update

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/common_tests.py

@@ -0,0 +1,354 @@
+import pickle
+
+import numpy as np
+import numpy.testing as npt
+from numpy.testing import assert_allclose, assert_equal
+from pytest import raises as assert_raises
+
+import numpy.ma.testutils as ma_npt
+
+from scipy._lib._util import (
+    getfullargspec_no_self as _getfullargspec, np_long
+)
+from scipy._lib._array_api import xp_assert_equal
+from scipy import stats
+
+
+def check_named_results(res, attributes, ma=False, xp=None):
+    for i, attr in enumerate(attributes):
+        if ma:
+            ma_npt.assert_equal(res[i], getattr(res, attr))
+        elif xp is not None:
+            xp_assert_equal(res[i], getattr(res, attr))
+        else:
+            npt.assert_equal(res[i], getattr(res, attr))
+
+
+def check_normalization(distfn, args, distname):
+    norm_moment = distfn.moment(0, *args)
+    npt.assert_allclose(norm_moment, 1.0)
+
+    if distname == "rv_histogram_instance":
+        atol, rtol = 1e-5, 0
+    else:
+        atol, rtol = 1e-7, 1e-7
+
+    normalization_expect = distfn.expect(lambda x: 1, args=args)
+    npt.assert_allclose(normalization_expect, 1.0, atol=atol, rtol=rtol,
+                        err_msg=distname, verbose=True)
+
+    _a, _b = distfn.support(*args)
+    normalization_cdf = distfn.cdf(_b, *args)
+    npt.assert_allclose(normalization_cdf, 1.0)
+
+
+def check_moment(distfn, arg, m, v, msg):
+    m1 = distfn.moment(1, *arg)
+    m2 = distfn.moment(2, *arg)
+    if not np.isinf(m):
+        npt.assert_almost_equal(m1, m, decimal=10,
+                                err_msg=msg + ' - 1st moment')
+    else:                     # or np.isnan(m1),
+        npt.assert_(np.isinf(m1),
+                    msg + ' - 1st moment -infinite, m1=%s' % str(m1))
+
+    if not np.isinf(v):
+        npt.assert_almost_equal(m2 - m1 * m1, v, decimal=10,
+                                err_msg=msg + ' - 2ndt moment')
+    else:                     # or np.isnan(m2),
+        npt.assert_(np.isinf(m2), msg + f' - 2nd moment -infinite, {m2=}')
+
+
+def check_mean_expect(distfn, arg, m, msg):
+    if np.isfinite(m):
+        m1 = distfn.expect(lambda x: x, arg)
+        npt.assert_almost_equal(m1, m, decimal=5,
+                                err_msg=msg + ' - 1st moment (expect)')
+
+
+def check_var_expect(distfn, arg, m, v, msg):
+    dist_looser_tolerances = {"rv_histogram_instance" , "ksone"}
+    kwargs = {'rtol': 5e-6} if msg in dist_looser_tolerances else {}
+    if np.isfinite(v):
+        m2 = distfn.expect(lambda x: x*x, arg)
+        npt.assert_allclose(m2, v + m*m, **kwargs)
+
+
+def check_skew_expect(distfn, arg, m, v, s, msg):
+    if np.isfinite(s):
+        m3e = distfn.expect(lambda x: np.power(x-m, 3), arg)
+        npt.assert_almost_equal(m3e, s * np.power(v, 1.5),
+                                decimal=5, err_msg=msg + ' - skew')
+    else:
+        npt.assert_(np.isnan(s))
+
+
+def check_kurt_expect(distfn, arg, m, v, k, msg):
+    if np.isfinite(k):
+        m4e = distfn.expect(lambda x: np.power(x-m, 4), arg)
+        npt.assert_allclose(m4e, (k + 3.) * np.power(v, 2),
+                            atol=1e-5, rtol=1e-5,
+                            err_msg=msg + ' - kurtosis')
+    elif not np.isposinf(k):
+        npt.assert_(np.isnan(k))
+
+
+def check_munp_expect(dist, args, msg):
+    # If _munp is overridden, test a higher moment. (Before gh-18634, some
+    # distributions had issues with moments 5 and higher.)
+    if dist._munp.__func__ != stats.rv_continuous._munp:
+        res = dist.moment(5, *args)  # shouldn't raise an error
+        ref = dist.expect(lambda x: x ** 5, args, lb=-np.inf, ub=np.inf)
+        if not np.isfinite(res):  # could be valid; automated test can't know
+            return
+        # loose tolerance, mostly to see whether _munp returns *something*
+        assert_allclose(res, ref, atol=1e-10, rtol=1e-4,
+                        err_msg=msg + ' - higher moment / _munp')
+
+
+def check_entropy(distfn, arg, msg):
+    ent = distfn.entropy(*arg)
+    npt.assert_(not np.isnan(ent), msg + 'test Entropy is nan')
+
+
+def check_private_entropy(distfn, args, superclass):
+    # compare a generic _entropy with the distribution-specific implementation
+    npt.assert_allclose(distfn._entropy(*args),
+                        superclass._entropy(distfn, *args))
+
+
+def check_entropy_vect_scale(distfn, arg):
+    # check 2-d
+    sc = np.asarray([[1, 2], [3, 4]])
+    v_ent = distfn.entropy(*arg, scale=sc)
+    s_ent = [distfn.entropy(*arg, scale=s) for s in sc.ravel()]
+    s_ent = np.asarray(s_ent).reshape(v_ent.shape)
+    assert_allclose(v_ent, s_ent, atol=1e-14)
+
+    # check invalid value, check cast
+    sc = [1, 2, -3]
+    v_ent = distfn.entropy(*arg, scale=sc)
+    s_ent = [distfn.entropy(*arg, scale=s) for s in sc]
+    s_ent = np.asarray(s_ent).reshape(v_ent.shape)
+    assert_allclose(v_ent, s_ent, atol=1e-14)
+
+
+def check_edge_support(distfn, args):
+    # Make sure that x=self.a and self.b are handled correctly.
+    x = distfn.support(*args)
+    if isinstance(distfn, stats.rv_discrete):
+        x = x[0]-1, x[1]
+
+    npt.assert_equal(distfn.cdf(x, *args), [0.0, 1.0])
+    npt.assert_equal(distfn.sf(x, *args), [1.0, 0.0])
+
+    if distfn.name not in ('skellam', 'dlaplace'):
+        # with a = -inf, log(0) generates warnings
+        npt.assert_equal(distfn.logcdf(x, *args), [-np.inf, 0.0])
+        npt.assert_equal(distfn.logsf(x, *args), [0.0, -np.inf])
+
+    npt.assert_equal(distfn.ppf([0.0, 1.0], *args), x)
+    npt.assert_equal(distfn.isf([0.0, 1.0], *args), x[::-1])
+
+    # out-of-bounds for isf & ppf
+    npt.assert_(np.isnan(distfn.isf([-1, 2], *args)).all())
+    npt.assert_(np.isnan(distfn.ppf([-1, 2], *args)).all())
+
+
+def check_named_args(distfn, x, shape_args, defaults, meths):
+    ## Check calling w/ named arguments.
+
+    # check consistency of shapes, numargs and _parse signature
+    signature = _getfullargspec(distfn._parse_args)
+    npt.assert_(signature.varargs is None)
+    npt.assert_(signature.varkw is None)
+    npt.assert_(not signature.kwonlyargs)
+    npt.assert_(list(signature.defaults) == list(defaults))
+
+    shape_argnames = signature.args[:-len(defaults)]  # a, b, loc=0, scale=1
+    if distfn.shapes:
+        shapes_ = distfn.shapes.replace(',', ' ').split()
+    else:
+        shapes_ = ''
+    npt.assert_(len(shapes_) == distfn.numargs)
+    npt.assert_(len(shapes_) == len(shape_argnames))
+
+    # check calling w/ named arguments
+    shape_args = list(shape_args)
+
+    vals = [meth(x, *shape_args) for meth in meths]
+    npt.assert_(np.all(np.isfinite(vals)))
+
+    names, a, k = shape_argnames[:], shape_args[:], {}
+    while names:
+        k.update({names.pop(): a.pop()})
+        v = [meth(x, *a, **k) for meth in meths]
+        npt.assert_array_equal(vals, v)
+        if 'n' not in k.keys():
+            # `n` is first parameter of moment(), so can't be used as named arg
+            npt.assert_equal(distfn.moment(1, *a, **k),
+                             distfn.moment(1, *shape_args))
+
+    # unknown arguments should not go through:
+    k.update({'kaboom': 42})
+    assert_raises(TypeError, distfn.cdf, x, **k)
+
+
+def check_random_state_property(distfn, args):
+    # check the random_state attribute of a distribution *instance*
+
+    # This test fiddles with distfn.random_state. This breaks other tests,
+    # hence need to save it and then restore.
+    rndm = distfn.random_state
+
+    # baseline: this relies on the global state
+    np.random.seed(1234)
+    distfn.random_state = None
+    r0 = distfn.rvs(*args, size=8)
+
+    # use an explicit instance-level random_state
+    distfn.random_state = 1234
+    r1 = distfn.rvs(*args, size=8)
+    npt.assert_equal(r0, r1)
+
+    distfn.random_state = np.random.RandomState(1234)
+    r2 = distfn.rvs(*args, size=8)
+    npt.assert_equal(r0, r2)
+
+    # check that np.random.Generator can be used (numpy >= 1.17)
+    if hasattr(np.random, 'default_rng'):
+        # obtain a np.random.Generator object
+        rng = np.random.default_rng(1234)
+        distfn.rvs(*args, size=1, random_state=rng)
+
+    # can override the instance-level random_state for an individual .rvs call
+    distfn.random_state = 2
+    orig_state = distfn.random_state.get_state()
+
+    r3 = distfn.rvs(*args, size=8, random_state=np.random.RandomState(1234))
+    npt.assert_equal(r0, r3)
+
+    # ... and that does not alter the instance-level random_state!
+    npt.assert_equal(distfn.random_state.get_state(), orig_state)
+
+    # finally, restore the random_state
+    distfn.random_state = rndm
+
+
+def check_meth_dtype(distfn, arg, meths):
+    q0 = [0.25, 0.5, 0.75]
+    x0 = distfn.ppf(q0, *arg)
+    x_cast = [x0.astype(tp) for tp in (np_long, np.float16, np.float32,
+                                       np.float64)]
+
+    for x in x_cast:
+        # casting may have clipped the values, exclude those
+        distfn._argcheck(*arg)
+        x = x[(distfn.a < x) & (x < distfn.b)]
+        for meth in meths:
+            val = meth(x, *arg)
+            npt.assert_(val.dtype == np.float64)
+
+
+def check_ppf_dtype(distfn, arg):
+    q0 = np.asarray([0.25, 0.5, 0.75])
+    q_cast = [q0.astype(tp) for tp in (np.float16, np.float32, np.float64)]
+    for q in q_cast:
+        for meth in [distfn.ppf, distfn.isf]:
+            val = meth(q, *arg)
+            npt.assert_(val.dtype == np.float64)
+
+
+def check_cmplx_deriv(distfn, arg):
+    # Distributions allow complex arguments.
+    def deriv(f, x, *arg):
+        x = np.asarray(x)
+        h = 1e-10
+        return (f(x + h*1j, *arg)/h).imag
+
+    x0 = distfn.ppf([0.25, 0.51, 0.75], *arg)
+    x_cast = [x0.astype(tp) for tp in (np_long, np.float16, np.float32,
+                                       np.float64)]
+
+    for x in x_cast:
+        # casting may have clipped the values, exclude those
+        distfn._argcheck(*arg)
+        x = x[(distfn.a < x) & (x < distfn.b)]
+
+        pdf, cdf, sf = distfn.pdf(x, *arg), distfn.cdf(x, *arg), distfn.sf(x, *arg)
+        assert_allclose(deriv(distfn.cdf, x, *arg), pdf, rtol=1e-5)
+        assert_allclose(deriv(distfn.logcdf, x, *arg), pdf/cdf, rtol=1e-5)
+
+        assert_allclose(deriv(distfn.sf, x, *arg), -pdf, rtol=1e-5)
+        assert_allclose(deriv(distfn.logsf, x, *arg), -pdf/sf, rtol=1e-5)
+
+        assert_allclose(deriv(distfn.logpdf, x, *arg),
+                        deriv(distfn.pdf, x, *arg) / distfn.pdf(x, *arg),
+                        rtol=1e-5)
+
+
+def check_pickling(distfn, args):
+    # check that a distribution instance pickles and unpickles
+    # pay special attention to the random_state property
+
+    # save the random_state (restore later)
+    rndm = distfn.random_state
+
+    # check unfrozen
+    distfn.random_state = 1234
+    distfn.rvs(*args, size=8)
+    s = pickle.dumps(distfn)
+    r0 = distfn.rvs(*args, size=8)
+
+    unpickled = pickle.loads(s)
+    r1 = unpickled.rvs(*args, size=8)
+    npt.assert_equal(r0, r1)
+
+    # also smoke test some methods
+    medians = [distfn.ppf(0.5, *args), unpickled.ppf(0.5, *args)]
+    npt.assert_equal(medians[0], medians[1])
+    npt.assert_equal(distfn.cdf(medians[0], *args),
+                     unpickled.cdf(medians[1], *args))
+
+    # check frozen pickling/unpickling with rvs
+    frozen_dist = distfn(*args)
+    pkl = pickle.dumps(frozen_dist)
+    unpickled = pickle.loads(pkl)
+
+    r0 = frozen_dist.rvs(size=8)
+    r1 = unpickled.rvs(size=8)
+    npt.assert_equal(r0, r1)
+
+    # check pickling/unpickling of .fit method
+    if hasattr(distfn, "fit"):
+        fit_function = distfn.fit
+        pickled_fit_function = pickle.dumps(fit_function)
+        unpickled_fit_function = pickle.loads(pickled_fit_function)
+        assert fit_function.__name__ == unpickled_fit_function.__name__ == "fit"
+
+    # restore the random_state
+    distfn.random_state = rndm
+
+
+def check_freezing(distfn, args):
+    # regression test for gh-11089: freezing a distribution fails
+    # if loc and/or scale are specified
+    if isinstance(distfn, stats.rv_continuous):
+        locscale = {'loc': 1, 'scale': 2}
+    else:
+        locscale = {'loc': 1}
+
+    rv = distfn(*args, **locscale)
+    assert rv.a == distfn(*args).a
+    assert rv.b == distfn(*args).b
+
+
+def check_rvs_broadcast(distfunc, distname, allargs, shape, shape_only, otype):
+    np.random.seed(123)
+    sample = distfunc.rvs(*allargs)
+    assert_equal(sample.shape, shape, "%s: rvs failed to broadcast" % distname)
+    if not shape_only:
+        rvs = np.vectorize(lambda *allargs: distfunc.rvs(*allargs), otypes=otype)
+        np.random.seed(123)
+        expected = rvs(*allargs)
+        assert_allclose(sample, expected, rtol=1e-13)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/_mvt.py

@@ -0,0 +1,171 @@
+import math
+import numpy as np
+from scipy import special
+from scipy.stats._qmc import primes_from_2_to
+
+
+def _primes(n):
+    # Defined to facilitate comparison between translation and source
+    # In Matlab, primes(10.5) -> first four primes, primes(11.5) -> first five
+    return primes_from_2_to(math.ceil(n))
+
+
+def _gaminv(a, b):
+    # Defined to facilitate comparison between translation and source
+    # Matlab's `gaminv` is like `special.gammaincinv` but args are reversed
+    return special.gammaincinv(b, a)
+
+
+def _qsimvtv(m, nu, sigma, a, b, rng):
+    """Estimates the multivariate t CDF using randomized QMC
+
+    Parameters
+    ----------
+    m : int
+        The number of points
+    nu : float
+        Degrees of freedom
+    sigma : ndarray
+        A 2D positive semidefinite covariance matrix
+    a : ndarray
+        Lower integration limits
+    b : ndarray
+        Upper integration limits.
+    rng : Generator
+        Pseudorandom number generator
+
+    Returns
+    -------
+    p : float
+        The estimated CDF.
+    e : float
+        An absolute error estimate.
+
+    """
+    # _qsimvtv is a Python translation of the Matlab function qsimvtv,
+    # semicolons and all.
+    #
+    #   This function uses an algorithm given in the paper
+    #      "Comparison of Methods for the Numerical Computation of
+    #       Multivariate t Probabilities", in
+    #      J. of Computational and Graphical Stat., 11(2002), pp. 950-971, by
+    #          Alan Genz and Frank Bretz
+    #
+    #   The primary references for the numerical integration are
+    #    "On a Number-Theoretical Integration Method"
+    #    H. Niederreiter, Aequationes Mathematicae, 8(1972), pp. 304-11.
+    #    and
+    #    "Randomization of Number Theoretic Methods for Multiple Integration"
+    #     R. Cranley & T.N.L. Patterson, SIAM J Numer Anal, 13(1976), pp. 904-14.
+    #
+    #   Alan Genz is the author of this function and following Matlab functions.
+    #          Alan Genz, WSU Math, PO Box 643113, Pullman, WA 99164-3113
+    #          Email : alangenz@wsu.edu
+    #
+    # Copyright (C) 2013, Alan Genz,  All rights reserved.
+    #
+    # Redistribution and use in source and binary forms, with or without
+    # modification, are permitted provided 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 contributor name(s) may not be used to endorse or promote
+    #      products derived from this software without specific prior
+    #      written permission.
+    # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+    # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+    # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+    # FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+    # COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+    # INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+    # BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
+    # OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+    # ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+    # TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF USE
+    # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+    # Initialization
+    sn = max(1, math.sqrt(nu)); ch, az, bz = _chlrps(sigma, a/sn, b/sn)
+    n = len(sigma); N = 10; P = math.ceil(m/N); on = np.ones(P); p = 0; e = 0
+    ps = np.sqrt(_primes(5*n*math.log(n+4)/4)); q = ps[:, np.newaxis]  # Richtmyer gens.
+
+    # Randomization loop for ns samples
+    c = None; dc = None
+    for S in range(N):
+        vp = on.copy(); s = np.zeros((n, P))
+        for i in range(n):
+            x = np.abs(2*np.mod(q[i]*np.arange(1, P+1) + rng.random(), 1)-1)  # periodizing transform
+            if i == 0:
+                r = on
+                if nu > 0:
+                    r = np.sqrt(2*_gaminv(x, nu/2))
+            else:
+                y = _Phinv(c + x*dc)
+                s[i:] += ch[i:, i-1:i] * y
+            si = s[i, :]; c = on.copy(); ai = az[i]*r - si; d = on.copy(); bi = bz[i]*r - si
+            c[ai <= -9] = 0; tl = abs(ai) < 9; c[tl] = _Phi(ai[tl])
+            d[bi <= -9] = 0; tl = abs(bi) < 9; d[tl] = _Phi(bi[tl])
+            dc = d - c; vp = vp * dc
+        d = (np.mean(vp) - p)/(S + 1); p = p + d; e = (S - 1)*e/(S + 1) + d**2
+    e = math.sqrt(e)  # error estimate is 3 times std error with N samples.
+    return p, e
+
+
+#  Standard statistical normal distribution functions
+def _Phi(z):
+    return special.ndtr(z)
+
+
+def _Phinv(p):
+    return special.ndtri(p)
+
+
+def _chlrps(R, a, b):
+    """
+    Computes permuted and scaled lower Cholesky factor c for R which may be
+    singular, also permuting and scaling integration limit vectors a and b.
+    """
+    ep = 1e-10  # singularity tolerance
+    eps = np.finfo(R.dtype).eps
+
+    n = len(R); c = R.copy(); ap = a.copy(); bp = b.copy(); d = np.sqrt(np.maximum(np.diag(c), 0))
+    for i in range(n):
+        if d[i] > 0:
+            c[:, i] /= d[i]; c[i, :] /= d[i]
+            ap[i] /= d[i]; bp[i] /= d[i]
+    y = np.zeros((n, 1)); sqtp = math.sqrt(2*math.pi)
+
+    for k in range(n):
+        im = k; ckk = 0; dem = 1; s = 0
+        for i in range(k, n):
+            if c[i, i] > eps:
+                cii = math.sqrt(max(c[i, i], 0))
+                if i > 0: s = c[i, :k] @ y[:k]
+                ai = (ap[i]-s)/cii; bi = (bp[i]-s)/cii; de = _Phi(bi)-_Phi(ai)
+                if de <= dem:
+                    ckk = cii; dem = de; am = ai; bm = bi; im = i
+        if im > k:
+            ap[[im, k]] = ap[[k, im]]; bp[[im, k]] = bp[[k, im]]; c[im, im] = c[k, k]
+            t = c[im, :k].copy(); c[im, :k] = c[k, :k]; c[k, :k] = t
+            t = c[im+1:, im].copy(); c[im+1:, im] = c[im+1:, k]; c[im+1:, k] = t
+            t = c[k+1:im, k].copy(); c[k+1:im, k] = c[im, k+1:im].T; c[im, k+1:im] = t.T
+        if ckk > ep*(k+1):
+            c[k, k] = ckk; c[k, k+1:] = 0
+            for i in range(k+1, n):
+                c[i, k] = c[i, k]/ckk; c[i, k+1:i+1] = c[i, k+1:i+1] - c[i, k]*c[k+1:i+1, k].T
+            if abs(dem) > ep:
+                y[k] = (np.exp(-am**2/2) - np.exp(-bm**2/2)) / (sqtp*dem)
+            else:
+                y[k] = (am + bm) / 2
+                if am < -10:
+                    y[k] = bm
+                elif bm > 10:
+                    y[k] = am
+            c[k, :k+1] /= ckk; ap[k] /= ckk; bp[k] /= ckk
+        else:
+            c[k:, k] = 0; y[k] = (ap[k] + bp[k])/2
+        pass
+    return c, ap, bp

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/fisher_exact_results_from_r.py

@@ -0,0 +1,607 @@
+# DO NOT EDIT THIS FILE!
+# This file was generated by the R script
+#     generate_fisher_exact_results_from_r.R
+# The script was run with R version 3.6.2 (2019-12-12) at 2020-11-09 06:16:09
+
+
+from collections import namedtuple
+import numpy as np
+
+
+Inf = np.inf
+
+Parameters = namedtuple('Parameters',
+                        ['table', 'confidence_level', 'alternative'])
+RResults = namedtuple('RResults',
+                      ['pvalue', 'conditional_odds_ratio',
+                       'conditional_odds_ratio_ci'])
+data = [
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.1300759363430016,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0.04035202926536294,
+                                         2.662846672960251))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.02301413756522116,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0.004668988338943325,
+                                         0.895792956493601))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.1973244147157191,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0.4153910882532168,
+                                         259.2593661129417))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.09580440012477633,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0.08056337526385809,
+                                         1.22704788545557))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.2697004098849359,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0.1176691231650079,
+                                         1.787463657995973))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.1973244147157192,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0.003857141267422399,
+                                         2.407369893767229))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.06126482213438735,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         1.451643573543705))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.04761904761904762,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(1.024822256141754,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         39.00054996869288))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.04761904761904761,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(1.024822256141754,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         39.00054996869287))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=2.005657880389071e-122,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(349.2595113327733,
+                                         3630.382605689872))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=5.728437460831947e-44,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(152.4166024390096,
+                                         1425.700792178893))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.95,
+                alternative='two.sided'),
+     RResults(pvalue=0.574111858126088,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0.8520462587912048,
+                                         1.340148950273938))),
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.1300759363430016,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0.02502345007115455,
+                                         6.304424772117853))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.02301413756522116,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0.001923034001462487,
+                                         1.53670836950172))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.1973244147157191,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0.2397970951413721,
+                                         1291.342011095509))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.09580440012477633,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0.05127576113762925,
+                                         1.717176678806983))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.2697004098849359,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0.07498546954483619,
+                                         2.506969905199901))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.1973244147157192,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0.0007743881879531337,
+                                         4.170192301163831))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.06126482213438735,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         2.642491011905582))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.04761904761904762,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0.496935393325443,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         198.019801980198))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.04761904761904761,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0.496935393325443,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         198.019801980198))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=2.005657880389071e-122,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(270.0334165523604,
+                                         5461.333333326708))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=5.728437460831947e-44,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(116.7944750275836,
+                                         1931.995993191814))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.99,
+                alternative='two.sided'),
+     RResults(pvalue=0.574111858126088,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0.7949398282935892,
+                                         1.436229679394333))),
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.1300759363430016,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0,
+                                         1.797867027270803))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.0185217259520665,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0,
+                                         0.6785254803404526))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.9782608695652173,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0,
+                                         127.8497388102893))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.05625775074399956,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0,
+                                         1.032332939718425))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.1808979350599346,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0,
+                                         1.502407513296985))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.1652173913043479,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0,
+                                         1.820421051562392))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.0565217391304348,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         1.06224603077045))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.5,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         19.00192394479939))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.4999999999999999,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         19.00192394479939))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(0,
+                                         3045.460216525746))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(0,
+                                         1186.440170942579))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.95,
+                alternative='less'),
+     RResults(pvalue=0.7416227010368963,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0,
+                                         1.293551891610822))),
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.1300759363430016,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0,
+                                         4.375946050832565))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.0185217259520665,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0,
+                                         1.235282118191202))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.9782608695652173,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0,
+                                         657.2063583945989))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.05625775074399956,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0,
+                                         1.498867660683128))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.1808979350599346,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0,
+                                         2.186159386716762))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.1652173913043479,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0,
+                                         3.335351451901569))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.0565217391304348,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         2.075407697450433))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.5,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         99.00009507969122))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.4999999999999999,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         99.00009507969123))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(0,
+                                         4503.078257659934))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(0,
+                                         1811.766127544222))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.99,
+                alternative='less'),
+     RResults(pvalue=0.7416227010368963,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0,
+                                         1.396522811516685))),
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.979790445314723,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0.05119649909830196,
+                                         Inf))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.9990149169715733,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0.007163749169069961,
+                                         Inf))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.1652173913043478,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0.5493234651081089,
+                                         Inf))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.9849086665340765,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0.1003538933958604,
+                                         Inf))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.9330176609214881,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0.146507416280863,
+                                         Inf))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.9782608695652174,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0.007821681994077808,
+                                         Inf))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.02380952380952382,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(1.487678929918272,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.0238095238095238,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(1.487678929918272,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=2.005657880388915e-122,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(397.784359748113,
+                                         Inf))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=5.728437460831983e-44,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(174.7148056880929,
+                                         Inf))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.95,
+                alternative='greater'),
+     RResults(pvalue=0.2959825901308897,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0.8828406663967776,
+                                         Inf))),
+    (Parameters(table=[[100, 2], [1000, 5]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.979790445314723,
+              conditional_odds_ratio=0.25055839934223,
+              conditional_odds_ratio_ci=(0.03045407081240429,
+                                         Inf))),
+    (Parameters(table=[[2, 7], [8, 2]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.9990149169715733,
+              conditional_odds_ratio=0.0858623513573622,
+              conditional_odds_ratio_ci=(0.002768053063547901,
+                                         Inf))),
+    (Parameters(table=[[5, 1], [10, 10]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.1652173913043478,
+              conditional_odds_ratio=4.725646047336587,
+              conditional_odds_ratio_ci=(0.2998184792279909,
+                                         Inf))),
+    (Parameters(table=[[5, 15], [20, 20]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.9849086665340765,
+              conditional_odds_ratio=0.3394396617440851,
+              conditional_odds_ratio_ci=(0.06180414342643172,
+                                         Inf))),
+    (Parameters(table=[[5, 16], [16, 25]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.9330176609214881,
+              conditional_odds_ratio=0.4937791394540491,
+              conditional_odds_ratio_ci=(0.09037094010066403,
+                                         Inf))),
+    (Parameters(table=[[10, 5], [10, 1]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.9782608695652174,
+              conditional_odds_ratio=0.2116112781158479,
+              conditional_odds_ratio_ci=(0.001521592095430679,
+                                         Inf))),
+    (Parameters(table=[[10, 5], [10, 0]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[5, 0], [1, 4]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.02380952380952382,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0.6661157890359722,
+                                         Inf))),
+    (Parameters(table=[[0, 5], [1, 4]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[5, 1], [0, 4]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.0238095238095238,
+              conditional_odds_ratio=Inf,
+              conditional_odds_ratio_ci=(0.6661157890359725,
+                                         Inf))),
+    (Parameters(table=[[0, 1], [3, 2]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=1,
+              conditional_odds_ratio=0,
+              conditional_odds_ratio_ci=(0,
+                                         Inf))),
+    (Parameters(table=[[200, 7], [8, 300]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=2.005657880388915e-122,
+              conditional_odds_ratio=977.7866978606228,
+              conditional_odds_ratio_ci=(297.9619252357688,
+                                         Inf))),
+    (Parameters(table=[[28, 21], [6, 1957]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=5.728437460831983e-44,
+              conditional_odds_ratio=425.2403028434684,
+              conditional_odds_ratio_ci=(130.3213490295859,
+                                         Inf))),
+    (Parameters(table=[[190, 800], [200, 900]],
+                confidence_level=0.99,
+                alternative='greater'),
+     RResults(pvalue=0.2959825901308897,
+              conditional_odds_ratio=1.068697577856801,
+              conditional_odds_ratio_ci=(0.8176272148267533,
+                                         Inf))),
+]

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_anova/AtmWtAg.dat

@@ -0,0 +1,108 @@
+NIST/ITL StRD 
+Dataset Name:   AtmWtAg   (AtmWtAg.dat)
+
+
+File Format:    ASCII
+                Certified Values   (lines 41 to 47)
+                Data               (lines 61 to 108) 
+
+
+Procedure:      Analysis of Variance
+
+
+Reference:      Powell, L.J., Murphy, T.J. and Gramlich, J.W. (1982).
+                "The Absolute Isotopic Abundance & Atomic Weight
+                of a Reference Sample of Silver".
+                NBS Journal of Research, 87, pp. 9-19.
+
+
+Data:           1 Factor
+                2 Treatments
+                24 Replicates/Cell
+                48 Observations
+                7 Constant Leading Digits
+                Average Level of Difficulty
+                Observed Data
+
+
+Model:          3 Parameters (mu, tau_1, tau_2)
+                y_{ij} = mu + tau_i + epsilon_{ij}
+
+
+
+
+
+
+Certified Values:
+
+Source of                  Sums of               Mean               
+Variation          df      Squares              Squares             F Statistic
+
+
+Between Instrument  1 3.63834187500000E-09 3.63834187500000E-09 1.59467335677930E+01
+Within Instrument  46 1.04951729166667E-08 2.28155932971014E-10
+
+                   Certified R-Squared 2.57426544538321E-01
+
+                   Certified Residual
+                   Standard Deviation  1.51048314446410E-05
+
+
+
+
+
+
+
+
+
+
+
+Data:  Instrument           AgWt
+           1            107.8681568
+           1            107.8681465
+           1            107.8681572
+           1            107.8681785
+           1            107.8681446
+           1            107.8681903
+           1            107.8681526
+           1            107.8681494
+           1            107.8681616
+           1            107.8681587
+           1            107.8681519
+           1            107.8681486
+           1            107.8681419
+           1            107.8681569
+           1            107.8681508
+           1            107.8681672
+           1            107.8681385
+           1            107.8681518
+           1            107.8681662
+           1            107.8681424
+           1            107.8681360
+           1            107.8681333
+           1            107.8681610
+           1            107.8681477
+           2            107.8681079
+           2            107.8681344
+           2            107.8681513
+           2            107.8681197
+           2            107.8681604
+           2            107.8681385
+           2            107.8681642
+           2            107.8681365
+           2            107.8681151
+           2            107.8681082
+           2            107.8681517
+           2            107.8681448
+           2            107.8681198
+           2            107.8681482
+           2            107.8681334
+           2            107.8681609
+           2            107.8681101
+           2            107.8681512
+           2            107.8681469
+           2            107.8681360
+           2            107.8681254
+           2            107.8681261
+           2            107.8681450
+           2            107.8681368

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_anova/SiRstv.dat

@@ -0,0 +1,85 @@
+NIST/ITL StRD 
+Dataset Name:   SiRstv     (SiRstv.dat)
+
+
+File Format:    ASCII
+                Certified Values   (lines 41 to 47)
+                Data               (lines 61 to 85) 
+
+
+Procedure:      Analysis of Variance
+
+
+Reference:      Ehrstein, James and Croarkin, M. Carroll.
+                Unpublished NIST dataset.
+
+
+Data:           1 Factor
+                5 Treatments
+                5  Replicates/Cell
+                25 Observations
+                3 Constant Leading Digits
+                Lower Level of Difficulty
+                Observed Data
+
+
+Model:          6 Parameters (mu,tau_1, ... , tau_5)
+                y_{ij} = mu + tau_i + epsilon_{ij}
+
+
+
+
+
+
+
+
+Certified Values:
+
+Source of                  Sums of               Mean               
+Variation          df      Squares              Squares             F Statistic
+
+Between Instrument  4 5.11462616000000E-02 1.27865654000000E-02 1.18046237440255E+00
+Within Instrument  20 2.16636560000000E-01 1.08318280000000E-02
+
+                   Certified R-Squared 1.90999039051129E-01
+
+                   Certified Residual
+                   Standard Deviation  1.04076068334656E-01
+
+
+
+
+
+
+
+
+
+
+
+
+Data:  Instrument   Resistance
+           1         196.3052
+           1         196.1240
+           1         196.1890
+           1         196.2569
+           1         196.3403
+           2         196.3042
+           2         196.3825
+           2         196.1669
+           2         196.3257
+           2         196.0422
+           3         196.1303
+           3         196.2005
+           3         196.2889
+           3         196.0343
+           3         196.1811
+           4         196.2795
+           4         196.1748
+           4         196.1494
+           4         196.1485
+           4         195.9885
+           5         196.2119
+           5         196.1051
+           5         196.1850
+           5         196.0052
+           5         196.2090

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_anova/SmLs01.dat

@@ -0,0 +1,249 @@
+NIST/ITL StRD 
+Dataset Name:   SmLs01   (SmLs01.dat)
+
+
+File Format:    ASCII
+                Certified Values   (lines 41 to 47)
+                Data               (lines 61 to 249) 
+
+
+Procedure:      Analysis of Variance
+
+
+Reference:      Simon, Stephen D. and Lesage, James P. (1989).
+                "Assessing the Accuracy of ANOVA Calculations in
+                Statistical Software".
+                Computational Statistics & Data Analysis, 8, pp. 325-332.
+
+
+Data:           1 Factor
+                9 Treatments
+                21 Replicates/Cell
+                189 Observations
+                1 Constant Leading Digit
+                Lower Level of Difficulty
+                Generated Data
+
+
+Model:          10 Parameters (mu,tau_1, ... , tau_9)
+                y_{ij} = mu + tau_i + epsilon_{ij}
+
+
+
+
+
+
+Certified Values:
+
+Source of                  Sums of               Mean               
+Variation          df      Squares              Squares            F Statistic
+
+Between Treatment   8 1.68000000000000E+00 2.10000000000000E-01 2.10000000000000E+01
+Within Treatment  180 1.80000000000000E+00 1.00000000000000E-02
+
+                  Certified R-Squared 4.82758620689655E-01
+
+                  Certified Residual
+                  Standard Deviation  1.00000000000000E-01
+
+
+
+
+
+
+
+
+
+
+
+
+Data:  Treatment   Response
+           1         1.4
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           1         1.3
+           1         1.5
+           2         1.3
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           2         1.2
+           2         1.4
+           3         1.5
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           3         1.4
+           3         1.6
+           4         1.3
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           4         1.2
+           4         1.4
+           5         1.5
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           5         1.4
+           5         1.6
+           6         1.3
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           6         1.2
+           6         1.4
+           7         1.5
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           7         1.4
+           7         1.6
+           8         1.3
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           8         1.2
+           8         1.4
+           9         1.5
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6
+           9         1.4
+           9         1.6

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_anova/SmLs04.dat

@@ -0,0 +1,249 @@
+NIST/ITL StRD 
+Dataset Name:   SmLs04   (SmLs04.dat)
+
+
+File Format:    ASCII
+                Certified Values   (lines 41 to 47)
+                Data               (lines 61 to 249) 
+
+
+Procedure:      Analysis of Variance
+
+
+Reference:      Simon, Stephen D. and Lesage, James P. (1989).
+                "Assessing the Accuracy of ANOVA Calculations in
+                Statistical Software".
+                Computational Statistics & Data Analysis, 8, pp. 325-332.
+
+
+Data:           1 Factor
+                9 Treatments
+                21 Replicates/Cell
+                189 Observations
+                7 Constant Leading Digits
+                Average Level of Difficulty
+                Generated Data
+
+
+Model:          10 Parameters (mu,tau_1, ... , tau_9)
+                y_{ij} = mu + tau_i + epsilon_{ij}
+
+
+
+
+
+
+Certified Values:
+
+Source of                  Sums of               Mean               
+Variation          df      Squares              Squares             F Statistic
+
+Between Treatment   8 1.68000000000000E+00 2.10000000000000E-01 2.10000000000000E+01
+Within Treatment  180 1.80000000000000E+00 1.00000000000000E-02
+
+                  Certified R-Squared 4.82758620689655E-01
+
+                  Certified Residual
+                  Standard Deviation  1.00000000000000E-01
+
+
+
+
+
+
+
+
+
+
+
+
+Data:  Treatment   Response
+           1       1000000.4
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           1       1000000.3
+           1       1000000.5
+           2       1000000.3
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           2       1000000.2
+           2       1000000.4
+           3       1000000.5
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           3       1000000.4
+           3       1000000.6
+           4       1000000.3
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           4       1000000.2
+           4       1000000.4
+           5       1000000.5
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           5       1000000.4
+           5       1000000.6
+           6       1000000.3
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           6       1000000.2
+           6       1000000.4
+           7       1000000.5
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           7       1000000.4
+           7       1000000.6
+           8       1000000.3
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           8       1000000.2
+           8       1000000.4
+           9       1000000.5
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6
+           9       1000000.4
+           9       1000000.6

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_anova/SmLs07.dat

@@ -0,0 +1,249 @@
+NIST/ITL StRD 
+Dataset Name:   SmLs07   (SmLs07.dat)
+
+
+File Format:    ASCII
+                Certified Values   (lines 41 to 47)
+                Data               (lines 61 to 249) 
+
+
+Procedure:      Analysis of Variance
+
+
+Reference:      Simon, Stephen D. and Lesage, James P. (1989).
+                "Assessing the Accuracy of ANOVA Calculations in
+                Statistical Software".
+                Computational Statistics & Data Analysis, 8, pp. 325-332.
+
+
+Data:           1 Factor
+                9 Treatments
+                21 Replicates/Cell
+                189 Observations
+                13 Constant Leading Digits
+                Higher Level of Difficulty
+                Generated Data
+
+
+Model:          10 Parameters (mu,tau_1, ... , tau_9)
+                y_{ij} = mu + tau_i + epsilon_{ij}
+
+
+
+
+
+
+Certified Values:
+
+Source of                  Sums of               Mean               
+Variation          df      Squares              Squares            F Statistic
+
+Between Treatment   8 1.68000000000000E+00 2.10000000000000E-01 2.10000000000000E+01
+Within Treatment  180 1.80000000000000E+00 1.00000000000000E-02
+
+                  Certified R-Squared 4.82758620689655E-01
+
+                  Certified Residual
+                  Standard Deviation  1.00000000000000E-01
+
+
+
+
+
+
+
+
+
+
+
+
+Data:  Treatment   Response
+           1    1000000000000.4
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           1    1000000000000.3
+           1    1000000000000.5
+           2    1000000000000.3
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           2    1000000000000.2
+           2    1000000000000.4
+           3    1000000000000.5
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           3    1000000000000.4
+           3    1000000000000.6
+           4    1000000000000.3
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           4    1000000000000.2
+           4    1000000000000.4
+           5    1000000000000.5
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           5    1000000000000.4
+           5    1000000000000.6
+           6    1000000000000.3
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           6    1000000000000.2
+           6    1000000000000.4
+           7    1000000000000.5
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           7    1000000000000.4
+           7    1000000000000.6
+           8    1000000000000.3
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           8    1000000000000.2
+           8    1000000000000.4
+           9    1000000000000.5
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6
+           9    1000000000000.4
+           9    1000000000000.6

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/data/nist_linregress/Norris.dat

