.2000000e-01   4.7000000e-01   4.2000000e-01   4.9000000e-01   4.7000000e-01   5.5000000e-01   3.9000000e-01   5.5000000e-01   4.6000000e-01   4.5000000e-01   4.0000000e-01   4.8000000e-01   4.5000000e-01   4.8000000e-01   4.8000000e-01   5.0000000e-01   4.8000000e-01   4.5000000e-01   6.4000000e-01   5.7000000e-01   4.6000000e-01   5.4000000e-01   5.6000000e-01   4.8000000e-01   4.8000000e-01   5.3000000e-01   5.4000000e-01   5.3000000e-01   4.5000000e-01   5.8000000e-01   4.2000000e-01   5.4000000e-01   6.0000000e-01   5.1000000e-01   4.6000000e-01   4.1000000e-01   4.4000000e-01   5.6000000e-01   5.4000000e-01   4.8000000e-01   4.8000000e-01   5.1000000e-01   5.2000000e-01   5.5000000e-01   4.5000000e-01   4.3000000e-01   4.7000000e-01   4.7000000e-01   5.6000000e-01   4.9000000e-01   4.8000000e-01   4.5000000e-01   4.9000000e-01   4.7000000e-01   4.5000000e-01   4.5000000e-01   5.6000000e-01   4.9000000e-01   5.8000000e-01   5.4000000e-01   4.6000000e-01   5.8000000e-01   5.3000000e-01   5.4000000e-01   5.5000000e-01   5.0000000e-01   5.2000000e-01   4.8000000e-01   5.0000000e-01   3.8000000e-01   5.3000000e-01   4.8000000e-01   5.1000000e-01   4.8000000e-01   5.2000000e-01   4.7000000e-01   5.0000000e-01   4.3000000e-01   4.8000000e-01   5.2000000e-01   5.0000000e-01   4.2000000e-01   4.2000000e-01   4.7000000e-01   5.4000000e-01   5.1000000e-01   5.4000000e-01   5.1000000e-01   4.8000000e-01   4.7000000e-01   5.2000000e-01   5.2000000e-01   5.4000000e-01   5.4000000e-01   5.0000000e-01   4.5000000e-01   4.4000000e-01   4.1000000e-01   5.7000000e-01   4.6000000e-01   5.1000000e-01   5.2000000e-01   5.0000000e-01   4.8000000e-01   5.0000000e-01   4.4000000e-01   5.3000000e-01   5.2000000e-01   4.9000000e-01   5.7000000e-01   5.8000000e-01   4.9000000e-01   5.1000000e-01   4.5000000e-01   5.3000000e-01   4.5000000e-01   4.4000000e-01   3.5000000e-01   4.2000000e-01   5.3000000e-01   5.2000000e-01   5.0000000e-01   3.8000000e-01   5.2000000e-01   5.6000000e-01   4.7000000e-01   4.4000000e-01   5.1000000e-01   5.7000000e-01   4.5000000e-01   5.7000000e-01   4.3000000e-01   5.1000000e-01   3.8000000e-01   5.3000000e-01   4.8000000e-01   4.4000000e-01   5.0000000e-01   4.8000000e-01   5.0000000e-01   4.7000000e-01   6.4000000e-01   4.9000000e-01   5.2000000e-01   4.8000000e-01   5.6000000e-01   4.3000000e-01   4.8000000e-01   4.7000000e-01   6.0000000e-01   5.4000000e-01   5.5000000e-01   4.0000000e-01   5.5000000e-01   5.6000000e-01   4.9000000e-01   5.0000000e-01   4.3000000e-01   5.7000000e-01   5.0000000e-01   5.7000000e-01   4.9000000e-01   4.2000000e-01   3.9000000e-01

openflamingo/lib/python3.10/site-packages/scipy/spatial/tests/test__plotutils.py

@@ -0,0 +1,91 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_, assert_array_equal, assert_allclose
+
+try:
+    import matplotlib
+    matplotlib.rcParams['backend'] = 'Agg'
+    import matplotlib.pyplot as plt
+    has_matplotlib = True
+except Exception:
+    has_matplotlib = False
+
+from scipy.spatial import \
+     delaunay_plot_2d, voronoi_plot_2d, convex_hull_plot_2d, \
+     Delaunay, Voronoi, ConvexHull
+
+
+@pytest.mark.skipif(not has_matplotlib, reason="Matplotlib not available")
+class TestPlotting:
+    points = [(0,0), (0,1), (1,0), (1,1)]
+
+    def test_delaunay(self):
+        # Smoke test
+        fig = plt.figure()
+        obj = Delaunay(self.points)
+        s_before = obj.simplices.copy()
+        r = delaunay_plot_2d(obj, ax=fig.gca())
+        assert_array_equal(obj.simplices, s_before)  # shouldn't modify
+        assert_(r is fig)
+        delaunay_plot_2d(obj, ax=fig.gca())
+
+    def test_voronoi(self):
+        # Smoke test
+        fig = plt.figure()
+        obj = Voronoi(self.points)
+        r = voronoi_plot_2d(obj, ax=fig.gca())
+        assert_(r is fig)
+        voronoi_plot_2d(obj)
+        voronoi_plot_2d(obj, show_vertices=False)
+
+    def test_convex_hull(self):
+        # Smoke test
+        fig = plt.figure()
+        tri = ConvexHull(self.points)
+        r = convex_hull_plot_2d(tri, ax=fig.gca())
+        assert_(r is fig)
+        convex_hull_plot_2d(tri)
+
+    def test_gh_19653(self):
+        # aspect ratio sensitivity of voronoi_plot_2d
+        # infinite Voronoi edges
+        points = np.array([[245.059986986012, 10.971011721360075],
+                           [320.49044143557785, 10.970258360366753],
+                           [239.79023081978914, 13.108487516946218],
+                           [263.38325791238833, 12.93241352743668],
+                           [219.53334398353175, 13.346107628161008]])
+        vor = Voronoi(points)
+        fig = voronoi_plot_2d(vor)
+        ax = fig.gca()
+        infinite_segments = ax.collections[1].get_segments()
+        expected_segments = np.array([[[282.77256, -254.76904],
+                                       [282.729714, -4544.744698]],
+                                      [[282.77256014, -254.76904029],
+                                       [430.08561382, 4032.67658742]],
+                                      [[229.26733285,  -20.39957514],
+                                       [-168.17167404, -4291.92545966]],
+                                      [[289.93433364, 5151.40412217],
+                                       [330.40553385, 9441.18887532]]])
+        assert_allclose(infinite_segments, expected_segments)
+
+    def test_gh_19653_smaller_aspect(self):
+        # reasonable behavior for less extreme aspect
+        # ratio
+        points = np.array([[24.059986986012, 10.971011721360075],
+                           [32.49044143557785, 10.970258360366753],
+                           [23.79023081978914, 13.108487516946218],
+                           [26.38325791238833, 12.93241352743668],
+                           [21.53334398353175, 13.346107628161008]])
+        vor = Voronoi(points)
+        fig = voronoi_plot_2d(vor)
+        ax = fig.gca()
+        infinite_segments = ax.collections[1].get_segments()
+        expected_segments = np.array([[[28.274979, 8.335027],
+                                       [28.270463, -42.19763338]],
+                                      [[28.27497869, 8.33502697],
+                                       [43.73223829, 56.44555501]],
+                                      [[22.51805823, 11.8621754],
+                                       [-12.09266506, -24.95694485]],
+                                      [[29.53092448, 78.46952378],
+                                       [33.82572726, 128.81934455]]])
+        assert_allclose(infinite_segments, expected_segments)

openflamingo/lib/python3.10/site-packages/scipy/spatial/tests/test__procrustes.py

@@ -0,0 +1,116 @@
+import numpy as np
+from numpy.testing import assert_allclose, assert_equal, assert_almost_equal
+from pytest import raises as assert_raises
+
+from scipy.spatial import procrustes
+
+
+class TestProcrustes:
+    def setup_method(self):
+        """creates inputs"""
+        # an L
+        self.data1 = np.array([[1, 3], [1, 2], [1, 1], [2, 1]], 'd')
+
+        # a larger, shifted, mirrored L
+        self.data2 = np.array([[4, -2], [4, -4], [4, -6], [2, -6]], 'd')
+
+        # an L shifted up 1, right 1, and with point 4 shifted an extra .5
+        # to the right
+        # pointwise distance disparity with data1: 3*(2) + (1 + 1.5^2)
+        self.data3 = np.array([[2, 4], [2, 3], [2, 2], [3, 2.5]], 'd')
+
+        # data4, data5 are standardized (trace(A*A') = 1).
+        # procrustes should return an identical copy if they are used
+        # as the first matrix argument.
+        shiftangle = np.pi / 8
+        self.data4 = np.array([[1, 0], [0, 1], [-1, 0],
+                              [0, -1]], 'd') / np.sqrt(4)
+        self.data5 = np.array([[np.cos(shiftangle), np.sin(shiftangle)],
+                              [np.cos(np.pi / 2 - shiftangle),
+                               np.sin(np.pi / 2 - shiftangle)],
+                              [-np.cos(shiftangle),
+                               -np.sin(shiftangle)],
+                              [-np.cos(np.pi / 2 - shiftangle),
+                               -np.sin(np.pi / 2 - shiftangle)]],
+                              'd') / np.sqrt(4)
+
+    def test_procrustes(self):
+        # tests procrustes' ability to match two matrices.
+        #
+        # the second matrix is a rotated, shifted, scaled, and mirrored version
+        # of the first, in two dimensions only
+        #
+        # can shift, mirror, and scale an 'L'?
+        a, b, disparity = procrustes(self.data1, self.data2)
+        assert_allclose(b, a)
+        assert_almost_equal(disparity, 0.)
+
+        # if first mtx is standardized, leaves first mtx unchanged?
+        m4, m5, disp45 = procrustes(self.data4, self.data5)
+        assert_equal(m4, self.data4)
+
+        # at worst, data3 is an 'L' with one point off by .5
+        m1, m3, disp13 = procrustes(self.data1, self.data3)
+        #assert_(disp13 < 0.5 ** 2)
+
+    def test_procrustes2(self):
+        # procrustes disparity should not depend on order of matrices
+        m1, m3, disp13 = procrustes(self.data1, self.data3)
+        m3_2, m1_2, disp31 = procrustes(self.data3, self.data1)
+        assert_almost_equal(disp13, disp31)
+
+        # try with 3d, 8 pts per
+        rand1 = np.array([[2.61955202, 0.30522265, 0.55515826],
+                         [0.41124708, -0.03966978, -0.31854548],
+                         [0.91910318, 1.39451809, -0.15295084],
+                         [2.00452023, 0.50150048, 0.29485268],
+                         [0.09453595, 0.67528885, 0.03283872],
+                         [0.07015232, 2.18892599, -1.67266852],
+                         [0.65029688, 1.60551637, 0.80013549],
+                         [-0.6607528, 0.53644208, 0.17033891]])
+
+        rand3 = np.array([[0.0809969, 0.09731461, -0.173442],
+                         [-1.84888465, -0.92589646, -1.29335743],
+                         [0.67031855, -1.35957463, 0.41938621],
+                         [0.73967209, -0.20230757, 0.52418027],
+                         [0.17752796, 0.09065607, 0.29827466],
+                         [0.47999368, -0.88455717, -0.57547934],
+                         [-0.11486344, -0.12608506, -0.3395779],
+                         [-0.86106154, -0.28687488, 0.9644429]])
+        res1, res3, disp13 = procrustes(rand1, rand3)
+        res3_2, res1_2, disp31 = procrustes(rand3, rand1)
+        assert_almost_equal(disp13, disp31)
+
+    def test_procrustes_shape_mismatch(self):
+        assert_raises(ValueError, procrustes,
+                      np.array([[1, 2], [3, 4]]),
+                      np.array([[5, 6, 7], [8, 9, 10]]))
+
+    def test_procrustes_empty_rows_or_cols(self):
+        empty = np.array([[]])
+        assert_raises(ValueError, procrustes, empty, empty)
+
+    def test_procrustes_no_variation(self):
+        assert_raises(ValueError, procrustes,
+                      np.array([[42, 42], [42, 42]]),
+                      np.array([[45, 45], [45, 45]]))
+
+    def test_procrustes_bad_number_of_dimensions(self):
+        # fewer dimensions in one dataset
+        assert_raises(ValueError, procrustes,
+                      np.array([1, 1, 2, 3, 5, 8]),
+                      np.array([[1, 2], [3, 4]]))
+
+        # fewer dimensions in both datasets
+        assert_raises(ValueError, procrustes,
+                      np.array([1, 1, 2, 3, 5, 8]),
+                      np.array([1, 1, 2, 3, 5, 8]))
+
+        # zero dimensions
+        assert_raises(ValueError, procrustes, np.array(7), np.array(11))
+
+        # extra dimensions
+        assert_raises(ValueError, procrustes,
+                      np.array([[[11], [7]]]),
+                      np.array([[[5, 13]]]))
+

openflamingo/lib/python3.10/site-packages/scipy/spatial/tests/test_spherical_voronoi.py

