Add files using upload-large-folder tool

ckpts/universal/global_step40/zero/11.input_layernorm.weight/fp32.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f744b2dee30f8590d57d433571c451f71516cfc0d8dda4aeb56cdb49f8ab3e69
+size 9293

ckpts/universal/global_step40/zero/5.mlp.dense_h_to_4h.weight/exp_avg.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a33f07f55c8a1ab36bf4ff987be5711b50931635a3de9d5197d6759952d70b87
+size 33555612

ckpts/universal/global_step40/zero/5.mlp.dense_h_to_4h.weight/exp_avg_sq.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3cba805c3aad0e844d7f976deb1110bd57596a4c1fbc043a118bcb534d97dea9
+size 33555627

venv/lib/python3.10/site-packages/scipy/cluster/__init__.py

@@ -0,0 +1,31 @@
+"""
+=========================================
+Clustering package (:mod:`scipy.cluster`)
+=========================================
+
+.. currentmodule:: scipy.cluster
+
+.. toctree::
+   :hidden:
+
+   cluster.vq
+   cluster.hierarchy
+
+Clustering algorithms are useful in information theory, target detection,
+communications, compression, and other areas. The `vq` module only
+supports vector quantization and the k-means algorithms.
+
+The `hierarchy` module provides functions for hierarchical and
+agglomerative clustering.  Its features include generating hierarchical
+clusters from distance matrices,
+calculating statistics on clusters, cutting linkages
+to generate flat clusters, and visualizing clusters with dendrograms.
+
+"""
+__all__ = ['vq', 'hierarchy']
+
+from . import vq, hierarchy
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

venv/lib/python3.10/site-packages/scipy/cluster/tests/hierarchy_test_data.py

@@ -0,0 +1,145 @@
+from numpy import array
+
+
+Q_X = array([[5.26563660e-01, 3.14160190e-01, 8.00656370e-02],
+             [7.50205180e-01, 4.60299830e-01, 8.98696460e-01],
+             [6.65461230e-01, 6.94011420e-01, 9.10465700e-01],
+             [9.64047590e-01, 1.43082200e-03, 7.39874220e-01],
+             [1.08159060e-01, 5.53028790e-01, 6.63804780e-02],
+             [9.31359130e-01, 8.25424910e-01, 9.52315440e-01],
+             [6.78086960e-01, 3.41903970e-01, 5.61481950e-01],
+             [9.82730940e-01, 7.04605210e-01, 8.70978630e-02],
+             [6.14691610e-01, 4.69989230e-02, 6.02406450e-01],
+             [5.80161260e-01, 9.17354970e-01, 5.88163850e-01],
+             [1.38246310e+00, 1.96358160e+00, 1.94437880e+00],
+             [2.10675860e+00, 1.67148730e+00, 1.34854480e+00],
+             [1.39880070e+00, 1.66142050e+00, 1.32224550e+00],
+             [1.71410460e+00, 1.49176380e+00, 1.45432170e+00],
+             [1.54102340e+00, 1.84374950e+00, 1.64658950e+00],
+             [2.08512480e+00, 1.84524350e+00, 2.17340850e+00],
+             [1.30748740e+00, 1.53801650e+00, 2.16007740e+00],
+             [1.41447700e+00, 1.99329070e+00, 1.99107420e+00],
+             [1.61943490e+00, 1.47703280e+00, 1.89788160e+00],
+             [1.59880600e+00, 1.54988980e+00, 1.57563350e+00],
+             [3.37247380e+00, 2.69635310e+00, 3.39981700e+00],
+             [3.13705120e+00, 3.36528090e+00, 3.06089070e+00],
+             [3.29413250e+00, 3.19619500e+00, 2.90700170e+00],
+             [2.65510510e+00, 3.06785900e+00, 2.97198540e+00],
+             [3.30941040e+00, 2.59283970e+00, 2.57714110e+00],
+             [2.59557220e+00, 3.33477370e+00, 3.08793190e+00],
+             [2.58206180e+00, 3.41615670e+00, 3.26441990e+00],
+             [2.71127000e+00, 2.77032450e+00, 2.63466500e+00],
+             [2.79617850e+00, 3.25473720e+00, 3.41801560e+00],
+             [2.64741750e+00, 2.54538040e+00, 3.25354110e+00]])
+
+ytdist = array([662., 877., 255., 412., 996., 295., 468., 268., 400., 754.,
+                564., 138., 219., 869., 669.])
+
+linkage_ytdist_single = array([[2., 5., 138., 2.],
+                               [3., 4., 219., 2.],
+                               [0., 7., 255., 3.],
+                               [1., 8., 268., 4.],
+                               [6., 9., 295., 6.]])
+
+linkage_ytdist_complete = array([[2., 5., 138., 2.],
+                                 [3., 4., 219., 2.],
+                                 [1., 6., 400., 3.],
+                                 [0., 7., 412., 3.],
+                                 [8., 9., 996., 6.]])
+
+linkage_ytdist_average = array([[2., 5., 138., 2.],
+                                [3., 4., 219., 2.],
+                                [0., 7., 333.5, 3.],
+                                [1., 6., 347.5, 3.],
+                                [8., 9., 680.77777778, 6.]])
+
+linkage_ytdist_weighted = array([[2., 5., 138., 2.],
+                                 [3., 4., 219., 2.],
+                                 [0., 7., 333.5, 3.],
+                                 [1., 6., 347.5, 3.],
+                                 [8., 9., 670.125, 6.]])
+
+# the optimal leaf ordering of linkage_ytdist_single
+linkage_ytdist_single_olo = array([[5., 2., 138., 2.],
+                                   [4., 3., 219., 2.],
+                                   [7., 0., 255., 3.],
+                                   [1., 8., 268., 4.],
+                                   [6., 9., 295., 6.]])
+
+X = array([[1.43054825, -7.5693489],
+           [6.95887839, 6.82293382],
+           [2.87137846, -9.68248579],
+           [7.87974764, -6.05485803],
+           [8.24018364, -6.09495602],
+           [7.39020262, 8.54004355]])
+ 
+linkage_X_centroid = array([[3., 4., 0.36265956, 2.],
+                            [1., 5., 1.77045373, 2.],
+                            [0., 2., 2.55760419, 2.],
+                            [6., 8., 6.43614494, 4.],
+                            [7., 9., 15.17363237, 6.]])
+
+linkage_X_median = array([[3., 4., 0.36265956, 2.],
+                          [1., 5., 1.77045373, 2.],
+                          [0., 2., 2.55760419, 2.],
+                          [6., 8., 6.43614494, 4.],
+                          [7., 9., 15.17363237, 6.]])
+
+linkage_X_ward = array([[3., 4., 0.36265956, 2.],
+                        [1., 5., 1.77045373, 2.],
+                        [0., 2., 2.55760419, 2.],
+                        [6., 8., 9.10208346, 4.],
+                        [7., 9., 24.7784379, 6.]])
+
+# the optimal leaf ordering of linkage_X_ward
+linkage_X_ward_olo = array([[4., 3., 0.36265956, 2.],
+                            [5., 1., 1.77045373, 2.],
+                            [2., 0., 2.55760419, 2.],
+                            [6., 8., 9.10208346, 4.],
+                            [7., 9., 24.7784379, 6.]])
+
+inconsistent_ytdist = {
+    1: array([[138., 0., 1., 0.],
+              [219., 0., 1., 0.],
+              [255., 0., 1., 0.],
+              [268., 0., 1., 0.],
+              [295., 0., 1., 0.]]),
+    2: array([[138., 0., 1., 0.],
+              [219., 0., 1., 0.],
+              [237., 25.45584412, 2., 0.70710678],
+              [261.5, 9.19238816, 2., 0.70710678],
+              [233.66666667, 83.9424406, 3., 0.7306594]]),
+    3: array([[138., 0., 1., 0.],
+              [219., 0., 1., 0.],
+              [237., 25.45584412, 2., 0.70710678],
+              [247.33333333, 25.38372182, 3., 0.81417007],
+              [239., 69.36377537, 4., 0.80733783]]),
+    4: array([[138., 0., 1., 0.],
+              [219., 0., 1., 0.],
+              [237., 25.45584412, 2., 0.70710678],
+              [247.33333333, 25.38372182, 3., 0.81417007],
+              [235., 60.73302232, 5., 0.98793042]])}
+
+fcluster_inconsistent = {
+    0.8: array([6, 2, 2, 4, 6, 2, 3, 7, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1]),
+    1.0: array([6, 2, 2, 4, 6, 2, 3, 7, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1]),
+    2.0: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1])}
+
+fcluster_distance = {
+    0.6: array([4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 6, 6, 6, 6, 6, 7, 6, 6, 6, 6, 3,
+                1, 1, 1, 2, 1, 1, 1, 1, 1]),
+    1.0: array([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1]),
+    2.0: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1])}
+
+fcluster_maxclust = {
+    8.0: array([5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 7, 7, 7, 7, 7, 8, 7, 7, 7, 7, 4,
+                1, 1, 1, 3, 1, 1, 1, 1, 2]),
+    4.0: array([3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2,
+                1, 1, 1, 1, 1, 1, 1, 1, 1]),
+    1.0: array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
+                1, 1, 1, 1, 1, 1, 1, 1, 1])}