@@ -0,0 +1,97 @@
+NIST/ITL StRD
+Dataset Name:  Norris (Norris.dat)
+
+File Format:   ASCII
+               Certified Values  (lines 31 to 46)
+               Data              (lines 61 to 96)
+
+Procedure:     Linear Least Squares Regression
+
+Reference:     Norris, J., NIST.  
+               Calibration of Ozone Monitors.
+
+Data:          1 Response Variable (y)
+               1 Predictor Variable (x)
+               36 Observations
+               Lower Level of Difficulty
+               Observed Data
+
+Model:         Linear Class
+               2 Parameters (B0,B1)
+
+               y = B0 + B1*x + e
+
+
+
+               Certified Regression Statistics
+
+                                          Standard Deviation
+     Parameter          Estimate             of Estimate
+
+        B0        -0.262323073774029     0.232818234301152
+        B1         1.00211681802045      0.429796848199937E-03
+
+     Residual
+     Standard Deviation   0.884796396144373
+
+     R-Squared            0.999993745883712
+
+
+               Certified Analysis of Variance Table
+
+Source of Degrees of    Sums of             Mean  
+Variation  Freedom      Squares            Squares           F Statistic
+              
+Regression    1     4255954.13232369   4255954.13232369   5436385.54079785
+Residual     34     26.6173985294224   0.782864662630069
+
+                 
+                                          
+                                          
+                                                           
+
+                            
+                                   
+                                                       
+
+
+
+
+Data:       y          x
+           0.1        0.2
+         338.8      337.4
+         118.1      118.2
+         888.0      884.6
+           9.2       10.1
+         228.1      226.5
+         668.5      666.3
+         998.5      996.3
+         449.1      448.6
+         778.9      777.0
+         559.2      558.2
+           0.3        0.4
+           0.1        0.6
+         778.1      775.5
+         668.8      666.9
+         339.3      338.0
+         448.9      447.5
+          10.8       11.6
+         557.7      556.0
+         228.3      228.1
+         998.0      995.8
+         888.8      887.6
+         119.6      120.2
+           0.3        0.3
+           0.6        0.3
+         557.6      556.8
+         339.3      339.1
+         888.0      887.2
+         998.5      999.0
+         778.9      779.0
+          10.2       11.1
+         117.6      118.3
+         228.9      229.2
+         668.4      669.1
+         449.2      448.9
+           0.2        0.5
+                                   

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_binned_statistic.py

@@ -0,0 +1,568 @@
+import numpy as np
+from numpy.testing import assert_allclose
+import pytest
+from pytest import raises as assert_raises
+from scipy.stats import (binned_statistic, binned_statistic_2d,
+                         binned_statistic_dd)
+from scipy._lib._util import check_random_state
+
+from .common_tests import check_named_results
+
+
+class TestBinnedStatistic:
+
+    @classmethod
+    def setup_class(cls):
+        rng = check_random_state(9865)
+        cls.x = rng.uniform(size=100)
+        cls.y = rng.uniform(size=100)
+        cls.v = rng.uniform(size=100)
+        cls.X = rng.uniform(size=(100, 3))
+        cls.w = rng.uniform(size=100)
+        cls.u = rng.uniform(size=100) + 1e6
+
+    def test_1d_count(self):
+        x = self.x
+        v = self.v
+
+        count1, edges1, bc = binned_statistic(x, v, 'count', bins=10)
+        count2, edges2 = np.histogram(x, bins=10)
+
+        assert_allclose(count1, count2)
+        assert_allclose(edges1, edges2)
+
+    def test_gh5927(self):
+        # smoke test for gh5927 - binned_statistic was using `is` for string
+        # comparison
+        x = self.x
+        v = self.v
+        statistics = ['mean', 'median', 'count', 'sum']
+        for statistic in statistics:
+            binned_statistic(x, v, statistic, bins=10)
+
+    def test_big_number_std(self):
+        # tests for numerical stability of std calculation
+        # see issue gh-10126 for more
+        x = self.x
+        u = self.u
+        stat1, edges1, bc = binned_statistic(x, u, 'std', bins=10)
+        stat2, edges2, bc = binned_statistic(x, u, np.std, bins=10)
+
+        assert_allclose(stat1, stat2)
+
+    def test_empty_bins_std(self):
+        # tests that std returns gives nan for empty bins
+        x = self.x
+        u = self.u
+        print(binned_statistic(x, u, 'count', bins=1000))
+        stat1, edges1, bc = binned_statistic(x, u, 'std', bins=1000)
+        stat2, edges2, bc = binned_statistic(x, u, np.std, bins=1000)
+
+        assert_allclose(stat1, stat2)
+
+    def test_non_finite_inputs_and_int_bins(self):
+        # if either `values` or `sample` contain np.inf or np.nan throw
+        # see issue gh-9010 for more
+        x = self.x
+        u = self.u
+        orig = u[0]
+        u[0] = np.inf
+        assert_raises(ValueError, binned_statistic, u, x, 'std', bins=10)
+        # need to test for non-python specific ints, e.g. np.int8, np.int64
+        assert_raises(ValueError, binned_statistic, u, x, 'std',
+                      bins=np.int64(10))
+        u[0] = np.nan
+        assert_raises(ValueError, binned_statistic, u, x, 'count', bins=10)
+        # replace original value, u belongs the class
+        u[0] = orig
+
+    def test_1d_result_attributes(self):
+        x = self.x
+        v = self.v
+
+        res = binned_statistic(x, v, 'count', bins=10)
+        attributes = ('statistic', 'bin_edges', 'binnumber')
+        check_named_results(res, attributes)
+
+    def test_1d_sum(self):
+        x = self.x
+        v = self.v
+
+        sum1, edges1, bc = binned_statistic(x, v, 'sum', bins=10)
+        sum2, edges2 = np.histogram(x, bins=10, weights=v)
+
+        assert_allclose(sum1, sum2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_mean(self):
+        x = self.x
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic(x, v, 'mean', bins=10)
+        stat2, edges2, bc = binned_statistic(x, v, np.mean, bins=10)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_std(self):
+        x = self.x
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic(x, v, 'std', bins=10)
+        stat2, edges2, bc = binned_statistic(x, v, np.std, bins=10)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_min(self):
+        x = self.x
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic(x, v, 'min', bins=10)
+        stat2, edges2, bc = binned_statistic(x, v, np.min, bins=10)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_max(self):
+        x = self.x
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic(x, v, 'max', bins=10)
+        stat2, edges2, bc = binned_statistic(x, v, np.max, bins=10)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_median(self):
+        x = self.x
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic(x, v, 'median', bins=10)
+        stat2, edges2, bc = binned_statistic(x, v, np.median, bins=10)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_1d_bincode(self):
+        x = self.x[:20]
+        v = self.v[:20]
+
+        count1, edges1, bc = binned_statistic(x, v, 'count', bins=3)
+        bc2 = np.array([3, 2, 1, 3, 2, 3, 3, 3, 3, 1, 1, 3, 3, 1, 2, 3, 1,
+                        1, 2, 1])
+
+        bcount = [(bc == i).sum() for i in np.unique(bc)]
+
+        assert_allclose(bc, bc2)
+        assert_allclose(bcount, count1)
+
+    def test_1d_range_keyword(self):
+        # Regression test for gh-3063, range can be (min, max) or [(min, max)]
+        np.random.seed(9865)
+        x = np.arange(30)
+        data = np.random.random(30)
+
+        mean, bins, _ = binned_statistic(x[:15], data[:15])
+        mean_range, bins_range, _ = binned_statistic(x, data, range=[(0, 14)])
+        mean_range2, bins_range2, _ = binned_statistic(x, data, range=(0, 14))
+
+        assert_allclose(mean, mean_range)
+        assert_allclose(bins, bins_range)
+        assert_allclose(mean, mean_range2)
+        assert_allclose(bins, bins_range2)
+
+    def test_1d_multi_values(self):
+        x = self.x
+        v = self.v
+        w = self.w
+
+        stat1v, edges1v, bc1v = binned_statistic(x, v, 'mean', bins=10)
+        stat1w, edges1w, bc1w = binned_statistic(x, w, 'mean', bins=10)
+        stat2, edges2, bc2 = binned_statistic(x, [v, w], 'mean', bins=10)
+
+        assert_allclose(stat2[0], stat1v)
+        assert_allclose(stat2[1], stat1w)
+        assert_allclose(edges1v, edges2)
+        assert_allclose(bc1v, bc2)
+
+    def test_2d_count(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        count1, binx1, biny1, bc = binned_statistic_2d(
+            x, y, v, 'count', bins=5)
+        count2, binx2, biny2 = np.histogram2d(x, y, bins=5)
+
+        assert_allclose(count1, count2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_result_attributes(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        res = binned_statistic_2d(x, y, v, 'count', bins=5)
+        attributes = ('statistic', 'x_edge', 'y_edge', 'binnumber')
+        check_named_results(res, attributes)
+
+    def test_2d_sum(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        sum1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'sum', bins=5)
+        sum2, binx2, biny2 = np.histogram2d(x, y, bins=5, weights=v)
+
+        assert_allclose(sum1, sum2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_mean(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'mean', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.mean, bins=5)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_mean_unicode(self):
+        x = self.x
+        y = self.y
+        v = self.v
+        stat1, binx1, biny1, bc = binned_statistic_2d(
+            x, y, v, 'mean', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.mean, bins=5)
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_std(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'std', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.std, bins=5)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_min(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'min', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.min, bins=5)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_max(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'max', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.max, bins=5)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_median(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat1, binx1, biny1, bc = binned_statistic_2d(
+            x, y, v, 'median', bins=5)
+        stat2, binx2, biny2, bc = binned_statistic_2d(
+            x, y, v, np.median, bins=5)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(binx1, binx2)
+        assert_allclose(biny1, biny2)
+
+    def test_2d_bincode(self):
+        x = self.x[:20]
+        y = self.y[:20]
+        v = self.v[:20]
+
+        count1, binx1, biny1, bc = binned_statistic_2d(
+            x, y, v, 'count', bins=3)
+        bc2 = np.array([17, 11, 6, 16, 11, 17, 18, 17, 17, 7, 6, 18, 16,
+                        6, 11, 16, 6, 6, 11, 8])
+
+        bcount = [(bc == i).sum() for i in np.unique(bc)]
+
+        assert_allclose(bc, bc2)
+        count1adj = count1[count1.nonzero()]
+        assert_allclose(bcount, count1adj)
+
+    def test_2d_multi_values(self):
+        x = self.x
+        y = self.y
+        v = self.v
+        w = self.w
+
+        stat1v, binx1v, biny1v, bc1v = binned_statistic_2d(
+            x, y, v, 'mean', bins=8)
+        stat1w, binx1w, biny1w, bc1w = binned_statistic_2d(
+            x, y, w, 'mean', bins=8)
+        stat2, binx2, biny2, bc2 = binned_statistic_2d(
+            x, y, [v, w], 'mean', bins=8)
+
+        assert_allclose(stat2[0], stat1v)
+        assert_allclose(stat2[1], stat1w)
+        assert_allclose(binx1v, binx2)
+        assert_allclose(biny1w, biny2)
+        assert_allclose(bc1v, bc2)
+
+    def test_2d_binnumbers_unraveled(self):
+        x = self.x
+        y = self.y
+        v = self.v
+
+        stat, edgesx, bcx = binned_statistic(x, v, 'mean', bins=20)
+        stat, edgesy, bcy = binned_statistic(y, v, 'mean', bins=10)
+
+        stat2, edgesx2, edgesy2, bc2 = binned_statistic_2d(
+            x, y, v, 'mean', bins=(20, 10), expand_binnumbers=True)
+
+        bcx3 = np.searchsorted(edgesx, x, side='right')
+        bcy3 = np.searchsorted(edgesy, y, side='right')
+
+        # `numpy.searchsorted` is non-inclusive on right-edge, compensate
+        bcx3[x == x.max()] -= 1
+        bcy3[y == y.max()] -= 1
+
+        assert_allclose(bcx, bc2[0])
+        assert_allclose(bcy, bc2[1])
+        assert_allclose(bcx3, bc2[0])
+        assert_allclose(bcy3, bc2[1])
+
+    def test_dd_count(self):
+        X = self.X
+        v = self.v
+
+        count1, edges1, bc = binned_statistic_dd(X, v, 'count', bins=3)
+        count2, edges2 = np.histogramdd(X, bins=3)
+
+        assert_allclose(count1, count2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_result_attributes(self):
+        X = self.X
+        v = self.v
+
+        res = binned_statistic_dd(X, v, 'count', bins=3)
+        attributes = ('statistic', 'bin_edges', 'binnumber')
+        check_named_results(res, attributes)
+
+    def test_dd_sum(self):
+        X = self.X
+        v = self.v
+
+        sum1, edges1, bc = binned_statistic_dd(X, v, 'sum', bins=3)
+        sum2, edges2 = np.histogramdd(X, bins=3, weights=v)
+        sum3, edges3, bc = binned_statistic_dd(X, v, np.sum, bins=3)
+
+        assert_allclose(sum1, sum2)
+        assert_allclose(edges1, edges2)
+        assert_allclose(sum1, sum3)
+        assert_allclose(edges1, edges3)
+
+    def test_dd_mean(self):
+        X = self.X
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic_dd(X, v, 'mean', bins=3)
+        stat2, edges2, bc = binned_statistic_dd(X, v, np.mean, bins=3)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_std(self):
+        X = self.X
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic_dd(X, v, 'std', bins=3)
+        stat2, edges2, bc = binned_statistic_dd(X, v, np.std, bins=3)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_min(self):
+        X = self.X
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic_dd(X, v, 'min', bins=3)
+        stat2, edges2, bc = binned_statistic_dd(X, v, np.min, bins=3)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_max(self):
+        X = self.X
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic_dd(X, v, 'max', bins=3)
+        stat2, edges2, bc = binned_statistic_dd(X, v, np.max, bins=3)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_median(self):
+        X = self.X
+        v = self.v
+
+        stat1, edges1, bc = binned_statistic_dd(X, v, 'median', bins=3)
+        stat2, edges2, bc = binned_statistic_dd(X, v, np.median, bins=3)
+
+        assert_allclose(stat1, stat2)
+        assert_allclose(edges1, edges2)
+
+    def test_dd_bincode(self):
+        X = self.X[:20]
+        v = self.v[:20]
+
+        count1, edges1, bc = binned_statistic_dd(X, v, 'count', bins=3)
+        bc2 = np.array([63, 33, 86, 83, 88, 67, 57, 33, 42, 41, 82, 83, 92,
+                        32, 36, 91, 43, 87, 81, 81])
+
+        bcount = [(bc == i).sum() for i in np.unique(bc)]
+
+        assert_allclose(bc, bc2)
+        count1adj = count1[count1.nonzero()]
+        assert_allclose(bcount, count1adj)
+
+    def test_dd_multi_values(self):
+        X = self.X
+        v = self.v
+        w = self.w
+
+        for stat in ["count", "sum", "mean", "std", "min", "max", "median",
+                     np.std]:
+            stat1v, edges1v, bc1v = binned_statistic_dd(X, v, stat, bins=8)
+            stat1w, edges1w, bc1w = binned_statistic_dd(X, w, stat, bins=8)
+            stat2, edges2, bc2 = binned_statistic_dd(X, [v, w], stat, bins=8)
+            assert_allclose(stat2[0], stat1v)
+            assert_allclose(stat2[1], stat1w)
+            assert_allclose(edges1v, edges2)
+            assert_allclose(edges1w, edges2)
+            assert_allclose(bc1v, bc2)
+
+    def test_dd_binnumbers_unraveled(self):
+        X = self.X
+        v = self.v
+
+        stat, edgesx, bcx = binned_statistic(X[:, 0], v, 'mean', bins=15)
+        stat, edgesy, bcy = binned_statistic(X[:, 1], v, 'mean', bins=20)
+        stat, edgesz, bcz = binned_statistic(X[:, 2], v, 'mean', bins=10)
+
+        stat2, edges2, bc2 = binned_statistic_dd(
+            X, v, 'mean', bins=(15, 20, 10), expand_binnumbers=True)
+
+        assert_allclose(bcx, bc2[0])
+        assert_allclose(bcy, bc2[1])
+        assert_allclose(bcz, bc2[2])
+
+    def test_dd_binned_statistic_result(self):
+        # NOTE: tests the reuse of bin_edges from previous call
+        x = np.random.random((10000, 3))
+        v = np.random.random(10000)
+        bins = np.linspace(0, 1, 10)
+        bins = (bins, bins, bins)
+
+        result = binned_statistic_dd(x, v, 'mean', bins=bins)
+        stat = result.statistic
+
+        result = binned_statistic_dd(x, v, 'mean',
+                                     binned_statistic_result=result)
+        stat2 = result.statistic
+
+        assert_allclose(stat, stat2)
+
+    def test_dd_zero_dedges(self):
+        x = np.random.random((10000, 3))
+        v = np.random.random(10000)
+        bins = np.linspace(0, 1, 10)
+        bins = np.append(bins, 1)
+        bins = (bins, bins, bins)
+        with assert_raises(ValueError, match='difference is numerically 0'):
+            binned_statistic_dd(x, v, 'mean', bins=bins)
+
+    def test_dd_range_errors(self):
+        # Test that descriptive exceptions are raised as appropriate for bad
+        # values of the `range` argument. (See gh-12996)
+        with assert_raises(ValueError,
+                           match='In range, start must be <= stop'):
+            binned_statistic_dd([self.y], self.v,
+                                range=[[1, 0]])
+        with assert_raises(
+                ValueError,
+                match='In dimension 1 of range, start must be <= stop'):
+            binned_statistic_dd([self.x, self.y], self.v,
+                                range=[[1, 0], [0, 1]])
+        with assert_raises(
+                ValueError,
+                match='In dimension 2 of range, start must be <= stop'):
+            binned_statistic_dd([self.x, self.y], self.v,
+                                range=[[0, 1], [1, 0]])
+        with assert_raises(
+                ValueError,
+                match='range given for 1 dimensions; 2 required'):
+            binned_statistic_dd([self.x, self.y], self.v,
+                                range=[[0, 1]])
+
+    def test_binned_statistic_float32(self):
+        X = np.array([0, 0.42358226], dtype=np.float32)
+        stat, _, _ = binned_statistic(X, None, 'count', bins=5)
+        assert_allclose(stat, np.array([1, 0, 0, 0, 1], dtype=np.float64))
+
+    def test_gh14332(self):
+        # Test the wrong output when the `sample` is close to bin edge
+        x = []
+        size = 20
+        for i in range(size):
+            x += [1-0.1**i]
+
+        bins = np.linspace(0,1,11)
+        sum1, edges1, bc = binned_statistic_dd(x, np.ones(len(x)),
+                                               bins=[bins], statistic='sum')
+        sum2, edges2 = np.histogram(x, bins=bins)
+
+        assert_allclose(sum1, sum2)
+        assert_allclose(edges1[0], edges2)
+
+    @pytest.mark.parametrize("dtype", [np.float64, np.complex128])
+    @pytest.mark.parametrize("statistic", [np.mean, np.median, np.sum, np.std,
+                                           np.min, np.max, 'count',
+                                           lambda x: (x**2).sum(),
+                                           lambda x: (x**2).sum() * 1j])
+    def test_dd_all(self, dtype, statistic):
+        def ref_statistic(x):
+            return len(x) if statistic == 'count' else statistic(x)
+
+        rng = np.random.default_rng(3704743126639371)
+        n = 10
+        x = rng.random(size=n)
+        i = x >= 0.5
+        v = rng.random(size=n)
+        if dtype is np.complex128:
+            v = v + rng.random(size=n)*1j
+
+        stat, _, _ = binned_statistic_dd(x, v, statistic, bins=2)
+        ref = np.array([ref_statistic(v[~i]), ref_statistic(v[i])])
+        assert_allclose(stat, ref)
+        assert stat.dtype == np.result_type(ref.dtype, np.float64)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_censored_data.py

@@ -0,0 +1,152 @@
+# Tests for the CensoredData class.
+
+import pytest
+import numpy as np
+from numpy.testing import assert_equal, assert_array_equal
+from scipy.stats import CensoredData
+
+
+class TestCensoredData:
+
+    def test_basic(self):
+        uncensored = [1]
+        left = [0]
+        right = [2, 5]
+        interval = [[2, 3]]
+        data = CensoredData(uncensored, left=left, right=right,
+                            interval=interval)
+        assert_equal(data._uncensored, uncensored)
+        assert_equal(data._left, left)
+        assert_equal(data._right, right)
+        assert_equal(data._interval, interval)
+
+        udata = data._uncensor()
+        assert_equal(udata, np.concatenate((uncensored, left, right,
+                                            np.mean(interval, axis=1))))
+
+    def test_right_censored(self):
+        x = np.array([0, 3, 2.5])
+        is_censored = np.array([0, 1, 0], dtype=bool)
+        data = CensoredData.right_censored(x, is_censored)
+        assert_equal(data._uncensored, x[~is_censored])
+        assert_equal(data._right, x[is_censored])
+        assert_equal(data._left, [])
+        assert_equal(data._interval, np.empty((0, 2)))
+
+    def test_left_censored(self):
+        x = np.array([0, 3, 2.5])
+        is_censored = np.array([0, 1, 0], dtype=bool)
+        data = CensoredData.left_censored(x, is_censored)
+        assert_equal(data._uncensored, x[~is_censored])
+        assert_equal(data._left, x[is_censored])
+        assert_equal(data._right, [])
+        assert_equal(data._interval, np.empty((0, 2)))
+
+    def test_interval_censored_basic(self):
+        a = [0.5, 2.0, 3.0, 5.5]
+        b = [1.0, 2.5, 3.5, 7.0]
+        data = CensoredData.interval_censored(low=a, high=b)
+        assert_array_equal(data._interval, np.array(list(zip(a, b))))
+        assert data._uncensored.shape == (0,)
+        assert data._left.shape == (0,)
+        assert data._right.shape == (0,)
+
+    def test_interval_censored_mixed(self):
+        # This is actually a mix of uncensored, left-censored, right-censored
+        # and interval-censored data.  Check that when the `interval_censored`
+        # class method is used, the data is correctly separated into the
+        # appropriate arrays.
+        a = [0.5, -np.inf, -13.0, 2.0, 1.0, 10.0, -1.0]
+        b = [0.5, 2500.0, np.inf, 3.0, 1.0, 11.0, np.inf]
+        data = CensoredData.interval_censored(low=a, high=b)
+        assert_array_equal(data._interval, [[2.0, 3.0], [10.0, 11.0]])
+        assert_array_equal(data._uncensored, [0.5, 1.0])
+        assert_array_equal(data._left, [2500.0])
+        assert_array_equal(data._right, [-13.0, -1.0])
+
+    def test_interval_to_other_types(self):
+        # The interval parameter can represent uncensored and
+        # left- or right-censored data.  Test the conversion of such
+        # an example to the canonical form in which the different
+        # types have been split into the separate arrays.
+        interval = np.array([[0, 1],        # interval-censored
+                             [2, 2],        # not censored
+                             [3, 3],        # not censored
+                             [9, np.inf],   # right-censored
+                             [8, np.inf],   # right-censored
+                             [-np.inf, 0],  # left-censored
+                             [1, 2]])       # interval-censored
+        data = CensoredData(interval=interval)
+        assert_equal(data._uncensored, [2, 3])
+        assert_equal(data._left, [0])
+        assert_equal(data._right, [9, 8])
+        assert_equal(data._interval, [[0, 1], [1, 2]])
+
+    def test_empty_arrays(self):
+        data = CensoredData(uncensored=[], left=[], right=[], interval=[])
+        assert data._uncensored.shape == (0,)
+        assert data._left.shape == (0,)
+        assert data._right.shape == (0,)
+        assert data._interval.shape == (0, 2)
+        assert len(data) == 0
+
+    def test_invalid_constructor_args(self):
+        with pytest.raises(ValueError, match='must be a one-dimensional'):
+            CensoredData(uncensored=[[1, 2, 3]])
+        with pytest.raises(ValueError, match='must be a one-dimensional'):
+            CensoredData(left=[[1, 2, 3]])
+        with pytest.raises(ValueError, match='must be a one-dimensional'):
+            CensoredData(right=[[1, 2, 3]])
+        with pytest.raises(ValueError, match='must be a two-dimensional'):
+            CensoredData(interval=[[1, 2, 3]])
+
+        with pytest.raises(ValueError, match='must not contain nan'):
+            CensoredData(uncensored=[1, np.nan, 2])
+        with pytest.raises(ValueError, match='must not contain nan'):
+            CensoredData(left=[1, np.nan, 2])
+        with pytest.raises(ValueError, match='must not contain nan'):
+            CensoredData(right=[1, np.nan, 2])
+        with pytest.raises(ValueError, match='must not contain nan'):
+            CensoredData(interval=[[1, np.nan], [2, 3]])
+
+        with pytest.raises(ValueError,
+                           match='both values must not be infinite'):
+            CensoredData(interval=[[1, 3], [2, 9], [np.inf, np.inf]])
+
+        with pytest.raises(ValueError,
+                           match='left value must not exceed the right'):
+            CensoredData(interval=[[1, 0], [2, 2]])
+
+    @pytest.mark.parametrize('func', [CensoredData.left_censored,
+                                      CensoredData.right_censored])
+    def test_invalid_left_right_censored_args(self, func):
+        with pytest.raises(ValueError,
+                           match='`x` must be one-dimensional'):
+            func([[1, 2, 3]], [0, 1, 1])
+        with pytest.raises(ValueError,
+                           match='`censored` must be one-dimensional'):
+            func([1, 2, 3], [[0, 1, 1]])
+        with pytest.raises(ValueError, match='`x` must not contain'):
+            func([1, 2, np.nan], [0, 1, 1])
+        with pytest.raises(ValueError, match='must have the same length'):
+            func([1, 2, 3], [0, 0, 1, 1])
+
+    def test_invalid_censored_args(self):
+        with pytest.raises(ValueError,
+                           match='`low` must be a one-dimensional'):
+            CensoredData.interval_censored(low=[[3]], high=[4, 5])
+        with pytest.raises(ValueError,
+                           match='`high` must be a one-dimensional'):
+            CensoredData.interval_censored(low=[3], high=[[4, 5]])
+        with pytest.raises(ValueError, match='`low` must not contain'):
+            CensoredData.interval_censored([1, 2, np.nan], [0, 1, 1])
+        with pytest.raises(ValueError, match='must have the same length'):
+            CensoredData.interval_censored([1, 2, 3], [0, 0, 1, 1])
+
+    def test_count_censored(self):
+        x = [1, 2, 3]
+        # data1 has no censored data.
+        data1 = CensoredData(x)
+        assert data1.num_censored() == 0
+        data2 = CensoredData(uncensored=[2.5], left=[10], interval=[[0, 1]])
+        assert data2.num_censored() == 2

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_contingency.py

@@ -0,0 +1,241 @@
+import numpy as np
+from numpy.testing import (assert_equal, assert_array_equal,
+                           assert_array_almost_equal, assert_approx_equal,
+                           assert_allclose)
+import pytest
+from pytest import raises as assert_raises
+from scipy.special import xlogy
+from scipy.stats.contingency import (margins, expected_freq,
+                                     chi2_contingency, association)
+
+
+def test_margins():
+    a = np.array([1])
+    m = margins(a)
+    assert_equal(len(m), 1)
+    m0 = m[0]
+    assert_array_equal(m0, np.array([1]))
+
+    a = np.array([[1]])
+    m0, m1 = margins(a)
+    expected0 = np.array([[1]])
+    expected1 = np.array([[1]])
+    assert_array_equal(m0, expected0)
+    assert_array_equal(m1, expected1)
+
+    a = np.arange(12).reshape(2, 6)
+    m0, m1 = margins(a)
+    expected0 = np.array([[15], [51]])
+    expected1 = np.array([[6, 8, 10, 12, 14, 16]])
+    assert_array_equal(m0, expected0)
+    assert_array_equal(m1, expected1)
+
+    a = np.arange(24).reshape(2, 3, 4)
+    m0, m1, m2 = margins(a)
+    expected0 = np.array([[[66]], [[210]]])
+    expected1 = np.array([[[60], [92], [124]]])
+    expected2 = np.array([[[60, 66, 72, 78]]])
+    assert_array_equal(m0, expected0)
+    assert_array_equal(m1, expected1)
+    assert_array_equal(m2, expected2)
+
+
+def test_expected_freq():
+    assert_array_equal(expected_freq([1]), np.array([1.0]))
+
+    observed = np.array([[[2, 0], [0, 2]], [[0, 2], [2, 0]], [[1, 1], [1, 1]]])
+    e = expected_freq(observed)
+    assert_array_equal(e, np.ones_like(observed))
+
+    observed = np.array([[10, 10, 20], [20, 20, 20]])
+    e = expected_freq(observed)
+    correct = np.array([[12., 12., 16.], [18., 18., 24.]])
+    assert_array_almost_equal(e, correct)
+
+
+def test_chi2_contingency_trivial():
+    # Some very simple tests for chi2_contingency.
+
+    # A trivial case
+    obs = np.array([[1, 2], [1, 2]])
+    chi2, p, dof, expected = chi2_contingency(obs, correction=False)
+    assert_equal(chi2, 0.0)
+    assert_equal(p, 1.0)
+    assert_equal(dof, 1)
+    assert_array_equal(obs, expected)
+
+    # A *really* trivial case: 1-D data.
+    obs = np.array([1, 2, 3])
+    chi2, p, dof, expected = chi2_contingency(obs, correction=False)
+    assert_equal(chi2, 0.0)
+    assert_equal(p, 1.0)
+    assert_equal(dof, 0)
+    assert_array_equal(obs, expected)
+
+
+def test_chi2_contingency_R():
+    # Some test cases that were computed independently, using R.
+
+    # Rcode = \
+    # """
+    # # Data vector.
+    # data <- c(
+    #   12, 34, 23,     4,  47,  11,
+    #   35, 31, 11,    34,  10,  18,
+    #   12, 32,  9,    18,  13,  19,
+    #   12, 12, 14,     9,  33,  25
+    #   )
+    #
+    # # Create factor tags:r=rows, c=columns, t=tiers
+    # r <- factor(gl(4, 2*3, 2*3*4, labels=c("r1", "r2", "r3", "r4")))
+    # c <- factor(gl(3, 1,   2*3*4, labels=c("c1", "c2", "c3")))
+    # t <- factor(gl(2, 3,   2*3*4, labels=c("t1", "t2")))
+    #
+    # # 3-way Chi squared test of independence
+    # s = summary(xtabs(data~r+c+t))
+    # print(s)
+    # """
+    # Routput = \
+    # """
+    # Call: xtabs(formula = data ~ r + c + t)
+    # Number of cases in table: 478
+    # Number of factors: 3
+    # Test for independence of all factors:
+    #         Chisq = 102.17, df = 17, p-value = 3.514e-14
+    # """
+    obs = np.array(
+        [[[12, 34, 23],
+          [35, 31, 11],
+          [12, 32, 9],
+          [12, 12, 14]],
+         [[4, 47, 11],
+          [34, 10, 18],
+          [18, 13, 19],
+          [9, 33, 25]]])
+    chi2, p, dof, expected = chi2_contingency(obs)
+    assert_approx_equal(chi2, 102.17, significant=5)
+    assert_approx_equal(p, 3.514e-14, significant=4)
+    assert_equal(dof, 17)
+
+    # Rcode = \
+    # """
+    # # Data vector.
+    # data <- c(
+    #     #
+    #     12, 17,
+    #     11, 16,
+    #     #
+    #     11, 12,
+    #     15, 16,
+    #     #
+    #     23, 15,
+    #     30, 22,
+    #     #
+    #     14, 17,
+    #     15, 16
+    #     )
+    #
+    # # Create factor tags:r=rows, c=columns, d=depths(?), t=tiers
+    # r <- factor(gl(2, 2,  2*2*2*2, labels=c("r1", "r2")))
+    # c <- factor(gl(2, 1,  2*2*2*2, labels=c("c1", "c2")))
+    # d <- factor(gl(2, 4,  2*2*2*2, labels=c("d1", "d2")))
+    # t <- factor(gl(2, 8,  2*2*2*2, labels=c("t1", "t2")))
+    #
+    # # 4-way Chi squared test of independence
+    # s = summary(xtabs(data~r+c+d+t))
+    # print(s)
+    # """
+    # Routput = \
+    # """
+    # Call: xtabs(formula = data ~ r + c + d + t)
+    # Number of cases in table: 262
+    # Number of factors: 4
+    # Test for independence of all factors:
+    #         Chisq = 8.758, df = 11, p-value = 0.6442
+    # """
+    obs = np.array(
+        [[[[12, 17],
+           [11, 16]],
+          [[11, 12],
+           [15, 16]]],
+         [[[23, 15],
+           [30, 22]],
+          [[14, 17],
+           [15, 16]]]])
+    chi2, p, dof, expected = chi2_contingency(obs)
+    assert_approx_equal(chi2, 8.758, significant=4)
+    assert_approx_equal(p, 0.6442, significant=4)
+    assert_equal(dof, 11)
+
+
+def test_chi2_contingency_g():
+    c = np.array([[15, 60], [15, 90]])
+    g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood',
+                                    correction=False)
+    assert_allclose(g, 2*xlogy(c, c/e).sum())
+
+    g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood',
+                                    correction=True)
+    c_corr = c + np.array([[-0.5, 0.5], [0.5, -0.5]])
+    assert_allclose(g, 2*xlogy(c_corr, c_corr/e).sum())
+
+    c = np.array([[10, 12, 10], [12, 10, 10]])
+    g, p, dof, e = chi2_contingency(c, lambda_='log-likelihood')
+    assert_allclose(g, 2*xlogy(c, c/e).sum())
+
+
+def test_chi2_contingency_bad_args():
+    # Test that "bad" inputs raise a ValueError.
+
+    # Negative value in the array of observed frequencies.
+    obs = np.array([[-1, 10], [1, 2]])
+    assert_raises(ValueError, chi2_contingency, obs)
+
+    # The zeros in this will result in zeros in the array
+    # of expected frequencies.
+    obs = np.array([[0, 1], [0, 1]])
+    assert_raises(ValueError, chi2_contingency, obs)
+
+    # A degenerate case: `observed` has size 0.
+    obs = np.empty((0, 8))
+    assert_raises(ValueError, chi2_contingency, obs)
+
+
+def test_chi2_contingency_yates_gh13875():
+    # Magnitude of Yates' continuity correction should not exceed difference
+    # between expected and observed value of the statistic; see gh-13875
+    observed = np.array([[1573, 3], [4, 0]])
+    p = chi2_contingency(observed)[1]
+    assert_allclose(p, 1, rtol=1e-12)
+
+
+@pytest.mark.parametrize("correction", [False, True])
+def test_result(correction):
+    obs = np.array([[1, 2], [1, 2]])
+    res = chi2_contingency(obs, correction=correction)
+    assert_equal((res.statistic, res.pvalue, res.dof, res.expected_freq), res)
+
+
+def test_bad_association_args():
+    # Invalid Test Statistic
+    assert_raises(ValueError, association, [[1, 2], [3, 4]], "X")
+    # Invalid array shape
+    assert_raises(ValueError, association, [[[1, 2]], [[3, 4]]], "cramer")
+    # chi2_contingency exception
+    assert_raises(ValueError, association, [[-1, 10], [1, 2]], 'cramer')
+    # Invalid Array Item Data Type
+    assert_raises(ValueError, association,
+                  np.array([[1, 2], ["dd", 4]], dtype=object), 'cramer')
+
+
+@pytest.mark.parametrize('stat, expected',
+                         [('cramer', 0.09222412010290792),
+                          ('tschuprow', 0.0775509319944633),
+                          ('pearson', 0.12932925727138758)])
+def test_assoc(stat, expected):
+    # 2d Array
+    obs1 = np.array([[12, 13, 14, 15, 16],
+                     [17, 16, 18, 19, 11],
+                     [9, 15, 14, 12, 11]])
+    a = association(observed=obs1, method=stat)
+    assert_allclose(a, expected)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_continuous_fit_censored.py

