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env-llmeval/lib/python3.10/site-packages/scipy/spatial/__init__.py

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+"""
+=============================================================
+Spatial algorithms and data structures (:mod:`scipy.spatial`)
+=============================================================
+
+.. currentmodule:: scipy.spatial
+
+.. toctree::
+   :hidden:
+
+   spatial.distance
+
+Spatial transformations
+=======================
+
+These are contained in the `scipy.spatial.transform` submodule.
+
+Nearest-neighbor queries
+========================
+.. autosummary::
+   :toctree: generated/
+
+   KDTree      -- class for efficient nearest-neighbor queries
+   cKDTree     -- class for efficient nearest-neighbor queries (faster implementation)
+   Rectangle
+
+Distance metrics
+================
+
+Distance metrics are contained in the :mod:`scipy.spatial.distance` submodule.
+
+Delaunay triangulation, convex hulls, and Voronoi diagrams
+==========================================================
+
+.. autosummary::
+   :toctree: generated/
+
+   Delaunay    -- compute Delaunay triangulation of input points
+   ConvexHull  -- compute a convex hull for input points
+   Voronoi     -- compute a Voronoi diagram hull from input points
+   SphericalVoronoi -- compute a Voronoi diagram from input points on the surface of a sphere
+   HalfspaceIntersection -- compute the intersection points of input halfspaces
+
+Plotting helpers
+================
+
+.. autosummary::
+   :toctree: generated/
+
+   delaunay_plot_2d     -- plot 2-D triangulation
+   convex_hull_plot_2d  -- plot 2-D convex hull
+   voronoi_plot_2d      -- plot 2-D Voronoi diagram
+
+.. seealso:: :ref:`Tutorial <qhulltutorial>`
+
+
+Simplex representation
+======================
+The simplices (triangles, tetrahedra, etc.) appearing in the Delaunay
+tessellation (N-D simplices), convex hull facets, and Voronoi ridges
+(N-1-D simplices) are represented in the following scheme::
+
+    tess = Delaunay(points)
+    hull = ConvexHull(points)
+    voro = Voronoi(points)
+
+    # coordinates of the jth vertex of the ith simplex
+    tess.points[tess.simplices[i, j], :]        # tessellation element
+    hull.points[hull.simplices[i, j], :]        # convex hull facet
+    voro.vertices[voro.ridge_vertices[i, j], :] # ridge between Voronoi cells
+
+For Delaunay triangulations and convex hulls, the neighborhood
+structure of the simplices satisfies the condition:
+``tess.neighbors[i,j]`` is the neighboring simplex of the ith
+simplex, opposite to the ``j``-vertex. It is -1 in case of no neighbor.
+
+Convex hull facets also define a hyperplane equation::
+
+    (hull.equations[i,:-1] * coord).sum() + hull.equations[i,-1] == 0
+
+Similar hyperplane equations for the Delaunay triangulation correspond
+to the convex hull facets on the corresponding N+1-D
+paraboloid.
+
+The Delaunay triangulation objects offer a method for locating the
+simplex containing a given point, and barycentric coordinate
+computations.
+
+Functions
+---------
+
+.. autosummary::
+   :toctree: generated/
+
+   tsearch
+   distance_matrix
+   minkowski_distance
+   minkowski_distance_p
+   procrustes
+   geometric_slerp
+
+Warnings / Errors used in :mod:`scipy.spatial`
+----------------------------------------------
+.. autosummary::
+   :toctree: generated/
+
+   QhullError
+"""  # noqa: E501
+
+from ._kdtree import *
+from ._ckdtree import *
+from ._qhull import *
+from ._spherical_voronoi import SphericalVoronoi
+from ._plotutils import *
+from ._procrustes import procrustes
+from ._geometric_slerp import geometric_slerp
+
+# Deprecated namespaces, to be removed in v2.0.0
+from . import ckdtree, kdtree, qhull
+
+__all__ = [s for s in dir() if not s.startswith('_')]
+
+from . import distance, transform
+
+__all__ += ['distance', 'transform']
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

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

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+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]: ...

env-llmeval/lib/python3.10/site-packages/scipy/spatial/_geometric_slerp.py

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+from __future__ import annotations
+
+__all__ = ['geometric_slerp']
+
+import warnings
+from typing import TYPE_CHECKING
+
+import numpy as np
+from scipy.spatial.distance import euclidean
+
+if TYPE_CHECKING:
+    import numpy.typing as npt
+
+
+def _geometric_slerp(start, end, t):
+    # create an orthogonal basis using QR decomposition
+    basis = np.vstack([start, end])
+    Q, R = np.linalg.qr(basis.T)
+    signs = 2 * (np.diag(R) >= 0) - 1
+    Q = Q.T * signs.T[:, np.newaxis]
+    R = R.T * signs.T[:, np.newaxis]
+
+    # calculate the angle between `start` and `end`
+    c = np.dot(start, end)
+    s = np.linalg.det(R)
+    omega = np.arctan2(s, c)
+
+    # interpolate
+    start, end = Q
+    s = np.sin(t * omega)
+    c = np.cos(t * omega)
+    return start * c[:, np.newaxis] + end * s[:, np.newaxis]
+
+
+def geometric_slerp(
+    start: npt.ArrayLike,
+    end: npt.ArrayLike,
+    t: npt.ArrayLike,
+    tol: float = 1e-7,
+) -> np.ndarray:
+    """
+    Geometric spherical linear interpolation.
+
+    The interpolation occurs along a unit-radius
+    great circle arc in arbitrary dimensional space.
+
+    Parameters
+    ----------
+    start : (n_dimensions, ) array-like
+        Single n-dimensional input coordinate in a 1-D array-like
+        object. `n` must be greater than 1.
+    end : (n_dimensions, ) array-like
+        Single n-dimensional input coordinate in a 1-D array-like
+        object. `n` must be greater than 1.
+    t : float or (n_points,) 1D array-like
+        A float or 1D array-like of doubles representing interpolation
+        parameters, with values required in the inclusive interval
+        between 0 and 1. A common approach is to generate the array
+        with ``np.linspace(0, 1, n_pts)`` for linearly spaced points.
+        Ascending, descending, and scrambled orders are permitted.
+    tol : float
+        The absolute tolerance for determining if the start and end
+        coordinates are antipodes.
+
+    Returns
+    -------
+    result : (t.size, D)
+        An array of doubles containing the interpolated
+        spherical path and including start and
+        end when 0 and 1 t are used. The
+        interpolated values should correspond to the
+        same sort order provided in the t array. The result
+        may be 1-dimensional if ``t`` is a float.
+
+    Raises
+    ------
+    ValueError
+        If ``start`` and ``end`` are antipodes, not on the
+        unit n-sphere, or for a variety of degenerate conditions.
+
+    See Also
+    --------
+    scipy.spatial.transform.Slerp : 3-D Slerp that works with quaternions
+
+    Notes
+    -----
+    The implementation is based on the mathematical formula provided in [1]_,
+    and the first known presentation of this algorithm, derived from study of
+    4-D geometry, is credited to Glenn Davis in a footnote of the original
+    quaternion Slerp publication by Ken Shoemake [2]_.
+
+    .. versionadded:: 1.5.0
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Slerp#Geometric_Slerp
+    .. [2] Ken Shoemake (1985) Animating rotation with quaternion curves.
+           ACM SIGGRAPH Computer Graphics, 19(3): 245-254.
+
+    Examples
+    --------
+    Interpolate four linearly-spaced values on the circumference of
+    a circle spanning 90 degrees:
+
+    >>> import numpy as np
+    >>> from scipy.spatial import geometric_slerp
+    >>> import matplotlib.pyplot as plt
+    >>> fig = plt.figure()
+    >>> ax = fig.add_subplot(111)
+    >>> start = np.array([1, 0])
+    >>> end = np.array([0, 1])
+    >>> t_vals = np.linspace(0, 1, 4)
+    >>> result = geometric_slerp(start,
+    ...                          end,
+    ...                          t_vals)
+
+    The interpolated results should be at 30 degree intervals
+    recognizable on the unit circle:
+
+    >>> ax.scatter(result[...,0], result[...,1], c='k')
+    >>> circle = plt.Circle((0, 0), 1, color='grey')
+    >>> ax.add_artist(circle)
+    >>> ax.set_aspect('equal')
+    >>> plt.show()
+
+    Attempting to interpolate between antipodes on a circle is
+    ambiguous because there are two possible paths, and on a
+    sphere there are infinite possible paths on the geodesic surface.
+    Nonetheless, one of the ambiguous paths is returned along
+    with a warning:
+
+    >>> opposite_pole = np.array([-1, 0])
+    >>> with np.testing.suppress_warnings() as sup:
+    ...     sup.filter(UserWarning)
+    ...     geometric_slerp(start,
+    ...                     opposite_pole,
+    ...                     t_vals)
+    array([[ 1.00000000e+00,  0.00000000e+00],
+           [ 5.00000000e-01,  8.66025404e-01],
+           [-5.00000000e-01,  8.66025404e-01],
+           [-1.00000000e+00,  1.22464680e-16]])
+
+    Extend the original example to a sphere and plot interpolation
+    points in 3D:
+
+    >>> from mpl_toolkits.mplot3d import proj3d
+    >>> fig = plt.figure()
+    >>> ax = fig.add_subplot(111, projection='3d')
+
+    Plot the unit sphere for reference (optional):
+
+    >>> u = np.linspace(0, 2 * np.pi, 100)
+    >>> v = np.linspace(0, np.pi, 100)
+    >>> x = np.outer(np.cos(u), np.sin(v))
+    >>> y = np.outer(np.sin(u), np.sin(v))
+    >>> z = np.outer(np.ones(np.size(u)), np.cos(v))
+    >>> ax.plot_surface(x, y, z, color='y', alpha=0.1)
+
+    Interpolating over a larger number of points
+    may provide the appearance of a smooth curve on
+    the surface of the sphere, which is also useful
+    for discretized integration calculations on a
+    sphere surface:
+
+    >>> start = np.array([1, 0, 0])
+    >>> end = np.array([0, 0, 1])
+    >>> t_vals = np.linspace(0, 1, 200)
+    >>> result = geometric_slerp(start,
+    ...                          end,
+    ...                          t_vals)
+    >>> ax.plot(result[...,0],
+    ...         result[...,1],
+    ...         result[...,2],
+    ...         c='k')
+    >>> plt.show()
+    """
+
+    start = np.asarray(start, dtype=np.float64)
+    end = np.asarray(end, dtype=np.float64)
+    t = np.asarray(t)
+
+    if t.ndim > 1:
+        raise ValueError("The interpolation parameter "
+                         "value must be one dimensional.")
+
+    if start.ndim != 1 or end.ndim != 1:
+        raise ValueError("Start and end coordinates "
+                         "must be one-dimensional")
+
+    if start.size != end.size:
+        raise ValueError("The dimensions of start and "
+                         "end must match (have same size)")
+
+    if start.size < 2 or end.size < 2:
+        raise ValueError("The start and end coordinates must "
+                         "both be in at least two-dimensional "
+                         "space")
+
+    if np.array_equal(start, end):
+        return np.linspace(start, start, t.size)
+
+    # for points that violate equation for n-sphere
+    for coord in [start, end]:
+        if not np.allclose(np.linalg.norm(coord), 1.0,
+                           rtol=1e-9,
+                           atol=0):
+            raise ValueError("start and end are not"
+                             " on a unit n-sphere")
+
+    if not isinstance(tol, float):
+        raise ValueError("tol must be a float")
+    else:
+        tol = np.fabs(tol)
+
+    coord_dist = euclidean(start, end)
+
+    # diameter of 2 within tolerance means antipodes, which is a problem
+    # for all unit n-spheres (even the 0-sphere would have an ambiguous path)
+    if np.allclose(coord_dist, 2.0, rtol=0, atol=tol):
+        warnings.warn("start and end are antipodes "
+                      "using the specified tolerance; "
+                      "this may cause ambiguous slerp paths",
+                      stacklevel=2)
+
+    t = np.asarray(t, dtype=np.float64)
+
+    if t.size == 0:
+        return np.empty((0, start.size))
+
+    if t.min() < 0 or t.max() > 1:
+        raise ValueError("interpolation parameter must be in [0, 1]")
+
+    if t.ndim == 0:
+        return _geometric_slerp(start,
+                                end,
+                                np.atleast_1d(t)).ravel()
+    else:
+        return _geometric_slerp(start,
+                                end,
+                                t)

env-llmeval/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

env-llmeval/lib/python3.10/site-packages/scipy/spatial/_plotutils.py

@@ -0,0 +1,270 @@
+import numpy as np
+from scipy._lib.decorator import decorator as _decorator
+
+__all__ = ['delaunay_plot_2d', 'convex_hull_plot_2d', 'voronoi_plot_2d']
+
+
+@_decorator
+def _held_figure(func, obj, ax=None, **kw):
+    import matplotlib.pyplot as plt
+
+    if ax is None:
+        fig = plt.figure()
+        ax = fig.gca()
+        return func(obj, ax=ax, **kw)
+
+    # As of matplotlib 2.0, the "hold" mechanism is deprecated.
+    # When matplotlib 1.x is no longer supported, this check can be removed.
+    was_held = getattr(ax, 'ishold', lambda: True)()
+    if was_held:
+        return func(obj, ax=ax, **kw)
+    try:
+        ax.hold(True)
+        return func(obj, ax=ax, **kw)
+    finally:
+        ax.hold(was_held)
+
+
+def _adjust_bounds(ax, points):
+    margin = 0.1 * np.ptp(points, axis=0)
+    xy_min = points.min(axis=0) - margin
+    xy_max = points.max(axis=0) + margin
+    ax.set_xlim(xy_min[0], xy_max[0])
+    ax.set_ylim(xy_min[1], xy_max[1])
+
+
+@_held_figure
+def delaunay_plot_2d(tri, ax=None):
+    """
+    Plot the given Delaunay triangulation in 2-D
+
+    Parameters
+    ----------
+    tri : scipy.spatial.Delaunay instance
+        Triangulation to plot
+    ax : matplotlib.axes.Axes instance, optional
+        Axes to plot on
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure instance
+        Figure for the plot
+
+    See Also
+    --------
+    Delaunay
+    matplotlib.pyplot.triplot
+
+    Notes
+    -----
+    Requires Matplotlib.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> from scipy.spatial import Delaunay, delaunay_plot_2d
+
+    The Delaunay triangulation of a set of random points:
+
+    >>> rng = np.random.default_rng()
+    >>> points = rng.random((30, 2))
+    >>> tri = Delaunay(points)
+
+    Plot it:
+
+    >>> _ = delaunay_plot_2d(tri)
+    >>> plt.show()
+
+    """
+    if tri.points.shape[1] != 2:
+        raise ValueError("Delaunay triangulation is not 2-D")
+
+    x, y = tri.points.T
+    ax.plot(x, y, 'o')
+    ax.triplot(x, y, tri.simplices.copy())
+
+    _adjust_bounds(ax, tri.points)
+
+    return ax.figure
+
+
+@_held_figure
+def convex_hull_plot_2d(hull, ax=None):
+    """
+    Plot the given convex hull diagram in 2-D
+
+    Parameters
+    ----------
+    hull : scipy.spatial.ConvexHull instance
+        Convex hull to plot
+    ax : matplotlib.axes.Axes instance, optional
+        Axes to plot on
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure instance
+        Figure for the plot
+
+    See Also
+    --------
+    ConvexHull
+
+    Notes
+    -----
+    Requires Matplotlib.
+
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> from scipy.spatial import ConvexHull, convex_hull_plot_2d
+
+    The convex hull of a random set of points:
+
+    >>> rng = np.random.default_rng()
+    >>> points = rng.random((30, 2))
+    >>> hull = ConvexHull(points)
+
+    Plot it:
+
+    >>> _ = convex_hull_plot_2d(hull)
+    >>> plt.show()
+
+    """
+    from matplotlib.collections import LineCollection
+
+    if hull.points.shape[1] != 2:
+        raise ValueError("Convex hull is not 2-D")
+
+    ax.plot(hull.points[:, 0], hull.points[:, 1], 'o')
+    line_segments = [hull.points[simplex] for simplex in hull.simplices]
+    ax.add_collection(LineCollection(line_segments,
+                                     colors='k',
+                                     linestyle='solid'))
+    _adjust_bounds(ax, hull.points)
+
+    return ax.figure
+
+
+@_held_figure
+def voronoi_plot_2d(vor, ax=None, **kw):
+    """
+    Plot the given Voronoi diagram in 2-D
+
+    Parameters
+    ----------
+    vor : scipy.spatial.Voronoi instance
+        Diagram to plot
+    ax : matplotlib.axes.Axes instance, optional
+        Axes to plot on
+    show_points : bool, optional
+        Add the Voronoi points to the plot.
+    show_vertices : bool, optional
+        Add the Voronoi vertices to the plot.
+    line_colors : string, optional
+        Specifies the line color for polygon boundaries
+    line_width : float, optional
+        Specifies the line width for polygon boundaries
+    line_alpha : float, optional
+        Specifies the line alpha for polygon boundaries
+    point_size : float, optional
+        Specifies the size of points
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure instance
+        Figure for the plot
+
+    See Also
+    --------
+    Voronoi
+
+    Notes
+    -----
+    Requires Matplotlib.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> from scipy.spatial import Voronoi, voronoi_plot_2d
+
+    Create a set of points for the example:
+
+    >>> rng = np.random.default_rng()
+    >>> points = rng.random((10,2))
+
+    Generate the Voronoi diagram for the points:
+
+    >>> vor = Voronoi(points)
+
+    Use `voronoi_plot_2d` to plot the diagram:
+
+    >>> fig = voronoi_plot_2d(vor)
+
+    Use `voronoi_plot_2d` to plot the diagram again, with some settings
+    customized:
+
+    >>> fig = voronoi_plot_2d(vor, show_vertices=False, line_colors='orange',
+    ...                       line_width=2, line_alpha=0.6, point_size=2)
+    >>> plt.show()
+
+    """
+    from matplotlib.collections import LineCollection
+
+    if vor.points.shape[1] != 2:
+        raise ValueError("Voronoi diagram is not 2-D")
+
+    if kw.get('show_points', True):
+        point_size = kw.get('point_size', None)
+        ax.plot(vor.points[:, 0], vor.points[:, 1], '.', markersize=point_size)
+    if kw.get('show_vertices', True):
+        ax.plot(vor.vertices[:, 0], vor.vertices[:, 1], 'o')
+
+    line_colors = kw.get('line_colors', 'k')
+    line_width = kw.get('line_width', 1.0)
+    line_alpha = kw.get('line_alpha', 1.0)
+
+    center = vor.points.mean(axis=0)
+    ptp_bound = np.ptp(vor.points, axis=0)
+
+    finite_segments = []
+    infinite_segments = []
+    for pointidx, simplex in zip(vor.ridge_points, vor.ridge_vertices):
+        simplex = np.asarray(simplex)
+        if np.all(simplex >= 0):
+            finite_segments.append(vor.vertices[simplex])
+        else:
+            i = simplex[simplex >= 0][0]  # finite end Voronoi vertex
+
+            t = vor.points[pointidx[1]] - vor.points[pointidx[0]]  # tangent
+            t /= np.linalg.norm(t)
+            n = np.array([-t[1], t[0]])  # normal
+
+            midpoint = vor.points[pointidx].mean(axis=0)
+            direction = np.sign(np.dot(midpoint - center, n)) * n
+            if (vor.furthest_site):
+                direction = -direction
+            aspect_factor = abs(ptp_bound.max() / ptp_bound.min())
+            far_point = vor.vertices[i] + direction * ptp_bound.max() * aspect_factor
+
+            infinite_segments.append([vor.vertices[i], far_point])
+
+    ax.add_collection(LineCollection(finite_segments,
+                                     colors=line_colors,
+                                     lw=line_width,
+                                     alpha=line_alpha,
+                                     linestyle='solid'))
+    ax.add_collection(LineCollection(infinite_segments,
+                                     colors=line_colors,
+                                     lw=line_width,
+                                     alpha=line_alpha,
+                                     linestyle='dashed'))
+
+    _adjust_bounds(ax, vor.points)
+
+    return ax.figure

env-llmeval/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
+

env-llmeval/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]: ...