venv/lib/python3.10/site-packages/scipy/cluster/tests/test_hierarchy.py

@@ -0,0 +1,1225 @@
+#
+# Author: Damian Eads
+# Date: April 17, 2008
+#
+# Copyright (C) 2008 Damian Eads
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above
+#    copyright notice, this list of conditions and the following
+#    disclaimer in the documentation and/or other materials provided
+#    with the distribution.
+#
+# 3. The name of the author may not be used to endorse or promote
+#    products derived from this software without specific prior
+#    written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+# OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+import numpy as np
+from numpy.testing import assert_allclose, assert_equal, assert_, assert_warns
+import pytest
+from pytest import raises as assert_raises
+
+import scipy.cluster.hierarchy
+from scipy.cluster.hierarchy import (
+    ClusterWarning, linkage, from_mlab_linkage, to_mlab_linkage,
+    num_obs_linkage, inconsistent, cophenet, fclusterdata, fcluster,
+    is_isomorphic, single, leaders,
+    correspond, is_monotonic, maxdists, maxinconsts, maxRstat,
+    is_valid_linkage, is_valid_im, to_tree, leaves_list, dendrogram,
+    set_link_color_palette, cut_tree, optimal_leaf_ordering,
+    _order_cluster_tree, _hierarchy, _LINKAGE_METHODS)
+from scipy.spatial.distance import pdist
+from scipy.cluster._hierarchy import Heap
+from scipy.conftest import array_api_compatible
+from scipy._lib._array_api import xp_assert_close, xp_assert_equal
+
+from . import hierarchy_test_data
+
+
+# Matplotlib is not a scipy dependency but is optionally used in dendrogram, so
+# check if it's available
+try:
+    import matplotlib
+    # and set the backend to be Agg (no gui)
+    matplotlib.use('Agg')
+    # before importing pyplot
+    import matplotlib.pyplot as plt
+    have_matplotlib = True
+except Exception:
+    have_matplotlib = False
+
+
+pytestmark = [array_api_compatible, pytest.mark.usefixtures("skip_if_array_api")]
+skip_if_array_api = pytest.mark.skip_if_array_api
+
+
+class TestLinkage:
+
+    @skip_if_array_api(cpu_only=True)
+    def test_linkage_non_finite_elements_in_distance_matrix(self, xp):
+        # Tests linkage(Y) where Y contains a non-finite element (e.g. NaN or Inf).
+        # Exception expected.
+        y = xp.zeros((6,))
+        y[0] = xp.nan
+        assert_raises(ValueError, linkage, y)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_linkage_empty_distance_matrix(self, xp):
+        # Tests linkage(Y) where Y is a 0x4 linkage matrix. Exception expected.
+        y = xp.zeros((0,))
+        assert_raises(ValueError, linkage, y)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_linkage_tdist(self, xp):
+        for method in ['single', 'complete', 'average', 'weighted']:
+            self.check_linkage_tdist(method, xp)
+
+    def check_linkage_tdist(self, method, xp):
+        # Tests linkage(Y, method) on the tdist data set.
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), method)
+        expectedZ = getattr(hierarchy_test_data, 'linkage_ytdist_' + method)
+        xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-10)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_linkage_X(self, xp):
+        for method in ['centroid', 'median', 'ward']:
+            self.check_linkage_q(method, xp)
+
+    def check_linkage_q(self, method, xp):
+        # Tests linkage(Y, method) on the Q data set.
+        Z = linkage(xp.asarray(hierarchy_test_data.X), method)
+        expectedZ = getattr(hierarchy_test_data, 'linkage_X_' + method)
+        xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-06)
+
+        y = scipy.spatial.distance.pdist(hierarchy_test_data.X,
+                                         metric="euclidean")
+        Z = linkage(xp.asarray(y), method)
+        xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-06)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_compare_with_trivial(self, xp):
+        rng = np.random.RandomState(0)
+        n = 20
+        X = rng.rand(n, 2)
+        d = pdist(X)
+
+        for method, code in _LINKAGE_METHODS.items():
+            Z_trivial = _hierarchy.linkage(d, n, code)
+            Z = linkage(xp.asarray(d), method)
+            xp_assert_close(Z, xp.asarray(Z_trivial), rtol=1e-14, atol=1e-15)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_optimal_leaf_ordering(self, xp):
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), optimal_ordering=True)
+        expectedZ = getattr(hierarchy_test_data, 'linkage_ytdist_single_olo')
+        xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-10)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestLinkageTies:
+
+    _expectations = {
+        'single': np.array([[0, 1, 1.41421356, 2],
+                            [2, 3, 1.41421356, 3]]),
+        'complete': np.array([[0, 1, 1.41421356, 2],
+                              [2, 3, 2.82842712, 3]]),
+        'average': np.array([[0, 1, 1.41421356, 2],
+                             [2, 3, 2.12132034, 3]]),
+        'weighted': np.array([[0, 1, 1.41421356, 2],
+                              [2, 3, 2.12132034, 3]]),
+        'centroid': np.array([[0, 1, 1.41421356, 2],
+                              [2, 3, 2.12132034, 3]]),
+        'median': np.array([[0, 1, 1.41421356, 2],
+                            [2, 3, 2.12132034, 3]]),
+        'ward': np.array([[0, 1, 1.41421356, 2],
+                          [2, 3, 2.44948974, 3]]),
+    }
+
+    def test_linkage_ties(self, xp):
+        for method in ['single', 'complete', 'average', 'weighted',
+                       'centroid', 'median', 'ward']:
+            self.check_linkage_ties(method, xp)
+
+    def check_linkage_ties(self, method, xp):
+        X = xp.asarray([[-1, -1], [0, 0], [1, 1]])
+        Z = linkage(X, method=method)
+        expectedZ = self._expectations[method]
+        xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-06)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestInconsistent:
+
+    def test_inconsistent_tdist(self, xp):
+        for depth in hierarchy_test_data.inconsistent_ytdist:
+            self.check_inconsistent_tdist(depth, xp)
+
+    def check_inconsistent_tdist(self, depth, xp):
+        Z = xp.asarray(hierarchy_test_data.linkage_ytdist_single)
+        xp_assert_close(inconsistent(Z, depth),
+                        xp.asarray(hierarchy_test_data.inconsistent_ytdist[depth]))
+
+
+@skip_if_array_api(cpu_only=True)
+class TestCopheneticDistance:
+
+    def test_linkage_cophenet_tdist_Z(self, xp):
+        # Tests cophenet(Z) on tdist data set.
+        expectedM = xp.asarray([268, 295, 255, 255, 295, 295, 268, 268, 295, 295,
+                                295, 138, 219, 295, 295])
+        Z = xp.asarray(hierarchy_test_data.linkage_ytdist_single)
+        M = cophenet(Z)
+        xp_assert_close(M, xp.asarray(expectedM, dtype=xp.float64), atol=1e-10)
+
+    def test_linkage_cophenet_tdist_Z_Y(self, xp):
+        # Tests cophenet(Z, Y) on tdist data set.
+        Z = xp.asarray(hierarchy_test_data.linkage_ytdist_single)
+        (c, M) = cophenet(Z, xp.asarray(hierarchy_test_data.ytdist))
+        expectedM = xp.asarray([268, 295, 255, 255, 295, 295, 268, 268, 295, 295,
+                                295, 138, 219, 295, 295], dtype=xp.float64)
+        expectedc = xp.asarray(0.639931296433393415057366837573, dtype=xp.float64)[()]
+        xp_assert_close(c, expectedc, atol=1e-10)
+        xp_assert_close(M, expectedM, atol=1e-10)
+
+
+class TestMLabLinkageConversion:
+
+    def test_mlab_linkage_conversion_empty(self, xp):
+        # Tests from/to_mlab_linkage on empty linkage array.
+        X = xp.asarray([], dtype=xp.float64)
+        xp_assert_equal(from_mlab_linkage(X), X)
+        xp_assert_equal(to_mlab_linkage(X), X)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_mlab_linkage_conversion_single_row(self, xp):
+        # Tests from/to_mlab_linkage on linkage array with single row.
+        Z = xp.asarray([[0., 1., 3., 2.]])
+        Zm = xp.asarray([[1, 2, 3]])
+        xp_assert_close(from_mlab_linkage(Zm), xp.asarray(Z, dtype=xp.float64),
+                        rtol=1e-15)
+        xp_assert_close(to_mlab_linkage(Z), xp.asarray(Zm, dtype=xp.float64),
+                        rtol=1e-15)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_mlab_linkage_conversion_multiple_rows(self, xp):
+        # Tests from/to_mlab_linkage on linkage array with multiple rows.
+        Zm = xp.asarray([[3, 6, 138], [4, 5, 219],
+                         [1, 8, 255], [2, 9, 268], [7, 10, 295]])
+        Z = xp.asarray([[2., 5., 138., 2.],
+                        [3., 4., 219., 2.],
+                        [0., 7., 255., 3.],
+                        [1., 8., 268., 4.],
+                        [6., 9., 295., 6.]],
+                       dtype=xp.float64)
+        xp_assert_close(from_mlab_linkage(Zm), Z, rtol=1e-15)
+        xp_assert_close(to_mlab_linkage(Z), xp.asarray(Zm, dtype=xp.float64),
+                        rtol=1e-15)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestFcluster:
+
+    def test_fclusterdata(self, xp):
+        for t in hierarchy_test_data.fcluster_inconsistent:
+            self.check_fclusterdata(t, 'inconsistent', xp)
+        for t in hierarchy_test_data.fcluster_distance:
+            self.check_fclusterdata(t, 'distance', xp)
+        for t in hierarchy_test_data.fcluster_maxclust:
+            self.check_fclusterdata(t, 'maxclust', xp)
+
+    def check_fclusterdata(self, t, criterion, xp):
+        # Tests fclusterdata(X, criterion=criterion, t=t) on a random 3-cluster data set
+        expectedT = xp.asarray(getattr(hierarchy_test_data, 'fcluster_' + criterion)[t])
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        T = fclusterdata(X, criterion=criterion, t=t)
+        assert_(is_isomorphic(T, expectedT))
+
+    def test_fcluster(self, xp):
+        for t in hierarchy_test_data.fcluster_inconsistent:
+            self.check_fcluster(t, 'inconsistent', xp)
+        for t in hierarchy_test_data.fcluster_distance:
+            self.check_fcluster(t, 'distance', xp)
+        for t in hierarchy_test_data.fcluster_maxclust:
+            self.check_fcluster(t, 'maxclust', xp)
+
+    def check_fcluster(self, t, criterion, xp):
+        # Tests fcluster(Z, criterion=criterion, t=t) on a random 3-cluster data set.
+        expectedT = xp.asarray(getattr(hierarchy_test_data, 'fcluster_' + criterion)[t])
+        Z = single(xp.asarray(hierarchy_test_data.Q_X))
+        T = fcluster(Z, criterion=criterion, t=t)
+        assert_(is_isomorphic(T, expectedT))
+
+    def test_fcluster_monocrit(self, xp):
+        for t in hierarchy_test_data.fcluster_distance:
+            self.check_fcluster_monocrit(t, xp)
+        for t in hierarchy_test_data.fcluster_maxclust:
+            self.check_fcluster_maxclust_monocrit(t, xp)
+
+    def check_fcluster_monocrit(self, t, xp):
+        expectedT = xp.asarray(hierarchy_test_data.fcluster_distance[t])
+        Z = single(xp.asarray(hierarchy_test_data.Q_X))
+        T = fcluster(Z, t, criterion='monocrit', monocrit=maxdists(Z))
+        assert_(is_isomorphic(T, expectedT))
+
+    def check_fcluster_maxclust_monocrit(self, t, xp):
+        expectedT = xp.asarray(hierarchy_test_data.fcluster_maxclust[t])
+        Z = single(xp.asarray(hierarchy_test_data.Q_X))
+        T = fcluster(Z, t, criterion='maxclust_monocrit', monocrit=maxdists(Z))
+        assert_(is_isomorphic(T, expectedT))
+
+
+@skip_if_array_api(cpu_only=True)
+class TestLeaders:
+
+    def test_leaders_single(self, xp):
+        # Tests leaders using a flat clustering generated by single linkage.
+        X = hierarchy_test_data.Q_X
+        Y = pdist(X)
+        Y = xp.asarray(Y)
+        Z = linkage(Y)
+        T = fcluster(Z, criterion='maxclust', t=3)
+        Lright = (xp.asarray([53, 55, 56]), xp.asarray([2, 3, 1]))