@@ -0,0 +1,683 @@
+# Tests for fitting specific distributions to censored data.
+
+import numpy as np
+from numpy.testing import assert_allclose
+
+from scipy.optimize import fmin
+from scipy.stats import (CensoredData, beta, cauchy, chi2, expon, gamma,
+                         gumbel_l, gumbel_r, invgauss, invweibull, laplace,
+                         logistic, lognorm, nct, ncx2, norm, weibull_max,
+                         weibull_min)
+
+
+# In some tests, we'll use this optimizer for improved accuracy.
+def optimizer(func, x0, args=(), disp=0):
+    return fmin(func, x0, args=args, disp=disp, xtol=1e-12, ftol=1e-12)
+
+
+def test_beta():
+    """
+    Test fitting beta shape parameters to interval-censored data.
+
+    Calculation in R:
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(0.10, 0.50, 0.75, 0.80),
+    +                    right=c(0.20, 0.55, 0.90, 0.95))
+    > result = fitdistcens(data, 'beta', control=list(reltol=1e-14))
+
+    > result
+    Fitting of the distribution ' beta ' on censored data by maximum likelihood
+    Parameters:
+           estimate
+    shape1 1.419941
+    shape2 1.027066
+    > result$sd
+       shape1    shape2
+    0.9914177 0.6866565
+    """
+    data = CensoredData(interval=[[0.10, 0.20],
+                                  [0.50, 0.55],
+                                  [0.75, 0.90],
+                                  [0.80, 0.95]])
+
+    # For this test, fit only the shape parameters; loc and scale are fixed.
+    a, b, loc, scale = beta.fit(data, floc=0, fscale=1, optimizer=optimizer)
+
+    assert_allclose(a, 1.419941, rtol=5e-6)
+    assert_allclose(b, 1.027066, rtol=5e-6)
+    assert loc == 0
+    assert scale == 1
+
+
+def test_cauchy_right_censored():
+    """
+    Test fitting the Cauchy distribution to right-censored data.
+
+    Calculation in R, with two values not censored [1, 10] and
+    one right-censored value [30].
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(1, 10, 30), right=c(1, 10, NA))
+    > result = fitdistcens(data, 'cauchy', control=list(reltol=1e-14))
+    > result
+    Fitting of the distribution ' cauchy ' on censored data by maximum
+    likelihood
+    Parameters:
+             estimate
+    location 7.100001
+    scale    7.455866
+    """
+    data = CensoredData(uncensored=[1, 10], right=[30])
+    loc, scale = cauchy.fit(data, optimizer=optimizer)
+    assert_allclose(loc, 7.10001, rtol=5e-6)
+    assert_allclose(scale, 7.455866, rtol=5e-6)
+
+
+def test_cauchy_mixed():
+    """
+    Test fitting the Cauchy distribution to data with mixed censoring.
+
+    Calculation in R, with:
+    * two values not censored [1, 10],
+    * one left-censored [1],
+    * one right-censored [30], and
+    * one interval-censored [[4, 8]].
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(NA, 1, 4, 10, 30), right=c(1, 1, 8, 10, NA))
+    > result = fitdistcens(data, 'cauchy', control=list(reltol=1e-14))
+    > result
+    Fitting of the distribution ' cauchy ' on censored data by maximum
+    likelihood
+    Parameters:
+             estimate
+    location 4.605150
+    scale    5.900852
+    """
+    data = CensoredData(uncensored=[1, 10], left=[1], right=[30],
+                        interval=[[4, 8]])
+    loc, scale = cauchy.fit(data, optimizer=optimizer)
+    assert_allclose(loc, 4.605150, rtol=5e-6)
+    assert_allclose(scale, 5.900852, rtol=5e-6)
+
+
+def test_chi2_mixed():
+    """
+    Test fitting just the shape parameter (df) of chi2 to mixed data.
+
+    Calculation in R, with:
+    * two values not censored [1, 10],
+    * one left-censored [1],
+    * one right-censored [30], and
+    * one interval-censored [[4, 8]].
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(NA, 1, 4, 10, 30), right=c(1, 1, 8, 10, NA))
+    > result = fitdistcens(data, 'chisq', control=list(reltol=1e-14))
+    > result
+    Fitting of the distribution ' chisq ' on censored data by maximum
+    likelihood
+    Parameters:
+             estimate
+    df 5.060329
+    """
+    data = CensoredData(uncensored=[1, 10], left=[1], right=[30],
+                        interval=[[4, 8]])
+    df, loc, scale = chi2.fit(data, floc=0, fscale=1, optimizer=optimizer)
+    assert_allclose(df, 5.060329, rtol=5e-6)
+    assert loc == 0
+    assert scale == 1
+
+
+def test_expon_right_censored():
+    """
+    For the exponential distribution with loc=0, the exact solution for
+    fitting n uncensored points x[0]...x[n-1] and m right-censored points
+    x[n]..x[n+m-1] is
+
+        scale = sum(x)/n
+
+    That is, divide the sum of all the values (not censored and
+    right-censored) by the number of uncensored values.  (See, for example,
+    https://en.wikipedia.org/wiki/Censoring_(statistics)#Likelihood.)
+
+    The second derivative of the log-likelihood function is
+
+        n/scale**2 - 2*sum(x)/scale**3
+
+    from which the estimate of the standard error can be computed.
+
+    -----
+
+    Calculation in R, for reference only. The R results are not
+    used in the test.
+
+    > library(fitdistrplus)
+    > dexps <- function(x, scale) {
+    +     return(dexp(x, 1/scale))
+    + }
+    > pexps <- function(q, scale) {
+    +     return(pexp(q, 1/scale))
+    + }
+    > left <- c(1, 2.5, 3, 6, 7.5, 10, 12, 12, 14.5, 15,
+    +                                     16, 16, 20, 20, 21, 22)
+    > right <- c(1, 2.5, 3, 6, 7.5, 10, 12, 12, 14.5, 15,
+    +                                     NA, NA, NA, NA, NA, NA)
+    > result = fitdistcens(data, 'exps', start=list(scale=mean(data$left)),
+    +                      control=list(reltol=1e-14))
+    > result
+    Fitting of the distribution ' exps ' on censored data by maximum likelihood
+    Parameters:
+          estimate
+    scale    19.85
+    > result$sd
+       scale
+    6.277119
+    """
+    # This data has 10 uncensored values and 6 right-censored values.
+    obs = [1, 2.5, 3, 6, 7.5, 10, 12, 12, 14.5, 15, 16, 16, 20, 20, 21, 22]
+    cens = [False]*10 + [True]*6
+    data = CensoredData.right_censored(obs, cens)
+
+    loc, scale = expon.fit(data, floc=0, optimizer=optimizer)
+
+    assert loc == 0
+    # Use the analytical solution to compute the expected value.  This
+    # is the sum of the observed values divided by the number of uncensored
+    # values.
+    n = len(data) - data.num_censored()
+    total = data._uncensored.sum() + data._right.sum()
+    expected = total / n
+    assert_allclose(scale, expected, 1e-8)
+
+
+def test_gamma_right_censored():
+    """
+    Fit gamma shape and scale to data with one right-censored value.
+
+    Calculation in R:
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(2.5, 2.9, 3.8, 9.1, 9.3, 12.0, 23.0, 25.0),
+    +                    right=c(2.5, 2.9, 3.8, 9.1, 9.3, 12.0, 23.0, NA))
+    > result = fitdistcens(data, 'gamma', start=list(shape=1, scale=10),
+    +                      control=list(reltol=1e-13))
+    > result
+    Fitting of the distribution ' gamma ' on censored data by maximum
+      likelihood
+    Parameters:
+          estimate
+    shape 1.447623
+    scale 8.360197
+    > result$sd
+        shape     scale
+    0.7053086 5.1016531
+    """
+    # The last value is right-censored.
+    x = CensoredData.right_censored([2.5, 2.9, 3.8, 9.1, 9.3, 12.0, 23.0,
+                                     25.0],
+                                    [0]*7 + [1])
+
+    a, loc, scale = gamma.fit(x, floc=0, optimizer=optimizer)
+
+    assert_allclose(a, 1.447623, rtol=5e-6)
+    assert loc == 0
+    assert_allclose(scale, 8.360197, rtol=5e-6)
+
+
+def test_gumbel():
+    """
+    Fit gumbel_l and gumbel_r to censored data.
+
+    This R calculation should match gumbel_r.
+
+    > library(evd)
+    > library(fitdistrplus)
+    > data = data.frame(left=c(0, 2, 3, 9, 10, 10),
+    +                   right=c(1, 2, 3, 9, NA, NA))
+    > result = fitdistcens(data, 'gumbel',
+    +                      control=list(reltol=1e-14),
+    +                      start=list(loc=4, scale=5))
+    > result
+    Fitting of the distribution ' gumbel ' on censored data by maximum
+    likelihood
+    Parameters:
+          estimate
+    loc   4.487853
+    scale 4.843640
+    """
+    # First value is interval-censored. Last two are right-censored.
+    uncensored = np.array([2, 3, 9])
+    right = np.array([10, 10])
+    interval = np.array([[0, 1]])
+    data = CensoredData(uncensored, right=right, interval=interval)
+    loc, scale = gumbel_r.fit(data, optimizer=optimizer)
+    assert_allclose(loc, 4.487853, rtol=5e-6)
+    assert_allclose(scale, 4.843640, rtol=5e-6)
+
+    # Negate the data and reverse the intervals, and test with gumbel_l.
+    data2 = CensoredData(-uncensored, left=-right,
+                         interval=-interval[:, ::-1])
+    # Fitting gumbel_l to data2 should give the same result as above, but
+    # with loc negated.
+    loc2, scale2 = gumbel_l.fit(data2, optimizer=optimizer)
+    assert_allclose(loc2, -4.487853, rtol=5e-6)
+    assert_allclose(scale2, 4.843640, rtol=5e-6)
+
+
+def test_invgauss():
+    """
+    Fit just the shape parameter of invgauss to data with one value
+    left-censored and one value right-censored.
+
+    Calculation in R; using a fixed dispersion parameter amounts to fixing
+    the scale to be 1.
+
+    > library(statmod)
+    > library(fitdistrplus)
+    > left <- c(NA, 0.4813096, 0.5571880, 0.5132463, 0.3801414, 0.5904386,
+    +           0.4822340, 0.3478597, 3, 0.7191797, 1.5810902, 0.4442299)
+    > right <- c(0.15, 0.4813096, 0.5571880, 0.5132463, 0.3801414, 0.5904386,
+    +            0.4822340, 0.3478597, NA, 0.7191797, 1.5810902, 0.4442299)
+    > data <- data.frame(left=left, right=right)
+    > result = fitdistcens(data, 'invgauss', control=list(reltol=1e-12),
+    +                      fix.arg=list(dispersion=1), start=list(mean=3))
+    > result
+    Fitting of the distribution ' invgauss ' on censored data by maximum
+      likelihood
+    Parameters:
+         estimate
+    mean 0.853469
+    Fixed parameters:
+               value
+    dispersion     1
+    > result$sd
+        mean
+    0.247636
+
+    Here's the R calculation with the dispersion as a free parameter to
+    be fit.
+
+    > result = fitdistcens(data, 'invgauss', control=list(reltol=1e-12),
+    +                      start=list(mean=3, dispersion=1))
+    > result
+    Fitting of the distribution ' invgauss ' on censored data by maximum
+    likelihood
+    Parameters:
+                estimate
+    mean       0.8699819
+    dispersion 1.2261362
+
+    The parametrization of the inverse Gaussian distribution in the
+    `statmod` package is not the same as in SciPy (see
+        https://arxiv.org/abs/1603.06687
+    for details).  The translation from R to SciPy is
+
+        scale = 1/dispersion
+        mu    = mean * dispersion
+
+    > 1/result$estimate['dispersion']  # 1/dispersion
+    dispersion
+     0.8155701
+    > result$estimate['mean'] * result$estimate['dispersion']
+        mean
+    1.066716
+
+    Those last two values are the SciPy scale and shape parameters.
+    """
+    # One point is left-censored, and one is right-censored.
+    x = [0.4813096, 0.5571880, 0.5132463, 0.3801414,
+         0.5904386, 0.4822340, 0.3478597, 0.7191797,
+         1.5810902, 0.4442299]
+    data = CensoredData(uncensored=x, left=[0.15], right=[3])
+
+    # Fit only the shape parameter.
+    mu, loc, scale = invgauss.fit(data, floc=0, fscale=1, optimizer=optimizer)
+
+    assert_allclose(mu, 0.853469, rtol=5e-5)
+    assert loc == 0
+    assert scale == 1
+
+    # Fit the shape and scale.
+    mu, loc, scale = invgauss.fit(data, floc=0, optimizer=optimizer)
+
+    assert_allclose(mu, 1.066716, rtol=5e-5)
+    assert loc == 0
+    assert_allclose(scale, 0.8155701, rtol=5e-5)
+
+
+def test_invweibull():
+    """
+    Fit invweibull to censored data.
+
+    Here is the calculation in R.  The 'frechet' distribution from the evd
+    package matches SciPy's invweibull distribution.  The `loc` parameter
+    is fixed at 0.
+
+    > library(evd)
+    > library(fitdistrplus)
+    > data = data.frame(left=c(0, 2, 3, 9, 10, 10),
+    +                   right=c(1, 2, 3, 9, NA, NA))
+    > result = fitdistcens(data, 'frechet',
+    +                      control=list(reltol=1e-14),
+    +                      start=list(loc=4, scale=5))
+    > result
+    Fitting of the distribution ' frechet ' on censored data by maximum
+    likelihood
+    Parameters:
+           estimate
+    scale 2.7902200
+    shape 0.6379845
+    Fixed parameters:
+        value
+    loc     0
+    """
+    # In the R data, the first value is interval-censored, and the last
+    # two are right-censored.  The rest are not censored.
+    data = CensoredData(uncensored=[2, 3, 9], right=[10, 10],
+                        interval=[[0, 1]])
+    c, loc, scale = invweibull.fit(data, floc=0, optimizer=optimizer)
+    assert_allclose(c, 0.6379845, rtol=5e-6)
+    assert loc == 0
+    assert_allclose(scale, 2.7902200, rtol=5e-6)
+
+
+def test_laplace():
+    """
+    Fir the Laplace distribution to left- and right-censored data.
+
+    Calculation in R:
+
+    > library(fitdistrplus)
+    > dlaplace <- function(x, location=0, scale=1) {
+    +     return(0.5*exp(-abs((x - location)/scale))/scale)
+    + }
+    > plaplace <- function(q, location=0, scale=1) {
+    +     z <- (q - location)/scale
+    +     s <- sign(z)
+    +     f <- -s*0.5*exp(-abs(z)) + (s+1)/2
+    +     return(f)
+    + }
+    > left <- c(NA, -41.564, 50.0, 15.7384, 50.0, 10.0452, -2.0684,
+    +           -19.5399, 50.0,   9.0005, 27.1227, 4.3113, -3.7372,
+    +           25.3111, 14.7987,  34.0887,  50.0, 42.8496, 18.5862,
+    +           32.8921, 9.0448, -27.4591, NA, 19.5083, -9.7199)
+    > right <- c(-50.0, -41.564,  NA, 15.7384, NA, 10.0452, -2.0684,
+    +            -19.5399, NA, 9.0005, 27.1227, 4.3113, -3.7372,
+    +            25.3111, 14.7987, 34.0887, NA,  42.8496, 18.5862,
+    +            32.8921, 9.0448, -27.4591, -50.0, 19.5083, -9.7199)
+    > data <- data.frame(left=left, right=right)
+    > result <- fitdistcens(data, 'laplace', start=list(location=10, scale=10),
+    +                       control=list(reltol=1e-13))
+    > result
+    Fitting of the distribution ' laplace ' on censored data by maximum
+      likelihood
+    Parameters:
+             estimate
+    location 14.79870
+    scale    30.93601
+    > result$sd
+         location     scale
+    0.1758864 7.0972125
+    """
+    # The value -50 is left-censored, and the value 50 is right-censored.
+    obs = np.array([-50.0, -41.564, 50.0, 15.7384, 50.0, 10.0452, -2.0684,
+                    -19.5399, 50.0, 9.0005, 27.1227, 4.3113, -3.7372,
+                    25.3111, 14.7987, 34.0887, 50.0, 42.8496, 18.5862,
+                    32.8921, 9.0448, -27.4591, -50.0, 19.5083, -9.7199])
+    x = obs[(obs != -50.0) & (obs != 50)]
+    left = obs[obs == -50.0]
+    right = obs[obs == 50.0]
+    data = CensoredData(uncensored=x, left=left, right=right)
+    loc, scale = laplace.fit(data, loc=10, scale=10, optimizer=optimizer)
+    assert_allclose(loc, 14.79870, rtol=5e-6)
+    assert_allclose(scale, 30.93601, rtol=5e-6)
+
+
+def test_logistic():
+    """
+    Fit the logistic distribution to left-censored data.
+
+    Calculation in R:
+    > library(fitdistrplus)
+    > left = c(13.5401, 37.4235, 11.906 , 13.998 ,  NA    ,  0.4023,  NA    ,
+    +          10.9044, 21.0629,  9.6985,  NA    , 12.9016, 39.164 , 34.6396,
+    +          NA    , 20.3665, 16.5889, 18.0952, 45.3818, 35.3306,  8.4949,
+    +          3.4041,  NA    ,  7.2828, 37.1265,  6.5969, 17.6868, 17.4977,
+    +          16.3391, 36.0541)
+    > right = c(13.5401, 37.4235, 11.906 , 13.998 ,  0.    ,  0.4023,  0.    ,
+    +           10.9044, 21.0629,  9.6985,  0.    , 12.9016, 39.164 , 34.6396,
+    +           0.    , 20.3665, 16.5889, 18.0952, 45.3818, 35.3306,  8.4949,
+    +           3.4041,  0.    ,  7.2828, 37.1265,  6.5969, 17.6868, 17.4977,
+    +           16.3391, 36.0541)
+    > data = data.frame(left=left, right=right)
+    > result = fitdistcens(data, 'logis', control=list(reltol=1e-14))
+    > result
+    Fitting of the distribution ' logis ' on censored data by maximum
+      likelihood
+    Parameters:
+              estimate
+    location 14.633459
+    scale     9.232736
+    > result$sd
+    location    scale
+    2.931505 1.546879
+    """
+    # Values that are zero are left-censored; the true values are less than 0.
+    x = np.array([13.5401, 37.4235, 11.906, 13.998, 0.0, 0.4023, 0.0, 10.9044,
+                  21.0629, 9.6985, 0.0, 12.9016, 39.164, 34.6396, 0.0, 20.3665,
+                  16.5889, 18.0952, 45.3818, 35.3306, 8.4949, 3.4041, 0.0,
+                  7.2828, 37.1265, 6.5969, 17.6868, 17.4977, 16.3391,
+                  36.0541])
+    data = CensoredData.left_censored(x, censored=(x == 0))
+    loc, scale = logistic.fit(data, optimizer=optimizer)
+    assert_allclose(loc, 14.633459, rtol=5e-7)
+    assert_allclose(scale, 9.232736, rtol=5e-6)
+
+
+def test_lognorm():
+    """
+    Ref: https://math.montana.edu/jobo/st528/documents/relc.pdf
+
+    The data is the locomotive control time to failure example that starts
+    on page 8.  That's the 8th page in the PDF; the page number shown in
+    the text is 270).
+    The document includes SAS output for the data.
+    """
+    # These are the uncensored measurements.  There are also 59 right-censored
+    # measurements where the lower bound is 135.
+    miles_to_fail = [22.5, 37.5, 46.0, 48.5, 51.5, 53.0, 54.5, 57.5, 66.5,
+                     68.0, 69.5, 76.5, 77.0, 78.5, 80.0, 81.5, 82.0, 83.0,
+                     84.0, 91.5, 93.5, 102.5, 107.0, 108.5, 112.5, 113.5,
+                     116.0, 117.0, 118.5, 119.0, 120.0, 122.5, 123.0, 127.5,
+                     131.0, 132.5, 134.0]
+
+    data = CensoredData.right_censored(miles_to_fail + [135]*59,
+                                       [0]*len(miles_to_fail) + [1]*59)
+    sigma, loc, scale = lognorm.fit(data, floc=0)
+
+    assert loc == 0
+    # Convert the lognorm parameters to the mu and sigma of the underlying
+    # normal distribution.
+    mu = np.log(scale)
+    # The expected results are from the 17th page of the PDF document
+    # (labeled page 279), in the SAS output on the right side of the page.
+    assert_allclose(mu, 5.1169, rtol=5e-4)
+    assert_allclose(sigma, 0.7055, rtol=5e-3)
+
+
+def test_nct():
+    """
+    Test fitting the noncentral t distribution to censored data.
+
+    Calculation in R:
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(1, 2, 3, 5, 8, 10, 25, 25),
+    +                    right=c(1, 2, 3, 5, 8, 10, NA, NA))
+    > result = fitdistcens(data, 't', control=list(reltol=1e-14),
+    +                      start=list(df=1, ncp=2))
+    > result
+    Fitting of the distribution ' t ' on censored data by maximum likelihood
+    Parameters:
+         estimate
+    df  0.5432336
+    ncp 2.8893565
+
+    """
+    data = CensoredData.right_censored([1, 2, 3, 5, 8, 10, 25, 25],
+                                       [0, 0, 0, 0, 0, 0, 1, 1])
+    # Fit just the shape parameter df and nc; loc and scale are fixed.
+    with np.errstate(over='ignore'):  # remove context when gh-14901 is closed
+        df, nc, loc, scale = nct.fit(data, floc=0, fscale=1,
+                                     optimizer=optimizer)
+    assert_allclose(df, 0.5432336, rtol=5e-6)
+    assert_allclose(nc, 2.8893565, rtol=5e-6)
+    assert loc == 0
+    assert scale == 1
+
+
+def test_ncx2():
+    """
+    Test fitting the shape parameters (df, ncp) of ncx2 to mixed data.
+
+    Calculation in R, with
+    * 5 not censored values [2.7, 0.2, 6.5, 0.4, 0.1],
+    * 1 interval-censored value [[0.6, 1.0]], and
+    * 2 right-censored values [8, 8].
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(2.7, 0.2, 6.5, 0.4, 0.1, 0.6, 8, 8),
+    +                    right=c(2.7, 0.2, 6.5, 0.4, 0.1, 1.0, NA, NA))
+    > result = fitdistcens(data, 'chisq', control=list(reltol=1e-14),
+    +                      start=list(df=1, ncp=2))
+    > result
+    Fitting of the distribution ' chisq ' on censored data by maximum
+    likelihood
+    Parameters:
+        estimate
+    df  1.052871
+    ncp 2.362934
+    """
+    data = CensoredData(uncensored=[2.7, 0.2, 6.5, 0.4, 0.1], right=[8, 8],
+                        interval=[[0.6, 1.0]])
+    with np.errstate(over='ignore'):  # remove context when gh-14901 is closed
+        df, ncp, loc, scale = ncx2.fit(data, floc=0, fscale=1,
+                                       optimizer=optimizer)
+    assert_allclose(df, 1.052871, rtol=5e-6)
+    assert_allclose(ncp, 2.362934, rtol=5e-6)
+    assert loc == 0
+    assert scale == 1
+
+
+def test_norm():
+    """
+    Test fitting the normal distribution to interval-censored data.
+
+    Calculation in R:
+
+    > library(fitdistrplus)
+    > data <- data.frame(left=c(0.10, 0.50, 0.75, 0.80),
+    +                    right=c(0.20, 0.55, 0.90, 0.95))
+    > result = fitdistcens(data, 'norm', control=list(reltol=1e-14))
+
+    > result
+    Fitting of the distribution ' norm ' on censored data by maximum likelihood
+    Parameters:
+          estimate
+    mean 0.5919990
+    sd   0.2868042
+    > result$sd
+         mean        sd
+    0.1444432 0.1029451
+    """
+    data = CensoredData(interval=[[0.10, 0.20],
+                                  [0.50, 0.55],
+                                  [0.75, 0.90],
+                                  [0.80, 0.95]])
+
+    loc, scale = norm.fit(data, optimizer=optimizer)
+
+    assert_allclose(loc, 0.5919990, rtol=5e-6)
+    assert_allclose(scale, 0.2868042, rtol=5e-6)
+
+
+def test_weibull_censored1():
+    # Ref: http://www.ams.sunysb.edu/~zhu/ams588/Lecture_3_likelihood.pdf
+
+    # Survival times; '*' indicates right-censored.
+    s = "3,5,6*,8,10*,11*,15,20*,22,23,27*,29,32,35,40,26,28,33*,21,24*"
+
+    times, cens = zip(*[(float(t[0]), len(t) == 2)
+                        for t in [w.split('*') for w in s.split(',')]])
+    data = CensoredData.right_censored(times, cens)
+
+    c, loc, scale = weibull_min.fit(data, floc=0)
+
+    # Expected values are from the reference.
+    assert_allclose(c, 2.149, rtol=1e-3)
+    assert loc == 0
+    assert_allclose(scale, 28.99, rtol=1e-3)
+
+    # Flip the sign of the data, and make the censored values
+    # left-censored. We should get the same parameters when we fit
+    # weibull_max to the flipped data.
+    data2 = CensoredData.left_censored(-np.array(times), cens)
+
+    c2, loc2, scale2 = weibull_max.fit(data2, floc=0)
+
+    assert_allclose(c2, 2.149, rtol=1e-3)
+    assert loc2 == 0
+    assert_allclose(scale2, 28.99, rtol=1e-3)
+
+
+def test_weibull_min_sas1():
+    # Data and SAS results from
+    #   https://support.sas.com/documentation/cdl/en/qcug/63922/HTML/default/
+    #         viewer.htm#qcug_reliability_sect004.htm
+
+    text = """
+           450 0    460 1   1150 0   1150 0   1560 1
+          1600 0   1660 1   1850 1   1850 1   1850 1
+          1850 1   1850 1   2030 1   2030 1   2030 1
+          2070 0   2070 0   2080 0   2200 1   3000 1
+          3000 1   3000 1   3000 1   3100 0   3200 1
+          3450 0   3750 1   3750 1   4150 1   4150 1
+          4150 1   4150 1   4300 1   4300 1   4300 1
+          4300 1   4600 0   4850 1   4850 1   4850 1
+          4850 1   5000 1   5000 1   5000 1   6100 1
+          6100 0   6100 1   6100 1   6300 1   6450 1
+          6450 1   6700 1   7450 1   7800 1   7800 1
+          8100 1   8100 1   8200 1   8500 1   8500 1
+          8500 1   8750 1   8750 0   8750 1   9400 1
+          9900 1  10100 1  10100 1  10100 1  11500 1
+    """
+
+    life, cens = np.array([int(w) for w in text.split()]).reshape(-1, 2).T
+    life = life/1000.0
+
+    data = CensoredData.right_censored(life, cens)
+
+    c, loc, scale = weibull_min.fit(data, floc=0, optimizer=optimizer)
+    assert_allclose(c, 1.0584, rtol=1e-4)
+    assert_allclose(scale, 26.2968, rtol=1e-5)
+    assert loc == 0
+
+
+def test_weibull_min_sas2():
+    # http://support.sas.com/documentation/cdl/en/ormpug/67517/HTML/default/
+    #      viewer.htm#ormpug_nlpsolver_examples06.htm
+
+    # The last two values are right-censored.
+    days = np.array([143, 164, 188, 188, 190, 192, 206, 209, 213, 216, 220,
+                     227, 230, 234, 246, 265, 304, 216, 244])
+
+    data = CensoredData.right_censored(days, [0]*(len(days) - 2) + [1]*2)
+
+    c, loc, scale = weibull_min.fit(data, 1, loc=100, scale=100,
+                                    optimizer=optimizer)
+
+    assert_allclose(c, 2.7112, rtol=5e-4)
+    assert_allclose(loc, 122.03, rtol=5e-4)
+    assert_allclose(scale, 108.37, rtol=5e-4)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_crosstab.py

@@ -0,0 +1,115 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_array_equal, assert_equal
+from scipy.stats.contingency import crosstab
+
+
+@pytest.mark.parametrize('sparse', [False, True])
+def test_crosstab_basic(sparse):
+    a = [0, 0, 9, 9, 0, 0, 9]
+    b = [2, 1, 3, 1, 2, 3, 3]
+    expected_avals = [0, 9]
+    expected_bvals = [1, 2, 3]
+    expected_count = np.array([[1, 2, 1],
+                               [1, 0, 2]])
+    (avals, bvals), count = crosstab(a, b, sparse=sparse)
+    assert_array_equal(avals, expected_avals)
+    assert_array_equal(bvals, expected_bvals)
+    if sparse:
+        assert_array_equal(count.toarray(), expected_count)
+    else:
+        assert_array_equal(count, expected_count)
+
+
+def test_crosstab_basic_1d():
+    # Verify that a single input sequence works as expected.
+    x = [1, 2, 3, 1, 2, 3, 3]
+    expected_xvals = [1, 2, 3]
+    expected_count = np.array([2, 2, 3])
+    (xvals,), count = crosstab(x)
+    assert_array_equal(xvals, expected_xvals)
+    assert_array_equal(count, expected_count)
+
+
+def test_crosstab_basic_3d():
+    # Verify the function for three input sequences.
+    a = 'a'
+    b = 'b'
+    x = [0, 0, 9, 9, 0, 0, 9, 9]
+    y = [a, a, a, a, b, b, b, a]
+    z = [1, 2, 3, 1, 2, 3, 3, 1]
+    expected_xvals = [0, 9]
+    expected_yvals = [a, b]
+    expected_zvals = [1, 2, 3]
+    expected_count = np.array([[[1, 1, 0],
+                                [0, 1, 1]],
+                               [[2, 0, 1],
+                                [0, 0, 1]]])
+    (xvals, yvals, zvals), count = crosstab(x, y, z)
+    assert_array_equal(xvals, expected_xvals)
+    assert_array_equal(yvals, expected_yvals)
+    assert_array_equal(zvals, expected_zvals)
+    assert_array_equal(count, expected_count)
+
+
+@pytest.mark.parametrize('sparse', [False, True])
+def test_crosstab_levels(sparse):
+    a = [0, 0, 9, 9, 0, 0, 9]
+    b = [1, 2, 3, 1, 2, 3, 3]
+    expected_avals = [0, 9]
+    expected_bvals = [0, 1, 2, 3]
+    expected_count = np.array([[0, 1, 2, 1],
+                               [0, 1, 0, 2]])
+    (avals, bvals), count = crosstab(a, b, levels=[None, [0, 1, 2, 3]],
+                                     sparse=sparse)
+    assert_array_equal(avals, expected_avals)
+    assert_array_equal(bvals, expected_bvals)
+    if sparse:
+        assert_array_equal(count.toarray(), expected_count)
+    else:
+        assert_array_equal(count, expected_count)
+
+
+@pytest.mark.parametrize('sparse', [False, True])
+def test_crosstab_extra_levels(sparse):
+    # The pair of values (-1, 3) will be ignored, because we explicitly
+    # request the counted `a` values to be [0, 9].
+    a = [0, 0, 9, 9, 0, 0, 9, -1]
+    b = [1, 2, 3, 1, 2, 3, 3, 3]
+    expected_avals = [0, 9]
+    expected_bvals = [0, 1, 2, 3]
+    expected_count = np.array([[0, 1, 2, 1],
+                               [0, 1, 0, 2]])
+    (avals, bvals), count = crosstab(a, b, levels=[[0, 9], [0, 1, 2, 3]],
+                                     sparse=sparse)
+    assert_array_equal(avals, expected_avals)
+    assert_array_equal(bvals, expected_bvals)
+    if sparse:
+        assert_array_equal(count.toarray(), expected_count)
+    else:
+        assert_array_equal(count, expected_count)
+
+
+def test_validation_at_least_one():
+    with pytest.raises(TypeError, match='At least one'):
+        crosstab()
+
+
+def test_validation_same_lengths():
+    with pytest.raises(ValueError, match='must have the same length'):
+        crosstab([1, 2], [1, 2, 3, 4])
+
+
+def test_validation_sparse_only_two_args():
+    with pytest.raises(ValueError, match='only two input sequences'):
+        crosstab([0, 1, 1], [8, 8, 9], [1, 3, 3], sparse=True)
+
+
+def test_validation_len_levels_matches_args():
+    with pytest.raises(ValueError, match='number of input sequences'):
+        crosstab([0, 1, 1], [8, 8, 9], levels=([0, 1, 2, 3],))
+
+
+def test_result():
+    res = crosstab([0, 1], [1, 2])
+    assert_equal((res.elements, res.count), res)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_discrete_basic.py

@@ -0,0 +1,563 @@
+import numpy.testing as npt
+from numpy.testing import assert_allclose
+
+import numpy as np
+import pytest
+
+from scipy import stats
+from .common_tests import (check_normalization, check_moment,
+                           check_mean_expect,
+                           check_var_expect, check_skew_expect,
+                           check_kurt_expect, check_entropy,
+                           check_private_entropy, check_edge_support,
+                           check_named_args, check_random_state_property,
+                           check_pickling, check_rvs_broadcast,
+                           check_freezing,)
+from scipy.stats._distr_params import distdiscrete, invdistdiscrete
+from scipy.stats._distn_infrastructure import rv_discrete_frozen
+
+vals = ([1, 2, 3, 4], [0.1, 0.2, 0.3, 0.4])
+distdiscrete += [[stats.rv_discrete(values=vals), ()]]
+
+# For these distributions, test_discrete_basic only runs with test mode full
+distslow = {'zipfian', 'nhypergeom'}
+
+# Override number of ULPs adjustment for `check_cdf_ppf`
+roundtrip_cdf_ppf_exceptions = {'nbinom': 30}
+
+def cases_test_discrete_basic():
+    seen = set()
+    for distname, arg in distdiscrete:
+        if distname in distslow:
+            yield pytest.param(distname, arg, distname, marks=pytest.mark.slow)
+        else:
+            yield distname, arg, distname not in seen
+        seen.add(distname)
+
+
+@pytest.mark.parametrize('distname,arg,first_case', cases_test_discrete_basic())
+def test_discrete_basic(distname, arg, first_case):
+    try:
+        distfn = getattr(stats, distname)
+    except TypeError:
+        distfn = distname
+        distname = 'sample distribution'
+    np.random.seed(9765456)
+    rvs = distfn.rvs(size=2000, *arg)
+    supp = np.unique(rvs)
+    m, v = distfn.stats(*arg)
+    check_cdf_ppf(distfn, arg, supp, distname + ' cdf_ppf')
+
+    check_pmf_cdf(distfn, arg, distname)
+    check_oth(distfn, arg, supp, distname + ' oth')
+    check_edge_support(distfn, arg)
+
+    alpha = 0.01
+    check_discrete_chisquare(distfn, arg, rvs, alpha,
+                             distname + ' chisquare')
+
+    if first_case:
+        locscale_defaults = (0,)
+        meths = [distfn.pmf, distfn.logpmf, distfn.cdf, distfn.logcdf,
+                 distfn.logsf]
+        # make sure arguments are within support
+        # for some distributions, this needs to be overridden
+        spec_k = {'randint': 11, 'hypergeom': 4, 'bernoulli': 0,
+                  'nchypergeom_wallenius': 6}
+        k = spec_k.get(distname, 1)
+        check_named_args(distfn, k, arg, locscale_defaults, meths)
+        if distname != 'sample distribution':
+            check_scale_docstring(distfn)
+        check_random_state_property(distfn, arg)
+        check_pickling(distfn, arg)
+        check_freezing(distfn, arg)
+
+        # Entropy
+        check_entropy(distfn, arg, distname)
+        if distfn.__class__._entropy != stats.rv_discrete._entropy:
+            check_private_entropy(distfn, arg, stats.rv_discrete)
+
+
+@pytest.mark.parametrize('distname,arg', distdiscrete)
+def test_moments(distname, arg):
+    try:
+        distfn = getattr(stats, distname)
+    except TypeError:
+        distfn = distname
+        distname = 'sample distribution'
+    m, v, s, k = distfn.stats(*arg, moments='mvsk')
+    check_normalization(distfn, arg, distname)
+
+    # compare `stats` and `moment` methods
+    check_moment(distfn, arg, m, v, distname)
+    check_mean_expect(distfn, arg, m, distname)
+    check_var_expect(distfn, arg, m, v, distname)
+    check_skew_expect(distfn, arg, m, v, s, distname)
+    with np.testing.suppress_warnings() as sup:
+        if distname in ['zipf', 'betanbinom']:
+            sup.filter(RuntimeWarning)
+        check_kurt_expect(distfn, arg, m, v, k, distname)
+
+    # frozen distr moments
+    check_moment_frozen(distfn, arg, m, 1)
+    check_moment_frozen(distfn, arg, v+m*m, 2)
+
+
+@pytest.mark.parametrize('dist,shape_args', distdiscrete)
+def test_rvs_broadcast(dist, shape_args):
+    # If shape_only is True, it means the _rvs method of the
+    # distribution uses more than one random number to generate a random
+    # variate.  That means the result of using rvs with broadcasting or
+    # with a nontrivial size will not necessarily be the same as using the
+    # numpy.vectorize'd version of rvs(), so we can only compare the shapes
+    # of the results, not the values.
+    # Whether or not a distribution is in the following list is an
+    # implementation detail of the distribution, not a requirement.  If
+    # the implementation the rvs() method of a distribution changes, this
+    # test might also have to be changed.
+    shape_only = dist in ['betabinom', 'betanbinom', 'skellam', 'yulesimon',
+                          'dlaplace', 'nchypergeom_fisher',
+                          'nchypergeom_wallenius']
+
+    try:
+        distfunc = getattr(stats, dist)
+    except TypeError:
+        distfunc = dist
+        dist = f'rv_discrete(values=({dist.xk!r}, {dist.pk!r}))'
+    loc = np.zeros(2)
+    nargs = distfunc.numargs
+    allargs = []
+    bshape = []
+    # Generate shape parameter arguments...
+    for k in range(nargs):
+        shp = (k + 3,) + (1,)*(k + 1)
+        param_val = shape_args[k]
+        allargs.append(np.full(shp, param_val))
+        bshape.insert(0, shp[0])
+    allargs.append(loc)
+    bshape.append(loc.size)
+    # bshape holds the expected shape when loc, scale, and the shape
+    # parameters are all broadcast together.
+    check_rvs_broadcast(
+        distfunc, dist, allargs, bshape, shape_only, [np.dtype(int)]
+    )
+
+
+@pytest.mark.parametrize('dist,args', distdiscrete)
+def test_ppf_with_loc(dist, args):
+    try:
+        distfn = getattr(stats, dist)
+    except TypeError:
+        distfn = dist
+    #check with a negative, no and positive relocation.
+    np.random.seed(1942349)
+    re_locs = [np.random.randint(-10, -1), 0, np.random.randint(1, 10)]
+    _a, _b = distfn.support(*args)
+    for loc in re_locs:
+        npt.assert_array_equal(
+            [_a-1+loc, _b+loc],
+            [distfn.ppf(0.0, *args, loc=loc), distfn.ppf(1.0, *args, loc=loc)]
+            )
+
+
+@pytest.mark.parametrize('dist, args', distdiscrete)
+def test_isf_with_loc(dist, args):
+    try:
+        distfn = getattr(stats, dist)
+    except TypeError:
+        distfn = dist
+    # check with a negative, no and positive relocation.
+    np.random.seed(1942349)
+    re_locs = [np.random.randint(-10, -1), 0, np.random.randint(1, 10)]
+    _a, _b = distfn.support(*args)
+    for loc in re_locs:
+        expected = _b + loc, _a - 1 + loc
+        res = distfn.isf(0., *args, loc=loc), distfn.isf(1., *args, loc=loc)
+        npt.assert_array_equal(expected, res)
+    # test broadcasting behaviour
+    re_locs = [np.random.randint(-10, -1, size=(5, 3)),
+               np.zeros((5, 3)),
+               np.random.randint(1, 10, size=(5, 3))]
+    _a, _b = distfn.support(*args)
+    for loc in re_locs:
+        expected = _b + loc, _a - 1 + loc
+        res = distfn.isf(0., *args, loc=loc), distfn.isf(1., *args, loc=loc)
+        npt.assert_array_equal(expected, res)
+
+
+def check_cdf_ppf(distfn, arg, supp, msg):
+    # supp is assumed to be an array of integers in the support of distfn
+    # (but not necessarily all the integers in the support).
+    # This test assumes that the PMF of any value in the support of the
+    # distribution is greater than 1e-8.
+
+    # cdf is a step function, and ppf(q) = min{k : cdf(k) >= q, k integer}
+    cdf_supp = distfn.cdf(supp, *arg)
+    # In very rare cases, the finite precision calculation of ppf(cdf(supp))
+    # can produce an array in which an element is off by one.  We nudge the
+    # CDF values down by a few ULPs help to avoid this.
+    n_ulps = roundtrip_cdf_ppf_exceptions.get(distfn.name, 15)
+    cdf_supp0 = cdf_supp - n_ulps*np.spacing(cdf_supp)
+    npt.assert_array_equal(distfn.ppf(cdf_supp0, *arg),
+                           supp, msg + '-roundtrip')
+    # Repeat the same calculation, but with the CDF values decreased by 1e-8.
+    npt.assert_array_equal(distfn.ppf(distfn.cdf(supp, *arg) - 1e-8, *arg),
+                           supp, msg + '-roundtrip')
+
+    if not hasattr(distfn, 'xk'):
+        _a, _b = distfn.support(*arg)
+        supp1 = supp[supp < _b]
+        npt.assert_array_equal(distfn.ppf(distfn.cdf(supp1, *arg) + 1e-8, *arg),
+                               supp1 + distfn.inc, msg + ' ppf-cdf-next')
+
+
+def check_pmf_cdf(distfn, arg, distname):
+    if hasattr(distfn, 'xk'):
+        index = distfn.xk
+    else:
+        startind = int(distfn.ppf(0.01, *arg) - 1)
+        index = list(range(startind, startind + 10))
+    cdfs = distfn.cdf(index, *arg)
+    pmfs_cum = distfn.pmf(index, *arg).cumsum()
+
+    atol, rtol = 1e-10, 1e-10
+    if distname == 'skellam':    # ncx2 accuracy
+        atol, rtol = 1e-5, 1e-5
+    npt.assert_allclose(cdfs - cdfs[0], pmfs_cum - pmfs_cum[0],
+                        atol=atol, rtol=rtol)
+
+    # also check that pmf at non-integral k is zero
+    k = np.asarray(index)
+    k_shifted = k[:-1] + np.diff(k)/2
+    npt.assert_equal(distfn.pmf(k_shifted, *arg), 0)
+
+    # better check frozen distributions, and also when loc != 0
+    loc = 0.5
+    dist = distfn(loc=loc, *arg)
+    npt.assert_allclose(dist.pmf(k[1:] + loc), np.diff(dist.cdf(k + loc)))
+    npt.assert_equal(dist.pmf(k_shifted + loc), 0)
+
+
+def check_moment_frozen(distfn, arg, m, k):
+    npt.assert_allclose(distfn(*arg).moment(k), m,
+                        atol=1e-10, rtol=1e-10)
+
+
+def check_oth(distfn, arg, supp, msg):
+    # checking other methods of distfn
+    npt.assert_allclose(distfn.sf(supp, *arg), 1. - distfn.cdf(supp, *arg),
+                        atol=1e-10, rtol=1e-10)
+
+    q = np.linspace(0.01, 0.99, 20)
+    npt.assert_allclose(distfn.isf(q, *arg), distfn.ppf(1. - q, *arg),
+                        atol=1e-10, rtol=1e-10)
+
+    median_sf = distfn.isf(0.5, *arg)
+    npt.assert_(distfn.sf(median_sf - 1, *arg) > 0.5)
+    npt.assert_(distfn.cdf(median_sf + 1, *arg) > 0.5)
+
+
+def check_discrete_chisquare(distfn, arg, rvs, alpha, msg):
+    """Perform chisquare test for random sample of a discrete distribution
+
+    Parameters
+    ----------
+    distname : string
+        name of distribution function
+    arg : sequence
+        parameters of distribution
+    alpha : float
+        significance level, threshold for p-value
+
+    Returns
+    -------
+    result : bool
+        0 if test passes, 1 if test fails
+
+    """
+    wsupp = 0.05
+
+    # construct intervals with minimum mass `wsupp`.
+    # intervals are left-half-open as in a cdf difference
+    _a, _b = distfn.support(*arg)
+    lo = int(max(_a, -1000))
+    high = int(min(_b, 1000)) + 1
+    distsupport = range(lo, high)
+    last = 0
+    distsupp = [lo]
+    distmass = []
+    for ii in distsupport:
+        current = distfn.cdf(ii, *arg)
+        if current - last >= wsupp - 1e-14:
+            distsupp.append(ii)
+            distmass.append(current - last)
+            last = current
+            if current > (1 - wsupp):
+                break
+    if distsupp[-1] < _b:
+        distsupp.append(_b)
+        distmass.append(1 - last)
+    distsupp = np.array(distsupp)
+    distmass = np.array(distmass)
+
+    # convert intervals to right-half-open as required by histogram
+    histsupp = distsupp + 1e-8
+    histsupp[0] = _a
+
+    # find sample frequencies and perform chisquare test
+    freq, hsupp = np.histogram(rvs, histsupp)
+    chis, pval = stats.chisquare(np.array(freq), len(rvs)*distmass)
+
+    npt.assert_(
+        pval > alpha,
+        f'chisquare - test for {msg} at arg = {str(arg)} with pval = {str(pval)}'
+    )
+
+
+def check_scale_docstring(distfn):
+    if distfn.__doc__ is not None:
+        # Docstrings can be stripped if interpreter is run with -OO
+        npt.assert_('scale' not in distfn.__doc__)
+
+
+@pytest.mark.parametrize('method', ['pmf', 'logpmf', 'cdf', 'logcdf',
+                                    'sf', 'logsf', 'ppf', 'isf'])
+@pytest.mark.parametrize('distname, args', distdiscrete)
+def test_methods_with_lists(method, distname, args):
+    # Test that the discrete distributions can accept Python lists
+    # as arguments.
+    try:
+        dist = getattr(stats, distname)
+    except TypeError:
+        return
+    if method in ['ppf', 'isf']:
+        z = [0.1, 0.2]
+    else:
+        z = [0, 1]
+    p2 = [[p]*2 for p in args]
+    loc = [0, 1]
+    result = dist.pmf(z, *p2, loc=loc)
+    npt.assert_allclose(result,
+                        [dist.pmf(*v) for v in zip(z, *p2, loc)],
+                        rtol=1e-15, atol=1e-15)
+
+
+@pytest.mark.parametrize('distname, args', invdistdiscrete)
+def test_cdf_gh13280_regression(distname, args):
+    # Test for nan output when shape parameters are invalid
+    dist = getattr(stats, distname)
+    x = np.arange(-2, 15)
+    vals = dist.cdf(x, *args)
+    expected = np.nan
+    npt.assert_equal(vals, expected)
+
+
+def cases_test_discrete_integer_shapes():
+    # distributions parameters that are only allowed to be integral when
+    # fitting, but are allowed to be real as input to PDF, etc.
+    integrality_exceptions = {'nbinom': {'n'}, 'betanbinom': {'n'}}
+
+    seen = set()
+    for distname, shapes in distdiscrete:
+        if distname in seen:
+            continue
+        seen.add(distname)
+
+        try:
+            dist = getattr(stats, distname)
+        except TypeError:
+            continue
+
+        shape_info = dist._shape_info()
+
+        for i, shape in enumerate(shape_info):
+            if (shape.name in integrality_exceptions.get(distname, set()) or
+                    not shape.integrality):
+                continue
+
+            yield distname, shape.name, shapes
+
+
+@pytest.mark.parametrize('distname, shapename, shapes',
+                         cases_test_discrete_integer_shapes())
+def test_integer_shapes(distname, shapename, shapes):
+    dist = getattr(stats, distname)
+    shape_info = dist._shape_info()
+    shape_names = [shape.name for shape in shape_info]
+    i = shape_names.index(shapename)  # this element of params must be integral
+
+    shapes_copy = list(shapes)
+
+    valid_shape = shapes[i]
+    invalid_shape = valid_shape - 0.5  # arbitrary non-integral value
+    new_valid_shape = valid_shape - 1
+    shapes_copy[i] = [[valid_shape], [invalid_shape], [new_valid_shape]]
+
+    a, b = dist.support(*shapes)
+    x = np.round(np.linspace(a, b, 5))
+
+    pmf = dist.pmf(x, *shapes_copy)
+    assert not np.any(np.isnan(pmf[0, :]))
+    assert np.all(np.isnan(pmf[1, :]))
+    assert not np.any(np.isnan(pmf[2, :]))
+
+
+def test_frozen_attributes():
+    # gh-14827 reported that all frozen distributions had both pmf and pdf
+    # attributes; continuous should have pdf and discrete should have pmf.
+    message = "'rv_discrete_frozen' object has no attribute"
+    with pytest.raises(AttributeError, match=message):
+        stats.binom(10, 0.5).pdf
+    with pytest.raises(AttributeError, match=message):
+        stats.binom(10, 0.5).logpdf
+    stats.binom.pdf = "herring"
+    frozen_binom = stats.binom(10, 0.5)
+    assert isinstance(frozen_binom, rv_discrete_frozen)
+    delattr(stats.binom, 'pdf')
+
+
+@pytest.mark.parametrize('distname, shapes', distdiscrete)
+def test_interval(distname, shapes):
+    # gh-11026 reported that `interval` returns incorrect values when
+    # `confidence=1`. The values were not incorrect, but it was not intuitive
+    # that the left end of the interval should extend beyond the support of the
+    # distribution. Confirm that this is the behavior for all distributions.
+    if isinstance(distname, str):
+        dist = getattr(stats, distname)
+    else:
+        dist = distname
+    a, b = dist.support(*shapes)
+    npt.assert_equal(dist.ppf([0, 1], *shapes), (a-1, b))
+    npt.assert_equal(dist.isf([1, 0], *shapes), (a-1, b))
+    npt.assert_equal(dist.interval(1, *shapes), (a-1, b))
+
+
+@pytest.mark.xfail_on_32bit("Sensible to machine precision")
+def test_rv_sample():
+    # Thoroughly test rv_sample and check that gh-3758 is resolved
+
+    # Generate a random discrete distribution
+    rng = np.random.default_rng(98430143469)
+    xk = np.sort(rng.random(10) * 10)
+    pk = rng.random(10)
+    pk /= np.sum(pk)
+    dist = stats.rv_discrete(values=(xk, pk))
+
+    # Generate points to the left and right of xk
+    xk_left = (np.array([0] + xk[:-1].tolist()) + xk)/2
+    xk_right = (np.array(xk[1:].tolist() + [xk[-1]+1]) + xk)/2
+
+    # Generate points to the left and right of cdf
+    cdf2 = np.cumsum(pk)
+    cdf2_left = (np.array([0] + cdf2[:-1].tolist()) + cdf2)/2
+    cdf2_right = (np.array(cdf2[1:].tolist() + [1]) + cdf2)/2
+
+    # support - leftmost and rightmost xk
+    a, b = dist.support()
+    assert_allclose(a, xk[0])
+    assert_allclose(b, xk[-1])
+
+    # pmf - supported only on the xk
+    assert_allclose(dist.pmf(xk), pk)
+    assert_allclose(dist.pmf(xk_right), 0)
+    assert_allclose(dist.pmf(xk_left), 0)
+
+    # logpmf is log of the pmf; log(0) = -np.inf
+    with np.errstate(divide='ignore'):
+        assert_allclose(dist.logpmf(xk), np.log(pk))
+        assert_allclose(dist.logpmf(xk_right), -np.inf)
+        assert_allclose(dist.logpmf(xk_left), -np.inf)
+
+    # cdf - the cumulative sum of the pmf
+    assert_allclose(dist.cdf(xk), cdf2)
+    assert_allclose(dist.cdf(xk_right), cdf2)
+    assert_allclose(dist.cdf(xk_left), [0]+cdf2[:-1].tolist())
+
+    with np.errstate(divide='ignore'):
+        assert_allclose(dist.logcdf(xk), np.log(dist.cdf(xk)),
+                        atol=1e-15)
+        assert_allclose(dist.logcdf(xk_right), np.log(dist.cdf(xk_right)),
+                        atol=1e-15)
+        assert_allclose(dist.logcdf(xk_left), np.log(dist.cdf(xk_left)),
+                        atol=1e-15)
+
+    # sf is 1-cdf
+    assert_allclose(dist.sf(xk), 1-dist.cdf(xk))
+    assert_allclose(dist.sf(xk_right), 1-dist.cdf(xk_right))
+    assert_allclose(dist.sf(xk_left), 1-dist.cdf(xk_left))
+
+    with np.errstate(divide='ignore'):
+        assert_allclose(dist.logsf(xk), np.log(dist.sf(xk)),
+                        atol=1e-15)
+        assert_allclose(dist.logsf(xk_right), np.log(dist.sf(xk_right)),
+                        atol=1e-15)
+        assert_allclose(dist.logsf(xk_left), np.log(dist.sf(xk_left)),
+                        atol=1e-15)
+
+    # ppf
+    assert_allclose(dist.ppf(cdf2), xk)
+    assert_allclose(dist.ppf(cdf2_left), xk)
+    assert_allclose(dist.ppf(cdf2_right)[:-1], xk[1:])
+    assert_allclose(dist.ppf(0), a - 1)
+    assert_allclose(dist.ppf(1), b)
+
+    # isf
+    sf2 = dist.sf(xk)
+    assert_allclose(dist.isf(sf2), xk)
+    assert_allclose(dist.isf(1-cdf2_left), dist.ppf(cdf2_left))
+    assert_allclose(dist.isf(1-cdf2_right), dist.ppf(cdf2_right))
+    assert_allclose(dist.isf(0), b)
+    assert_allclose(dist.isf(1), a - 1)
+
+    # interval is (ppf(alpha/2), isf(alpha/2))
+    ps = np.linspace(0.01, 0.99, 10)
+    int2 = dist.ppf(ps/2), dist.isf(ps/2)
+    assert_allclose(dist.interval(1-ps), int2)
+    assert_allclose(dist.interval(0), dist.median())
+    assert_allclose(dist.interval(1), (a-1, b))
+
+    # median is simply ppf(0.5)
+    med2 = dist.ppf(0.5)
+    assert_allclose(dist.median(), med2)
+
+    # all four stats (mean, var, skew, and kurtosis) from the definitions
+    mean2 = np.sum(xk*pk)
+    var2 = np.sum((xk - mean2)**2 * pk)
+    skew2 = np.sum((xk - mean2)**3 * pk) / var2**(3/2)
+    kurt2 = np.sum((xk - mean2)**4 * pk) / var2**2 - 3
+    assert_allclose(dist.mean(), mean2)
+    assert_allclose(dist.std(), np.sqrt(var2))
+    assert_allclose(dist.var(), var2)
+    assert_allclose(dist.stats(moments='mvsk'), (mean2, var2, skew2, kurt2))
+
+    # noncentral moment against definition
+    mom3 = np.sum((xk**3) * pk)
+    assert_allclose(dist.moment(3), mom3)
+
+    # expect - check against moments
+    assert_allclose(dist.expect(lambda x: 1), 1)
+    assert_allclose(dist.expect(), mean2)
+    assert_allclose(dist.expect(lambda x: x**3), mom3)
+
+    # entropy is the negative of the expected value of log(p)
+    with np.errstate(divide='ignore'):
+        assert_allclose(-dist.expect(lambda x: dist.logpmf(x)), dist.entropy())
+
+    # RVS is just ppf of uniform random variates
+    rng = np.random.default_rng(98430143469)
+    rvs = dist.rvs(size=100, random_state=rng)
+    rng = np.random.default_rng(98430143469)
+    rvs0 = dist.ppf(rng.random(size=100))
+    assert_allclose(rvs, rvs0)
+
+def test__pmf_float_input():
+    # gh-21272
+    # test that `rvs()` can be computed when `_pmf` requires float input
+    
+    class rv_exponential(stats.rv_discrete):
+        def _pmf(self, i):
+            return (2/3)*3**(1 - i)
+    
+    rv = rv_exponential(a=0.0, b=float('inf'))
+    rvs = rv.rvs(random_state=42)  # should not crash due to integer input to `_pmf`
+    assert_allclose(rvs, 0)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_discrete_distns.py