env-llmeval/lib/python3.10/site-packages/scipy/spatial/_spherical_voronoi.py

@@ -0,0 +1,341 @@
+"""
+Spherical Voronoi Code
+
+.. versionadded:: 0.18.0
+
+"""
+#
+# Copyright (C)  Tyler Reddy, Ross Hemsley, Edd Edmondson,
+#                Nikolai Nowaczyk, Joe Pitt-Francis, 2015.
+#
+# Distributed under the same BSD license as SciPy.
+#
+
+import numpy as np
+import scipy
+from . import _voronoi
+from scipy.spatial import cKDTree
+
+__all__ = ['SphericalVoronoi']
+
+
+def calculate_solid_angles(R):
+    """Calculates the solid angles of plane triangles. Implements the method of
+    Van Oosterom and Strackee [VanOosterom]_ with some modifications. Assumes
+    that input points have unit norm."""
+    # Original method uses a triple product `R1 . (R2 x R3)` for the numerator.
+    # This is equal to the determinant of the matrix [R1 R2 R3], which can be
+    # computed with better stability.
+    numerator = np.linalg.det(R)
+    denominator = 1 + (np.einsum('ij,ij->i', R[:, 0], R[:, 1]) +
+                       np.einsum('ij,ij->i', R[:, 1], R[:, 2]) +
+                       np.einsum('ij,ij->i', R[:, 2], R[:, 0]))
+    return np.abs(2 * np.arctan2(numerator, denominator))
+
+
+class SphericalVoronoi:
+    """ Voronoi diagrams on the surface of a sphere.
+
+    .. versionadded:: 0.18.0
+
+    Parameters
+    ----------
+    points : ndarray of floats, shape (npoints, ndim)
+        Coordinates of points from which to construct a spherical
+        Voronoi diagram.
+    radius : float, optional
+        Radius of the sphere (Default: 1)
+    center : ndarray of floats, shape (ndim,)
+        Center of sphere (Default: origin)
+    threshold : float
+        Threshold for detecting duplicate points and
+        mismatches between points and sphere parameters.
+        (Default: 1e-06)
+
+    Attributes
+    ----------
+    points : double array of shape (npoints, ndim)
+        the points in `ndim` dimensions to generate the Voronoi diagram from
+    radius : double
+        radius of the sphere
+    center : double array of shape (ndim,)
+        center of the sphere
+    vertices : double array of shape (nvertices, ndim)
+        Voronoi vertices corresponding to points
+    regions : list of list of integers of shape (npoints, _ )
+        the n-th entry is a list consisting of the indices
+        of the vertices belonging to the n-th point in points
+
+    Methods
+    -------
+    calculate_areas
+        Calculates the areas of the Voronoi regions. For 2D point sets, the
+        regions are circular arcs. The sum of the areas is `2 * pi * radius`.
+        For 3D point sets, the regions are spherical polygons. The sum of the
+        areas is `4 * pi * radius**2`.
+
+    Raises
+    ------
+    ValueError
+        If there are duplicates in `points`.
+        If the provided `radius` is not consistent with `points`.
+
+    Notes
+    -----
+    The spherical Voronoi diagram algorithm proceeds as follows. The Convex
+    Hull of the input points (generators) is calculated, and is equivalent to
+    their Delaunay triangulation on the surface of the sphere [Caroli]_.
+    The Convex Hull neighbour information is then used to
+    order the Voronoi region vertices around each generator. The latter
+    approach is substantially less sensitive to floating point issues than
+    angle-based methods of Voronoi region vertex sorting.
+
+    Empirical assessment of spherical Voronoi algorithm performance suggests
+    quadratic time complexity (loglinear is optimal, but algorithms are more
+    challenging to implement).
+
+    References
+    ----------
+    .. [Caroli] Caroli et al. Robust and Efficient Delaunay triangulations of
+                points on or close to a sphere. Research Report RR-7004, 2009.
+
+    .. [VanOosterom] Van Oosterom and Strackee. The solid angle of a plane
+                     triangle. IEEE Transactions on Biomedical Engineering,
+                     2, 1983, pp 125--126.
+
+    See Also
+    --------
+    Voronoi : Conventional Voronoi diagrams in N dimensions.
+
+    Examples
+    --------
+    Do some imports and take some points on a cube:
+
+    >>> import numpy as np
+    >>> import matplotlib.pyplot as plt
+    >>> from scipy.spatial import SphericalVoronoi, geometric_slerp
+    >>> from mpl_toolkits.mplot3d import proj3d
+    >>> # set input data
+    >>> points = np.array([[0, 0, 1], [0, 0, -1], [1, 0, 0],
+    ...                    [0, 1, 0], [0, -1, 0], [-1, 0, 0], ])
+
+    Calculate the spherical Voronoi diagram:
+
+    >>> radius = 1
+    >>> center = np.array([0, 0, 0])
+    >>> sv = SphericalVoronoi(points, radius, center)
+
+    Generate plot:
+
+    >>> # sort vertices (optional, helpful for plotting)
+    >>> sv.sort_vertices_of_regions()
+    >>> t_vals = np.linspace(0, 1, 2000)
+    >>> fig = plt.figure()
+    >>> ax = fig.add_subplot(111, projection='3d')
+    >>> # plot the unit sphere for reference (optional)
+    >>> u = np.linspace(0, 2 * np.pi, 100)
+    >>> v = np.linspace(0, np.pi, 100)
+    >>> x = np.outer(np.cos(u), np.sin(v))
+    >>> y = np.outer(np.sin(u), np.sin(v))
+    >>> z = np.outer(np.ones(np.size(u)), np.cos(v))
+    >>> ax.plot_surface(x, y, z, color='y', alpha=0.1)
+    >>> # plot generator points
+    >>> ax.scatter(points[:, 0], points[:, 1], points[:, 2], c='b')
+    >>> # plot Voronoi vertices
+    >>> ax.scatter(sv.vertices[:, 0], sv.vertices[:, 1], sv.vertices[:, 2],
+    ...                    c='g')
+    >>> # indicate Voronoi regions (as Euclidean polygons)
+    >>> for region in sv.regions:
+    ...    n = len(region)
+    ...    for i in range(n):
+    ...        start = sv.vertices[region][i]
+    ...        end = sv.vertices[region][(i + 1) % n]
+    ...        result = geometric_slerp(start, end, t_vals)
+    ...        ax.plot(result[..., 0],
+    ...                result[..., 1],
+    ...                result[..., 2],
+    ...                c='k')
+    >>> ax.azim = 10
+    >>> ax.elev = 40
+    >>> _ = ax.set_xticks([])
+    >>> _ = ax.set_yticks([])
+    >>> _ = ax.set_zticks([])
+    >>> fig.set_size_inches(4, 4)
+    >>> plt.show()
+
+    """
+    def __init__(self, points, radius=1, center=None, threshold=1e-06):
+
+        if radius is None:
+            raise ValueError('`radius` is `None`. '
+                             'Please provide a floating point number '
+                             '(i.e. `radius=1`).')
+
+        self.radius = float(radius)
+        self.points = np.array(points).astype(np.float64)
+        self._dim = self.points.shape[1]
+        if center is None:
+            self.center = np.zeros(self._dim)
+        else:
+            self.center = np.array(center, dtype=float)
+
+        # test degenerate input
+        self._rank = np.linalg.matrix_rank(self.points - self.points[0],
+                                           tol=threshold * self.radius)
+        if self._rank < self._dim:
+            raise ValueError(f"Rank of input points must be at least {self._dim}")
+
+        if cKDTree(self.points).query_pairs(threshold * self.radius):
+            raise ValueError("Duplicate generators present.")
+
+        radii = np.linalg.norm(self.points - self.center, axis=1)
+        max_discrepancy = np.abs(radii - self.radius).max()
+        if max_discrepancy >= threshold * self.radius:
+            raise ValueError("Radius inconsistent with generators.")
+
+        self._calc_vertices_regions()
+
+    def _calc_vertices_regions(self):
+        """
+        Calculates the Voronoi vertices and regions of the generators stored
+        in self.points. The vertices will be stored in self.vertices and the
+        regions in self.regions.
+
+        This algorithm was discussed at PyData London 2015 by
+        Tyler Reddy, Ross Hemsley and Nikolai Nowaczyk
+        """
+        # get Convex Hull
+        conv = scipy.spatial.ConvexHull(self.points)
+        # get circumcenters of Convex Hull triangles from facet equations
+        # for 3D input circumcenters will have shape: (2N-4, 3)
+        self.vertices = self.radius * conv.equations[:, :-1] + self.center
+        self._simplices = conv.simplices
+        # calculate regions from triangulation
+        # for 3D input simplex_indices will have shape: (2N-4,)
+        simplex_indices = np.arange(len(self._simplices))
+        # for 3D input tri_indices will have shape: (6N-12,)
+        tri_indices = np.column_stack([simplex_indices] * self._dim).ravel()
+        # for 3D input point_indices will have shape: (6N-12,)
+        point_indices = self._simplices.ravel()
+        # for 3D input indices will have shape: (6N-12,)
+        indices = np.argsort(point_indices, kind='mergesort')
+        # for 3D input flattened_groups will have shape: (6N-12,)
+        flattened_groups = tri_indices[indices].astype(np.intp)
+        # intervals will have shape: (N+1,)
+        intervals = np.cumsum(np.bincount(point_indices + 1))
+        # split flattened groups to get nested list of unsorted regions
+        groups = [list(flattened_groups[intervals[i]:intervals[i + 1]])
+                  for i in range(len(intervals) - 1)]
+        self.regions = groups
+
+    def sort_vertices_of_regions(self):
+        """Sort indices of the vertices to be (counter-)clockwise ordered.
+
+        Raises
+        ------
+        TypeError
+            If the points are not three-dimensional.
+
+        Notes
+        -----
+        For each region in regions, it sorts the indices of the Voronoi
+        vertices such that the resulting points are in a clockwise or
+        counterclockwise order around the generator point.
+
+        This is done as follows: Recall that the n-th region in regions
+        surrounds the n-th generator in points and that the k-th
+        Voronoi vertex in vertices is the circumcenter of the k-th triangle
+        in self._simplices.  For each region n, we choose the first triangle
+        (=Voronoi vertex) in self._simplices and a vertex of that triangle
+        not equal to the center n. These determine a unique neighbor of that
+        triangle, which is then chosen as the second triangle. The second
+        triangle will have a unique vertex not equal to the current vertex or
+        the center. This determines a unique neighbor of the second triangle,
+        which is then chosen as the third triangle and so forth. We proceed
+        through all the triangles (=Voronoi vertices) belonging to the
+        generator in points and obtain a sorted version of the vertices
+        of its surrounding region.
+        """
+        if self._dim != 3:
+            raise TypeError("Only supported for three-dimensional point sets")
+        _voronoi.sort_vertices_of_regions(self._simplices, self.regions)
+
+    def _calculate_areas_3d(self):
+        self.sort_vertices_of_regions()
+        sizes = [len(region) for region in self.regions]
+        csizes = np.cumsum(sizes)
+        num_regions = csizes[-1]
+
+        # We create a set of triangles consisting of one point and two Voronoi
+        # vertices. The vertices of each triangle are adjacent in the sorted
+        # regions list.
+        point_indices = [i for i, size in enumerate(sizes)
+                         for j in range(size)]
+
+        nbrs1 = np.array([r for region in self.regions for r in region])
+
+        # The calculation of nbrs2 is a vectorized version of:
+        # np.array([r for region in self.regions for r in np.roll(region, 1)])
+        nbrs2 = np.roll(nbrs1, 1)
+        indices = np.roll(csizes, 1)
+        indices[0] = 0
+        nbrs2[indices] = nbrs1[csizes - 1]
+
+        # Normalize points and vertices.
+        pnormalized = (self.points - self.center) / self.radius
+        vnormalized = (self.vertices - self.center) / self.radius
+
+        # Create the complete set of triangles and calculate their solid angles
+        triangles = np.hstack([pnormalized[point_indices],
+                               vnormalized[nbrs1],
+                               vnormalized[nbrs2]
+                               ]).reshape((num_regions, 3, 3))
+        triangle_solid_angles = calculate_solid_angles(triangles)
+
+        # Sum the solid angles of the triangles in each region
+        solid_angles = np.cumsum(triangle_solid_angles)[csizes - 1]
+        solid_angles[1:] -= solid_angles[:-1]
+
+        # Get polygon areas using A = omega * r**2
+        return solid_angles * self.radius**2
+
+    def _calculate_areas_2d(self):
+        # Find start and end points of arcs
+        arcs = self.points[self._simplices] - self.center
+
+        # Calculate the angle subtended by arcs
+        d = np.sum((arcs[:, 1] - arcs[:, 0]) ** 2, axis=1)
+        theta = np.arccos(1 - (d / (2 * (self.radius ** 2))))
+
+        # Get areas using A = r * theta
+        areas = self.radius * theta
+
+        # Correct arcs which go the wrong way (single-hemisphere inputs)
+        signs = np.sign(np.einsum('ij,ij->i', arcs[:, 0],
+                                              self.vertices - self.center))
+        indices = np.where(signs < 0)
+        areas[indices] = 2 * np.pi * self.radius - areas[indices]
+        return areas
+
+    def calculate_areas(self):
+        """Calculates the areas of the Voronoi regions.
+
+        For 2D point sets, the regions are circular arcs. The sum of the areas
+        is `2 * pi * radius`.
+
+        For 3D point sets, the regions are spherical polygons. The sum of the
+        areas is `4 * pi * radius**2`.
+
+        .. versionadded:: 1.5.0
+
+        Returns
+        -------
+        areas : double array of shape (npoints,)
+            The areas of the Voronoi regions.
+        """
+        if self._dim == 2:
+            return self._calculate_areas_2d()
+        elif self._dim == 3:
+            return self._calculate_areas_3d()
+        else:
+            raise TypeError("Only supported for 2D and 3D point sets")

env-llmeval/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

env-llmeval/lib/python3.10/site-packages/scipy/spatial/ckdtree.py

@@ -0,0 +1,27 @@
+# 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
+    'cKDTree',
+    'cKDTreeNode',
+    'coo_entries',
+    'operator',
+    'ordered_pairs',
+    'os',
+    'scipy',
+    'threading',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="spatial", module="ckdtree",
+                                   private_modules=["_ckdtree"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/spatial/distance.py