+        T = xp.asarray(T, dtype=xp.int32)
+        L = leaders(Z, T)
+        assert_allclose(np.concatenate(L), np.concatenate(Lright), rtol=1e-15)
+
+
+@skip_if_array_api(np_only=True,
+                   reasons=['`is_isomorphic` only supports NumPy backend'])
+class TestIsIsomorphic:
+
+    @skip_if_array_api(np_only=True,
+                       reasons=['array-likes only supported for NumPy backend'])
+    def test_array_like(self, xp):
+        assert is_isomorphic([1, 1, 1], [2, 2, 2])
+        assert is_isomorphic([], [])
+
+    def test_is_isomorphic_1(self, xp):
+        # Tests is_isomorphic on test case #1 (one flat cluster, different labellings)
+        a = xp.asarray([1, 1, 1])
+        b = xp.asarray([2, 2, 2])
+        assert is_isomorphic(a, b)
+        assert is_isomorphic(b, a)
+
+    def test_is_isomorphic_2(self, xp):
+        # Tests is_isomorphic on test case #2 (two flat clusters, different labelings)
+        a = xp.asarray([1, 7, 1])
+        b = xp.asarray([2, 3, 2])
+        assert is_isomorphic(a, b)
+        assert is_isomorphic(b, a)
+
+    def test_is_isomorphic_3(self, xp):
+        # Tests is_isomorphic on test case #3 (no flat clusters)
+        a = xp.asarray([])
+        b = xp.asarray([])
+        assert is_isomorphic(a, b)
+
+    def test_is_isomorphic_4A(self, xp):
+        # Tests is_isomorphic on test case #4A
+        # (3 flat clusters, different labelings, isomorphic)
+        a = xp.asarray([1, 2, 3])
+        b = xp.asarray([1, 3, 2])
+        assert is_isomorphic(a, b)
+        assert is_isomorphic(b, a)
+
+    def test_is_isomorphic_4B(self, xp):
+        # Tests is_isomorphic on test case #4B
+        # (3 flat clusters, different labelings, nonisomorphic)
+        a = xp.asarray([1, 2, 3, 3])
+        b = xp.asarray([1, 3, 2, 3])
+        assert is_isomorphic(a, b) is False
+        assert is_isomorphic(b, a) is False
+
+    def test_is_isomorphic_4C(self, xp):
+        # Tests is_isomorphic on test case #4C
+        # (3 flat clusters, different labelings, isomorphic)
+        a = xp.asarray([7, 2, 3])
+        b = xp.asarray([6, 3, 2])
+        assert is_isomorphic(a, b)
+        assert is_isomorphic(b, a)
+
+    def test_is_isomorphic_5(self, xp):
+        # Tests is_isomorphic on test case #5 (1000 observations, 2/3/5 random
+        # clusters, random permutation of the labeling).
+        for nc in [2, 3, 5]:
+            self.help_is_isomorphic_randperm(1000, nc, xp=xp)
+
+    def test_is_isomorphic_6(self, xp):
+        # Tests is_isomorphic on test case #5A (1000 observations, 2/3/5 random
+        # clusters, random permutation of the labeling, slightly
+        # nonisomorphic.)
+        for nc in [2, 3, 5]:
+            self.help_is_isomorphic_randperm(1000, nc, True, 5, xp=xp)
+
+    def test_is_isomorphic_7(self, xp):
+        # Regression test for gh-6271
+        a = xp.asarray([1, 2, 3])
+        b = xp.asarray([1, 1, 1])
+        assert not is_isomorphic(a, b)
+
+    def help_is_isomorphic_randperm(self, nobs, nclusters, noniso=False, nerrors=0,
+                                    *, xp):
+        for k in range(3):
+            a = (np.random.rand(nobs) * nclusters).astype(int)
+            b = np.zeros(a.size, dtype=int)
+            P = np.random.permutation(nclusters)
+            for i in range(0, a.shape[0]):
+                b[i] = P[a[i]]
+            if noniso:
+                Q = np.random.permutation(nobs)
+                b[Q[0:nerrors]] += 1
+                b[Q[0:nerrors]] %= nclusters
+            a = xp.asarray(a)
+            b = xp.asarray(b)
+            assert is_isomorphic(a, b) == (not noniso)
+            assert is_isomorphic(b, a) == (not noniso)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestIsValidLinkage:
+
+    def test_is_valid_linkage_various_size(self, xp):
+        for nrow, ncol, valid in [(2, 5, False), (2, 3, False),
+                                  (1, 4, True), (2, 4, True)]:
+            self.check_is_valid_linkage_various_size(nrow, ncol, valid, xp)
+
+    def check_is_valid_linkage_various_size(self, nrow, ncol, valid, xp):
+        # Tests is_valid_linkage(Z) with linkage matrices of various sizes
+        Z = xp.asarray([[0, 1, 3.0, 2, 5],
+                        [3, 2, 4.0, 3, 3]], dtype=xp.float64)
+        Z = Z[:nrow, :ncol]
+        assert_(is_valid_linkage(Z) == valid)
+        if not valid:
+            assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_int_type(self, xp):
+        # Tests is_valid_linkage(Z) with integer type.
+        Z = xp.asarray([[0, 1, 3.0, 2],
+                        [3, 2, 4.0, 3]], dtype=xp.int64)
+        assert_(is_valid_linkage(Z) is False)
+        assert_raises(TypeError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_empty(self, xp):
+        # Tests is_valid_linkage(Z) with empty linkage.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        assert_(is_valid_linkage(Z) is False)
+        assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_4_and_up(self, xp):
+        # Tests is_valid_linkage(Z) on linkage on observation sets between
+        # sizes 4 and 15 (step size 3).
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            assert_(is_valid_linkage(Z) is True)
+
+    def test_is_valid_linkage_4_and_up_neg_index_left(self, xp):
+        # Tests is_valid_linkage(Z) on linkage on observation sets between
+        # sizes 4 and 15 (step size 3) with negative indices (left).
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            Z[i//2,0] = -2
+            assert_(is_valid_linkage(Z) is False)
+            assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_4_and_up_neg_index_right(self, xp):
+        # Tests is_valid_linkage(Z) on linkage on observation sets between
+        # sizes 4 and 15 (step size 3) with negative indices (right).
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            Z[i//2,1] = -2
+            assert_(is_valid_linkage(Z) is False)
+            assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_4_and_up_neg_dist(self, xp):
+        # Tests is_valid_linkage(Z) on linkage on observation sets between
+        # sizes 4 and 15 (step size 3) with negative distances.
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            Z[i//2,2] = -0.5
+            assert_(is_valid_linkage(Z) is False)
+            assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+    def test_is_valid_linkage_4_and_up_neg_counts(self, xp):
+        # Tests is_valid_linkage(Z) on linkage on observation sets between
+        # sizes 4 and 15 (step size 3) with negative counts.
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            Z[i//2,3] = -2
+            assert_(is_valid_linkage(Z) is False)
+            assert_raises(ValueError, is_valid_linkage, Z, throw=True)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestIsValidInconsistent:
+
+    def test_is_valid_im_int_type(self, xp):
+        # Tests is_valid_im(R) with integer type.
+        R = xp.asarray([[0, 1, 3.0, 2],
+                        [3, 2, 4.0, 3]], dtype=xp.int64)
+        assert_(is_valid_im(R) is False)
+        assert_raises(TypeError, is_valid_im, R, throw=True)
+
+    def test_is_valid_im_various_size(self, xp):
+        for nrow, ncol, valid in [(2, 5, False), (2, 3, False),
+                                  (1, 4, True), (2, 4, True)]:
+            self.check_is_valid_im_various_size(nrow, ncol, valid, xp)
+
+    def check_is_valid_im_various_size(self, nrow, ncol, valid, xp):
+        # Tests is_valid_im(R) with linkage matrices of various sizes
+        R = xp.asarray([[0, 1, 3.0, 2, 5],
+                        [3, 2, 4.0, 3, 3]], dtype=xp.float64)
+        R = R[:nrow, :ncol]
+        assert_(is_valid_im(R) == valid)
+        if not valid:
+            assert_raises(ValueError, is_valid_im, R, throw=True)
+
+    def test_is_valid_im_empty(self, xp):
+        # Tests is_valid_im(R) with empty inconsistency matrix.
+        R = xp.zeros((0, 4), dtype=xp.float64)
+        assert_(is_valid_im(R) is False)
+        assert_raises(ValueError, is_valid_im, R, throw=True)
+
+    def test_is_valid_im_4_and_up(self, xp):
+        # Tests is_valid_im(R) on im on observation sets between sizes 4 and 15
+        # (step size 3).
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            R = inconsistent(Z)
+            assert_(is_valid_im(R) is True)
+
+    def test_is_valid_im_4_and_up_neg_index_left(self, xp):
+        # Tests is_valid_im(R) on im on observation sets between sizes 4 and 15
+        # (step size 3) with negative link height means.
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            R = inconsistent(Z)
+            R[i//2,0] = -2.0
+            assert_(is_valid_im(R) is False)
+            assert_raises(ValueError, is_valid_im, R, throw=True)
+
+    def test_is_valid_im_4_and_up_neg_index_right(self, xp):
+        # Tests is_valid_im(R) on im on observation sets between sizes 4 and 15
+        # (step size 3) with negative link height standard deviations.
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            R = inconsistent(Z)
+            R[i//2,1] = -2.0
+            assert_(is_valid_im(R) is False)
+            assert_raises(ValueError, is_valid_im, R, throw=True)
+
+    def test_is_valid_im_4_and_up_neg_dist(self, xp):
+        # Tests is_valid_im(R) on im on observation sets between sizes 4 and 15
+        # (step size 3) with negative link counts.
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            R = inconsistent(Z)
+            R[i//2,2] = -0.5
+            assert_(is_valid_im(R) is False)
+            assert_raises(ValueError, is_valid_im, R, throw=True)
+
+
+class TestNumObsLinkage:
+
+    @skip_if_array_api(cpu_only=True)
+    def test_num_obs_linkage_empty(self, xp):
+        # Tests num_obs_linkage(Z) with empty linkage.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        assert_raises(ValueError, num_obs_linkage, Z)
+
+    def test_num_obs_linkage_1x4(self, xp):
+        # Tests num_obs_linkage(Z) on linkage over 2 observations.
+        Z = xp.asarray([[0, 1, 3.0, 2]], dtype=xp.float64)
+        assert_equal(num_obs_linkage(Z), 2)
+
+    def test_num_obs_linkage_2x4(self, xp):
+        # Tests num_obs_linkage(Z) on linkage over 3 observations.
+        Z = xp.asarray([[0, 1, 3.0, 2],
+                        [3, 2, 4.0, 3]], dtype=xp.float64)
+        assert_equal(num_obs_linkage(Z), 3)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_num_obs_linkage_4_and_up(self, xp):
+        # Tests num_obs_linkage(Z) on linkage on observation sets between sizes
+        # 4 and 15 (step size 3).
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            assert_equal(num_obs_linkage(Z), i)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestLeavesList:
+
+    def test_leaves_list_1x4(self, xp):
+        # Tests leaves_list(Z) on a 1x4 linkage.
+        Z = xp.asarray([[0, 1, 3.0, 2]], dtype=xp.float64)
+        to_tree(Z)
+        assert_allclose(leaves_list(Z), [0, 1], rtol=1e-15)
+
+    def test_leaves_list_2x4(self, xp):
+        # Tests leaves_list(Z) on a 2x4 linkage.
+        Z = xp.asarray([[0, 1, 3.0, 2],
+                        [3, 2, 4.0, 3]], dtype=xp.float64)
+        to_tree(Z)
+        assert_allclose(leaves_list(Z), [0, 1, 2], rtol=1e-15)
+
+    def test_leaves_list_Q(self, xp):
+        for method in ['single', 'complete', 'average', 'weighted', 'centroid',
+                       'median', 'ward']:
+            self.check_leaves_list_Q(method, xp)
+
+    def check_leaves_list_Q(self, method, xp):
+        # Tests leaves_list(Z) on the Q data set
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, method)
+        node = to_tree(Z)
+        assert_allclose(node.pre_order(), leaves_list(Z), rtol=1e-15)
+
+    def test_Q_subtree_pre_order(self, xp):
+        # Tests that pre_order() works when called on sub-trees.