@@ -0,0 +1,648 @@
+import pytest
+import itertools
+
+from scipy.stats import (betabinom, betanbinom, hypergeom, nhypergeom,
+                         bernoulli, boltzmann, skellam, zipf, zipfian, binom,
+                         nbinom, nchypergeom_fisher, nchypergeom_wallenius,
+                         randint)
+
+import numpy as np
+from numpy.testing import (
+    assert_almost_equal, assert_equal, assert_allclose, suppress_warnings
+)
+from scipy.special import binom as special_binom
+from scipy.optimize import root_scalar
+from scipy.integrate import quad
+
+
+# The expected values were computed with Wolfram Alpha, using
+# the expression CDF[HypergeometricDistribution[N, n, M], k].
+@pytest.mark.parametrize('k, M, n, N, expected, rtol',
+                         [(3, 10, 4, 5,
+                           0.9761904761904762, 1e-15),
+                          (107, 10000, 3000, 215,
+                           0.9999999997226765, 1e-15),
+                          (10, 10000, 3000, 215,
+                           2.681682217692179e-21, 5e-11)])
+def test_hypergeom_cdf(k, M, n, N, expected, rtol):
+    p = hypergeom.cdf(k, M, n, N)
+    assert_allclose(p, expected, rtol=rtol)
+
+
+# The expected values were computed with Wolfram Alpha, using
+# the expression SurvivalFunction[HypergeometricDistribution[N, n, M], k].
+@pytest.mark.parametrize('k, M, n, N, expected, rtol',
+                         [(25, 10000, 3000, 215,
+                           0.9999999999052958, 1e-15),
+                          (125, 10000, 3000, 215,
+                           1.4416781705752128e-18, 5e-11)])
+def test_hypergeom_sf(k, M, n, N, expected, rtol):
+    p = hypergeom.sf(k, M, n, N)
+    assert_allclose(p, expected, rtol=rtol)
+
+
+def test_hypergeom_logpmf():
+    # symmetries test
+    # f(k,N,K,n) = f(n-k,N,N-K,n) = f(K-k,N,K,N-n) = f(k,N,n,K)
+    k = 5
+    N = 50
+    K = 10
+    n = 5
+    logpmf1 = hypergeom.logpmf(k, N, K, n)
+    logpmf2 = hypergeom.logpmf(n - k, N, N - K, n)
+    logpmf3 = hypergeom.logpmf(K - k, N, K, N - n)
+    logpmf4 = hypergeom.logpmf(k, N, n, K)
+    assert_almost_equal(logpmf1, logpmf2, decimal=12)
+    assert_almost_equal(logpmf1, logpmf3, decimal=12)
+    assert_almost_equal(logpmf1, logpmf4, decimal=12)
+
+    # test related distribution
+    # Bernoulli distribution if n = 1
+    k = 1
+    N = 10
+    K = 7
+    n = 1
+    hypergeom_logpmf = hypergeom.logpmf(k, N, K, n)
+    bernoulli_logpmf = bernoulli.logpmf(k, K/N)
+    assert_almost_equal(hypergeom_logpmf, bernoulli_logpmf, decimal=12)
+
+
+def test_nhypergeom_pmf():
+    # test with hypergeom
+    M, n, r = 45, 13, 8
+    k = 6
+    NHG = nhypergeom.pmf(k, M, n, r)
+    HG = hypergeom.pmf(k, M, n, k+r-1) * (M - n - (r-1)) / (M - (k+r-1))
+    assert_allclose(HG, NHG, rtol=1e-10)
+
+
+def test_nhypergeom_pmfcdf():
+    # test pmf and cdf with arbitrary values.
+    M = 8
+    n = 3
+    r = 4
+    support = np.arange(n+1)
+    pmf = nhypergeom.pmf(support, M, n, r)
+    cdf = nhypergeom.cdf(support, M, n, r)
+    assert_allclose(pmf, [1/14, 3/14, 5/14, 5/14], rtol=1e-13)
+    assert_allclose(cdf, [1/14, 4/14, 9/14, 1.0], rtol=1e-13)
+
+
+def test_nhypergeom_r0():
+    # test with `r = 0`.
+    M = 10
+    n = 3
+    r = 0
+    pmf = nhypergeom.pmf([[0, 1, 2, 0], [1, 2, 0, 3]], M, n, r)
+    assert_allclose(pmf, [[1, 0, 0, 1], [0, 0, 1, 0]], rtol=1e-13)
+
+
+def test_nhypergeom_rvs_shape():
+    # Check that when given a size with more dimensions than the
+    # dimensions of the broadcast parameters, rvs returns an array
+    # with the correct shape.
+    x = nhypergeom.rvs(22, [7, 8, 9], [[12], [13]], size=(5, 1, 2, 3))
+    assert x.shape == (5, 1, 2, 3)
+
+
+def test_nhypergeom_accuracy():
+    # Check that nhypergeom.rvs post-gh-13431 gives the same values as
+    # inverse transform sampling
+    np.random.seed(0)
+    x = nhypergeom.rvs(22, 7, 11, size=100)
+    np.random.seed(0)
+    p = np.random.uniform(size=100)
+    y = nhypergeom.ppf(p, 22, 7, 11)
+    assert_equal(x, y)
+
+
+def test_boltzmann_upper_bound():
+    k = np.arange(-3, 5)
+
+    N = 1
+    p = boltzmann.pmf(k, 0.123, N)
+    expected = k == 0
+    assert_equal(p, expected)
+
+    lam = np.log(2)
+    N = 3
+    p = boltzmann.pmf(k, lam, N)
+    expected = [0, 0, 0, 4/7, 2/7, 1/7, 0, 0]
+    assert_allclose(p, expected, rtol=1e-13)
+
+    c = boltzmann.cdf(k, lam, N)
+    expected = [0, 0, 0, 4/7, 6/7, 1, 1, 1]
+    assert_allclose(c, expected, rtol=1e-13)
+
+
+def test_betabinom_a_and_b_unity():
+    # test limiting case that betabinom(n, 1, 1) is a discrete uniform
+    # distribution from 0 to n
+    n = 20
+    k = np.arange(n + 1)
+    p = betabinom(n, 1, 1).pmf(k)
+    expected = np.repeat(1 / (n + 1), n + 1)
+    assert_almost_equal(p, expected)
+
+
+@pytest.mark.parametrize('dtypes', itertools.product(*[(int, float)]*3))
+def test_betabinom_stats_a_and_b_integers_gh18026(dtypes):
+    # gh-18026 reported that `betabinom` kurtosis calculation fails when some
+    # parameters are integers. Check that this is resolved.
+    n_type, a_type, b_type = dtypes
+    n, a, b = n_type(10), a_type(2), b_type(3)
+    assert_allclose(betabinom.stats(n, a, b, moments='k'), -0.6904761904761907)
+
+
+def test_betabinom_bernoulli():
+    # test limiting case that betabinom(1, a, b) = bernoulli(a / (a + b))
+    a = 2.3
+    b = 0.63
+    k = np.arange(2)
+    p = betabinom(1, a, b).pmf(k)
+    expected = bernoulli(a / (a + b)).pmf(k)
+    assert_almost_equal(p, expected)
+
+
+def test_issue_10317():
+    alpha, n, p = 0.9, 10, 1
+    assert_equal(nbinom.interval(confidence=alpha, n=n, p=p), (0, 0))
+
+
+def test_issue_11134():
+    alpha, n, p = 0.95, 10, 0
+    assert_equal(binom.interval(confidence=alpha, n=n, p=p), (0, 0))
+
+
+def test_issue_7406():
+    np.random.seed(0)
+    assert_equal(binom.ppf(np.random.rand(10), 0, 0.5), 0)
+
+    # Also check that endpoints (q=0, q=1) are correct
+    assert_equal(binom.ppf(0, 0, 0.5), -1)
+    assert_equal(binom.ppf(1, 0, 0.5), 0)
+
+
+def test_issue_5122():
+    p = 0
+    n = np.random.randint(100, size=10)
+
+    x = 0
+    ppf = binom.ppf(x, n, p)
+    assert_equal(ppf, -1)
+
+    x = np.linspace(0.01, 0.99, 10)
+    ppf = binom.ppf(x, n, p)
+    assert_equal(ppf, 0)
+
+    x = 1
+    ppf = binom.ppf(x, n, p)
+    assert_equal(ppf, n)
+
+
+def test_issue_1603():
+    assert_equal(binom(1000, np.logspace(-3, -100)).ppf(0.01), 0)
+
+
+def test_issue_5503():
+    p = 0.5
+    x = np.logspace(3, 14, 12)
+    assert_allclose(binom.cdf(x, 2*x, p), 0.5, atol=1e-2)
+
+
+@pytest.mark.parametrize('x, n, p, cdf_desired', [
+    (300, 1000, 3/10, 0.51559351981411995636),
+    (3000, 10000, 3/10, 0.50493298381929698016),
+    (30000, 100000, 3/10, 0.50156000591726422864),
+    (300000, 1000000, 3/10, 0.50049331906666960038),
+    (3000000, 10000000, 3/10, 0.50015600124585261196),
+    (30000000, 100000000, 3/10, 0.50004933192735230102),
+    (30010000, 100000000, 3/10, 0.98545384016570790717),
+    (29990000, 100000000, 3/10, 0.01455017177985268670),
+    (29950000, 100000000, 3/10, 5.02250963487432024943e-28),
+])
+def test_issue_5503pt2(x, n, p, cdf_desired):
+    assert_allclose(binom.cdf(x, n, p), cdf_desired)
+
+
+def test_issue_5503pt3():
+    # From Wolfram Alpha: CDF[BinomialDistribution[1e12, 1e-12], 2]
+    assert_allclose(binom.cdf(2, 10**12, 10**-12), 0.91969860292869777384)
+
+
+def test_issue_6682():
+    # Reference value from R:
+    # options(digits=16)
+    # print(pnbinom(250, 50, 32/63, lower.tail=FALSE))
+    assert_allclose(nbinom.sf(250, 50, 32./63.), 1.460458510976452e-35)
+
+
+def test_issue_19747():
+    # test that negative k does not raise an error in nbinom.logcdf
+    result = nbinom.logcdf([5, -1, 1], 5, 0.5)
+    reference = [-0.47313352, -np.inf, -2.21297293]
+    assert_allclose(result, reference)
+
+
+def test_boost_divide_by_zero_issue_15101():
+    n = 1000
+    p = 0.01
+    k = 996
+    assert_allclose(binom.pmf(k, n, p), 0.0)
+
+
+def test_skellam_gh11474():
+    # test issue reported in gh-11474 caused by `cdfchn`
+    mu = [1, 10, 100, 1000, 5000, 5050, 5100, 5250, 6000]
+    cdf = skellam.cdf(0, mu, mu)
+    # generated in R
+    # library(skellam)
+    # options(digits = 16)
+    # mu = c(1, 10, 100, 1000, 5000, 5050, 5100, 5250, 6000)
+    # pskellam(0, mu, mu, TRUE)
+    cdf_expected = [0.6542541612768356, 0.5448901559424127, 0.5141135799745580,
+                    0.5044605891382528, 0.5019947363350450, 0.5019848365953181,
+                    0.5019750827993392, 0.5019466621805060, 0.5018209330219539]
+    assert_allclose(cdf, cdf_expected)
+
+
+class TestZipfian:
+    def test_zipfian_asymptotic(self):
+        # test limiting case that zipfian(a, n) -> zipf(a) as n-> oo
+        a = 6.5
+        N = 10000000
+        k = np.arange(1, 21)
+        assert_allclose(zipfian.pmf(k, a, N), zipf.pmf(k, a))
+        assert_allclose(zipfian.cdf(k, a, N), zipf.cdf(k, a))
+        assert_allclose(zipfian.sf(k, a, N), zipf.sf(k, a))
+        assert_allclose(zipfian.stats(a, N, moments='msvk'),
+                        zipf.stats(a, moments='msvk'))
+
+    def test_zipfian_continuity(self):
+        # test that zipfian(0.999999, n) ~ zipfian(1.000001, n)
+        # (a = 1 switches between methods of calculating harmonic sum)
+        alt1, agt1 = 0.99999999, 1.00000001
+        N = 30
+        k = np.arange(1, N + 1)
+        assert_allclose(zipfian.pmf(k, alt1, N), zipfian.pmf(k, agt1, N),
+                        rtol=5e-7)
+        assert_allclose(zipfian.cdf(k, alt1, N), zipfian.cdf(k, agt1, N),
+                        rtol=5e-7)
+        assert_allclose(zipfian.sf(k, alt1, N), zipfian.sf(k, agt1, N),
+                        rtol=5e-7)
+        assert_allclose(zipfian.stats(alt1, N, moments='msvk'),
+                        zipfian.stats(agt1, N, moments='msvk'), rtol=5e-7)
+
+    def test_zipfian_R(self):
+        # test against R VGAM package
+        # library(VGAM)
+        # k <- c(13, 16,  1,  4,  4,  8, 10, 19,  5,  7)
+        # a <- c(1.56712977, 3.72656295, 5.77665117, 9.12168729, 5.79977172,
+        #        4.92784796, 9.36078764, 4.3739616 , 7.48171872, 4.6824154)
+        # n <- c(70, 80, 48, 65, 83, 89, 50, 30, 20, 20)
+        # pmf <- dzipf(k, N = n, shape = a)
+        # cdf <- pzipf(k, N = n, shape = a)
+        # print(pmf)
+        # print(cdf)
+        np.random.seed(0)
+        k = np.random.randint(1, 20, size=10)
+        a = np.random.rand(10)*10 + 1
+        n = np.random.randint(1, 100, size=10)
+        pmf = [8.076972e-03, 2.950214e-05, 9.799333e-01, 3.216601e-06,
+               3.158895e-04, 3.412497e-05, 4.350472e-10, 2.405773e-06,
+               5.860662e-06, 1.053948e-04]
+        cdf = [0.8964133, 0.9998666, 0.9799333, 0.9999995, 0.9998584,
+               0.9999458, 1.0000000, 0.9999920, 0.9999977, 0.9998498]
+        # skip the first point; zipUC is not accurate for low a, n
+        assert_allclose(zipfian.pmf(k, a, n)[1:], pmf[1:], rtol=1e-6)
+        assert_allclose(zipfian.cdf(k, a, n)[1:], cdf[1:], rtol=5e-5)
+
+    np.random.seed(0)
+    naive_tests = np.vstack((np.logspace(-2, 1, 10),
+                             np.random.randint(2, 40, 10))).T
+
+    @pytest.mark.parametrize("a, n", naive_tests)
+    def test_zipfian_naive(self, a, n):
+        # test against bare-bones implementation
+
+        @np.vectorize
+        def Hns(n, s):
+            """Naive implementation of harmonic sum"""
+            return (1/np.arange(1, n+1)**s).sum()
+
+        @np.vectorize
+        def pzip(k, a, n):
+            """Naive implementation of zipfian pmf"""
+            if k < 1 or k > n:
+                return 0.
+            else:
+                return 1 / k**a / Hns(n, a)
+
+        k = np.arange(n+1)
+        pmf = pzip(k, a, n)
+        cdf = np.cumsum(pmf)
+        mean = np.average(k, weights=pmf)
+        var = np.average((k - mean)**2, weights=pmf)
+        std = var**0.5
+        skew = np.average(((k-mean)/std)**3, weights=pmf)
+        kurtosis = np.average(((k-mean)/std)**4, weights=pmf) - 3
+        assert_allclose(zipfian.pmf(k, a, n), pmf)
+        assert_allclose(zipfian.cdf(k, a, n), cdf)
+        assert_allclose(zipfian.stats(a, n, moments="mvsk"),
+                        [mean, var, skew, kurtosis])
+
+    def test_pmf_integer_k(self):
+        k = np.arange(0, 1000)
+        k_int32 = k.astype(np.int32)
+        dist = zipfian(111, 22)
+        pmf = dist.pmf(k)
+        pmf_k_int32 = dist.pmf(k_int32)
+        assert_equal(pmf, pmf_k_int32)
+
+
+class TestNCH:
+    np.random.seed(2)  # seeds 0 and 1 had some xl = xu; randint failed
+    shape = (2, 4, 3)
+    max_m = 100
+    m1 = np.random.randint(1, max_m, size=shape)    # red balls
+    m2 = np.random.randint(1, max_m, size=shape)    # white balls
+    N = m1 + m2                                     # total balls
+    n = randint.rvs(0, N, size=N.shape)             # number of draws
+    xl = np.maximum(0, n-m2)                        # lower bound of support
+    xu = np.minimum(n, m1)                          # upper bound of support
+    x = randint.rvs(xl, xu, size=xl.shape)
+    odds = np.random.rand(*x.shape)*2
+
+    # test output is more readable when function names (strings) are passed
+    @pytest.mark.parametrize('dist_name',
+                             ['nchypergeom_fisher', 'nchypergeom_wallenius'])
+    def test_nch_hypergeom(self, dist_name):
+        # Both noncentral hypergeometric distributions reduce to the
+        # hypergeometric distribution when odds = 1
+        dists = {'nchypergeom_fisher': nchypergeom_fisher,
+                 'nchypergeom_wallenius': nchypergeom_wallenius}
+        dist = dists[dist_name]
+        x, N, m1, n = self.x, self.N, self.m1, self.n
+        assert_allclose(dist.pmf(x, N, m1, n, odds=1),
+                        hypergeom.pmf(x, N, m1, n))
+
+    def test_nchypergeom_fisher_naive(self):
+        # test against a very simple implementation
+        x, N, m1, n, odds = self.x, self.N, self.m1, self.n, self.odds
+
+        @np.vectorize
+        def pmf_mean_var(x, N, m1, n, w):
+            # simple implementation of nchypergeom_fisher pmf
+            m2 = N - m1
+            xl = np.maximum(0, n-m2)
+            xu = np.minimum(n, m1)
+
+            def f(x):
+                t1 = special_binom(m1, x)
+                t2 = special_binom(m2, n - x)
+                return t1 * t2 * w**x
+
+            def P(k):
+                return sum(f(y)*y**k for y in range(xl, xu + 1))
+
+            P0 = P(0)
+            P1 = P(1)
+            P2 = P(2)
+            pmf = f(x) / P0
+            mean = P1 / P0
+            var = P2 / P0 - (P1 / P0)**2
+            return pmf, mean, var
+
+        pmf, mean, var = pmf_mean_var(x, N, m1, n, odds)
+        assert_allclose(nchypergeom_fisher.pmf(x, N, m1, n, odds), pmf)
+        assert_allclose(nchypergeom_fisher.stats(N, m1, n, odds, moments='m'),
+                        mean)
+        assert_allclose(nchypergeom_fisher.stats(N, m1, n, odds, moments='v'),
+                        var)
+
+    def test_nchypergeom_wallenius_naive(self):
+        # test against a very simple implementation
+
+        np.random.seed(2)
+        shape = (2, 4, 3)
+        max_m = 100
+        m1 = np.random.randint(1, max_m, size=shape)
+        m2 = np.random.randint(1, max_m, size=shape)
+        N = m1 + m2
+        n = randint.rvs(0, N, size=N.shape)
+        xl = np.maximum(0, n-m2)
+        xu = np.minimum(n, m1)
+        x = randint.rvs(xl, xu, size=xl.shape)
+        w = np.random.rand(*x.shape)*2
+
+        def support(N, m1, n, w):
+            m2 = N - m1
+            xl = np.maximum(0, n-m2)
+            xu = np.minimum(n, m1)
+            return xl, xu
+
+        @np.vectorize
+        def mean(N, m1, n, w):
+            m2 = N - m1
+            xl, xu = support(N, m1, n, w)
+
+            def fun(u):
+                return u/m1 + (1 - (n-u)/m2)**w - 1
+
+            return root_scalar(fun, bracket=(xl, xu)).root
+
+        with suppress_warnings() as sup:
+            sup.filter(RuntimeWarning,
+                       message="invalid value encountered in mean")
+            assert_allclose(nchypergeom_wallenius.mean(N, m1, n, w),
+                            mean(N, m1, n, w), rtol=2e-2)
+
+        @np.vectorize
+        def variance(N, m1, n, w):
+            m2 = N - m1
+            u = mean(N, m1, n, w)
+            a = u * (m1 - u)
+            b = (n-u)*(u + m2 - n)
+            return N*a*b / ((N-1) * (m1*b + m2*a))
+
+        with suppress_warnings() as sup:
+            sup.filter(RuntimeWarning,
+                       message="invalid value encountered in mean")
+            assert_allclose(
+                nchypergeom_wallenius.stats(N, m1, n, w, moments='v'),
+                variance(N, m1, n, w),
+                rtol=5e-2
+            )
+
+        @np.vectorize
+        def pmf(x, N, m1, n, w):
+            m2 = N - m1
+            xl, xu = support(N, m1, n, w)
+
+            def integrand(t):
+                D = w*(m1 - x) + (m2 - (n-x))
+                res = (1-t**(w/D))**x * (1-t**(1/D))**(n-x)
+                return res
+
+            def f(x):
+                t1 = special_binom(m1, x)
+                t2 = special_binom(m2, n - x)
+                the_integral = quad(integrand, 0, 1,
+                                    epsrel=1e-16, epsabs=1e-16)
+                return t1 * t2 * the_integral[0]
+
+            return f(x)
+
+        pmf0 = pmf(x, N, m1, n, w)
+        pmf1 = nchypergeom_wallenius.pmf(x, N, m1, n, w)
+
+        atol, rtol = 1e-6, 1e-6
+        i = np.abs(pmf1 - pmf0) < atol + rtol*np.abs(pmf0)
+        assert i.sum() > np.prod(shape) / 2  # works at least half the time
+
+        # for those that fail, discredit the naive implementation
+        for N, m1, n, w in zip(N[~i], m1[~i], n[~i], w[~i]):
+            # get the support
+            m2 = N - m1
+            xl, xu = support(N, m1, n, w)
+            x = np.arange(xl, xu + 1)
+
+            # calculate sum of pmf over the support
+            # the naive implementation is very wrong in these cases
+            assert pmf(x, N, m1, n, w).sum() < .5
+            assert_allclose(nchypergeom_wallenius.pmf(x, N, m1, n, w).sum(), 1)
+
+    def test_wallenius_against_mpmath(self):
+        # precompute data with mpmath since naive implementation above
+        # is not reliable. See source code in gh-13330.
+        M = 50
+        n = 30
+        N = 20
+        odds = 2.25
+        # Expected results, computed with mpmath.
+        sup = np.arange(21)
+        pmf = np.array([3.699003068656875e-20,
+                        5.89398584245431e-17,
+                        2.1594437742911123e-14,
+                        3.221458044649955e-12,
+                        2.4658279241205077e-10,
+                        1.0965862603981212e-08,
+                        3.057890479665704e-07,
+                        5.622818831643761e-06,
+                        7.056482841531681e-05,
+                        0.000618899425358671,
+                        0.003854172932571669,
+                        0.01720592676256026,
+                        0.05528844897093792,
+                        0.12772363313574242,
+                        0.21065898367825722,
+                        0.24465958845359234,
+                        0.1955114898110033,
+                        0.10355390084949237,
+                        0.03414490375225675,
+                        0.006231989845775931,
+                        0.0004715577304677075])
+        mean = 14.808018384813426
+        var = 2.6085975877923717
+
+        # nchypergeom_wallenius.pmf returns 0 for pmf(0) and pmf(1), and pmf(2)
+        # has only three digits of accuracy (~ 2.1511e-14).
+        assert_allclose(nchypergeom_wallenius.pmf(sup, M, n, N, odds), pmf,
+                        rtol=1e-13, atol=1e-13)
+        assert_allclose(nchypergeom_wallenius.mean(M, n, N, odds),
+                        mean, rtol=1e-13)
+        assert_allclose(nchypergeom_wallenius.var(M, n, N, odds),
+                        var, rtol=1e-11)
+
+    @pytest.mark.parametrize('dist_name',
+                             ['nchypergeom_fisher', 'nchypergeom_wallenius'])
+    def test_rvs_shape(self, dist_name):
+        # Check that when given a size with more dimensions than the
+        # dimensions of the broadcast parameters, rvs returns an array
+        # with the correct shape.
+        dists = {'nchypergeom_fisher': nchypergeom_fisher,
+                 'nchypergeom_wallenius': nchypergeom_wallenius}
+        dist = dists[dist_name]
+        x = dist.rvs(50, 30, [[10], [20]], [0.5, 1.0, 2.0], size=(5, 1, 2, 3))
+        assert x.shape == (5, 1, 2, 3)
+
+
+@pytest.mark.parametrize("mu, q, expected",
+                         [[10, 120, -1.240089881791596e-38],
+                          [1500, 0, -86.61466680572661]])
+def test_nbinom_11465(mu, q, expected):
+    # test nbinom.logcdf at extreme tails
+    size = 20
+    n, p = size, size/(size+mu)
+    # In R:
+    # options(digits=16)
+    # pnbinom(mu=10, size=20, q=120, log.p=TRUE)
+    assert_allclose(nbinom.logcdf(q, n, p), expected)
+
+
+def test_gh_17146():
+    # Check that discrete distributions return PMF of zero at non-integral x.
+    # See gh-17146.
+    x = np.linspace(0, 1, 11)
+    p = 0.8
+    pmf = bernoulli(p).pmf(x)
+    i = (x % 1 == 0)
+    assert_allclose(pmf[-1], p)
+    assert_allclose(pmf[0], 1-p)
+    assert_equal(pmf[~i], 0)
+
+
+class TestBetaNBinom:
+    @pytest.mark.parametrize('x, n, a, b, ref',
+                            [[5, 5e6, 5, 20, 1.1520944824139114e-107],
+                            [100, 50, 5, 20, 0.002855762954310226],
+                            [10000, 1000, 5, 20, 1.9648515726019154e-05]])
+    def test_betanbinom_pmf(self, x, n, a, b, ref):
+        # test that PMF stays accurate in the distribution tails
+        # reference values computed with mpmath
+        # from mpmath import mp
+        # mp.dps = 500
+        # def betanbinom_pmf(k, n, a, b):
+        #     k = mp.mpf(k)
+        #     a = mp.mpf(a)
+        #     b = mp.mpf(b)
+        #     n = mp.mpf(n)
+        #     return float(mp.binomial(n + k - mp.one, k)
+        #                  * mp.beta(a + n, b + k) / mp.beta(a, b))
+        assert_allclose(betanbinom.pmf(x, n, a, b), ref, rtol=1e-10)
+
+
+    @pytest.mark.parametrize('n, a, b, ref',
+                            [[10000, 5000, 50, 0.12841520515722202],
+                            [10, 9, 9, 7.9224400871459695],
+                            [100, 1000, 10, 1.5849602176622748]])
+    def test_betanbinom_kurtosis(self, n, a, b, ref):
+        # reference values were computed via mpmath
+        # from mpmath import mp
+        # def kurtosis_betanegbinom(n, a, b):
+        #     n = mp.mpf(n)
+        #     a = mp.mpf(a)
+        #     b = mp.mpf(b)
+        #     four = mp.mpf(4.)
+        #     mean = n * b / (a - mp.one)
+        #     var = (n * b * (n + a - 1.) * (a + b - 1.)
+        #            / ((a - 2.) * (a - 1.)**2.))
+        #     def f(k):
+        #         return (mp.binomial(n + k - mp.one, k)
+        #                 * mp.beta(a + n, b + k) / mp.beta(a, b)
+        #                 * (k - mean)**four)
+        #      fourth_moment = mp.nsum(f, [0, mp.inf])
+        #      return float(fourth_moment/var**2 - 3.)
+        assert_allclose(betanbinom.stats(n, a, b, moments="k"),
+                        ref, rtol=3e-15)
+
+
+class TestZipf:
+    def test_gh20692(self):
+        # test that int32 data for k generates same output as double
+        k = np.arange(0, 1000)
+        k_int32 = k.astype(np.int32)
+        dist = zipf(9)
+        pmf = dist.pmf(k)
+        pmf_k_int32 = dist.pmf(k_int32)
+        assert_equal(pmf, pmf_k_int32)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_entropy.py