@@ -0,0 +1,2993 @@
+"""
+Distance computations (:mod:`scipy.spatial.distance`)
+=====================================================
+
+.. sectionauthor:: Damian Eads
+
+Function reference
+------------------
+
+Distance matrix computation from a collection of raw observation vectors
+stored in a rectangular array.
+
+.. autosummary::
+   :toctree: generated/
+
+   pdist   -- pairwise distances between observation vectors.
+   cdist   -- distances between two collections of observation vectors
+   squareform -- convert distance matrix to a condensed one and vice versa
+   directed_hausdorff -- directed Hausdorff distance between arrays
+
+Predicates for checking the validity of distance matrices, both
+condensed and redundant. Also contained in this module are functions
+for computing the number of observations in a distance matrix.
+
+.. autosummary::
+   :toctree: generated/
+
+   is_valid_dm -- checks for a valid distance matrix
+   is_valid_y  -- checks for a valid condensed distance matrix
+   num_obs_dm  -- # of observations in a distance matrix
+   num_obs_y   -- # of observations in a condensed distance matrix
+
+Distance functions between two numeric vectors ``u`` and ``v``. Computing
+distances over a large collection of vectors is inefficient for these
+functions. Use ``pdist`` for this purpose.
+
+.. autosummary::
+   :toctree: generated/
+
+   braycurtis       -- the Bray-Curtis distance.
+   canberra         -- the Canberra distance.
+   chebyshev        -- the Chebyshev distance.
+   cityblock        -- the Manhattan distance.
+   correlation      -- the Correlation distance.
+   cosine           -- the Cosine distance.
+   euclidean        -- the Euclidean distance.
+   jensenshannon    -- the Jensen-Shannon distance.
+   mahalanobis      -- the Mahalanobis distance.
+   minkowski        -- the Minkowski distance.
+   seuclidean       -- the normalized Euclidean distance.
+   sqeuclidean      -- the squared Euclidean distance.
+
+Distance functions between two boolean vectors (representing sets) ``u`` and
+``v``.  As in the case of numerical vectors, ``pdist`` is more efficient for
+computing the distances between all pairs.
+
+.. autosummary::
+   :toctree: generated/
+
+   dice             -- the Dice dissimilarity.
+   hamming          -- the Hamming distance.
+   jaccard          -- the Jaccard distance.
+   kulczynski1      -- the Kulczynski 1 distance.
+   rogerstanimoto   -- the Rogers-Tanimoto dissimilarity.
+   russellrao       -- the Russell-Rao dissimilarity.
+   sokalmichener    -- the Sokal-Michener dissimilarity.
+   sokalsneath      -- the Sokal-Sneath dissimilarity.
+   yule             -- the Yule dissimilarity.
+
+:func:`hamming` also operates over discrete numerical vectors.
+"""
+
+# Copyright (C) Damian Eads, 2007-2008. New BSD License.
+
+__all__ = [
+    'braycurtis',
+    'canberra',
+    'cdist',
+    'chebyshev',
+    'cityblock',
+    'correlation',
+    'cosine',
+    'dice',
+    'directed_hausdorff',
+    'euclidean',
+    'hamming',
+    'is_valid_dm',
+    'is_valid_y',
+    'jaccard',
+    'jensenshannon',
+    'kulczynski1',
+    'mahalanobis',
+    'minkowski',
+    'num_obs_dm',
+    'num_obs_y',
+    'pdist',
+    'rogerstanimoto',
+    'russellrao',
+    'seuclidean',
+    'sokalmichener',
+    'sokalsneath',
+    'sqeuclidean',
+    'squareform',
+    'yule'
+]
+
+
+import math
+import warnings
+import numpy as np
+import dataclasses
+
+from typing import Optional, Callable
+
+from functools import partial
+from scipy._lib._util import _asarray_validated
+
+from . import _distance_wrap
+from . import _hausdorff
+from ..linalg import norm
+from ..special import rel_entr
+
+from . import _distance_pybind
+
+
+def _copy_array_if_base_present(a):
+    """Copy the array if its base points to a parent array."""
+    if a.base is not None:
+        return a.copy()
+    return a
+
+
+def _correlation_cdist_wrap(XA, XB, dm, **kwargs):
+    XA = XA - XA.mean(axis=1, keepdims=True)
+    XB = XB - XB.mean(axis=1, keepdims=True)
+    _distance_wrap.cdist_cosine_double_wrap(XA, XB, dm, **kwargs)
+
+
+def _correlation_pdist_wrap(X, dm, **kwargs):
+    X2 = X - X.mean(axis=1, keepdims=True)
+    _distance_wrap.pdist_cosine_double_wrap(X2, dm, **kwargs)
+
+
+def _convert_to_type(X, out_type):
+    return np.ascontiguousarray(X, dtype=out_type)
+
+
+def _nbool_correspond_all(u, v, w=None):
+    if u.dtype == v.dtype == bool and w is None:
+        not_u = ~u
+        not_v = ~v
+        nff = (not_u & not_v).sum()
+        nft = (not_u & v).sum()
+        ntf = (u & not_v).sum()
+        ntt = (u & v).sum()
+    else:
+        dtype = np.result_type(int, u.dtype, v.dtype)
+        u = u.astype(dtype)
+        v = v.astype(dtype)
+        not_u = 1.0 - u
+        not_v = 1.0 - v
+        if w is not None:
+            not_u = w * not_u
+            u = w * u
+        nff = (not_u * not_v).sum()
+        nft = (not_u * v).sum()
+        ntf = (u * not_v).sum()
+        ntt = (u * v).sum()
+    return (nff, nft, ntf, ntt)
+
+
+def _nbool_correspond_ft_tf(u, v, w=None):
+    if u.dtype == v.dtype == bool and w is None:
+        not_u = ~u
+        not_v = ~v
+        nft = (not_u & v).sum()
+        ntf = (u & not_v).sum()
+    else:
+        dtype = np.result_type(int, u.dtype, v.dtype)
+        u = u.astype(dtype)
+        v = v.astype(dtype)
+        not_u = 1.0 - u
+        not_v = 1.0 - v
+        if w is not None:
+            not_u = w * not_u
+            u = w * u
+        nft = (not_u * v).sum()
+        ntf = (u * not_v).sum()
+    return (nft, ntf)
+
+
+def _validate_cdist_input(XA, XB, mA, mB, n, metric_info, **kwargs):
+    # get supported types
+    types = metric_info.types
+    # choose best type
+    typ = types[types.index(XA.dtype)] if XA.dtype in types else types[0]
+    # validate data
+    XA = _convert_to_type(XA, out_type=typ)
+    XB = _convert_to_type(XB, out_type=typ)
+
+    # validate kwargs
+    _validate_kwargs = metric_info.validator
+    if _validate_kwargs:
+        kwargs = _validate_kwargs((XA, XB), mA + mB, n, **kwargs)
+    return XA, XB, typ, kwargs
+
+
+def _validate_weight_with_size(X, m, n, **kwargs):
+    w = kwargs.pop('w', None)
+    if w is None:
+        return kwargs
+
+    if w.ndim != 1 or w.shape[0] != n:
+        raise ValueError("Weights must have same size as input vector. "
+                         f"{w.shape[0]} vs. {n}")
+
+    kwargs['w'] = _validate_weights(w)
+    return kwargs
+
+
+def _validate_hamming_kwargs(X, m, n, **kwargs):
+    w = kwargs.get('w', np.ones((n,), dtype='double'))
+
+    if w.ndim != 1 or w.shape[0] != n:
+        raise ValueError(
+            "Weights must have same size as input vector. %d vs. %d" % (w.shape[0], n)
+        )
+
+    kwargs['w'] = _validate_weights(w)
+    return kwargs
+
+
+def _validate_mahalanobis_kwargs(X, m, n, **kwargs):
+    VI = kwargs.pop('VI', None)
+    if VI is None:
+        if m <= n:
+            # There are fewer observations than the dimension of
+            # the observations.
+            raise ValueError("The number of observations (%d) is too "
+                             "small; the covariance matrix is "
+                             "singular. For observations with %d "
+                             "dimensions, at least %d observations "
+                             "are required." % (m, n, n + 1))
+        if isinstance(X, tuple):
+            X = np.vstack(X)
+        CV = np.atleast_2d(np.cov(X.astype(np.float64, copy=False).T))
+        VI = np.linalg.inv(CV).T.copy()
+    kwargs["VI"] = _convert_to_double(VI)
+    return kwargs
+
+
+def _validate_minkowski_kwargs(X, m, n, **kwargs):
+    kwargs = _validate_weight_with_size(X, m, n, **kwargs)
+    if 'p' not in kwargs:
+        kwargs['p'] = 2.
+    else:
+        if kwargs['p'] <= 0:
+            raise ValueError("p must be greater than 0")
+
+    return kwargs
+
+
+def _validate_pdist_input(X, m, n, metric_info, **kwargs):
+    # get supported types
+    types = metric_info.types
+    # choose best type
+    typ = types[types.index(X.dtype)] if X.dtype in types else types[0]
+    # validate data
+    X = _convert_to_type(X, out_type=typ)
+
+    # validate kwargs
+    _validate_kwargs = metric_info.validator
+    if _validate_kwargs:
+        kwargs = _validate_kwargs(X, m, n, **kwargs)
+    return X, typ, kwargs
+
+
+def _validate_seuclidean_kwargs(X, m, n, **kwargs):
+    V = kwargs.pop('V', None)
+    if V is None:
+        if isinstance(X, tuple):
+            X = np.vstack(X)
+        V = np.var(X.astype(np.float64, copy=False), axis=0, ddof=1)
+    else:
+        V = np.asarray(V, order='c')
+        if len(V.shape) != 1:
+            raise ValueError('Variance vector V must '
+                             'be one-dimensional.')
+        if V.shape[0] != n:
+            raise ValueError('Variance vector V must be of the same '
+                             'dimension as the vectors on which the distances '
+                             'are computed.')
+    kwargs['V'] = _convert_to_double(V)
+    return kwargs
+
+
+def _validate_vector(u, dtype=None):
+    # XXX Is order='c' really necessary?
+    u = np.asarray(u, dtype=dtype, order='c')
+    if u.ndim == 1:
+        return u
+    raise ValueError("Input vector should be 1-D.")
+
+
+def _validate_weights(w, dtype=np.float64):
+    w = _validate_vector(w, dtype=dtype)
+    if np.any(w < 0):
+        raise ValueError("Input weights should be all non-negative")
+    return w
+
+
+def directed_hausdorff(u, v, seed=0):
+    """
+    Compute the directed Hausdorff distance between two 2-D arrays.
+
+    Distances between pairs are calculated using a Euclidean metric.
+
+    Parameters
+    ----------
+    u : (M,N) array_like
+        Input array with M points in N dimensions.
+    v : (O,N) array_like
+        Input array with O points in N dimensions.
+    seed : int or None, optional
+        Local `numpy.random.RandomState` seed. Default is 0, a random
+        shuffling of u and v that guarantees reproducibility.
+
+    Returns
+    -------
+    d : double
+        The directed Hausdorff distance between arrays `u` and `v`,
+
+    index_1 : int
+        index of point contributing to Hausdorff pair in `u`
+
+    index_2 : int
+        index of point contributing to Hausdorff pair in `v`
+
+    Raises
+    ------
+    ValueError
+        An exception is thrown if `u` and `v` do not have
+        the same number of columns.
+
+    See Also
+    --------
+    scipy.spatial.procrustes : Another similarity test for two data sets
+
+    Notes
+    -----
+    Uses the early break technique and the random sampling approach
+    described by [1]_. Although worst-case performance is ``O(m * o)``
+    (as with the brute force algorithm), this is unlikely in practice
+    as the input data would have to require the algorithm to explore
+    every single point interaction, and after the algorithm shuffles
+    the input points at that. The best case performance is O(m), which
+    is satisfied by selecting an inner loop distance that is less than
+    cmax and leads to an early break as often as possible. The authors
+    have formally shown that the average runtime is closer to O(m).
+
+    .. versionadded:: 0.19.0
+
+    References
+    ----------
+    .. [1] A. A. Taha and A. Hanbury, "An efficient algorithm for
+           calculating the exact Hausdorff distance." IEEE Transactions On
+           Pattern Analysis And Machine Intelligence, vol. 37 pp. 2153-63,
+           2015.
+
+    Examples
+    --------
+    Find the directed Hausdorff distance between two 2-D arrays of
+    coordinates:
+
+    >>> from scipy.spatial.distance import directed_hausdorff
+    >>> import numpy as np
+    >>> u = np.array([(1.0, 0.0),
+    ...               (0.0, 1.0),
+    ...               (-1.0, 0.0),
+    ...               (0.0, -1.0)])
+    >>> v = np.array([(2.0, 0.0),
+    ...               (0.0, 2.0),
+    ...               (-2.0, 0.0),
+    ...               (0.0, -4.0)])
+
+    >>> directed_hausdorff(u, v)[0]
+    2.23606797749979
+    >>> directed_hausdorff(v, u)[0]
+    3.0
+
+    Find the general (symmetric) Hausdorff distance between two 2-D
+    arrays of coordinates:
+
+    >>> max(directed_hausdorff(u, v)[0], directed_hausdorff(v, u)[0])
+    3.0
+
+    Find the indices of the points that generate the Hausdorff distance
+    (the Hausdorff pair):
+
+    >>> directed_hausdorff(v, u)[1:]
+    (3, 3)
+
+    """
+    u = np.asarray(u, dtype=np.float64, order='c')
+    v = np.asarray(v, dtype=np.float64, order='c')
+    if u.shape[1] != v.shape[1]:
+        raise ValueError('u and v need to have the same '
+                         'number of columns')
+    result = _hausdorff.directed_hausdorff(u, v, seed)
+    return result
+
+
+def minkowski(u, v, p=2, w=None):
+    """
+    Compute the Minkowski distance between two 1-D arrays.
+
+    The Minkowski distance between 1-D arrays `u` and `v`,
+    is defined as
+
+    .. math::
+
+       {\\|u-v\\|}_p = (\\sum{|u_i - v_i|^p})^{1/p}.
+
+
+       \\left(\\sum{w_i(|(u_i - v_i)|^p)}\\right)^{1/p}.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    p : scalar
+        The order of the norm of the difference :math:`{\\|u-v\\|}_p`. Note
+        that for :math:`0 < p < 1`, the triangle inequality only holds with
+        an additional multiplicative factor, i.e. it is only a quasi-metric.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    minkowski : double
+        The Minkowski distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.minkowski([1, 0, 0], [0, 1, 0], 1)
+    2.0
+    >>> distance.minkowski([1, 0, 0], [0, 1, 0], 2)
+    1.4142135623730951
+    >>> distance.minkowski([1, 0, 0], [0, 1, 0], 3)
+    1.2599210498948732
+    >>> distance.minkowski([1, 1, 0], [0, 1, 0], 1)
+    1.0
+    >>> distance.minkowski([1, 1, 0], [0, 1, 0], 2)
+    1.0
+    >>> distance.minkowski([1, 1, 0], [0, 1, 0], 3)
+    1.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if p <= 0:
+        raise ValueError("p must be greater than 0")
+    u_v = u - v
+    if w is not None:
+        w = _validate_weights(w)
+        if p == 1:
+            root_w = w
+        elif p == 2:
+            # better precision and speed
+            root_w = np.sqrt(w)
+        elif p == np.inf:
+            root_w = (w != 0)
+        else:
+            root_w = np.power(w, 1/p)
+        u_v = root_w * u_v
+    dist = norm(u_v, ord=p)
+    return dist
+
+
+def euclidean(u, v, w=None):
+    """
+    Computes the Euclidean distance between two 1-D arrays.
+
+    The Euclidean distance between 1-D arrays `u` and `v`, is defined as
+
+    .. math::
+
+       {\\|u-v\\|}_2
+
+       \\left(\\sum{(w_i |(u_i - v_i)|^2)}\\right)^{1/2}
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    euclidean : double
+        The Euclidean distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.euclidean([1, 0, 0], [0, 1, 0])
+    1.4142135623730951
+    >>> distance.euclidean([1, 1, 0], [0, 1, 0])
+    1.0
+
+    """
+    return minkowski(u, v, p=2, w=w)
+
+
+def sqeuclidean(u, v, w=None):
+    """
+    Compute the squared Euclidean distance between two 1-D arrays.
+
+    The squared Euclidean distance between `u` and `v` is defined as
+
+    .. math::
+
+       \\sum_i{w_i |u_i - v_i|^2}
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    sqeuclidean : double
+        The squared Euclidean distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.sqeuclidean([1, 0, 0], [0, 1, 0])
+    2.0
+    >>> distance.sqeuclidean([1, 1, 0], [0, 1, 0])
+    1.0
+
+    """
+    # Preserve float dtypes, but convert everything else to np.float64
+    # for stability.
+    utype, vtype = None, None
+    if not (hasattr(u, "dtype") and np.issubdtype(u.dtype, np.inexact)):
+        utype = np.float64
+    if not (hasattr(v, "dtype") and np.issubdtype(v.dtype, np.inexact)):
+        vtype = np.float64
+
+    u = _validate_vector(u, dtype=utype)
+    v = _validate_vector(v, dtype=vtype)
+    u_v = u - v
+    u_v_w = u_v  # only want weights applied once
+    if w is not None:
+        w = _validate_weights(w)
+        u_v_w = w * u_v
+    return np.dot(u_v, u_v_w)
+
+
+def correlation(u, v, w=None, centered=True):
+    """
+    Compute the correlation distance between two 1-D arrays.
+
+    The correlation distance between `u` and `v`, is
+    defined as
+
+    .. math::
+
+        1 - \\frac{(u - \\bar{u}) \\cdot (v - \\bar{v})}
+                  {{\\|(u - \\bar{u})\\|}_2 {\\|(v - \\bar{v})\\|}_2}
+
+    where :math:`\\bar{u}` is the mean of the elements of `u`
+    and :math:`x \\cdot y` is the dot product of :math:`x` and :math:`y`.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+    centered : bool, optional
+        If True, `u` and `v` will be centered. Default is True.
+
+    Returns
+    -------
+    correlation : double
+        The correlation distance between 1-D array `u` and `v`.
+
+    Examples
+    --------
+    Find the correlation between two arrays.
+
+    >>> from scipy.spatial.distance import correlation
+    >>> correlation([1, 0, 1], [1, 1, 0])
+    1.5
+
+    Using a weighting array, the correlation can be calculated as:
+
+    >>> correlation([1, 0, 1], [1, 1, 0], w=[0.9, 0.1, 0.1])
+    1.1
+
+    If centering is not needed, the correlation can be calculated as:
+
+    >>> correlation([1, 0, 1], [1, 1, 0], centered=False)
+    0.5
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+        w = w / w.sum()
+    if centered:
+        if w is not None:
+            umu = np.dot(u, w)
+            vmu = np.dot(v, w)
+        else:
+            umu = np.mean(u)
+            vmu = np.mean(v)
+        u = u - umu
+        v = v - vmu
+    if w is not None:
+        vw = v * w
+        uw = u * w
+    else:
+        vw, uw = v, u
+    uv = np.dot(u, vw)
+    uu = np.dot(u, uw)
+    vv = np.dot(v, vw)
+    dist = 1.0 - uv / math.sqrt(uu * vv)
+    # Clip the result to avoid rounding error
+    return np.clip(dist, 0.0, 2.0)
+
+
+def cosine(u, v, w=None):
+    """
+    Compute the Cosine distance between 1-D arrays.
+
+    The Cosine distance between `u` and `v`, is defined as
+
+    .. math::
+
+        1 - \\frac{u \\cdot v}
+                  {\\|u\\|_2 \\|v\\|_2}.
+
+    where :math:`u \\cdot v` is the dot product of :math:`u` and
+    :math:`v`.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    cosine : double
+        The Cosine distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.cosine([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.cosine([100, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.cosine([1, 1, 0], [0, 1, 0])
+    0.29289321881345254
+
+    """
+    # cosine distance is also referred to as 'uncentered correlation',
+    #   or 'reflective correlation'
+    return correlation(u, v, w=w, centered=False)
+
+
+def hamming(u, v, w=None):
+    """
+    Compute the Hamming distance between two 1-D arrays.
+
+    The Hamming distance between 1-D arrays `u` and `v`, is simply the
+    proportion of disagreeing components in `u` and `v`. If `u` and `v` are
+    boolean vectors, the Hamming distance is
+
+    .. math::
+
+       \\frac{c_{01} + c_{10}}{n}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n`.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    hamming : double
+        The Hamming distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.hamming([1, 0, 0], [0, 1, 0])
+    0.66666666666666663
+    >>> distance.hamming([1, 0, 0], [1, 1, 0])
+    0.33333333333333331
+    >>> distance.hamming([1, 0, 0], [2, 0, 0])
+    0.33333333333333331
+    >>> distance.hamming([1, 0, 0], [3, 0, 0])
+    0.33333333333333331
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if u.shape != v.shape:
+        raise ValueError('The 1d arrays must have equal lengths.')
+    u_ne_v = u != v
+    if w is not None:
+        w = _validate_weights(w)
+        if w.shape != u.shape:
+            raise ValueError("'w' should have the same length as 'u' and 'v'.")
+        w = w / w.sum()
+        return np.dot(u_ne_v, w)
+    return np.mean(u_ne_v)
+
+
+def jaccard(u, v, w=None):
+    """
+    Compute the Jaccard-Needham dissimilarity between two boolean 1-D arrays.
+
+    The Jaccard-Needham dissimilarity between 1-D boolean arrays `u` and `v`,
+    is defined as
+
+    .. math::
+
+       \\frac{c_{TF} + c_{FT}}
+            {c_{TT} + c_{FT} + c_{TF}}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    jaccard : double
+        The Jaccard distance between vectors `u` and `v`.
+
+    Notes
+    -----
+    When both `u` and `v` lead to a `0/0` division i.e. there is no overlap
+    between the items in the vectors the returned distance is 0. See the
+    Wikipedia page on the Jaccard index [1]_, and this paper [2]_.
+
+    .. versionchanged:: 1.2.0
+        Previously, when `u` and `v` lead to a `0/0` division, the function
+        would return NaN. This was changed to return 0 instead.
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Jaccard_index
+    .. [2] S. Kosub, "A note on the triangle inequality for the Jaccard
+       distance", 2016, :arxiv:`1612.02696`
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.jaccard([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.jaccard([1, 0, 0], [1, 1, 0])
+    0.5
+    >>> distance.jaccard([1, 0, 0], [1, 2, 0])
+    0.5
+    >>> distance.jaccard([1, 0, 0], [1, 1, 1])
+    0.66666666666666663
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+
+    nonzero = np.bitwise_or(u != 0, v != 0)
+    unequal_nonzero = np.bitwise_and((u != v), nonzero)
+    if w is not None:
+        w = _validate_weights(w)
+        nonzero = w * nonzero
+        unequal_nonzero = w * unequal_nonzero
+    a = np.float64(unequal_nonzero.sum())
+    b = np.float64(nonzero.sum())
+    return (a / b) if b != 0 else 0
+
+
+def kulczynski1(u, v, *, w=None):
+    """