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, 'single')
+        node = to_tree(Z)
+        assert_allclose(node.pre_order(), (node.get_left().pre_order()
+                                           + node.get_right().pre_order()),
+                        rtol=1e-15)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestCorrespond:
+
+    def test_correspond_empty(self, xp):
+        # Tests correspond(Z, y) with empty linkage and condensed distance matrix.
+        y = xp.zeros((0,), dtype=xp.float64)
+        Z = xp.zeros((0,4), dtype=xp.float64)
+        assert_raises(ValueError, correspond, Z, y)
+
+    def test_correspond_2_and_up(self, xp):
+        # Tests correspond(Z, y) on linkage and CDMs over observation sets of
+        # different sizes.
+        for i in range(2, 4):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            assert_(correspond(Z, y))
+        for i in range(4, 15, 3):
+            y = np.random.rand(i*(i-1)//2)
+            y = xp.asarray(y)
+            Z = linkage(y)
+            assert_(correspond(Z, y))
+
+    def test_correspond_4_and_up(self, xp):
+        # Tests correspond(Z, y) on linkage and CDMs over observation sets of
+        # different sizes. Correspondence should be false.
+        for (i, j) in (list(zip(list(range(2, 4)), list(range(3, 5)))) +
+                       list(zip(list(range(3, 5)), list(range(2, 4))))):
+            y = np.random.rand(i*(i-1)//2)
+            y2 = np.random.rand(j*(j-1)//2)
+            y = xp.asarray(y)
+            y2 = xp.asarray(y2)
+            Z = linkage(y)
+            Z2 = linkage(y2)
+            assert not correspond(Z, y2)
+            assert not correspond(Z2, y)
+
+    def test_correspond_4_and_up_2(self, xp):
+        # Tests correspond(Z, y) on linkage and CDMs over observation sets of
+        # different sizes. Correspondence should be false.
+        for (i, j) in (list(zip(list(range(2, 7)), list(range(16, 21)))) +
+                       list(zip(list(range(2, 7)), list(range(16, 21))))):
+            y = np.random.rand(i*(i-1)//2)
+            y2 = np.random.rand(j*(j-1)//2)
+            y = xp.asarray(y)
+            y2 = xp.asarray(y2)
+            Z = linkage(y)
+            Z2 = linkage(y2)
+            assert not correspond(Z, y2)
+            assert not correspond(Z2, y)
+
+    def test_num_obs_linkage_multi_matrix(self, xp):
+        # Tests num_obs_linkage with observation matrices of multiple sizes.
+        for n in range(2, 10):
+            X = np.random.rand(n, 4)
+            Y = pdist(X)
+            Y = xp.asarray(Y)
+            Z = linkage(Y)
+            assert_equal(num_obs_linkage(Z), n)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestIsMonotonic:
+
+    def test_is_monotonic_empty(self, xp):
+        # Tests is_monotonic(Z) on an empty linkage.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        assert_raises(ValueError, is_monotonic, Z)
+
+    def test_is_monotonic_1x4(self, xp):
+        # Tests is_monotonic(Z) on 1x4 linkage. Expecting True.
+        Z = xp.asarray([[0, 1, 0.3, 2]], dtype=xp.float64)
+        assert is_monotonic(Z)
+
+    def test_is_monotonic_2x4_T(self, xp):
+        # Tests is_monotonic(Z) on 2x4 linkage. Expecting True.
+        Z = xp.asarray([[0, 1, 0.3, 2],
+                        [2, 3, 0.4, 3]], dtype=xp.float64)
+        assert is_monotonic(Z)
+
+    def test_is_monotonic_2x4_F(self, xp):
+        # Tests is_monotonic(Z) on 2x4 linkage. Expecting False.
+        Z = xp.asarray([[0, 1, 0.4, 2],
+                        [2, 3, 0.3, 3]], dtype=xp.float64)
+        assert not is_monotonic(Z)
+
+    def test_is_monotonic_3x4_T(self, xp):
+        # Tests is_monotonic(Z) on 3x4 linkage. Expecting True.
+        Z = xp.asarray([[0, 1, 0.3, 2],
+                        [2, 3, 0.4, 2],
+                        [4, 5, 0.6, 4]], dtype=xp.float64)
+        assert is_monotonic(Z)
+
+    def test_is_monotonic_3x4_F1(self, xp):
+        # Tests is_monotonic(Z) on 3x4 linkage (case 1). Expecting False.
+        Z = xp.asarray([[0, 1, 0.3, 2],
+                        [2, 3, 0.2, 2],
+                        [4, 5, 0.6, 4]], dtype=xp.float64)
+        assert not is_monotonic(Z)
+
+    def test_is_monotonic_3x4_F2(self, xp):
+        # Tests is_monotonic(Z) on 3x4 linkage (case 2). Expecting False.
+        Z = xp.asarray([[0, 1, 0.8, 2],
+                        [2, 3, 0.4, 2],
+                        [4, 5, 0.6, 4]], dtype=xp.float64)
+        assert not is_monotonic(Z)
+
+    def test_is_monotonic_3x4_F3(self, xp):
+        # Tests is_monotonic(Z) on 3x4 linkage (case 3). Expecting False
+        Z = xp.asarray([[0, 1, 0.3, 2],
+                        [2, 3, 0.4, 2],
+                        [4, 5, 0.2, 4]], dtype=xp.float64)
+        assert not is_monotonic(Z)
+
+    def test_is_monotonic_tdist_linkage1(self, xp):
+        # Tests is_monotonic(Z) on clustering generated by single linkage on
+        # tdist data set. Expecting True.
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        assert is_monotonic(Z)
+
+    def test_is_monotonic_tdist_linkage2(self, xp):
+        # Tests is_monotonic(Z) on clustering generated by single linkage on
+        # tdist data set. Perturbing. Expecting False.
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        Z[2,2] = 0.0
+        assert not is_monotonic(Z)
+
+    def test_is_monotonic_Q_linkage(self, xp):
+        # Tests is_monotonic(Z) on clustering generated by single linkage on
+        # Q data set. Expecting True.
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, 'single')
+        assert is_monotonic(Z)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestMaxDists:
+
+    def test_maxdists_empty_linkage(self, xp):
+        # Tests maxdists(Z) on empty linkage. Expecting exception.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        assert_raises(ValueError, maxdists, Z)
+
+    def test_maxdists_one_cluster_linkage(self, xp):
+        # Tests maxdists(Z) on linkage with one cluster.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        MD = maxdists(Z)
+        expectedMD = calculate_maximum_distances(Z, xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+    def test_maxdists_Q_linkage(self, xp):
+        for method in ['single', 'complete', 'ward', 'centroid', 'median']:
+            self.check_maxdists_Q_linkage(method, xp)
+
+    def check_maxdists_Q_linkage(self, method, xp):
+        # Tests maxdists(Z) on the Q data set
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, method)
+        MD = maxdists(Z)
+        expectedMD = calculate_maximum_distances(Z, xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+
+class TestMaxInconsts:
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxinconsts_empty_linkage(self, xp):
+        # Tests maxinconsts(Z, R) on empty linkage. Expecting exception.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        R = xp.zeros((0, 4), dtype=xp.float64)
+        assert_raises(ValueError, maxinconsts, Z, R)
+
+    def test_maxinconsts_difrow_linkage(self, xp):
+        # Tests maxinconsts(Z, R) on linkage and inconsistency matrices with
+        # different numbers of clusters. Expecting exception.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        R = np.random.rand(2, 4)
+        R = xp.asarray(R)
+        assert_raises(ValueError, maxinconsts, Z, R)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxinconsts_one_cluster_linkage(self, xp):
+        # Tests maxinconsts(Z, R) on linkage with one cluster.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        R = xp.asarray([[0, 0, 0, 0.3]], dtype=xp.float64)
+        MD = maxinconsts(Z, R)
+        expectedMD = calculate_maximum_inconsistencies(Z, R, xp=xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxinconsts_Q_linkage(self, xp):
+        for method in ['single', 'complete', 'ward', 'centroid', 'median']:
+            self.check_maxinconsts_Q_linkage(method, xp)
+
+    def check_maxinconsts_Q_linkage(self, method, xp):
+        # Tests maxinconsts(Z, R) on the Q data set
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, method)
+        R = inconsistent(Z)
+        MD = maxinconsts(Z, R)
+        expectedMD = calculate_maximum_inconsistencies(Z, R, xp=xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+
+class TestMaxRStat:
+
+    def test_maxRstat_invalid_index(self, xp):
+        for i in [3.3, -1, 4]:
+            self.check_maxRstat_invalid_index(i, xp)
+
+    def check_maxRstat_invalid_index(self, i, xp):
+        # Tests maxRstat(Z, R, i). Expecting exception.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        R = xp.asarray([[0, 0, 0, 0.3]], dtype=xp.float64)
+        if isinstance(i, int):
+            assert_raises(ValueError, maxRstat, Z, R, i)
+        else:
+            assert_raises(TypeError, maxRstat, Z, R, i)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxRstat_empty_linkage(self, xp):
+        for i in range(4):
+            self.check_maxRstat_empty_linkage(i, xp)
+
+    def check_maxRstat_empty_linkage(self, i, xp):
+        # Tests maxRstat(Z, R, i) on empty linkage. Expecting exception.
+        Z = xp.zeros((0, 4), dtype=xp.float64)
+        R = xp.zeros((0, 4), dtype=xp.float64)
+        assert_raises(ValueError, maxRstat, Z, R, i)
+
+    def test_maxRstat_difrow_linkage(self, xp):
+        for i in range(4):
+            self.check_maxRstat_difrow_linkage(i, xp)
+
+    def check_maxRstat_difrow_linkage(self, i, xp):
+        # Tests maxRstat(Z, R, i) on linkage and inconsistency matrices with
+        # different numbers of clusters. Expecting exception.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        R = np.random.rand(2, 4)
+        R = xp.asarray(R)
+        assert_raises(ValueError, maxRstat, Z, R, i)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxRstat_one_cluster_linkage(self, xp):
+        for i in range(4):
+            self.check_maxRstat_one_cluster_linkage(i, xp)
+
+    def check_maxRstat_one_cluster_linkage(self, i, xp):
+        # Tests maxRstat(Z, R, i) on linkage with one cluster.
+        Z = xp.asarray([[0, 1, 0.3, 4]], dtype=xp.float64)
+        R = xp.asarray([[0, 0, 0, 0.3]], dtype=xp.float64)
+        MD = maxRstat(Z, R, 1)
+        expectedMD = calculate_maximum_inconsistencies(Z, R, 1, xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+    @skip_if_array_api(cpu_only=True)
+    def test_maxRstat_Q_linkage(self, xp):
+        for method in ['single', 'complete', 'ward', 'centroid', 'median']:
+            for i in range(4):
+                self.check_maxRstat_Q_linkage(method, i, xp)
+
+    def check_maxRstat_Q_linkage(self, method, i, xp):
+        # Tests maxRstat(Z, R, i) on the Q data set
+        X = xp.asarray(hierarchy_test_data.Q_X)
+        Z = linkage(X, method)
+        R = inconsistent(Z)
+        MD = maxRstat(Z, R, 1)
+        expectedMD = calculate_maximum_inconsistencies(Z, R, 1, xp)
+        xp_assert_close(MD, expectedMD, atol=1e-15)
+
+
+@skip_if_array_api(cpu_only=True)
+class TestDendrogram:
+
+    def test_dendrogram_single_linkage_tdist(self, xp):
+        # Tests dendrogram calculation on single linkage of the tdist data set.
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        R = dendrogram(Z, no_plot=True)
+        leaves = R["leaves"]
+        assert_equal(leaves, [2, 5, 1, 0, 3, 4])
+
+    def test_valid_orientation(self, xp):
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        assert_raises(ValueError, dendrogram, Z, orientation="foo")
+
+    def test_labels_as_array_or_list(self, xp):
+        # test for gh-12418
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        labels = xp.asarray([1, 3, 2, 6, 4, 5])
+        result1 = dendrogram(Z, labels=labels, no_plot=True)
+        result2 = dendrogram(Z, labels=list(labels), no_plot=True)
+        assert result1 == result2
+