@@ -0,0 +1,304 @@
+import math
+import pytest
+from pytest import raises as assert_raises
+
+import numpy as np
+from numpy.testing import assert_allclose
+
+from scipy import stats
+from scipy.conftest import array_api_compatible
+from scipy._lib._array_api import xp_assert_close, xp_assert_equal, xp_assert_less
+
+class TestEntropy:
+    @array_api_compatible
+    def test_entropy_positive(self, xp):
+        # See ticket #497
+        pk = xp.asarray([0.5, 0.2, 0.3])
+        qk = xp.asarray([0.1, 0.25, 0.65])
+        eself = stats.entropy(pk, pk)
+        edouble = stats.entropy(pk, qk)
+        xp_assert_equal(eself, xp.asarray(0.))
+        xp_assert_less(-edouble, xp.asarray(0.))
+
+    @array_api_compatible
+    def test_entropy_base(self, xp):
+        pk = xp.ones(16)
+        S = stats.entropy(pk, base=2.)
+        xp_assert_less(xp.abs(S - 4.), xp.asarray(1.e-5))
+
+        qk = xp.ones(16)
+        qk = xp.where(xp.arange(16) < 8, xp.asarray(2.), qk)
+        S = stats.entropy(pk, qk)
+        S2 = stats.entropy(pk, qk, base=2.)
+        xp_assert_less(xp.abs(S/S2 - math.log(2.)), xp.asarray(1.e-5))
+
+    @array_api_compatible
+    def test_entropy_zero(self, xp):
+        # Test for PR-479
+        x = xp.asarray([0., 1., 2.])
+        xp_assert_close(stats.entropy(x),
+                        xp.asarray(0.63651416829481278))
+
+    @array_api_compatible
+    def test_entropy_2d(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.2, 0.1], [0.3, 0.6], [0.5, 0.3]])
+        xp_assert_close(stats.entropy(pk, qk),
+                        xp.asarray([0.1933259, 0.18609809]))
+
+    @array_api_compatible
+    def test_entropy_2d_zero(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.0, 0.1], [0.3, 0.6], [0.5, 0.3]])
+        xp_assert_close(stats.entropy(pk, qk),
+                        xp.asarray([xp.inf, 0.18609809]))
+
+        pk = xp.asarray([[0.0, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        xp_assert_close(stats.entropy(pk, qk),
+                        xp.asarray([0.17403988, 0.18609809]))
+
+    @array_api_compatible
+    def test_entropy_base_2d_nondefault_axis(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        xp_assert_close(stats.entropy(pk, axis=1),
+                        xp.asarray([0.63651417, 0.63651417, 0.66156324]))
+
+    @array_api_compatible
+    def test_entropy_2d_nondefault_axis(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.2, 0.1], [0.3, 0.6], [0.5, 0.3]])
+        xp_assert_close(stats.entropy(pk, qk, axis=1),
+                        xp.asarray([0.23104906, 0.23104906, 0.12770641]))
+
+    @array_api_compatible
+    def test_entropy_raises_value_error(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.1, 0.2], [0.6, 0.3]])
+        message = "Array shapes are incompatible for broadcasting."
+        with pytest.raises(ValueError, match=message):
+            stats.entropy(pk, qk)
+
+    @array_api_compatible
+    def test_base_entropy_with_axis_0_is_equal_to_default(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        xp_assert_close(stats.entropy(pk, axis=0),
+                        stats.entropy(pk))
+
+    @array_api_compatible
+    def test_entropy_with_axis_0_is_equal_to_default(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.2, 0.1], [0.3, 0.6], [0.5, 0.3]])
+        xp_assert_close(stats.entropy(pk, qk, axis=0),
+                        stats.entropy(pk, qk))
+
+    @array_api_compatible
+    def test_base_entropy_transposed(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        xp_assert_close(stats.entropy(pk.T),
+                        stats.entropy(pk, axis=1))
+
+    @array_api_compatible
+    def test_entropy_transposed(self, xp):
+        pk = xp.asarray([[0.1, 0.2], [0.6, 0.3], [0.3, 0.5]])
+        qk = xp.asarray([[0.2, 0.1], [0.3, 0.6], [0.5, 0.3]])
+        xp_assert_close(stats.entropy(pk.T, qk.T),
+                        stats.entropy(pk, qk, axis=1))
+
+    @array_api_compatible
+    def test_entropy_broadcasting(self, xp):
+        rng = np.random.default_rng(74187315492831452)
+        x = xp.asarray(rng.random(3))
+        y = xp.asarray(rng.random((2, 1)))
+        res = stats.entropy(x, y, axis=-1)
+        xp_assert_equal(res[0], stats.entropy(x, y[0, ...]))
+        xp_assert_equal(res[1], stats.entropy(x, y[1, ...]))
+
+    @array_api_compatible
+    def test_entropy_shape_mismatch(self, xp):
+        x = xp.ones((10, 1, 12))
+        y = xp.ones((11, 2))
+        message = "Array shapes are incompatible for broadcasting."
+        with pytest.raises(ValueError, match=message):
+            stats.entropy(x, y)
+
+    @array_api_compatible
+    def test_input_validation(self, xp):
+        x = xp.ones(10)
+        message = "`base` must be a positive number."
+        with pytest.raises(ValueError, match=message):
+            stats.entropy(x, base=-2)
+
+
+class TestDifferentialEntropy:
+    """
+    Vasicek results are compared with the R package vsgoftest.
+
+    # library(vsgoftest)
+    #
+    # samp <- c(<values>)
+    # entropy.estimate(x = samp, window = <window_length>)
+
+    """
+
+    def test_differential_entropy_vasicek(self):
+
+        random_state = np.random.RandomState(0)
+        values = random_state.standard_normal(100)
+
+        entropy = stats.differential_entropy(values, method='vasicek')
+        assert_allclose(entropy, 1.342551, rtol=1e-6)
+
+        entropy = stats.differential_entropy(values, window_length=1,
+                                             method='vasicek')
+        assert_allclose(entropy, 1.122044, rtol=1e-6)
+
+        entropy = stats.differential_entropy(values, window_length=8,
+                                             method='vasicek')
+        assert_allclose(entropy, 1.349401, rtol=1e-6)
+
+    def test_differential_entropy_vasicek_2d_nondefault_axis(self):
+        random_state = np.random.RandomState(0)
+        values = random_state.standard_normal((3, 100))
+
+        entropy = stats.differential_entropy(values, axis=1, method='vasicek')
+        assert_allclose(
+            entropy,
+            [1.342551, 1.341826, 1.293775],
+            rtol=1e-6,
+        )
+
+        entropy = stats.differential_entropy(values, axis=1, window_length=1,
+                                             method='vasicek')
+        assert_allclose(
+            entropy,
+            [1.122044, 1.102944, 1.129616],
+            rtol=1e-6,
+        )
+
+        entropy = stats.differential_entropy(values, axis=1, window_length=8,
+                                             method='vasicek')
+        assert_allclose(
+            entropy,
+            [1.349401, 1.338514, 1.292332],
+            rtol=1e-6,
+        )
+
+    def test_differential_entropy_raises_value_error(self):
+        random_state = np.random.RandomState(0)
+        values = random_state.standard_normal((3, 100))
+
+        error_str = (
+            r"Window length \({window_length}\) must be positive and less "
+            r"than half the sample size \({sample_size}\)."
+        )
+
+        sample_size = values.shape[1]
+
+        for window_length in {-1, 0, sample_size//2, sample_size}:
+
+            formatted_error_str = error_str.format(
+                window_length=window_length,
+                sample_size=sample_size,
+            )
+
+            with assert_raises(ValueError, match=formatted_error_str):
+                stats.differential_entropy(
+                    values,
+                    window_length=window_length,
+                    axis=1,
+                )
+
+    def test_base_differential_entropy_with_axis_0_is_equal_to_default(self):
+        random_state = np.random.RandomState(0)
+        values = random_state.standard_normal((100, 3))
+
+        entropy = stats.differential_entropy(values, axis=0)
+        default_entropy = stats.differential_entropy(values)
+        assert_allclose(entropy, default_entropy)
+
+    def test_base_differential_entropy_transposed(self):
+        random_state = np.random.RandomState(0)
+        values = random_state.standard_normal((3, 100))
+
+        assert_allclose(
+            stats.differential_entropy(values.T).T,
+            stats.differential_entropy(values, axis=1),
+        )
+
+    def test_input_validation(self):
+        x = np.random.rand(10)
+
+        message = "`base` must be a positive number or `None`."
+        with pytest.raises(ValueError, match=message):
+            stats.differential_entropy(x, base=-2)
+
+        message = "`method` must be one of..."
+        with pytest.raises(ValueError, match=message):
+            stats.differential_entropy(x, method='ekki-ekki')
+
+    @pytest.mark.parametrize('method', ['vasicek', 'van es',
+                                        'ebrahimi', 'correa'])
+    def test_consistency(self, method):
+        # test that method is a consistent estimator
+        n = 10000 if method == 'correa' else 1000000
+        rvs = stats.norm.rvs(size=n, random_state=0)
+        expected = stats.norm.entropy()
+        res = stats.differential_entropy(rvs, method=method)
+        assert_allclose(res, expected, rtol=0.005)
+
+    # values from differential_entropy reference [6], table 1, n=50, m=7
+    norm_rmse_std_cases = {  # method: (RMSE, STD)
+                           'vasicek': (0.198, 0.109),
+                           'van es': (0.212, 0.110),
+                           'correa': (0.135, 0.112),
+                           'ebrahimi': (0.128, 0.109)
+                           }
+
+    @pytest.mark.parametrize('method, expected',
+                             list(norm_rmse_std_cases.items()))
+    def test_norm_rmse_std(self, method, expected):
+        # test that RMSE and standard deviation of estimators matches values
+        # given in differential_entropy reference [6]. Incidentally, also
+        # tests vectorization.
+        reps, n, m = 10000, 50, 7
+        rmse_expected, std_expected = expected
+        rvs = stats.norm.rvs(size=(reps, n), random_state=0)
+        true_entropy = stats.norm.entropy()
+        res = stats.differential_entropy(rvs, window_length=m,
+                                         method=method, axis=-1)
+        assert_allclose(np.sqrt(np.mean((res - true_entropy)**2)),
+                        rmse_expected, atol=0.005)
+        assert_allclose(np.std(res), std_expected, atol=0.002)
+
+    # values from differential_entropy reference [6], table 2, n=50, m=7
+    expon_rmse_std_cases = {  # method: (RMSE, STD)
+                            'vasicek': (0.194, 0.148),
+                            'van es': (0.179, 0.149),
+                            'correa': (0.155, 0.152),
+                            'ebrahimi': (0.151, 0.148)
+                            }
+
+    @pytest.mark.parametrize('method, expected',
+                             list(expon_rmse_std_cases.items()))
+    def test_expon_rmse_std(self, method, expected):
+        # test that RMSE and standard deviation of estimators matches values
+        # given in differential_entropy reference [6]. Incidentally, also
+        # tests vectorization.
+        reps, n, m = 10000, 50, 7
+        rmse_expected, std_expected = expected
+        rvs = stats.expon.rvs(size=(reps, n), random_state=0)
+        true_entropy = stats.expon.entropy()
+        res = stats.differential_entropy(rvs, window_length=m,
+                                         method=method, axis=-1)
+        assert_allclose(np.sqrt(np.mean((res - true_entropy)**2)),
+                        rmse_expected, atol=0.005)
+        assert_allclose(np.std(res), std_expected, atol=0.002)
+
+    @pytest.mark.parametrize('n, method', [(8, 'van es'),
+                                           (12, 'ebrahimi'),
+                                           (1001, 'vasicek')])
+    def test_method_auto(self, n, method):
+        rvs = stats.norm.rvs(size=(n,), random_state=0)
+        res1 = stats.differential_entropy(rvs)
+        res2 = stats.differential_entropy(rvs, method=method)
+        assert res1 == res2

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_fast_gen_inversion.py

@@ -0,0 +1,432 @@
+import pytest
+import warnings
+import numpy as np
+from numpy.testing import (assert_array_equal, assert_allclose,
+                           suppress_warnings)
+from copy import deepcopy
+from scipy.stats.sampling import FastGeneratorInversion
+from scipy import stats
+
+
+def test_bad_args():
+    # loc and scale must be scalar
+    with pytest.raises(ValueError, match="loc must be scalar"):
+        FastGeneratorInversion(stats.norm(loc=(1.2, 1.3)))
+    with pytest.raises(ValueError, match="scale must be scalar"):
+        FastGeneratorInversion(stats.norm(scale=[1.5, 5.7]))
+
+    with pytest.raises(ValueError, match="'test' cannot be used to seed"):
+        FastGeneratorInversion(stats.norm(), random_state="test")
+
+    msg = "Each of the 1 shape parameters must be a scalar"
+    with pytest.raises(ValueError, match=msg):
+        FastGeneratorInversion(stats.gamma([1.3, 2.5]))
+
+    with pytest.raises(ValueError, match="`dist` must be a frozen"):
+        FastGeneratorInversion("xy")
+
+    with pytest.raises(ValueError, match="Distribution 'truncnorm' is not"):
+        FastGeneratorInversion(stats.truncnorm(1.3, 4.5))
+
+
+def test_random_state():
+    # fixed seed
+    gen = FastGeneratorInversion(stats.norm(), random_state=68734509)
+    x1 = gen.rvs(size=10)
+    gen.random_state = 68734509
+    x2 = gen.rvs(size=10)
+    assert_array_equal(x1, x2)
+
+    # Generator
+    urng = np.random.default_rng(20375857)
+    gen = FastGeneratorInversion(stats.norm(), random_state=urng)
+    x1 = gen.rvs(size=10)
+    gen.random_state = np.random.default_rng(20375857)
+    x2 = gen.rvs(size=10)
+    assert_array_equal(x1, x2)
+
+    # RandomState
+    urng = np.random.RandomState(2364)
+    gen = FastGeneratorInversion(stats.norm(), random_state=urng)
+    x1 = gen.rvs(size=10)
+    gen.random_state = np.random.RandomState(2364)
+    x2 = gen.rvs(size=10)
+    assert_array_equal(x1, x2)
+
+    # if evaluate_error is called, it must not interfere with the random_state
+    # used by rvs
+    gen = FastGeneratorInversion(stats.norm(), random_state=68734509)
+    x1 = gen.rvs(size=10)
+    _ = gen.evaluate_error(size=5)  # this will generate 5 uniform rvs
+    x2 = gen.rvs(size=10)
+    gen.random_state = 68734509
+    x3 = gen.rvs(size=20)
+    assert_array_equal(x2, x3[10:])
+
+
+dists_with_params = [
+    ("alpha", (3.5,)),
+    ("anglit", ()),
+    ("argus", (3.5,)),
+    ("argus", (5.1,)),
+    ("beta", (1.5, 0.9)),
+    ("cosine", ()),
+    ("betaprime", (2.5, 3.3)),
+    ("bradford", (1.2,)),
+    ("burr", (1.3, 2.4)),
+    ("burr12", (0.7, 1.2)),
+    ("cauchy", ()),
+    ("chi2", (3.5,)),
+    ("chi", (4.5,)),
+    ("crystalball", (0.7, 1.2)),
+    ("expon", ()),
+    ("gamma", (1.5,)),
+    ("gennorm", (2.7,)),
+    ("gumbel_l", ()),
+    ("gumbel_r", ()),
+    ("hypsecant", ()),
+    ("invgauss", (3.1,)),
+    ("invweibull", (1.5,)),
+    ("laplace", ()),
+    ("logistic", ()),
+    ("maxwell", ()),
+    ("moyal", ()),
+    ("norm", ()),
+    ("pareto", (1.3,)),
+    ("powerlaw", (7.6,)),
+    ("rayleigh", ()),
+    ("semicircular", ()),
+    ("t", (5.7,)),
+    ("wald", ()),
+    ("weibull_max", (2.4,)),
+    ("weibull_min", (1.2,)),
+]
+
+
+@pytest.mark.parametrize(("distname, args"), dists_with_params)
+def test_rvs_and_ppf(distname, args):
+    # check sample against rvs generated by rv_continuous
+    urng = np.random.default_rng(9807324628097097)
+    rng1 = getattr(stats, distname)(*args)
+    rvs1 = rng1.rvs(size=500, random_state=urng)
+    rng2 = FastGeneratorInversion(rng1, random_state=urng)
+    rvs2 = rng2.rvs(size=500)
+    assert stats.cramervonmises_2samp(rvs1, rvs2).pvalue > 0.01
+
+    # check ppf
+    q = [0.001, 0.1, 0.5, 0.9, 0.999]
+    assert_allclose(rng1.ppf(q), rng2.ppf(q), atol=1e-10)
+
+
+@pytest.mark.parametrize(("distname, args"), dists_with_params)
+def test_u_error(distname, args):
+    # check sample against rvs generated by rv_continuous
+    dist = getattr(stats, distname)(*args)
+    with suppress_warnings() as sup:
+        # filter the warnings thrown by UNU.RAN
+        sup.filter(RuntimeWarning)
+        rng = FastGeneratorInversion(dist)
+    u_error, x_error = rng.evaluate_error(
+        size=10_000, random_state=9807324628097097, x_error=False
+    )
+    assert u_error <= 1e-10
+
+
+@pytest.mark.xslow
+@pytest.mark.xfail(reason="geninvgauss CDF is not accurate")
+def test_geninvgauss_uerror():
+    dist = stats.geninvgauss(3.2, 1.5)
+    rng = FastGeneratorInversion(dist)
+    err = rng.evaluate_error(size=10_000, random_state=67982)
+    assert err[0] < 1e-10
+
+
+# TODO: add more distributions
+@pytest.mark.parametrize(("distname, args"), [("beta", (0.11, 0.11))])
+def test_error_extreme_params(distname, args):
+    # take extreme parameters where u-error might not be below the tolerance
+    # due to limitations of floating point arithmetic
+    with suppress_warnings() as sup:
+        # filter the warnings thrown by UNU.RAN for such extreme parameters
+        sup.filter(RuntimeWarning)
+        dist = getattr(stats, distname)(*args)
+        rng = FastGeneratorInversion(dist)
+    u_error, x_error = rng.evaluate_error(
+        size=10_000, random_state=980732462809709732623, x_error=True
+    )
+    if u_error >= 2.5 * 1e-10:
+        assert x_error < 1e-9
+
+
+def test_evaluate_error_inputs():
+    gen = FastGeneratorInversion(stats.norm())
+    with pytest.raises(ValueError, match="size must be an integer"):
+        gen.evaluate_error(size=3.5)
+    with pytest.raises(ValueError, match="size must be an integer"):
+        gen.evaluate_error(size=(3, 3))
+
+
+def test_rvs_ppf_loc_scale():
+    loc, scale = 3.5, 2.3
+    dist = stats.norm(loc=loc, scale=scale)
+    rng = FastGeneratorInversion(dist, random_state=1234)
+    r = rng.rvs(size=1000)
+    r_rescaled = (r - loc) / scale
+    assert stats.cramervonmises(r_rescaled, "norm").pvalue > 0.01
+    q = [0.001, 0.1, 0.5, 0.9, 0.999]
+    assert_allclose(rng._ppf(q), rng.ppf(q), atol=1e-10)
+
+
+def test_domain():
+    # only a basic check that the domain argument is passed to the
+    # UNU.RAN generators
+    rng = FastGeneratorInversion(stats.norm(), domain=(-1, 1))
+    r = rng.rvs(size=100)
+    assert -1 <= r.min() < r.max() <= 1
+
+    # if loc and scale are used, new domain is loc + scale*domain
+    loc, scale = 3.5, 1.3
+    dist = stats.norm(loc=loc, scale=scale)
+    rng = FastGeneratorInversion(dist, domain=(-1.5, 2))
+    r = rng.rvs(size=100)
+    lb, ub = loc - scale * 1.5, loc + scale * 2
+    assert lb <= r.min() < r.max() <= ub
+
+
+@pytest.mark.parametrize(("distname, args, expected"),
+                         [("beta", (3.5, 2.5), (0, 1)),
+                          ("norm", (), (-np.inf, np.inf))])
+def test_support(distname, args, expected):
+    # test that the support is updated if truncation and loc/scale are applied
+    # use beta distribution since it is a transformed betaprime distribution,
+    # so it is important that the correct support is considered
+    # (i.e., the support of beta is (0,1), while betaprime is (0, inf))
+    dist = getattr(stats, distname)(*args)
+    rng = FastGeneratorInversion(dist)
+    assert_array_equal(rng.support(), expected)
+    rng.loc = 1
+    rng.scale = 2
+    assert_array_equal(rng.support(), 1 + 2*np.array(expected))
+
+
+@pytest.mark.parametrize(("distname, args"),
+                         [("beta", (3.5, 2.5)), ("norm", ())])
+def test_support_truncation(distname, args):
+    # similar test for truncation
+    dist = getattr(stats, distname)(*args)
+    rng = FastGeneratorInversion(dist, domain=(0.5, 0.7))
+    assert_array_equal(rng.support(), (0.5, 0.7))
+    rng.loc = 1
+    rng.scale = 2
+    assert_array_equal(rng.support(), (1 + 2 * 0.5, 1 + 2 * 0.7))
+
+
+def test_domain_shift_truncation():
+    # center of norm is zero, it should be shifted to the left endpoint of
+    # domain. if this was not the case, PINV in UNURAN would raise a warning
+    # as the center is not inside the domain
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
+        rng = FastGeneratorInversion(stats.norm(), domain=(1, 2))
+    r = rng.rvs(size=100)
+    assert 1 <= r.min() < r.max() <= 2
+
+
+def test_non_rvs_methods_with_domain():
+    # as a first step, compare truncated normal against stats.truncnorm
+    rng = FastGeneratorInversion(stats.norm(), domain=(2.3, 3.2))
+    trunc_norm = stats.truncnorm(2.3, 3.2)
+    # take values that are inside and outside the domain
+    x = (2.0, 2.4, 3.0, 3.4)
+    p = (0.01, 0.5, 0.99)
+    assert_allclose(rng._cdf(x), trunc_norm.cdf(x))
+    assert_allclose(rng._ppf(p), trunc_norm.ppf(p))
+    loc, scale = 2, 3
+    rng.loc = 2
+    rng.scale = 3
+    trunc_norm = stats.truncnorm(2.3, 3.2, loc=loc, scale=scale)
+    x = np.array(x) * scale + loc
+    assert_allclose(rng._cdf(x), trunc_norm.cdf(x))
+    assert_allclose(rng._ppf(p), trunc_norm.ppf(p))
+
+    # do another sanity check with beta distribution
+    # in that case, it is important to use the correct domain since beta
+    # is a transformation of betaprime which has a different support
+    rng = FastGeneratorInversion(stats.beta(2.5, 3.5), domain=(0.3, 0.7))
+    rng.loc = 2
+    rng.scale = 2.5
+    # the support is 2.75, , 3.75 (2 + 2.5 * 0.3, 2 + 2.5 * 0.7)
+    assert_array_equal(rng.support(), (2.75, 3.75))
+    x = np.array([2.74, 2.76, 3.74, 3.76])
+    # the cdf needs to be zero outside of the domain
+    y_cdf = rng._cdf(x)
+    assert_array_equal((y_cdf[0], y_cdf[3]), (0, 1))
+    assert np.min(y_cdf[1:3]) > 0
+    # ppf needs to map 0 and 1 to the boundaries
+    assert_allclose(rng._ppf(y_cdf), (2.75, 2.76, 3.74, 3.75))
+
+
+def test_non_rvs_methods_without_domain():
+    norm_dist = stats.norm()
+    rng = FastGeneratorInversion(norm_dist)
+    x = np.linspace(-3, 3, num=10)
+    p = (0.01, 0.5, 0.99)
+    assert_allclose(rng._cdf(x), norm_dist.cdf(x))
+    assert_allclose(rng._ppf(p), norm_dist.ppf(p))
+    loc, scale = 0.5, 1.3
+    rng.loc = loc
+    rng.scale = scale
+    norm_dist = stats.norm(loc=loc, scale=scale)
+    assert_allclose(rng._cdf(x), norm_dist.cdf(x))
+    assert_allclose(rng._ppf(p), norm_dist.ppf(p))
+
+@pytest.mark.parametrize(("domain, x"),
+                         [(None, 0.5),
+                         ((0, 1), 0.5),
+                         ((0, 1), 1.5)])
+def test_scalar_inputs(domain, x):
+    """ pdf, cdf etc should map scalar values to scalars. check with and
+    w/o domain since domain impacts pdf, cdf etc
+    Take x inside and outside of domain """
+    rng = FastGeneratorInversion(stats.norm(), domain=domain)
+    assert np.isscalar(rng._cdf(x))
+    assert np.isscalar(rng._ppf(0.5))
+
+
+def test_domain_argus_large_chi():
+    # for large chi, the Gamma distribution is used and the domain has to be
+    # transformed. this is a test to ensure that the transformation works
+    chi, lb, ub = 5.5, 0.25, 0.75
+    rng = FastGeneratorInversion(stats.argus(chi), domain=(lb, ub))
+    rng.random_state = 4574
+    r = rng.rvs(size=500)
+    assert lb <= r.min() < r.max() <= ub
+    # perform goodness of fit test with conditional cdf
+    cdf = stats.argus(chi).cdf
+    prob = cdf(ub) - cdf(lb)
+    assert stats.cramervonmises(r, lambda x: cdf(x) / prob).pvalue > 0.05
+
+
+def test_setting_loc_scale():
+    rng = FastGeneratorInversion(stats.norm(), random_state=765765864)
+    r1 = rng.rvs(size=1000)
+    rng.loc = 3.0
+    rng.scale = 2.5
+    r2 = rng.rvs(1000)
+    # rescaled r2 should be again standard normal
+    assert stats.cramervonmises_2samp(r1, (r2 - 3) / 2.5).pvalue > 0.05
+    # reset values to default loc=0, scale=1
+    rng.loc = 0
+    rng.scale = 1
+    r2 = rng.rvs(1000)
+    assert stats.cramervonmises_2samp(r1, r2).pvalue > 0.05
+
+
+def test_ignore_shape_range():
+    msg = "No generator is defined for the shape parameters"
+    with pytest.raises(ValueError, match=msg):
+        rng = FastGeneratorInversion(stats.t(0.03))
+    rng = FastGeneratorInversion(stats.t(0.03), ignore_shape_range=True)
+    # we can ignore the recommended range of shape parameters
+    # but u-error can be expected to be too large in that case
+    u_err, _ = rng.evaluate_error(size=1000, random_state=234)
+    assert u_err >= 1e-6
+
+@pytest.mark.xfail_on_32bit(
+    "NumericalInversePolynomial.qrvs fails for Win 32-bit"
+)
+class TestQRVS:
+    def test_input_validation(self):
+        gen = FastGeneratorInversion(stats.norm())
+
+        match = "`qmc_engine` must be an instance of..."
+        with pytest.raises(ValueError, match=match):
+            gen.qrvs(qmc_engine=0)
+
+        match = "`d` must be consistent with dimension of `qmc_engine`."
+        with pytest.raises(ValueError, match=match):
+            gen.qrvs(d=3, qmc_engine=stats.qmc.Halton(2))
+
+    qrngs = [None, stats.qmc.Sobol(1, seed=0), stats.qmc.Halton(3, seed=0)]
+    # `size=None` should not add anything to the shape, `size=1` should
+    sizes = [
+        (None, tuple()),
+        (1, (1,)),
+        (4, (4,)),
+        ((4,), (4,)),
+        ((2, 4), (2, 4)),
+    ]
+    # Neither `d=None` nor `d=1` should add anything to the shape
+    ds = [(None, tuple()), (1, tuple()), (3, (3,))]
+
+    @pytest.mark.parametrize("qrng", qrngs)
+    @pytest.mark.parametrize("size_in, size_out", sizes)
+    @pytest.mark.parametrize("d_in, d_out", ds)
+    def test_QRVS_shape_consistency(self, qrng, size_in, size_out,
+                                    d_in, d_out):
+        gen = FastGeneratorInversion(stats.norm())
+
+        # If d and qrng.d are inconsistent, an error is raised
+        if d_in is not None and qrng is not None and qrng.d != d_in:
+            match = "`d` must be consistent with dimension of `qmc_engine`."
+            with pytest.raises(ValueError, match=match):
+                gen.qrvs(size_in, d=d_in, qmc_engine=qrng)
+            return
+
+        # Sometimes d is really determined by qrng
+        if d_in is None and qrng is not None and qrng.d != 1:
+            d_out = (qrng.d,)
+
+        shape_expected = size_out + d_out
+
+        qrng2 = deepcopy(qrng)
+        qrvs = gen.qrvs(size=size_in, d=d_in, qmc_engine=qrng)
+        if size_in is not None:
+            assert qrvs.shape == shape_expected
+
+        if qrng2 is not None:
+            uniform = qrng2.random(np.prod(size_in) or 1)
+            qrvs2 = stats.norm.ppf(uniform).reshape(shape_expected)
+            assert_allclose(qrvs, qrvs2, atol=1e-12)
+
+    def test_QRVS_size_tuple(self):
+        # QMCEngine samples are always of shape (n, d). When `size` is a tuple,
+        # we set `n = prod(size)` in the call to qmc_engine.random, transform
+        # the sample, and reshape it to the final dimensions. When we reshape,
+        # we need to be careful, because the _columns_ of the sample returned
+        # by a QMCEngine are "independent"-ish, but the elements within the
+        # columns are not. We need to make sure that this doesn't get mixed up
+        # by reshaping: qrvs[..., i] should remain "independent"-ish of
+        # qrvs[..., i+1], but the elements within qrvs[..., i] should be
+        # transformed from the same low-discrepancy sequence.
+
+        gen = FastGeneratorInversion(stats.norm())
+
+        size = (3, 4)
+        d = 5
+        qrng = stats.qmc.Halton(d, seed=0)
+        qrng2 = stats.qmc.Halton(d, seed=0)
+
+        uniform = qrng2.random(np.prod(size))
+
+        qrvs = gen.qrvs(size=size, d=d, qmc_engine=qrng)
+        qrvs2 = stats.norm.ppf(uniform)
+
+        for i in range(d):
+            sample = qrvs[..., i]
+            sample2 = qrvs2[:, i].reshape(size)
+            assert_allclose(sample, sample2, atol=1e-12)
+
+
+def test_burr_overflow():
+    # this case leads to an overflow error if math.exp is used
+    # in the definition of the burr pdf instead of np.exp
+    # a direct implementation of the PDF as x**(-c-1) / (1+x**(-c))**(d+1)
+    # also leads to an overflow error in the setup
+    args = (1.89128135, 0.30195177)
+    with suppress_warnings() as sup:
+        # filter potential overflow warning
+        sup.filter(RuntimeWarning)
+        gen = FastGeneratorInversion(stats.burr(*args))
+    u_error, _ = gen.evaluate_error(random_state=4326)
+    assert u_error <= 1e-10