@@ -0,0 +1,358 @@
+import numpy as np
+import itertools
+from numpy.testing import (assert_equal,
+                           assert_almost_equal,
+                           assert_array_equal,
+                           assert_array_almost_equal)
+import pytest
+from pytest import raises as assert_raises
+from scipy.spatial import SphericalVoronoi, distance
+from scipy.optimize import linear_sum_assignment
+from scipy.constants import golden as phi
+from scipy.special import gamma
+
+
+TOL = 1E-10
+
+
+def _generate_tetrahedron():
+    return np.array([[1, 1, 1], [1, -1, -1], [-1, 1, -1], [-1, -1, 1]])
+
+
+def _generate_cube():
+    return np.array(list(itertools.product([-1, 1.], repeat=3)))
+
+
+def _generate_octahedron():
+    return np.array([[-1, 0, 0], [+1, 0, 0], [0, -1, 0],
+                     [0, +1, 0], [0, 0, -1], [0, 0, +1]])
+
+
+def _generate_dodecahedron():
+
+    x1 = _generate_cube()
+    x2 = np.array([[0, -phi, -1 / phi],
+                   [0, -phi, +1 / phi],
+                   [0, +phi, -1 / phi],
+                   [0, +phi, +1 / phi]])
+    x3 = np.array([[-1 / phi, 0, -phi],
+                   [+1 / phi, 0, -phi],
+                   [-1 / phi, 0, +phi],
+                   [+1 / phi, 0, +phi]])
+    x4 = np.array([[-phi, -1 / phi, 0],
+                   [-phi, +1 / phi, 0],
+                   [+phi, -1 / phi, 0],
+                   [+phi, +1 / phi, 0]])
+    return np.concatenate((x1, x2, x3, x4))
+
+
+def _generate_icosahedron():
+    x = np.array([[0, -1, -phi],
+                  [0, -1, +phi],
+                  [0, +1, -phi],
+                  [0, +1, +phi]])
+    return np.concatenate([np.roll(x, i, axis=1) for i in range(3)])
+
+
+def _generate_polytope(name):
+    polygons = ["triangle", "square", "pentagon", "hexagon", "heptagon",
+                "octagon", "nonagon", "decagon", "undecagon", "dodecagon"]
+    polyhedra = ["tetrahedron", "cube", "octahedron", "dodecahedron",
+                 "icosahedron"]
+    if name not in polygons and name not in polyhedra:
+        raise ValueError("unrecognized polytope")
+
+    if name in polygons:
+        n = polygons.index(name) + 3
+        thetas = np.linspace(0, 2 * np.pi, n, endpoint=False)
+        p = np.vstack([np.cos(thetas), np.sin(thetas)]).T
+    elif name == "tetrahedron":
+        p = _generate_tetrahedron()
+    elif name == "cube":
+        p = _generate_cube()
+    elif name == "octahedron":
+        p = _generate_octahedron()
+    elif name == "dodecahedron":
+        p = _generate_dodecahedron()
+    elif name == "icosahedron":
+        p = _generate_icosahedron()
+
+    return p / np.linalg.norm(p, axis=1, keepdims=True)
+
+
+def _hypersphere_area(dim, radius):
+    # https://en.wikipedia.org/wiki/N-sphere#Closed_forms
+    return 2 * np.pi**(dim / 2) / gamma(dim / 2) * radius**(dim - 1)
+
+
+def _sample_sphere(n, dim, seed=None):
+    # Sample points uniformly at random from the hypersphere
+    rng = np.random.RandomState(seed=seed)
+    points = rng.randn(n, dim)
+    points /= np.linalg.norm(points, axis=1, keepdims=True)
+    return points
+
+
+class TestSphericalVoronoi:
+
+    def setup_method(self):
+        self.points = np.array([
+            [-0.78928481, -0.16341094, 0.59188373],
+            [-0.66839141, 0.73309634, 0.12578818],
+            [0.32535778, -0.92476944, -0.19734181],
+            [-0.90177102, -0.03785291, -0.43055335],
+            [0.71781344, 0.68428936, 0.12842096],
+            [-0.96064876, 0.23492353, -0.14820556],
+            [0.73181537, -0.22025898, -0.6449281],
+            [0.79979205, 0.54555747, 0.25039913]]
+        )
+
+    def test_constructor(self):
+        center = np.array([1, 2, 3])
+        radius = 2
+        s1 = SphericalVoronoi(self.points)
+        # user input checks in SphericalVoronoi now require
+        # the radius / center to match the generators so adjust
+        # accordingly here
+        s2 = SphericalVoronoi(self.points * radius, radius)
+        s3 = SphericalVoronoi(self.points + center, center=center)
+        s4 = SphericalVoronoi(self.points * radius + center, radius, center)
+        assert_array_equal(s1.center, np.array([0, 0, 0]))
+        assert_equal(s1.radius, 1)
+        assert_array_equal(s2.center, np.array([0, 0, 0]))
+        assert_equal(s2.radius, 2)
+        assert_array_equal(s3.center, center)
+        assert_equal(s3.radius, 1)
+        assert_array_equal(s4.center, center)
+        assert_equal(s4.radius, radius)
+
+        # Test a non-sequence/-ndarray based array-like
+        s5 = SphericalVoronoi(memoryview(self.points))  # type: ignore[arg-type]
+        assert_array_equal(s5.center, np.array([0, 0, 0]))
+        assert_equal(s5.radius, 1)
+
+    def test_vertices_regions_translation_invariance(self):
+        sv_origin = SphericalVoronoi(self.points)
+        center = np.array([1, 1, 1])
+        sv_translated = SphericalVoronoi(self.points + center, center=center)
+        assert_equal(sv_origin.regions, sv_translated.regions)
+        assert_array_almost_equal(sv_origin.vertices + center,
+                                  sv_translated.vertices)
+
+    def test_vertices_regions_scaling_invariance(self):
+        sv_unit = SphericalVoronoi(self.points)
+        sv_scaled = SphericalVoronoi(self.points * 2, 2)
+        assert_equal(sv_unit.regions, sv_scaled.regions)
+        assert_array_almost_equal(sv_unit.vertices * 2,
+                                  sv_scaled.vertices)
+
+    def test_old_radius_api_error(self):
+        with pytest.raises(ValueError, match='`radius` is `None`. *'):
+            SphericalVoronoi(self.points, radius=None)
+
+    def test_sort_vertices_of_regions(self):
+        sv = SphericalVoronoi(self.points)
+        unsorted_regions = sv.regions
+        sv.sort_vertices_of_regions()
+        assert_equal(sorted(sv.regions), sorted(unsorted_regions))
+
+    def test_sort_vertices_of_regions_flattened(self):
+        expected = sorted([[0, 6, 5, 2, 3], [2, 3, 10, 11, 8, 7], [0, 6, 4, 1],
+                           [4, 8, 7, 5, 6], [9, 11, 10], [2, 7, 5],
+                           [1, 4, 8, 11, 9], [0, 3, 10, 9, 1]])
+        expected = list(itertools.chain(*sorted(expected)))  # type: ignore
+        sv = SphericalVoronoi(self.points)
+        sv.sort_vertices_of_regions()
+        actual = list(itertools.chain(*sorted(sv.regions)))
+        assert_array_equal(actual, expected)
+
+    def test_sort_vertices_of_regions_dimensionality(self):
+        points = np.array([[1, 0, 0, 0],
+                           [0, 1, 0, 0],
+                           [0, 0, 1, 0],
+                           [0, 0, 0, 1],
+                           [0.5, 0.5, 0.5, 0.5]])
+        with pytest.raises(TypeError, match="three-dimensional"):
+            sv = SphericalVoronoi(points)
+            sv.sort_vertices_of_regions()
+
+    def test_num_vertices(self):
+        # for any n >= 3, a spherical Voronoi diagram has 2n - 4
+        # vertices; this is a direct consequence of Euler's formula
+        # as explained by Dinis and Mamede (2010) Proceedings of the
+        # 2010 International Symposium on Voronoi Diagrams in Science
+        # and Engineering
+        sv = SphericalVoronoi(self.points)
+        expected = self.points.shape[0] * 2 - 4
+        actual = sv.vertices.shape[0]
+        assert_equal(actual, expected)
+
+    def test_voronoi_circles(self):
+        sv = SphericalVoronoi(self.points)
+        for vertex in sv.vertices:
+            distances = distance.cdist(sv.points, np.array([vertex]))
+            closest = np.array(sorted(distances)[0:3])
+            assert_almost_equal(closest[0], closest[1], 7, str(vertex))
+            assert_almost_equal(closest[0], closest[2], 7, str(vertex))
+
+    def test_duplicate_point_handling(self):
+        # an exception should be raised for degenerate generators
+        # related to Issue# 7046
+        self.degenerate = np.concatenate((self.points, self.points))
+        with assert_raises(ValueError):
+            SphericalVoronoi(self.degenerate)
+
+    def test_incorrect_radius_handling(self):
+        # an exception should be raised if the radius provided
+        # cannot possibly match the input generators
+        with assert_raises(ValueError):
+            SphericalVoronoi(self.points, radius=0.98)
+
+    def test_incorrect_center_handling(self):
+        # an exception should be raised if the center provided
+        # cannot possibly match the input generators
+        with assert_raises(ValueError):
+            SphericalVoronoi(self.points, center=[0.1, 0, 0])
+
+    @pytest.mark.parametrize("dim", range(2, 6))
+    @pytest.mark.parametrize("shift", [False, True])
+    def test_single_hemisphere_handling(self, dim, shift):
+        n = 10
+        points = _sample_sphere(n, dim, seed=0)
+        points[:, 0] = np.abs(points[:, 0])
+        center = (np.arange(dim) + 1) * shift
+        sv = SphericalVoronoi(points + center, center=center)
+        dots = np.einsum('ij,ij->i', sv.vertices - center,
+                                     sv.points[sv._simplices[:, 0]] - center)
+        circumradii = np.arccos(np.clip(dots, -1, 1))
+        assert np.max(circumradii) > np.pi / 2
+
+    @pytest.mark.parametrize("n", [1, 2, 10])
+    @pytest.mark.parametrize("dim", range(2, 6))
+    @pytest.mark.parametrize("shift", [False, True])
+    def test_rank_deficient(self, n, dim, shift):
+        center = (np.arange(dim) + 1) * shift
+        points = _sample_sphere(n, dim - 1, seed=0)
+        points = np.hstack([points, np.zeros((n, 1))])
+        with pytest.raises(ValueError, match="Rank of input points"):
+            SphericalVoronoi(points + center, center=center)
+
+    @pytest.mark.parametrize("dim", range(2, 6))
+    def test_higher_dimensions(self, dim):
+        n = 100
+        points = _sample_sphere(n, dim, seed=0)
+        sv = SphericalVoronoi(points)
+        assert sv.vertices.shape[1] == dim
+        assert len(sv.regions) == n
+
+        # verify Euler characteristic
+        cell_counts = []
+        simplices = np.sort(sv._simplices)
+        for i in range(1, dim + 1):
+            cells = []
+            for indices in itertools.combinations(range(dim), i):
+                cells.append(simplices[:, list(indices)])
+            cells = np.unique(np.concatenate(cells), axis=0)
+            cell_counts.append(len(cells))
+        expected_euler = 1 + (-1)**(dim-1)
+        actual_euler = sum([(-1)**i * e for i, e in enumerate(cell_counts)])
+        assert expected_euler == actual_euler
+
+    @pytest.mark.parametrize("dim", range(2, 6))
+    def test_cross_polytope_regions(self, dim):
+        # The hypercube is the dual of the cross-polytope, so the voronoi
+        # vertices of the cross-polytope lie on the points of the hypercube.
+
+        # generate points of the cross-polytope
+        points = np.concatenate((-np.eye(dim), np.eye(dim)))
+        sv = SphericalVoronoi(points)
+        assert all([len(e) == 2**(dim - 1) for e in sv.regions])
+
+        # generate points of the hypercube
+        expected = np.vstack(list(itertools.product([-1, 1], repeat=dim)))
+        expected = expected.astype(np.float64) / np.sqrt(dim)
+
+        # test that Voronoi vertices are correctly placed
+        dist = distance.cdist(sv.vertices, expected)
+        res = linear_sum_assignment(dist)
+        assert dist[res].sum() < TOL
+
+    @pytest.mark.parametrize("dim", range(2, 6))
+    def test_hypercube_regions(self, dim):
+        # The cross-polytope is the dual of the hypercube, so the voronoi
+        # vertices of the hypercube lie on the points of the cross-polytope.
+
+        # generate points of the hypercube
+        points = np.vstack(list(itertools.product([-1, 1], repeat=dim)))
+        points = points.astype(np.float64) / np.sqrt(dim)
+        sv = SphericalVoronoi(points)
+
+        # generate points of the cross-polytope
+        expected = np.concatenate((-np.eye(dim), np.eye(dim)))
+
+        # test that Voronoi vertices are correctly placed
+        dist = distance.cdist(sv.vertices, expected)
+        res = linear_sum_assignment(dist)
+        assert dist[res].sum() < TOL
+
+    @pytest.mark.parametrize("n", [10, 500])
+    @pytest.mark.parametrize("dim", [2, 3])
+    @pytest.mark.parametrize("radius", [0.5, 1, 2])
+    @pytest.mark.parametrize("shift", [False, True])
+    @pytest.mark.parametrize("single_hemisphere", [False, True])
+    def test_area_reconstitution(self, n, dim, radius, shift,
+                                 single_hemisphere):
+        points = _sample_sphere(n, dim, seed=0)
+
+        # move all points to one side of the sphere for single-hemisphere test
+        if single_hemisphere:
+            points[:, 0] = np.abs(points[:, 0])
+
+        center = (np.arange(dim) + 1) * shift
+        points = radius * points + center
+
+        sv = SphericalVoronoi(points, radius=radius, center=center)
+        areas = sv.calculate_areas()
+        assert_almost_equal(areas.sum(), _hypersphere_area(dim, radius))
+
+    @pytest.mark.parametrize("poly", ["triangle", "dodecagon",
+                                      "tetrahedron", "cube", "octahedron",
+                                      "dodecahedron", "icosahedron"])
+    def test_equal_area_reconstitution(self, poly):
+        points = _generate_polytope(poly)
+        n, dim = points.shape
+        sv = SphericalVoronoi(points)
+        areas = sv.calculate_areas()
+        assert_almost_equal(areas, _hypersphere_area(dim, 1) / n)
+
+    def test_area_unsupported_dimension(self):
+        dim = 4
+        points = np.concatenate((-np.eye(dim), np.eye(dim)))
+        sv = SphericalVoronoi(points)
+        with pytest.raises(TypeError, match="Only supported"):
+            sv.calculate_areas()
+
+    @pytest.mark.parametrize("radius", [1, 1.])
+    @pytest.mark.parametrize("center", [None, (1, 2, 3), (1., 2., 3.)])
+    def test_attribute_types(self, radius, center):
+        points = radius * self.points
+        if center is not None:
+            points += center
+
+        sv = SphericalVoronoi(points, radius=radius, center=center)
+        assert sv.points.dtype is np.dtype(np.float64)
+        assert sv.center.dtype is np.dtype(np.float64)
+        assert isinstance(sv.radius, float)
+
+    def test_region_types(self):
+        # Tests that region integer type does not change
+        # See Issue #13412
+        sv = SphericalVoronoi(self.points)
+        dtype = type(sv.regions[0][0])
+        # also enforce nested list type per gh-19177
+        for region in sv.regions:
+            assert isinstance(region, list)
+        sv.sort_vertices_of_regions()
+        assert type(sv.regions[0][0]) == dtype
+        sv.sort_vertices_of_regions()
+        assert type(sv.regions[0][0]) == dtype

phi4/lib/python3.10/site-packages/numpy/_core/__pycache__/fromnumeric.cpython-310.pyc

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:cf135b5f582a3ff2dc30b3e7699e7af572e82048a193bf6c1b2589997c2d67b4
+size 139645