+    @pytest.mark.skipif(not have_matplotlib, reason="no matplotlib")
+    def test_valid_label_size(self, xp):
+        link = xp.asarray([
+            [0, 1, 1.0, 4],
+            [2, 3, 1.0, 5],
+            [4, 5, 2.0, 6],
+        ])
+        plt.figure()
+        with pytest.raises(ValueError) as exc_info:
+            dendrogram(link, labels=list(range(100)))
+        assert "Dimensions of Z and labels must be consistent."\
+               in str(exc_info.value)
+
+        with pytest.raises(
+                ValueError,
+                match="Dimensions of Z and labels must be consistent."):
+            dendrogram(link, labels=[])
+
+        plt.close()
+
+    @pytest.mark.skipif(not have_matplotlib, reason="no matplotlib")
+    def test_dendrogram_plot(self, xp):
+        for orientation in ['top', 'bottom', 'left', 'right']:
+            self.check_dendrogram_plot(orientation, xp)
+
+    def check_dendrogram_plot(self, orientation, xp):
+        # Tests dendrogram plotting.
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+        expected = {'color_list': ['C1', 'C0', 'C0', 'C0', 'C0'],
+                    'dcoord': [[0.0, 138.0, 138.0, 0.0],
+                               [0.0, 219.0, 219.0, 0.0],
+                               [0.0, 255.0, 255.0, 219.0],
+                               [0.0, 268.0, 268.0, 255.0],
+                               [138.0, 295.0, 295.0, 268.0]],
+                    'icoord': [[5.0, 5.0, 15.0, 15.0],
+                               [45.0, 45.0, 55.0, 55.0],
+                               [35.0, 35.0, 50.0, 50.0],
+                               [25.0, 25.0, 42.5, 42.5],
+                               [10.0, 10.0, 33.75, 33.75]],
+                    'ivl': ['2', '5', '1', '0', '3', '4'],
+                    'leaves': [2, 5, 1, 0, 3, 4],
+                    'leaves_color_list': ['C1', 'C1', 'C0', 'C0', 'C0', 'C0'],
+                    }
+
+        fig = plt.figure()
+        ax = fig.add_subplot(221)
+
+        # test that dendrogram accepts ax keyword
+        R1 = dendrogram(Z, ax=ax, orientation=orientation)
+        R1['dcoord'] = np.asarray(R1['dcoord'])
+        assert_equal(R1, expected)
+
+        # test that dendrogram accepts and handle the leaf_font_size and
+        # leaf_rotation keywords
+        dendrogram(Z, ax=ax, orientation=orientation,
+                   leaf_font_size=20, leaf_rotation=90)
+        testlabel = (
+            ax.get_xticklabels()[0]
+            if orientation in ['top', 'bottom']
+            else ax.get_yticklabels()[0]
+        )
+        assert_equal(testlabel.get_rotation(), 90)
+        assert_equal(testlabel.get_size(), 20)
+        dendrogram(Z, ax=ax, orientation=orientation,
+                   leaf_rotation=90)
+        testlabel = (
+            ax.get_xticklabels()[0]
+            if orientation in ['top', 'bottom']
+            else ax.get_yticklabels()[0]
+        )
+        assert_equal(testlabel.get_rotation(), 90)
+        dendrogram(Z, ax=ax, orientation=orientation,
+                   leaf_font_size=20)
+        testlabel = (
+            ax.get_xticklabels()[0]
+            if orientation in ['top', 'bottom']
+            else ax.get_yticklabels()[0]
+        )
+        assert_equal(testlabel.get_size(), 20)
+        plt.close()
+
+        # test plotting to gca (will import pylab)
+        R2 = dendrogram(Z, orientation=orientation)
+        plt.close()
+        R2['dcoord'] = np.asarray(R2['dcoord'])
+        assert_equal(R2, expected)
+
+    @pytest.mark.skipif(not have_matplotlib, reason="no matplotlib")
+    def test_dendrogram_truncate_mode(self, xp):
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+
+        R = dendrogram(Z, 2, 'lastp', show_contracted=True)
+        plt.close()
+        R['dcoord'] = np.asarray(R['dcoord'])
+        assert_equal(R, {'color_list': ['C0'],
+                         'dcoord': [[0.0, 295.0, 295.0, 0.0]],
+                         'icoord': [[5.0, 5.0, 15.0, 15.0]],
+                         'ivl': ['(2)', '(4)'],
+                         'leaves': [6, 9],
+                         'leaves_color_list': ['C0', 'C0'],
+                         })
+
+        R = dendrogram(Z, 2, 'mtica', show_contracted=True)
+        plt.close()
+        R['dcoord'] = np.asarray(R['dcoord'])
+        assert_equal(R, {'color_list': ['C1', 'C0', 'C0', 'C0'],
+                         'dcoord': [[0.0, 138.0, 138.0, 0.0],
+                                    [0.0, 255.0, 255.0, 0.0],
+                                    [0.0, 268.0, 268.0, 255.0],
+                                    [138.0, 295.0, 295.0, 268.0]],
+                         'icoord': [[5.0, 5.0, 15.0, 15.0],
+                                    [35.0, 35.0, 45.0, 45.0],
+                                    [25.0, 25.0, 40.0, 40.0],
+                                    [10.0, 10.0, 32.5, 32.5]],
+                         'ivl': ['2', '5', '1', '0', '(2)'],
+                         'leaves': [2, 5, 1, 0, 7],
+                         'leaves_color_list': ['C1', 'C1', 'C0', 'C0', 'C0'],
+                         })
+
+    def test_dendrogram_colors(self, xp):
+        # Tests dendrogram plots with alternate colors
+        Z = linkage(xp.asarray(hierarchy_test_data.ytdist), 'single')
+
+        set_link_color_palette(['c', 'm', 'y', 'k'])
+        R = dendrogram(Z, no_plot=True,
+                       above_threshold_color='g', color_threshold=250)
+        set_link_color_palette(['g', 'r', 'c', 'm', 'y', 'k'])
+
+        color_list = R['color_list']
+        assert_equal(color_list, ['c', 'm', 'g', 'g', 'g'])
+
+        # reset color palette (global list)
+        set_link_color_palette(None)
+
+    def test_dendrogram_leaf_colors_zero_dist(self, xp):
+        # tests that the colors of leafs are correct for tree
+        # with two identical points
+        x = xp.asarray([[1, 0, 0],
+                        [0, 0, 1],
+                        [0, 2, 0],
+                        [0, 0, 1],
+                        [0, 1, 0],
+                        [0, 1, 0]])
+        z = linkage(x, "single")
+        d = dendrogram(z, no_plot=True)
+        exp_colors = ['C0', 'C1', 'C1', 'C0', 'C2', 'C2']
+        colors = d["leaves_color_list"]
+        assert_equal(colors, exp_colors)
+
+    def test_dendrogram_leaf_colors(self, xp):
+        # tests that the colors are correct for a tree
+        # with two near points ((0, 0, 1.1) and (0, 0, 1))
+        x = xp.asarray([[1, 0, 0],
+                        [0, 0, 1.1],
+                        [0, 2, 0],
+                        [0, 0, 1],
+                        [0, 1, 0],
+                        [0, 1, 0]])
+        z = linkage(x, "single")
+        d = dendrogram(z, no_plot=True)
+        exp_colors = ['C0', 'C1', 'C1', 'C0', 'C2', 'C2']
+        colors = d["leaves_color_list"]
+        assert_equal(colors, exp_colors)
+
+
+def calculate_maximum_distances(Z, xp):
+    # Used for testing correctness of maxdists.
+    n = Z.shape[0] + 1
+    B = xp.zeros((n-1,), dtype=Z.dtype)
+    q = xp.zeros((3,))
+    for i in range(0, n - 1):
+        q[:] = 0.0
+        left = Z[i, 0]
+        right = Z[i, 1]
+        if left >= n:
+            q[0] = B[xp.asarray(left, dtype=xp.int64) - n]
+        if right >= n:
+            q[1] = B[xp.asarray(right, dtype=xp.int64) - n]
+        q[2] = Z[i, 2]
+        B[i] = xp.max(q)
+    return B
+
+
+def calculate_maximum_inconsistencies(Z, R, k=3, xp=np):
+    # Used for testing correctness of maxinconsts.
+    n = Z.shape[0] + 1
+    dtype = xp.result_type(Z, R)
+    B = xp.zeros((n-1,), dtype=dtype)
+    q = xp.zeros((3,))
+    for i in range(0, n - 1):
+        q[:] = 0.0
+        left = Z[i, 0]
+        right = Z[i, 1]
+        if left >= n:
+            q[0] = B[xp.asarray(left, dtype=xp.int64) - n]
+        if right >= n:
+            q[1] = B[xp.asarray(right, dtype=xp.int64) - n]
+        q[2] = R[i, k]
+        B[i] = xp.max(q)
+    return B
+
+
+@skip_if_array_api(cpu_only=True)
+def test_unsupported_uncondensed_distance_matrix_linkage_warning(xp):
+    assert_warns(ClusterWarning, linkage, xp.asarray([[0, 1], [1, 0]]))
+
+
+def test_euclidean_linkage_value_error(xp):
+    for method in scipy.cluster.hierarchy._EUCLIDEAN_METHODS:
+        assert_raises(ValueError, linkage, xp.asarray([[1, 1], [1, 1]]),
+                      method=method, metric='cityblock')
+
+
+@skip_if_array_api(cpu_only=True)
+def test_2x2_linkage(xp):
+    Z1 = linkage(xp.asarray([1]), method='single', metric='euclidean')
+    Z2 = linkage(xp.asarray([[0, 1], [0, 0]]), method='single', metric='euclidean')
+    xp_assert_close(Z1, Z2, rtol=1e-15)
+
+
+@skip_if_array_api(cpu_only=True)
+def test_node_compare(xp):
+    np.random.seed(23)
+    nobs = 50
+    X = np.random.randn(nobs, 4)
+    X = xp.asarray(X)
+    Z = scipy.cluster.hierarchy.ward(X)
+    tree = to_tree(Z)
+    assert_(tree > tree.get_left())
+    assert_(tree.get_right() > tree.get_left())
+    assert_(tree.get_right() == tree.get_right())
+    assert_(tree.get_right() != tree.get_left())
+
+
+@skip_if_array_api(np_only=True, reasons=['`cut_tree` uses non-standard indexing'])
+def test_cut_tree(xp):
+    np.random.seed(23)
+    nobs = 50
+    X = np.random.randn(nobs, 4)
+    X = xp.asarray(X)
+    Z = scipy.cluster.hierarchy.ward(X)
+    cutree = cut_tree(Z)
+
+    # cutree.dtype varies between int32 and int64 over platforms
+    xp_assert_close(cutree[:, 0], xp.arange(nobs), rtol=1e-15, check_dtype=False)
+    xp_assert_close(cutree[:, -1], xp.zeros(nobs), rtol=1e-15, check_dtype=False)
+    assert_equal(np.asarray(cutree).max(0), np.arange(nobs - 1, -1, -1))
+
+    xp_assert_close(cutree[:, [-5]], cut_tree(Z, n_clusters=5), rtol=1e-15)
+    xp_assert_close(cutree[:, [-5, -10]], cut_tree(Z, n_clusters=[5, 10]), rtol=1e-15)
+    xp_assert_close(cutree[:, [-10, -5]], cut_tree(Z, n_clusters=[10, 5]), rtol=1e-15)
+
+    nodes = _order_cluster_tree(Z)
+    heights = xp.asarray([node.dist for node in nodes])
+
+    xp_assert_close(cutree[:, np.searchsorted(heights, [5])],
+                    cut_tree(Z, height=5), rtol=1e-15)
+    xp_assert_close(cutree[:, np.searchsorted(heights, [5, 10])],
+                    cut_tree(Z, height=[5, 10]), rtol=1e-15)
+    xp_assert_close(cutree[:, np.searchsorted(heights, [10, 5])],
+                    cut_tree(Z, height=[10, 5]), rtol=1e-15)
+
+
+@skip_if_array_api(cpu_only=True)
+def test_optimal_leaf_ordering(xp):
+    # test with the distance vector y
+    Z = optimal_leaf_ordering(linkage(xp.asarray(hierarchy_test_data.ytdist)),
+                              xp.asarray(hierarchy_test_data.ytdist))
+    expectedZ = hierarchy_test_data.linkage_ytdist_single_olo
+    xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-10)
+
+    # test with the observation matrix X
+    Z = optimal_leaf_ordering(linkage(xp.asarray(hierarchy_test_data.X), 'ward'),
+                              xp.asarray(hierarchy_test_data.X))
+    expectedZ = hierarchy_test_data.linkage_X_ward_olo
+    xp_assert_close(Z, xp.asarray(expectedZ), atol=1e-06)
+
+
+@skip_if_array_api(np_only=True, reasons=['`Heap` only supports NumPy backend'])
+def test_Heap(xp):
+    values = xp.asarray([2, -1, 0, -1.5, 3])
+    heap = Heap(values)
+
+    pair = heap.get_min()
+    assert_equal(pair['key'], 3)
+    assert_equal(pair['value'], -1.5)
+
+    heap.remove_min()
+    pair = heap.get_min()
+    assert_equal(pair['key'], 1)
+    assert_equal(pair['value'], -1)
+
+    heap.change_value(1, 2.5)
+    pair = heap.get_min()
+    assert_equal(pair['key'], 2)
+    assert_equal(pair['value'], 0)
+
+    heap.remove_min()
+    heap.remove_min()
+
+    heap.change_value(1, 10)
+    pair = heap.get_min()
+    assert_equal(pair['key'], 4)
+    assert_equal(pair['value'], 3)
+
+    heap.remove_min()
+    pair = heap.get_min()
+    assert_equal(pair['key'], 1)
+    assert_equal(pair['value'], 10)