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_kdeoth.py

@@ -0,0 +1,608 @@
+from scipy import stats, linalg, integrate
+import numpy as np
+from numpy.testing import (assert_almost_equal, assert_, assert_equal,
+                           assert_array_almost_equal,
+                           assert_array_almost_equal_nulp, assert_allclose)
+import pytest
+from pytest import raises as assert_raises
+
+
+def test_kde_1d():
+    #some basic tests comparing to normal distribution
+    np.random.seed(8765678)
+    n_basesample = 500
+    xn = np.random.randn(n_basesample)
+    xnmean = xn.mean()
+    xnstd = xn.std(ddof=1)
+
+    # get kde for original sample
+    gkde = stats.gaussian_kde(xn)
+
+    # evaluate the density function for the kde for some points
+    xs = np.linspace(-7,7,501)
+    kdepdf = gkde.evaluate(xs)
+    normpdf = stats.norm.pdf(xs, loc=xnmean, scale=xnstd)
+    intervall = xs[1] - xs[0]
+
+    assert_(np.sum((kdepdf - normpdf)**2)*intervall < 0.01)
+    prob1 = gkde.integrate_box_1d(xnmean, np.inf)
+    prob2 = gkde.integrate_box_1d(-np.inf, xnmean)
+    assert_almost_equal(prob1, 0.5, decimal=1)
+    assert_almost_equal(prob2, 0.5, decimal=1)
+    assert_almost_equal(gkde.integrate_box(xnmean, np.inf), prob1, decimal=13)
+    assert_almost_equal(gkde.integrate_box(-np.inf, xnmean), prob2, decimal=13)
+
+    assert_almost_equal(gkde.integrate_kde(gkde),
+                        (kdepdf**2).sum()*intervall, decimal=2)
+    assert_almost_equal(gkde.integrate_gaussian(xnmean, xnstd**2),
+                        (kdepdf*normpdf).sum()*intervall, decimal=2)
+
+
+def test_kde_1d_weighted():
+    #some basic tests comparing to normal distribution
+    np.random.seed(8765678)
+    n_basesample = 500
+    xn = np.random.randn(n_basesample)
+    wn = np.random.rand(n_basesample)
+    xnmean = np.average(xn, weights=wn)
+    xnstd = np.sqrt(np.average((xn-xnmean)**2, weights=wn))
+
+    # get kde for original sample
+    gkde = stats.gaussian_kde(xn, weights=wn)
+
+    # evaluate the density function for the kde for some points
+    xs = np.linspace(-7,7,501)
+    kdepdf = gkde.evaluate(xs)
+    normpdf = stats.norm.pdf(xs, loc=xnmean, scale=xnstd)
+    intervall = xs[1] - xs[0]
+
+    assert_(np.sum((kdepdf - normpdf)**2)*intervall < 0.01)
+    prob1 = gkde.integrate_box_1d(xnmean, np.inf)
+    prob2 = gkde.integrate_box_1d(-np.inf, xnmean)
+    assert_almost_equal(prob1, 0.5, decimal=1)
+    assert_almost_equal(prob2, 0.5, decimal=1)
+    assert_almost_equal(gkde.integrate_box(xnmean, np.inf), prob1, decimal=13)
+    assert_almost_equal(gkde.integrate_box(-np.inf, xnmean), prob2, decimal=13)
+
+    assert_almost_equal(gkde.integrate_kde(gkde),
+                        (kdepdf**2).sum()*intervall, decimal=2)
+    assert_almost_equal(gkde.integrate_gaussian(xnmean, xnstd**2),
+                        (kdepdf*normpdf).sum()*intervall, decimal=2)
+
+
+@pytest.mark.xslow
+def test_kde_2d():
+    #some basic tests comparing to normal distribution
+    np.random.seed(8765678)
+    n_basesample = 500
+
+    mean = np.array([1.0, 3.0])
+    covariance = np.array([[1.0, 2.0], [2.0, 6.0]])
+
+    # Need transpose (shape (2, 500)) for kde
+    xn = np.random.multivariate_normal(mean, covariance, size=n_basesample).T
+
+    # get kde for original sample
+    gkde = stats.gaussian_kde(xn)
+
+    # evaluate the density function for the kde for some points
+    x, y = np.mgrid[-7:7:500j, -7:7:500j]
+    grid_coords = np.vstack([x.ravel(), y.ravel()])
+    kdepdf = gkde.evaluate(grid_coords)
+    kdepdf = kdepdf.reshape(500, 500)
+
+    normpdf = stats.multivariate_normal.pdf(np.dstack([x, y]),
+                                            mean=mean, cov=covariance)
+    intervall = y.ravel()[1] - y.ravel()[0]
+
+    assert_(np.sum((kdepdf - normpdf)**2) * (intervall**2) < 0.01)
+
+    small = -1e100
+    large = 1e100
+    prob1 = gkde.integrate_box([small, mean[1]], [large, large])
+    prob2 = gkde.integrate_box([small, small], [large, mean[1]])
+
+    assert_almost_equal(prob1, 0.5, decimal=1)
+    assert_almost_equal(prob2, 0.5, decimal=1)
+    assert_almost_equal(gkde.integrate_kde(gkde),
+                        (kdepdf**2).sum()*(intervall**2), decimal=2)
+    assert_almost_equal(gkde.integrate_gaussian(mean, covariance),
+                        (kdepdf*normpdf).sum()*(intervall**2), decimal=2)
+
+
+@pytest.mark.xslow
+def test_kde_2d_weighted():
+    #some basic tests comparing to normal distribution
+    np.random.seed(8765678)
+    n_basesample = 500
+
+    mean = np.array([1.0, 3.0])
+    covariance = np.array([[1.0, 2.0], [2.0, 6.0]])
+
+    # Need transpose (shape (2, 500)) for kde
+    xn = np.random.multivariate_normal(mean, covariance, size=n_basesample).T
+    wn = np.random.rand(n_basesample)
+
+    # get kde for original sample
+    gkde = stats.gaussian_kde(xn, weights=wn)
+
+    # evaluate the density function for the kde for some points
+    x, y = np.mgrid[-7:7:500j, -7:7:500j]
+    grid_coords = np.vstack([x.ravel(), y.ravel()])
+    kdepdf = gkde.evaluate(grid_coords)
+    kdepdf = kdepdf.reshape(500, 500)
+
+    normpdf = stats.multivariate_normal.pdf(np.dstack([x, y]),
+                                            mean=mean, cov=covariance)
+    intervall = y.ravel()[1] - y.ravel()[0]
+
+    assert_(np.sum((kdepdf - normpdf)**2) * (intervall**2) < 0.01)
+
+    small = -1e100
+    large = 1e100
+    prob1 = gkde.integrate_box([small, mean[1]], [large, large])
+    prob2 = gkde.integrate_box([small, small], [large, mean[1]])
+
+    assert_almost_equal(prob1, 0.5, decimal=1)
+    assert_almost_equal(prob2, 0.5, decimal=1)
+    assert_almost_equal(gkde.integrate_kde(gkde),
+                        (kdepdf**2).sum()*(intervall**2), decimal=2)
+    assert_almost_equal(gkde.integrate_gaussian(mean, covariance),
+                        (kdepdf*normpdf).sum()*(intervall**2), decimal=2)
+
+
+def test_kde_bandwidth_method():
+    def scotts_factor(kde_obj):
+        """Same as default, just check that it works."""
+        return np.power(kde_obj.n, -1./(kde_obj.d+4))
+
+    np.random.seed(8765678)
+    n_basesample = 50
+    xn = np.random.randn(n_basesample)
+
+    # Default
+    gkde = stats.gaussian_kde(xn)
+    # Supply a callable
+    gkde2 = stats.gaussian_kde(xn, bw_method=scotts_factor)
+    # Supply a scalar
+    gkde3 = stats.gaussian_kde(xn, bw_method=gkde.factor)
+
+    xs = np.linspace(-7,7,51)
+    kdepdf = gkde.evaluate(xs)
+    kdepdf2 = gkde2.evaluate(xs)
+    assert_almost_equal(kdepdf, kdepdf2)
+    kdepdf3 = gkde3.evaluate(xs)
+    assert_almost_equal(kdepdf, kdepdf3)
+
+    assert_raises(ValueError, stats.gaussian_kde, xn, bw_method='wrongstring')
+
+
+def test_kde_bandwidth_method_weighted():
+    def scotts_factor(kde_obj):
+        """Same as default, just check that it works."""
+        return np.power(kde_obj.neff, -1./(kde_obj.d+4))
+
+    np.random.seed(8765678)
+    n_basesample = 50
+    xn = np.random.randn(n_basesample)
+
+    # Default
+    gkde = stats.gaussian_kde(xn)
+    # Supply a callable
+    gkde2 = stats.gaussian_kde(xn, bw_method=scotts_factor)
+    # Supply a scalar
+    gkde3 = stats.gaussian_kde(xn, bw_method=gkde.factor)
+
+    xs = np.linspace(-7,7,51)
+    kdepdf = gkde.evaluate(xs)
+    kdepdf2 = gkde2.evaluate(xs)
+    assert_almost_equal(kdepdf, kdepdf2)
+    kdepdf3 = gkde3.evaluate(xs)
+    assert_almost_equal(kdepdf, kdepdf3)
+
+    assert_raises(ValueError, stats.gaussian_kde, xn, bw_method='wrongstring')
+
+
+# Subclasses that should stay working (extracted from various sources).
+# Unfortunately the earlier design of gaussian_kde made it necessary for users
+# to create these kinds of subclasses, or call _compute_covariance() directly.
+
+class _kde_subclass1(stats.gaussian_kde):
+    def __init__(self, dataset):
+        self.dataset = np.atleast_2d(dataset)
+        self.d, self.n = self.dataset.shape
+        self.covariance_factor = self.scotts_factor
+        self._compute_covariance()
+
+
+class _kde_subclass2(stats.gaussian_kde):
+    def __init__(self, dataset):
+        self.covariance_factor = self.scotts_factor
+        super().__init__(dataset)
+
+
+class _kde_subclass4(stats.gaussian_kde):
+    def covariance_factor(self):
+        return 0.5 * self.silverman_factor()
+
+
+def test_gaussian_kde_subclassing():
+    x1 = np.array([-7, -5, 1, 4, 5], dtype=float)
+    xs = np.linspace(-10, 10, num=50)
+
+    # gaussian_kde itself
+    kde = stats.gaussian_kde(x1)
+    ys = kde(xs)
+
+    # subclass 1
+    kde1 = _kde_subclass1(x1)
+    y1 = kde1(xs)
+    assert_array_almost_equal_nulp(ys, y1, nulp=10)
+
+    # subclass 2
+    kde2 = _kde_subclass2(x1)
+    y2 = kde2(xs)
+    assert_array_almost_equal_nulp(ys, y2, nulp=10)
+
+    # subclass 3 was removed because we have no obligation to maintain support
+    # for user invocation of private methods
+
+    # subclass 4
+    kde4 = _kde_subclass4(x1)
+    y4 = kde4(x1)
+    y_expected = [0.06292987, 0.06346938, 0.05860291, 0.08657652, 0.07904017]
+
+    assert_array_almost_equal(y_expected, y4, decimal=6)
+
+    # Not a subclass, but check for use of _compute_covariance()
+    kde5 = kde
+    kde5.covariance_factor = lambda: kde.factor
+    kde5._compute_covariance()
+    y5 = kde5(xs)
+    assert_array_almost_equal_nulp(ys, y5, nulp=10)
+
+
+def test_gaussian_kde_covariance_caching():
+    x1 = np.array([-7, -5, 1, 4, 5], dtype=float)
+    xs = np.linspace(-10, 10, num=5)
+    # These expected values are from scipy 0.10, before some changes to
+    # gaussian_kde.  They were not compared with any external reference.
+    y_expected = [0.02463386, 0.04689208, 0.05395444, 0.05337754, 0.01664475]
+
+    # Set the bandwidth, then reset it to the default.
+    kde = stats.gaussian_kde(x1)
+    kde.set_bandwidth(bw_method=0.5)
+    kde.set_bandwidth(bw_method='scott')
+    y2 = kde(xs)
+
+    assert_array_almost_equal(y_expected, y2, decimal=7)
+
+
+def test_gaussian_kde_monkeypatch():
+    """Ugly, but people may rely on this.  See scipy pull request 123,
+    specifically the linked ML thread "Width of the Gaussian in stats.kde".
+    If it is necessary to break this later on, that is to be discussed on ML.
+    """
+    x1 = np.array([-7, -5, 1, 4, 5], dtype=float)
+    xs = np.linspace(-10, 10, num=50)
+
+    # The old monkeypatched version to get at Silverman's Rule.
+    kde = stats.gaussian_kde(x1)
+    kde.covariance_factor = kde.silverman_factor
+    kde._compute_covariance()
+    y1 = kde(xs)
+
+    # The new saner version.
+    kde2 = stats.gaussian_kde(x1, bw_method='silverman')
+    y2 = kde2(xs)
+
+    assert_array_almost_equal_nulp(y1, y2, nulp=10)
+
+
+def test_kde_integer_input():
+    """Regression test for #1181."""
+    x1 = np.arange(5)
+    kde = stats.gaussian_kde(x1)
+    y_expected = [0.13480721, 0.18222869, 0.19514935, 0.18222869, 0.13480721]
+    assert_array_almost_equal(kde(x1), y_expected, decimal=6)
+
+
+_ftypes = ['float32', 'float64', 'float96', 'float128', 'int32', 'int64']
+
+
+@pytest.mark.parametrize("bw_type", _ftypes + ["scott", "silverman"])
+@pytest.mark.parametrize("dtype", _ftypes)
+def test_kde_output_dtype(dtype, bw_type):
+    # Check whether the datatypes are available
+    dtype = getattr(np, dtype, None)
+
+    if bw_type in ["scott", "silverman"]:
+        bw = bw_type
+    else:
+        bw_type = getattr(np, bw_type, None)
+        bw = bw_type(3) if bw_type else None
+
+    if any(dt is None for dt in [dtype, bw]):
+        pytest.skip()
+
+    weights = np.arange(5, dtype=dtype)
+    dataset = np.arange(5, dtype=dtype)
+    k = stats.gaussian_kde(dataset, bw_method=bw, weights=weights)
+    points = np.arange(5, dtype=dtype)
+    result = k(points)
+    # weights are always cast to float64
+    assert result.dtype == np.result_type(dataset, points, np.float64(weights),
+                                          k.factor)
+
+
+def test_pdf_logpdf_validation():
+    rng = np.random.default_rng(64202298293133848336925499069837723291)
+    xn = rng.standard_normal((2, 10))
+    gkde = stats.gaussian_kde(xn)
+    xs = rng.standard_normal((3, 10))
+
+    msg = "points have dimension 3, dataset has dimension 2"
+    with pytest.raises(ValueError, match=msg):
+        gkde.logpdf(xs)
+
+
+def test_pdf_logpdf():
+    np.random.seed(1)
+    n_basesample = 50
+    xn = np.random.randn(n_basesample)
+
+    # Default
+    gkde = stats.gaussian_kde(xn)
+
+    xs = np.linspace(-15, 12, 25)
+    pdf = gkde.evaluate(xs)
+    pdf2 = gkde.pdf(xs)
+    assert_almost_equal(pdf, pdf2, decimal=12)
+
+    logpdf = np.log(pdf)
+    logpdf2 = gkde.logpdf(xs)
+    assert_almost_equal(logpdf, logpdf2, decimal=12)
+
+    # There are more points than data
+    gkde = stats.gaussian_kde(xs)
+    pdf = np.log(gkde.evaluate(xn))
+    pdf2 = gkde.logpdf(xn)
+    assert_almost_equal(pdf, pdf2, decimal=12)
+
+
+def test_pdf_logpdf_weighted():
+    np.random.seed(1)
+    n_basesample = 50
+    xn = np.random.randn(n_basesample)
+    wn = np.random.rand(n_basesample)
+
+    # Default
+    gkde = stats.gaussian_kde(xn, weights=wn)
+
+    xs = np.linspace(-15, 12, 25)
+    pdf = gkde.evaluate(xs)
+    pdf2 = gkde.pdf(xs)
+    assert_almost_equal(pdf, pdf2, decimal=12)
+
+    logpdf = np.log(pdf)
+    logpdf2 = gkde.logpdf(xs)
+    assert_almost_equal(logpdf, logpdf2, decimal=12)
+
+    # There are more points than data
+    gkde = stats.gaussian_kde(xs, weights=np.random.rand(len(xs)))
+    pdf = np.log(gkde.evaluate(xn))
+    pdf2 = gkde.logpdf(xn)
+    assert_almost_equal(pdf, pdf2, decimal=12)
+
+
+def test_marginal_1_axis():
+    rng = np.random.default_rng(6111799263660870475)
+    n_data = 50
+    n_dim = 10
+    dataset = rng.normal(size=(n_dim, n_data))
+    points = rng.normal(size=(n_dim, 3))
+
+    dimensions = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9])  # dimensions to keep
+
+    kde = stats.gaussian_kde(dataset)
+    marginal = kde.marginal(dimensions)
+    pdf = marginal.pdf(points[dimensions])
+
+    def marginal_pdf_single(point):
+        def f(x):
+            x = np.concatenate(([x], point[dimensions]))
+            return kde.pdf(x)[0]
+        return integrate.quad(f, -np.inf, np.inf)[0]
+
+    def marginal_pdf(points):
+        return np.apply_along_axis(marginal_pdf_single, axis=0, arr=points)
+
+    ref = marginal_pdf(points)
+
+    assert_allclose(pdf, ref, rtol=1e-6)
+
+
+@pytest.mark.xslow
+def test_marginal_2_axis():
+    rng = np.random.default_rng(6111799263660870475)
+    n_data = 30
+    n_dim = 4
+    dataset = rng.normal(size=(n_dim, n_data))
+    points = rng.normal(size=(n_dim, 3))
+
+    dimensions = np.array([1, 3])  # dimensions to keep
+
+    kde = stats.gaussian_kde(dataset)
+    marginal = kde.marginal(dimensions)
+    pdf = marginal.pdf(points[dimensions])
+
+    def marginal_pdf(points):
+        def marginal_pdf_single(point):
+            def f(y, x):
+                w, z = point[dimensions]
+                x = np.array([x, w, y, z])
+                return kde.pdf(x)[0]
+            return integrate.dblquad(f, -np.inf, np.inf, -np.inf, np.inf)[0]
+
+        return np.apply_along_axis(marginal_pdf_single, axis=0, arr=points)
+
+    ref = marginal_pdf(points)
+
+    assert_allclose(pdf, ref, rtol=1e-6)
+
+
+def test_marginal_iv():
+    # test input validation
+    rng = np.random.default_rng(6111799263660870475)
+    n_data = 30
+    n_dim = 4
+    dataset = rng.normal(size=(n_dim, n_data))
+    points = rng.normal(size=(n_dim, 3))
+
+    kde = stats.gaussian_kde(dataset)
+
+    # check that positive and negative indices are equivalent
+    dimensions1 = [-1, 1]
+    marginal1 = kde.marginal(dimensions1)
+    pdf1 = marginal1.pdf(points[dimensions1])
+
+    dimensions2 = [3, -3]
+    marginal2 = kde.marginal(dimensions2)
+    pdf2 = marginal2.pdf(points[dimensions2])
+
+    assert_equal(pdf1, pdf2)
+
+    # IV for non-integer dimensions
+    message = "Elements of `dimensions` must be integers..."
+    with pytest.raises(ValueError, match=message):
+        kde.marginal([1, 2.5])
+
+    # IV for uniquenes
+    message = "All elements of `dimensions` must be unique."
+    with pytest.raises(ValueError, match=message):
+        kde.marginal([1, 2, 2])
+
+    # IV for non-integer dimensions
+    message = (r"Dimensions \[-5  6\] are invalid for a distribution in 4...")
+    with pytest.raises(ValueError, match=message):
+        kde.marginal([1, -5, 6])
+
+
+@pytest.mark.xslow
+def test_logpdf_overflow():
+    # regression test for gh-12988; testing against linalg instability for
+    # very high dimensionality kde
+    np.random.seed(1)
+    n_dimensions = 2500
+    n_samples = 5000
+    xn = np.array([np.random.randn(n_samples) + (n) for n in range(
+        0, n_dimensions)])
+
+    # Default
+    gkde = stats.gaussian_kde(xn)
+
+    logpdf = gkde.logpdf(np.arange(0, n_dimensions))
+    np.testing.assert_equal(np.isneginf(logpdf[0]), False)
+    np.testing.assert_equal(np.isnan(logpdf[0]), False)
+
+
+def test_weights_intact():
+    # regression test for gh-9709: weights are not modified
+    np.random.seed(12345)
+    vals = np.random.lognormal(size=100)
+    weights = np.random.choice([1.0, 10.0, 100], size=vals.size)
+    orig_weights = weights.copy()
+
+    stats.gaussian_kde(np.log10(vals), weights=weights)
+    assert_allclose(weights, orig_weights, atol=1e-14, rtol=1e-14)
+
+
+def test_weights_integer():
+    # integer weights are OK, cf gh-9709 (comment)
+    np.random.seed(12345)
+    values = [0.2, 13.5, 21.0, 75.0, 99.0]
+    weights = [1, 2, 4, 8, 16]  # a list of integers
+    pdf_i = stats.gaussian_kde(values, weights=weights)
+    pdf_f = stats.gaussian_kde(values, weights=np.float64(weights))
+
+    xn = [0.3, 11, 88]
+    assert_allclose(pdf_i.evaluate(xn),
+                    pdf_f.evaluate(xn), atol=1e-14, rtol=1e-14)
+
+
+def test_seed():
+    # Test the seed option of the resample method
+    def test_seed_sub(gkde_trail):
+        n_sample = 200
+        # The results should be different without using seed
+        samp1 = gkde_trail.resample(n_sample)
+        samp2 = gkde_trail.resample(n_sample)
+        assert_raises(
+            AssertionError, assert_allclose, samp1, samp2, atol=1e-13
+        )
+        # Use integer seed
+        seed = 831
+        samp1 = gkde_trail.resample(n_sample, seed=seed)
+        samp2 = gkde_trail.resample(n_sample, seed=seed)
+        assert_allclose(samp1, samp2, atol=1e-13)
+        # Use RandomState
+        rstate1 = np.random.RandomState(seed=138)
+        samp1 = gkde_trail.resample(n_sample, seed=rstate1)
+        rstate2 = np.random.RandomState(seed=138)
+        samp2 = gkde_trail.resample(n_sample, seed=rstate2)
+        assert_allclose(samp1, samp2, atol=1e-13)
+
+        # check that np.random.Generator can be used (numpy >= 1.17)
+        if hasattr(np.random, 'default_rng'):
+            # obtain a np.random.Generator object
+            rng = np.random.default_rng(1234)
+            gkde_trail.resample(n_sample, seed=rng)
+
+    np.random.seed(8765678)
+    n_basesample = 500
+    wn = np.random.rand(n_basesample)
+    # Test 1D case
+    xn_1d = np.random.randn(n_basesample)
+
+    gkde_1d = stats.gaussian_kde(xn_1d)
+    test_seed_sub(gkde_1d)
+    gkde_1d_weighted = stats.gaussian_kde(xn_1d, weights=wn)
+    test_seed_sub(gkde_1d_weighted)
+
+    # Test 2D case
+    mean = np.array([1.0, 3.0])
+    covariance = np.array([[1.0, 2.0], [2.0, 6.0]])
+    xn_2d = np.random.multivariate_normal(mean, covariance, size=n_basesample).T
+
+    gkde_2d = stats.gaussian_kde(xn_2d)
+    test_seed_sub(gkde_2d)
+    gkde_2d_weighted = stats.gaussian_kde(xn_2d, weights=wn)
+    test_seed_sub(gkde_2d_weighted)
+
+
+def test_singular_data_covariance_gh10205():
+    # When the data lie in a lower-dimensional subspace and this causes
+    # and exception, check that the error message is informative.
+    rng = np.random.default_rng(2321583144339784787)
+    mu = np.array([1, 10, 20])
+    sigma = np.array([[4, 10, 0], [10, 25, 0], [0, 0, 100]])
+    data = rng.multivariate_normal(mu, sigma, 1000)
+    try:  # doesn't raise any error on some platforms, and that's OK
+        stats.gaussian_kde(data.T)
+    except linalg.LinAlgError:
+        msg = "The data appears to lie in a lower-dimensional subspace..."
+        with assert_raises(linalg.LinAlgError, match=msg):
+            stats.gaussian_kde(data.T)
+
+
+def test_fewer_points_than_dimensions_gh17436():
+    # When the number of points is fewer than the number of dimensions, the
+    # the covariance matrix would be singular, and the exception tested in
+    # test_singular_data_covariance_gh10205 would occur. However, sometimes
+    # this occurs when the user passes in the transpose of what `gaussian_kde`
+    # expects. This can result in a huge covariance matrix, so bail early.
+    rng = np.random.default_rng(2046127537594925772)
+    rvs = rng.multivariate_normal(np.zeros(3), np.eye(3), size=5)
+    message = "Number of dimensions is greater than number of samples..."
+    with pytest.raises(ValueError, match=message):
+        stats.gaussian_kde(rvs)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_mgc.py

@@ -0,0 +1,217 @@
+import pytest
+from pytest import raises as assert_raises, warns as assert_warns
+
+import numpy as np
+from numpy.testing import assert_approx_equal, assert_allclose, assert_equal
+
+from scipy.spatial.distance import cdist
+from scipy import stats
+
+class TestMGCErrorWarnings:
+    """ Tests errors and warnings derived from MGC.
+    """
+    def test_error_notndarray(self):
+        # raises error if x or y is not a ndarray
+        x = np.arange(20)
+        y = [5] * 20
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, y)
+        assert_raises(ValueError, stats.multiscale_graphcorr, y, x)
+
+    def test_error_shape(self):
+        # raises error if number of samples different (n)
+        x = np.arange(100).reshape(25, 4)
+        y = x.reshape(10, 10)
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, y)
+
+    def test_error_lowsamples(self):
+        # raises error if samples are low (< 3)
+        x = np.arange(3)
+        y = np.arange(3)
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, y)
+
+    def test_error_nans(self):
+        # raises error if inputs contain NaNs
+        x = np.arange(20, dtype=float)
+        x[0] = np.nan
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, x)
+
+        y = np.arange(20)
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, y)
+
+    def test_error_wrongdisttype(self):
+        # raises error if metric is not a function
+        x = np.arange(20)
+        compute_distance = 0
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, x,
+                      compute_distance=compute_distance)
+
+    @pytest.mark.parametrize("reps", [
+        -1,    # reps is negative
+        '1',   # reps is not integer
+    ])
+    def test_error_reps(self, reps):
+        # raises error if reps is negative
+        x = np.arange(20)
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, x, reps=reps)
+
+    def test_warns_reps(self):
+        # raises warning when reps is less than 1000
+        x = np.arange(20)
+        reps = 100
+        assert_warns(RuntimeWarning, stats.multiscale_graphcorr, x, x, reps=reps)
+
+    def test_error_infty(self):
+        # raises error if input contains infinities
+        x = np.arange(20)
+        y = np.ones(20) * np.inf
+        assert_raises(ValueError, stats.multiscale_graphcorr, x, y)
+
+
+class TestMGCStat:
+    """ Test validity of MGC test statistic
+    """
+    def _simulations(self, samps=100, dims=1, sim_type=""):
+        # linear simulation
+        if sim_type == "linear":
+            x = np.random.uniform(-1, 1, size=(samps, 1))
+            y = x + 0.3 * np.random.random_sample(size=(x.size, 1))
+
+        # spiral simulation
+        elif sim_type == "nonlinear":
+            unif = np.array(np.random.uniform(0, 5, size=(samps, 1)))
+            x = unif * np.cos(np.pi * unif)
+            y = (unif * np.sin(np.pi * unif) +
+                 0.4*np.random.random_sample(size=(x.size, 1)))
+
+        # independence (tests type I simulation)
+        elif sim_type == "independence":
+            u = np.random.normal(0, 1, size=(samps, 1))
+            v = np.random.normal(0, 1, size=(samps, 1))
+            u_2 = np.random.binomial(1, p=0.5, size=(samps, 1))
+            v_2 = np.random.binomial(1, p=0.5, size=(samps, 1))
+            x = u/3 + 2*u_2 - 1
+            y = v/3 + 2*v_2 - 1
+
+        # raises error if not approved sim_type
+        else:
+            raise ValueError("sim_type must be linear, nonlinear, or "
+                             "independence")
+
+        # add dimensions of noise for higher dimensions
+        if dims > 1:
+            dims_noise = np.random.normal(0, 1, size=(samps, dims-1))
+            x = np.concatenate((x, dims_noise), axis=1)
+
+        return x, y
+
+    @pytest.mark.xslow
+    @pytest.mark.parametrize("sim_type, obs_stat, obs_pvalue", [
+        ("linear", 0.97, 1/1000),           # test linear simulation
+        ("nonlinear", 0.163, 1/1000),       # test spiral simulation
+        ("independence", -0.0094, 0.78)     # test independence simulation
+    ])
+    def test_oned(self, sim_type, obs_stat, obs_pvalue):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type=sim_type)
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y)
+        assert_approx_equal(stat, obs_stat, significant=1)
+        assert_approx_equal(pvalue, obs_pvalue, significant=1)
+
+    @pytest.mark.xslow
+    @pytest.mark.parametrize("sim_type, obs_stat, obs_pvalue", [
+        ("linear", 0.184, 1/1000),           # test linear simulation
+        ("nonlinear", 0.0190, 0.117),        # test spiral simulation
+    ])
+    def test_fived(self, sim_type, obs_stat, obs_pvalue):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=5, sim_type=sim_type)
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y)
+        assert_approx_equal(stat, obs_stat, significant=1)
+        assert_approx_equal(pvalue, obs_pvalue, significant=1)
+
+    @pytest.mark.xslow
+    def test_twosamp(self):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x = np.random.binomial(100, 0.5, size=(100, 5))
+        y = np.random.normal(0, 1, size=(80, 5))
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y)
+        assert_approx_equal(stat, 1.0, significant=1)
+        assert_approx_equal(pvalue, 0.001, significant=1)
+
+        # generate x and y
+        y = np.random.normal(0, 1, size=(100, 5))
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y, is_twosamp=True)
+        assert_approx_equal(stat, 1.0, significant=1)
+        assert_approx_equal(pvalue, 0.001, significant=1)
+
+    @pytest.mark.xslow
+    def test_workers(self):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type="linear")
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y, workers=2)
+        assert_approx_equal(stat, 0.97, significant=1)
+        assert_approx_equal(pvalue, 0.001, significant=1)
+
+    @pytest.mark.xslow
+    def test_random_state(self):
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type="linear")
+
+        # test stat and pvalue
+        stat, pvalue, _ = stats.multiscale_graphcorr(x, y, random_state=1)
+        assert_approx_equal(stat, 0.97, significant=1)
+        assert_approx_equal(pvalue, 0.001, significant=1)
+
+    @pytest.mark.xslow
+    def test_dist_perm(self):
+        np.random.seed(12345678)
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type="nonlinear")
+        distx = cdist(x, x, metric="euclidean")
+        disty = cdist(y, y, metric="euclidean")
+
+        stat_dist, pvalue_dist, _ = stats.multiscale_graphcorr(distx, disty,
+                                                               compute_distance=None,
+                                                               random_state=1)
+        assert_approx_equal(stat_dist, 0.163, significant=1)
+        assert_approx_equal(pvalue_dist, 0.001, significant=1)
+
+    @pytest.mark.fail_slow(10)  # all other tests are XSLOW; we need at least one to run
+    @pytest.mark.slow
+    def test_pvalue_literature(self):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type="linear")
+
+        # test stat and pvalue
+        _, pvalue, _ = stats.multiscale_graphcorr(x, y, random_state=1)
+        assert_allclose(pvalue, 1/1001)
+
+    @pytest.mark.xslow
+    def test_alias(self):
+        np.random.seed(12345678)
+
+        # generate x and y
+        x, y = self._simulations(samps=100, dims=1, sim_type="linear")
+
+        res = stats.multiscale_graphcorr(x, y, random_state=1)
+        assert_equal(res.stat, res.statistic)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_mstats_extras.py

@@ -0,0 +1,172 @@
+import numpy as np
+import numpy.ma as ma
+import scipy.stats.mstats as ms
+
+from numpy.testing import (assert_equal, assert_almost_equal, assert_,
+                           assert_allclose)
+
+
+def test_compare_medians_ms():
+    x = np.arange(7)
+    y = x + 10
+    assert_almost_equal(ms.compare_medians_ms(x, y), 0)
+
+    y2 = np.linspace(0, 1, num=10)
+    assert_almost_equal(ms.compare_medians_ms(x, y2), 0.017116406778)
+
+
+def test_hdmedian():
+    # 1-D array
+    x = ma.arange(11)
+    assert_allclose(ms.hdmedian(x), 5, rtol=1e-14)
+    x.mask = ma.make_mask(x)
+    x.mask[:7] = False
+    assert_allclose(ms.hdmedian(x), 3, rtol=1e-14)
+
+    # Check that `var` keyword returns a value.  TODO: check whether returned
+    # value is actually correct.
+    assert_(ms.hdmedian(x, var=True).size == 2)
+
+    # 2-D array
+    x2 = ma.arange(22).reshape((11, 2))
+    assert_allclose(ms.hdmedian(x2, axis=0), [10, 11])
+    x2.mask = ma.make_mask(x2)
+    x2.mask[:7, :] = False
+    assert_allclose(ms.hdmedian(x2, axis=0), [6, 7])
+
+
+def test_rsh():
+    np.random.seed(132345)
+    x = np.random.randn(100)
+    res = ms.rsh(x)
+    # Just a sanity check that the code runs and output shape is correct.
+    # TODO: check that implementation is correct.
+    assert_(res.shape == x.shape)
+
+    # Check points keyword
+    res = ms.rsh(x, points=[0, 1.])
+    assert_(res.size == 2)
+
+
+def test_mjci():
+    # Tests the Marits-Jarrett estimator
+    data = ma.array([77, 87, 88,114,151,210,219,246,253,262,
+                     296,299,306,376,428,515,666,1310,2611])
+    assert_almost_equal(ms.mjci(data),[55.76819,45.84028,198.87875],5)
+
+
+def test_trimmed_mean_ci():
+    # Tests the confidence intervals of the trimmed mean.
+    data = ma.array([545,555,558,572,575,576,578,580,
+                     594,605,635,651,653,661,666])
+    assert_almost_equal(ms.trimmed_mean(data,0.2), 596.2, 1)
+    assert_equal(np.round(ms.trimmed_mean_ci(data,(0.2,0.2)),1),
+                 [561.8, 630.6])
+
+
+def test_idealfourths():
+    # Tests ideal-fourths
+    test = np.arange(100)
+    assert_almost_equal(np.asarray(ms.idealfourths(test)),
+                        [24.416667,74.583333],6)
+    test_2D = test.repeat(3).reshape(-1,3)
+    assert_almost_equal(ms.idealfourths(test_2D, axis=0),
+                        [[24.416667,24.416667,24.416667],
+                         [74.583333,74.583333,74.583333]],6)
+    assert_almost_equal(ms.idealfourths(test_2D, axis=1),
+                        test.repeat(2).reshape(-1,2))
+    test = [0, 0]
+    _result = ms.idealfourths(test)
+    assert_(np.isnan(_result).all())
+
+
+class TestQuantiles:
+    data = [0.706560797,0.727229578,0.990399276,0.927065621,0.158953014,
+            0.887764025,0.239407086,0.349638551,0.972791145,0.149789972,
+            0.936947700,0.132359948,0.046041972,0.641675031,0.945530547,
+            0.224218684,0.771450991,0.820257774,0.336458052,0.589113496,
+            0.509736129,0.696838829,0.491323573,0.622767425,0.775189248,
+            0.641461450,0.118455200,0.773029450,0.319280007,0.752229111,
+            0.047841438,0.466295911,0.583850781,0.840581845,0.550086491,
+            0.466470062,0.504765074,0.226855960,0.362641207,0.891620942,
+            0.127898691,0.490094097,0.044882048,0.041441695,0.317976349,
+            0.504135618,0.567353033,0.434617473,0.636243375,0.231803616,
+            0.230154113,0.160011327,0.819464108,0.854706985,0.438809221,
+            0.487427267,0.786907310,0.408367937,0.405534192,0.250444460,
+            0.995309248,0.144389588,0.739947527,0.953543606,0.680051621,
+            0.388382017,0.863530727,0.006514031,0.118007779,0.924024803,
+            0.384236354,0.893687694,0.626534881,0.473051932,0.750134705,
+            0.241843555,0.432947602,0.689538104,0.136934797,0.150206859,
+            0.474335206,0.907775349,0.525869295,0.189184225,0.854284286,
+            0.831089744,0.251637345,0.587038213,0.254475554,0.237781276,
+            0.827928620,0.480283781,0.594514455,0.213641488,0.024194386,
+            0.536668589,0.699497811,0.892804071,0.093835427,0.731107772]
+
+    def test_hdquantiles(self):
+        data = self.data
+        assert_almost_equal(ms.hdquantiles(data,[0., 1.]),
+                            [0.006514031, 0.995309248])
+        hdq = ms.hdquantiles(data,[0.25, 0.5, 0.75])
+        assert_almost_equal(hdq, [0.253210762, 0.512847491, 0.762232442,])
+
+        data = np.array(data).reshape(10,10)
+        hdq = ms.hdquantiles(data,[0.25,0.5,0.75],axis=0)
+        assert_almost_equal(hdq[:,0], ms.hdquantiles(data[:,0],[0.25,0.5,0.75]))
+        assert_almost_equal(hdq[:,-1], ms.hdquantiles(data[:,-1],[0.25,0.5,0.75]))
+        hdq = ms.hdquantiles(data,[0.25,0.5,0.75],axis=0,var=True)
+        assert_almost_equal(hdq[...,0],
+                            ms.hdquantiles(data[:,0],[0.25,0.5,0.75],var=True))
+        assert_almost_equal(hdq[...,-1],
+                            ms.hdquantiles(data[:,-1],[0.25,0.5,0.75], var=True))
+
+    def test_hdquantiles_sd(self):
+        # Standard deviation is a jackknife estimator, so we can check if
+        # the efficient version (hdquantiles_sd) matches a rudimentary,
+        # but clear version here.
+
+        hd_std_errs = ms.hdquantiles_sd(self.data)
+
+        # jacknnife standard error, Introduction to the Bootstrap Eq. 11.5
+        n = len(self.data)
+        jdata = np.broadcast_to(self.data, (n, n))
+        jselector = np.logical_not(np.eye(n))  # leave out one sample each row
+        jdata = jdata[jselector].reshape(n, n-1)
+        jdist = ms.hdquantiles(jdata, axis=1)
+        jdist_mean = np.mean(jdist, axis=0)
+        jstd = ((n-1)/n * np.sum((jdist - jdist_mean)**2, axis=0))**.5
+
+        assert_almost_equal(hd_std_errs, jstd)
+        # Test actual values for good measure
+        assert_almost_equal(hd_std_errs, [0.0379258, 0.0380656, 0.0380013])
+
+        two_data_points = ms.hdquantiles_sd([1, 2])
+        assert_almost_equal(two_data_points, [0.5, 0.5, 0.5])
+
+    def test_mquantiles_cimj(self):
+        # Only test that code runs, implementation not checked for correctness
+        ci_lower, ci_upper = ms.mquantiles_cimj(self.data)
+        assert_(ci_lower.size == ci_upper.size == 3)
+
+
+def test_median_cihs():
+    # Basic test against R library EnvStats function `eqnpar`, e.g.
+    # library(EnvStats)
+    # options(digits=8)
+    # x = c(0.88612955, 0.35242375, 0.66240904, 0.94617974, 0.10929913,
+    #       0.76699506, 0.88550655, 0.62763754, 0.76818588, 0.68506508,
+    #       0.88043148, 0.03911248, 0.93805564, 0.95326961, 0.25291112,
+    #       0.16128487, 0.49784577, 0.24588924, 0.6597, 0.92239679)
+    # eqnpar(x, p=0.5,
+    #        ci.method = "interpolate", approx.conf.level = 0.95, ci = TRUE)
+    rng = np.random.default_rng(8824288259505800535)
+    x = rng.random(size=20)
+    assert_allclose(ms.median_cihs(x), (0.38663198, 0.88431272))
+
+    # SciPy's 90% CI upper limit doesn't match that of EnvStats eqnpar. SciPy
+    # doesn't look wrong, and it agrees with a different reference,
+    # `median_confint_hs` from `hoehleatsu/quantileCI`.
+    # In (e.g.) Colab with R runtime:
+    # devtools::install_github("hoehleatsu/quantileCI")
+    # library(quantileCI)
+    # median_confint_hs(x=x, conf.level=0.90, interpolate=TRUE)
+    assert_allclose(ms.median_cihs(x, 0.1), (0.48319773366, 0.88094268050))

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_multicomp.py

@@ -0,0 +1,404 @@
+import copy
+
+import numpy as np
+import pytest
+from numpy.testing import assert_allclose
+
+from scipy import stats
+from scipy.stats._multicomp import _pvalue_dunnett, DunnettResult
+
+
+class TestDunnett:
+    # For the following tests, p-values were computed using Matlab, e.g.
+    #     sample = [18.  15.  18.  16.  17.  15.  14.  14.  14.  15.  15....
+    #               14.  15.  14.  22.  18.  21.  21.  10.  10.  11.  9....
+    #               25.  26.  17.5 16.  15.5 14.5 22.  22.  24.  22.5 29....
+    #               24.5 20.  18.  18.5 17.5 26.5 13.  16.5 13.  13.  13....
+    #               28.  27.  34.  31.  29.  27.  24.  23.  38.  36.  25....
+    #               38. 26.  22.  36.  27.  27.  32.  28.  31....
+    #               24.  27.  33.  32.  28.  19. 37.  31.  36.  36....
+    #               34.  38.  32.  38.  32....
+    #               26.  24.  26.  25.  29. 29.5 16.5 36.  44....
+    #               25.  27.  19....
+    #               25.  20....
+    #               28.];
+    #     j = [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
+    #          0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
+    #          0 0 0 0...
+    #          1 1 1 1 1 1 1 1 1 1 1 1 1 1 1...
+    #          2 2 2 2 2 2 2 2 2...
+    #          3 3 3...
+    #          4 4...
+    #          5];
+    #     [~, ~, stats] = anova1(sample, j, "off");
+    #     [results, ~, ~, gnames] = multcompare(stats, ...
+    #     "CriticalValueType", "dunnett", ...
+    #     "Approximate", false);
+    #     tbl = array2table(results, "VariableNames", ...
+    #     ["Group", "Control Group", "Lower Limit", ...
+    #     "Difference", "Upper Limit", "P-value"]);
+    #     tbl.("Group") = gnames(tbl.("Group"));
+    #     tbl.("Control Group") = gnames(tbl.("Control Group"))
+
+    # Matlab doesn't report the statistic, so the statistics were
+    # computed using R multcomp `glht`, e.g.:
+    #     library(multcomp)
+    #     options(digits=16)
+    #     control < - c(18.0, 15.0, 18.0, 16.0, 17.0, 15.0, 14.0, 14.0, 14.0,
+    #                   15.0, 15.0, 14.0, 15.0, 14.0, 22.0, 18.0, 21.0, 21.0,
+    #                   10.0, 10.0, 11.0, 9.0, 25.0, 26.0, 17.5, 16.0, 15.5,
+    #                   14.5, 22.0, 22.0, 24.0, 22.5, 29.0, 24.5, 20.0, 18.0,
+    #                   18.5, 17.5, 26.5, 13.0, 16.5, 13.0, 13.0, 13.0, 28.0,
+    #                   27.0, 34.0, 31.0, 29.0, 27.0, 24.0, 23.0, 38.0, 36.0,
+    #                   25.0, 38.0, 26.0, 22.0, 36.0, 27.0, 27.0, 32.0, 28.0,
+    #                   31.0)
+    #     t < - c(24.0, 27.0, 33.0, 32.0, 28.0, 19.0, 37.0, 31.0, 36.0, 36.0,
+    #             34.0, 38.0, 32.0, 38.0, 32.0)
+    #     w < - c(26.0, 24.0, 26.0, 25.0, 29.0, 29.5, 16.5, 36.0, 44.0)
+    #     x < - c(25.0, 27.0, 19.0)
+    #     y < - c(25.0, 20.0)
+    #     z < - c(28.0)
+    #
+    #     groups = factor(rep(c("control", "t", "w", "x", "y", "z"),
+    #                         times=c(length(control), length(t), length(w),
+    #                                 length(x), length(y), length(z))))
+    #     df < - data.frame(response=c(control, t, w, x, y, z),
+    #                       group=groups)
+    #     model < - aov(response
+    #     ~group, data = df)
+    #     test < - glht(model=model,
+    #                   linfct=mcp(group="Dunnett"),
+    #                   alternative="g")
+    #     summary(test)
+    #     confint(test)
+    # p-values agreed with those produced by Matlab to at least atol=1e-3
+
+    # From Matlab's documentation on multcompare
+    samples_1 = [
+        [
+            24.0, 27.0, 33.0, 32.0, 28.0, 19.0, 37.0, 31.0, 36.0, 36.0,
+            34.0, 38.0, 32.0, 38.0, 32.0
+        ],
+        [26.0, 24.0, 26.0, 25.0, 29.0, 29.5, 16.5, 36.0, 44.0],
+        [25.0, 27.0, 19.0],
+        [25.0, 20.0],
+        [28.0]
+    ]
+    control_1 = [
+        18.0, 15.0, 18.0, 16.0, 17.0, 15.0, 14.0, 14.0, 14.0, 15.0, 15.0,
+        14.0, 15.0, 14.0, 22.0, 18.0, 21.0, 21.0, 10.0, 10.0, 11.0, 9.0,
+        25.0, 26.0, 17.5, 16.0, 15.5, 14.5, 22.0, 22.0, 24.0, 22.5, 29.0,
+        24.5, 20.0, 18.0, 18.5, 17.5, 26.5, 13.0, 16.5, 13.0, 13.0, 13.0,
+        28.0, 27.0, 34.0, 31.0, 29.0, 27.0, 24.0, 23.0, 38.0, 36.0, 25.0,
+        38.0, 26.0, 22.0, 36.0, 27.0, 27.0, 32.0, 28.0, 31.0
+    ]
+    pvalue_1 = [4.727e-06, 0.022346, 0.97912, 0.99953, 0.86579]  # Matlab
+    # Statistic, alternative p-values, and CIs computed with R multcomp `glht`
+    p_1_twosided = [1e-4, 0.02237, 0.97913, 0.99953, 0.86583]
+    p_1_greater = [1e-4, 0.011217, 0.768500, 0.896991, 0.577211]
+    p_1_less = [1, 1, 0.99660, 0.98398, .99953]
+    statistic_1 = [5.27356, 2.91270, 0.60831, 0.27002, 0.96637]
+    ci_1_twosided = [[5.3633917835622, 0.7296142201217, -8.3879817106607,
+                      -11.9090753452911, -11.7655021543469],
+                     [15.9709832164378, 13.8936496687672, 13.4556900439941,
+                      14.6434503452911, 25.4998771543469]]
+    ci_1_greater = [5.9036402398526, 1.4000632918725, -7.2754756323636,
+                    -10.5567456382391, -9.8675629499576]
+    ci_1_less = [15.4306165948619, 13.2230539537359, 12.3429406339544,
+                 13.2908248513211, 23.6015228251660]
+    pvalues_1 = dict(twosided=p_1_twosided, less=p_1_less, greater=p_1_greater)
+    cis_1 = dict(twosided=ci_1_twosided, less=ci_1_less, greater=ci_1_greater)
+    case_1 = dict(samples=samples_1, control=control_1, statistic=statistic_1,
+                  pvalues=pvalues_1, cis=cis_1)
+
+    # From Dunnett1955 comparing with R's DescTools: DunnettTest
+    samples_2 = [[9.76, 8.80, 7.68, 9.36], [12.80, 9.68, 12.16, 9.20, 10.55]]
+    control_2 = [7.40, 8.50, 7.20, 8.24, 9.84, 8.32]
+    pvalue_2 = [0.6201, 0.0058]
+    # Statistic, alternative p-values, and CIs computed with R multcomp `glht`
+    p_2_twosided = [0.6201020, 0.0058254]
+    p_2_greater = [0.3249776, 0.0029139]
+    p_2_less = [0.91676, 0.99984]
+    statistic_2 = [0.85703, 3.69375]
+    ci_2_twosided = [[-1.2564116462124, 0.8396273539789],
+                     [2.5564116462124, 4.4163726460211]]
+    ci_2_greater = [-0.9588591188156, 1.1187563667543]
+    ci_2_less = [2.2588591188156, 4.1372436332457]
+    pvalues_2 = dict(twosided=p_2_twosided, less=p_2_less, greater=p_2_greater)
+    cis_2 = dict(twosided=ci_2_twosided, less=ci_2_less, greater=ci_2_greater)
+    case_2 = dict(samples=samples_2, control=control_2, statistic=statistic_2,
+                  pvalues=pvalues_2, cis=cis_2)
+
+    samples_3 = [[55, 64, 64], [55, 49, 52], [50, 44, 41]]
+    control_3 = [55, 47, 48]
+    pvalue_3 = [0.0364, 0.8966, 0.4091]
+    # Statistic, alternative p-values, and CIs computed with R multcomp `glht`
+    p_3_twosided = [0.036407, 0.896539, 0.409295]
+    p_3_greater = [0.018277, 0.521109, 0.981892]
+    p_3_less = [0.99944, 0.90054, 0.20974]
+    statistic_3 = [3.09073, 0.56195, -1.40488]
+    ci_3_twosided = [[0.7529028025053, -8.2470971974947, -15.2470971974947],
+                     [21.2470971974947, 12.2470971974947, 5.2470971974947]]
+    ci_3_greater = [2.4023682323149, -6.5976317676851, -13.5976317676851]
+    ci_3_less = [19.5984402363662, 10.5984402363662, 3.5984402363662]
+    pvalues_3 = dict(twosided=p_3_twosided, less=p_3_less, greater=p_3_greater)
+    cis_3 = dict(twosided=ci_3_twosided, less=ci_3_less, greater=ci_3_greater)
+    case_3 = dict(samples=samples_3, control=control_3, statistic=statistic_3,
+                  pvalues=pvalues_3, cis=cis_3)
+
+    # From Thomson and Short,
+    # Mucociliary function in health, chronic obstructive airway disease,
+    # and asbestosis, Journal of Applied Physiology, 1969. Table 1
+    # Comparing with R's DescTools: DunnettTest
+    samples_4 = [[3.8, 2.7, 4.0, 2.4], [2.8, 3.4, 3.7, 2.2, 2.0]]
+    control_4 = [2.9, 3.0, 2.5, 2.6, 3.2]
+    pvalue_4 = [0.5832, 0.9982]
+    # Statistic, alternative p-values, and CIs computed with R multcomp `glht`
+    p_4_twosided = [0.58317, 0.99819]
+    p_4_greater = [0.30225, 0.69115]
+    p_4_less = [0.91929, 0.65212]
+    statistic_4 = [0.90875, -0.05007]
+    ci_4_twosided = [[-0.6898153448579, -1.0333456251632],
+                     [1.4598153448579, 0.9933456251632]]
+    ci_4_greater = [-0.5186459268412, -0.8719655502147 ]
+    ci_4_less = [1.2886459268412, 0.8319655502147]
+    pvalues_4 = dict(twosided=p_4_twosided, less=p_4_less, greater=p_4_greater)
+    cis_4 = dict(twosided=ci_4_twosided, less=ci_4_less, greater=ci_4_greater)
+    case_4 = dict(samples=samples_4, control=control_4, statistic=statistic_4,
+                  pvalues=pvalues_4, cis=cis_4)
+
+    @pytest.mark.parametrize(
+        'rho, n_groups, df, statistic, pvalue, alternative',
+        [
+            # From Dunnett1955
+            # Tables 1a and 1b pages 1117-1118
+            (0.5, 1, 10, 1.81, 0.05, "greater"),  # different than two-sided
+            (0.5, 3, 10, 2.34, 0.05, "greater"),
+            (0.5, 2, 30, 1.99, 0.05, "greater"),
+            (0.5, 5, 30, 2.33, 0.05, "greater"),
+            (0.5, 4, 12, 3.32, 0.01, "greater"),
+            (0.5, 7, 12, 3.56, 0.01, "greater"),
+            (0.5, 2, 60, 2.64, 0.01, "greater"),
+            (0.5, 4, 60, 2.87, 0.01, "greater"),
+            (0.5, 4, 60, [2.87, 2.21], [0.01, 0.05], "greater"),
+            # Tables 2a and 2b pages 1119-1120
+            (0.5, 1, 10, 2.23, 0.05, "two-sided"),  # two-sided
+            (0.5, 3, 10, 2.81, 0.05, "two-sided"),
+            (0.5, 2, 30, 2.32, 0.05, "two-sided"),
+            (0.5, 3, 20, 2.57, 0.05, "two-sided"),
+            (0.5, 4, 12, 3.76, 0.01, "two-sided"),
+            (0.5, 7, 12, 4.08, 0.01, "two-sided"),
+            (0.5, 2, 60, 2.90, 0.01, "two-sided"),
+            (0.5, 4, 60, 3.14, 0.01, "two-sided"),
+            (0.5, 4, 60, [3.14, 2.55], [0.01, 0.05], "two-sided"),
+        ],
+    )
+    def test_critical_values(
+        self, rho, n_groups, df, statistic, pvalue, alternative
+    ):
+        rng = np.random.default_rng(165250594791731684851746311027739134893)
+        rho = np.full((n_groups, n_groups), rho)
+        np.fill_diagonal(rho, 1)
+
+        statistic = np.array(statistic)
+        res = _pvalue_dunnett(
+            rho=rho, df=df, statistic=statistic,
+            alternative=alternative,
+            rng=rng
+        )
+        assert_allclose(res, pvalue, atol=5e-3)
+
+    @pytest.mark.parametrize(
+        'samples, control, pvalue, statistic',
+        [
+            (samples_1, control_1, pvalue_1, statistic_1),
+            (samples_2, control_2, pvalue_2, statistic_2),
+            (samples_3, control_3, pvalue_3, statistic_3),
+            (samples_4, control_4, pvalue_4, statistic_4),
+        ]
+    )
+    def test_basic(self, samples, control, pvalue, statistic):
+        rng = np.random.default_rng(11681140010308601919115036826969764808)
+
+        res = stats.dunnett(*samples, control=control, random_state=rng)
+
+        assert isinstance(res, DunnettResult)
+        assert_allclose(res.statistic, statistic, rtol=5e-5)
+        assert_allclose(res.pvalue, pvalue, rtol=1e-2, atol=1e-4)
+
+    @pytest.mark.parametrize(
+        'alternative',
+        ['two-sided', 'less', 'greater']
+    )
+    def test_ttest_ind(self, alternative):
+        # check that `dunnett` agrees with `ttest_ind`
+        # when there are only two groups
+        rng = np.random.default_rng(114184017807316971636137493526995620351)
+
+        for _ in range(10):
+            sample = rng.integers(-100, 100, size=(10,))
+            control = rng.integers(-100, 100, size=(10,))
+
+            res = stats.dunnett(
+                sample, control=control,
+                alternative=alternative, random_state=rng
+            )
+            ref = stats.ttest_ind(
+                sample, control,
+                alternative=alternative, random_state=rng
+            )
+
+            assert_allclose(res.statistic, ref.statistic, rtol=1e-3, atol=1e-5)
+            assert_allclose(res.pvalue, ref.pvalue, rtol=1e-3, atol=1e-5)
+
+    @pytest.mark.parametrize(
+        'alternative, pvalue',
+        [
+            ('less', [0, 1]),
+            ('greater', [1, 0]),
+            ('two-sided', [0, 0]),
+        ]
+    )
+    def test_alternatives(self, alternative, pvalue):
+        rng = np.random.default_rng(114184017807316971636137493526995620351)
+
+        # width of 20 and min diff between samples/control is 60
+        # and maximal diff would be 100
+        sample_less = rng.integers(0, 20, size=(10,))
+        control = rng.integers(80, 100, size=(10,))
+        sample_greater = rng.integers(160, 180, size=(10,))
+
+        res = stats.dunnett(
+            sample_less, sample_greater, control=control,
+            alternative=alternative, random_state=rng
+        )
+        assert_allclose(res.pvalue, pvalue, atol=1e-7)
+
+        ci = res.confidence_interval()
+        # two-sided is comparable for high/low
+        if alternative == 'less':
+            assert np.isneginf(ci.low).all()
+            assert -100 < ci.high[0] < -60
+            assert 60 < ci.high[1] < 100
+        elif alternative == 'greater':
+            assert -100 < ci.low[0] < -60
+            assert 60 < ci.low[1] < 100
+            assert np.isposinf(ci.high).all()
+        elif alternative == 'two-sided':
+            assert -100 < ci.low[0] < -60
+            assert 60 < ci.low[1] < 100
+            assert -100 < ci.high[0] < -60
+            assert 60 < ci.high[1] < 100
+
+    @pytest.mark.parametrize("case", [case_1, case_2, case_3, case_4])
+    @pytest.mark.parametrize("alternative", ['less', 'greater', 'two-sided'])
+    def test_against_R_multicomp_glht(self, case, alternative):
+        rng = np.random.default_rng(189117774084579816190295271136455278291)
+        samples = case['samples']
+        control = case['control']
+        alternatives = {'less': 'less', 'greater': 'greater',
+                        'two-sided': 'twosided'}
+        p_ref = case['pvalues'][alternative.replace('-', '')]
+
+        res = stats.dunnett(*samples, control=control, alternative=alternative,
+                            random_state=rng)
+        # atol can't be tighter because R reports some pvalues as "< 1e-4"
+        assert_allclose(res.pvalue, p_ref, rtol=5e-3, atol=1e-4)
+
+        ci_ref = case['cis'][alternatives[alternative]]
+        if alternative == "greater":
+            ci_ref = [ci_ref, np.inf]
+        elif alternative == "less":
+            ci_ref = [-np.inf, ci_ref]
+        assert res._ci is None
+        assert res._ci_cl is None
+        ci = res.confidence_interval(confidence_level=0.95)
+        assert_allclose(ci.low, ci_ref[0], rtol=5e-3, atol=1e-5)
+        assert_allclose(ci.high, ci_ref[1], rtol=5e-3, atol=1e-5)
+
+        # re-run to use the cached value "is" to check id as same object
+        assert res._ci is ci
+        assert res._ci_cl == 0.95
+        ci_ = res.confidence_interval(confidence_level=0.95)
+        assert ci_ is ci
+
+    @pytest.mark.parametrize('alternative', ["two-sided", "less", "greater"])
+    def test_str(self, alternative):
+        rng = np.random.default_rng(189117774084579816190295271136455278291)
+
+        res = stats.dunnett(
+            *self.samples_3, control=self.control_3, alternative=alternative,
+            random_state=rng
+        )
+
+        # check some str output
+        res_str = str(res)
+        assert '(Sample 2 - Control)' in res_str
+        assert '95.0%' in res_str
+
+        if alternative == 'less':
+            assert '-inf' in res_str
+            assert '19.' in res_str
+        elif alternative == 'greater':
+            assert 'inf' in res_str
+            assert '-13.' in res_str
+        else:
+            assert 'inf' not in res_str
+            assert '21.' in res_str
+
+    def test_warnings(self):
+        rng = np.random.default_rng(189117774084579816190295271136455278291)
+
+        res = stats.dunnett(
+            *self.samples_3, control=self.control_3, random_state=rng
+        )
+        msg = r"Computation of the confidence interval did not converge"
+        with pytest.warns(UserWarning, match=msg):
+            res._allowance(tol=1e-5)
+
+    def test_raises(self):
+        samples, control = self.samples_3, self.control_3
+
+        # alternative
+        with pytest.raises(ValueError, match="alternative must be"):
+            stats.dunnett(*samples, control=control, alternative='bob')
+
+        # 2D for a sample
+        samples_ = copy.deepcopy(samples)
+        samples_[0] = [samples_[0]]
+        with pytest.raises(ValueError, match="must be 1D arrays"):
+            stats.dunnett(*samples_, control=control)
+
+        # 2D for control
+        control_ = copy.deepcopy(control)
+        control_ = [control_]
+        with pytest.raises(ValueError, match="must be 1D arrays"):
+            stats.dunnett(*samples, control=control_)
+
+        # No obs in a sample
+        samples_ = copy.deepcopy(samples)
+        samples_[1] = []
+        with pytest.raises(ValueError, match="at least 1 observation"):
+            stats.dunnett(*samples_, control=control)
+
+        # No obs in control
+        control_ = []
+        with pytest.raises(ValueError, match="at least 1 observation"):
+            stats.dunnett(*samples, control=control_)
+
+        res = stats.dunnett(*samples, control=control)
+        with pytest.raises(ValueError, match="Confidence level must"):
+            res.confidence_interval(confidence_level=3)
+
+    @pytest.mark.filterwarnings("ignore:Computation of the confidence")
+    @pytest.mark.parametrize('n_samples', [1, 2, 3])
+    def test_shapes(self, n_samples):
+        rng = np.random.default_rng(689448934110805334)
+        samples = rng.normal(size=(n_samples, 10))
+        control = rng.normal(size=10)
+        res = stats.dunnett(*samples, control=control, random_state=rng)
+        assert res.statistic.shape == (n_samples,)
+        assert res.pvalue.shape == (n_samples,)
+        ci = res.confidence_interval()
+        assert ci.low.shape == (n_samples,)
+        assert ci.high.shape == (n_samples,)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_odds_ratio.py