phi4/lib/python3.10/site-packages/scipy/_lib/_array_api.py

@@ -0,0 +1,595 @@
+"""Utility functions to use Python Array API compatible libraries.
+
+For the context about the Array API see:
+https://data-apis.org/array-api/latest/purpose_and_scope.html
+
+The SciPy use case of the Array API is described on the following page:
+https://data-apis.org/array-api/latest/use_cases.html#use-case-scipy
+"""
+import os
+
+from types import ModuleType
+from typing import Any, Literal, TypeAlias
+
+import numpy as np
+import numpy.typing as npt
+
+from scipy._lib import array_api_compat
+from scipy._lib.array_api_compat import (
+    is_array_api_obj,
+    size as xp_size,
+    numpy as np_compat,
+    device as xp_device,
+    is_numpy_namespace as is_numpy,
+    is_cupy_namespace as is_cupy,
+    is_torch_namespace as is_torch,
+    is_jax_namespace as is_jax,
+    is_array_api_strict_namespace as is_array_api_strict
+)
+
+__all__ = [
+    '_asarray', 'array_namespace', 'assert_almost_equal', 'assert_array_almost_equal',
+    'get_xp_devices',
+    'is_array_api_strict', 'is_complex', 'is_cupy', 'is_jax', 'is_numpy', 'is_torch', 
+    'SCIPY_ARRAY_API', 'SCIPY_DEVICE', 'scipy_namespace_for',
+    'xp_assert_close', 'xp_assert_equal', 'xp_assert_less',
+    'xp_copy', 'xp_copysign', 'xp_device',
+    'xp_moveaxis_to_end', 'xp_ravel', 'xp_real', 'xp_sign', 'xp_size',
+    'xp_take_along_axis', 'xp_unsupported_param_msg', 'xp_vector_norm',
+]
+
+
+# To enable array API and strict array-like input validation
+SCIPY_ARRAY_API: str | bool = os.environ.get("SCIPY_ARRAY_API", False)
+# To control the default device - for use in the test suite only
+SCIPY_DEVICE = os.environ.get("SCIPY_DEVICE", "cpu")
+
+_GLOBAL_CONFIG = {
+    "SCIPY_ARRAY_API": SCIPY_ARRAY_API,
+    "SCIPY_DEVICE": SCIPY_DEVICE,
+}
+
+
+Array: TypeAlias = Any  # To be changed to a Protocol later (see array-api#589)
+ArrayLike: TypeAlias = Array | npt.ArrayLike
+
+
+def _compliance_scipy(arrays):
+    """Raise exceptions on known-bad subclasses.
+
+    The following subclasses are not supported and raise and error:
+    - `numpy.ma.MaskedArray`
+    - `numpy.matrix`
+    - NumPy arrays which do not have a boolean or numerical dtype
+    - Any array-like which is neither array API compatible nor coercible by NumPy
+    - Any array-like which is coerced by NumPy to an unsupported dtype
+    """
+    for i in range(len(arrays)):
+        array = arrays[i]
+
+        from scipy.sparse import issparse
+        # this comes from `_util._asarray_validated`
+        if issparse(array):
+            msg = ('Sparse arrays/matrices are not supported by this function. '
+                   'Perhaps one of the `scipy.sparse.linalg` functions '
+                   'would work instead.')
+            raise ValueError(msg)
+
+        if isinstance(array, np.ma.MaskedArray):
+            raise TypeError("Inputs of type `numpy.ma.MaskedArray` are not supported.")
+        elif isinstance(array, np.matrix):
+            raise TypeError("Inputs of type `numpy.matrix` are not supported.")
+        if isinstance(array, np.ndarray | np.generic):
+            dtype = array.dtype
+            if not (np.issubdtype(dtype, np.number) or np.issubdtype(dtype, np.bool_)):
+                raise TypeError(f"An argument has dtype `{dtype!r}`; "
+                                f"only boolean and numerical dtypes are supported.")
+        elif not is_array_api_obj(array):
+            try:
+                array = np.asanyarray(array)
+            except TypeError:
+                raise TypeError("An argument is neither array API compatible nor "
+                                "coercible by NumPy.")
+            dtype = array.dtype
+            if not (np.issubdtype(dtype, np.number) or np.issubdtype(dtype, np.bool_)):
+                message = (
+                    f"An argument was coerced to an unsupported dtype `{dtype!r}`; "
+                    f"only boolean and numerical dtypes are supported."
+                )
+                raise TypeError(message)
+            arrays[i] = array
+    return arrays
+
+
+def _check_finite(array: Array, xp: ModuleType) -> None:
+    """Check for NaNs or Infs."""
+    msg = "array must not contain infs or NaNs"
+    try:
+        if not xp.all(xp.isfinite(array)):
+            raise ValueError(msg)
+    except TypeError:
+        raise ValueError(msg)
+
+
+def array_namespace(*arrays: Array) -> ModuleType:
+    """Get the array API compatible namespace for the arrays xs.
+
+    Parameters
+    ----------
+    *arrays : sequence of array_like
+        Arrays used to infer the common namespace.
+
+    Returns
+    -------
+    namespace : module
+        Common namespace.
+
+    Notes
+    -----
+    Thin wrapper around `array_api_compat.array_namespace`.
+
+    1. Check for the global switch: SCIPY_ARRAY_API. This can also be accessed
+       dynamically through ``_GLOBAL_CONFIG['SCIPY_ARRAY_API']``.
+    2. `_compliance_scipy` raise exceptions on known-bad subclasses. See
+       its definition for more details.
+
+    When the global switch is False, it defaults to the `numpy` namespace.
+    In that case, there is no compliance check. This is a convenience to
+    ease the adoption. Otherwise, arrays must comply with the new rules.
+    """
+    if not _GLOBAL_CONFIG["SCIPY_ARRAY_API"]:
+        # here we could wrap the namespace if needed
+        return np_compat
+
+    _arrays = [array for array in arrays if array is not None]
+
+    _arrays = _compliance_scipy(_arrays)
+
+    return array_api_compat.array_namespace(*_arrays)
+
+
+def _asarray(
+        array: ArrayLike,
+        dtype: Any = None,
+        order: Literal['K', 'A', 'C', 'F'] | None = None,
+        copy: bool | None = None,
+        *,
+        xp: ModuleType | None = None,
+        check_finite: bool = False,
+        subok: bool = False,
+    ) -> Array:
+    """SciPy-specific replacement for `np.asarray` with `order`, `check_finite`, and
+    `subok`.
+
+    Memory layout parameter `order` is not exposed in the Array API standard.
+    `order` is only enforced if the input array implementation
+    is NumPy based, otherwise `order` is just silently ignored.
+
+    `check_finite` is also not a keyword in the array API standard; included
+    here for convenience rather than that having to be a separate function
+    call inside SciPy functions.
+
+    `subok` is included to allow this function to preserve the behaviour of
+    `np.asanyarray` for NumPy based inputs.
+    """
+    if xp is None:
+        xp = array_namespace(array)
+    if is_numpy(xp):
+        # Use NumPy API to support order
+        if copy is True:
+            array = np.array(array, order=order, dtype=dtype, subok=subok)
+        elif subok:
+            array = np.asanyarray(array, order=order, dtype=dtype)
+        else:
+            array = np.asarray(array, order=order, dtype=dtype)
+    else:
+        try:
+            array = xp.asarray(array, dtype=dtype, copy=copy)
+        except TypeError:
+            coerced_xp = array_namespace(xp.asarray(3))
+            array = coerced_xp.asarray(array, dtype=dtype, copy=copy)
+
+    if check_finite:
+        _check_finite(array, xp)
+
+    return array
+
+
+def xp_copy(x: Array, *, xp: ModuleType | None = None) -> Array:
+    """
+    Copies an array.
+
+    Parameters
+    ----------
+    x : array
+
+    xp : array_namespace
+
+    Returns
+    -------
+    copy : array
+        Copied array
+
+    Notes
+    -----
+    This copy function does not offer all the semantics of `np.copy`, i.e. the
+    `subok` and `order` keywords are not used.
+    """
+    # Note: for older NumPy versions, `np.asarray` did not support the `copy` kwarg,
+    # so this uses our other helper `_asarray`.
+    if xp is None:
+        xp = array_namespace(x)
+
+    return _asarray(x, copy=True, xp=xp)
+
+
+def _strict_check(actual, desired, xp, *,
+                  check_namespace=True, check_dtype=True, check_shape=True,
+                  check_0d=True):
+    __tracebackhide__ = True  # Hide traceback for py.test
+    if check_namespace:
+        _assert_matching_namespace(actual, desired)
+
+    # only NumPy distinguishes between scalars and arrays; we do if check_0d=True.
+    # do this first so we can then cast to array (and thus use the array API) below.
+    if is_numpy(xp) and check_0d:
+        _msg = ("Array-ness does not match:\n Actual: "
+                f"{type(actual)}\n Desired: {type(desired)}")
+        assert ((xp.isscalar(actual) and xp.isscalar(desired))
+                or (not xp.isscalar(actual) and not xp.isscalar(desired))), _msg
+
+    actual = xp.asarray(actual)
+    desired = xp.asarray(desired)
+
+    if check_dtype:
+        _msg = f"dtypes do not match.\nActual: {actual.dtype}\nDesired: {desired.dtype}"
+        assert actual.dtype == desired.dtype, _msg
+
+    if check_shape:
+        _msg = f"Shapes do not match.\nActual: {actual.shape}\nDesired: {desired.shape}"
+        assert actual.shape == desired.shape, _msg
+
+    desired = xp.broadcast_to(desired, actual.shape)
+    return actual, desired
+
+
+def _assert_matching_namespace(actual, desired):
+    __tracebackhide__ = True  # Hide traceback for py.test
+    actual = actual if isinstance(actual, tuple) else (actual,)
+    desired_space = array_namespace(desired)
+    for arr in actual:
+        arr_space = array_namespace(arr)
+        _msg = (f"Namespaces do not match.\n"
+                f"Actual: {arr_space.__name__}\n"
+                f"Desired: {desired_space.__name__}")
+        assert arr_space == desired_space, _msg
+
+
+def xp_assert_equal(actual, desired, *, check_namespace=True, check_dtype=True,
+                    check_shape=True, check_0d=True, err_msg='', xp=None):
+    __tracebackhide__ = True  # Hide traceback for py.test
+    if xp is None:
+        xp = array_namespace(actual)
+
+    actual, desired = _strict_check(
+        actual, desired, xp, check_namespace=check_namespace,
+        check_dtype=check_dtype, check_shape=check_shape,
+        check_0d=check_0d
+    )
+
+    if is_cupy(xp):
+        return xp.testing.assert_array_equal(actual, desired, err_msg=err_msg)
+    elif is_torch(xp):
+        # PyTorch recommends using `rtol=0, atol=0` like this
+        # to test for exact equality
+        err_msg = None if err_msg == '' else err_msg
+        return xp.testing.assert_close(actual, desired, rtol=0, atol=0, equal_nan=True,
+                                       check_dtype=False, msg=err_msg)
+    # JAX uses `np.testing`
+    return np.testing.assert_array_equal(actual, desired, err_msg=err_msg)
+
+
+def xp_assert_close(actual, desired, *, rtol=None, atol=0, check_namespace=True,
+                    check_dtype=True, check_shape=True, check_0d=True,
+                    err_msg='', xp=None):
+    __tracebackhide__ = True  # Hide traceback for py.test
+    if xp is None:
+        xp = array_namespace(actual)
+
+    actual, desired = _strict_check(
+        actual, desired, xp,
+        check_namespace=check_namespace, check_dtype=check_dtype,
+        check_shape=check_shape, check_0d=check_0d
+    )
+
+    floating = xp.isdtype(actual.dtype, ('real floating', 'complex floating'))
+    if rtol is None and floating:
+        # multiplier of 4 is used as for `np.float64` this puts the default `rtol`
+        # roughly half way between sqrt(eps) and the default for
+        # `numpy.testing.assert_allclose`, 1e-7
+        rtol = xp.finfo(actual.dtype).eps**0.5 * 4
+    elif rtol is None:
+        rtol = 1e-7
+
+    if is_cupy(xp):
+        return xp.testing.assert_allclose(actual, desired, rtol=rtol,
+                                          atol=atol, err_msg=err_msg)
+    elif is_torch(xp):
+        err_msg = None if err_msg == '' else err_msg
+        return xp.testing.assert_close(actual, desired, rtol=rtol, atol=atol,
+                                       equal_nan=True, check_dtype=False, msg=err_msg)
+    # JAX uses `np.testing`
+    return np.testing.assert_allclose(actual, desired, rtol=rtol,
+                                      atol=atol, err_msg=err_msg)
+
+
+def xp_assert_less(actual, desired, *, check_namespace=True, check_dtype=True,
+                   check_shape=True, check_0d=True, err_msg='', verbose=True, xp=None):
+    __tracebackhide__ = True  # Hide traceback for py.test
+    if xp is None:
+        xp = array_namespace(actual)
+
+    actual, desired = _strict_check(
+        actual, desired, xp, check_namespace=check_namespace,
+        check_dtype=check_dtype, check_shape=check_shape,
+        check_0d=check_0d
+    )
+
+    if is_cupy(xp):
+        return xp.testing.assert_array_less(actual, desired,
+                                            err_msg=err_msg, verbose=verbose)
+    elif is_torch(xp):
+        if actual.device.type != 'cpu':
+            actual = actual.cpu()
+        if desired.device.type != 'cpu':
+            desired = desired.cpu()
+    # JAX uses `np.testing`
+    return np.testing.assert_array_less(actual, desired,
+                                        err_msg=err_msg, verbose=verbose)
+
+
+def assert_array_almost_equal(actual, desired, decimal=6, *args, **kwds):
+    """Backwards compatible replacement. In new code, use xp_assert_close instead.
+    """
+    rtol, atol = 0, 1.5*10**(-decimal)
+    return xp_assert_close(actual, desired,
+                           atol=atol, rtol=rtol, check_dtype=False, check_shape=False,
+                           *args, **kwds)
+
+
+def assert_almost_equal(actual, desired, decimal=7, *args, **kwds):
+    """Backwards compatible replacement. In new code, use xp_assert_close instead.
+    """
+    rtol, atol = 0, 1.5*10**(-decimal)
+    return xp_assert_close(actual, desired,
+                           atol=atol, rtol=rtol, check_dtype=False, check_shape=False,
+                           *args, **kwds)
+
+
+def xp_unsupported_param_msg(param: Any) -> str:
+    return f'Providing {param!r} is only supported for numpy arrays.'
+
+
+def is_complex(x: Array, xp: ModuleType) -> bool:
+    return xp.isdtype(x.dtype, 'complex floating')
+
+
+def get_xp_devices(xp: ModuleType) -> list[str] | list[None]:
+    """Returns a list of available devices for the given namespace."""
+    devices: list[str] = []
+    if is_torch(xp):
+        devices += ['cpu']
+        import torch # type: ignore[import]
+        num_cuda = torch.cuda.device_count()
+        for i in range(0, num_cuda):
+            devices += [f'cuda:{i}']
+        if torch.backends.mps.is_available():
+            devices += ['mps']
+        return devices
+    elif is_cupy(xp):
+        import cupy # type: ignore[import]
+        num_cuda = cupy.cuda.runtime.getDeviceCount()
+        for i in range(0, num_cuda):
+            devices += [f'cuda:{i}']
+        return devices
+    elif is_jax(xp):
+        import jax # type: ignore[import]
+        num_cpu = jax.device_count(backend='cpu')
+        for i in range(0, num_cpu):
+            devices += [f'cpu:{i}']
+        num_gpu = jax.device_count(backend='gpu')
+        for i in range(0, num_gpu):
+            devices += [f'gpu:{i}']
+        num_tpu = jax.device_count(backend='tpu')
+        for i in range(0, num_tpu):
+            devices += [f'tpu:{i}']
+        return devices
+
+    # given namespace is not known to have a list of available devices;
+    # return `[None]` so that one can use this in tests for `device=None`.
+    return [None]
+
+
+def scipy_namespace_for(xp: ModuleType) -> ModuleType | None:
+    """Return the `scipy`-like namespace of a non-NumPy backend
+
+    That is, return the namespace corresponding with backend `xp` that contains
+    `scipy` sub-namespaces like `linalg` and `special`. If no such namespace
+    exists, return ``None``. Useful for dispatching.
+    """
+
+    if is_cupy(xp):
+        import cupyx  # type: ignore[import-not-found,import-untyped]
+        return cupyx.scipy
+
+    if is_jax(xp):
+        import jax  # type: ignore[import-not-found]
+        return jax.scipy
+
+    if is_torch(xp):
+        return xp
+
+    return None
+
+
+# temporary substitute for xp.moveaxis, which is not yet in all backends
+# or covered by array_api_compat.
+def xp_moveaxis_to_end(
+        x: Array,
+        source: int,
+        /, *,
+        xp: ModuleType | None = None) -> Array:
+    xp = array_namespace(xp) if xp is None else xp
+    axes = list(range(x.ndim))
+    temp = axes.pop(source)
+    axes = axes + [temp]
+    return xp.permute_dims(x, axes)
+
+
+# temporary substitute for xp.copysign, which is not yet in all backends
+# or covered by array_api_compat.
+def xp_copysign(x1: Array, x2: Array, /, *, xp: ModuleType | None = None) -> Array:
+    # no attempt to account for special cases
+    xp = array_namespace(x1, x2) if xp is None else xp
+    abs_x1 = xp.abs(x1)
+    return xp.where(x2 >= 0, abs_x1, -abs_x1)
+
+
+# partial substitute for xp.sign, which does not cover the NaN special case
+# that I need. (https://github.com/data-apis/array-api-compat/issues/136)
+def xp_sign(x: Array, /, *, xp: ModuleType | None = None) -> Array:
+    xp = array_namespace(x) if xp is None else xp
+    if is_numpy(xp):  # only NumPy implements the special cases correctly
+        return xp.sign(x)
+    sign = xp.zeros_like(x)
+    one = xp.asarray(1, dtype=x.dtype)
+    sign = xp.where(x > 0, one, sign)
+    sign = xp.where(x < 0, -one, sign)
+    sign = xp.where(xp.isnan(x), xp.nan*one, sign)
+    return sign
+
+# maybe use `scipy.linalg` if/when array API support is added
+def xp_vector_norm(x: Array, /, *,
+                   axis: int | tuple[int] | None = None,
+                   keepdims: bool = False,
+                   ord: int | float = 2,
+                   xp: ModuleType | None = None) -> Array:
+    xp = array_namespace(x) if xp is None else xp
+
+    if SCIPY_ARRAY_API:
+        # check for optional `linalg` extension
+        if hasattr(xp, 'linalg'):
+            return xp.linalg.vector_norm(x, axis=axis, keepdims=keepdims, ord=ord)
+        else:
+            if ord != 2:
+                raise ValueError(
+                    "only the Euclidean norm (`ord=2`) is currently supported in "
+                    "`xp_vector_norm` for backends not implementing the `linalg` "
+                    "extension."
+                )
+            # return (x @ x)**0.5
+            # or to get the right behavior with nd, complex arrays
+            return xp.sum(xp.conj(x) * x, axis=axis, keepdims=keepdims)**0.5
+    else:
+        # to maintain backwards compatibility
+        return np.linalg.norm(x, ord=ord, axis=axis, keepdims=keepdims)
+
+
+def xp_ravel(x: Array, /, *, xp: ModuleType | None = None) -> Array:
+    # Equivalent of np.ravel written in terms of array API
+    # Even though it's one line, it comes up so often that it's worth having
+    # this function for readability
+    xp = array_namespace(x) if xp is None else xp
+    return xp.reshape(x, (-1,))
+
+
+def xp_real(x: Array, /, *, xp: ModuleType | None = None) -> Array:
+    # Convenience wrapper of xp.real that allows non-complex input;
+    # see data-apis/array-api#824
+    xp = array_namespace(x) if xp is None else xp
+    return xp.real(x) if xp.isdtype(x.dtype, 'complex floating') else x
+
+
+def xp_take_along_axis(arr: Array,
+                       indices: Array, /, *,
+                       axis: int = -1,
+                       xp: ModuleType | None = None) -> Array:
+    # Dispatcher for np.take_along_axis for backends that support it;
+    # see data-apis/array-api/pull#816
+    xp = array_namespace(arr) if xp is None else xp
+    if is_torch(xp):
+        return xp.take_along_dim(arr, indices, dim=axis)
+    elif is_array_api_strict(xp):
+        raise NotImplementedError("Array API standard does not define take_along_axis")
+    else:
+        return xp.take_along_axis(arr, indices, axis)
+
+
+# utility to broadcast arrays and promote to common dtype
+def xp_broadcast_promote(*args, ensure_writeable=False, force_floating=False, xp=None):
+    xp = array_namespace(*args) if xp is None else xp
+
+    args = [(_asarray(arg, subok=True) if arg is not None else arg) for arg in args]
+    args_not_none = [arg for arg in args if arg is not None]
+
+    # determine minimum dtype
+    default_float = xp.asarray(1.).dtype
+    dtypes = [arg.dtype for arg in args_not_none]
+    try:  # follow library's prefered mixed promotion rules
+        dtype = xp.result_type(*dtypes)
+        if force_floating and xp.isdtype(dtype, 'integral'):
+            # If we were to add `default_float` before checking whether the result
+            # type is otherwise integral, we risk promotion from lower float.
+            dtype = xp.result_type(dtype, default_float)
+    except TypeError:  # mixed type promotion isn't defined
+        float_dtypes = [dtype for dtype in dtypes
+                        if not xp.isdtype(dtype, 'integral')]
+        if float_dtypes:
+            dtype = xp.result_type(*float_dtypes, default_float)
+        elif force_floating:
+            dtype = default_float
+        else:
+            dtype = xp.result_type(*dtypes)
+
+    # determine result shape
+    shapes = {arg.shape for arg in args_not_none}
+    try:
+        shape = (np.broadcast_shapes(*shapes) if len(shapes) != 1
+                 else args_not_none[0].shape)
+    except ValueError as e:
+        message = "Array shapes are incompatible for broadcasting."
+        raise ValueError(message) from e
+
+    out = []
+    for arg in args:
+        if arg is None:
+            out.append(arg)
+            continue
+
+        # broadcast only if needed
+        # Even if two arguments need broadcasting, this is faster than
+        # `broadcast_arrays`, especially since we've already determined `shape`
+        if arg.shape != shape:
+            kwargs = {'subok': True} if is_numpy(xp) else {}
+            arg = xp.broadcast_to(arg, shape, **kwargs)
+
+        # convert dtype/copy only if needed
+        if (arg.dtype != dtype) or ensure_writeable:
+            arg = xp.astype(arg, dtype, copy=True)
+        out.append(arg)
+
+    return out
+
+
+def xp_float_to_complex(arr: Array, xp: ModuleType | None = None) -> Array:
+    xp = array_namespace(arr) if xp is None else xp
+    arr_dtype = arr.dtype
+    # The standard float dtypes are float32 and float64.
+    # Convert float32 to complex64,
+    # and float64 (and non-standard real dtypes) to complex128
+    if xp.isdtype(arr_dtype, xp.float32):
+        arr = xp.astype(arr, xp.complex64)
+    elif xp.isdtype(arr_dtype, 'real floating'):
+        arr = xp.astype(arr, xp.complex128)
+
+    return arr