+    Compute the Kulczynski 1 dissimilarity between two boolean 1-D arrays.
+
+    The Kulczynski 1 dissimilarity between two boolean 1-D arrays `u` and `v`
+    of length ``n``, is defined as
+
+    .. math::
+
+         \\frac{c_{11}}
+              {c_{01} + c_{10}}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k \\in {0, 1, ..., n-1}`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    kulczynski1 : float
+        The Kulczynski 1 distance between vectors `u` and `v`.
+
+    Notes
+    -----
+    This measure has a minimum value of 0 and no upper limit.
+    It is un-defined when there are no non-matches.
+
+    .. versionadded:: 1.8.0
+
+    References
+    ----------
+    .. [1] Kulczynski S. et al. Bulletin
+           International de l'Academie Polonaise des Sciences
+           et des Lettres, Classe des Sciences Mathematiques
+           et Naturelles, Serie B (Sciences Naturelles). 1927;
+           Supplement II: 57-203.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.kulczynski1([1, 0, 0], [0, 1, 0])
+    0.0
+    >>> distance.kulczynski1([True, False, False], [True, True, False])
+    1.0
+    >>> distance.kulczynski1([True, False, False], [True])
+    0.5
+    >>> distance.kulczynski1([1, 0, 0], [3, 1, 0])
+    -3.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+    (_, nft, ntf, ntt) = _nbool_correspond_all(u, v, w=w)
+
+    return ntt / (ntf + nft)
+
+
+def seuclidean(u, v, V):
+    """
+    Return the standardized Euclidean distance between two 1-D arrays.
+
+    The standardized Euclidean distance between two n-vectors `u` and `v` is
+
+    .. math::
+
+       \\sqrt{\\sum\\limits_i \\frac{1}{V_i} \\left(u_i-v_i \\right)^2}
+
+    ``V`` is the variance vector; ``V[I]`` is the variance computed over all the i-th
+    components of the points. If not passed, it is automatically computed.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    V : (N,) array_like
+        `V` is an 1-D array of component variances. It is usually computed
+        among a larger collection vectors.
+
+    Returns
+    -------
+    seuclidean : double
+        The standardized Euclidean distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.seuclidean([1, 0, 0], [0, 1, 0], [0.1, 0.1, 0.1])
+    4.4721359549995796
+    >>> distance.seuclidean([1, 0, 0], [0, 1, 0], [1, 0.1, 0.1])
+    3.3166247903553998
+    >>> distance.seuclidean([1, 0, 0], [0, 1, 0], [10, 0.1, 0.1])
+    3.1780497164141406
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    V = _validate_vector(V, dtype=np.float64)
+    if V.shape[0] != u.shape[0] or u.shape[0] != v.shape[0]:
+        raise TypeError('V must be a 1-D array of the same dimension '
+                        'as u and v.')
+    return euclidean(u, v, w=1/V)
+
+
+def cityblock(u, v, w=None):
+    """
+    Compute the City Block (Manhattan) distance.
+
+    Computes the Manhattan distance between two 1-D arrays `u` and `v`,
+    which is defined as
+
+    .. math::
+
+       \\sum_i {\\left| u_i - v_i \\right|}.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    cityblock : double
+        The City Block (Manhattan) distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.cityblock([1, 0, 0], [0, 1, 0])
+    2
+    >>> distance.cityblock([1, 0, 0], [0, 2, 0])
+    3
+    >>> distance.cityblock([1, 0, 0], [1, 1, 0])
+    1
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    l1_diff = abs(u - v)
+    if w is not None:
+        w = _validate_weights(w)
+        l1_diff = w * l1_diff
+    return l1_diff.sum()
+
+
+def mahalanobis(u, v, VI):
+    """
+    Compute the Mahalanobis distance between two 1-D arrays.
+
+    The Mahalanobis distance between 1-D arrays `u` and `v`, is defined as
+
+    .. math::
+
+       \\sqrt{ (u-v) V^{-1} (u-v)^T }
+
+    where ``V`` is the covariance matrix.  Note that the argument `VI`
+    is the inverse of ``V``.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    VI : array_like
+        The inverse of the covariance matrix.
+
+    Returns
+    -------
+    mahalanobis : double
+        The Mahalanobis distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> iv = [[1, 0.5, 0.5], [0.5, 1, 0.5], [0.5, 0.5, 1]]
+    >>> distance.mahalanobis([1, 0, 0], [0, 1, 0], iv)
+    1.0
+    >>> distance.mahalanobis([0, 2, 0], [0, 1, 0], iv)
+    1.0
+    >>> distance.mahalanobis([2, 0, 0], [0, 1, 0], iv)
+    1.7320508075688772
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    VI = np.atleast_2d(VI)
+    delta = u - v
+    m = np.dot(np.dot(delta, VI), delta)
+    return np.sqrt(m)
+
+
+def chebyshev(u, v, w=None):
+    """
+    Compute the Chebyshev distance.
+
+    Computes the Chebyshev distance between two 1-D arrays `u` and `v`,
+    which is defined as
+
+    .. math::
+
+       \\max_i {|u_i-v_i|}.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input vector.
+    v : (N,) array_like
+        Input vector.
+    w : (N,) array_like, optional
+        Unused, as 'max' is a weightless operation. Here for API consistency.
+
+    Returns
+    -------
+    chebyshev : double
+        The Chebyshev distance between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.chebyshev([1, 0, 0], [0, 1, 0])
+    1
+    >>> distance.chebyshev([1, 1, 0], [0, 1, 0])
+    1
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+        has_weight = w > 0
+        if has_weight.sum() < w.size:
+            u = u[has_weight]
+            v = v[has_weight]
+    return max(abs(u - v))
+
+
+def braycurtis(u, v, w=None):
+    """
+    Compute the Bray-Curtis distance between two 1-D arrays.
+
+    Bray-Curtis distance is defined as
+
+    .. math::
+
+       \\sum{|u_i-v_i|} / \\sum{|u_i+v_i|}
+
+    The Bray-Curtis distance is in the range [0, 1] if all coordinates are
+    positive, and is undefined if the inputs are of length zero.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    braycurtis : double
+        The Bray-Curtis distance between 1-D arrays `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.braycurtis([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.braycurtis([1, 1, 0], [0, 1, 0])
+    0.33333333333333331
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v, dtype=np.float64)
+    l1_diff = abs(u - v)
+    l1_sum = abs(u + v)
+    if w is not None:
+        w = _validate_weights(w)
+        l1_diff = w * l1_diff
+        l1_sum = w * l1_sum
+    return l1_diff.sum() / l1_sum.sum()
+
+
+def canberra(u, v, w=None):
+    """
+    Compute the Canberra distance between two 1-D arrays.
+
+    The Canberra distance is defined as
+
+    .. math::
+
+         d(u,v) = \\sum_i \\frac{|u_i-v_i|}
+                              {|u_i|+|v_i|}.
+
+    Parameters
+    ----------
+    u : (N,) array_like
+        Input array.
+    v : (N,) array_like
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    canberra : double
+        The Canberra distance between vectors `u` and `v`.
+
+    Notes
+    -----
+    When `u[i]` and `v[i]` are 0 for given i, then the fraction 0/0 = 0 is
+    used in the calculation.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.canberra([1, 0, 0], [0, 1, 0])
+    2.0
+    >>> distance.canberra([1, 1, 0], [0, 1, 0])
+    1.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v, dtype=np.float64)
+    if w is not None:
+        w = _validate_weights(w)
+    with np.errstate(invalid='ignore'):
+        abs_uv = abs(u - v)
+        abs_u = abs(u)
+        abs_v = abs(v)
+        d = abs_uv / (abs_u + abs_v)
+        if w is not None:
+            d = w * d
+        d = np.nansum(d)
+    return d
+
+
+def jensenshannon(p, q, base=None, *, axis=0, keepdims=False):
+    """
+    Compute the Jensen-Shannon distance (metric) between
+    two probability arrays. This is the square root
+    of the Jensen-Shannon divergence.
+
+    The Jensen-Shannon distance between two probability
+    vectors `p` and `q` is defined as,
+
+    .. math::
+
+       \\sqrt{\\frac{D(p \\parallel m) + D(q \\parallel m)}{2}}
+
+    where :math:`m` is the pointwise mean of :math:`p` and :math:`q`
+    and :math:`D` is the Kullback-Leibler divergence.
+
+    This routine will normalize `p` and `q` if they don't sum to 1.0.
+
+    Parameters
+    ----------
+    p : (N,) array_like
+        left probability vector
+    q : (N,) array_like
+        right probability vector
+    base : double, optional
+        the base of the logarithm used to compute the output
+        if not given, then the routine uses the default base of
+        scipy.stats.entropy.
+    axis : int, optional
+        Axis along which the Jensen-Shannon distances are computed. The default
+        is 0.
+
+        .. versionadded:: 1.7.0
+    keepdims : bool, optional
+        If this is set to `True`, the reduced axes are left in the
+        result as dimensions with size one. With this option,
+        the result will broadcast correctly against the input array.
+        Default is False.
+
+        .. versionadded:: 1.7.0
+
+    Returns
+    -------
+    js : double or ndarray
+        The Jensen-Shannon distances between `p` and `q` along the `axis`.
+
+    Notes
+    -----
+
+    .. versionadded:: 1.2.0
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> import numpy as np
+    >>> distance.jensenshannon([1.0, 0.0, 0.0], [0.0, 1.0, 0.0], 2.0)
+    1.0
+    >>> distance.jensenshannon([1.0, 0.0], [0.5, 0.5])
+    0.46450140402245893
+    >>> distance.jensenshannon([1.0, 0.0, 0.0], [1.0, 0.0, 0.0])
+    0.0
+    >>> a = np.array([[1, 2, 3, 4],
+    ...               [5, 6, 7, 8],
+    ...               [9, 10, 11, 12]])
+    >>> b = np.array([[13, 14, 15, 16],
+    ...               [17, 18, 19, 20],
+    ...               [21, 22, 23, 24]])
+    >>> distance.jensenshannon(a, b, axis=0)
+    array([0.1954288, 0.1447697, 0.1138377, 0.0927636])
+    >>> distance.jensenshannon(a, b, axis=1)
+    array([0.1402339, 0.0399106, 0.0201815])
+
+    """
+    p = np.asarray(p)
+    q = np.asarray(q)
+    p = p / np.sum(p, axis=axis, keepdims=True)
+    q = q / np.sum(q, axis=axis, keepdims=True)
+    m = (p + q) / 2.0
+    left = rel_entr(p, m)
+    right = rel_entr(q, m)
+    left_sum = np.sum(left, axis=axis, keepdims=keepdims)
+    right_sum = np.sum(right, axis=axis, keepdims=keepdims)
+    js = left_sum + right_sum
+    if base is not None:
+        js /= np.log(base)
+    return np.sqrt(js / 2.0)
+
+
+def yule(u, v, w=None):
+    """
+    Compute the Yule dissimilarity between two boolean 1-D arrays.
+
+    The Yule dissimilarity is defined as
+
+    .. math::
+
+         \\frac{R}{c_{TT} * c_{FF} + \\frac{R}{2}}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n` and :math:`R = 2.0 * c_{TF} * c_{FT}`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    yule : double
+        The Yule dissimilarity between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.yule([1, 0, 0], [0, 1, 0])
+    2.0
+    >>> distance.yule([1, 1, 0], [0, 1, 0])
+    0.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+    (nff, nft, ntf, ntt) = _nbool_correspond_all(u, v, w=w)
+    half_R = ntf * nft
+    if half_R == 0:
+        return 0.0
+    else:
+        return float(2.0 * half_R / (ntt * nff + half_R))
+
+
+def dice(u, v, w=None):
+    """
+    Compute the Dice dissimilarity between two boolean 1-D arrays.
+
+    The Dice dissimilarity between `u` and `v`, is
+
+    .. math::
+
+         \\frac{c_{TF} + c_{FT}}
+              {2c_{TT} + c_{FT} + c_{TF}}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input 1-D array.
+    v : (N,) array_like, bool
+        Input 1-D array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    dice : double
+        The Dice dissimilarity between 1-D arrays `u` and `v`.
+
+    Notes
+    -----
+    This function computes the Dice dissimilarity index. To compute the
+    Dice similarity index, convert one to the other with similarity =
+    1 - dissimilarity.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.dice([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.dice([1, 0, 0], [1, 1, 0])
+    0.3333333333333333
+    >>> distance.dice([1, 0, 0], [2, 0, 0])
+    -0.3333333333333333
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+    if u.dtype == v.dtype == bool and w is None:
+        ntt = (u & v).sum()
+    else:
+        dtype = np.result_type(int, u.dtype, v.dtype)
+        u = u.astype(dtype)
+        v = v.astype(dtype)
+        if w is None:
+            ntt = (u * v).sum()
+        else:
+            ntt = (u * v * w).sum()
+    (nft, ntf) = _nbool_correspond_ft_tf(u, v, w=w)
+    return float((ntf + nft) / np.array(2.0 * ntt + ntf + nft))
+
+
+def rogerstanimoto(u, v, w=None):
+    """
+    Compute the Rogers-Tanimoto dissimilarity between two boolean 1-D arrays.
+
+    The Rogers-Tanimoto dissimilarity between two boolean 1-D arrays
+    `u` and `v`, is defined as
+
+    .. math::
+       \\frac{R}
+            {c_{TT} + c_{FF} + R}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n` and :math:`R = 2(c_{TF} + c_{FT})`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    rogerstanimoto : double
+        The Rogers-Tanimoto dissimilarity between vectors
+        `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.rogerstanimoto([1, 0, 0], [0, 1, 0])
+    0.8
+    >>> distance.rogerstanimoto([1, 0, 0], [1, 1, 0])
+    0.5
+    >>> distance.rogerstanimoto([1, 0, 0], [2, 0, 0])
+    -1.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+    (nff, nft, ntf, ntt) = _nbool_correspond_all(u, v, w=w)
+    return float(2.0 * (ntf + nft)) / float(ntt + nff + (2.0 * (ntf + nft)))
+
+
+def russellrao(u, v, w=None):
+    """
+    Compute the Russell-Rao dissimilarity between two boolean 1-D arrays.
+
+    The Russell-Rao dissimilarity between two boolean 1-D arrays, `u` and
+    `v`, is defined as
+
+    .. math::
+
+      \\frac{n - c_{TT}}
+           {n}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    russellrao : double
+        The Russell-Rao dissimilarity between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.russellrao([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.russellrao([1, 0, 0], [1, 1, 0])
+    0.6666666666666666
+    >>> distance.russellrao([1, 0, 0], [2, 0, 0])
+    0.3333333333333333
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if u.dtype == v.dtype == bool and w is None:
+        ntt = (u & v).sum()
+        n = float(len(u))
+    elif w is None:
+        ntt = (u * v).sum()
+        n = float(len(u))
+    else:
+        w = _validate_weights(w)
+        ntt = (u * v * w).sum()
+        n = w.sum()
+    return float(n - ntt) / n
+
+
+def sokalmichener(u, v, w=None):
+    """
+    Compute the Sokal-Michener dissimilarity between two boolean 1-D arrays.
+
+    The Sokal-Michener dissimilarity between boolean 1-D arrays `u` and `v`,
+    is defined as
+
+    .. math::
+
+       \\frac{R}
+            {S + R}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n`, :math:`R = 2 * (c_{TF} + c_{FT})` and
+    :math:`S = c_{FF} + c_{TT}`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    sokalmichener : double
+        The Sokal-Michener dissimilarity between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.sokalmichener([1, 0, 0], [0, 1, 0])
+    0.8
+    >>> distance.sokalmichener([1, 0, 0], [1, 1, 0])
+    0.5
+    >>> distance.sokalmichener([1, 0, 0], [2, 0, 0])
+    -1.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if w is not None:
+        w = _validate_weights(w)
+    nff, nft, ntf, ntt = _nbool_correspond_all(u, v, w=w)
+    return float(2.0 * (ntf + nft)) / float(ntt + nff + 2.0 * (ntf + nft))
+
+
+def sokalsneath(u, v, w=None):
+    """
+    Compute the Sokal-Sneath dissimilarity between two boolean 1-D arrays.
+
+    The Sokal-Sneath dissimilarity between `u` and `v`,
+
+    .. math::
+
+       \\frac{R}
+            {c_{TT} + R}
+
+    where :math:`c_{ij}` is the number of occurrences of
+    :math:`\\mathtt{u[k]} = i` and :math:`\\mathtt{v[k]} = j` for
+    :math:`k < n` and :math:`R = 2(c_{TF} + c_{FT})`.
+
+    Parameters
+    ----------
+    u : (N,) array_like, bool
+        Input array.
+    v : (N,) array_like, bool
+        Input array.
+    w : (N,) array_like, optional
+        The weights for each value in `u` and `v`. Default is None,
+        which gives each value a weight of 1.0
+
+    Returns
+    -------
+    sokalsneath : double
+        The Sokal-Sneath dissimilarity between vectors `u` and `v`.
+
+    Examples
+    --------
+    >>> from scipy.spatial import distance
+    >>> distance.sokalsneath([1, 0, 0], [0, 1, 0])
+    1.0
+    >>> distance.sokalsneath([1, 0, 0], [1, 1, 0])
+    0.66666666666666663
+    >>> distance.sokalsneath([1, 0, 0], [2, 1, 0])
+    0.0
+    >>> distance.sokalsneath([1, 0, 0], [3, 1, 0])
+    -2.0
+
+    """
+    u = _validate_vector(u)
+    v = _validate_vector(v)
+    if u.dtype == v.dtype == bool and w is None:
+        ntt = (u & v).sum()
+    elif w is None:
+        ntt = (u * v).sum()
+    else:
+        w = _validate_weights(w)
+        ntt = (u * v * w).sum()
+    (nft, ntf) = _nbool_correspond_ft_tf(u, v, w=w)
+    denom = np.array(ntt + 2.0 * (ntf + nft))
+    if not denom.any():
+        raise ValueError('Sokal-Sneath dissimilarity is not defined for '
+                         'vectors that are entirely false.')
+    return float(2.0 * (ntf + nft)) / denom
+
+
+_convert_to_double = partial(_convert_to_type, out_type=np.float64)
+_convert_to_bool = partial(_convert_to_type, out_type=bool)
+
+# adding python-only wrappers to _distance_wrap module
+_distance_wrap.pdist_correlation_double_wrap = _correlation_pdist_wrap
+_distance_wrap.cdist_correlation_double_wrap = _correlation_cdist_wrap
+
+
+@dataclasses.dataclass(frozen=True)
+class CDistMetricWrapper:
+    metric_name: str
+
+    def __call__(self, XA, XB, *, out=None, **kwargs):
+        XA = np.ascontiguousarray(XA)
+        XB = np.ascontiguousarray(XB)
+        mA, n = XA.shape
+        mB, _ = XB.shape
+        metric_name = self.metric_name
+        metric_info = _METRICS[metric_name]
+        XA, XB, typ, kwargs = _validate_cdist_input(
+            XA, XB, mA, mB, n, metric_info, **kwargs)
+
+        w = kwargs.pop('w', None)
+        if w is not None:
+            metric = metric_info.dist_func
+            return _cdist_callable(
+                XA, XB, metric=metric, out=out, w=w, **kwargs)
+
+        dm = _prepare_out_argument(out, np.float64, (mA, mB))
+        # get cdist wrapper
+        cdist_fn = getattr(_distance_wrap, f'cdist_{metric_name}_{typ}_wrap')
+        cdist_fn(XA, XB, dm, **kwargs)
+        return dm
+
+
+@dataclasses.dataclass(frozen=True)
+class PDistMetricWrapper:
+    metric_name: str
+
+    def __call__(self, X, *, out=None, **kwargs):
+        X = np.ascontiguousarray(X)
+        m, n = X.shape
+        metric_name = self.metric_name
+        metric_info = _METRICS[metric_name]
+        X, typ, kwargs = _validate_pdist_input(
+            X, m, n, metric_info, **kwargs)
+        out_size = (m * (m - 1)) // 2
+        w = kwargs.pop('w', None)
+        if w is not None:
+            metric = metric_info.dist_func
+            return _pdist_callable(
+                X, metric=metric, out=out, w=w, **kwargs)
+
+        dm = _prepare_out_argument(out, np.float64, (out_size,))
+        # get pdist wrapper
+        pdist_fn = getattr(_distance_wrap, f'pdist_{metric_name}_{typ}_wrap')
+        pdist_fn(X, dm, **kwargs)
+        return dm
+
+
+@dataclasses.dataclass(frozen=True)
+class MetricInfo:
+    # Name of python distance function
+    canonical_name: str
+    # All aliases, including canonical_name
+    aka: set[str]
+    # unvectorized distance function
+    dist_func: Callable
+    # Optimized cdist function
+    cdist_func: Callable
+    # Optimized pdist function
+    pdist_func: Callable
+    # function that checks kwargs and computes default values:
+    # f(X, m, n, **kwargs)
+    validator: Optional[Callable] = None
+    # list of supported types:
+    # X (pdist) and XA (cdist) are used to choose the type. if there is no
+    # match the first type is used. Default double
+    types: list[str] = dataclasses.field(default_factory=lambda: ['double'])
+    # true if out array must be C-contiguous
+    requires_contiguous_out: bool = True
+
+
+# Registry of implemented metrics:
+_METRIC_INFOS = [
+    MetricInfo(
+        canonical_name='braycurtis',
+        aka={'braycurtis'},
+        dist_func=braycurtis,
+        cdist_func=_distance_pybind.cdist_braycurtis,
+        pdist_func=_distance_pybind.pdist_braycurtis,
+    ),
+    MetricInfo(
+        canonical_name='canberra',
+        aka={'canberra'},
+        dist_func=canberra,
+        cdist_func=_distance_pybind.cdist_canberra,
+        pdist_func=_distance_pybind.pdist_canberra,
+    ),
+    MetricInfo(
+        canonical_name='chebyshev',
+        aka={'chebychev', 'chebyshev', 'cheby', 'cheb', 'ch'},
+        dist_func=chebyshev,
+        cdist_func=_distance_pybind.cdist_chebyshev,
+        pdist_func=_distance_pybind.pdist_chebyshev,
+    ),
+    MetricInfo(
+        canonical_name='cityblock',
+        aka={'cityblock', 'cblock', 'cb', 'c'},
+        dist_func=cityblock,
+        cdist_func=_distance_pybind.cdist_cityblock,
+        pdist_func=_distance_pybind.pdist_cityblock,
+    ),
+    MetricInfo(
+        canonical_name='correlation',
+        aka={'correlation', 'co'},
+        dist_func=correlation,
+        cdist_func=CDistMetricWrapper('correlation'),
+        pdist_func=PDistMetricWrapper('correlation'),
+    ),
+    MetricInfo(
+        canonical_name='cosine',
+        aka={'cosine', 'cos'},
+        dist_func=cosine,
+        cdist_func=CDistMetricWrapper('cosine'),
+        pdist_func=PDistMetricWrapper('cosine'),
+    ),
+    MetricInfo(
+        canonical_name='dice',
+        aka={'dice'},
+        types=['bool'],
+        dist_func=dice,
+        cdist_func=_distance_pybind.cdist_dice,
+        pdist_func=_distance_pybind.pdist_dice,