venv/lib/python3.10/site-packages/scipy/cluster/vq.py

@@ -0,0 +1,835 @@
+"""
+K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
+====================================================================
+
+Provides routines for k-means clustering, generating code books
+from k-means models and quantizing vectors by comparing them with
+centroids in a code book.
+
+.. autosummary::
+   :toctree: generated/
+
+   whiten -- Normalize a group of observations so each feature has unit variance
+   vq -- Calculate code book membership of a set of observation vectors
+   kmeans -- Perform k-means on a set of observation vectors forming k clusters
+   kmeans2 -- A different implementation of k-means with more methods
+           -- for initializing centroids
+
+Background information
+----------------------
+The k-means algorithm takes as input the number of clusters to
+generate, k, and a set of observation vectors to cluster. It
+returns a set of centroids, one for each of the k clusters. An
+observation vector is classified with the cluster number or
+centroid index of the centroid closest to it.
+
+A vector v belongs to cluster i if it is closer to centroid i than
+any other centroid. If v belongs to i, we say centroid i is the
+dominating centroid of v. The k-means algorithm tries to
+minimize distortion, which is defined as the sum of the squared distances
+between each observation vector and its dominating centroid.
+The minimization is achieved by iteratively reclassifying
+the observations into clusters and recalculating the centroids until
+a configuration is reached in which the centroids are stable. One can
+also define a maximum number of iterations.
+
+Since vector quantization is a natural application for k-means,
+information theory terminology is often used. The centroid index
+or cluster index is also referred to as a "code" and the table
+mapping codes to centroids and, vice versa, is often referred to as a
+"code book". The result of k-means, a set of centroids, can be
+used to quantize vectors. Quantization aims to find an encoding of
+vectors that reduces the expected distortion.
+
+All routines expect obs to be an M by N array, where the rows are
+the observation vectors. The codebook is a k by N array, where the
+ith row is the centroid of code word i. The observation vectors
+and centroids have the same feature dimension.
+
+As an example, suppose we wish to compress a 24-bit color image
+(each pixel is represented by one byte for red, one for blue, and
+one for green) before sending it over the web. By using a smaller
+8-bit encoding, we can reduce the amount of data by two
+thirds. Ideally, the colors for each of the 256 possible 8-bit
+encoding values should be chosen to minimize distortion of the
+color. Running k-means with k=256 generates a code book of 256
+codes, which fills up all possible 8-bit sequences. Instead of
+sending a 3-byte value for each pixel, the 8-bit centroid index
+(or code word) of the dominating centroid is transmitted. The code
+book is also sent over the wire so each 8-bit code can be
+translated back to a 24-bit pixel value representation. If the
+image of interest was of an ocean, we would expect many 24-bit
+blues to be represented by 8-bit codes. If it was an image of a
+human face, more flesh-tone colors would be represented in the
+code book.
+
+"""
+import warnings
+import numpy as np
+from collections import deque
+from scipy._lib._array_api import (
+    _asarray, array_namespace, size, atleast_nd, copy, cov
+)
+from scipy._lib._util import check_random_state, rng_integers
+from scipy.spatial.distance import cdist
+
+from . import _vq
+
+__docformat__ = 'restructuredtext'
+
+__all__ = ['whiten', 'vq', 'kmeans', 'kmeans2']
+
+
+class ClusterError(Exception):
+    pass
+
+
+def whiten(obs, check_finite=True):
+    """
+    Normalize a group of observations on a per feature basis.
+
+    Before running k-means, it is beneficial to rescale each feature
+    dimension of the observation set by its standard deviation (i.e. "whiten"
+    it - as in "white noise" where each frequency has equal power).
+    Each feature is divided by its standard deviation across all observations
+    to give it unit variance.
+
+    Parameters
+    ----------
+    obs : ndarray
+        Each row of the array is an observation.  The
+        columns are the features seen during each observation.
+
+        >>> #         f0    f1    f2
+        >>> obs = [[  1.,   1.,   1.],  #o0
+        ...        [  2.,   2.,   2.],  #o1
+        ...        [  3.,   3.,   3.],  #o2
+        ...        [  4.,   4.,   4.]]  #o3
+
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+
+    Returns
+    -------
+    result : ndarray
+        Contains the values in `obs` scaled by the standard deviation
+        of each column.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.cluster.vq import whiten
+    >>> features  = np.array([[1.9, 2.3, 1.7],
+    ...                       [1.5, 2.5, 2.2],
+    ...                       [0.8, 0.6, 1.7,]])
+    >>> whiten(features)
+    array([[ 4.17944278,  2.69811351,  7.21248917],
+           [ 3.29956009,  2.93273208,  9.33380951],
+           [ 1.75976538,  0.7038557 ,  7.21248917]])
+
+    """
+    xp = array_namespace(obs)
+    obs = _asarray(obs, check_finite=check_finite, xp=xp)
+    std_dev = xp.std(obs, axis=0)
+    zero_std_mask = std_dev == 0
+    if xp.any(zero_std_mask):
+        std_dev[zero_std_mask] = 1.0
+        warnings.warn("Some columns have standard deviation zero. "
+                      "The values of these columns will not change.",
+                      RuntimeWarning, stacklevel=2)
+    return obs / std_dev
+
+
+def vq(obs, code_book, check_finite=True):
+    """
+    Assign codes from a code book to observations.
+
+    Assigns a code from a code book to each observation. Each
+    observation vector in the 'M' by 'N' `obs` array is compared with the
+    centroids in the code book and assigned the code of the closest
+    centroid.
+
+    The features in `obs` should have unit variance, which can be
+    achieved by passing them through the whiten function. The code
+    book can be created with the k-means algorithm or a different
+    encoding algorithm.
+
+    Parameters
+    ----------
+    obs : ndarray
+        Each row of the 'M' x 'N' array is an observation. The columns are
+        the "features" seen during each observation. The features must be
+        whitened first using the whiten function or something equivalent.
+    code_book : ndarray
+        The code book is usually generated using the k-means algorithm.
+        Each row of the array holds a different code, and the columns are
+        the features of the code.
+
+         >>> #              f0    f1    f2   f3
+         >>> code_book = [
+         ...             [  1.,   2.,   3.,   4.],  #c0
+         ...             [  1.,   2.,   3.,   4.],  #c1
+         ...             [  1.,   2.,   3.,   4.]]  #c2
+
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+
+    Returns
+    -------
+    code : ndarray
+        A length M array holding the code book index for each observation.
+    dist : ndarray
+        The distortion (distance) between the observation and its nearest
+        code.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.cluster.vq import vq
+    >>> code_book = np.array([[1., 1., 1.],
+    ...                       [2., 2., 2.]])
+    >>> features  = np.array([[1.9, 2.3, 1.7],
+    ...                       [1.5, 2.5, 2.2],
+    ...                       [0.8, 0.6, 1.7]])
+    >>> vq(features, code_book)
+    (array([1, 1, 0], dtype=int32), array([0.43588989, 0.73484692, 0.83066239]))
+
+    """
+    xp = array_namespace(obs, code_book)
+    obs = _asarray(obs, xp=xp, check_finite=check_finite)
+    code_book = _asarray(code_book, xp=xp, check_finite=check_finite)
+    ct = xp.result_type(obs, code_book)
+
+    c_obs = xp.astype(obs, ct, copy=False)
+    c_code_book = xp.astype(code_book, ct, copy=False)
+
+    if xp.isdtype(ct, kind='real floating'):
+        c_obs = np.asarray(c_obs)
+        c_code_book = np.asarray(c_code_book)
+        result = _vq.vq(c_obs, c_code_book)
+        return xp.asarray(result[0]), xp.asarray(result[1])
+    return py_vq(obs, code_book, check_finite=False)
+
+
+def py_vq(obs, code_book, check_finite=True):
+    """ Python version of vq algorithm.
+
+    The algorithm computes the Euclidean distance between each
+    observation and every frame in the code_book.
+
+    Parameters
+    ----------
+    obs : ndarray
+        Expects a rank 2 array. Each row is one observation.
+    code_book : ndarray
+        Code book to use. Same format than obs. Should have same number of
+        features (e.g., columns) than obs.
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+
+    Returns
+    -------
+    code : ndarray
+        code[i] gives the label of the ith obversation; its code is
+        code_book[code[i]].
+    mind_dist : ndarray
+        min_dist[i] gives the distance between the ith observation and its
+        corresponding code.
+
+    Notes
+    -----
+    This function is slower than the C version but works for
+    all input types. If the inputs have the wrong types for the
+    C versions of the function, this one is called as a last resort.
+
+    It is about 20 times slower than the C version.
+
+    """
+    xp = array_namespace(obs, code_book)
+    obs = _asarray(obs, xp=xp, check_finite=check_finite)
+    code_book = _asarray(code_book, xp=xp, check_finite=check_finite)
+
+    if obs.ndim != code_book.ndim:
+        raise ValueError("Observation and code_book should have the same rank")
+
+    if obs.ndim == 1:
+        obs = obs[:, xp.newaxis]
+        code_book = code_book[:, xp.newaxis]
+
+    # Once `cdist` has array API support, this `xp.asarray` call can be removed
+    dist = xp.asarray(cdist(obs, code_book))
+    code = xp.argmin(dist, axis=1)
+    min_dist = xp.min(dist, axis=1)
+    return code, min_dist
+
+
+def _kmeans(obs, guess, thresh=1e-5, xp=None):
+    """ "raw" version of k-means.
+
+    Returns
+    -------
+    code_book
+        The lowest distortion codebook found.
+    avg_dist
+        The average distance a observation is from a code in the book.
+        Lower means the code_book matches the data better.
+
+    See Also
+    --------
+    kmeans : wrapper around k-means
+
+    Examples
+    --------
+    Note: not whitened in this example.
+
+    >>> import numpy as np
+    >>> from scipy.cluster.vq import _kmeans
+    >>> features  = np.array([[ 1.9,2.3],
+    ...                       [ 1.5,2.5],
+    ...                       [ 0.8,0.6],
+    ...                       [ 0.4,1.8],
+    ...                       [ 1.0,1.0]])
+    >>> book = np.array((features[0],features[2]))
+    >>> _kmeans(features,book)
+    (array([[ 1.7       ,  2.4       ],
+           [ 0.73333333,  1.13333333]]), 0.40563916697728591)
+
+    """
+    xp = np if xp is None else xp
+    code_book = guess
+    diff = xp.inf
+    prev_avg_dists = deque([diff], maxlen=2)
+    while diff > thresh:
+        # compute membership and distances between obs and code_book
+        obs_code, distort = vq(obs, code_book, check_finite=False)
+        prev_avg_dists.append(xp.mean(distort, axis=-1))
+        # recalc code_book as centroids of associated obs
+        obs = np.asarray(obs)
+        obs_code = np.asarray(obs_code)
+        code_book, has_members = _vq.update_cluster_means(obs, obs_code,
+                                                          code_book.shape[0])
+        obs = xp.asarray(obs)
+        obs_code = xp.asarray(obs_code)
+        code_book = xp.asarray(code_book)
+        has_members = xp.asarray(has_members)
+        code_book = code_book[has_members]
+        diff = xp.abs(prev_avg_dists[0] - prev_avg_dists[1])
+
+    return code_book, prev_avg_dists[1]
+
+
+def kmeans(obs, k_or_guess, iter=20, thresh=1e-5, check_finite=True,
+           *, seed=None):
+    """
+    Performs k-means on a set of observation vectors forming k clusters.
+
+    The k-means algorithm adjusts the classification of the observations
+    into clusters and updates the cluster centroids until the position of
+    the centroids is stable over successive iterations. In this
+    implementation of the algorithm, the stability of the centroids is
+    determined by comparing the absolute value of the change in the average
+    Euclidean distance between the observations and their corresponding
+    centroids against a threshold. This yields
+    a code book mapping centroids to codes and vice versa.
+
+    Parameters
+    ----------
+    obs : ndarray
+       Each row of the M by N array is an observation vector. The
+       columns are the features seen during each observation.
+       The features must be whitened first with the `whiten` function.
+
+    k_or_guess : int or ndarray
+       The number of centroids to generate. A code is assigned to
+       each centroid, which is also the row index of the centroid
+       in the code_book matrix generated.
+
+       The initial k centroids are chosen by randomly selecting
+       observations from the observation matrix. Alternatively,
+       passing a k by N array specifies the initial k centroids.
+
+    iter : int, optional
+       The number of times to run k-means, returning the codebook
+       with the lowest distortion. This argument is ignored if
+       initial centroids are specified with an array for the
+       ``k_or_guess`` parameter. This parameter does not represent the
+       number of iterations of the k-means algorithm.
+
+    thresh : float, optional
+       Terminates the k-means algorithm if the change in
+       distortion since the last k-means iteration is less than
+       or equal to threshold.
+
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+
+    seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional
+        Seed for initializing the pseudo-random number generator.
+        If `seed` is None (or `numpy.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+        The default is None.
+
+    Returns
+    -------
+    codebook : ndarray
+       A k by N array of k centroids. The ith centroid
+       codebook[i] is represented with the code i. The centroids
+       and codes generated represent the lowest distortion seen,
+       not necessarily the globally minimal distortion.
+       Note that the number of centroids is not necessarily the same as the
+       ``k_or_guess`` parameter, because centroids assigned to no observations
+       are removed during iterations.
+
+    distortion : float
+       The mean (non-squared) Euclidean distance between the observations
+       passed and the centroids generated. Note the difference to the standard
+       definition of distortion in the context of the k-means algorithm, which
+       is the sum of the squared distances.
+
+    See Also
+    --------
+    kmeans2 : a different implementation of k-means clustering
+       with more methods for generating initial centroids but without