phi4/lib/python3.10/site-packages/scipy/_lib/_bunch.py

@@ -0,0 +1,225 @@
+import sys as _sys
+from keyword import iskeyword as _iskeyword
+
+
+def _validate_names(typename, field_names, extra_field_names):
+    """
+    Ensure that all the given names are valid Python identifiers that
+    do not start with '_'.  Also check that there are no duplicates
+    among field_names + extra_field_names.
+    """
+    for name in [typename] + field_names + extra_field_names:
+        if not isinstance(name, str):
+            raise TypeError('typename and all field names must be strings')
+        if not name.isidentifier():
+            raise ValueError('typename and all field names must be valid '
+                             f'identifiers: {name!r}')
+        if _iskeyword(name):
+            raise ValueError('typename and all field names cannot be a '
+                             f'keyword: {name!r}')
+
+    seen = set()
+    for name in field_names + extra_field_names:
+        if name.startswith('_'):
+            raise ValueError('Field names cannot start with an underscore: '
+                             f'{name!r}')
+        if name in seen:
+            raise ValueError(f'Duplicate field name: {name!r}')
+        seen.add(name)
+
+
+# Note: This code is adapted from CPython:Lib/collections/__init__.py
+def _make_tuple_bunch(typename, field_names, extra_field_names=None,
+                      module=None):
+    """
+    Create a namedtuple-like class with additional attributes.
+
+    This function creates a subclass of tuple that acts like a namedtuple
+    and that has additional attributes.
+
+    The additional attributes are listed in `extra_field_names`.  The
+    values assigned to these attributes are not part of the tuple.
+
+    The reason this function exists is to allow functions in SciPy
+    that currently return a tuple or a namedtuple to returned objects
+    that have additional attributes, while maintaining backwards
+    compatibility.
+
+    This should only be used to enhance *existing* functions in SciPy.
+    New functions are free to create objects as return values without
+    having to maintain backwards compatibility with an old tuple or
+    namedtuple return value.
+
+    Parameters
+    ----------
+    typename : str
+        The name of the type.
+    field_names : list of str
+        List of names of the values to be stored in the tuple. These names
+        will also be attributes of instances, so the values in the tuple
+        can be accessed by indexing or as attributes.  At least one name
+        is required.  See the Notes for additional restrictions.
+    extra_field_names : list of str, optional
+        List of names of values that will be stored as attributes of the
+        object.  See the notes for additional restrictions.
+
+    Returns
+    -------
+    cls : type
+        The new class.
+
+    Notes
+    -----
+    There are restrictions on the names that may be used in `field_names`
+    and `extra_field_names`:
+
+    * The names must be unique--no duplicates allowed.
+    * The names must be valid Python identifiers, and must not begin with
+      an underscore.
+    * The names must not be Python keywords (e.g. 'def', 'and', etc., are
+      not allowed).
+
+    Examples
+    --------
+    >>> from scipy._lib._bunch import _make_tuple_bunch
+
+    Create a class that acts like a namedtuple with length 2 (with field
+    names `x` and `y`) that will also have the attributes `w` and `beta`:
+
+    >>> Result = _make_tuple_bunch('Result', ['x', 'y'], ['w', 'beta'])
+
+    `Result` is the new class.  We call it with keyword arguments to create
+    a new instance with given values.
+
+    >>> result1 = Result(x=1, y=2, w=99, beta=0.5)
+    >>> result1
+    Result(x=1, y=2, w=99, beta=0.5)
+
+    `result1` acts like a tuple of length 2:
+
+    >>> len(result1)
+    2
+    >>> result1[:]
+    (1, 2)
+
+    The values assigned when the instance was created are available as
+    attributes:
+
+    >>> result1.y
+    2
+    >>> result1.beta
+    0.5
+    """
+    if len(field_names) == 0:
+        raise ValueError('field_names must contain at least one name')
+
+    if extra_field_names is None:
+        extra_field_names = []
+    _validate_names(typename, field_names, extra_field_names)
+
+    typename = _sys.intern(str(typename))
+    field_names = tuple(map(_sys.intern, field_names))
+    extra_field_names = tuple(map(_sys.intern, extra_field_names))
+
+    all_names = field_names + extra_field_names
+    arg_list = ', '.join(field_names)
+    full_list = ', '.join(all_names)
+    repr_fmt = ''.join(('(',
+                        ', '.join(f'{name}=%({name})r' for name in all_names),
+                        ')'))
+    tuple_new = tuple.__new__
+    _dict, _tuple, _zip = dict, tuple, zip
+
+    # Create all the named tuple methods to be added to the class namespace
+
+    s = f"""\
+def __new__(_cls, {arg_list}, **extra_fields):
+    return _tuple_new(_cls, ({arg_list},))
+
+def __init__(self, {arg_list}, **extra_fields):
+    for key in self._extra_fields:
+        if key not in extra_fields:
+            raise TypeError("missing keyword argument '%s'" % (key,))
+    for key, val in extra_fields.items():
+        if key not in self._extra_fields:
+            raise TypeError("unexpected keyword argument '%s'" % (key,))
+        self.__dict__[key] = val
+
+def __setattr__(self, key, val):
+    if key in {repr(field_names)}:
+        raise AttributeError("can't set attribute %r of class %r"
+                             % (key, self.__class__.__name__))
+    else:
+        self.__dict__[key] = val
+"""
+    del arg_list
+    namespace = {'_tuple_new': tuple_new,
+                 '__builtins__': dict(TypeError=TypeError,
+                                      AttributeError=AttributeError),
+                 '__name__': f'namedtuple_{typename}'}
+    exec(s, namespace)
+    __new__ = namespace['__new__']
+    __new__.__doc__ = f'Create new instance of {typename}({full_list})'
+    __init__ = namespace['__init__']
+    __init__.__doc__ = f'Instantiate instance of {typename}({full_list})'
+    __setattr__ = namespace['__setattr__']
+
+    def __repr__(self):
+        'Return a nicely formatted representation string'
+        return self.__class__.__name__ + repr_fmt % self._asdict()
+
+    def _asdict(self):
+        'Return a new dict which maps field names to their values.'
+        out = _dict(_zip(self._fields, self))
+        out.update(self.__dict__)
+        return out
+
+    def __getnewargs_ex__(self):
+        'Return self as a plain tuple.  Used by copy and pickle.'
+        return _tuple(self), self.__dict__
+
+    # Modify function metadata to help with introspection and debugging
+    for method in (__new__, __repr__, _asdict, __getnewargs_ex__):
+        method.__qualname__ = f'{typename}.{method.__name__}'
+
+    # Build-up the class namespace dictionary
+    # and use type() to build the result class
+    class_namespace = {
+        '__doc__': f'{typename}({full_list})',
+        '_fields': field_names,
+        '__new__': __new__,
+        '__init__': __init__,
+        '__repr__': __repr__,
+        '__setattr__': __setattr__,
+        '_asdict': _asdict,
+        '_extra_fields': extra_field_names,
+        '__getnewargs_ex__': __getnewargs_ex__,
+    }
+    for index, name in enumerate(field_names):
+
+        def _get(self, index=index):
+            return self[index]
+        class_namespace[name] = property(_get)
+    for name in extra_field_names:
+
+        def _get(self, name=name):
+            return self.__dict__[name]
+        class_namespace[name] = property(_get)
+
+    result = type(typename, (tuple,), class_namespace)
+
+    # For pickling to work, the __module__ variable needs to be set to the
+    # frame where the named tuple is created.  Bypass this step in environments
+    # where sys._getframe is not defined (Jython for example) or sys._getframe
+    # is not defined for arguments greater than 0 (IronPython), or where the
+    # user has specified a particular module.
+    if module is None:
+        try:
+            module = _sys._getframe(1).f_globals.get('__name__', '__main__')
+        except (AttributeError, ValueError):
+            pass
+    if module is not None:
+        result.__module__ = module
+        __new__.__module__ = module
+
+    return result

phi4/lib/python3.10/site-packages/scipy/_lib/_ccallback.py

@@ -0,0 +1,251 @@
+from . import _ccallback_c
+
+import ctypes
+
+PyCFuncPtr = ctypes.CFUNCTYPE(ctypes.c_void_p).__bases__[0]
+
+ffi = None
+
+class CData:
+    pass
+
+def _import_cffi():
+    global ffi, CData
+
+    if ffi is not None:
+        return
+
+    try:
+        import cffi
+        ffi = cffi.FFI()
+        CData = ffi.CData
+    except ImportError:
+        ffi = False
+
+
+class LowLevelCallable(tuple):
+    """
+    Low-level callback function.
+
+    Some functions in SciPy take as arguments callback functions, which
+    can either be python callables or low-level compiled functions. Using
+    compiled callback functions can improve performance somewhat by
+    avoiding wrapping data in Python objects.
+
+    Such low-level functions in SciPy are wrapped in `LowLevelCallable`
+    objects, which can be constructed from function pointers obtained from
+    ctypes, cffi, Cython, or contained in Python `PyCapsule` objects.
+
+    .. seealso::
+
+       Functions accepting low-level callables:
+
+       `scipy.integrate.quad`, `scipy.ndimage.generic_filter`,
+       `scipy.ndimage.generic_filter1d`, `scipy.ndimage.geometric_transform`
+
+       Usage examples:
+
+       :ref:`ndimage-ccallbacks`, :ref:`quad-callbacks`
+
+    Parameters
+    ----------
+    function : {PyCapsule, ctypes function pointer, cffi function pointer}
+        Low-level callback function.
+    user_data : {PyCapsule, ctypes void pointer, cffi void pointer}
+        User data to pass on to the callback function.
+    signature : str, optional
+        Signature of the function. If omitted, determined from *function*,
+        if possible.
+
+    Attributes
+    ----------
+    function
+        Callback function given.
+    user_data
+        User data given.
+    signature
+        Signature of the function.
+
+    Methods
+    -------
+    from_cython
+        Class method for constructing callables from Cython C-exported
+        functions.
+
+    Notes
+    -----
+    The argument ``function`` can be one of:
+
+    - PyCapsule, whose name contains the C function signature
+    - ctypes function pointer
+    - cffi function pointer
+
+    The signature of the low-level callback must match one of those expected
+    by the routine it is passed to.
+
+    If constructing low-level functions from a PyCapsule, the name of the
+    capsule must be the corresponding signature, in the format::
+
+        return_type (arg1_type, arg2_type, ...)
+
+    For example::
+
+        "void (double)"
+        "double (double, int *, void *)"
+
+    The context of a PyCapsule passed in as ``function`` is used as ``user_data``,
+    if an explicit value for ``user_data`` was not given.
+
+    """
+
+    # Make the class immutable
+    __slots__ = ()
+
+    def __new__(cls, function, user_data=None, signature=None):
+        # We need to hold a reference to the function & user data,
+        # to prevent them going out of scope
+        item = cls._parse_callback(function, user_data, signature)
+        return tuple.__new__(cls, (item, function, user_data))
+
+    def __repr__(self):
+        return f"LowLevelCallable({self.function!r}, {self.user_data!r})"
+
+    @property
+    def function(self):
+        return tuple.__getitem__(self, 1)
+
+    @property
+    def user_data(self):
+        return tuple.__getitem__(self, 2)
+
+    @property
+    def signature(self):
+        return _ccallback_c.get_capsule_signature(tuple.__getitem__(self, 0))
+
+    def __getitem__(self, idx):
+        raise ValueError()
+
+    @classmethod
+    def from_cython(cls, module, name, user_data=None, signature=None):
+        """
+        Create a low-level callback function from an exported Cython function.
+
+        Parameters
+        ----------
+        module : module
+            Cython module where the exported function resides
+        name : str
+            Name of the exported function
+        user_data : {PyCapsule, ctypes void pointer, cffi void pointer}, optional
+            User data to pass on to the callback function.
+        signature : str, optional
+            Signature of the function. If omitted, determined from *function*.
+
+        """
+        try:
+            function = module.__pyx_capi__[name]
+        except AttributeError as e:
+            message = "Given module is not a Cython module with __pyx_capi__ attribute"
+            raise ValueError(message) from e
+        except KeyError as e:
+            message = f"No function {name!r} found in __pyx_capi__ of the module"
+            raise ValueError(message) from e
+        return cls(function, user_data, signature)
+
+    @classmethod
+    def _parse_callback(cls, obj, user_data=None, signature=None):
+        _import_cffi()
+
+        if isinstance(obj, LowLevelCallable):
+            func = tuple.__getitem__(obj, 0)
+        elif isinstance(obj, PyCFuncPtr):
+            func, signature = _get_ctypes_func(obj, signature)
+        elif isinstance(obj, CData):
+            func, signature = _get_cffi_func(obj, signature)
+        elif _ccallback_c.check_capsule(obj):
+            func = obj
+        else:
+            raise ValueError("Given input is not a callable or a "
+                             "low-level callable (pycapsule/ctypes/cffi)")
+
+        if isinstance(user_data, ctypes.c_void_p):
+            context = _get_ctypes_data(user_data)
+        elif isinstance(user_data, CData):
+            context = _get_cffi_data(user_data)
+        elif user_data is None:
+            context = 0
+        elif _ccallback_c.check_capsule(user_data):
+            context = user_data
+        else:
+            raise ValueError("Given user data is not a valid "
+                             "low-level void* pointer (pycapsule/ctypes/cffi)")
+
+        return _ccallback_c.get_raw_capsule(func, signature, context)
+
+
+#
+# ctypes helpers
+#
+
+def _get_ctypes_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ctypes.cast(func, ctypes.c_void_p).value
+
+    # Construct function signature
+    if signature is None:
+        signature = _typename_from_ctypes(func.restype) + " ("
+        for j, arg in enumerate(func.argtypes):
+            if j == 0:
+                signature += _typename_from_ctypes(arg)
+            else:
+                signature += ", " + _typename_from_ctypes(arg)
+        signature += ")"
+
+    return func_ptr, signature
+
+
+def _typename_from_ctypes(item):
+    if item is None:
+        return "void"
+    elif item is ctypes.c_void_p:
+        return "void *"
+
+    name = item.__name__
+
+    pointer_level = 0
+    while name.startswith("LP_"):
+        pointer_level += 1
+        name = name[3:]
+
+    if name.startswith('c_'):
+        name = name[2:]
+
+    if pointer_level > 0:
+        name += " " + "*"*pointer_level
+
+    return name
+
+
+def _get_ctypes_data(data):
+    # Get voidp pointer
+    return ctypes.cast(data, ctypes.c_void_p).value
+
+
+#
+# CFFI helpers
+#
+
+def _get_cffi_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ffi.cast('uintptr_t', func)
+
+    # Get signature
+    if signature is None:
+        signature = ffi.getctype(ffi.typeof(func)).replace('(*)', ' ')
+
+    return func_ptr, signature
+
+
+def _get_cffi_data(data):
+    # Get pointer
+    return ffi.cast('uintptr_t', data)

phi4/lib/python3.10/site-packages/scipy/_lib/_disjoint_set.py

@@ -0,0 +1,254 @@
+"""
+Disjoint set data structure
+"""
+
+
+class DisjointSet:
+    """ Disjoint set data structure for incremental connectivity queries.
+
+    .. versionadded:: 1.6.0
+
+    Attributes
+    ----------
+    n_subsets : int
+        The number of subsets.
+
+    Methods
+    -------
+    add
+    merge
+    connected
+    subset
+    subset_size
+    subsets
+    __getitem__
+
+    Notes
+    -----
+    This class implements the disjoint set [1]_, also known as the *union-find*
+    or *merge-find* data structure. The *find* operation (implemented in
+    `__getitem__`) implements the *path halving* variant. The *merge* method
+    implements the *merge by size* variant.
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Disjoint-set_data_structure
+
+    Examples
+    --------
+    >>> from scipy.cluster.hierarchy import DisjointSet
+
+    Initialize a disjoint set:
+
+    >>> disjoint_set = DisjointSet([1, 2, 3, 'a', 'b'])
+
+    Merge some subsets:
+
+    >>> disjoint_set.merge(1, 2)
+    True
+    >>> disjoint_set.merge(3, 'a')
+    True
+    >>> disjoint_set.merge('a', 'b')
+    True
+    >>> disjoint_set.merge('b', 'b')
+    False
+
+    Find root elements:
+
+    >>> disjoint_set[2]
+    1
+    >>> disjoint_set['b']
+    3
+
+    Test connectivity:
+
+    >>> disjoint_set.connected(1, 2)
+    True
+    >>> disjoint_set.connected(1, 'b')
+    False
+
+    List elements in disjoint set:
+
+    >>> list(disjoint_set)
+    [1, 2, 3, 'a', 'b']
+
+    Get the subset containing 'a':
+
+    >>> disjoint_set.subset('a')
+    {'a', 3, 'b'}
+
+    Get the size of the subset containing 'a' (without actually instantiating
+    the subset):
+
+    >>> disjoint_set.subset_size('a')
+    3
+
+    Get all subsets in the disjoint set:
+
+    >>> disjoint_set.subsets()
+    [{1, 2}, {'a', 3, 'b'}]
+    """
+    def __init__(self, elements=None):
+        self.n_subsets = 0
+        self._sizes = {}
+        self._parents = {}
+        # _nbrs is a circular linked list which links connected elements.
+        self._nbrs = {}
+        # _indices tracks the element insertion order in `__iter__`.
+        self._indices = {}
+        if elements is not None:
+            for x in elements:
+                self.add(x)
+
+    def __iter__(self):
+        """Returns an iterator of the elements in the disjoint set.
+
+        Elements are ordered by insertion order.
+        """
+        return iter(self._indices)
+
+    def __len__(self):
+        return len(self._indices)
+
+    def __contains__(self, x):
+        return x in self._indices
+
+    def __getitem__(self, x):
+        """Find the root element of `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        root : hashable object
+            Root element of `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        # find by "path halving"
+        parents = self._parents
+        while self._indices[x] != self._indices[parents[x]]:
+            parents[x] = parents[parents[x]]
+            x = parents[x]
+        return x
+
+    def add(self, x):
+        """Add element `x` to disjoint set
+        """
+        if x in self._indices:
+            return
+
+        self._sizes[x] = 1
+        self._parents[x] = x
+        self._nbrs[x] = x
+        self._indices[x] = len(self._indices)
+        self.n_subsets += 1
+
+    def merge(self, x, y):
+        """Merge the subsets of `x` and `y`.
+
+        The smaller subset (the child) is merged into the larger subset (the
+        parent). If the subsets are of equal size, the root element which was
+        first inserted into the disjoint set is selected as the parent.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to merge.
+
+        Returns
+        -------
+        merged : bool
+            True if `x` and `y` were in disjoint sets, False otherwise.
+        """
+        xr = self[x]
+        yr = self[y]
+        if self._indices[xr] == self._indices[yr]:
+            return False
+
+        sizes = self._sizes
+        if (sizes[xr], self._indices[yr]) < (sizes[yr], self._indices[xr]):
+            xr, yr = yr, xr
+        self._parents[yr] = xr
+        self._sizes[xr] += self._sizes[yr]
+        self._nbrs[xr], self._nbrs[yr] = self._nbrs[yr], self._nbrs[xr]
+        self.n_subsets -= 1
+        return True
+
+    def connected(self, x, y):
+        """Test whether `x` and `y` are in the same subset.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to test.
+
+        Returns
+        -------
+        result : bool
+            True if `x` and `y` are in the same set, False otherwise.
+        """
+        return self._indices[self[x]] == self._indices[self[y]]
+
+    def subset(self, x):
+        """Get the subset containing `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        result : set
+            Subset containing `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        result = [x]
+        nxt = self._nbrs[x]
+        while self._indices[nxt] != self._indices[x]:
+            result.append(nxt)
+            nxt = self._nbrs[nxt]
+        return set(result)
+
+    def subset_size(self, x):
+        """Get the size of the subset containing `x`.
+
+        Note that this method is faster than ``len(self.subset(x))`` because
+        the size is directly read off an internal field, without the need to
+        instantiate the full subset.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        result : int
+            Size of the subset containing `x`.
+        """
+        return self._sizes[self[x]]
+
+    def subsets(self):
+        """Get all the subsets in the disjoint set.
+
+        Returns
+        -------
+        result : list
+            Subsets in the disjoint set.
+        """
+        result = []
+        visited = set()
+        for x in self:
+            if x not in visited:
+                xset = self.subset(x)
+                visited.update(xset)
+                result.append(xset)
+        return result

