import numpy as np import numpy.testing as npt import pytest from pytest import raises as assert_raises from scipy.integrate import IntegrationWarning import itertools 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_entropy_vect_scale, check_edge_support, check_named_args, check_random_state_property, check_meth_dtype, check_ppf_dtype, check_cmplx_deriv, check_pickling, check_rvs_broadcast, check_freezing, check_deprecation_warning_gh5982_moment, check_deprecation_warning_gh5982_interval) from scipy.stats._distr_params import distcont from scipy.stats._distn_infrastructure import rv_continuous_frozen """ Test all continuous distributions. Parameters were chosen for those distributions that pass the Kolmogorov-Smirnov test. This provides safe parameters for each distributions so that we can perform further testing of class methods. These tests currently check only/mostly for serious errors and exceptions, not for numerically exact results. """ # Note that you need to add new distributions you want tested # to _distr_params DECIMAL = 5 # specify the precision of the tests # increased from 0 to 5 # For skipping test_cont_basic distslow = ['recipinvgauss', 'vonmises', 'kappa4', 'vonmises_line', 'gausshyper', 'norminvgauss', 'geninvgauss', 'genhyperbolic', 'truncnorm', 'truncweibull_min'] # distxslow are sorted by speed (very slow to slow) distxslow = ['studentized_range', 'kstwo', 'ksone', 'wrapcauchy', 'genexpon'] # For skipping test_moments, which is already marked slow distxslow_test_moments = ['studentized_range', 'vonmises', 'vonmises_line', 'ksone', 'kstwo', 'recipinvgauss', 'genexpon'] # skip check_fit_args (test is slow) skip_fit_test_mle = ['exponpow', 'exponweib', 'gausshyper', 'genexpon', 'halfgennorm', 'gompertz', 'johnsonsb', 'johnsonsu', 'kappa4', 'ksone', 'kstwo', 'kstwobign', 'mielke', 'ncf', 'nct', 'powerlognorm', 'powernorm', 'recipinvgauss', 'trapezoid', 'vonmises', 'vonmises_line', 'levy_stable', 'rv_histogram_instance', 'studentized_range'] # these were really slow in `test_fit`.py. # note that this list is used to skip both fit_test and fit_fix tests slow_fit_test_mm = ['argus', 'exponpow', 'exponweib', 'gausshyper', 'genexpon', 'genhalflogistic', 'halfgennorm', 'gompertz', 'johnsonsb', 'kappa4', 'kstwobign', 'recipinvgauss', 'trapezoid', 'truncexpon', 'vonmises', 'vonmises_line', 'studentized_range'] # pearson3 fails due to something weird # the first list fails due to non-finite distribution moments encountered # most of the rest fail due to integration warnings # pearson3 is overriden as not implemented due to gh-11746 fail_fit_test_mm = (['alpha', 'betaprime', 'bradford', 'burr', 'burr12', 'cauchy', 'crystalball', 'f', 'fisk', 'foldcauchy', 'genextreme', 'genpareto', 'halfcauchy', 'invgamma', 'kappa3', 'levy', 'levy_l', 'loglaplace', 'lomax', 'mielke', 'nakagami', 'ncf', 'skewcauchy', 't', 'tukeylambda', 'invweibull'] + ['genhyperbolic', 'johnsonsu', 'ksone', 'kstwo', 'nct', 'pareto', 'powernorm', 'powerlognorm'] + ['pearson3']) skip_fit_test = {"MLE": skip_fit_test_mle, "MM": slow_fit_test_mm + fail_fit_test_mm} # skip check_fit_args_fix (test is slow) skip_fit_fix_test_mle = ['burr', 'exponpow', 'exponweib', 'gausshyper', 'genexpon', 'halfgennorm', 'gompertz', 'johnsonsb', 'johnsonsu', 'kappa4', 'ksone', 'kstwo', 'kstwobign', 'levy_stable', 'mielke', 'ncf', 'ncx2', 'powerlognorm', 'powernorm', 'rdist', 'recipinvgauss', 'trapezoid', 'vonmises', 'vonmises_line', 'studentized_range'] # the first list fails due to non-finite distribution moments encountered # most of the rest fail due to integration warnings # pearson3 is overriden as not implemented due to gh-11746 fail_fit_fix_test_mm = (['alpha', 'betaprime', 'burr', 'burr12', 'cauchy', 'crystalball', 'f', 'fisk', 'foldcauchy', 'genextreme', 'genpareto', 'halfcauchy', 'invgamma', 'kappa3', 'levy', 'levy_l', 'loglaplace', 'lomax', 'mielke', 'nakagami', 'ncf', 'nct', 'skewcauchy', 't', 'truncpareto', 'invweibull'] + ['genhyperbolic', 'johnsonsu', 'ksone', 'kstwo', 'pareto', 'powernorm', 'powerlognorm'] + ['pearson3']) skip_fit_fix_test = {"MLE": skip_fit_fix_test_mle, "MM": slow_fit_test_mm + fail_fit_fix_test_mm} # These distributions fail the complex derivative test below. # Here 'fail' mean produce wrong results and/or raise exceptions, depending # on the implementation details of corresponding special functions. # cf https://github.com/scipy/scipy/pull/4979 for a discussion. fails_cmplx = set(['argus', 'beta', 'betaprime', 'chi', 'chi2', 'cosine', 'dgamma', 'dweibull', 'erlang', 'f', 'gamma', 'gausshyper', 'gengamma', 'genhyperbolic', 'geninvgauss', 'gennorm', 'genpareto', 'halfgennorm', 'invgamma', 'ksone', 'kstwo', 'kstwobign', 'levy_l', 'loggamma', 'logistic', 'loguniform', 'maxwell', 'nakagami', 'ncf', 'nct', 'ncx2', 'norminvgauss', 'pearson3', 'rdist', 'reciprocal', 'rice', 'skewnorm', 't', 'truncweibull_min', 'tukeylambda', 'vonmises', 'vonmises_line', 'rv_histogram_instance', 'truncnorm', 'studentized_range']) # rv_histogram instances, with uniform and non-uniform bins; # stored as (dist, arg) tuples for cases_test_cont_basic # and cases_test_moments. histogram_test_instances = [] case1 = {'a': [1, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9], 'bins': 8} # equal width bins case2 = {'a': [1, 1], 'bins': [0, 1, 10]} # unequal width bins for case, density in itertools.product([case1, case2], [True, False]): _hist = np.histogram(**case, density=density) _rv_hist = stats.rv_histogram(_hist, density=density) histogram_test_instances.append((_rv_hist, tuple())) def cases_test_cont_basic(): for distname, arg in distcont[:] + histogram_test_instances: if distname == 'levy_stable': continue elif distname in distslow: yield pytest.param(distname, arg, marks=pytest.mark.slow) elif distname in distxslow: yield pytest.param(distname, arg, marks=pytest.mark.xslow) else: yield distname, arg @pytest.mark.filterwarnings('ignore::RuntimeWarning') @pytest.mark.parametrize('distname,arg', cases_test_cont_basic()) @pytest.mark.parametrize('sn, n_fit_samples', [(500, 200)]) def test_cont_basic(distname, arg, sn, n_fit_samples): # this test skips slow distributions try: distfn = getattr(stats, distname) except TypeError: distfn = distname distname = 'rv_histogram_instance' rng = np.random.RandomState(765456) rvs = distfn.rvs(size=sn, *arg, random_state=rng) m, v = distfn.stats(*arg) if distname not in {'laplace_asymmetric'}: check_sample_meanvar_(m, v, rvs) check_cdf_ppf(distfn, arg, distname) check_sf_isf(distfn, arg, distname) check_pdf(distfn, arg, distname) check_pdf_logpdf(distfn, arg, distname) check_pdf_logpdf_at_endpoints(distfn, arg, distname) check_cdf_logcdf(distfn, arg, distname) check_sf_logsf(distfn, arg, distname) check_ppf_broadcast(distfn, arg, distname) check_deprecation_warning_gh5982_moment(distfn, arg, distname) check_deprecation_warning_gh5982_interval(distfn, arg, distname) alpha = 0.01 if distname == 'rv_histogram_instance': check_distribution_rvs(distfn.cdf, arg, alpha, rvs) elif distname != 'geninvgauss': # skip kstest for geninvgauss since cdf is too slow; see test for # rv generation in TestGenInvGauss in test_distributions.py check_distribution_rvs(distname, arg, alpha, rvs) locscale_defaults = (0, 1) meths = [distfn.pdf, distfn.logpdf, distfn.cdf, distfn.logcdf, distfn.logsf] # make sure arguments are within support spec_x = {'weibull_max': -0.5, 'levy_l': -0.5, 'pareto': 1.5, 'truncpareto': 3.2, 'tukeylambda': 0.3, 'rv_histogram_instance': 5.0} x = spec_x.get(distname, 0.5) if distname == 'invweibull': arg = (1,) elif distname == 'ksone': arg = (3,) check_named_args(distfn, x, arg, locscale_defaults, meths) check_random_state_property(distfn, arg) check_pickling(distfn, arg) check_freezing(distfn, arg) # Entropy if distname not in ['kstwobign', 'kstwo', 'ncf']: check_entropy(distfn, arg, distname) if distfn.numargs == 0: check_vecentropy(distfn, arg) if (distfn.