+       using a distortion change threshold as a stopping criterion.
+
+    whiten : must be called prior to passing an observation matrix
+       to kmeans.
+
+    Notes
+    -----
+    For more functionalities or optimal performance, you can use
+    `sklearn.cluster.KMeans <https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html>`_.
+    `This <https://hdbscan.readthedocs.io/en/latest/performance_and_scalability.html#comparison-of-high-performance-implementations>`_
+    is a benchmark result of several implementations.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.cluster.vq import vq, kmeans, whiten
+    >>> import matplotlib.pyplot as plt
+    >>> features  = np.array([[ 1.9,2.3],
+    ...                       [ 1.5,2.5],
+    ...                       [ 0.8,0.6],
+    ...                       [ 0.4,1.8],
+    ...                       [ 0.1,0.1],
+    ...                       [ 0.2,1.8],
+    ...                       [ 2.0,0.5],
+    ...                       [ 0.3,1.5],
+    ...                       [ 1.0,1.0]])
+    >>> whitened = whiten(features)
+    >>> book = np.array((whitened[0],whitened[2]))
+    >>> kmeans(whitened,book)
+    (array([[ 2.3110306 ,  2.86287398],    # random
+           [ 0.93218041,  1.24398691]]), 0.85684700941625547)
+
+    >>> codes = 3
+    >>> kmeans(whitened,codes)
+    (array([[ 2.3110306 ,  2.86287398],    # random
+           [ 1.32544402,  0.65607529],
+           [ 0.40782893,  2.02786907]]), 0.5196582527686241)
+
+    >>> # Create 50 datapoints in two clusters a and b
+    >>> pts = 50
+    >>> rng = np.random.default_rng()
+    >>> a = rng.multivariate_normal([0, 0], [[4, 1], [1, 4]], size=pts)
+    >>> b = rng.multivariate_normal([30, 10],
+    ...                             [[10, 2], [2, 1]],
+    ...                             size=pts)
+    >>> features = np.concatenate((a, b))
+    >>> # Whiten data
+    >>> whitened = whiten(features)
+    >>> # Find 2 clusters in the data
+    >>> codebook, distortion = kmeans(whitened, 2)
+    >>> # Plot whitened data and cluster centers in red
+    >>> plt.scatter(whitened[:, 0], whitened[:, 1])
+    >>> plt.scatter(codebook[:, 0], codebook[:, 1], c='r')
+    >>> plt.show()
+
+    """
+    if isinstance(k_or_guess, int):
+        xp = array_namespace(obs)
+    else:
+        xp = array_namespace(obs, k_or_guess)
+    obs = _asarray(obs, xp=xp, check_finite=check_finite)
+    guess = _asarray(k_or_guess, xp=xp, check_finite=check_finite)
+    if iter < 1:
+        raise ValueError("iter must be at least 1, got %s" % iter)
+
+    # Determine whether a count (scalar) or an initial guess (array) was passed.
+    if size(guess) != 1:
+        if size(guess) < 1:
+            raise ValueError("Asked for 0 clusters. Initial book was %s" %
+                             guess)
+        return _kmeans(obs, guess, thresh=thresh, xp=xp)
+
+    # k_or_guess is a scalar, now verify that it's an integer
+    k = int(guess)
+    if k != guess:
+        raise ValueError("If k_or_guess is a scalar, it must be an integer.")
+    if k < 1:
+        raise ValueError("Asked for %d clusters." % k)
+
+    rng = check_random_state(seed)
+
+    # initialize best distance value to a large value
+    best_dist = xp.inf
+    for i in range(iter):
+        # the initial code book is randomly selected from observations
+        guess = _kpoints(obs, k, rng, xp)
+        book, dist = _kmeans(obs, guess, thresh=thresh, xp=xp)
+        if dist < best_dist:
+            best_book = book
+            best_dist = dist
+    return best_book, best_dist
+
+
+def _kpoints(data, k, rng, xp):
+    """Pick k points at random in data (one row = one observation).
+
+    Parameters
+    ----------
+    data : ndarray
+        Expect a rank 1 or 2 array. Rank 1 are assumed to describe one
+        dimensional data, rank 2 multidimensional data, in which case one
+        row is one observation.
+    k : int
+        Number of samples to generate.
+    rng : `numpy.random.Generator` or `numpy.random.RandomState`
+        Random number generator.
+
+    Returns
+    -------
+    x : ndarray
+        A 'k' by 'N' containing the initial centroids
+
+    """
+    idx = rng.choice(data.shape[0], size=int(k), replace=False)
+    # convert to array with default integer dtype (avoids numpy#25607)
+    idx = xp.asarray(idx, dtype=xp.asarray([1]).dtype)
+    return xp.take(data, idx, axis=0)
+
+
+def _krandinit(data, k, rng, xp):
+    """Returns k samples of a random variable whose parameters depend on data.
+
+    More precisely, it returns k observations sampled from a Gaussian random
+    variable whose mean and covariances are the ones estimated from the data.
+
+    Parameters
+    ----------
+    data : ndarray
+        Expect a rank 1 or 2 array. Rank 1 is assumed to describe 1-D
+        data, rank 2 multidimensional data, in which case one
+        row is one observation.
+    k : int
+        Number of samples to generate.
+    rng : `numpy.random.Generator` or `numpy.random.RandomState`
+        Random number generator.
+
+    Returns
+    -------
+    x : ndarray
+        A 'k' by 'N' containing the initial centroids
+
+    """
+    mu = xp.mean(data, axis=0)
+    k = np.asarray(k)
+
+    if data.ndim == 1:
+        _cov = cov(data)
+        x = rng.standard_normal(size=k)
+        x = xp.asarray(x)
+        x *= xp.sqrt(_cov)
+    elif data.shape[1] > data.shape[0]:
+        # initialize when the covariance matrix is rank deficient
+        _, s, vh = xp.linalg.svd(data - mu, full_matrices=False)
+        x = rng.standard_normal(size=(k, size(s)))
+        x = xp.asarray(x)
+        sVh = s[:, None] * vh / xp.sqrt(data.shape[0] - xp.asarray(1.))
+        x = x @ sVh
+    else:
+        _cov = atleast_nd(cov(data.T), ndim=2)
+
+        # k rows, d cols (one row = one obs)
+        # Generate k sample of a random variable ~ Gaussian(mu, cov)
+        x = rng.standard_normal(size=(k, size(mu)))
+        x = xp.asarray(x)
+        x = x @ xp.linalg.cholesky(_cov).T
+
+    x += mu
+    return x
+
+
+def _kpp(data, k, rng, xp):
+    """ Picks k points in the data based on the kmeans++ method.
+
+    Parameters
+    ----------
+    data : ndarray
+        Expect a rank 1 or 2 array. Rank 1 is assumed to describe 1-D
+        data, rank 2 multidimensional data, in which case one
+        row is one observation.
+    k : int
+        Number of samples to generate.
+    rng : `numpy.random.Generator` or `numpy.random.RandomState`
+        Random number generator.
+
+    Returns
+    -------
+    init : ndarray
+        A 'k' by 'N' containing the initial centroids.
+
+    References
+    ----------
+    .. [1] D. Arthur and S. Vassilvitskii, "k-means++: the advantages of
+       careful seeding", Proceedings of the Eighteenth Annual ACM-SIAM Symposium
+       on Discrete Algorithms, 2007.
+    """
+
+    ndim = len(data.shape)
+    if ndim == 1:
+        data = data[:, None]
+
+    dims = data.shape[1]
+
+    init = xp.empty((int(k), dims))
+
+    for i in range(k):
+        if i == 0:
+            init[i, :] = data[rng_integers(rng, data.shape[0]), :]
+
+        else:
+            D2 = cdist(init[:i,:], data, metric='sqeuclidean').min(axis=0)
+            probs = D2/D2.sum()
+            cumprobs = probs.cumsum()
+            r = rng.uniform()
+            cumprobs = np.asarray(cumprobs)
+            init[i, :] = data[np.searchsorted(cumprobs, r), :]
+
+    if ndim == 1:
+        init = init[:, 0]
+    return init
+
+
+_valid_init_meth = {'random': _krandinit, 'points': _kpoints, '++': _kpp}
+
+
+def _missing_warn():
+    """Print a warning when called."""
+    warnings.warn("One of the clusters is empty. "
+                  "Re-run kmeans with a different initialization.",
+                  stacklevel=3)
+
+
+def _missing_raise():
+    """Raise a ClusterError when called."""
+    raise ClusterError("One of the clusters is empty. "
+                       "Re-run kmeans with a different initialization.")
+
+
+_valid_miss_meth = {'warn': _missing_warn, 'raise': _missing_raise}
+
+
+def kmeans2(data, k, iter=10, thresh=1e-5, minit='random',
+            missing='warn', check_finite=True, *, seed=None):
+    """
+    Classify a set of observations into k clusters using the k-means algorithm.
+
+    The algorithm attempts to minimize the Euclidean distance between
+    observations and centroids. Several initialization methods are
+    included.
+
+    Parameters
+    ----------
+    data : ndarray
+        A 'M' by 'N' array of 'M' observations in 'N' dimensions or a length
+        'M' array of 'M' 1-D observations.
+    k : int or ndarray
+        The number of clusters to form as well as the number of
+        centroids to generate. If `minit` initialization string is
+        'matrix', or if a ndarray is given instead, it is
+        interpreted as initial cluster to use instead.
+    iter : int, optional
+        Number of iterations of the k-means algorithm to run. Note
+        that this differs in meaning from the iters parameter to
+        the kmeans function.
+    thresh : float, optional
+        (not used yet)
+    minit : str, optional
+        Method for initialization. Available methods are 'random',
+        'points', '++' and 'matrix':
+
+        'random': generate k centroids from a Gaussian with mean and
+        variance estimated from the data.
+
+        'points': choose k observations (rows) at random from data for
+        the initial centroids.
+
+        '++': choose k observations accordingly to the kmeans++ method
+        (careful seeding)
+
+        'matrix': interpret the k parameter as a k by M (or length k
+        array for 1-D data) array of initial centroids.
+    missing : str, optional
+        Method to deal with empty clusters. Available methods are
+        'warn' and 'raise':
+
+        'warn': give a warning and continue.
+
+        'raise': raise an ClusterError and terminate the algorithm.
+    check_finite : bool, optional
+        Whether to check that the input matrices contain only finite numbers.
+        Disabling may give a performance gain, but may result in problems
+        (crashes, non-termination) if the inputs do contain infinities or NaNs.
+        Default: True
+    seed : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional
+        Seed for initializing the pseudo-random number generator.
+        If `seed` is None (or `numpy.random`), the `numpy.random.RandomState`
+        singleton is used.
+        If `seed` is an int, a new ``RandomState`` instance is used,
+        seeded with `seed`.
+        If `seed` is already a ``Generator`` or ``RandomState`` instance then
+        that instance is used.
+        The default is None.
+
+    Returns
+    -------
+    centroid : ndarray
+        A 'k' by 'N' array of centroids found at the last iteration of
+        k-means.
+    label : ndarray
+        label[i] is the code or index of the centroid the
+        ith observation is closest to.
+
+    See Also
+    --------
+    kmeans
+
+    References
+    ----------
+    .. [1] D. Arthur and S. Vassilvitskii, "k-means++: the advantages of
+       careful seeding", Proceedings of the Eighteenth Annual ACM-SIAM Symposium
+       on Discrete Algorithms, 2007.
+
+    Examples
+    --------
+    >>> from scipy.cluster.vq import kmeans2
+    >>> import matplotlib.pyplot as plt
+    >>> import numpy as np
+
+    Create z, an array with shape (100, 2) containing a mixture of samples
+    from three multivariate normal distributions.
+
+    >>> rng = np.random.default_rng()
+    >>> a = rng.multivariate_normal([0, 6], [[2, 1], [1, 1.5]], size=45)
+    >>> b = rng.multivariate_normal([2, 0], [[1, -1], [-1, 3]], size=30)
+    >>> c = rng.multivariate_normal([6, 4], [[5, 0], [0, 1.2]], size=25)
+    >>> z = np.concatenate((a, b, c))
+    >>> rng.shuffle(z)
+
+    Compute three clusters.
+
+    >>> centroid, label = kmeans2(z, 3, minit='points')
+    >>> centroid
+    array([[ 2.22274463, -0.61666946],  # may vary
+           [ 0.54069047,  5.86541444],
+           [ 6.73846769,  4.01991898]])
+
+    How many points are in each cluster?
+
+    >>> counts = np.bincount(label)
+    >>> counts
+    array([29, 51, 20])  # may vary
+
+    Plot the clusters.
+
+    >>> w0 = z[label == 0]
+    >>> w1 = z[label == 1]
+    >>> w2 = z[label == 2]
+    >>> plt.plot(w0[:, 0], w0[:, 1], 'o', alpha=0.5, label='cluster 0')
+    >>> plt.plot(w1[:, 0], w1[:, 1], 'd', alpha=0.5, label='cluster 1')
+    >>> plt.plot(w2[:, 0], w2[:, 1], 's', alpha=0.5, label='cluster 2')
+    >>> plt.plot(centroid[:, 0], centroid[:, 1], 'k*', label='centroids')
+    >>> plt.axis('equal')
+    >>> plt.legend(shadow=True)
+    >>> plt.show()
+
+    """
+    if int(iter) < 1:
+        raise ValueError("Invalid iter (%s), "
+                         "must be a positive integer." % iter)
+    try:
+        miss_meth = _valid_miss_meth[missing]
+    except KeyError as e:
+        raise ValueError(f"Unknown missing method {missing!r}") from e
+
+    if isinstance(k, int):
+        xp = array_namespace(data)
+    else:
+        xp = array_namespace(data, k)
+    data = _asarray(data, xp=xp, check_finite=check_finite)
+    code_book = copy(k, xp=xp)
+    if data.ndim == 1:
+        d = 1
+    elif data.ndim == 2:
+        d = data.shape[1]
+    else:
+        raise ValueError("Input of rank > 2 is not supported.")
+
+    if size(data) < 1 or size(code_book) < 1:
+        raise ValueError("Empty input is not supported.")
+
+    # If k is not a single value, it should be compatible with data's shape
+    if minit == 'matrix' or size(code_book) > 1:
+        if data.ndim != code_book.ndim:
+            raise ValueError("k array doesn't match data rank")
+        nc = code_book.shape[0]
+        if data.ndim > 1 and code_book.shape[1] != d:
+            raise ValueError("k array doesn't match data dimension")
+    else:
+        nc = int(code_book)
+
+        if nc < 1:
+            raise ValueError("Cannot ask kmeans2 for %d clusters"
+                             " (k was %s)" % (nc, code_book))
+        elif nc != code_book:
+            warnings.warn("k was not an integer, was converted.", stacklevel=2)
+
+        try:
+            init_meth = _valid_init_meth[minit]
+        except KeyError as e:
+            raise ValueError(f"Unknown init method {minit!r}") from e
+        else:
+            rng = check_random_state(seed)
+            code_book = init_meth(data, code_book, rng, xp)
+
+    data = np.asarray(data)
+    code_book = np.asarray(code_book)
+    for i in range(iter):
+        # Compute the nearest neighbor for each obs using the current code book
+        label = vq(data, code_book, check_finite=check_finite)[0]
+        # Update the code book by computing centroids
+        new_code_book, has_members = _vq.update_cluster_means(data, label, nc)
+        if not has_members.all():
+            miss_meth()
+            # Set the empty clusters to their previous positions
+            new_code_book[~has_members] = code_book[~has_members]
+        code_book = new_code_book
+
+    return xp.asarray(code_book), xp.asarray(label)