phi4/lib/python3.10/site-packages/scipy/_lib/_gcutils.py

@@ -0,0 +1,105 @@
+"""
+Module for testing automatic garbage collection of objects
+
+.. autosummary::
+   :toctree: generated/
+
+   set_gc_state - enable or disable garbage collection
+   gc_state - context manager for given state of garbage collector
+   assert_deallocated - context manager to check for circular references on object
+
+"""
+import weakref
+import gc
+
+from contextlib import contextmanager
+from platform import python_implementation
+
+__all__ = ['set_gc_state', 'gc_state', 'assert_deallocated']
+
+
+IS_PYPY = python_implementation() == 'PyPy'
+
+
+class ReferenceError(AssertionError):
+    pass
+
+
+def set_gc_state(state):
+    """ Set status of garbage collector """
+    if gc.isenabled() == state:
+        return
+    if state:
+        gc.enable()
+    else:
+        gc.disable()
+
+
+@contextmanager
+def gc_state(state):
+    """ Context manager to set state of garbage collector to `state`
+
+    Parameters
+    ----------
+    state : bool
+        True for gc enabled, False for disabled
+
+    Examples
+    --------
+    >>> with gc_state(False):
+    ...     assert not gc.isenabled()
+    >>> with gc_state(True):
+    ...     assert gc.isenabled()
+    """
+    orig_state = gc.isenabled()
+    set_gc_state(state)
+    yield
+    set_gc_state(orig_state)
+
+
+@contextmanager
+def assert_deallocated(func, *args, **kwargs):
+    """Context manager to check that object is deallocated
+
+    This is useful for checking that an object can be freed directly by
+    reference counting, without requiring gc to break reference cycles.
+    GC is disabled inside the context manager.
+
+    This check is not available on PyPy.
+
+    Parameters
+    ----------
+    func : callable
+        Callable to create object to check
+    \\*args : sequence
+        positional arguments to `func` in order to create object to check
+    \\*\\*kwargs : dict
+        keyword arguments to `func` in order to create object to check
+
+    Examples
+    --------
+    >>> class C: pass
+    >>> with assert_deallocated(C) as c:
+    ...     # do something
+    ...     del c
+
+    >>> class C:
+    ...     def __init__(self):
+    ...         self._circular = self # Make circular reference
+    >>> with assert_deallocated(C) as c: #doctest: +IGNORE_EXCEPTION_DETAIL
+    ...     # do something
+    ...     del c
+    Traceback (most recent call last):
+        ...
+    ReferenceError: Remaining reference(s) to object
+    """
+    if IS_PYPY:
+        raise RuntimeError("assert_deallocated is unavailable on PyPy")
+
+    with gc_state(False):
+        obj = func(*args, **kwargs)
+        ref = weakref.ref(obj)
+        yield obj
+        del obj
+        if ref() is not None:
+            raise ReferenceError("Remaining reference(s) to object")

phi4/lib/python3.10/site-packages/scipy/_lib/_pep440.py

@@ -0,0 +1,487 @@
+"""Utility to compare pep440 compatible version strings.
+
+The LooseVersion and StrictVersion classes that distutils provides don't
+work; they don't recognize anything like alpha/beta/rc/dev versions.
+"""
+
+# Copyright (c) Donald Stufft and individual contributors.
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+
+#     1. Redistributions of source code must retain the above copyright notice,
+#        this list of conditions and the following disclaimer.
+
+#     2. Redistributions in binary form must reproduce the above copyright
+#        notice, this list of conditions and the following disclaimer in the
+#        documentation and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+import collections
+import itertools
+import re
+
+
+__all__ = [
+    "parse", "Version", "LegacyVersion", "InvalidVersion", "VERSION_PATTERN",
+]
+
+
+# BEGIN packaging/_structures.py
+
+
+class Infinity:
+    def __repr__(self):
+        return "Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return False
+
+    def __le__(self, other):
+        return False
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return True
+
+    def __ge__(self, other):
+        return True
+
+    def __neg__(self):
+        return NegativeInfinity
+
+
+Infinity = Infinity()
+
+
+class NegativeInfinity:
+    def __repr__(self):
+        return "-Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return True
+
+    def __le__(self, other):
+        return True
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return False
+
+    def __ge__(self, other):
+        return False
+
+    def __neg__(self):
+        return Infinity
+
+
+# BEGIN packaging/version.py
+
+
+NegativeInfinity = NegativeInfinity()
+
+_Version = collections.namedtuple(
+    "_Version",
+    ["epoch", "release", "dev", "pre", "post", "local"],
+)
+
+
+def parse(version):
+    """
+    Parse the given version string and return either a :class:`Version` object
+    or a :class:`LegacyVersion` object depending on if the given version is
+    a valid PEP 440 version or a legacy version.
+    """
+    try:
+        return Version(version)
+    except InvalidVersion:
+        return LegacyVersion(version)
+
+
+class InvalidVersion(ValueError):
+    """
+    An invalid version was found, users should refer to PEP 440.
+    """
+
+
+class _BaseVersion:
+
+    def __hash__(self):
+        return hash(self._key)
+
+    def __lt__(self, other):
+        return self._compare(other, lambda s, o: s < o)
+
+    def __le__(self, other):
+        return self._compare(other, lambda s, o: s <= o)
+
+    def __eq__(self, other):
+        return self._compare(other, lambda s, o: s == o)
+
+    def __ge__(self, other):
+        return self._compare(other, lambda s, o: s >= o)
+
+    def __gt__(self, other):
+        return self._compare(other, lambda s, o: s > o)
+
+    def __ne__(self, other):
+        return self._compare(other, lambda s, o: s != o)
+
+    def _compare(self, other, method):
+        if not isinstance(other, _BaseVersion):
+            return NotImplemented
+
+        return method(self._key, other._key)
+
+
+class LegacyVersion(_BaseVersion):
+
+    def __init__(self, version):
+        self._version = str(version)
+        self._key = _legacy_cmpkey(self._version)
+
+    def __str__(self):
+        return self._version
+
+    def __repr__(self):
+        return f"<LegacyVersion({repr(str(self))})>"
+
+    @property
+    def public(self):
+        return self._version
+
+    @property
+    def base_version(self):
+        return self._version
+
+    @property
+    def local(self):
+        return None
+
+    @property
+    def is_prerelease(self):
+        return False
+
+    @property
+    def is_postrelease(self):
+        return False
+
+
+_legacy_version_component_re = re.compile(
+    r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE,
+)
+
+_legacy_version_replacement_map = {
+    "pre": "c", "preview": "c", "-": "final-", "rc": "c", "dev": "@",
+}
+
+
+def _parse_version_parts(s):
+    for part in _legacy_version_component_re.split(s):
+        part = _legacy_version_replacement_map.get(part, part)
+
+        if not part or part == ".":
+            continue
+
+        if part[:1] in "0123456789":
+            # pad for numeric comparison
+            yield part.zfill(8)
+        else:
+            yield "*" + part
+
+    # ensure that alpha/beta/candidate are before final
+    yield "*final"
+
+
+def _legacy_cmpkey(version):
+    # We hardcode an epoch of -1 here. A PEP 440 version can only have an epoch
+    # greater than or equal to 0. This will effectively put the LegacyVersion,
+    # which uses the defacto standard originally implemented by setuptools,
+    # as before all PEP 440 versions.
+    epoch = -1
+
+    # This scheme is taken from pkg_resources.parse_version setuptools prior to
+    # its adoption of the packaging library.
+    parts = []
+    for part in _parse_version_parts(version.lower()):
+        if part.startswith("*"):
+            # remove "-" before a prerelease tag
+            if part < "*final":
+                while parts and parts[-1] == "*final-":
+                    parts.pop()
+
+            # remove trailing zeros from each series of numeric parts
+            while parts and parts[-1] == "00000000":
+                parts.pop()
+
+        parts.append(part)
+    parts = tuple(parts)
+
+    return epoch, parts
+
+
+# Deliberately not anchored to the start and end of the string, to make it
+# easier for 3rd party code to reuse
+VERSION_PATTERN = r"""
+    v?
+    (?:
+        (?:(?P<epoch>[0-9]+)!)?                           # epoch
+        (?P<release>[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P<pre>                                          # pre-release
+            [-_\.]?
+            (?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
+            [-_\.]?
+            (?P<pre_n>[0-9]+)?
+        )?
+        (?P<post>                                         # post release
+            (?:-(?P<post_n1>[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?P<post_l>post|rev|r)
+                [-_\.]?
+                (?P<post_n2>[0-9]+)?
+            )
+        )?
+        (?P<dev>                                          # dev release
+            [-_\.]?
+            (?P<dev_l>dev)
+            [-_\.]?
+            (?P<dev_n>[0-9]+)?
+        )?
+    )
+    (?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+"""
+
+
+class Version(_BaseVersion):
+
+    _regex = re.compile(
+        r"^\s*" + VERSION_PATTERN + r"\s*$",
+        re.VERBOSE | re.IGNORECASE,
+    )
+
+    def __init__(self, version):
+        # Validate the version and parse it into pieces
+        match = self._regex.search(version)
+        if not match:
+            raise InvalidVersion(f"Invalid version: '{version}'")
+
+        # Store the parsed out pieces of the version
+        self._version = _Version(
+            epoch=int(match.group("epoch")) if match.group("epoch") else 0,
+            release=tuple(int(i) for i in match.group("release").split(".")),
+            pre=_parse_letter_version(
+                match.group("pre_l"),
+                match.group("pre_n"),
+            ),
+            post=_parse_letter_version(
+                match.group("post_l"),
+                match.group("post_n1") or match.group("post_n2"),
+            ),
+            dev=_parse_letter_version(
+                match.group("dev_l"),
+                match.group("dev_n"),
+            ),
+            local=_parse_local_version(match.group("local")),
+        )
+
+        # Generate a key which will be used for sorting
+        self._key = _cmpkey(
+            self._version.epoch,
+            self._version.release,
+            self._version.pre,
+            self._version.post,
+            self._version.dev,
+            self._version.local,
+        )
+
+    def __repr__(self):
+        return f"<Version({repr(str(self))})>"
+
+    def __str__(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append(f"{self._version.epoch}!")
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        # Pre-release
+        if self._version.pre is not None:
+            parts.append("".join(str(x) for x in self._version.pre))
+
+        # Post-release
+        if self._version.post is not None:
+            parts.append(f".post{self._version.post[1]}")
+
+        # Development release
+        if self._version.dev is not None:
+            parts.append(f".dev{self._version.dev[1]}")
+
+        # Local version segment
+        if self._version.local is not None:
+            parts.append(
+                "+{}".format(".".join(str(x) for x in self._version.local))
+            )
+
+        return "".join(parts)
+
+    @property
+    def public(self):
+        return str(self).split("+", 1)[0]
+
+    @property
+    def base_version(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append(f"{self._version.epoch}!")
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        return "".join(parts)
+
+    @property
+    def local(self):
+        version_string = str(self)
+        if "+" in version_string:
+            return version_string.split("+", 1)[1]
+
+    @property
+    def is_prerelease(self):
+        return bool(self._version.dev or self._version.pre)
+
+    @property
+    def is_postrelease(self):
+        return bool(self._version.post)
+
+
+def _parse_letter_version(letter, number):
+    if letter:
+        # We assume there is an implicit 0 in a pre-release if there is
+        # no numeral associated with it.
+        if number is None:
+            number = 0
+
+        # We normalize any letters to their lower-case form
+        letter = letter.lower()
+
+        # We consider some words to be alternate spellings of other words and
+        # in those cases we want to normalize the spellings to our preferred
+        # spelling.
+        if letter == "alpha":
+            letter = "a"
+        elif letter == "beta":
+            letter = "b"
+        elif letter in ["c", "pre", "preview"]:
+            letter = "rc"
+        elif letter in ["rev", "r"]:
+            letter = "post"
+
+        return letter, int(number)
+    if not letter and number:
+        # We assume that if we are given a number but not given a letter,
+        # then this is using the implicit post release syntax (e.g., 1.0-1)
+        letter = "post"
+
+        return letter, int(number)
+
+
+_local_version_seperators = re.compile(r"[\._-]")
+
+
+def _parse_local_version(local):
+    """
+    Takes a string like abc.1.twelve and turns it into ("abc", 1, "twelve").
+    """
+    if local is not None:
+        return tuple(
+            part.lower() if not part.isdigit() else int(part)
+            for part in _local_version_seperators.split(local)
+        )
+
+
+def _cmpkey(epoch, release, pre, post, dev, local):
+    # When we compare a release version, we want to compare it with all of the
+    # trailing zeros removed. So we'll use a reverse the list, drop all the now
+    # leading zeros until we come to something non-zero, then take the rest,
+    # re-reverse it back into the correct order, and make it a tuple and use
+    # that for our sorting key.
+    release = tuple(
+        reversed(list(
+            itertools.dropwhile(
+                lambda x: x == 0,
+                reversed(release),
+            )
+        ))
+    )
+
+    # We need to "trick" the sorting algorithm to put 1.0.dev0 before 1.0a0.
+    # We'll do this by abusing the pre-segment, but we _only_ want to do this
+    # if there is no pre- or a post-segment. If we have one of those, then
+    # the normal sorting rules will handle this case correctly.
+    if pre is None and post is None and dev is not None:
+        pre = -Infinity
+    # Versions without a pre-release (except as noted above) should sort after
+    # those with one.
+    elif pre is None:
+        pre = Infinity
+
+    # Versions without a post-segment should sort before those with one.
+    if post is None:
+        post = -Infinity
+
+    # Versions without a development segment should sort after those with one.
+    if dev is None:
+        dev = Infinity
+
+    if local is None:
+        # Versions without a local segment should sort before those with one.
+        local = -Infinity
+    else:
+        # Versions with a local segment need that segment parsed to implement
+        # the sorting rules in PEP440.
+        # - Alphanumeric segments sort before numeric segments
+        # - Alphanumeric segments sort lexicographically
+        # - Numeric segments sort numerically
+        # - Shorter versions sort before longer versions when the prefixes
+        #   match exactly
+        local = tuple(
+            (i, "") if isinstance(i, int) else (-Infinity, i)
+            for i in local
+        )
+
+    return epoch, release, pre, post, dev, local