@@ -0,0 +1,148 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_equal, assert_allclose
+from .._discrete_distns import nchypergeom_fisher, hypergeom
+from scipy.stats._odds_ratio import odds_ratio
+from .data.fisher_exact_results_from_r import data
+
+
+class TestOddsRatio:
+
+    @pytest.mark.parametrize('parameters, rresult', data)
+    def test_results_from_r(self, parameters, rresult):
+        alternative = parameters.alternative.replace('.', '-')
+        result = odds_ratio(parameters.table)
+        # The results computed by R are not very accurate.
+        if result.statistic < 400:
+            or_rtol = 5e-4
+            ci_rtol = 2e-2
+        else:
+            or_rtol = 5e-2
+            ci_rtol = 1e-1
+        assert_allclose(result.statistic,
+                        rresult.conditional_odds_ratio, rtol=or_rtol)
+        ci = result.confidence_interval(parameters.confidence_level,
+                                        alternative)
+        assert_allclose((ci.low, ci.high), rresult.conditional_odds_ratio_ci,
+                        rtol=ci_rtol)
+
+        # Also do a self-check for the conditional odds ratio.
+        # With the computed conditional odds ratio as the noncentrality
+        # parameter of the noncentral hypergeometric distribution with
+        # parameters table.sum(), table[0].sum(), and table[:,0].sum() as
+        # total, ngood and nsample, respectively, the mean of the distribution
+        # should equal table[0, 0].
+        cor = result.statistic
+        table = np.array(parameters.table)
+        total = table.sum()
+        ngood = table[0].sum()
+        nsample = table[:, 0].sum()
+        # nchypergeom_fisher does not allow the edge cases where the
+        # noncentrality parameter is 0 or inf, so handle those values
+        # separately here.
+        if cor == 0:
+            nchg_mean = hypergeom.support(total, ngood, nsample)[0]
+        elif cor == np.inf:
+            nchg_mean = hypergeom.support(total, ngood, nsample)[1]
+        else:
+            nchg_mean = nchypergeom_fisher.mean(total, ngood, nsample, cor)
+        assert_allclose(nchg_mean, table[0, 0], rtol=1e-13)
+
+        # Check that the confidence interval is correct.
+        alpha = 1 - parameters.confidence_level
+        if alternative == 'two-sided':
+            if ci.low > 0:
+                sf = nchypergeom_fisher.sf(table[0, 0] - 1,
+                                           total, ngood, nsample, ci.low)
+                assert_allclose(sf, alpha/2, rtol=1e-11)
+            if np.isfinite(ci.high):
+                cdf = nchypergeom_fisher.cdf(table[0, 0],
+                                             total, ngood, nsample, ci.high)
+                assert_allclose(cdf, alpha/2, rtol=1e-11)
+        elif alternative == 'less':
+            if np.isfinite(ci.high):
+                cdf = nchypergeom_fisher.cdf(table[0, 0],
+                                             total, ngood, nsample, ci.high)
+                assert_allclose(cdf, alpha, rtol=1e-11)
+        else:
+            # alternative == 'greater'
+            if ci.low > 0:
+                sf = nchypergeom_fisher.sf(table[0, 0] - 1,
+                                           total, ngood, nsample, ci.low)
+                assert_allclose(sf, alpha, rtol=1e-11)
+
+    @pytest.mark.parametrize('table', [
+        [[0, 0], [5, 10]],
+        [[5, 10], [0, 0]],
+        [[0, 5], [0, 10]],
+        [[5, 0], [10, 0]],
+    ])
+    def test_row_or_col_zero(self, table):
+        result = odds_ratio(table)
+        assert_equal(result.statistic, np.nan)
+        ci = result.confidence_interval()
+        assert_equal((ci.low, ci.high), (0, np.inf))
+
+    @pytest.mark.parametrize("case",
+                             [[0.95, 'two-sided', 0.4879913, 2.635883],
+                              [0.90, 'two-sided', 0.5588516, 2.301663]])
+    def test_sample_odds_ratio_ci(self, case):
+        # Compare the sample odds ratio confidence interval to the R function
+        # oddsratio.wald from the epitools package, e.g.
+        # > library(epitools)
+        # > table = matrix(c(10, 20, 41, 93), nrow=2, ncol=2, byrow=TRUE)
+        # > result = oddsratio.wald(table)
+        # > result$measure
+        #           odds ratio with 95% C.I.
+        # Predictor  estimate     lower    upper
+        #   Exposed1 1.000000        NA       NA
+        #   Exposed2 1.134146 0.4879913 2.635883
+
+        confidence_level, alternative, ref_low, ref_high = case
+        table = [[10, 20], [41, 93]]
+        result = odds_ratio(table, kind='sample')
+        assert_allclose(result.statistic, 1.134146, rtol=1e-6)
+        ci = result.confidence_interval(confidence_level, alternative)
+        assert_allclose([ci.low, ci.high], [ref_low, ref_high], rtol=1e-6)
+
+    @pytest.mark.slow
+    @pytest.mark.parametrize('alternative', ['less', 'greater', 'two-sided'])
+    def test_sample_odds_ratio_one_sided_ci(self, alternative):
+        # can't find a good reference for one-sided CI, so bump up the sample
+        # size and compare against the conditional odds ratio CI
+        table = [[1000, 2000], [4100, 9300]]
+        res = odds_ratio(table, kind='sample')
+        ref = odds_ratio(table, kind='conditional')
+        assert_allclose(res.statistic, ref.statistic, atol=1e-5)
+        assert_allclose(res.confidence_interval(alternative=alternative),
+                        ref.confidence_interval(alternative=alternative),
+                        atol=2e-3)
+
+    @pytest.mark.parametrize('kind', ['sample', 'conditional'])
+    @pytest.mark.parametrize('bad_table', [123, "foo", [10, 11, 12]])
+    def test_invalid_table_shape(self, kind, bad_table):
+        with pytest.raises(ValueError, match="Invalid shape"):
+            odds_ratio(bad_table, kind=kind)
+
+    def test_invalid_table_type(self):
+        with pytest.raises(ValueError, match='must be an array of integers'):
+            odds_ratio([[1.0, 3.4], [5.0, 9.9]])
+
+    def test_negative_table_values(self):
+        with pytest.raises(ValueError, match='must be nonnegative'):
+            odds_ratio([[1, 2], [3, -4]])
+
+    def test_invalid_kind(self):
+        with pytest.raises(ValueError, match='`kind` must be'):
+            odds_ratio([[10, 20], [30, 14]], kind='magnetoreluctance')
+
+    def test_invalid_alternative(self):
+        result = odds_ratio([[5, 10], [2, 32]])
+        with pytest.raises(ValueError, match='`alternative` must be'):
+            result.confidence_interval(alternative='depleneration')
+
+    @pytest.mark.parametrize('level', [-0.5, 1.5])
+    def test_invalid_confidence_level(self, level):
+        result = odds_ratio([[5, 10], [2, 32]])
+        with pytest.raises(ValueError, match='must be between 0 and 1'):
+            result.confidence_interval(confidence_level=level)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_rank.py

@@ -0,0 +1,338 @@
+import numpy as np
+from numpy.testing import assert_equal, assert_array_equal
+import pytest
+
+from scipy.conftest import skip_xp_invalid_arg
+from scipy.stats import rankdata, tiecorrect
+from scipy._lib._util import np_long
+
+
+class TestTieCorrect:
+
+    def test_empty(self):
+        """An empty array requires no correction, should return 1.0."""
+        ranks = np.array([], dtype=np.float64)
+        c = tiecorrect(ranks)
+        assert_equal(c, 1.0)
+
+    def test_one(self):
+        """A single element requires no correction, should return 1.0."""
+        ranks = np.array([1.0], dtype=np.float64)
+        c = tiecorrect(ranks)
+        assert_equal(c, 1.0)
+
+    def test_no_correction(self):
+        """Arrays with no ties require no correction."""
+        ranks = np.arange(2.0)
+        c = tiecorrect(ranks)
+        assert_equal(c, 1.0)
+        ranks = np.arange(3.0)
+        c = tiecorrect(ranks)
+        assert_equal(c, 1.0)
+
+    def test_basic(self):
+        """Check a few basic examples of the tie correction factor."""
+        # One tie of two elements
+        ranks = np.array([1.0, 2.5, 2.5])
+        c = tiecorrect(ranks)
+        T = 2.0
+        N = ranks.size
+        expected = 1.0 - (T**3 - T) / (N**3 - N)
+        assert_equal(c, expected)
+
+        # One tie of two elements (same as above, but tie is not at the end)
+        ranks = np.array([1.5, 1.5, 3.0])
+        c = tiecorrect(ranks)
+        T = 2.0
+        N = ranks.size
+        expected = 1.0 - (T**3 - T) / (N**3 - N)
+        assert_equal(c, expected)
+
+        # One tie of three elements
+        ranks = np.array([1.0, 3.0, 3.0, 3.0])
+        c = tiecorrect(ranks)
+        T = 3.0
+        N = ranks.size
+        expected = 1.0 - (T**3 - T) / (N**3 - N)
+        assert_equal(c, expected)
+
+        # Two ties, lengths 2 and 3.
+        ranks = np.array([1.5, 1.5, 4.0, 4.0, 4.0])
+        c = tiecorrect(ranks)
+        T1 = 2.0
+        T2 = 3.0
+        N = ranks.size
+        expected = 1.0 - ((T1**3 - T1) + (T2**3 - T2)) / (N**3 - N)
+        assert_equal(c, expected)
+
+    def test_overflow(self):
+        ntie, k = 2000, 5
+        a = np.repeat(np.arange(k), ntie)
+        n = a.size  # ntie * k
+        out = tiecorrect(rankdata(a))
+        assert_equal(out, 1.0 - k * (ntie**3 - ntie) / float(n**3 - n))
+
+
+class TestRankData:
+
+    def test_empty(self):
+        """stats.rankdata([]) should return an empty array."""
+        a = np.array([], dtype=int)
+        r = rankdata(a)
+        assert_array_equal(r, np.array([], dtype=np.float64))
+        r = rankdata([])
+        assert_array_equal(r, np.array([], dtype=np.float64))
+
+    @pytest.mark.parametrize("shape", [(0, 1, 2)])
+    @pytest.mark.parametrize("axis", [None, *range(3)])
+    def test_empty_multidim(self, shape, axis):
+        a = np.empty(shape, dtype=int)
+        r = rankdata(a, axis=axis)
+        expected_shape = (0,) if axis is None else shape
+        assert_equal(r.shape, expected_shape)
+        assert_equal(r.dtype, np.float64)
+
+    def test_one(self):
+        """Check stats.rankdata with an array of length 1."""
+        data = [100]
+        a = np.array(data, dtype=int)
+        r = rankdata(a)
+        assert_array_equal(r, np.array([1.0], dtype=np.float64))
+        r = rankdata(data)
+        assert_array_equal(r, np.array([1.0], dtype=np.float64))
+
+    def test_basic(self):
+        """Basic tests of stats.rankdata."""
+        data = [100, 10, 50]
+        expected = np.array([3.0, 1.0, 2.0], dtype=np.float64)
+        a = np.array(data, dtype=int)
+        r = rankdata(a)
+        assert_array_equal(r, expected)
+        r = rankdata(data)
+        assert_array_equal(r, expected)
+
+        data = [40, 10, 30, 10, 50]
+        expected = np.array([4.0, 1.5, 3.0, 1.5, 5.0], dtype=np.float64)
+        a = np.array(data, dtype=int)
+        r = rankdata(a)
+        assert_array_equal(r, expected)
+        r = rankdata(data)
+        assert_array_equal(r, expected)
+
+        data = [20, 20, 20, 10, 10, 10]
+        expected = np.array([5.0, 5.0, 5.0, 2.0, 2.0, 2.0], dtype=np.float64)
+        a = np.array(data, dtype=int)
+        r = rankdata(a)
+        assert_array_equal(r, expected)
+        r = rankdata(data)
+        assert_array_equal(r, expected)
+        # The docstring states explicitly that the argument is flattened.
+        a2d = a.reshape(2, 3)
+        r = rankdata(a2d)
+        assert_array_equal(r, expected)
+
+    @skip_xp_invalid_arg
+    def test_rankdata_object_string(self):
+
+        def min_rank(a):
+            return [1 + sum(i < j for i in a) for j in a]
+
+        def max_rank(a):
+            return [sum(i <= j for i in a) for j in a]
+
+        def ordinal_rank(a):
+            return min_rank([(x, i) for i, x in enumerate(a)])
+
+        def average_rank(a):
+            return [(i + j) / 2.0 for i, j in zip(min_rank(a), max_rank(a))]
+
+        def dense_rank(a):
+            b = np.unique(a)
+            return [1 + sum(i < j for i in b) for j in a]
+
+        rankf = dict(min=min_rank, max=max_rank, ordinal=ordinal_rank,
+                     average=average_rank, dense=dense_rank)
+
+        def check_ranks(a):
+            for method in 'min', 'max', 'dense', 'ordinal', 'average':
+                out = rankdata(a, method=method)
+                assert_array_equal(out, rankf[method](a))
+
+        val = ['foo', 'bar', 'qux', 'xyz', 'abc', 'efg', 'ace', 'qwe', 'qaz']
+        check_ranks(np.random.choice(val, 200))
+        check_ranks(np.random.choice(val, 200).astype('object'))
+
+        val = np.array([0, 1, 2, 2.718, 3, 3.141], dtype='object')
+        check_ranks(np.random.choice(val, 200).astype('object'))
+
+    def test_large_int(self):
+        data = np.array([2**60, 2**60+1], dtype=np.uint64)
+        r = rankdata(data)
+        assert_array_equal(r, [1.0, 2.0])
+
+        data = np.array([2**60, 2**60+1], dtype=np.int64)
+        r = rankdata(data)
+        assert_array_equal(r, [1.0, 2.0])
+
+        data = np.array([2**60, -2**60+1], dtype=np.int64)
+        r = rankdata(data)
+        assert_array_equal(r, [2.0, 1.0])
+
+    def test_big_tie(self):
+        for n in [10000, 100000, 1000000]:
+            data = np.ones(n, dtype=int)
+            r = rankdata(data)
+            expected_rank = 0.5 * (n + 1)
+            assert_array_equal(r, expected_rank * data,
+                               "test failed with n=%d" % n)
+
+    def test_axis(self):
+        data = [[0, 2, 1],
+                [4, 2, 2]]
+        expected0 = [[1., 1.5, 1.],
+                     [2., 1.5, 2.]]
+        r0 = rankdata(data, axis=0)
+        assert_array_equal(r0, expected0)
+        expected1 = [[1., 3., 2.],
+                     [3., 1.5, 1.5]]
+        r1 = rankdata(data, axis=1)
+        assert_array_equal(r1, expected1)
+
+    methods = ["average", "min", "max", "dense", "ordinal"]
+    dtypes = [np.float64] + [np_long]*4
+
+    @pytest.mark.parametrize("axis", [0, 1])
+    @pytest.mark.parametrize("method, dtype", zip(methods, dtypes))
+    def test_size_0_axis(self, axis, method, dtype):
+        shape = (3, 0)
+        data = np.zeros(shape)
+        r = rankdata(data, method=method, axis=axis)
+        assert_equal(r.shape, shape)
+        assert_equal(r.dtype, dtype)
+
+    @pytest.mark.parametrize('axis', range(3))
+    @pytest.mark.parametrize('method', methods)
+    def test_nan_policy_omit_3d(self, axis, method):
+        shape = (20, 21, 22)
+        rng = np.random.RandomState(23983242)
+
+        a = rng.random(size=shape)
+        i = rng.random(size=shape) < 0.4
+        j = rng.random(size=shape) < 0.1
+        k = rng.random(size=shape) < 0.1
+        a[i] = np.nan
+        a[j] = -np.inf
+        a[k] - np.inf
+
+        def rank_1d_omit(a, method):
+            out = np.zeros_like(a)
+            i = np.isnan(a)
+            a_compressed = a[~i]
+            res = rankdata(a_compressed, method)
+            out[~i] = res
+            out[i] = np.nan
+            return out
+
+        def rank_omit(a, method, axis):
+            return np.apply_along_axis(lambda a: rank_1d_omit(a, method),
+                                       axis, a)
+
+        res = rankdata(a, method, axis=axis, nan_policy='omit')
+        res0 = rank_omit(a, method, axis=axis)
+
+        assert_array_equal(res, res0)
+
+    def test_nan_policy_2d_axis_none(self):
+        # 2 2d-array test with axis=None
+        data = [[0, np.nan, 3],
+                [4, 2, np.nan],
+                [1, 2, 2]]
+        assert_array_equal(rankdata(data, axis=None, nan_policy='omit'),
+                           [1., np.nan, 6., 7., 4., np.nan, 2., 4., 4.])
+        assert_array_equal(rankdata(data, axis=None, nan_policy='propagate'),
+                           [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan,
+                            np.nan, np.nan, np.nan])
+
+    def test_nan_policy_raise(self):
+        # 1 1d-array test
+        data = [0, 2, 3, -2, np.nan, np.nan]
+        with pytest.raises(ValueError, match="The input contains nan"):
+            rankdata(data, nan_policy='raise')
+
+        # 2 2d-array test
+        data = [[0, np.nan, 3],
+                [4, 2, np.nan],
+                [np.nan, 2, 2]]
+
+        with pytest.raises(ValueError, match="The input contains nan"):
+            rankdata(data, axis=0, nan_policy="raise")
+
+        with pytest.raises(ValueError, match="The input contains nan"):
+            rankdata(data, axis=1, nan_policy="raise")
+
+    def test_nan_policy_propagate(self):
+        # 1 1d-array test
+        data = [0, 2, 3, -2, np.nan, np.nan]
+        assert_array_equal(rankdata(data, nan_policy='propagate'),
+                           [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan])
+
+        # 2 2d-array test
+        data = [[0, np.nan, 3],
+                [4, 2, np.nan],
+                [1, 2, 2]]
+        assert_array_equal(rankdata(data, axis=0, nan_policy='propagate'),
+                           [[1, np.nan, np.nan],
+                            [3, np.nan, np.nan],
+                            [2, np.nan, np.nan]])
+        assert_array_equal(rankdata(data, axis=1, nan_policy='propagate'),
+                           [[np.nan, np.nan, np.nan],
+                            [np.nan, np.nan, np.nan],
+                            [1, 2.5, 2.5]])
+
+
+_cases = (
+    # values, method, expected
+    ([], 'average', []),
+    ([], 'min', []),
+    ([], 'max', []),
+    ([], 'dense', []),
+    ([], 'ordinal', []),
+    #
+    ([100], 'average', [1.0]),
+    ([100], 'min', [1.0]),
+    ([100], 'max', [1.0]),
+    ([100], 'dense', [1.0]),
+    ([100], 'ordinal', [1.0]),
+    #
+    ([100, 100, 100], 'average', [2.0, 2.0, 2.0]),
+    ([100, 100, 100], 'min', [1.0, 1.0, 1.0]),
+    ([100, 100, 100], 'max', [3.0, 3.0, 3.0]),
+    ([100, 100, 100], 'dense', [1.0, 1.0, 1.0]),
+    ([100, 100, 100], 'ordinal', [1.0, 2.0, 3.0]),
+    #
+    ([100, 300, 200], 'average', [1.0, 3.0, 2.0]),
+    ([100, 300, 200], 'min', [1.0, 3.0, 2.0]),
+    ([100, 300, 200], 'max', [1.0, 3.0, 2.0]),
+    ([100, 300, 200], 'dense', [1.0, 3.0, 2.0]),
+    ([100, 300, 200], 'ordinal', [1.0, 3.0, 2.0]),
+    #
+    ([100, 200, 300, 200], 'average', [1.0, 2.5, 4.0, 2.5]),
+    ([100, 200, 300, 200], 'min', [1.0, 2.0, 4.0, 2.0]),
+    ([100, 200, 300, 200], 'max', [1.0, 3.0, 4.0, 3.0]),
+    ([100, 200, 300, 200], 'dense', [1.0, 2.0, 3.0, 2.0]),
+    ([100, 200, 300, 200], 'ordinal', [1.0, 2.0, 4.0, 3.0]),
+    #
+    ([100, 200, 300, 200, 100], 'average', [1.5, 3.5, 5.0, 3.5, 1.5]),
+    ([100, 200, 300, 200, 100], 'min', [1.0, 3.0, 5.0, 3.0, 1.0]),
+    ([100, 200, 300, 200, 100], 'max', [2.0, 4.0, 5.0, 4.0, 2.0]),
+    ([100, 200, 300, 200, 100], 'dense', [1.0, 2.0, 3.0, 2.0, 1.0]),
+    ([100, 200, 300, 200, 100], 'ordinal', [1.0, 3.0, 5.0, 4.0, 2.0]),
+    #
+    ([10] * 30, 'ordinal', np.arange(1.0, 31.0)),
+)
+
+
+def test_cases():
+    for values, method, expected in _cases:
+        r = rankdata(values, method=method)
+        assert_array_equal(r, expected)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_relative_risk.py

@@ -0,0 +1,95 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_allclose, assert_equal
+from scipy.stats.contingency import relative_risk
+
+
+# Test just the calculation of the relative risk, including edge
+# cases that result in a relative risk of 0, inf or nan.
+@pytest.mark.parametrize(
+    'exposed_cases, exposed_total, control_cases, control_total, expected_rr',
+    [(1, 4, 3, 8, 0.25 / 0.375),
+     (0, 10, 5, 20, 0),
+     (0, 10, 0, 20, np.nan),
+     (5, 15, 0, 20, np.inf)]
+)
+def test_relative_risk(exposed_cases, exposed_total,
+                       control_cases, control_total, expected_rr):
+    result = relative_risk(exposed_cases, exposed_total,
+                           control_cases, control_total)
+    assert_allclose(result.relative_risk, expected_rr, rtol=1e-13)
+
+
+def test_relative_risk_confidence_interval():
+    result = relative_risk(exposed_cases=16, exposed_total=128,
+                           control_cases=24, control_total=256)
+    rr = result.relative_risk
+    ci = result.confidence_interval(confidence_level=0.95)
+    # The corresponding calculation in R using the epitools package.
+    #
+    # > library(epitools)
+    # > c <- matrix(c(232, 112, 24, 16), nrow=2)
+    # > result <- riskratio(c)
+    # > result$measure
+    #               risk ratio with 95% C.I.
+    # Predictor  estimate     lower    upper
+    #   Exposed1 1.000000        NA       NA
+    #   Exposed2 1.333333 0.7347317 2.419628
+    #
+    # The last line is the result that we want.
+    assert_allclose(rr, 4/3)
+    assert_allclose((ci.low, ci.high), (0.7347317, 2.419628), rtol=5e-7)
+
+
+def test_relative_risk_ci_conflevel0():
+    result = relative_risk(exposed_cases=4, exposed_total=12,
+                           control_cases=5, control_total=30)
+    rr = result.relative_risk
+    assert_allclose(rr, 2.0, rtol=1e-14)
+    ci = result.confidence_interval(0)
+    assert_allclose((ci.low, ci.high), (2.0, 2.0), rtol=1e-12)
+
+
+def test_relative_risk_ci_conflevel1():
+    result = relative_risk(exposed_cases=4, exposed_total=12,
+                           control_cases=5, control_total=30)
+    ci = result.confidence_interval(1)
+    assert_equal((ci.low, ci.high), (0, np.inf))
+
+
+def test_relative_risk_ci_edge_cases_00():
+    result = relative_risk(exposed_cases=0, exposed_total=12,
+                           control_cases=0, control_total=30)
+    assert_equal(result.relative_risk, np.nan)
+    ci = result.confidence_interval()
+    assert_equal((ci.low, ci.high), (np.nan, np.nan))
+
+
+def test_relative_risk_ci_edge_cases_01():
+    result = relative_risk(exposed_cases=0, exposed_total=12,
+                           control_cases=1, control_total=30)
+    assert_equal(result.relative_risk, 0)
+    ci = result.confidence_interval()
+    assert_equal((ci.low, ci.high), (0.0, np.nan))
+
+
+def test_relative_risk_ci_edge_cases_10():
+    result = relative_risk(exposed_cases=1, exposed_total=12,
+                           control_cases=0, control_total=30)
+    assert_equal(result.relative_risk, np.inf)
+    ci = result.confidence_interval()
+    assert_equal((ci.low, ci.high), (np.nan, np.inf))
+
+
+@pytest.mark.parametrize('ec, et, cc, ct', [(0, 0, 10, 20),
+                                            (-1, 10, 1, 5),
+                                            (1, 10, 0, 0),
+                                            (1, 10, -1, 4)])
+def test_relative_risk_bad_value(ec, et, cc, ct):
+    with pytest.raises(ValueError, match="must be an integer not less than"):
+        relative_risk(ec, et, cc, ct)
+
+
+def test_relative_risk_bad_type():
+    with pytest.raises(TypeError, match="must be an integer"):
+        relative_risk(1, 10, 2.0, 40)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_sensitivity_analysis.py

@@ -0,0 +1,301 @@
+import numpy as np
+from numpy.testing import assert_allclose, assert_array_less
+import pytest
+
+from scipy import stats
+from scipy.stats import sobol_indices
+from scipy.stats._resampling import BootstrapResult
+from scipy.stats._sensitivity_analysis import (
+    BootstrapSobolResult, f_ishigami, sample_AB, sample_A_B
+)
+
+
+@pytest.fixture(scope='session')
+def ishigami_ref_indices():
+    """Reference values for Ishigami from Saltelli2007.
+
+    Chapter 4, exercise 5 pages 179-182.
+    """
+    a = 7.
+    b = 0.1
+
+    var = 0.5 + a**2/8 + b*np.pi**4/5 + b**2*np.pi**8/18
+    v1 = 0.5 + b*np.pi**4/5 + b**2*np.pi**8/50
+    v2 = a**2/8
+    v3 = 0
+    v12 = 0
+    # v13: mistake in the book, see other derivations e.g. in 10.1002/nme.4856
+    v13 = b**2*np.pi**8*8/225
+    v23 = 0
+
+    s_first = np.array([v1, v2, v3])/var
+    s_second = np.array([
+        [0., 0., v13],
+        [v12, 0., v23],
+        [v13, v23, 0.]
+    ])/var
+    s_total = s_first + s_second.sum(axis=1)
+
+    return s_first, s_total
+
+
+def f_ishigami_vec(x):
+    """Output of shape (2, n)."""
+    res = f_ishigami(x)
+    return res, res
+
+
+class TestSobolIndices:
+
+    dists = [
+        stats.uniform(loc=-np.pi, scale=2*np.pi)  # type: ignore[attr-defined]
+    ] * 3
+
+    def test_sample_AB(self):
+        # (d, n)
+        A = np.array(
+            [[1, 4, 7, 10],
+             [2, 5, 8, 11],
+             [3, 6, 9, 12]]
+        )
+        B = A + 100
+        # (d, d, n)
+        ref = np.array(
+            [[[101, 104, 107, 110],
+              [2, 5, 8, 11],
+              [3, 6, 9, 12]],
+             [[1, 4, 7, 10],
+              [102, 105, 108, 111],
+              [3, 6, 9, 12]],
+             [[1, 4, 7, 10],
+              [2, 5, 8, 11],
+              [103, 106, 109, 112]]]
+        )
+        AB = sample_AB(A=A, B=B)
+        assert_allclose(AB, ref)
+
+    @pytest.mark.xslow
+    @pytest.mark.xfail_on_32bit("Can't create large array for test")
+    @pytest.mark.parametrize(
+        'func',
+        [f_ishigami, pytest.param(f_ishigami_vec, marks=pytest.mark.slow)],
+        ids=['scalar', 'vector']
+    )
+    def test_ishigami(self, ishigami_ref_indices, func):
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        res = sobol_indices(
+            func=func, n=4096,
+            dists=self.dists,
+            random_state=rng
+        )
+
+        if func.__name__ == 'f_ishigami_vec':
+            ishigami_ref_indices = [
+                    [ishigami_ref_indices[0], ishigami_ref_indices[0]],
+                    [ishigami_ref_indices[1], ishigami_ref_indices[1]]
+            ]
+
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-2)
+        assert_allclose(res.total_order, ishigami_ref_indices[1], atol=1e-2)
+
+        assert res._bootstrap_result is None
+        bootstrap_res = res.bootstrap(n_resamples=99)
+        assert isinstance(bootstrap_res, BootstrapSobolResult)
+        assert isinstance(res._bootstrap_result, BootstrapResult)
+
+        assert res._bootstrap_result.confidence_interval.low.shape[0] == 2
+        assert res._bootstrap_result.confidence_interval.low[1].shape \
+               == res.first_order.shape
+
+        assert bootstrap_res.first_order.confidence_interval.low.shape \
+               == res.first_order.shape
+        assert bootstrap_res.total_order.confidence_interval.low.shape \
+               == res.total_order.shape
+
+        assert_array_less(
+            bootstrap_res.first_order.confidence_interval.low, res.first_order
+        )
+        assert_array_less(
+            res.first_order, bootstrap_res.first_order.confidence_interval.high
+        )
+        assert_array_less(
+            bootstrap_res.total_order.confidence_interval.low, res.total_order
+        )
+        assert_array_less(
+            res.total_order, bootstrap_res.total_order.confidence_interval.high
+        )
+
+        # call again to use previous results and change a param
+        assert isinstance(
+            res.bootstrap(confidence_level=0.9, n_resamples=99),
+            BootstrapSobolResult
+        )
+        assert isinstance(res._bootstrap_result, BootstrapResult)
+
+    def test_func_dict(self, ishigami_ref_indices):
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        n = 4096
+        dists = [
+            stats.uniform(loc=-np.pi, scale=2*np.pi),
+            stats.uniform(loc=-np.pi, scale=2*np.pi),
+            stats.uniform(loc=-np.pi, scale=2*np.pi)
+        ]
+
+        A, B = sample_A_B(n=n, dists=dists, random_state=rng)
+        AB = sample_AB(A=A, B=B)
+
+        func = {
+            'f_A': f_ishigami(A).reshape(1, -1),
+            'f_B': f_ishigami(B).reshape(1, -1),
+            'f_AB': f_ishigami(AB).reshape((3, 1, -1))
+        }
+
+        res = sobol_indices(
+            func=func, n=n,
+            dists=dists,
+            random_state=rng
+        )
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-2)
+
+        res = sobol_indices(
+            func=func, n=n,
+            random_state=rng
+        )
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-2)
+
+    def test_method(self, ishigami_ref_indices):
+        def jansen_sobol(f_A, f_B, f_AB):
+            """Jansen for S and Sobol' for St.
+
+            From Saltelli2010, table 2 formulations (c) and (e)."""
+            var = np.var([f_A, f_B], axis=(0, -1))
+
+            s = (var - 0.5*np.mean((f_B - f_AB)**2, axis=-1)) / var
+            st = np.mean(f_A*(f_A - f_AB), axis=-1) / var
+
+            return s.T, st.T
+
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        res = sobol_indices(
+            func=f_ishigami, n=4096,
+            dists=self.dists,
+            method=jansen_sobol,
+            random_state=rng
+        )
+
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-2)
+        assert_allclose(res.total_order, ishigami_ref_indices[1], atol=1e-2)
+
+        def jansen_sobol_typed(
+            f_A: np.ndarray, f_B: np.ndarray, f_AB: np.ndarray
+        ) -> tuple[np.ndarray, np.ndarray]:
+            return jansen_sobol(f_A, f_B, f_AB)
+
+        _ = sobol_indices(
+            func=f_ishigami, n=8,
+            dists=self.dists,
+            method=jansen_sobol_typed,
+            random_state=rng
+        )
+
+    def test_normalization(self, ishigami_ref_indices):
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        res = sobol_indices(
+            func=lambda x: f_ishigami(x) + 1000, n=4096,
+            dists=self.dists,
+            random_state=rng
+        )
+
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-2)
+        assert_allclose(res.total_order, ishigami_ref_indices[1], atol=1e-2)
+
+    def test_constant_function(self, ishigami_ref_indices):
+
+        def f_ishigami_vec_const(x):
+            """Output of shape (3, n)."""
+            res = f_ishigami(x)
+            return res, res * 0 + 10, res
+
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        res = sobol_indices(
+            func=f_ishigami_vec_const, n=4096,
+            dists=self.dists,
+            random_state=rng
+        )
+
+        ishigami_vec_indices = [
+                [ishigami_ref_indices[0], [0, 0, 0], ishigami_ref_indices[0]],
+                [ishigami_ref_indices[1], [0, 0, 0], ishigami_ref_indices[1]]
+        ]
+
+        assert_allclose(res.first_order, ishigami_vec_indices[0], atol=1e-2)
+        assert_allclose(res.total_order, ishigami_vec_indices[1], atol=1e-2)
+
+    @pytest.mark.xfail_on_32bit("Can't create large array for test")
+    def test_more_converged(self, ishigami_ref_indices):
+        rng = np.random.default_rng(28631265345463262246170309650372465332)
+        res = sobol_indices(
+            func=f_ishigami, n=2**19,  # 524288
+            dists=self.dists,
+            random_state=rng
+        )
+
+        assert_allclose(res.first_order, ishigami_ref_indices[0], atol=1e-4)
+        assert_allclose(res.total_order, ishigami_ref_indices[1], atol=1e-4)
+
+    def test_raises(self):
+
+        message = r"Each distribution in `dists` must have method `ppf`"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=0, func=f_ishigami, dists="uniform")
+
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=0, func=f_ishigami, dists=[lambda x: x])
+
+        message = r"The balance properties of Sobol'"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=7, func=f_ishigami, dists=[stats.uniform()])
+
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=4.1, func=f_ishigami, dists=[stats.uniform()])
+
+        message = r"'toto' is not a valid 'method'"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=0, func=f_ishigami, method='toto')
+
+        message = r"must have the following signature"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=0, func=f_ishigami, method=lambda x: x)
+
+        message = r"'dists' must be defined when 'func' is a callable"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(n=0, func=f_ishigami)
+
+        def func_wrong_shape_output(x):
+            return x.reshape(-1, 1)
+
+        message = r"'func' output should have a shape"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(
+                n=2, func=func_wrong_shape_output, dists=[stats.uniform()]
+            )
+
+        message = r"When 'func' is a dictionary"
+        with pytest.raises(ValueError, match=message):
+            sobol_indices(
+                n=2, func={'f_A': [], 'f_AB': []}, dists=[stats.uniform()]
+            )
+
+        with pytest.raises(ValueError, match=message):
+            # f_B malformed
+            sobol_indices(
+                n=2,
+                func={'f_A': [1, 2], 'f_B': [3], 'f_AB': [5, 6, 7, 8]},
+            )
+
+        with pytest.raises(ValueError, match=message):
+            # f_AB malformed
+            sobol_indices(
+                n=2,
+                func={'f_A': [1, 2], 'f_B': [3, 4], 'f_AB': [5, 6, 7]},
+            )