+    ),
+    MetricInfo(
+        canonical_name='euclidean',
+        aka={'euclidean', 'euclid', 'eu', 'e'},
+        dist_func=euclidean,
+        cdist_func=_distance_pybind.cdist_euclidean,
+        pdist_func=_distance_pybind.pdist_euclidean,
+    ),
+    MetricInfo(
+        canonical_name='hamming',
+        aka={'matching', 'hamming', 'hamm', 'ha', 'h'},
+        types=['double', 'bool'],
+        validator=_validate_hamming_kwargs,
+        dist_func=hamming,
+        cdist_func=_distance_pybind.cdist_hamming,
+        pdist_func=_distance_pybind.pdist_hamming,
+    ),
+    MetricInfo(
+        canonical_name='jaccard',
+        aka={'jaccard', 'jacc', 'ja', 'j'},
+        types=['double', 'bool'],
+        dist_func=jaccard,
+        cdist_func=_distance_pybind.cdist_jaccard,
+        pdist_func=_distance_pybind.pdist_jaccard,
+    ),
+    MetricInfo(
+        canonical_name='jensenshannon',
+        aka={'jensenshannon', 'js'},
+        dist_func=jensenshannon,
+        cdist_func=CDistMetricWrapper('jensenshannon'),
+        pdist_func=PDistMetricWrapper('jensenshannon'),
+    ),
+    MetricInfo(
+        canonical_name='kulczynski1',
+        aka={'kulczynski1'},
+        types=['bool'],
+        dist_func=kulczynski1,
+        cdist_func=_distance_pybind.cdist_kulczynski1,
+        pdist_func=_distance_pybind.pdist_kulczynski1,
+    ),
+    MetricInfo(
+        canonical_name='mahalanobis',
+        aka={'mahalanobis', 'mahal', 'mah'},
+        validator=_validate_mahalanobis_kwargs,
+        dist_func=mahalanobis,
+        cdist_func=CDistMetricWrapper('mahalanobis'),
+        pdist_func=PDistMetricWrapper('mahalanobis'),
+    ),
+    MetricInfo(
+        canonical_name='minkowski',
+        aka={'minkowski', 'mi', 'm', 'pnorm'},
+        validator=_validate_minkowski_kwargs,
+        dist_func=minkowski,
+        cdist_func=_distance_pybind.cdist_minkowski,
+        pdist_func=_distance_pybind.pdist_minkowski,
+    ),
+    MetricInfo(
+        canonical_name='rogerstanimoto',
+        aka={'rogerstanimoto'},
+        types=['bool'],
+        dist_func=rogerstanimoto,
+        cdist_func=_distance_pybind.cdist_rogerstanimoto,
+        pdist_func=_distance_pybind.pdist_rogerstanimoto,
+    ),
+    MetricInfo(
+        canonical_name='russellrao',
+        aka={'russellrao'},
+        types=['bool'],
+        dist_func=russellrao,
+        cdist_func=_distance_pybind.cdist_russellrao,
+        pdist_func=_distance_pybind.pdist_russellrao,
+    ),
+    MetricInfo(
+        canonical_name='seuclidean',
+        aka={'seuclidean', 'se', 's'},
+        validator=_validate_seuclidean_kwargs,
+        dist_func=seuclidean,
+        cdist_func=CDistMetricWrapper('seuclidean'),
+        pdist_func=PDistMetricWrapper('seuclidean'),
+    ),
+    MetricInfo(
+        canonical_name='sokalmichener',
+        aka={'sokalmichener'},
+        types=['bool'],
+        dist_func=sokalmichener,
+        cdist_func=_distance_pybind.cdist_sokalmichener,
+        pdist_func=_distance_pybind.pdist_sokalmichener,
+    ),
+    MetricInfo(
+        canonical_name='sokalsneath',
+        aka={'sokalsneath'},
+        types=['bool'],
+        dist_func=sokalsneath,
+        cdist_func=_distance_pybind.cdist_sokalsneath,
+        pdist_func=_distance_pybind.pdist_sokalsneath,
+    ),
+    MetricInfo(
+        canonical_name='sqeuclidean',
+        aka={'sqeuclidean', 'sqe', 'sqeuclid'},
+        dist_func=sqeuclidean,
+        cdist_func=_distance_pybind.cdist_sqeuclidean,
+        pdist_func=_distance_pybind.pdist_sqeuclidean,
+    ),
+    MetricInfo(
+        canonical_name='yule',
+        aka={'yule'},
+        types=['bool'],
+        dist_func=yule,
+        cdist_func=_distance_pybind.cdist_yule,
+        pdist_func=_distance_pybind.pdist_yule,
+    ),
+]
+
+_METRICS = {info.canonical_name: info for info in _METRIC_INFOS}
+_METRIC_ALIAS = {alias: info
+                     for info in _METRIC_INFOS
+                     for alias in info.aka}
+
+_METRICS_NAMES = list(_METRICS.keys())
+
+_TEST_METRICS = {'test_' + info.canonical_name: info for info in _METRIC_INFOS}
+
+
+def pdist(X, metric='euclidean', *, out=None, **kwargs):
+    """
+    Pairwise distances between observations in n-dimensional space.
+
+    See Notes for common calling conventions.
+
+    Parameters
+    ----------
+    X : array_like
+        An m by n array of m original observations in an
+        n-dimensional space.
+    metric : str or function, optional
+        The distance metric to use. The distance function can
+        be 'braycurtis', 'canberra', 'chebyshev', 'cityblock',
+        'correlation', 'cosine', 'dice', 'euclidean', 'hamming',
+        'jaccard', 'jensenshannon', 'kulczynski1',
+        'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto',
+        'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath',
+        'sqeuclidean', 'yule'.
+    out : ndarray, optional
+        The output array.
+        If not None, condensed distance matrix Y is stored in this array.
+    **kwargs : dict, optional
+        Extra arguments to `metric`: refer to each metric documentation for a
+        list of all possible arguments.
+
+        Some possible arguments:
+
+        p : scalar
+        The p-norm to apply for Minkowski, weighted and unweighted.
+        Default: 2.
+
+        w : ndarray
+        The weight vector for metrics that support weights (e.g., Minkowski).
+
+        V : ndarray
+        The variance vector for standardized Euclidean.
+        Default: var(X, axis=0, ddof=1)
+
+        VI : ndarray
+        The inverse of the covariance matrix for Mahalanobis.
+        Default: inv(cov(X.T)).T
+
+    Returns
+    -------
+    Y : ndarray
+        Returns a condensed distance matrix Y. For each :math:`i` and :math:`j`
+        (where :math:`i<j<m`),where m is the number of original observations.
+        The metric ``dist(u=X[i], v=X[j])`` is computed and stored in entry ``m
+        * i + j - ((i + 2) * (i + 1)) // 2``.
+
+    See Also
+    --------
+    squareform : converts between condensed distance matrices and
+                 square distance matrices.
+
+    Notes
+    -----
+    See ``squareform`` for information on how to calculate the index of
+    this entry or to convert the condensed distance matrix to a
+    redundant square matrix.
+
+    The following are common calling conventions.
+
+    1. ``Y = pdist(X, 'euclidean')``
+
+       Computes the distance between m points using Euclidean distance
+       (2-norm) as the distance metric between the points. The points
+       are arranged as m n-dimensional row vectors in the matrix X.
+
+    2. ``Y = pdist(X, 'minkowski', p=2.)``
+
+       Computes the distances using the Minkowski distance
+       :math:`\\|u-v\\|_p` (:math:`p`-norm) where :math:`p > 0` (note
+       that this is only a quasi-metric if :math:`0 < p < 1`).
+
+    3. ``Y = pdist(X, 'cityblock')``
+
+       Computes the city block or Manhattan distance between the
+       points.
+
+    4. ``Y = pdist(X, 'seuclidean', V=None)``
+
+       Computes the standardized Euclidean distance. The standardized
+       Euclidean distance between two n-vectors ``u`` and ``v`` is
+
+       .. math::
+
+          \\sqrt{\\sum {(u_i-v_i)^2 / V[x_i]}}
+
+
+       V is the variance vector; V[i] is the variance computed over all
+       the i'th components of the points.  If not passed, it is
+       automatically computed.
+
+    5. ``Y = pdist(X, 'sqeuclidean')``
+
+       Computes the squared Euclidean distance :math:`\\|u-v\\|_2^2` between
+       the vectors.
+
+    6. ``Y = pdist(X, 'cosine')``
+
+       Computes the cosine distance between vectors u and v,
+
+       .. math::
+
+          1 - \\frac{u \\cdot v}
+                   {{\\|u\\|}_2 {\\|v\\|}_2}
+
+       where :math:`\\|*\\|_2` is the 2-norm of its argument ``*``, and
+       :math:`u \\cdot v` is the dot product of ``u`` and ``v``.
+
+    7. ``Y = pdist(X, 'correlation')``
+
+       Computes the correlation distance between vectors u and v. This is
+
+       .. math::
+
+          1 - \\frac{(u - \\bar{u}) \\cdot (v - \\bar{v})}
+                   {{\\|(u - \\bar{u})\\|}_2 {\\|(v - \\bar{v})\\|}_2}
+
+       where :math:`\\bar{v}` is the mean of the elements of vector v,
+       and :math:`x \\cdot y` is the dot product of :math:`x` and :math:`y`.
+
+    8. ``Y = pdist(X, 'hamming')``
+
+       Computes the normalized Hamming distance, or the proportion of
+       those vector elements between two n-vectors ``u`` and ``v``
+       which disagree. To save memory, the matrix ``X`` can be of type
+       boolean.
+
+    9. ``Y = pdist(X, 'jaccard')``
+
+       Computes the Jaccard distance between the points. Given two
+       vectors, ``u`` and ``v``, the Jaccard distance is the
+       proportion of those elements ``u[i]`` and ``v[i]`` that
+       disagree.
+
+    10. ``Y = pdist(X, 'jensenshannon')``
+
+        Computes the Jensen-Shannon distance between two probability arrays.
+        Given two probability vectors, :math:`p` and :math:`q`, the
+        Jensen-Shannon distance is
+
+        .. math::
+
+           \\sqrt{\\frac{D(p \\parallel m) + D(q \\parallel m)}{2}}
+
+        where :math:`m` is the pointwise mean of :math:`p` and :math:`q`
+        and :math:`D` is the Kullback-Leibler divergence.
+
+    11. ``Y = pdist(X, 'chebyshev')``
+
+        Computes the Chebyshev distance between the points. The
+        Chebyshev distance between two n-vectors ``u`` and ``v`` is the
+        maximum norm-1 distance between their respective elements. More
+        precisely, the distance is given by
+
+        .. math::
+
+           d(u,v) = \\max_i {|u_i-v_i|}
+
+    12. ``Y = pdist(X, 'canberra')``
+
+        Computes the Canberra distance between the points. The
+        Canberra distance between two points ``u`` and ``v`` is
+
+        .. math::
+
+          d(u,v) = \\sum_i \\frac{|u_i-v_i|}
+                               {|u_i|+|v_i|}
+
+
+    13. ``Y = pdist(X, 'braycurtis')``
+
+        Computes the Bray-Curtis distance between the points. The
+        Bray-Curtis distance between two points ``u`` and ``v`` is
+
+
+        .. math::
+
+             d(u,v) = \\frac{\\sum_i {|u_i-v_i|}}
+                            {\\sum_i {|u_i+v_i|}}
+
+    14. ``Y = pdist(X, 'mahalanobis', VI=None)``
+
+        Computes the Mahalanobis distance between the points. The
+        Mahalanobis distance between two points ``u`` and ``v`` is
+        :math:`\\sqrt{(u-v)(1/V)(u-v)^T}` where :math:`(1/V)` (the ``VI``
+        variable) is the inverse covariance. If ``VI`` is not None,
+        ``VI`` will be used as the inverse covariance matrix.
+
+    15. ``Y = pdist(X, 'yule')``
+
+        Computes the Yule distance between each pair of boolean
+        vectors. (see yule function documentation)
+
+    16. ``Y = pdist(X, 'matching')``
+
+        Synonym for 'hamming'.
+
+    17. ``Y = pdist(X, 'dice')``
+
+        Computes the Dice distance between each pair of boolean
+        vectors. (see dice function documentation)
+
+    18. ``Y = pdist(X, 'kulczynski1')``
+
+        Computes the kulczynski1 distance between each pair of
+        boolean vectors. (see kulczynski1 function documentation)
+
+    19. ``Y = pdist(X, 'rogerstanimoto')``
+
+        Computes the Rogers-Tanimoto distance between each pair of
+        boolean vectors. (see rogerstanimoto function documentation)
+
+    20. ``Y = pdist(X, 'russellrao')``
+
+        Computes the Russell-Rao distance between each pair of
+        boolean vectors. (see russellrao function documentation)
+
+    21. ``Y = pdist(X, 'sokalmichener')``
+
+        Computes the Sokal-Michener distance between each pair of
+        boolean vectors. (see sokalmichener function documentation)
+
+    22. ``Y = pdist(X, 'sokalsneath')``
+
+        Computes the Sokal-Sneath distance between each pair of
+        boolean vectors. (see sokalsneath function documentation)
+
+    23. ``Y = pdist(X, 'kulczynski1')``
+
+        Computes the Kulczynski 1 distance between each pair of
+        boolean vectors. (see kulczynski1 function documentation)
+
+    24. ``Y = pdist(X, f)``
+
+        Computes the distance between all pairs of vectors in X
+        using the user supplied 2-arity function f. For example,
+        Euclidean distance between the vectors could be computed
+        as follows::
+
+          dm = pdist(X, lambda u, v: np.sqrt(((u-v)**2).sum()))
+
+        Note that you should avoid passing a reference to one of
+        the distance functions defined in this library. For example,::
+
+          dm = pdist(X, sokalsneath)
+
+        would calculate the pair-wise distances between the vectors in
+        X using the Python function sokalsneath. This would result in
+        sokalsneath being called :math:`{n \\choose 2}` times, which
+        is inefficient. Instead, the optimized C version is more
+        efficient, and we call it using the following syntax.::
+
+          dm = pdist(X, 'sokalsneath')
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.spatial.distance import pdist
+
+    ``x`` is an array of five points in three-dimensional space.
+
+    >>> x = np.array([[2, 0, 2], [2, 2, 3], [-2, 4, 5], [0, 1, 9], [2, 2, 4]])
+
+    ``pdist(x)`` with no additional arguments computes the 10 pairwise
+    Euclidean distances:
+
+    >>> pdist(x)
+    array([2.23606798, 6.40312424, 7.34846923, 2.82842712, 4.89897949,
+           6.40312424, 1.        , 5.38516481, 4.58257569, 5.47722558])
+
+    The following computes the pairwise Minkowski distances with ``p = 3.5``:
+
+    >>> pdist(x, metric='minkowski', p=3.5)
+    array([2.04898923, 5.1154929 , 7.02700737, 2.43802731, 4.19042714,
+           6.03956994, 1.        , 4.45128103, 4.10636143, 5.0619695 ])
+
+    The pairwise city block or Manhattan distances:
+
+    >>> pdist(x, metric='cityblock')
+    array([ 3., 11., 10.,  4.,  8.,  9.,  1.,  9.,  7.,  8.])
+
+    """
+    # You can also call this as:
+    #     Y = pdist(X, 'test_abc')
+    # where 'abc' is the metric being tested.  This computes the distance
+    # between all pairs of vectors in X using the distance metric 'abc' but
+    # with a more succinct, verifiable, but less efficient implementation.
+
+    X = _asarray_validated(X, sparse_ok=False, objects_ok=True, mask_ok=True,
+                           check_finite=False)
+
+    s = X.shape
+    if len(s) != 2:
+        raise ValueError('A 2-dimensional array must be passed.')
+
+    m, n = s
+
+    if callable(metric):
+        mstr = getattr(metric, '__name__', 'UnknownCustomMetric')
+        metric_info = _METRIC_ALIAS.get(mstr, None)
+
+        if metric_info is not None:
+            X, typ, kwargs = _validate_pdist_input(
+                X, m, n, metric_info, **kwargs)
+
+        return _pdist_callable(X, metric=metric, out=out, **kwargs)
+    elif isinstance(metric, str):
+        mstr = metric.lower()
+        metric_info = _METRIC_ALIAS.get(mstr, None)
+
+        if metric_info is not None:
+            pdist_fn = metric_info.pdist_func
+            return pdist_fn(X, out=out, **kwargs)
+        elif mstr.startswith("test_"):
+            metric_info = _TEST_METRICS.get(mstr, None)
+            if metric_info is None:
+                raise ValueError(f'Unknown "Test" Distance Metric: {mstr[5:]}')
+            X, typ, kwargs = _validate_pdist_input(
+                X, m, n, metric_info, **kwargs)
+            return _pdist_callable(
+                X, metric=metric_info.dist_func, out=out, **kwargs)
+        else:
+            raise ValueError('Unknown Distance Metric: %s' % mstr)
+    else:
+        raise TypeError('2nd argument metric must be a string identifier '
+                        'or a function.')
+
+
+def squareform(X, force="no", checks=True):
+    """
+    Convert a vector-form distance vector to a square-form distance
+    matrix, and vice-versa.
+
+    Parameters
+    ----------
+    X : array_like
+        Either a condensed or redundant distance matrix.
+    force : str, optional
+        As with MATLAB(TM), if force is equal to ``'tovector'`` or
+        ``'tomatrix'``, the input will be treated as a distance matrix or
+        distance vector respectively.
+    checks : bool, optional
+        If set to False, no checks will be made for matrix
+        symmetry nor zero diagonals. This is useful if it is known that
+        ``X - X.T1`` is small and ``diag(X)`` is close to zero.
+        These values are ignored any way so they do not disrupt the
+        squareform transformation.
+
+    Returns
+    -------
+    Y : ndarray
+        If a condensed distance matrix is passed, a redundant one is
+        returned, or if a redundant one is passed, a condensed distance
+        matrix is returned.
+
+    Notes
+    -----
+    1. ``v = squareform(X)``
+
+       Given a square n-by-n symmetric distance matrix ``X``,
+       ``v = squareform(X)`` returns a ``n * (n-1) / 2``
+       (i.e. binomial coefficient n choose 2) sized vector `v`
+       where :math:`v[{n \\choose 2} - {n-i \\choose 2} + (j-i-1)]`
+       is the distance between distinct points ``i`` and ``j``.
+       If ``X`` is non-square or asymmetric, an error is raised.
+
+    2. ``X = squareform(v)``
+
+       Given a ``n * (n-1) / 2`` sized vector ``v``
+       for some integer ``n >= 1`` encoding distances as described,
+       ``X = squareform(v)`` returns a n-by-n distance matrix ``X``.
+       The ``X[i, j]`` and ``X[j, i]`` values are set to
+       :math:`v[{n \\choose 2} - {n-i \\choose 2} + (j-i-1)]`
+       and all diagonal elements are zero.
+
+    In SciPy 0.19.0, ``squareform`` stopped casting all input types to
+    float64, and started returning arrays of the same dtype as the input.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.spatial.distance import pdist, squareform
+
+    ``x`` is an array of five points in three-dimensional space.
+
+    >>> x = np.array([[2, 0, 2], [2, 2, 3], [-2, 4, 5], [0, 1, 9], [2, 2, 4]])
+
+    ``pdist(x)`` computes the Euclidean distances between each pair of
+    points in ``x``.  The distances are returned in a one-dimensional
+    array with length ``5*(5 - 1)/2 = 10``.
+
+    >>> distvec = pdist(x)
+    >>> distvec
+    array([2.23606798, 6.40312424, 7.34846923, 2.82842712, 4.89897949,
+           6.40312424, 1.        , 5.38516481, 4.58257569, 5.47722558])
+
+    ``squareform(distvec)`` returns the 5x5 distance matrix.
+
+    >>> m = squareform(distvec)
+    >>> m
+    array([[0.        , 2.23606798, 6.40312424, 7.34846923, 2.82842712],
+           [2.23606798, 0.        , 4.89897949, 6.40312424, 1.        ],
+           [6.40312424, 4.89897949, 0.        , 5.38516481, 4.58257569],
+           [7.34846923, 6.40312424, 5.38516481, 0.        , 5.47722558],
+           [2.82842712, 1.        , 4.58257569, 5.47722558, 0.        ]])
+
+    When given a square distance matrix ``m``, ``squareform(m)`` returns
+    the one-dimensional condensed distance vector associated with the
+    matrix.  In this case, we recover ``distvec``.
+
+    >>> squareform(m)
+    array([2.23606798, 6.40312424, 7.34846923, 2.82842712, 4.89897949,
+           6.40312424, 1.        , 5.38516481, 4.58257569, 5.47722558])
+    """
+    X = np.ascontiguousarray(X)
+
+    s = X.shape
+
+    if force.lower() == 'tomatrix':
+        if len(s) != 1:
+            raise ValueError("Forcing 'tomatrix' but input X is not a "
+                             "distance vector.")
+    elif force.lower() == 'tovector':
+        if len(s) != 2:
+            raise ValueError("Forcing 'tovector' but input X is not a "
+                             "distance matrix.")
+
+    # X = squareform(v)
+    if len(s) == 1:
+        if s[0] == 0:
+            return np.zeros((1, 1), dtype=X.dtype)
+
+        # Grab the closest value to the square root of the number
+        # of elements times 2 to see if the number of elements
+        # is indeed a binomial coefficient.
+        d = int(np.ceil(np.sqrt(s[0] * 2)))
+
+        # Check that v is of valid dimensions.
+        if d * (d - 1) != s[0] * 2:
+            raise ValueError('Incompatible vector size. It must be a binomial '
+                             'coefficient n choose 2 for some integer n >= 2.')
+
+        # Allocate memory for the distance matrix.
+        M = np.zeros((d, d), dtype=X.dtype)
+
+        # Since the C code does not support striding using strides.
+        # The dimensions are used instead.
+        X = _copy_array_if_base_present(X)
+
+        # Fill in the values of the distance matrix.
+        _distance_wrap.to_squareform_from_vector_wrap(M, X)
+
+        # Return the distance matrix.
+        return M
+    elif len(s) == 2:
+        if s[0] != s[1]:
+            raise ValueError('The matrix argument must be square.')
+        if checks:
+            is_valid_dm(X, throw=True, name='X')
+
+        # One-side of the dimensions is set here.
+        d = s[0]
+
+        if d <= 1:
+            return np.array([], dtype=X.dtype)
+
+        # Create a vector.
+        v = np.zeros((d * (d - 1)) // 2, dtype=X.dtype)
+
+        # Since the C code does not support striding using strides.
+        # The dimensions are used instead.
+        X = _copy_array_if_base_present(X)
+
+        # Convert the vector to squareform.
+        _distance_wrap.to_vector_from_squareform_wrap(X, v)
+        return v
+    else:
+        raise ValueError(('The first argument must be one or two dimensional '
+                          'array. A %d-dimensional array is not '
+                          'permitted') % len(s))
+
+
+def is_valid_dm(D, tol=0.0, throw=False, name="D", warning=False):
+    """
+    Return True if input array is a valid distance matrix.
+
+    Distance matrices must be 2-dimensional numpy arrays.
+    They must have a zero-diagonal, and they must be symmetric.
+
+    Parameters