phi4/lib/python3.10/site-packages/scipy/_lib/_testutils.py

@@ -0,0 +1,369 @@
+"""
+Generic test utilities.
+
+"""
+
+import inspect
+import os
+import re
+import shutil
+import subprocess
+import sys
+import sysconfig
+import threading
+from importlib.util import module_from_spec, spec_from_file_location
+
+import numpy as np
+import scipy
+
+try:
+    # Need type: ignore[import-untyped] for mypy >= 1.6
+    import cython  # type: ignore[import-untyped]
+    from Cython.Compiler.Version import (  # type: ignore[import-untyped]
+        version as cython_version,
+    )
+except ImportError:
+    cython = None
+else:
+    from scipy._lib import _pep440
+    required_version = '3.0.8'
+    if _pep440.parse(cython_version) < _pep440.Version(required_version):
+        # too old or wrong cython, skip Cython API tests
+        cython = None
+
+
+__all__ = ['PytestTester', 'check_free_memory', '_TestPythranFunc', 'IS_MUSL']
+
+
+IS_MUSL = False
+# alternate way is
+# from packaging.tags import sys_tags
+#     _tags = list(sys_tags())
+#     if 'musllinux' in _tags[0].platform:
+_v = sysconfig.get_config_var('HOST_GNU_TYPE') or ''
+if 'musl' in _v:
+    IS_MUSL = True
+
+
+IS_EDITABLE = 'editable' in scipy.__path__[0]
+
+
+class FPUModeChangeWarning(RuntimeWarning):
+    """Warning about FPU mode change"""
+    pass
+
+
+class PytestTester:
+    """
+    Run tests for this namespace
+
+    ``scipy.test()`` runs tests for all of SciPy, with the default settings.
+    When used from a submodule (e.g., ``scipy.cluster.test()``, only the tests
+    for that namespace are run.
+
+    Parameters
+    ----------
+    label : {'fast', 'full'}, optional
+        Whether to run only the fast tests, or also those marked as slow.
+        Default is 'fast'.
+    verbose : int, optional
+        Test output verbosity. Default is 1.
+    extra_argv : list, optional
+        Arguments to pass through to Pytest.
+    doctests : bool, optional
+        Whether to run doctests or not. Default is False.
+    coverage : bool, optional
+        Whether to run tests with code coverage measurements enabled.
+        Default is False.
+    tests : list of str, optional
+        List of module names to run tests for. By default, uses the module
+        from which the ``test`` function is called.
+    parallel : int, optional
+        Run tests in parallel with pytest-xdist, if number given is larger than
+        1. Default is 1.
+
+    """
+    def __init__(self, module_name):
+        self.module_name = module_name
+
+    def __call__(self, label="fast", verbose=1, extra_argv=None, doctests=False,
+                 coverage=False, tests=None, parallel=None):
+        import pytest
+
+        module = sys.modules[self.module_name]
+        module_path = os.path.abspath(module.__path__[0])
+
+        pytest_args = ['--showlocals', '--tb=short']
+
+        if extra_argv:
+            pytest_args += list(extra_argv)
+
+        if verbose and int(verbose) > 1:
+            pytest_args += ["-" + "v"*(int(verbose)-1)]
+
+        if coverage:
+            pytest_args += ["--cov=" + module_path]
+
+        if label == "fast":
+            pytest_args += ["-m", "not slow"]
+        elif label != "full":
+            pytest_args += ["-m", label]
+
+        if tests is None:
+            tests = [self.module_name]
+
+        if parallel is not None and parallel > 1:
+            if _pytest_has_xdist():
+                pytest_args += ['-n', str(parallel)]
+            else:
+                import warnings
+                warnings.warn('Could not run tests in parallel because '
+                              'pytest-xdist plugin is not available.',
+                              stacklevel=2)
+
+        pytest_args += ['--pyargs'] + list(tests)
+
+        try:
+            code = pytest.main(pytest_args)
+        except SystemExit as exc:
+            code = exc.code
+
+        return (code == 0)
+
+
+class _TestPythranFunc:
+    '''
+    These are situations that can be tested in our pythran tests:
+    - A function with multiple array arguments and then
+      other positional and keyword arguments.
+    - A function with array-like keywords (e.g. `def somefunc(x0, x1=None)`.
+    Note: list/tuple input is not yet tested!
+
+    `self.arguments`: A dictionary which key is the index of the argument,
+                      value is tuple(array value, all supported dtypes)
+    `self.partialfunc`: A function used to freeze some non-array argument
+                        that of no interests in the original function
+    '''
+    ALL_INTEGER = [np.int8, np.int16, np.int32, np.int64, np.intc, np.intp]
+    ALL_FLOAT = [np.float32, np.float64]
+    ALL_COMPLEX = [np.complex64, np.complex128]
+
+    def setup_method(self):
+        self.arguments = {}
+        self.partialfunc = None
+        self.expected = None
+
+    def get_optional_args(self, func):
+        # get optional arguments with its default value,
+        # used for testing keywords
+        signature = inspect.signature(func)
+        optional_args = {}
+        for k, v in signature.parameters.items():
+            if v.default is not inspect.Parameter.empty:
+                optional_args[k] = v.default
+        return optional_args
+
+    def get_max_dtype_list_length(self):
+        # get the max supported dtypes list length in all arguments
+        max_len = 0
+        for arg_idx in self.arguments:
+            cur_len = len(self.arguments[arg_idx][1])
+            if cur_len > max_len:
+                max_len = cur_len
+        return max_len
+
+    def get_dtype(self, dtype_list, dtype_idx):
+        # get the dtype from dtype_list via index
+        # if the index is out of range, then return the last dtype
+        if dtype_idx > len(dtype_list)-1:
+            return dtype_list[-1]
+        else:
+            return dtype_list[dtype_idx]
+
+    def test_all_dtypes(self):
+        for type_idx in range(self.get_max_dtype_list_length()):
+            args_array = []
+            for arg_idx in self.arguments:
+                new_dtype = self.get_dtype(self.arguments[arg_idx][1],
+                                           type_idx)
+                args_array.append(self.arguments[arg_idx][0].astype(new_dtype))
+            self.pythranfunc(*args_array)
+
+    def test_views(self):
+        args_array = []
+        for arg_idx in self.arguments:
+            args_array.append(self.arguments[arg_idx][0][::-1][::-1])
+        self.pythranfunc(*args_array)
+
+    def test_strided(self):
+        args_array = []
+        for arg_idx in self.arguments:
+            args_array.append(np.repeat(self.arguments[arg_idx][0],
+                                        2, axis=0)[::2])
+        self.pythranfunc(*args_array)
+
+
+def _pytest_has_xdist():
+    """
+    Check if the pytest-xdist plugin is installed, providing parallel tests
+    """
+    # Check xdist exists without importing, otherwise pytests emits warnings
+    from importlib.util import find_spec
+    return find_spec('xdist') is not None
+
+
+def check_free_memory(free_mb):
+    """
+    Check *free_mb* of memory is available, otherwise do pytest.skip
+    """
+    import pytest
+
+    try:
+        mem_free = _parse_size(os.environ['SCIPY_AVAILABLE_MEM'])
+        msg = '{} MB memory required, but environment SCIPY_AVAILABLE_MEM={}'.format(
+            free_mb, os.environ['SCIPY_AVAILABLE_MEM'])
+    except KeyError:
+        mem_free = _get_mem_available()
+        if mem_free is None:
+            pytest.skip("Could not determine available memory; set SCIPY_AVAILABLE_MEM "
+                        "variable to free memory in MB to run the test.")
+        msg = f'{free_mb} MB memory required, but {mem_free/1e6} MB available'
+
+    if mem_free < free_mb * 1e6:
+        pytest.skip(msg)
+
+
+def _parse_size(size_str):
+    suffixes = {'': 1e6,
+                'b': 1.0,
+                'k': 1e3, 'M': 1e6, 'G': 1e9, 'T': 1e12,
+                'kb': 1e3, 'Mb': 1e6, 'Gb': 1e9, 'Tb': 1e12,
+                'kib': 1024.0, 'Mib': 1024.0**2, 'Gib': 1024.0**3, 'Tib': 1024.0**4}
+    m = re.match(r'^\s*(\d+)\s*({})\s*$'.format('|'.join(suffixes.keys())),
+                 size_str,
+                 re.I)
+    if not m or m.group(2) not in suffixes:
+        raise ValueError("Invalid size string")
+
+    return float(m.group(1)) * suffixes[m.group(2)]
+
+
+def _get_mem_available():
+    """
+    Get information about memory available, not counting swap.
+    """
+    try:
+        import psutil
+        return psutil.virtual_memory().available
+    except (ImportError, AttributeError):
+        pass
+
+    if sys.platform.startswith('linux'):
+        info = {}
+        with open('/proc/meminfo') as f:
+            for line in f:
+                p = line.split()
+                info[p[0].strip(':').lower()] = float(p[1]) * 1e3
+
+        if 'memavailable' in info:
+            # Linux >= 3.14
+            return info['memavailable']
+        else:
+            return info['memfree'] + info['cached']
+
+    return None
+
+def _test_cython_extension(tmp_path, srcdir):
+    """
+    Helper function to test building and importing Cython modules that
+    make use of the Cython APIs for BLAS, LAPACK, optimize, and special.
+    """
+    import pytest
+    try:
+        subprocess.check_call(["meson", "--version"])
+    except FileNotFoundError:
+        pytest.skip("No usable 'meson' found")
+
+    # Make safe for being called by multiple threads within one test
+    tmp_path = tmp_path / str(threading.get_ident())
+
+    # build the examples in a temporary directory
+    mod_name = os.path.split(srcdir)[1]
+    shutil.copytree(srcdir, tmp_path / mod_name)
+    build_dir = tmp_path / mod_name / 'tests' / '_cython_examples'
+    target_dir = build_dir / 'build'
+    os.makedirs(target_dir, exist_ok=True)
+
+    # Ensure we use the correct Python interpreter even when `meson` is
+    # installed in a different Python environment (see numpy#24956)
+    native_file = str(build_dir / 'interpreter-native-file.ini')
+    with open(native_file, 'w') as f:
+        f.write("[binaries]\n")
+        f.write(f"python = '{sys.executable}'")
+
+    if sys.platform == "win32":
+        subprocess.check_call(["meson", "setup",
+                               "--buildtype=release",
+                               "--native-file", native_file,
+                               "--vsenv", str(build_dir)],
+                              cwd=target_dir,
+                              )
+    else:
+        subprocess.check_call(["meson", "setup",
+                               "--native-file", native_file, str(build_dir)],
+                              cwd=target_dir
+                              )
+    subprocess.check_call(["meson", "compile", "-vv"], cwd=target_dir)
+
+    # import without adding the directory to sys.path
+    suffix = sysconfig.get_config_var('EXT_SUFFIX')
+
+    def load(modname):
+        so = (target_dir / modname).with_suffix(suffix)
+        spec = spec_from_file_location(modname, so)
+        mod = module_from_spec(spec)
+        spec.loader.exec_module(mod)
+        return mod
+
+    # test that the module can be imported
+    return load("extending"), load("extending_cpp")
+
+
+def _run_concurrent_barrier(n_workers, fn, *args, **kwargs):
+    """
+    Run a given function concurrently across a given number of threads.
+
+    This is equivalent to using a ThreadPoolExecutor, but using the threading
+    primitives instead. This function ensures that the closure passed by
+    parameter gets called concurrently by setting up a barrier before it gets
+    called before any of the threads.
+
+    Arguments
+    ---------
+    n_workers: int
+        Number of concurrent threads to spawn.
+    fn: callable
+        Function closure to execute concurrently. Its first argument will
+        be the thread id.
+    *args: tuple
+        Variable number of positional arguments to pass to the function.
+    **kwargs: dict
+        Keyword arguments to pass to the function.
+    """
+    barrier = threading.Barrier(n_workers)
+
+    def closure(i, *args, **kwargs):
+        barrier.wait()
+        fn(i, *args, **kwargs)
+
+    workers = []
+    for i in range(0, n_workers):
+        workers.append(threading.Thread(
+            target=closure,
+            args=(i,) + args, kwargs=kwargs))
+
+    for worker in workers:
+        worker.start()
+
+    for worker in workers:
+        worker.join()

phi4/lib/python3.10/site-packages/scipy/_lib/_tmpdirs.py

@@ -0,0 +1,86 @@
+''' Contexts for *with* statement providing temporary directories
+'''
+import os
+from contextlib import contextmanager
+from shutil import rmtree
+from tempfile import mkdtemp
+
+
+@contextmanager
+def tempdir():
+    """Create and return a temporary directory. This has the same
+    behavior as mkdtemp but can be used as a context manager.
+
+    Upon exiting the context, the directory and everything contained
+    in it are removed.
+
+    Examples
+    --------
+    >>> import os
+    >>> with tempdir() as tmpdir:
+    ...     fname = os.path.join(tmpdir, 'example_file.txt')
+    ...     with open(fname, 'wt') as fobj:
+    ...         _ = fobj.write('a string\\n')
+    >>> os.path.exists(tmpdir)
+    False
+    """
+    d = mkdtemp()
+    yield d
+    rmtree(d)
+
+
+@contextmanager
+def in_tempdir():
+    ''' Create, return, and change directory to a temporary directory
+
+    Examples
+    --------
+    >>> import os
+    >>> my_cwd = os.getcwd()
+    >>> with in_tempdir() as tmpdir:
+    ...     _ = open('test.txt', 'wt').write('some text')
+    ...     assert os.path.isfile('test.txt')
+    ...     assert os.path.isfile(os.path.join(tmpdir, 'test.txt'))
+    >>> os.path.exists(tmpdir)
+    False
+    >>> os.getcwd() == my_cwd
+    True
+    '''
+    pwd = os.getcwd()
+    d = mkdtemp()
+    os.chdir(d)
+    yield d
+    os.chdir(pwd)
+    rmtree(d)
+
+
+@contextmanager
+def in_dir(dir=None):
+    """ Change directory to given directory for duration of ``with`` block
+
+    Useful when you want to use `in_tempdir` for the final test, but
+    you are still debugging. For example, you may want to do this in the end:
+
+    >>> with in_tempdir() as tmpdir:
+    ...     # do something complicated which might break
+    ...     pass
+
+    But, indeed, the complicated thing does break, and meanwhile, the
+    ``in_tempdir`` context manager wiped out the directory with the
+    temporary files that you wanted for debugging. So, while debugging, you
+    replace with something like:
+
+    >>> with in_dir() as tmpdir: # Use working directory by default
+    ...     # do something complicated which might break
+    ...     pass
+
+    You can then look at the temporary file outputs to debug what is happening,
+    fix, and finally replace ``in_dir`` with ``in_tempdir`` again.
+    """
+    cwd = os.getcwd()
+    if dir is None:
+        yield cwd
+        return
+    os.chdir(dir)
+    yield dir
+    os.chdir(cwd)