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_survival.py

@@ -0,0 +1,470 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_equal, assert_allclose
+from scipy import stats
+from scipy.stats import _survival
+
+
+def _kaplan_meier_reference(times, censored):
+    # This is a very straightforward implementation of the Kaplan-Meier
+    # estimator that does almost everything differently from the implementation
+    # in stats.ecdf.
+
+    # Begin by sorting the raw data. Note that the order of death and loss
+    # at a given time matters: death happens first. See [2] page 461:
+    # "These conventions may be paraphrased by saying that deaths recorded as
+    # of an age t are treated as if they occurred slightly before t, and losses
+    # recorded as of an age t are treated as occurring slightly after t."
+    # We implement this by sorting the data first by time, then by `censored`,
+    # (which is 0 when there is a death and 1 when there is only a loss).
+    dtype = [('time', float), ('censored', int)]
+    data = np.array([(t, d) for t, d in zip(times, censored)], dtype=dtype)
+    data = np.sort(data, order=('time', 'censored'))
+    times = data['time']
+    died = np.logical_not(data['censored'])
+
+    m = times.size
+    n = np.arange(m, 0, -1)  # number at risk
+    sf = np.cumprod((n - died) / n)
+
+    # Find the indices of the *last* occurrence of unique times. The
+    # corresponding entries of `times` and `sf` are what we want.
+    _, indices = np.unique(times[::-1], return_index=True)
+    ref_times = times[-indices - 1]
+    ref_sf = sf[-indices - 1]
+    return ref_times, ref_sf
+
+
+class TestSurvival:
+
+    @staticmethod
+    def get_random_sample(rng, n_unique):
+        # generate random sample
+        unique_times = rng.random(n_unique)
+        # convert to `np.int32` to resolve `np.repeat` failure in 32-bit CI
+        repeats = rng.integers(1, 4, n_unique).astype(np.int32)
+        times = rng.permuted(np.repeat(unique_times, repeats))
+        censored = rng.random(size=times.size) > rng.random()
+        sample = stats.CensoredData.right_censored(times, censored)
+        return sample, times, censored
+
+    def test_input_validation(self):
+        message = '`sample` must be a one-dimensional sequence.'
+        with pytest.raises(ValueError, match=message):
+            stats.ecdf([[1]])
+        with pytest.raises(ValueError, match=message):
+            stats.ecdf(1)
+
+        message = '`sample` must not contain nan'
+        with pytest.raises(ValueError, match=message):
+            stats.ecdf([np.nan])
+
+        message = 'Currently, only uncensored and right-censored data...'
+        with pytest.raises(NotImplementedError, match=message):
+            stats.ecdf(stats.CensoredData.left_censored([1], censored=[True]))
+
+        message = 'method` must be one of...'
+        res = stats.ecdf([1, 2, 3])
+        with pytest.raises(ValueError, match=message):
+            res.cdf.confidence_interval(method='ekki-ekki')
+        with pytest.raises(ValueError, match=message):
+            res.sf.confidence_interval(method='shrubbery')
+
+        message = 'confidence_level` must be a scalar between 0 and 1'
+        with pytest.raises(ValueError, match=message):
+            res.cdf.confidence_interval(-1)
+        with pytest.raises(ValueError, match=message):
+            res.sf.confidence_interval([0.5, 0.6])
+
+        message = 'The confidence interval is undefined at some observations.'
+        with pytest.warns(RuntimeWarning, match=message):
+            ci = res.cdf.confidence_interval()
+
+        message = 'Confidence interval bounds do not implement...'
+        with pytest.raises(NotImplementedError, match=message):
+            ci.low.confidence_interval()
+        with pytest.raises(NotImplementedError, match=message):
+            ci.high.confidence_interval()
+
+    def test_edge_cases(self):
+        res = stats.ecdf([])
+        assert_equal(res.cdf.quantiles, [])
+        assert_equal(res.cdf.probabilities, [])
+
+        res = stats.ecdf([1])
+        assert_equal(res.cdf.quantiles, [1])
+        assert_equal(res.cdf.probabilities, [1])
+
+    def test_unique(self):
+        # Example with unique observations; `stats.ecdf` ref. [1] page 80
+        sample = [6.23, 5.58, 7.06, 6.42, 5.20]
+        res = stats.ecdf(sample)
+        ref_x = np.sort(np.unique(sample))
+        ref_cdf = np.arange(1, 6) / 5
+        ref_sf = 1 - ref_cdf
+        assert_equal(res.cdf.quantiles, ref_x)
+        assert_equal(res.cdf.probabilities, ref_cdf)
+        assert_equal(res.sf.quantiles, ref_x)
+        assert_equal(res.sf.probabilities, ref_sf)
+
+    def test_nonunique(self):
+        # Example with non-unique observations; `stats.ecdf` ref. [1] page 82
+        sample = [0, 2, 1, 2, 3, 4]
+        res = stats.ecdf(sample)
+        ref_x = np.sort(np.unique(sample))
+        ref_cdf = np.array([1/6, 2/6, 4/6, 5/6, 1])
+        ref_sf = 1 - ref_cdf
+        assert_equal(res.cdf.quantiles, ref_x)
+        assert_equal(res.cdf.probabilities, ref_cdf)
+        assert_equal(res.sf.quantiles, ref_x)
+        assert_equal(res.sf.probabilities, ref_sf)
+
+    def test_evaluate_methods(self):
+        # Test CDF and SF `evaluate` methods
+        rng = np.random.default_rng(1162729143302572461)
+        sample, _, _ = self.get_random_sample(rng, 15)
+        res = stats.ecdf(sample)
+        x = res.cdf.quantiles
+        xr = x + np.diff(x, append=x[-1]+1)/2  # right shifted points
+
+        assert_equal(res.cdf.evaluate(x), res.cdf.probabilities)
+        assert_equal(res.cdf.evaluate(xr), res.cdf.probabilities)
+        assert_equal(res.cdf.evaluate(x[0]-1), 0)  # CDF starts at 0
+        assert_equal(res.cdf.evaluate([-np.inf, np.inf]), [0, 1])
+
+        assert_equal(res.sf.evaluate(x), res.sf.probabilities)
+        assert_equal(res.sf.evaluate(xr), res.sf.probabilities)
+        assert_equal(res.sf.evaluate(x[0]-1), 1)  # SF starts at 1
+        assert_equal(res.sf.evaluate([-np.inf, np.inf]), [1, 0])
+
+    # ref. [1] page 91
+    t1 = [37, 43, 47, 56, 60, 62, 71, 77, 80, 81]  # times
+    d1 = [0, 0, 1, 1, 0, 0, 0, 1, 1, 1]  # 1 means deaths (not censored)
+    r1 = [1, 1, 0.875, 0.75, 0.75, 0.75, 0.75, 0.5, 0.25, 0]  # reference SF
+
+    # https://sphweb.bumc.bu.edu/otlt/mph-modules/bs/bs704_survival/BS704_Survival5.html
+    t2 = [8, 12, 26, 14, 21, 27, 8, 32, 20, 40]
+    d2 = [1, 1, 1, 1, 1, 1, 0, 0, 0, 0]
+    r2 = [0.9, 0.788, 0.675, 0.675, 0.54, 0.405, 0.27, 0.27, 0.27]
+    t3 = [33, 28, 41, 48, 48, 25, 37, 48, 25, 43]
+    d3 = [1, 1, 1, 0, 0, 0, 0, 0, 0, 0]
+    r3 = [1, 0.875, 0.75, 0.75, 0.6, 0.6, 0.6]
+
+    # https://sphweb.bumc.bu.edu/otlt/mph-modules/bs/bs704_survival/bs704_survival4.html
+    t4 = [24, 3, 11, 19, 24, 13, 14, 2, 18, 17,
+          24, 21, 12, 1, 10, 23, 6, 5, 9, 17]
+    d4 = [0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1]
+    r4 = [0.95, 0.95, 0.897, 0.844, 0.844, 0.844, 0.844, 0.844, 0.844,
+          0.844, 0.76, 0.676, 0.676, 0.676, 0.676, 0.507, 0.507]
+
+    # https://www.real-statistics.com/survival-analysis/kaplan-meier-procedure/confidence-interval-for-the-survival-function/
+    t5 = [3, 5, 8, 10, 5, 5, 8, 12, 15, 14, 2, 11, 10, 9, 12, 5, 8, 11]
+    d5 = [1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1]
+    r5 = [0.944, 0.889, 0.722, 0.542, 0.542, 0.542, 0.361, 0.181, 0.181, 0.181]
+
+    @pytest.mark.parametrize("case", [(t1, d1, r1), (t2, d2, r2), (t3, d3, r3),
+                                      (t4, d4, r4), (t5, d5, r5)])
+    def test_right_censored_against_examples(self, case):
+        # test `ecdf` against other implementations on example problems
+        times, died, ref = case
+        sample = stats.CensoredData.right_censored(times, np.logical_not(died))
+        res = stats.ecdf(sample)
+        assert_allclose(res.sf.probabilities, ref, atol=1e-3)
+        assert_equal(res.sf.quantiles, np.sort(np.unique(times)))
+
+        # test reference implementation against other implementations
+        res = _kaplan_meier_reference(times, np.logical_not(died))
+        assert_equal(res[0], np.sort(np.unique(times)))
+        assert_allclose(res[1], ref, atol=1e-3)
+
+    @pytest.mark.parametrize('seed', [182746786639392128, 737379171436494115,
+                                      576033618403180168, 308115465002673650])
+    def test_right_censored_against_reference_implementation(self, seed):
+        # test `ecdf` against reference implementation on random problems
+        rng = np.random.default_rng(seed)
+        n_unique = rng.integers(10, 100)
+        sample, times, censored = self.get_random_sample(rng, n_unique)
+        res = stats.ecdf(sample)
+        ref = _kaplan_meier_reference(times, censored)
+        assert_allclose(res.sf.quantiles, ref[0])
+        assert_allclose(res.sf.probabilities, ref[1])
+
+        # If all observations are uncensored, the KM estimate should match
+        # the usual estimate for uncensored data
+        sample = stats.CensoredData(uncensored=times)
+        res = _survival._ecdf_right_censored(sample)  # force Kaplan-Meier
+        ref = stats.ecdf(times)
+        assert_equal(res[0], ref.sf.quantiles)
+        assert_allclose(res[1], ref.cdf.probabilities, rtol=1e-14)
+        assert_allclose(res[2], ref.sf.probabilities, rtol=1e-14)
+
+    def test_right_censored_ci(self):
+        # test "greenwood" confidence interval against example 4 (URL above).
+        times, died = self.t4, self.d4
+        sample = stats.CensoredData.right_censored(times, np.logical_not(died))
+        res = stats.ecdf(sample)
+        ref_allowance = [0.096, 0.096, 0.135, 0.162, 0.162, 0.162, 0.162,
+                         0.162, 0.162, 0.162, 0.214, 0.246, 0.246, 0.246,
+                         0.246, 0.341, 0.341]
+
+        sf_ci = res.sf.confidence_interval()
+        cdf_ci = res.cdf.confidence_interval()
+        allowance = res.sf.probabilities - sf_ci.low.probabilities
+
+        assert_allclose(allowance, ref_allowance, atol=1e-3)
+        assert_allclose(sf_ci.low.probabilities,
+                        np.clip(res.sf.probabilities - allowance, 0, 1))
+        assert_allclose(sf_ci.high.probabilities,
+                        np.clip(res.sf.probabilities + allowance, 0, 1))
+        assert_allclose(cdf_ci.low.probabilities,
+                        np.clip(res.cdf.probabilities - allowance, 0, 1))
+        assert_allclose(cdf_ci.high.probabilities,
+                        np.clip(res.cdf.probabilities + allowance, 0, 1))
+
+        # test "log-log" confidence interval against Mathematica
+        # e = {24, 3, 11, 19, 24, 13, 14, 2, 18, 17, 24, 21, 12, 1, 10, 23, 6, 5,
+        #      9, 17}
+        # ci = {1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0}
+        # R = EventData[e, ci]
+        # S = SurvivalModelFit[R]
+        # S["PointwiseIntervals", ConfidenceLevel->0.95,
+        #   ConfidenceTransform->"LogLog"]
+
+        ref_low = [0.694743, 0.694743, 0.647529, 0.591142, 0.591142, 0.591142,
+                   0.591142, 0.591142, 0.591142, 0.591142, 0.464605, 0.370359,
+                   0.370359, 0.370359, 0.370359, 0.160489, 0.160489]
+        ref_high = [0.992802, 0.992802, 0.973299, 0.947073, 0.947073, 0.947073,
+                    0.947073, 0.947073, 0.947073, 0.947073, 0.906422, 0.856521,
+                    0.856521, 0.856521, 0.856521, 0.776724, 0.776724]
+        sf_ci = res.sf.confidence_interval(method='log-log')
+        assert_allclose(sf_ci.low.probabilities, ref_low, atol=1e-6)
+        assert_allclose(sf_ci.high.probabilities, ref_high, atol=1e-6)
+
+    def test_right_censored_ci_example_5(self):
+        # test "exponential greenwood" confidence interval against example 5
+        times, died = self.t5, self.d5
+        sample = stats.CensoredData.right_censored(times, np.logical_not(died))
+        res = stats.ecdf(sample)
+        lower = np.array([0.66639, 0.624174, 0.456179, 0.287822, 0.287822,
+                          0.287822, 0.128489, 0.030957, 0.030957, 0.030957])
+        upper = np.array([0.991983, 0.970995, 0.87378, 0.739467, 0.739467,
+                          0.739467, 0.603133, 0.430365, 0.430365, 0.430365])
+
+        sf_ci = res.sf.confidence_interval(method='log-log')
+        cdf_ci = res.cdf.confidence_interval(method='log-log')
+
+        assert_allclose(sf_ci.low.probabilities, lower, atol=1e-5)
+        assert_allclose(sf_ci.high.probabilities, upper, atol=1e-5)
+        assert_allclose(cdf_ci.low.probabilities, 1-upper, atol=1e-5)
+        assert_allclose(cdf_ci.high.probabilities, 1-lower, atol=1e-5)
+
+        # Test against R's `survival` library `survfit` function, 90%CI
+        # library(survival)
+        # options(digits=16)
+        # time = c(3, 5, 8, 10, 5, 5, 8, 12, 15, 14, 2, 11, 10, 9, 12, 5, 8, 11)
+        # status = c(1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1)
+        # res = survfit(Surv(time, status)
+        # ~1, conf.type = "log-log", conf.int = 0.90)
+        # res$time; res$lower; res$upper
+        low = [0.74366748406861172, 0.68582332289196246, 0.50596835651480121,
+               0.32913131413336727, 0.32913131413336727, 0.32913131413336727,
+               0.15986912028781664, 0.04499539918147757, 0.04499539918147757,
+               0.04499539918147757]
+        high = [0.9890291867238429, 0.9638835422144144, 0.8560366823086629,
+                0.7130167643978450, 0.7130167643978450, 0.7130167643978450,
+                0.5678602982997164, 0.3887616766886558, 0.3887616766886558,
+                0.3887616766886558]
+        sf_ci = res.sf.confidence_interval(method='log-log',
+                                           confidence_level=0.9)
+        assert_allclose(sf_ci.low.probabilities, low)
+        assert_allclose(sf_ci.high.probabilities, high)
+
+        # And with conf.type = "plain"
+        low = [0.8556383113628162, 0.7670478794850761, 0.5485720663578469,
+               0.3441515412527123, 0.3441515412527123, 0.3441515412527123,
+               0.1449184105424544, 0., 0., 0.]
+        high = [1., 1., 0.8958723780865975, 0.7391817920806210,
+                0.7391817920806210, 0.7391817920806210, 0.5773038116797676,
+                0.3642270254596720, 0.3642270254596720, 0.3642270254596720]
+        sf_ci = res.sf.confidence_interval(confidence_level=0.9)
+        assert_allclose(sf_ci.low.probabilities, low)
+        assert_allclose(sf_ci.high.probabilities, high)
+
+    def test_right_censored_ci_nans(self):
+        # test `ecdf` confidence interval on a problem that results in NaNs
+        times, died = self.t1, self.d1
+        sample = stats.CensoredData.right_censored(times, np.logical_not(died))
+        res = stats.ecdf(sample)
+
+        # Reference values generated with Matlab
+        # format long
+        # t = [37 43 47 56 60 62 71 77 80 81];
+        # d = [0 0 1 1 0 0 0 1 1 1];
+        # censored = ~d1;
+        # [f, x, flo, fup] = ecdf(t, 'Censoring', censored, 'Alpha', 0.05);
+        x = [37, 47, 56, 77, 80, 81]
+        flo = [np.nan, 0, 0, 0.052701464070711, 0.337611126231790, np.nan]
+        fup = [np.nan, 0.35417230377, 0.5500569798, 0.9472985359, 1.0, np.nan]
+        i = np.searchsorted(res.cdf.quantiles, x)
+
+        message = "The confidence interval is undefined at some observations"
+        with pytest.warns(RuntimeWarning, match=message):
+            ci = res.cdf.confidence_interval()
+
+        # Matlab gives NaN as the first element of the CIs. Mathematica agrees,
+        # but R's survfit does not. It makes some sense, but it's not what the
+        # formula gives, so skip that element.
+        assert_allclose(ci.low.probabilities[i][1:], flo[1:])
+        assert_allclose(ci.high.probabilities[i][1:], fup[1:])
+
+        # [f, x, flo, fup] = ecdf(t, 'Censoring', censored, 'Function',
+        #                        'survivor', 'Alpha', 0.05);
+        flo = [np.nan, 0.64582769623, 0.449943020228, 0.05270146407, 0, np.nan]
+        fup = [np.nan, 1.0, 1.0, 0.947298535929289, 0.662388873768210, np.nan]
+        i = np.searchsorted(res.cdf.quantiles, x)
+
+        with pytest.warns(RuntimeWarning, match=message):
+            ci = res.sf.confidence_interval()
+
+        assert_allclose(ci.low.probabilities[i][1:], flo[1:])
+        assert_allclose(ci.high.probabilities[i][1:], fup[1:])
+
+        # With the same data, R's `survival` library `survfit` function
+        # doesn't produce the leading NaN
+        # library(survival)
+        # options(digits=16)
+        # time = c(37, 43, 47, 56, 60, 62, 71, 77, 80, 81)
+        # status = c(0, 0, 1, 1, 0, 0, 0, 1, 1, 1)
+        # res = survfit(Surv(time, status)
+        # ~1, conf.type = "plain", conf.int = 0.95)
+        # res$time
+        # res$lower
+        # res$upper
+        low = [1., 1., 0.64582769623233816, 0.44994302022779326,
+               0.44994302022779326, 0.44994302022779326, 0.44994302022779326,
+               0.05270146407071086, 0., np.nan]
+        high = [1., 1., 1., 1., 1., 1., 1., 0.9472985359292891,
+                0.6623888737682101, np.nan]
+        assert_allclose(ci.low.probabilities, low)
+        assert_allclose(ci.high.probabilities, high)
+
+        # It does with conf.type="log-log", as do we
+        with pytest.warns(RuntimeWarning, match=message):
+            ci = res.sf.confidence_interval(method='log-log')
+        low = [np.nan, np.nan, 0.38700001403202522, 0.31480711370551911,
+               0.31480711370551911, 0.31480711370551911, 0.31480711370551911,
+               0.08048821148507734, 0.01049958986680601, np.nan]
+        high = [np.nan, np.nan, 0.9813929658789660, 0.9308983170906275,
+                0.9308983170906275, 0.9308983170906275, 0.9308983170906275,
+                0.8263946341076415, 0.6558775085110887, np.nan]
+        assert_allclose(ci.low.probabilities, low)
+        assert_allclose(ci.high.probabilities, high)
+
+    def test_right_censored_against_uncensored(self):
+        rng = np.random.default_rng(7463952748044886637)
+        sample = rng.integers(10, 100, size=1000)
+        censored = np.zeros_like(sample)
+        censored[np.argmax(sample)] = True
+        res = stats.ecdf(sample)
+        ref = stats.ecdf(stats.CensoredData.right_censored(sample, censored))
+        assert_equal(res.sf.quantiles, ref.sf.quantiles)
+        assert_equal(res.sf._n, ref.sf._n)
+        assert_equal(res.sf._d[:-1], ref.sf._d[:-1])  # difference @ [-1]
+        assert_allclose(res.sf._sf[:-1], ref.sf._sf[:-1], rtol=1e-14)
+
+    def test_plot_iv(self):
+        rng = np.random.default_rng(1769658657308472721)
+        n_unique = rng.integers(10, 100)
+        sample, _, _ = self.get_random_sample(rng, n_unique)
+        res = stats.ecdf(sample)
+
+        try:
+            import matplotlib.pyplot as plt  # noqa: F401
+            res.sf.plot()  # no other errors occur
+        except (ModuleNotFoundError, ImportError):
+            # Avoid trying to call MPL with numpy 2.0-dev, because that fails
+            # too often due to ABI mismatches and is hard to avoid. This test
+            # will work fine again once MPL has done a 2.0-compatible release.
+            if not np.__version__.startswith('2.0.0.dev0'):
+                message = r"matplotlib must be installed to use method `plot`."
+                with pytest.raises(ModuleNotFoundError, match=message):
+                    res.sf.plot()
+
+
+class TestLogRank:
+
+    @pytest.mark.parametrize(
+        "x, y, statistic, pvalue",
+        # Results validate with R
+        # library(survival)
+        # options(digits=16)
+        #
+        # futime_1 <- c(8, 12, 26, 14, 21, 27, 8, 32, 20, 40)
+        # fustat_1 <- c(1, 1, 1, 1, 1, 1, 0, 0, 0, 0)
+        # rx_1 <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
+        #
+        # futime_2 <- c(33, 28, 41, 48, 48, 25, 37, 48, 25, 43)
+        # fustat_2 <- c(1, 1, 1, 0, 0, 0, 0, 0, 0, 0)
+        # rx_2 <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
+        #
+        # futime <- c(futime_1, futime_2)
+        # fustat <- c(fustat_1, fustat_2)
+        # rx <- c(rx_1, rx_2)
+        #
+        # survdiff(formula = Surv(futime, fustat) ~ rx)
+        #
+        # Also check against another library which handle alternatives
+        # library(nph)
+        # logrank.test(futime, fustat, rx, alternative = "two.sided")
+        # res["test"]
+        [(
+              # https://sphweb.bumc.bu.edu/otlt/mph-modules/bs/bs704_survival/BS704_Survival5.html
+              # uncensored, censored
+              [[8, 12, 26, 14, 21, 27], [8, 32, 20, 40]],
+              [[33, 28, 41], [48, 48, 25, 37, 48, 25, 43]],
+              # chi2, ["two-sided", "less", "greater"]
+              6.91598157449,
+              [0.008542873404, 0.9957285632979385, 0.004271436702061537]
+         ),
+         (
+              # https://sphweb.bumc.bu.edu/otlt/mph-modules/bs/bs704_survival/BS704_Survival5.html
+              [[19, 6, 5, 4], [20, 19, 17, 14]],
+              [[16, 21, 7], [21, 15, 18, 18, 5]],
+              0.835004855038,
+              [0.3608293039, 0.8195853480676912, 0.1804146519323088]
+         ),
+         (
+              # Bland, Altman, "The logrank test", BMJ, 2004
+              # https://www.bmj.com/content/328/7447/1073.short
+              [[6, 13, 21, 30, 37, 38, 49, 50, 63, 79, 86, 98, 202, 219],
+               [31, 47, 80, 82, 82, 149]],
+              [[10, 10, 12, 13, 14, 15, 16, 17, 18, 20, 24, 24, 25, 28, 30,
+                33, 35, 37, 40, 40, 46, 48, 76, 81, 82, 91, 112, 181],
+               [34, 40, 70]],
+              7.49659416854,
+              [0.006181578637, 0.003090789318730882, 0.9969092106812691]
+         )]
+    )
+    def test_log_rank(self, x, y, statistic, pvalue):
+        x = stats.CensoredData(uncensored=x[0], right=x[1])
+        y = stats.CensoredData(uncensored=y[0], right=y[1])
+
+        for i, alternative in enumerate(["two-sided", "less", "greater"]):
+            res = stats.logrank(x=x, y=y, alternative=alternative)
+
+            # we return z and use the normal distribution while other framework
+            # return z**2. The p-value are directly comparable, but we have to
+            # square the statistic
+            assert_allclose(res.statistic**2, statistic, atol=1e-10)
+            assert_allclose(res.pvalue, pvalue[i], atol=1e-10)
+
+    def test_raises(self):
+        sample = stats.CensoredData([1, 2])
+
+        msg = r"`y` must be"
+        with pytest.raises(ValueError, match=msg):
+            stats.logrank(x=sample, y=[[1, 2]])
+
+        msg = r"`x` must be"
+        with pytest.raises(ValueError, match=msg):
+            stats.logrank(x=[[1, 2]], y=sample)

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_tukeylambda_stats.py

@@ -0,0 +1,85 @@
+import numpy as np
+from numpy.testing import assert_allclose, assert_equal
+
+from scipy.stats._tukeylambda_stats import (tukeylambda_variance,
+                                            tukeylambda_kurtosis)
+
+
+def test_tukeylambda_stats_known_exact():
+    """Compare results with some known exact formulas."""
+    # Some exact values of the Tukey Lambda variance and kurtosis:
+    # lambda   var      kurtosis
+    #   0     pi**2/3     6/5     (logistic distribution)
+    #  0.5    4 - pi    (5/3 - pi/2)/(pi/4 - 1)**2 - 3
+    #   1      1/3       -6/5     (uniform distribution on (-1,1))
+    #   2      1/12      -6/5     (uniform distribution on (-1/2, 1/2))
+
+    # lambda = 0
+    var = tukeylambda_variance(0)
+    assert_allclose(var, np.pi**2 / 3, atol=1e-12)
+    kurt = tukeylambda_kurtosis(0)
+    assert_allclose(kurt, 1.2, atol=1e-10)
+
+    # lambda = 0.5
+    var = tukeylambda_variance(0.5)
+    assert_allclose(var, 4 - np.pi, atol=1e-12)
+    kurt = tukeylambda_kurtosis(0.5)
+    desired = (5./3 - np.pi/2) / (np.pi/4 - 1)**2 - 3
+    assert_allclose(kurt, desired, atol=1e-10)
+
+    # lambda = 1
+    var = tukeylambda_variance(1)
+    assert_allclose(var, 1.0 / 3, atol=1e-12)
+    kurt = tukeylambda_kurtosis(1)
+    assert_allclose(kurt, -1.2, atol=1e-10)
+
+    # lambda = 2
+    var = tukeylambda_variance(2)
+    assert_allclose(var, 1.0 / 12, atol=1e-12)
+    kurt = tukeylambda_kurtosis(2)
+    assert_allclose(kurt, -1.2, atol=1e-10)
+
+
+def test_tukeylambda_stats_mpmath():
+    """Compare results with some values that were computed using mpmath."""
+    a10 = dict(atol=1e-10, rtol=0)
+    a12 = dict(atol=1e-12, rtol=0)
+    data = [
+        # lambda        variance              kurtosis
+        [-0.1, 4.78050217874253547, 3.78559520346454510],
+        [-0.0649, 4.16428023599895777, 2.52019675947435718],
+        [-0.05, 3.93672267890775277, 2.13129793057777277],
+        [-0.001, 3.30128380390964882, 1.21452460083542988],
+        [0.001, 3.27850775649572176, 1.18560634779287585],
+        [0.03125, 2.95927803254615800, 0.804487555161819980],
+        [0.05, 2.78281053405464501, 0.611604043886644327],
+        [0.0649, 2.65282386754100551, 0.476834119532774540],
+        [1.2, 0.242153920578588346, -1.23428047169049726],
+        [10.0, 0.00095237579757703597, 2.37810697355144933],
+        [20.0, 0.00012195121951131043, 7.37654321002709531],
+    ]
+
+    for lam, var_expected, kurt_expected in data:
+        var = tukeylambda_variance(lam)
+        assert_allclose(var, var_expected, **a12)
+        kurt = tukeylambda_kurtosis(lam)
+        assert_allclose(kurt, kurt_expected, **a10)
+
+    # Test with vector arguments (most of the other tests are for single
+    # values).
+    lam, var_expected, kurt_expected = zip(*data)
+    var = tukeylambda_variance(lam)
+    assert_allclose(var, var_expected, **a12)
+    kurt = tukeylambda_kurtosis(lam)
+    assert_allclose(kurt, kurt_expected, **a10)
+
+
+def test_tukeylambda_stats_invalid():
+    """Test values of lambda outside the domains of the functions."""
+    lam = [-1.0, -0.5]
+    var = tukeylambda_variance(lam)
+    assert_equal(var, np.array([np.nan, np.inf]))
+
+    lam = [-1.0, -0.25]
+    kurt = tukeylambda_kurtosis(lam)
+    assert_equal(kurt, np.array([np.nan, np.inf]))

.CondaPkg/env/Lib/site-packages/scipy/stats/tests/test_variation.py

@@ -0,0 +1,213 @@
+import math
+
+import numpy as np
+import pytest
+from numpy.testing import suppress_warnings
+
+from scipy.stats import variation
+from scipy._lib._util import AxisError
+from scipy.conftest import array_api_compatible
+from scipy._lib._array_api import xp_assert_equal, xp_assert_close, is_numpy
+from scipy.stats._axis_nan_policy import (too_small_nd_omit, too_small_nd_not_omit,
+                                          SmallSampleWarning)
+
+pytestmark = [array_api_compatible, pytest.mark.usefixtures("skip_xp_backends")]
+skip_xp_backends = pytest.mark.skip_xp_backends
+
+
+class TestVariation:
+    """
+    Test class for scipy.stats.variation
+    """
+
+    def test_ddof(self, xp):
+        x = xp.arange(9.0)
+        xp_assert_close(variation(x, ddof=1), xp.asarray(math.sqrt(60/8)/4))
+
+    @pytest.mark.parametrize('sgn', [1, -1])
+    def test_sign(self, sgn, xp):
+        x = xp.asarray([1., 2., 3., 4., 5.])
+        v = variation(sgn*x)
+        expected = xp.asarray(sgn*math.sqrt(2)/3)
+        xp_assert_close(v, expected, rtol=1e-10)
+
+    def test_scalar(self, xp):
+        # A scalar is treated like a 1-d sequence with length 1.
+        xp_assert_equal(variation(4.0), 0.0)
+
+    @pytest.mark.parametrize('nan_policy, expected',
+                             [('propagate', np.nan),
+                              ('omit', np.sqrt(20/3)/4)])
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_variation_nan(self, nan_policy, expected, xp):
+        x = xp.arange(10.)
+        x[9] = xp.nan
+        xp_assert_close(variation(x, nan_policy=nan_policy), expected)
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_nan_policy_raise(self, xp):
+        x = xp.asarray([1.0, 2.0, xp.nan, 3.0])
+        with pytest.raises(ValueError, match='input contains nan'):
+            variation(x, nan_policy='raise')
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_bad_nan_policy(self, xp):
+        with pytest.raises(ValueError, match='must be one of'):
+            variation([1, 2, 3], nan_policy='foobar')
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`keepdims` only supports NumPy backend'])
+    def test_keepdims(self, xp):
+        x = xp.reshape(xp.arange(10), (2, 5))
+        y = variation(x, axis=1, keepdims=True)
+        expected = np.array([[np.sqrt(2)/2],
+                             [np.sqrt(2)/7]])
+        xp_assert_close(y, expected)
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`keepdims` only supports NumPy backend'])
+    @pytest.mark.parametrize('axis, expected',
+                             [(0, np.empty((1, 0))),
+                              (1, np.full((5, 1), fill_value=np.nan))])
+    def test_keepdims_size0(self, axis, expected, xp):
+        x = xp.zeros((5, 0))
+        if axis == 1:
+            with pytest.warns(SmallSampleWarning, match=too_small_nd_not_omit):
+                y = variation(x, axis=axis, keepdims=True)
+        else:
+            y = variation(x, axis=axis, keepdims=True)
+        xp_assert_equal(y, expected)
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`keepdims` only supports NumPy backend'])
+    @pytest.mark.parametrize('incr, expected_fill', [(0, np.inf), (1, np.nan)])
+    def test_keepdims_and_ddof_eq_len_plus_incr(self, incr, expected_fill, xp):
+        x = xp.asarray([[1, 1, 2, 2], [1, 2, 3, 3]])
+        y = variation(x, axis=1, ddof=x.shape[1] + incr, keepdims=True)
+        xp_assert_equal(y, xp.full((2, 1), fill_value=expected_fill))
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_propagate_nan(self, xp):
+        # Check that the shape of the result is the same for inputs
+        # with and without nans, cf gh-5817
+        a = xp.reshape(xp.arange(8, dtype=float), (2, -1))
+        a[1, 0] = xp.nan
+        v = variation(a, axis=1, nan_policy="propagate")
+        xp_assert_close(v, [math.sqrt(5/4)/1.5, xp.nan], atol=1e-15)
+
+    @skip_xp_backends(np_only=True, reasons=['Python list input uses NumPy backend'])
+    def test_axis_none(self, xp):
+        # Check that `variation` computes the result on the flattened
+        # input when axis is None.
+        y = variation([[0, 1], [2, 3]], axis=None)
+        xp_assert_close(y, math.sqrt(5/4)/1.5)
+
+    def test_bad_axis(self, xp):
+        # Check that an invalid axis raises np.exceptions.AxisError.
+        x = xp.asarray([[1, 2, 3], [4, 5, 6]])
+        with pytest.raises((AxisError, IndexError)):
+            variation(x, axis=10)
+
+    def test_mean_zero(self, xp):
+        # Check that `variation` returns inf for a sequence that is not
+        # identically zero but whose mean is zero.
+        x = xp.asarray([10., -3., 1., -4., -4.])
+        y = variation(x)
+        xp_assert_equal(y, xp.asarray(xp.inf))
+
+        x2 = xp.stack([x, -10.*x])
+        y2 = variation(x2, axis=1)
+        xp_assert_equal(y2, xp.asarray([xp.inf, xp.inf]))
+
+    @pytest.mark.parametrize('x', [[0.]*5, [1, 2, np.inf, 9]])
+    def test_return_nan(self, x, xp):
+        x = xp.asarray(x)
+        # Test some cases where `variation` returns nan.
+        y = variation(x)
+        xp_assert_equal(y, xp.asarray(xp.nan, dtype=x.dtype))
+
+    @pytest.mark.parametrize('axis, expected',
+                             [(0, []), (1, [np.nan]*3), (None, np.nan)])
+    def test_2d_size_zero_with_axis(self, axis, expected, xp):
+        x = xp.empty((3, 0))
+        with suppress_warnings() as sup:
+            # torch
+            sup.filter(UserWarning, "std*")
+            if axis != 0:
+                if is_numpy(xp):
+                    with pytest.warns(SmallSampleWarning, match="See documentation..."):
+                        y = variation(x, axis=axis)
+                else:
+                    y = variation(x, axis=axis)
+            else:
+                y = variation(x, axis=axis)
+        xp_assert_equal(y, xp.asarray(expected))
+
+    def test_neg_inf(self, xp):
+        # Edge case that produces -inf: ddof equals the number of non-nan
+        # values, the values are not constant, and the mean is negative.
+        x1 = xp.asarray([-3., -5.])
+        xp_assert_equal(variation(x1, ddof=2), xp.asarray(-xp.inf))
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_neg_inf_nan(self, xp):
+        x2 = xp.asarray([[xp.nan, 1, -10, xp.nan],
+                         [-20, -3, xp.nan, xp.nan]])
+        xp_assert_equal(variation(x2, axis=1, ddof=2, nan_policy='omit'),
+                        [-xp.inf, -xp.inf])
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    @pytest.mark.parametrize("nan_policy", ['propagate', 'omit'])
+    def test_combined_edge_cases(self, nan_policy, xp):
+        x = xp.array([[0, 10, xp.nan, 1],
+                      [0, -5, xp.nan, 2],
+                      [0, -5, xp.nan, 3]])
+        if nan_policy == 'omit':
+            with pytest.warns(SmallSampleWarning, match=too_small_nd_omit):
+                y = variation(x, axis=0, nan_policy=nan_policy)
+        else:
+            y = variation(x, axis=0, nan_policy=nan_policy)
+        xp_assert_close(y, [xp.nan, xp.inf, xp.nan, math.sqrt(2/3)/2])
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    @pytest.mark.parametrize(
+        'ddof, expected',
+        [(0, [np.sqrt(1/6), np.sqrt(5/8), np.inf, 0, np.nan, 0.0, np.nan]),
+         (1, [0.5, np.sqrt(5/6), np.inf, 0, np.nan, 0, np.nan]),
+         (2, [np.sqrt(0.5), np.sqrt(5/4), np.inf, np.nan, np.nan, 0, np.nan])]
+    )
+    def test_more_nan_policy_omit_tests(self, ddof, expected, xp):
+        # The slightly strange formatting in the follow array is my attempt to
+        # maintain a clean tabular arrangement of the data while satisfying
+        # the demands of pycodestyle.  Currently, E201 and E241 are not
+        # disabled by the `noqa` annotation.
+        nan = xp.nan
+        x = xp.asarray([[1.0, 2.0, nan, 3.0],
+                        [0.0, 4.0, 3.0, 1.0],
+                        [nan, -.5, 0.5, nan],
+                        [nan, 9.0, 9.0, nan],
+                        [nan, nan, nan, nan],
+                        [3.0, 3.0, 3.0, 3.0],
+                        [0.0, 0.0, 0.0, 0.0]])
+        with pytest.warns(SmallSampleWarning, match=too_small_nd_omit):
+            v = variation(x, axis=1, ddof=ddof, nan_policy='omit')
+        xp_assert_close(v, expected)
+
+    @skip_xp_backends(np_only=True,
+                      reasons=['`nan_policy` only supports NumPy backend'])
+    def test_variation_ddof(self, xp):
+        # test variation with delta degrees of freedom
+        # regression test for gh-13341
+        a = xp.asarray([1., 2., 3., 4., 5.])
+        nan_a = xp.asarray([1, 2, 3, xp.nan, 4, 5, xp.nan])
+        y = variation(a, ddof=1)
+        nan_y = variation(nan_a, nan_policy="omit", ddof=1)
+        xp_assert_close(y, math.sqrt(5/2)/3)
+        assert y == nan_y