+    ----------
+    D : array_like
+        The candidate object to test for validity.
+    tol : float, optional
+        The distance matrix should be symmetric. `tol` is the maximum
+        difference between entries ``ij`` and ``ji`` for the distance
+        metric to be considered symmetric.
+    throw : bool, optional
+        An exception is thrown if the distance matrix passed is not valid.
+    name : str, optional
+        The name of the variable to checked. This is useful if
+        throw is set to True so the offending variable can be identified
+        in the exception message when an exception is thrown.
+    warning : bool, optional
+        Instead of throwing an exception, a warning message is
+        raised.
+
+    Returns
+    -------
+    valid : bool
+        True if the variable `D` passed is a valid distance matrix.
+
+    Notes
+    -----
+    Small numerical differences in `D` and `D.T` and non-zeroness of
+    the diagonal are ignored if they are within the tolerance specified
+    by `tol`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.spatial.distance import is_valid_dm
+
+    This matrix is a valid distance matrix.
+
+    >>> d = np.array([[0.0, 1.1, 1.2, 1.3],
+    ...               [1.1, 0.0, 1.0, 1.4],
+    ...               [1.2, 1.0, 0.0, 1.5],
+    ...               [1.3, 1.4, 1.5, 0.0]])
+    >>> is_valid_dm(d)
+    True
+
+    In the following examples, the input is not a valid distance matrix.
+
+    Not square:
+
+    >>> is_valid_dm([[0, 2, 2], [2, 0, 2]])
+    False
+
+    Nonzero diagonal element:
+
+    >>> is_valid_dm([[0, 1, 1], [1, 2, 3], [1, 3, 0]])
+    False
+
+    Not symmetric:
+
+    >>> is_valid_dm([[0, 1, 3], [2, 0, 1], [3, 1, 0]])
+    False
+
+    """
+    D = np.asarray(D, order='c')
+    valid = True
+    try:
+        s = D.shape
+        if len(D.shape) != 2:
+            if name:
+                raise ValueError(('Distance matrix \'%s\' must have shape=2 '
+                                  '(i.e. be two-dimensional).') % name)
+            else:
+                raise ValueError('Distance matrix must have shape=2 (i.e. '
+                                 'be two-dimensional).')
+        if tol == 0.0:
+            if not (D == D.T).all():
+                if name:
+                    raise ValueError(('Distance matrix \'%s\' must be '
+                                     'symmetric.') % name)
+                else:
+                    raise ValueError('Distance matrix must be symmetric.')
+            if not (D[range(0, s[0]), range(0, s[0])] == 0).all():
+                if name:
+                    raise ValueError(('Distance matrix \'%s\' diagonal must '
+                                      'be zero.') % name)
+                else:
+                    raise ValueError('Distance matrix diagonal must be zero.')
+        else:
+            if not (D - D.T <= tol).all():
+                if name:
+                    raise ValueError(f'Distance matrix \'{name}\' must be '
+                                     f'symmetric within tolerance {tol:5.5f}.')
+                else:
+                    raise ValueError('Distance matrix must be symmetric within '
+                                     'tolerance %5.5f.' % tol)
+            if not (D[range(0, s[0]), range(0, s[0])] <= tol).all():
+                if name:
+                    raise ValueError(f'Distance matrix \'{name}\' diagonal must be '
+                                     f'close to zero within tolerance {tol:5.5f}.')
+                else:
+                    raise ValueError(('Distance matrix \'{}\' diagonal must be close '
+                                      'to zero within tolerance {:5.5f}.').format(*tol))
+    except Exception as e:
+        if throw:
+            raise
+        if warning:
+            warnings.warn(str(e), stacklevel=2)
+        valid = False
+    return valid
+
+
+def is_valid_y(y, warning=False, throw=False, name=None):
+    """
+    Return True if the input array is a valid condensed distance matrix.
+
+    Condensed distance matrices must be 1-dimensional numpy arrays.
+    Their length must be a binomial coefficient :math:`{n \\choose 2}`
+    for some positive integer n.
+
+    Parameters
+    ----------
+    y : array_like
+        The condensed distance matrix.
+    warning : bool, optional
+        Invokes a warning if the variable passed is not a valid
+        condensed distance matrix. The warning message explains why
+        the distance matrix is not valid.  `name` is used when
+        referencing the offending variable.
+    throw : bool, optional
+        Throws an exception if the variable passed is not a valid
+        condensed distance matrix.
+    name : bool, optional
+        Used when referencing the offending variable in the
+        warning or exception message.
+
+    Returns
+    -------
+    bool
+        True if the input array is a valid condensed distance matrix,
+        False otherwise.
+
+    Examples
+    --------
+    >>> from scipy.spatial.distance import is_valid_y
+
+    This vector is a valid condensed distance matrix.  The length is 6,
+    which corresponds to ``n = 4``, since ``4*(4 - 1)/2`` is 6.
+
+    >>> v = [1.0, 1.2, 1.0, 0.5, 1.3, 0.9]
+    >>> is_valid_y(v)
+    True
+
+    An input vector with length, say, 7, is not a valid condensed distance
+    matrix.
+
+    >>> is_valid_y([1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7])
+    False
+
+    """
+    y = np.asarray(y, order='c')
+    valid = True
+    try:
+        if len(y.shape) != 1:
+            if name:
+                raise ValueError(('Condensed distance matrix \'%s\' must '
+                                  'have shape=1 (i.e. be one-dimensional).')
+                                 % name)
+            else:
+                raise ValueError('Condensed distance matrix must have shape=1 '
+                                 '(i.e. be one-dimensional).')
+        n = y.shape[0]
+        d = int(np.ceil(np.sqrt(n * 2)))
+        if (d * (d - 1) / 2) != n:
+            if name:
+                raise ValueError(('Length n of condensed distance matrix '
+                                  '\'%s\' must be a binomial coefficient, i.e.'
+                                  'there must be a k such that '
+                                  '(k \\choose 2)=n)!') % name)
+            else:
+                raise ValueError('Length n of condensed distance matrix must '
+                                 'be a binomial coefficient, i.e. there must '
+                                 'be a k such that (k \\choose 2)=n)!')
+    except Exception as e:
+        if throw:
+            raise
+        if warning:
+            warnings.warn(str(e), stacklevel=2)
+        valid = False
+    return valid
+
+
+def num_obs_dm(d):
+    """
+    Return the number of original observations that correspond to a
+    square, redundant distance matrix.
+
+    Parameters
+    ----------
+    d : array_like
+        The target distance matrix.
+
+    Returns
+    -------
+    num_obs_dm : int
+        The number of observations in the redundant distance matrix.
+
+    Examples
+    --------
+    Find the number of original observations corresponding
+    to a square redundant distance matrix d.
+    
+    >>> from scipy.spatial.distance import num_obs_dm
+    >>> d = [[0, 100, 200], [100, 0, 150], [200, 150, 0]]
+    >>> num_obs_dm(d)
+    3
+    """
+    d = np.asarray(d, order='c')
+    is_valid_dm(d, tol=np.inf, throw=True, name='d')
+    return d.shape[0]
+
+
+def num_obs_y(Y):
+    """
+    Return the number of original observations that correspond to a
+    condensed distance matrix.
+
+    Parameters
+    ----------
+    Y : array_like
+        Condensed distance matrix.
+
+    Returns
+    -------
+    n : int
+        The number of observations in the condensed distance matrix `Y`.
+
+    Examples
+    --------
+    Find the number of original observations corresponding to a
+    condensed distance matrix Y.
+    
+    >>> from scipy.spatial.distance import num_obs_y
+    >>> Y = [1, 2, 3.5, 7, 10, 4]
+    >>> num_obs_y(Y)
+    4
+    """
+    Y = np.asarray(Y, order='c')
+    is_valid_y(Y, throw=True, name='Y')
+    k = Y.shape[0]
+    if k == 0:
+        raise ValueError("The number of observations cannot be determined on "
+                         "an empty distance matrix.")
+    d = int(np.ceil(np.sqrt(k * 2)))
+    if (d * (d - 1) / 2) != k:
+        raise ValueError("Invalid condensed distance matrix passed. Must be "
+                         "some k where k=(n choose 2) for some n >= 2.")
+    return d
+
+
+def _prepare_out_argument(out, dtype, expected_shape):
+    if out is None:
+        return np.empty(expected_shape, dtype=dtype)
+
+    if out.shape != expected_shape:
+        raise ValueError("Output array has incorrect shape.")
+    if not out.flags.c_contiguous:
+        raise ValueError("Output array must be C-contiguous.")
+    if out.dtype != np.float64:
+        raise ValueError("Output array must be double type.")
+    return out
+
+
+def _pdist_callable(X, *, out, metric, **kwargs):
+    n = X.shape[0]
+    out_size = (n * (n - 1)) // 2
+    dm = _prepare_out_argument(out, np.float64, (out_size,))
+    k = 0
+    for i in range(X.shape[0] - 1):
+        for j in range(i + 1, X.shape[0]):
+            dm[k] = metric(X[i], X[j], **kwargs)
+            k += 1
+    return dm
+
+
+def _cdist_callable(XA, XB, *, out, metric, **kwargs):
+    mA = XA.shape[0]
+    mB = XB.shape[0]
+    dm = _prepare_out_argument(out, np.float64, (mA, mB))
+    for i in range(mA):
+        for j in range(mB):
+            dm[i, j] = metric(XA[i], XB[j], **kwargs)
+    return dm
+
+
+def cdist(XA, XB, metric='euclidean', *, out=None, **kwargs):
+    """
+    Compute distance between each pair of the two collections of inputs.
+
+    See Notes for common calling conventions.
+
+    Parameters
+    ----------
+    XA : array_like
+        An :math:`m_A` by :math:`n` array of :math:`m_A`
+        original observations in an :math:`n`-dimensional space.
+        Inputs are converted to float type.
+    XB : array_like
+        An :math:`m_B` by :math:`n` array of :math:`m_B`
+        original observations in an :math:`n`-dimensional space.
+        Inputs are converted to float type.
+    metric : str or callable, optional
+        The distance metric to use. If a string, the distance function can be
+        'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation',
+        'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon',
+        'kulczynski1', 'mahalanobis', 'matching', 'minkowski',
+        'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener',
+        'sokalsneath', 'sqeuclidean', 'yule'.
+    **kwargs : dict, optional
+        Extra arguments to `metric`: refer to each metric documentation for a
+        list of all possible arguments.
+
+        Some possible arguments:
+
+        p : scalar
+        The p-norm to apply for Minkowski, weighted and unweighted.
+        Default: 2.
+
+        w : array_like
+        The weight vector for metrics that support weights (e.g., Minkowski).
+
+        V : array_like
+        The variance vector for standardized Euclidean.
+        Default: var(vstack([XA, XB]), axis=0, ddof=1)
+
+        VI : array_like
+        The inverse of the covariance matrix for Mahalanobis.
+        Default: inv(cov(vstack([XA, XB].T))).T
+
+        out : ndarray
+        The output array
+        If not None, the distance matrix Y is stored in this array.
+
+    Returns
+    -------
+    Y : ndarray
+        A :math:`m_A` by :math:`m_B` distance matrix is returned.
+        For each :math:`i` and :math:`j`, the metric
+        ``dist(u=XA[i], v=XB[j])`` is computed and stored in the
+        :math:`ij` th entry.
+
+    Raises
+    ------
+    ValueError
+        An exception is thrown if `XA` and `XB` do not have
+        the same number of columns.
+
+    Notes
+    -----
+    The following are common calling conventions:
+
+    1. ``Y = cdist(XA, XB, 'euclidean')``
+
+       Computes the distance between :math:`m` points using
+       Euclidean distance (2-norm) as the distance metric between the
+       points. The points are arranged as :math:`m`
+       :math:`n`-dimensional row vectors in the matrix X.
+
+    2. ``Y = cdist(XA, XB, 'minkowski', p=2.)``
+
+       Computes the distances using the Minkowski distance
+       :math:`\\|u-v\\|_p` (:math:`p`-norm) where :math:`p > 0` (note
+       that this is only a quasi-metric if :math:`0 < p < 1`).
+
+    3. ``Y = cdist(XA, XB, 'cityblock')``
+
+       Computes the city block or Manhattan distance between the
+       points.
+
+    4. ``Y = cdist(XA, XB, 'seuclidean', V=None)``
+
+       Computes the standardized Euclidean distance. The standardized
+       Euclidean distance between two n-vectors ``u`` and ``v`` is
+
+       .. math::
+
+          \\sqrt{\\sum {(u_i-v_i)^2 / V[x_i]}}.
+
+       V is the variance vector; V[i] is the variance computed over all
+       the i'th components of the points. If not passed, it is
+       automatically computed.
+
+    5. ``Y = cdist(XA, XB, 'sqeuclidean')``
+
+       Computes the squared Euclidean distance :math:`\\|u-v\\|_2^2` between
+       the vectors.
+
+    6. ``Y = cdist(XA, XB, 'cosine')``
+
+       Computes the cosine distance between vectors u and v,
+
+       .. math::
+
+          1 - \\frac{u \\cdot v}
+                   {{\\|u\\|}_2 {\\|v\\|}_2}
+
+       where :math:`\\|*\\|_2` is the 2-norm of its argument ``*``, and
+       :math:`u \\cdot v` is the dot product of :math:`u` and :math:`v`.
+
+    7. ``Y = cdist(XA, XB, 'correlation')``
+
+       Computes the correlation distance between vectors u and v. This is
+
+       .. math::
+
+          1 - \\frac{(u - \\bar{u}) \\cdot (v - \\bar{v})}
+                   {{\\|(u - \\bar{u})\\|}_2 {\\|(v - \\bar{v})\\|}_2}
+
+       where :math:`\\bar{v}` is the mean of the elements of vector v,
+       and :math:`x \\cdot y` is the dot product of :math:`x` and :math:`y`.
+
+
+    8. ``Y = cdist(XA, XB, 'hamming')``
+
+       Computes the normalized Hamming distance, or the proportion of
+       those vector elements between two n-vectors ``u`` and ``v``
+       which disagree. To save memory, the matrix ``X`` can be of type
+       boolean.
+
+    9. ``Y = cdist(XA, XB, 'jaccard')``
+
+       Computes the Jaccard distance between the points. Given two
+       vectors, ``u`` and ``v``, the Jaccard distance is the
+       proportion of those elements ``u[i]`` and ``v[i]`` that
+       disagree where at least one of them is non-zero.
+
+    10. ``Y = cdist(XA, XB, 'jensenshannon')``
+
+        Computes the Jensen-Shannon distance between two probability arrays.
+        Given two probability vectors, :math:`p` and :math:`q`, the
+        Jensen-Shannon distance is
+
+        .. math::
+
+           \\sqrt{\\frac{D(p \\parallel m) + D(q \\parallel m)}{2}}
+
+        where :math:`m` is the pointwise mean of :math:`p` and :math:`q`
+        and :math:`D` is the Kullback-Leibler divergence.
+
+    11. ``Y = cdist(XA, XB, 'chebyshev')``
+
+        Computes the Chebyshev distance between the points. The
+        Chebyshev distance between two n-vectors ``u`` and ``v`` is the
+        maximum norm-1 distance between their respective elements. More
+        precisely, the distance is given by
+
+        .. math::
+
+           d(u,v) = \\max_i {|u_i-v_i|}.
+
+    12. ``Y = cdist(XA, XB, 'canberra')``
+
+        Computes the Canberra distance between the points. The
+        Canberra distance between two points ``u`` and ``v`` is
+
+        .. math::
+
+          d(u,v) = \\sum_i \\frac{|u_i-v_i|}
+                               {|u_i|+|v_i|}.
+
+    13. ``Y = cdist(XA, XB, 'braycurtis')``
+
+        Computes the Bray-Curtis distance between the points. The
+        Bray-Curtis distance between two points ``u`` and ``v`` is
+
+
+        .. math::
+
+             d(u,v) = \\frac{\\sum_i (|u_i-v_i|)}
+                           {\\sum_i (|u_i+v_i|)}
+
+    14. ``Y = cdist(XA, XB, 'mahalanobis', VI=None)``
+
+        Computes the Mahalanobis distance between the points. The
+        Mahalanobis distance between two points ``u`` and ``v`` is
+        :math:`\\sqrt{(u-v)(1/V)(u-v)^T}` where :math:`(1/V)` (the ``VI``
+        variable) is the inverse covariance. If ``VI`` is not None,
+        ``VI`` will be used as the inverse covariance matrix.
+
+    15. ``Y = cdist(XA, XB, 'yule')``
+
+        Computes the Yule distance between the boolean
+        vectors. (see `yule` function documentation)
+
+    16. ``Y = cdist(XA, XB, 'matching')``
+
+        Synonym for 'hamming'.
+
+    17. ``Y = cdist(XA, XB, 'dice')``
+
+        Computes the Dice distance between the boolean vectors. (see
+        `dice` function documentation)
+
+    18. ``Y = cdist(XA, XB, 'kulczynski1')``
+
+        Computes the kulczynski distance between the boolean
+        vectors. (see `kulczynski1` function documentation)
+
+    19. ``Y = cdist(XA, XB, 'rogerstanimoto')``
+
+        Computes the Rogers-Tanimoto distance between the boolean
+        vectors. (see `rogerstanimoto` function documentation)
+
+    20. ``Y = cdist(XA, XB, 'russellrao')``
+
+        Computes the Russell-Rao distance between the boolean
+        vectors. (see `russellrao` function documentation)
+
+    21. ``Y = cdist(XA, XB, 'sokalmichener')``
+
+        Computes the Sokal-Michener distance between the boolean
+        vectors. (see `sokalmichener` function documentation)
+
+    22. ``Y = cdist(XA, XB, 'sokalsneath')``
+
+        Computes the Sokal-Sneath distance between the vectors. (see
+        `sokalsneath` function documentation)
+
+    23. ``Y = cdist(XA, XB, f)``
+
+        Computes the distance between all pairs of vectors in X
+        using the user supplied 2-arity function f. For example,
+        Euclidean distance between the vectors could be computed
+        as follows::
+
+          dm = cdist(XA, XB, lambda u, v: np.sqrt(((u-v)**2).sum()))
+
+        Note that you should avoid passing a reference to one of
+        the distance functions defined in this library. For example,::
+
+          dm = cdist(XA, XB, sokalsneath)
+
+        would calculate the pair-wise distances between the vectors in
+        X using the Python function `sokalsneath`. This would result in
+        sokalsneath being called :math:`{n \\choose 2}` times, which
+        is inefficient. Instead, the optimized C version is more
+        efficient, and we call it using the following syntax::
+
+          dm = cdist(XA, XB, 'sokalsneath')
+
+    Examples
+    --------
+    Find the Euclidean distances between four 2-D coordinates:
+
+    >>> from scipy.spatial import distance
+    >>> import numpy as np
+    >>> coords = [(35.0456, -85.2672),
+    ...           (35.1174, -89.9711),
+    ...           (35.9728, -83.9422),
+    ...           (36.1667, -86.7833)]
+    >>> distance.cdist(coords, coords, 'euclidean')
+    array([[ 0.    ,  4.7044,  1.6172,  1.8856],
+           [ 4.7044,  0.    ,  6.0893,  3.3561],
+           [ 1.6172,  6.0893,  0.    ,  2.8477],
+           [ 1.8856,  3.3561,  2.8477,  0.    ]])
+
+
+    Find the Manhattan distance from a 3-D point to the corners of the unit
+    cube:
+
+    >>> a = np.array([[0, 0, 0],
+    ...               [0, 0, 1],
+    ...               [0, 1, 0],
+    ...               [0, 1, 1],
+    ...               [1, 0, 0],
+    ...               [1, 0, 1],
+    ...               [1, 1, 0],
+    ...               [1, 1, 1]])
+    >>> b = np.array([[ 0.1,  0.2,  0.4]])
+    >>> distance.cdist(a, b, 'cityblock')
+    array([[ 0.7],
+           [ 0.9],
+           [ 1.3],
+           [ 1.5],
+           [ 1.5],
+           [ 1.7],
+           [ 2.1],
+           [ 2.3]])
+
+    """
+    # You can also call this as:
+    #     Y = cdist(XA, XB, 'test_abc')
+    # where 'abc' is the metric being tested.  This computes the distance
+    # between all pairs of vectors in XA and XB using the distance metric 'abc'
+    # but with a more succinct, verifiable, but less efficient implementation.
+
+    XA = np.asarray(XA)
+    XB = np.asarray(XB)
+
+    s = XA.shape
+    sB = XB.shape
+
+    if len(s) != 2:
+        raise ValueError('XA must be a 2-dimensional array.')
+    if len(sB) != 2:
+        raise ValueError('XB must be a 2-dimensional array.')
+    if s[1] != sB[1]:
+        raise ValueError('XA and XB must have the same number of columns '
+                         '(i.e. feature dimension.)')
+
+    mA = s[0]
+    mB = sB[0]
+    n = s[1]
+
+    if callable(metric):
+        mstr = getattr(metric, '__name__', 'Unknown')
+        metric_info = _METRIC_ALIAS.get(mstr, None)
+        if metric_info is not None:
+            XA, XB, typ, kwargs = _validate_cdist_input(
+                XA, XB, mA, mB, n, metric_info, **kwargs)
+        return _cdist_callable(XA, XB, metric=metric, out=out, **kwargs)
+    elif isinstance(metric, str):
+        mstr = metric.lower()
+        metric_info = _METRIC_ALIAS.get(mstr, None)
+        if metric_info is not None:
+            cdist_fn = metric_info.cdist_func
+            return cdist_fn(XA, XB, out=out, **kwargs)
+        elif mstr.startswith("test_"):
+            metric_info = _TEST_METRICS.get(mstr, None)
+            if metric_info is None:
+                raise ValueError(f'Unknown "Test" Distance Metric: {mstr[5:]}')
+            XA, XB, typ, kwargs = _validate_cdist_input(
+                XA, XB, mA, mB, n, metric_info, **kwargs)
+            return _cdist_callable(
+                XA, XB, metric=metric_info.dist_func, out=out, **kwargs)
+        else:
+            raise ValueError('Unknown Distance Metric: %s' % mstr)
+    else:
+        raise TypeError('2nd argument metric must be a string identifier '
+                        'or a function.')