phi4/lib/python3.10/site-packages/scipy/_lib/_util.py

@@ -0,0 +1,1179 @@
+import re
+from contextlib import contextmanager
+import functools
+import operator
+import warnings
+import numbers
+from collections import namedtuple
+import inspect
+import math
+from typing import TypeAlias, TypeVar
+
+import numpy as np
+from scipy._lib._array_api import array_namespace, is_numpy, xp_size
+from scipy._lib._docscrape import FunctionDoc, Parameter
+
+
+AxisError: type[Exception]
+ComplexWarning: type[Warning]
+VisibleDeprecationWarning: type[Warning]
+
+if np.lib.NumpyVersion(np.__version__) >= '1.25.0':
+    from numpy.exceptions import (
+        AxisError, ComplexWarning, VisibleDeprecationWarning,
+        DTypePromotionError
+    )
+else:
+    from numpy import (  # type: ignore[attr-defined, no-redef]
+        AxisError, ComplexWarning, VisibleDeprecationWarning  # noqa: F401
+    )
+    DTypePromotionError = TypeError  # type: ignore
+
+np_long: type
+np_ulong: type
+
+if np.lib.NumpyVersion(np.__version__) >= "2.0.0.dev0":
+    try:
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                r".*In the future `np\.long` will be defined as.*",
+                FutureWarning,
+            )
+            np_long = np.long  # type: ignore[attr-defined]
+            np_ulong = np.ulong  # type: ignore[attr-defined]
+    except AttributeError:
+            np_long = np.int_
+            np_ulong = np.uint
+else:
+    np_long = np.int_
+    np_ulong = np.uint
+
+IntNumber = int | np.integer
+DecimalNumber = float | np.floating | np.integer
+
+copy_if_needed: bool | None
+
+if np.lib.NumpyVersion(np.__version__) >= "2.0.0":
+    copy_if_needed = None
+elif np.lib.NumpyVersion(np.__version__) < "1.28.0":
+    copy_if_needed = False
+else:
+    # 2.0.0 dev versions, handle cases where copy may or may not exist
+    try:
+        np.array([1]).__array__(copy=None)  # type: ignore[call-overload]
+        copy_if_needed = None
+    except TypeError:
+        copy_if_needed = False
+
+
+_RNG: TypeAlias = np.random.Generator | np.random.RandomState
+SeedType: TypeAlias = IntNumber | _RNG | None
+
+GeneratorType = TypeVar("GeneratorType", bound=_RNG)
+
+# Since Generator was introduced in numpy 1.17, the following condition is needed for
+# backward compatibility
+try:
+    from numpy.random import Generator as Generator
+except ImportError:
+    class Generator:  # type: ignore[no-redef]
+        pass
+
+
+def _lazywhere(cond, arrays, f, fillvalue=None, f2=None):
+    """Return elements chosen from two possibilities depending on a condition
+
+    Equivalent to ``f(*arrays) if cond else fillvalue`` performed elementwise.
+
+    Parameters
+    ----------
+    cond : array
+        The condition (expressed as a boolean array).
+    arrays : tuple of array
+        Arguments to `f` (and `f2`). Must be broadcastable with `cond`.
+    f : callable
+        Where `cond` is True, output will be ``f(arr1[cond], arr2[cond], ...)``
+    fillvalue : object
+        If provided, value with which to fill output array where `cond` is
+        not True.
+    f2 : callable
+        If provided, output will be ``f2(arr1[cond], arr2[cond], ...)`` where
+        `cond` is not True.
+
+    Returns
+    -------
+    out : array
+        An array with elements from the output of `f` where `cond` is True
+        and `fillvalue` (or elements from the output of `f2`) elsewhere. The
+        returned array has data type determined by Type Promotion Rules
+        with the output of `f` and `fillvalue` (or the output of `f2`).
+
+    Notes
+    -----
+    ``xp.where(cond, x, fillvalue)`` requires explicitly forming `x` even where
+    `cond` is False. This function evaluates ``f(arr1[cond], arr2[cond], ...)``
+    onle where `cond` ``is True.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> a, b = np.array([1, 2, 3, 4]), np.array([5, 6, 7, 8])
+    >>> def f(a, b):
+    ...     return a*b
+    >>> _lazywhere(a > 2, (a, b), f, np.nan)
+    array([ nan,  nan,  21.,  32.])
+
+    """
+    xp = array_namespace(cond, *arrays)
+
+    if (f2 is fillvalue is None) or (f2 is not None and fillvalue is not None):
+        raise ValueError("Exactly one of `fillvalue` or `f2` must be given.")
+
+    args = xp.broadcast_arrays(cond, *arrays)
+    bool_dtype = xp.asarray([True]).dtype  # numpy 1.xx doesn't have `bool`
+    cond, arrays = xp.astype(args[0], bool_dtype, copy=False), args[1:]
+
+    temp1 = xp.asarray(f(*(arr[cond] for arr in arrays)))
+
+    if f2 is None:
+        # If `fillvalue` is a Python scalar and we convert to `xp.asarray`, it gets the
+        # default `int` or `float` type of `xp`, so `result_type` could be wrong.
+        # `result_type` should/will handle mixed array/Python scalars;
+        # remove this special logic when it does.
+        if type(fillvalue) in {bool, int, float, complex}:
+            with np.errstate(invalid='ignore'):
+                dtype = (temp1 * fillvalue).dtype
+        else:
+           dtype = xp.result_type(temp1.dtype, fillvalue)
+        out = xp.full(cond.shape, dtype=dtype,
+                      fill_value=xp.asarray(fillvalue, dtype=dtype))
+    else:
+        ncond = ~cond
+        temp2 = xp.asarray(f2(*(arr[ncond] for arr in arrays)))
+        dtype = xp.result_type(temp1, temp2)
+        out = xp.empty(cond.shape, dtype=dtype)
+        out[ncond] = temp2
+
+    out[cond] = temp1
+
+    return out
+
+
+def _lazyselect(condlist, choicelist, arrays, default=0):
+    """
+    Mimic `np.select(condlist, choicelist)`.
+
+    Notice, it assumes that all `arrays` are of the same shape or can be
+    broadcasted together.
+
+    All functions in `choicelist` must accept array arguments in the order
+    given in `arrays` and must return an array of the same shape as broadcasted
+    `arrays`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> x = np.arange(6)
+    >>> np.select([x <3, x > 3], [x**2, x**3], default=0)
+    array([  0,   1,   4,   0,  64, 125])
+
+    >>> _lazyselect([x < 3, x > 3], [lambda x: x**2, lambda x: x**3], (x,))
+    array([   0.,    1.,    4.,   0.,   64.,  125.])
+
+    >>> a = -np.ones_like(x)
+    >>> _lazyselect([x < 3, x > 3],
+    ...             [lambda x, a: x**2, lambda x, a: a * x**3],
+    ...             (x, a), default=np.nan)
+    array([   0.,    1.,    4.,   nan,  -64., -125.])
+
+    """
+    arrays = np.broadcast_arrays(*arrays)
+    tcode = np.mintypecode([a.dtype.char for a in arrays])
+    out = np.full(np.shape(arrays[0]), fill_value=default, dtype=tcode)
+    for func, cond in zip(choicelist, condlist):
+        if np.all(cond is False):
+            continue
+        cond, _ = np.broadcast_arrays(cond, arrays[0])
+        temp = tuple(np.extract(cond, arr) for arr in arrays)
+        np.place(out, cond, func(*temp))
+    return out
+
+
+def _aligned_zeros(shape, dtype=float, order="C", align=None):
+    """Allocate a new ndarray with aligned memory.
+
+    Primary use case for this currently is working around a f2py issue
+    in NumPy 1.9.1, where dtype.alignment is such that np.zeros() does
+    not necessarily create arrays aligned up to it.
+
+    """
+    dtype = np.dtype(dtype)
+    if align is None:
+        align = dtype.alignment
+    if not hasattr(shape, '__len__'):
+        shape = (shape,)
+    size = functools.reduce(operator.mul, shape) * dtype.itemsize
+    buf = np.empty(size + align + 1, np.uint8)
+    offset = buf.__array_interface__['data'][0] % align
+    if offset != 0:
+        offset = align - offset
+    # Note: slices producing 0-size arrays do not necessarily change
+    # data pointer --- so we use and allocate size+1
+    buf = buf[offset:offset+size+1][:-1]
+    data = np.ndarray(shape, dtype, buf, order=order)
+    data.fill(0)
+    return data
+
+
+def _prune_array(array):
+    """Return an array equivalent to the input array. If the input
+    array is a view of a much larger array, copy its contents to a
+    newly allocated array. Otherwise, return the input unchanged.
+    """
+    if array.base is not None and array.size < array.base.size // 2:
+        return array.copy()
+    return array
+
+
+def float_factorial(n: int) -> float:
+    """Compute the factorial and return as a float
+
+    Returns infinity when result is too large for a double
+    """
+    return float(math.factorial(n)) if n < 171 else np.inf
+
+
+_rng_desc = (
+    r"""If `rng` is passed by keyword, types other than `numpy.random.Generator` are
+    passed to `numpy.random.default_rng` to instantiate a ``Generator``.
+    If `rng` is already a ``Generator`` instance, then the provided instance is
+    used. Specify `rng` for repeatable function behavior.
+
+    If this argument is passed by position or `{old_name}` is passed by keyword,
+    legacy behavior for the argument `{old_name}` applies:
+
+    - If `{old_name}` is None (or `numpy.random`), the `numpy.random.RandomState`
+      singleton is used.
+    - If `{old_name}` is an int, a new ``RandomState`` instance is used,
+      seeded with `{old_name}`.
+    - If `{old_name}` is already a ``Generator`` or ``RandomState`` instance then
+      that instance is used.
+
+    .. versionchanged:: 1.15.0
+        As part of the `SPEC-007 <https://scientific-python.org/specs/spec-0007/>`_
+        transition from use of `numpy.random.RandomState` to
+        `numpy.random.Generator`, this keyword was changed from `{old_name}` to `rng`.
+        For an interim period, both keywords will continue to work, although only one
+        may be specified at a time. After the interim period, function calls using the
+        `{old_name}` keyword will emit warnings. The behavior of both `{old_name}` and
+        `rng` are outlined above, but only the `rng` keyword should be used in new code.
+        """
+)
+
+
+# SPEC 7
+def _transition_to_rng(old_name, *, position_num=None, end_version=None,
+                       replace_doc=True):
+    """Example decorator to transition from old PRNG usage to new `rng` behavior
+
+    Suppose the decorator is applied to a function that used to accept parameter
+    `old_name='random_state'` either by keyword or as a positional argument at
+    `position_num=1`. At the time of application, the name of the argument in the
+    function signature is manually changed to the new name, `rng`. If positional
+    use was allowed before, this is not changed.*
+
+    - If the function is called with both `random_state` and `rng`, the decorator
+      raises an error.
+    - If `random_state` is provided as a keyword argument, the decorator passes
+      `random_state` to the function's `rng` argument as a keyword. If `end_version`
+      is specified, the decorator will emit a `DeprecationWarning` about the
+      deprecation of keyword `random_state`.
+    - If `random_state` is provided as a positional argument, the decorator passes
+      `random_state` to the function's `rng` argument by position. If `end_version`
+      is specified, the decorator will emit a `FutureWarning` about the changing
+      interpretation of the argument.
+    - If `rng` is provided as a keyword argument, the decorator validates `rng` using
+      `numpy.random.default_rng` before passing it to the function.
+    - If `end_version` is specified and neither `random_state` nor `rng` is provided
+      by the user, the decorator checks whether `np.random.seed` has been used to set
+      the global seed. If so, it emits a `FutureWarning`, noting that usage of
+      `numpy.random.seed` will eventually have no effect. Either way, the decorator
+      calls the function without explicitly passing the `rng` argument.
+
+    If `end_version` is specified, a user must pass `rng` as a keyword to avoid
+    warnings.
+
+    After the deprecation period, the decorator can be removed, and the function
+    can simply validate the `rng` argument by calling `np.random.default_rng(rng)`.
+
+    * A `FutureWarning` is emitted when the PRNG argument is used by
+      position. It indicates that the "Hinsen principle" (same
+      code yielding different results in two versions of the software)
+      will be violated, unless positional use is deprecated. Specifically:
+
+      - If `None` is passed by position and `np.random.seed` has been used,
+        the function will change from being seeded to being unseeded.
+      - If an integer is passed by position, the random stream will change.
+      - If `np.random` or an instance of `RandomState` is passed by position,
+        an error will be raised.
+
+      We suggest that projects consider deprecating positional use of
+      `random_state`/`rng` (i.e., change their function signatures to
+      ``def my_func(..., *, rng=None)``); that might not make sense
+      for all projects, so this SPEC does not make that
+      recommendation, neither does this decorator enforce it.
+
+    Parameters
+    ----------
+    old_name : str
+        The old name of the PRNG argument (e.g. `seed` or `random_state`).
+    position_num : int, optional
+        The (0-indexed) position of the old PRNG argument (if accepted by position).
+        Maintainers are welcome to eliminate this argument and use, for example,
+        `inspect`, if preferred.
+    end_version : str, optional
+        The full version number of the library when the behavior described in
+        `DeprecationWarning`s and `FutureWarning`s will take effect. If left
+        unspecified, no warnings will be emitted by the decorator.
+    replace_doc : bool, default: True
+        Whether the decorator should replace the documentation for parameter `rng` with
+        `_rng_desc` (defined above), which documents both new `rng` keyword behavior
+        and typical legacy `random_state`/`seed` behavior. If True, manually replace
+        the first paragraph of the function's old `random_state`/`seed` documentation
+        with the desired *final* `rng` documentation; this way, no changes to
+        documentation are needed when the decorator is removed. Documentation of `rng`
+        after the first blank line is preserved. Use False if the function's old
+        `random_state`/`seed` behavior does not match that described by `_rng_desc`.
+
+    """
+    NEW_NAME = "rng"
+
+    cmn_msg = (
+        "To silence this warning and ensure consistent behavior in SciPy "
+        f"{end_version}, control the RNG using argument `{NEW_NAME}`. Arguments passed "
+        f"to keyword `{NEW_NAME}` will be validated by `np.random.default_rng`, so the "
+        "behavior corresponding with a given value may change compared to use of "
+        f"`{old_name}`. For example, "
+        "1) `None` will result in unpredictable random numbers, "
+        "2) an integer will result in a different stream of random numbers, (with the "
+        "same distribution), and "
+        "3) `np.random` or `RandomState` instances will result in an error. "
+        "See the documentation of `default_rng` for more information."
+    )
+
+    def decorator(fun):
+        @functools.wraps(fun)
+        def wrapper(*args, **kwargs):
+            # Determine how PRNG was passed
+            as_old_kwarg = old_name in kwargs
+            as_new_kwarg = NEW_NAME in kwargs
+            as_pos_arg = position_num is not None and len(args) >= position_num + 1
+            emit_warning = end_version is not None
+
+            # Can only specify PRNG one of the three ways
+            if int(as_old_kwarg) + int(as_new_kwarg) + int(as_pos_arg) > 1:
+                message = (
+                    f"{fun.__name__}() got multiple values for "
+                    f"argument now known as `{NEW_NAME}`. Specify one of "
+                    f"`{NEW_NAME}` or `{old_name}`."
+                )
+                raise TypeError(message)
+
+            # Check whether global random state has been set
+            global_seed_set = np.random.mtrand._rand._bit_generator._seed_seq is None
+
+            if as_old_kwarg:  # warn about deprecated use of old kwarg
+                kwargs[NEW_NAME] = kwargs.pop(old_name)
+                if emit_warning:
+                    message = (
+                        f"Use of keyword argument `{old_name}` is "
+                        f"deprecated and replaced by `{NEW_NAME}`.  "
+                        f"Support for `{old_name}` will be removed "
+                        f"in SciPy {end_version}. "
+                    ) + cmn_msg
+                    warnings.warn(message, DeprecationWarning, stacklevel=2)
+
+            elif as_pos_arg:
+                # Warn about changing meaning of positional arg
+
+                # Note that this decorator does not deprecate positional use of the
+                # argument; it only warns that the behavior will change in the future.
+                # Simultaneously transitioning to keyword-only use is another option.
+
+                arg = args[position_num]
+                # If the argument is None and the global seed wasn't set, or if the
+                # argument is one of a few new classes, the user will not notice change
+                # in behavior.
+                ok_classes = (
+                    np.random.Generator,
+                    np.random.SeedSequence,
+                    np.random.BitGenerator,
+                )
+                if (arg is None and not global_seed_set) or isinstance(arg, ok_classes):
+                    pass
+                elif emit_warning:
+                    message = (
+                        f"Positional use of `{NEW_NAME}` (formerly known as "
+                        f"`{old_name}`) is still allowed, but the behavior is "
+                        "changing: the argument will be normalized using "
+                        f"`np.random.default_rng` beginning in SciPy {end_version}, "
+                        "and the resulting `Generator` will be used to generate "
+                        "random numbers."
+                    ) + cmn_msg
+                    warnings.warn(message, FutureWarning, stacklevel=2)
+
+            elif as_new_kwarg:  # no warnings; this is the preferred use
+                # After the removal of the decorator, normalization with
+                # np.random.default_rng will be done inside the decorated function
+                kwargs[NEW_NAME] = np.random.default_rng(kwargs[NEW_NAME])
+
+            elif global_seed_set and emit_warning:
+                # Emit FutureWarning if `np.random.seed` was used and no PRNG was passed
+                message = (
+                    "The NumPy global RNG was seeded by calling "
+                    f"`np.random.seed`. Beginning in {end_version}, this "
+                    "function will no longer use the global RNG."
+                ) + cmn_msg
+                warnings.warn(message, FutureWarning, stacklevel=2)
+
+            return fun(*args, **kwargs)
+
+        if replace_doc:
+            doc = FunctionDoc(wrapper)
+            parameter_names = [param.name for param in doc['Parameters']]
+            if 'rng' in parameter_names:
+                _type = "{None, int, `numpy.random.Generator`}, optional"
+                _desc = _rng_desc.replace("{old_name}", old_name)
+                old_doc = doc['Parameters'][parameter_names.index('rng')].desc
+                old_doc_keep = old_doc[old_doc.index("") + 1:] if "" in old_doc else []
+                new_doc = [_desc] + old_doc_keep
+                _rng_parameter_doc = Parameter('rng', _type, new_doc)
+                doc['Parameters'][parameter_names.index('rng')] = _rng_parameter_doc
+                doc = str(doc).split("\n", 1)[1]  # remove signature
+                wrapper.__doc__ = str(doc)
+        return wrapper
+
+    return decorator
+
+
+# copy-pasted from scikit-learn utils/validation.py
+def check_random_state(seed):
+    """Turn `seed` into a `np.random.RandomState` instance.
+
+    Parameters
+    ----------
+    seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional
+        If `seed` is None (or `np.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+
+    Returns
+    -------
+    seed : {`numpy.random.Generator`, `numpy.random.RandomState`}
+        Random number generator.
+
+    """
+    if seed is None or seed is np.random:
+        return np.random.mtrand._rand
+    if isinstance(seed, numbers.Integral | np.integer):
+        return np.random.RandomState(seed)
+    if isinstance(seed, np.random.RandomState | np.random.Generator):
+        return seed
+
+    raise ValueError(f"'{seed}' cannot be used to seed a numpy.random.RandomState"
+                     " instance")
+
+
+def _asarray_validated(a, check_finite=True,
+                       sparse_ok=False, objects_ok=False, mask_ok=False,
+                       as_inexact=False):
+    """
+    Helper function for SciPy argument validation.
+
+    Many SciPy linear algebra functions do support arbitrary array-like
+    input arguments. Examples of commonly unsupported inputs include
+    matrices containing inf/nan, sparse matrix representations, and
+    matrices with complicated elements.
+
+    Parameters
+    ----------
+    a : array_like
+        The array-like input.
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+    sparse_ok : bool, optional
+        True if scipy sparse matrices are allowed.
+    objects_ok : bool, optional
+        True if arrays with dype('O') are allowed.
+    mask_ok : bool, optional
+        True if masked arrays are allowed.
+    as_inexact : bool, optional
+        True to convert the input array to a np.inexact dtype.
+
+    Returns
+    -------
+    ret : ndarray
+        The converted validated array.
+
+    """
+    if not sparse_ok:
+        import scipy.sparse
+        if scipy.sparse.issparse(a):
+            msg = ('Sparse arrays/matrices are not supported by this function. '
+                   'Perhaps one of the `scipy.sparse.linalg` functions '
+                   'would work instead.')
+            raise ValueError(msg)
+    if not mask_ok:
+        if np.ma.isMaskedArray(a):
+            raise ValueError('masked arrays are not supported')
+    toarray = np.asarray_chkfinite if check_finite else np.asarray
+    a = toarray(a)
+    if not objects_ok:
+        if a.dtype is np.dtype('O'):
+            raise ValueError('object arrays are not supported')
+    if as_inexact:
+        if not np.issubdtype(a.dtype, np.inexact):
+            a = toarray(a, dtype=np.float64)
+    return a
+
+
+def _validate_int(k, name, minimum=None):
+    """
+    Validate a scalar integer.
+
+    This function can be used to validate an argument to a function
+    that expects the value to be an integer.  It uses `operator.index`
+    to validate the value (so, for example, k=2.0 results in a
+    TypeError).
+
+    Parameters
+    ----------
+    k : int
+        The value to be validated.
+    name : str
+        The name of the parameter.
+    minimum : int, optional
+        An optional lower bound.
+    """
+    try:
+        k = operator.index(k)
+    except TypeError:
+        raise TypeError(f'{name} must be an integer.') from None
+    if minimum is not None and k < minimum:
+        raise ValueError(f'{name} must be an integer not less '
+                         f'than {minimum}') from None
+    return k
+
+
+# Add a replacement for inspect.getfullargspec()/
+# The version below is borrowed from Django,
+# https://github.com/django/django/pull/4846.
+
+# Note an inconsistency between inspect.getfullargspec(func) and
+# inspect.signature(func). If `func` is a bound method, the latter does *not*
+# list `self` as a first argument, while the former *does*.
+# Hence, cook up a common ground replacement: `getfullargspec_no_self` which
+# mimics `inspect.getfullargspec` but does not list `self`.
+#
+# This way, the caller code does not need to know whether it uses a legacy
+# .getfullargspec or a bright and shiny .signature.
+
+FullArgSpec = namedtuple('FullArgSpec',
+                         ['args', 'varargs', 'varkw', 'defaults',
+                          'kwonlyargs', 'kwonlydefaults', 'annotations'])
+
+
+def getfullargspec_no_self(func):
+    """inspect.getfullargspec replacement using inspect.signature.
+
+    If func is a bound method, do not list the 'self' parameter.
+
+    Parameters
+    ----------
+    func : callable
+        A callable to inspect
+
+    Returns
+    -------
+    fullargspec : FullArgSpec(args, varargs, varkw, defaults, kwonlyargs,
+                              kwonlydefaults, annotations)
+
+        NOTE: if the first argument of `func` is self, it is *not*, I repeat
+        *not*, included in fullargspec.args.
+        This is done for consistency between inspect.getargspec() under
+        Python 2.x, and inspect.signature() under Python 3.x.
+
+    """
+    sig = inspect.signature(func)
+    args = [
+        p.name for p in sig.parameters.values()
+        if p.kind in [inspect.Parameter.POSITIONAL_OR_KEYWORD,
+                      inspect.Parameter.POSITIONAL_ONLY]
+    ]
+    varargs = [
+        p.name for p in sig.parameters.values()
+        if p.kind == inspect.Parameter.VAR_POSITIONAL
+    ]
+    varargs = varargs[0] if varargs else None
+    varkw = [
+        p.name for p in sig.parameters.values()
+        if p.kind == inspect.Parameter.VAR_KEYWORD
+    ]
+    varkw = varkw[0] if varkw else None
+    defaults = tuple(
+        p.default for p in sig.parameters.values()
+        if (p.kind == inspect.Parameter.POSITIONAL_OR_KEYWORD and
+            p.default is not p.empty)
+    ) or None
+    kwonlyargs = [
+        p.name for p in sig.parameters.values()
+        if p.kind == inspect.Parameter.KEYWORD_ONLY
+    ]
+    kwdefaults = {p.name: p.default for p in sig.parameters.values()
+                  if p.kind == inspect.Parameter.KEYWORD_ONLY and
+                  p.default is not p.empty}
+    annotations = {p.name: p.annotation for p in sig.parameters.values()
+                   if p.annotation is not p.empty}
+    return FullArgSpec(args, varargs, varkw, defaults, kwonlyargs,
+                       kwdefaults or None, annotations)
+
+
+class _FunctionWrapper:
+    """
+    Object to wrap user's function, allowing picklability
+    """
+    def __init__(self, f, args):
+        self.f = f
+        self.args = [] if args is None else args
+
+    def __call__(self, x):
+        return self.f(x, *self.args)
+
+
+class MapWrapper:
+    """
+    Parallelisation wrapper for working with map-like callables, such as
+    `multiprocessing.Pool.map`.
+
+    Parameters
+    ----------
+    pool : int or map-like callable
+        If `pool` is an integer, then it specifies the number of threads to
+        use for parallelization. If ``int(pool) == 1``, then no parallel
+        processing is used and the map builtin is used.
+        If ``pool == -1``, then the pool will utilize all available CPUs.
+        If `pool` is a map-like callable that follows the same
+        calling sequence as the built-in map function, then this callable is
+        used for parallelization.
+    """
+    def __init__(self, pool=1):
+        self.pool = None
+        self._mapfunc = map
+        self._own_pool = False
+
+        if callable(pool):
+            self.pool = pool
+            self._mapfunc = self.pool
+        else:
+            from multiprocessing import Pool
+            # user supplies a number
+            if int(pool) == -1:
+                # use as many processors as possible
+                self.pool = Pool()
+                self._mapfunc = self.pool.map
+                self._own_pool = True
+            elif int(pool) == 1:
+                pass
+            elif int(pool) > 1:
+                # use the number of processors requested
+                self.pool = Pool(processes=int(pool))
+                self._mapfunc = self.pool.map
+                self._own_pool = True
+            else:
+                raise RuntimeError("Number of workers specified must be -1,"
+                                   " an int >= 1, or an object with a 'map' "
+                                   "method")
+
+    def __enter__(self):
+        return self
+
+    def terminate(self):
+        if self._own_pool:
+            self.pool.terminate()
+
+    def join(self):
+        if self._own_pool:
+            self.pool.join()
+
+    def close(self):
+        if self._own_pool:
+            self.pool.close()
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        if self._own_pool:
+            self.pool.close()
+            self.pool.terminate()
+
+    def __call__(self, func, iterable):
+        # only accept one iterable because that's all Pool.map accepts
+        try:
+            return self._mapfunc(func, iterable)
+        except TypeError as e:
+            # wrong number of arguments
+            raise TypeError("The map-like callable must be of the"
+                            " form f(func, iterable)") from e
+
+
+def rng_integers(gen, low, high=None, size=None, dtype='int64',
+                 endpoint=False):
+    """
+    Return random integers from low (inclusive) to high (exclusive), or if
+    endpoint=True, low (inclusive) to high (inclusive). Replaces
+    `RandomState.randint` (with endpoint=False) and
+    `RandomState.random_integers` (with endpoint=True).
+
+    Return random integers from the "discrete uniform" distribution of the
+    specified dtype. If high is None (the default), then results are from
+    0 to low.
+
+    Parameters
+    ----------
+    gen : {None, np.random.RandomState, np.random.Generator}
+        Random number generator. If None, then the np.random.RandomState
+        singleton is used.
+    low : int or array-like of ints
+        Lowest (signed) integers to be drawn from the distribution (unless
+        high=None, in which case this parameter is 0 and this value is used
+        for high).
+    high : int or array-like of ints
+        If provided, one above the largest (signed) integer to be drawn from
+        the distribution (see above for behavior if high=None). If array-like,
+        must contain integer values.
+    size : array-like of ints, optional
+        Output shape. If the given shape is, e.g., (m, n, k), then m * n * k
+        samples are drawn. Default is None, in which case a single value is
+        returned.
+    dtype : {str, dtype}, optional
+        Desired dtype of the result. All dtypes are determined by their name,
+        i.e., 'int64', 'int', etc, so byteorder is not available and a specific
+        precision may have different C types depending on the platform.
+        The default value is 'int64'.
+    endpoint : bool, optional
+        If True, sample from the interval [low, high] instead of the default
+        [low, high) Defaults to False.
+
+    Returns
+    -------
+    out: int or ndarray of ints
+        size-shaped array of random integers from the appropriate distribution,
+        or a single such random int if size not provided.
+    """
+    if isinstance(gen, Generator):
+        return gen.integers(low, high=high, size=size, dtype=dtype,
+                            endpoint=endpoint)
+    else:
+        if gen is None:
+            # default is RandomState singleton used by np.random.
+            gen = np.random.mtrand._rand
+        if endpoint:
+            # inclusive of endpoint
+            # remember that low and high can be arrays, so don't modify in
+            # place
+            if high is None:
+                return gen.randint(low + 1, size=size, dtype=dtype)
+            if high is not None:
+                return gen.randint(low, high=high + 1, size=size, dtype=dtype)
+
+        # exclusive
+        return gen.randint(low, high=high, size=size, dtype=dtype)
+
+
+@contextmanager
+def _fixed_default_rng(seed=1638083107694713882823079058616272161):
+    """Context with a fixed np.random.default_rng seed."""
+    orig_fun = np.random.default_rng
+    np.random.default_rng = lambda seed=seed: orig_fun(seed)
+    try:
+        yield
+    finally:
+        np.random.default_rng = orig_fun
+
+
+def _rng_html_rewrite(func):
+    """Rewrite the HTML rendering of ``np.random.default_rng``.
+
+    This is intended to decorate
+    ``numpydoc.docscrape_sphinx.SphinxDocString._str_examples``.
+
+    Examples are only run by Sphinx when there are plot involved. Even so,
+    it does not change the result values getting printed.
+    """
+    # hexadecimal or number seed, case-insensitive
+    pattern = re.compile(r'np.random.default_rng\((0x[0-9A-F]+|\d+)\)', re.I)
+
+    def _wrapped(*args, **kwargs):
+        res = func(*args, **kwargs)
+        lines = [
+            re.sub(pattern, 'np.random.default_rng()', line)
+            for line in res
+        ]
+        return lines
+
+    return _wrapped
+
+
+def _argmin(a, keepdims=False, axis=None):
+    """
+    argmin with a `keepdims` parameter.
+
+    See https://github.com/numpy/numpy/issues/8710
+
+    If axis is not None, a.shape[axis] must be greater than 0.
+    """
+    res = np.argmin(a, axis=axis)
+    if keepdims and axis is not None:
+        res = np.expand_dims(res, axis=axis)
+    return res
+
+
+def _first_nonnan(a, axis):
+    """
+    Return the first non-nan value along the given axis.
+
+    If a slice is all nan, nan is returned for that slice.
+
+    The shape of the return value corresponds to ``keepdims=True``.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> nan = np.nan
+    >>> a = np.array([[ 3.,  3., nan,  3.],
+                      [ 1., nan,  2.,  4.],
+                      [nan, nan,  9., -1.],
+                      [nan,  5.,  4.,  3.],
+                      [ 2.,  2.,  2.,  2.],
+                      [nan, nan, nan, nan]])
+    >>> _first_nonnan(a, axis=0)
+    array([[3., 3., 2., 3.]])
+    >>> _first_nonnan(a, axis=1)
+    array([[ 3.],
+           [ 1.],
+           [ 9.],
+           [ 5.],
+           [ 2.],
+           [nan]])
+    """
+    k = _argmin(np.isnan(a), axis=axis, keepdims=True)
+    return np.take_along_axis(a, k, axis=axis)
+
+
+def _nan_allsame(a, axis, keepdims=False):
+    """
+    Determine if the values along an axis are all the same.
+
+    nan values are ignored.
+
+    `a` must be a numpy array.
+
+    `axis` is assumed to be normalized; that is, 0 <= axis < a.ndim.
+
+    For an axis of length 0, the result is True.  That is, we adopt the
+    convention that ``allsame([])`` is True. (There are no values in the
+    input that are different.)
+
+    `True` is returned for slices that are all nan--not because all the
+    values are the same, but because this is equivalent to ``allsame([])``.
+
+    Examples
+    --------
+    >>> from numpy import nan, array
+    >>> a = array([[ 3.,  3., nan,  3.],
+    ...            [ 1., nan,  2.,  4.],
+    ...            [nan, nan,  9., -1.],
+    ...            [nan,  5.,  4.,  3.],
+    ...            [ 2.,  2.,  2.,  2.],
+    ...            [nan, nan, nan, nan]])
+    >>> _nan_allsame(a, axis=1, keepdims=True)
+    array([[ True],
+           [False],
+           [False],
+           [False],
+           [ True],
+           [ True]])
+    """
+    if axis is None:
+        if a.size == 0:
+            return True
+        a = a.ravel()
+        axis = 0
+    else:
+        shp = a.shape
+        if shp[axis] == 0:
+            shp = shp[:axis] + (1,)*keepdims + shp[axis + 1:]
+            return np.full(shp, fill_value=True, dtype=bool)
+    a0 = _first_nonnan(a, axis=axis)
+    return ((a0 == a) | np.isnan(a)).all(axis=axis, keepdims=keepdims)
+
+
+def _contains_nan(a, nan_policy='propagate', policies=None, *,
+                  xp_omit_okay=False, xp=None):
+    # Regarding `xp_omit_okay`: Temporarily, while `_axis_nan_policy` does not
+    # handle non-NumPy arrays, most functions that call `_contains_nan` want
+    # it to raise an error if `nan_policy='omit'` and `xp` is not `np`.
+    # Some functions support `nan_policy='omit'` natively, so setting this to
+    # `True` prevents the error from being raised.
+    if xp is None:
+        xp = array_namespace(a)
+    not_numpy = not is_numpy(xp)
+
+    if policies is None:
+        policies = {'propagate', 'raise', 'omit'}
+    if nan_policy not in policies:
+        raise ValueError(f"nan_policy must be one of {set(policies)}.")
+
+    if xp_size(a) == 0:
+        contains_nan = False
+    elif xp.isdtype(a.dtype, "real floating"):
+        # Faster and less memory-intensive than xp.any(xp.isnan(a)), and unlike other
+        # reductions, `max`/`min` won't return NaN unless there is a NaN in the data.
+        contains_nan = xp.isnan(xp.max(a))
+    elif xp.isdtype(a.dtype, "complex floating"):
+        # Typically `real` and `imag` produce views; otherwise, `xp.any(xp.isnan(a))`
+        # would be more efficient.
+        contains_nan = xp.isnan(xp.max(xp.real(a))) | xp.isnan(xp.max(xp.imag(a)))
+    elif is_numpy(xp) and np.issubdtype(a.dtype, object):
+        contains_nan = False
+        for el in a.ravel():
+            # isnan doesn't work on non-numeric elements
+            if np.issubdtype(type(el), np.number) and np.isnan(el):
+                contains_nan = True
+                break
+    else:
+        # Only `object` and `inexact` arrays can have NaNs
+        contains_nan = False
+
+    if contains_nan and nan_policy == 'raise':
+        raise ValueError("The input contains nan values")
+
+    if not xp_omit_okay and not_numpy and contains_nan and nan_policy=='omit':
+        message = "`nan_policy='omit' is incompatible with non-NumPy arrays."
+        raise ValueError(message)
+
+    return contains_nan, nan_policy
+
+
+def _rename_parameter(old_name, new_name, dep_version=None):
+    """
+    Generate decorator for backward-compatible keyword renaming.
+
+    Apply the decorator generated by `_rename_parameter` to functions with a
+    recently renamed parameter to maintain backward-compatibility.
+
+    After decoration, the function behaves as follows:
+    If only the new parameter is passed into the function, behave as usual.
+    If only the old parameter is passed into the function (as a keyword), raise
+    a DeprecationWarning if `dep_version` is provided, and behave as usual
+    otherwise.
+    If both old and new parameters are passed into the function, raise a
+    DeprecationWarning if `dep_version` is provided, and raise the appropriate
+    TypeError (function got multiple values for argument).
+
+    Parameters
+    ----------
+    old_name : str
+        Old name of parameter
+    new_name : str
+        New name of parameter
+    dep_version : str, optional
+        Version of SciPy in which old parameter was deprecated in the format
+        'X.Y.Z'. If supplied, the deprecation message will indicate that
+        support for the old parameter will be removed in version 'X.Y+2.Z'
+
+    Notes
+    -----
+    Untested with functions that accept *args. Probably won't work as written.
+
+    """
+    def decorator(fun):
+        @functools.wraps(fun)
+        def wrapper(*args, **kwargs):
+            if old_name in kwargs:
+                if dep_version:
+                    end_version = dep_version.split('.')
+                    end_version[1] = str(int(end_version[1]) + 2)
+                    end_version = '.'.join(end_version)
+                    message = (f"Use of keyword argument `{old_name}` is "
+                               f"deprecated and replaced by `{new_name}`.  "
+                               f"Support for `{old_name}` will be removed "
+                               f"in SciPy {end_version}.")
+                    warnings.warn(message, DeprecationWarning, stacklevel=2)
+                if new_name in kwargs:
+                    message = (f"{fun.__name__}() got multiple values for "
+                               f"argument now known as `{new_name}`")
+                    raise TypeError(message)
+                kwargs[new_name] = kwargs.pop(old_name)
+            return fun(*args, **kwargs)
+        return wrapper
+    return decorator
+
+
+def _rng_spawn(rng, n_children):
+    # spawns independent RNGs from a parent RNG
+    bg = rng._bit_generator
+    ss = bg._seed_seq
+    child_rngs = [np.random.Generator(type(bg)(child_ss))
+                  for child_ss in ss.spawn(n_children)]
+    return child_rngs
+
+
+def _get_nan(*data, xp=None):
+    xp = array_namespace(*data) if xp is None else xp
+    # Get NaN of appropriate dtype for data
+    data = [xp.asarray(item) for item in data]
+    try:
+        min_float = getattr(xp, 'float16', xp.float32)
+        dtype = xp.result_type(*data, min_float)  # must be at least a float
+    except DTypePromotionError:
+        # fallback to float64
+        dtype = xp.float64
+    return xp.asarray(xp.nan, dtype=dtype)[()]
+
+
+def normalize_axis_index(axis, ndim):
+    # Check if `axis` is in the correct range and normalize it
+    if axis < -ndim or axis >= ndim:
+        msg = f"axis {axis} is out of bounds for array of dimension {ndim}"
+        raise AxisError(msg)
+
+    if axis < 0:
+        axis = axis + ndim
+    return axis
+
+
+def _call_callback_maybe_halt(callback, res):
+    """Call wrapped callback; return True if algorithm should stop.
+
+    Parameters
+    ----------
+    callback : callable or None
+        A user-provided callback wrapped with `_wrap_callback`
+    res : OptimizeResult
+        Information about the current iterate
+
+    Returns
+    -------
+    halt : bool
+        True if minimization should stop
+
+    """
+    if callback is None:
+        return False
+    try:
+        callback(res)
+        return False
+    except StopIteration:
+        callback.stop_iteration = True
+        return True
+
+
+class _RichResult(dict):
+    """ Container for multiple outputs with pretty-printing """
+    def __getattr__(self, name):
+        try:
+            return self[name]
+        except KeyError as e:
+            raise AttributeError(name) from e
+
+    __setattr__ = dict.__setitem__  # type: ignore[assignment]
+    __delattr__ = dict.__delitem__  # type: ignore[assignment]
+
+    def __repr__(self):
+        order_keys = ['message', 'success', 'status', 'fun', 'funl', 'x', 'xl',
+                      'col_ind', 'nit', 'lower', 'upper', 'eqlin', 'ineqlin',
+                      'converged', 'flag', 'function_calls', 'iterations',
+                      'root']
+        order_keys = getattr(self, '_order_keys', order_keys)
+        # 'slack', 'con' are redundant with residuals
+        # 'crossover_nit' is probably not interesting to most users
+        omit_keys = {'slack', 'con', 'crossover_nit', '_order_keys'}
+
+        def key(item):
+            try:
+                return order_keys.index(item[0].lower())
+            except ValueError:  # item not in list
+                return np.inf
+
+        def omit_redundant(items):
+            for item in items:
+                if item[0] in omit_keys:
+                    continue
+                yield item
+
+        def item_sorter(d):
+            return sorted(omit_redundant(d.items()), key=key)
+
+        if self.keys():
+            return _dict_formatter(self, sorter=item_sorter)
+        else:
+            return self.__class__.__name__ + "()"
+
+    def __dir__(self):
+        return list(self.keys())
+
+
+def _indenter(s, n=0):
+    """
+    Ensures that lines after the first are indented by the specified amount
+    """
+    split = s.split("\n")
+    indent = " "*n
+    return ("\n" + indent).join(split)
+
+
+def _float_formatter_10(x):
+    """
+    Returns a string representation of a float with exactly ten characters
+    """
+    if np.isposinf(x):
+        return "       inf"
+    elif np.isneginf(x):
+        return "      -inf"
+    elif np.isnan(x):
+        return "       nan"
+    return np.format_float_scientific(x, precision=3, pad_left=2, unique=False)
+
+
+def _dict_formatter(d, n=0, mplus=1, sorter=None):
+    """
+    Pretty printer for dictionaries
+
+    `n` keeps track of the starting indentation;
+    lines are indented by this much after a line break.
+    `mplus` is additional left padding applied to keys
+    """
+    if isinstance(d, dict):
+        m = max(map(len, list(d.keys()))) + mplus  # width to print keys
+        s = '\n'.join([k.rjust(m) + ': ' +  # right justified, width m
+                       _indenter(_dict_formatter(v, m+n+2, 0, sorter), m+2)
+                       for k, v in sorter(d)])  # +2 for ': '
+    else:
+        # By default, NumPy arrays print with linewidth=76. `n` is
+        # the indent at which a line begins printing, so it is subtracted
+        # from the default to avoid exceeding 76 characters total.
+        # `edgeitems` is the number of elements to include before and after
+        # ellipses when arrays are not shown in full.
+        # `threshold` is the maximum number of elements for which an
+        # array is shown in full.
+        # These values tend to work well for use with OptimizeResult.
+        with np.printoptions(linewidth=76-n, edgeitems=2, threshold=12,
+                             formatter={'float_kind': _float_formatter_10}):
+            s = str(d)
+    return s