venv/lib/python3.10/site-packages/scipy/sparse/linalg/_dsolve/__init__.py

@@ -0,0 +1,71 @@
+"""
+Linear Solvers
+==============
+
+The default solver is SuperLU (included in the scipy distribution),
+which can solve real or complex linear systems in both single and
+double precisions.  It is automatically replaced by UMFPACK, if
+available.  Note that UMFPACK works in double precision only, so
+switch it off by::
+
+    >>> from scipy.sparse.linalg import spsolve, use_solver
+    >>> use_solver(useUmfpack=False)
+
+to solve in the single precision. See also use_solver documentation.
+
+Example session::
+
+    >>> from scipy.sparse import csc_matrix, spdiags
+    >>> from numpy import array
+    >>>
+    >>> print("Inverting a sparse linear system:")
+    >>> print("The sparse matrix (constructed from diagonals):")
+    >>> a = spdiags([[1, 2, 3, 4, 5], [6, 5, 8, 9, 10]], [0, 1], 5, 5)
+    >>> b = array([1, 2, 3, 4, 5])
+    >>> print("Solve: single precision complex:")
+    >>> use_solver( useUmfpack = False )
+    >>> a = a.astype('F')
+    >>> x = spsolve(a, b)
+    >>> print(x)
+    >>> print("Error: ", a@x-b)
+    >>>
+    >>> print("Solve: double precision complex:")
+    >>> use_solver( useUmfpack = True )
+    >>> a = a.astype('D')
+    >>> x = spsolve(a, b)
+    >>> print(x)
+    >>> print("Error: ", a@x-b)
+    >>>
+    >>> print("Solve: double precision:")
+    >>> a = a.astype('d')
+    >>> x = spsolve(a, b)
+    >>> print(x)
+    >>> print("Error: ", a@x-b)
+    >>>
+    >>> print("Solve: single precision:")
+    >>> use_solver( useUmfpack = False )
+    >>> a = a.astype('f')
+    >>> x = spsolve(a, b.astype('f'))
+    >>> print(x)
+    >>> print("Error: ", a@x-b)
+
+"""
+
+#import umfpack
+#__doc__ = '\n\n'.join( (__doc__,  umfpack.__doc__) )
+#del umfpack
+
+from .linsolve import *
+from ._superlu import SuperLU
+from . import _add_newdocs
+from . import linsolve
+
+__all__ = [
+    'MatrixRankWarning', 'SuperLU', 'factorized',
+    'spilu', 'splu', 'spsolve',
+    'spsolve_triangular', 'use_solver'
+]
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

venv/lib/python3.10/site-packages/scipy/sparse/linalg/_dsolve/_add_newdocs.py

@@ -0,0 +1,153 @@
+from numpy.lib import add_newdoc
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU',
+    """
+    LU factorization of a sparse matrix.
+
+    Factorization is represented as::
+
+        Pr @ A @ Pc = L @ U
+
+    To construct these `SuperLU` objects, call the `splu` and `spilu`
+    functions.
+
+    Attributes
+    ----------
+    shape
+    nnz
+    perm_c
+    perm_r
+    L
+    U
+
+    Methods
+    -------
+    solve
+
+    Notes
+    -----
+
+    .. versionadded:: 0.14.0
+
+    Examples
+    --------
+    The LU decomposition can be used to solve matrix equations. Consider:
+
+    >>> import numpy as np
+    >>> from scipy.sparse import csc_matrix
+    >>> from scipy.sparse.linalg import splu
+    >>> A = csc_matrix([[1,2,0,4], [1,0,0,1], [1,0,2,1], [2,2,1,0.]])
+
+    This can be solved for a given right-hand side:
+
+    >>> lu = splu(A)
+    >>> b = np.array([1, 2, 3, 4])
+    >>> x = lu.solve(b)
+    >>> A.dot(x)
+    array([ 1.,  2.,  3.,  4.])
+
+    The ``lu`` object also contains an explicit representation of the
+    decomposition. The permutations are represented as mappings of
+    indices:
+
+    >>> lu.perm_r
+    array([2, 1, 3, 0], dtype=int32)  # may vary
+    >>> lu.perm_c
+    array([0, 1, 3, 2], dtype=int32)  # may vary
+
+    The L and U factors are sparse matrices in CSC format:
+
+    >>> lu.L.toarray()
+    array([[ 1. ,  0. ,  0. ,  0. ],  # may vary
+           [ 0.5,  1. ,  0. ,  0. ],
+           [ 0.5, -1. ,  1. ,  0. ],
+           [ 0.5,  1. ,  0. ,  1. ]])
+    >>> lu.U.toarray()
+    array([[ 2. ,  2. ,  0. ,  1. ],  # may vary
+           [ 0. , -1. ,  1. , -0.5],
+           [ 0. ,  0. ,  5. , -1. ],
+           [ 0. ,  0. ,  0. ,  2. ]])
+
+    The permutation matrices can be constructed:
+
+    >>> Pr = csc_matrix((np.ones(4), (lu.perm_r, np.arange(4))))
+    >>> Pc = csc_matrix((np.ones(4), (np.arange(4), lu.perm_c)))
+
+    We can reassemble the original matrix:
+
+    >>> (Pr.T @ (lu.L @ lu.U) @ Pc.T).toarray()
+    array([[ 1.,  2.,  0.,  4.],
+           [ 1.,  0.,  0.,  1.],
+           [ 1.,  0.,  2.,  1.],
+           [ 2.,  2.,  1.,  0.]])
+    """)
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('solve',
+    """
+    solve(rhs[, trans])
+
+    Solves linear system of equations with one or several right-hand sides.
+
+    Parameters
+    ----------
+    rhs : ndarray, shape (n,) or (n, k)
+        Right hand side(s) of equation
+    trans : {'N', 'T', 'H'}, optional
+        Type of system to solve::
+
+            'N':   A   @ x == rhs  (default)
+            'T':   A^T @ x == rhs
+            'H':   A^H @ x == rhs
+
+        i.e., normal, transposed, and hermitian conjugate.
+
+    Returns
+    -------
+    x : ndarray, shape ``rhs.shape``
+        Solution vector(s)
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('L',
+    """
+    Lower triangular factor with unit diagonal as a
+    `scipy.sparse.csc_matrix`.
+
+    .. versionadded:: 0.14.0
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('U',
+    """
+    Upper triangular factor as a `scipy.sparse.csc_matrix`.
+
+    .. versionadded:: 0.14.0
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('shape',
+    """
+    Shape of the original matrix as a tuple of ints.
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('nnz',
+    """
+    Number of nonzero elements in the matrix.
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('perm_c',
+    """
+    Permutation Pc represented as an array of indices.
+
+    The column permutation matrix can be reconstructed via:
+
+    >>> Pc = np.zeros((n, n))
+    >>> Pc[np.arange(n), perm_c] = 1
+    """))
+
+add_newdoc('scipy.sparse.linalg._dsolve._superlu', 'SuperLU', ('perm_r',
+    """
+    Permutation Pr represented as an array of indices.
+
+    The row permutation matrix can be reconstructed via:
+
+    >>> Pr = np.zeros((n, n))
+    >>> Pr[perm_r, np.arange(n)] = 1
+    """))