env-llmeval/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: ...

env-llmeval/lib/python3.10/site-packages/scipy/spatial/kdtree.py

@@ -0,0 +1,26 @@
+# 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
+    'KDTree',
+    'Rectangle',
+    'cKDTree',
+    'cKDTreeNode',
+    'distance_matrix',
+    'minkowski_distance',
+    'minkowski_distance_p',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="spatial", module="kdtree",
+                                   private_modules=["_kdtree"], all=__all__,
+                                   attribute=name)

env-llmeval/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)

env-llmeval/lib/python3.10/site-packages/scipy/spatial/qhull_src/COPYING.txt

@@ -0,0 +1,38 @@
+                    Qhull, Copyright (c) 1993-2019
+                    
+                            C.B. Barber
+                           Arlington, MA 
+                          
+                               and
+
+       The National Science and Technology Research Center for
+        Computation and Visualization of Geometric Structures
+                        (The Geometry Center)
+                       University of Minnesota
+
+                       email: [email protected]
+
+This software includes Qhull from C.B. Barber and The Geometry Center.  
+Qhull is copyrighted as noted above.  Qhull is free software and may 
+be obtained via http from www.qhull.org.  It may be freely copied, modified, 
+and redistributed under the following conditions:
+
+1. All copyright notices must remain intact in all files.
+
+2. A copy of this text file must be distributed along with any copies 
+   of Qhull that you redistribute; this includes copies that you have 
+   modified, or copies of programs or other software products that 
+   include Qhull.
+
+3. If you modify Qhull, you must include a notice giving the
+   name of the person performing the modification, the date of
+   modification, and the reason for such modification.
+
+4. When distributing modified versions of Qhull, or other software 
+   products that include Qhull, you must provide notice that the original 
+   source code may be obtained as noted above.
+
+5. There is no warranty or other guarantee of fitness for Qhull, it is 
+   provided solely "as is".  Bug reports or fixes may be sent to 
+   [email protected]; the authors may or may not act on them as 
+   they desire.

env-llmeval/lib/python3.10/site-packages/scipy/spatial/transform/__init__.py

@@ -0,0 +1,29 @@
+"""
+Spatial Transformations (:mod:`scipy.spatial.transform`)
+========================================================
+
+.. currentmodule:: scipy.spatial.transform
+
+This package implements various spatial transformations. For now,
+only rotations are supported.
+
+Rotations in 3 dimensions
+-------------------------
+.. autosummary::
+   :toctree: generated/
+
+   Rotation
+   Slerp
+   RotationSpline
+"""
+from ._rotation import Rotation, Slerp
+from ._rotation_spline import RotationSpline
+
+# Deprecated namespaces, to be removed in v2.0.0
+from . import rotation
+
+__all__ = ['Rotation', 'Slerp', 'RotationSpline']
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

env-llmeval/lib/python3.10/site-packages/scipy/spatial/transform/_rotation_groups.py