phi4/lib/python3.10/site-packages/scipy/_lib/array_api_compat/__init__.py

@@ -0,0 +1,22 @@
+"""
+NumPy Array API compatibility library
+
+This is a small wrapper around NumPy and CuPy that is compatible with the
+Array API standard https://data-apis.org/array-api/latest/. See also NEP 47
+https://numpy.org/neps/nep-0047-array-api-standard.html.
+
+Unlike array_api_strict, this is not a strict minimal implementation of the
+Array API, but rather just an extension of the main NumPy namespace with
+changes needed to be compliant with the Array API. See
+https://numpy.org/doc/stable/reference/array_api.html for a full list of
+changes. In particular, unlike array_api_strict, this package does not use a
+separate Array object, but rather just uses numpy.ndarray directly.
+
+Library authors using the Array API may wish to test against array_api_strict
+to ensure they are not using functionality outside of the standard, but prefer
+this implementation for the default when working with NumPy arrays.
+
+"""
+__version__ = '1.9.1'
+
+from .common import *  # noqa: F401, F403

phi4/lib/python3.10/site-packages/scipy/_lib/array_api_compat/_internal.py

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+"""
+Internal helpers
+"""
+
+from functools import wraps
+from inspect import signature
+
+def get_xp(xp):
+    """
+    Decorator to automatically replace xp with the corresponding array module.
+
+    Use like
+
+    import numpy as np
+
+    @get_xp(np)
+    def func(x, /, xp, kwarg=None):
+        return xp.func(x, kwarg=kwarg)
+
+    Note that xp must be a keyword argument and come after all non-keyword
+    arguments.
+
+    """
+
+    def inner(f):
+        @wraps(f)
+        def wrapped_f(*args, **kwargs):
+            return f(*args, xp=xp, **kwargs)
+
+        sig = signature(f)
+        new_sig = sig.replace(
+            parameters=[sig.parameters[i] for i in sig.parameters if i != "xp"]
+        )
+
+        if wrapped_f.__doc__ is None:
+            wrapped_f.__doc__ = f"""\
+Array API compatibility wrapper for {f.__name__}.
+
+See the corresponding documentation in NumPy/CuPy and/or the array API
+specification for more details.
+
+"""
+        wrapped_f.__signature__ = new_sig
+        return wrapped_f
+
+    return inner

phi4/lib/python3.10/site-packages/scipy/_lib/array_api_compat/cupy/__init__.py

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+from cupy import * # noqa: F403
+
+# from cupy import * doesn't overwrite these builtin names
+from cupy import abs, max, min, round # noqa: F401
+
+# These imports may overwrite names from the import * above.
+from ._aliases import * # noqa: F403
+
+# See the comment in the numpy __init__.py
+__import__(__package__ + '.linalg')
+
+__import__(__package__ + '.fft')
+
+from ..common._helpers import * # noqa: F401,F403
+
+__array_api_version__ = '2023.12'