@@ -0,0 +1,140 @@
+import numpy as np
+from scipy.constants import golden as phi
+
+
+def icosahedral(cls):
+    g1 = tetrahedral(cls).as_quat()
+    a = 0.5
+    b = 0.5 / phi
+    c = phi / 2
+    g2 = np.array([[+a, +b, +c, 0],
+                   [+a, +b, -c, 0],
+                   [+a, +c, 0, +b],
+                   [+a, +c, 0, -b],
+                   [+a, -b, +c, 0],
+                   [+a, -b, -c, 0],
+                   [+a, -c, 0, +b],
+                   [+a, -c, 0, -b],
+                   [+a, 0, +b, +c],
+                   [+a, 0, +b, -c],
+                   [+a, 0, -b, +c],
+                   [+a, 0, -b, -c],
+                   [+b, +a, 0, +c],
+                   [+b, +a, 0, -c],
+                   [+b, +c, +a, 0],
+                   [+b, +c, -a, 0],
+                   [+b, -a, 0, +c],
+                   [+b, -a, 0, -c],
+                   [+b, -c, +a, 0],
+                   [+b, -c, -a, 0],
+                   [+b, 0, +c, +a],
+                   [+b, 0, +c, -a],
+                   [+b, 0, -c, +a],
+                   [+b, 0, -c, -a],
+                   [+c, +a, +b, 0],
+                   [+c, +a, -b, 0],
+                   [+c, +b, 0, +a],
+                   [+c, +b, 0, -a],
+                   [+c, -a, +b, 0],
+                   [+c, -a, -b, 0],
+                   [+c, -b, 0, +a],
+                   [+c, -b, 0, -a],
+                   [+c, 0, +a, +b],
+                   [+c, 0, +a, -b],
+                   [+c, 0, -a, +b],
+                   [+c, 0, -a, -b],
+                   [0, +a, +c, +b],
+                   [0, +a, +c, -b],
+                   [0, +a, -c, +b],
+                   [0, +a, -c, -b],
+                   [0, +b, +a, +c],
+                   [0, +b, +a, -c],
+                   [0, +b, -a, +c],
+                   [0, +b, -a, -c],
+                   [0, +c, +b, +a],
+                   [0, +c, +b, -a],
+                   [0, +c, -b, +a],
+                   [0, +c, -b, -a]])
+    return cls.from_quat(np.concatenate((g1, g2)))
+
+
+def octahedral(cls):
+    g1 = tetrahedral(cls).as_quat()
+    c = np.sqrt(2) / 2
+    g2 = np.array([[+c, 0, 0, +c],
+                   [0, +c, 0, +c],
+                   [0, 0, +c, +c],
+                   [0, 0, -c, +c],
+                   [0, -c, 0, +c],
+                   [-c, 0, 0, +c],
+                   [0, +c, +c, 0],
+                   [0, -c, +c, 0],
+                   [+c, 0, +c, 0],
+                   [-c, 0, +c, 0],
+                   [+c, +c, 0, 0],
+                   [-c, +c, 0, 0]])
+    return cls.from_quat(np.concatenate((g1, g2)))
+
+
+def tetrahedral(cls):
+    g1 = np.eye(4)
+    c = 0.5
+    g2 = np.array([[c, -c, -c, +c],
+                   [c, -c, +c, +c],
+                   [c, +c, -c, +c],
+                   [c, +c, +c, +c],
+                   [c, -c, -c, -c],
+                   [c, -c, +c, -c],
+                   [c, +c, -c, -c],
+                   [c, +c, +c, -c]])
+    return cls.from_quat(np.concatenate((g1, g2)))
+
+
+def dicyclic(cls, n, axis=2):
+    g1 = cyclic(cls, n, axis).as_rotvec()
+
+    thetas = np.linspace(0, np.pi, n, endpoint=False)
+    rv = np.pi * np.vstack([np.zeros(n), np.cos(thetas), np.sin(thetas)]).T
+    g2 = np.roll(rv, axis, axis=1)
+    return cls.from_rotvec(np.concatenate((g1, g2)))
+
+
+def cyclic(cls, n, axis=2):
+    thetas = np.linspace(0, 2 * np.pi, n, endpoint=False)
+    rv = np.vstack([thetas, np.zeros(n), np.zeros(n)]).T
+    return cls.from_rotvec(np.roll(rv, axis, axis=1))
+
+
+def create_group(cls, group, axis='Z'):
+    if not isinstance(group, str):
+        raise ValueError("`group` argument must be a string")
+
+    permitted_axes = ['x', 'y', 'z', 'X', 'Y', 'Z']
+    if axis not in permitted_axes:
+        raise ValueError("`axis` must be one of " + ", ".join(permitted_axes))
+
+    if group in ['I', 'O', 'T']:
+        symbol = group
+        order = 1
+    elif group[:1] in ['C', 'D'] and group[1:].isdigit():
+        symbol = group[:1]
+        order = int(group[1:])
+    else:
+        raise ValueError("`group` must be one of 'I', 'O', 'T', 'Dn', 'Cn'")
+
+    if order < 1:
+        raise ValueError("Group order must be positive")
+
+    axis = 'xyz'.index(axis.lower())
+    if symbol == 'I':
+        return icosahedral(cls)
+    elif symbol == 'O':
+        return octahedral(cls)
+    elif symbol == 'T':
+        return tetrahedral(cls)
+    elif symbol == 'D':
+        return dicyclic(cls, order, axis=axis)
+    elif symbol == 'C':
+        return cyclic(cls, order, axis=axis)
+    else:
+        assert False

env-llmeval/lib/python3.10/site-packages/scipy/special/_precompute/cosine_cdf.py

@@ -0,0 +1,17 @@
+import mpmath
+
+
+def f(x):
+    return (mpmath.pi + x + mpmath.sin(x)) / (2*mpmath.pi)
+
+
+# Note: 40 digits might be overkill; a few more digits than the default
+# might be sufficient.
+mpmath.mp.dps = 40
+ts = mpmath.taylor(f, -mpmath.pi, 20)
+p, q = mpmath.pade(ts, 9, 10)
+
+p = [float(c) for c in p]
+q = [float(c) for c in q]
+print('p =', p)
+print('q =', q)

env-llmeval/lib/python3.10/site-packages/scipy/special/_precompute/expn_asy.py

@@ -0,0 +1,54 @@
+"""Precompute the polynomials for the asymptotic expansion of the
+generalized exponential integral.
+
+Sources
+-------
+[1] NIST, Digital Library of Mathematical Functions,
+    https://dlmf.nist.gov/8.20#ii
+
+"""
+import os
+
+try:
+    import sympy
+    from sympy import Poly
+    x = sympy.symbols('x')
+except ImportError:
+    pass
+
+
+def generate_A(K):
+    A = [Poly(1, x)]
+    for k in range(K):
+        A.append(Poly(1 - 2*k*x, x)*A[k] + Poly(x*(x + 1))*A[k].diff())
+    return A
+
+
+WARNING = """\
+/* This file was automatically generated by _precompute/expn_asy.py.
+ * Do not edit it manually!
+ */
+"""
+
+
+def main():
+    print(__doc__)
+    fn = os.path.join('..', 'cephes', 'expn.h')
+
+    K = 12
+    A = generate_A(K)
+    with open(fn + '.new', 'w') as f:
+        f.write(WARNING)
+        f.write(f"#define nA {len(A)}\n")
+        for k, Ak in enumerate(A):
+            ', '.join([str(x.evalf(18)) for x in Ak.coeffs()])
+            f.write(f"static const double A{k}[] = {{tmp}};\n")
+        ", ".join([f"A{k}" for k in range(K + 1)])
+        f.write("static const double *A[] = {{tmp}};\n")
+        ", ".join([str(Ak.degree()) for Ak in A])
+        f.write("static const int Adegs[] = {{tmp}};\n")
+    os.rename(fn + '.new', fn)
+
+
+if __name__ == "__main__":
+    main()

env-llmeval/lib/python3.10/site-packages/scipy/special/_precompute/gammainc_asy.py

@@ -0,0 +1,116 @@
+"""
+Precompute coefficients of Temme's asymptotic expansion for gammainc.
+
+This takes about 8 hours to run on a 2.3 GHz Macbook Pro with 4GB ram.
+
+Sources:
+[1] NIST, "Digital Library of Mathematical Functions",
+    https://dlmf.nist.gov/
+
+"""
+import os
+from scipy.special._precompute.utils import lagrange_inversion
+
+try:
+    import mpmath as mp
+except ImportError:
+    pass
+
+
+def compute_a(n):
+    """a_k from DLMF 5.11.6"""
+    a = [mp.sqrt(2)/2]
+    for k in range(1, n):
+        ak = a[-1]/k
+        for j in range(1, len(a)):
+            ak -= a[j]*a[-j]/(j + 1)
+        ak /= a[0]*(1 + mp.mpf(1)/(k + 1))
+        a.append(ak)
+    return a
+
+
+def compute_g(n):
+    """g_k from DLMF 5.11.3/5.11.5"""
+    a = compute_a(2*n)
+    g = [mp.sqrt(2)*mp.rf(0.5, k)*a[2*k] for k in range(n)]
+    return g
+
+
+def eta(lam):
+    """Function from DLMF 8.12.1 shifted to be centered at 0."""
+    if lam > 0:
+        return mp.sqrt(2*(lam - mp.log(lam + 1)))
+    elif lam < 0:
+        return -mp.sqrt(2*(lam - mp.log(lam + 1)))
+    else:
+        return 0
+
+
+def compute_alpha(n):
+    """alpha_n from DLMF 8.12.13"""
+    coeffs = mp.taylor(eta, 0, n - 1)
+    return lagrange_inversion(coeffs)
+
+
+def compute_d(K, N):
+    """d_{k, n} from DLMF 8.12.12"""
+    M = N + 2*K
+    d0 = [-mp.mpf(1)/3]
+    alpha = compute_alpha(M + 2)
+    for n in range(1, M):
+        d0.append((n + 2)*alpha[n+2])
+    d = [d0]
+    g = compute_g(K)
+    for k in range(1, K):
+        dk = []
+        for n in range(M - 2*k):
+            dk.append((-1)**k*g[k]*d[0][n] + (n + 2)*d[k-1][n+2])
+        d.append(dk)
+    for k in range(K):
+        d[k] = d[k][:N]
+    return d
+
+
+header = \
+r"""/* This file was automatically generated by _precomp/gammainc.py.
+ * Do not edit it manually!
+ */
+
+#ifndef IGAM_H
+#define IGAM_H
+
+#define K {}
+#define N {}
+
+static const double d[K][N] =
+{{"""
+
+footer = \
+r"""
+#endif
+"""
+
+
+def main():
+    print(__doc__)
+    K = 25
+    N = 25
+    with mp.workdps(50):
+        d = compute_d(K, N)
+    fn = os.path.join(os.path.dirname(__file__), '..', 'cephes', 'igam.h')
+    with open(fn + '.new', 'w') as f:
+        f.write(header.format(K, N))
+        for k, row in enumerate(d):
+            row = [mp.nstr(x, 17, min_fixed=0, max_fixed=0) for x in row]
+            f.write('{')
+            f.write(", ".join(row))
+            if k < K - 1:
+                f.write('},\n')
+            else:
+                f.write('}};\n')
+        f.write(footer)
+    os.rename(fn + '.new', fn)
+
+
+if __name__ == "__main__":
+    main()

env-llmeval/lib/python3.10/site-packages/scipy/special/_precompute/gammainc_data.py

@@ -0,0 +1,124 @@
+"""Compute gammainc and gammaincc for large arguments and parameters
+and save the values to data files for use in tests. We can't just
+compare to mpmath's gammainc in test_mpmath.TestSystematic because it
+would take too long.
+
+Note that mpmath's gammainc is computed using hypercomb, but since it
+doesn't allow the user to increase the maximum number of terms used in
+the series it doesn't converge for many arguments. To get around this
+we copy the mpmath implementation but use more terms.
+
+This takes about 17 minutes to run on a 2.3 GHz Macbook Pro with 4GB
+ram.
+
+Sources:
+[1] Fredrik Johansson and others. mpmath: a Python library for
+    arbitrary-precision floating-point arithmetic (version 0.19),
+    December 2013. http://mpmath.org/.
+
+"""
+import os
+from time import time
+import numpy as np
+from numpy import pi
+
+from scipy.special._mptestutils import mpf2float
+
+try:
+    import mpmath as mp
+except ImportError:
+    pass
+
+
+def gammainc(a, x, dps=50, maxterms=10**8):
+    """Compute gammainc exactly like mpmath does but allow for more
+    summands in hypercomb. See
+
+    mpmath/functions/expintegrals.py#L134
+
+    in the mpmath github repository.
+
+    """
+    with mp.workdps(dps):
+        z, a, b = mp.mpf(a), mp.mpf(x), mp.mpf(x)
+        G = [z]
+        negb = mp.fneg(b, exact=True)
+
+        def h(z):
+            T1 = [mp.exp(negb), b, z], [1, z, -1], [], G, [1], [1+z], b
+            return (T1,)
+
+        res = mp.hypercomb(h, [z], maxterms=maxterms)
+        return mpf2float(res)
+
+
+def gammaincc(a, x, dps=50, maxterms=10**8):
+    """Compute gammaincc exactly like mpmath does but allow for more
+    terms in hypercomb. See
+
+    mpmath/functions/expintegrals.py#L187
+
+    in the mpmath github repository.
+
+    """
+    with mp.workdps(dps):
+        z, a = a, x
+
+        if mp.isint(z):
+            try:
+                # mpmath has a fast integer path
+                return mpf2float(mp.gammainc(z, a=a, regularized=True))
+            except mp.libmp.NoConvergence:
+                pass
+        nega = mp.fneg(a, exact=True)
+        G = [z]
+        # Use 2F0 series when possible; fall back to lower gamma representation
+        try:
+            def h(z):
+                r = z-1
+                return [([mp.exp(nega), a], [1, r], [], G, [1, -r], [], 1/nega)]
+            return mpf2float(mp.hypercomb(h, [z], force_series=True))
+        except mp.libmp.NoConvergence:
+            def h(z):
+                T1 = [], [1, z-1], [z], G, [], [], 0
+                T2 = [-mp.exp(nega), a, z], [1, z, -1], [], G, [1], [1+z], a
+                return T1, T2
+            return mpf2float(mp.hypercomb(h, [z], maxterms=maxterms))
+
+
+def main():
+    t0 = time()
+    # It would be nice to have data for larger values, but either this
+    # requires prohibitively large precision (dps > 800) or mpmath has
+    # a bug. For example, gammainc(1e20, 1e20, dps=800) returns a
+    # value around 0.03, while the true value should be close to 0.5
+    # (DLMF 8.12.15).
+    print(__doc__)
+    pwd = os.path.dirname(__file__)
+    r = np.logspace(4, 14, 30)
+    ltheta = np.logspace(np.log10(pi/4), np.log10(np.arctan(0.6)), 30)
+    utheta = np.logspace(np.log10(pi/4), np.log10(np.arctan(1.4)), 30)
+
+    regimes = [(gammainc, ltheta), (gammaincc, utheta)]
+    for func, theta in regimes:
+        rg, thetag = np.meshgrid(r, theta)
+        a, x = rg*np.cos(thetag), rg*np.sin(thetag)
+        a, x = a.flatten(), x.flatten()
+        dataset = []
+        for i, (a0, x0) in enumerate(zip(a, x)):
+            if func == gammaincc:
+                # Exploit the fast integer path in gammaincc whenever
+                # possible so that the computation doesn't take too
+                # long
+                a0, x0 = np.floor(a0), np.floor(x0)
+            dataset.append((a0, x0, func(a0, x0)))
+        dataset = np.array(dataset)
+        filename = os.path.join(pwd, '..', 'tests', 'data', 'local',
+                                f'{func.__name__}.txt')
+        np.savetxt(filename, dataset)
+
+    print(f"{(time() - t0)/60} minutes elapsed")
+
+
+if __name__ == "__main__":
+    main()

env-llmeval/lib/python3.10/site-packages/scipy/special/_precompute/lambertw.py

@@ -0,0 +1,68 @@
+"""Compute a Pade approximation for the principal branch of the
+Lambert W function around 0 and compare it to various other
+approximations.
+
+"""
+import numpy as np
+
+try:
+    import mpmath
+    import matplotlib.pyplot as plt
+except ImportError:
+    pass
+
+
+def lambertw_pade():
+    derivs = [mpmath.diff(mpmath.lambertw, 0, n=n) for n in range(6)]
+    p, q = mpmath.pade(derivs, 3, 2)
+    return p, q
+
+
+def main():
+    print(__doc__)
+    with mpmath.workdps(50):
+        p, q = lambertw_pade()
+        p, q = p[::-1], q[::-1]
+        print(f"p = {p}")
+        print(f"q = {q}")
+
+    x, y = np.linspace(-1.5, 1.5, 75), np.linspace(-1.5, 1.5, 75)
+    x, y = np.meshgrid(x, y)
+    z = x + 1j*y
+    lambertw_std = []
+    for z0 in z.flatten():
+        lambertw_std.append(complex(mpmath.lambertw(z0)))
+    lambertw_std = np.array(lambertw_std).reshape(x.shape)
+
+    fig, axes = plt.subplots(nrows=3, ncols=1)
+    # Compare Pade approximation to true result
+    p = np.array([float(p0) for p0 in p])
+    q = np.array([float(q0) for q0 in q])
+    pade_approx = np.polyval(p, z)/np.polyval(q, z)
+    pade_err = abs(pade_approx - lambertw_std)
+    axes[0].pcolormesh(x, y, pade_err)
+    # Compare two terms of asymptotic series to true result
+    asy_approx = np.log(z) - np.log(np.log(z))
+    asy_err = abs(asy_approx - lambertw_std)
+    axes[1].pcolormesh(x, y, asy_err)
+    # Compare two terms of the series around the branch point to the
+    # true result
+    p = np.sqrt(2*(np.exp(1)*z + 1))
+    series_approx = -1 + p - p**2/3
+    series_err = abs(series_approx - lambertw_std)
+    im = axes[2].pcolormesh(x, y, series_err)
+
+    fig.colorbar(im, ax=axes.ravel().tolist())
+    plt.show()
+
+    fig, ax = plt.subplots(nrows=1, ncols=1)
+    pade_better = pade_err < asy_err
+    im = ax.pcolormesh(x, y, pade_better)
+    t = np.linspace(-0.3, 0.3)
+    ax.plot(-2.5*abs(t) - 0.2, t, 'r')
+    fig.colorbar(im, ax=ax)
+    plt.show()
+
+
+if __name__ == '__main__':
+    main()