__class__._entropy != stats.rv_continuous._entropy and distname != 'vonmises'): check_private_entropy(distfn, arg, stats.rv_continuous) with npt.suppress_warnings() as sup: sup.filter(IntegrationWarning, "The occurrence of roundoff error") sup.filter(IntegrationWarning, "Extremely bad integrand") sup.filter(RuntimeWarning, "invalid value") check_entropy_vect_scale(distfn, arg) check_retrieving_support(distfn, arg) check_edge_support(distfn, arg) check_meth_dtype(distfn, arg, meths) check_ppf_dtype(distfn, arg) if distname not in fails_cmplx: check_cmplx_deriv(distfn, arg) if distname != 'truncnorm': check_ppf_private(distfn, arg, distname) for method in ["MLE", "MM"]: if distname not in skip_fit_test[method]: check_fit_args(distfn, arg, rvs[:n_fit_samples], method) if distname not in skip_fit_fix_test[method]: check_fit_args_fix(distfn, arg, rvs[:n_fit_samples], method) @pytest.mark.parametrize('distname,arg', cases_test_cont_basic()) def test_rvs_scalar(distname, arg): # rvs should return a scalar when given scalar arguments (gh-12428) try: distfn = getattr(stats, distname) except TypeError: distfn = distname distname = 'rv_histogram_instance' assert np.isscalar(distfn.rvs(*arg)) assert np.isscalar(distfn.rvs(*arg, size=())) assert np.isscalar(distfn.rvs(*arg, size=None)) def test_levy_stable_random_state_property(): # levy_stable only implements rvs(), so it is skipped in the # main loop in test_cont_basic(). Here we apply just the test # check_random_state_property to levy_stable. check_random_state_property(stats.levy_stable, (0.5, 0.1)) def cases_test_moments(): fail_normalization = set() fail_higher = set(['ncf']) for distname, arg in distcont[:] + histogram_test_instances: if distname == 'levy_stable': continue if distname in distxslow_test_moments: yield pytest.param(distname, arg, True, True, True, marks=pytest.mark.xslow(reason="too slow")) continue cond1 = distname not in fail_normalization cond2 = distname not in fail_higher marks = list() # Currently unused, `marks` can be used to add a timeout to a test of # a specific distribution. For example, this shows how a timeout could # be added for the 'skewnorm' distribution: # # marks = list() # if distname == 'skewnorm': # marks.append(pytest.mark.timeout(300)) yield pytest.param(distname, arg, cond1, cond2, False, marks=marks) if not cond1 or not cond2: # Run the distributions that have issues twice, once skipping the # not_ok parts, once with the not_ok parts but marked as knownfail yield pytest.param(distname, arg, True, True, True, marks=[pytest.mark.xfail] + marks) @pytest.mark.slow @pytest.mark.parametrize('distname,arg,normalization_ok,higher_ok,' 'is_xfailing', cases_test_moments()) def test_moments(distname, arg, normalization_ok, higher_ok, is_xfailing): try: distfn = getattr(stats, distname) except TypeError: distfn = distname distname = 'rv_histogram_instance' with npt.suppress_warnings() as sup: sup.filter(IntegrationWarning, "The integral is probably divergent, or slowly convergent.") sup.filter(IntegrationWarning, "The maximum number of subdivisions.") if is_xfailing: sup.filter(IntegrationWarning) m, v, s, k = distfn.stats(*arg, moments='mvsk') with np.errstate(all="ignore"): if normalization_ok: check_normalization(distfn, arg, distname) if higher_ok: check_mean_expect(distfn, arg, m, distname) check_skew_expect(distfn, arg, m, v, s, distname) check_var_expect(distfn, arg, m, v, distname) check_kurt_expect(distfn, arg, m, v, k, distname) check_moment(distfn, arg, m, v, distname) @pytest.mark.parametrize('dist,shape_args', distcont) def test_rvs_broadcast(dist, shape_args): if dist in ['gausshyper', 'genexpon', 'studentized_range']: pytest.skip("too slow") # 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 ['argus', 'betaprime', 'dgamma', 'dweibull', 'exponnorm', 'genhyperbolic', 'geninvgauss', 'levy_stable', 'nct', 'norminvgauss', 'rice', 'skewnorm', 'semicircular', 'gennorm', 'loggamma'] distfunc = getattr(stats, dist) loc = np.zeros(2) scale = np.ones((3, 1)) nargs = distfunc.numargs allargs = [] bshape = [3, 2] # Generate shape parameter arguments... for k in range(nargs): shp = (k + 4,) + (1,)*(k + 2) allargs.append(shape_args[k]*np.ones(shp)) bshape.insert(0, k + 4) allargs.extend([loc, scale]) # 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, 'd') # Expected values of the SF, CDF, PDF were computed using # mpmath with mpmath.mp.dps = 50 and output at 20: # # def ks(x, n): # x = mpmath.mpf(x) # logp = -mpmath.power(6.0*n*x+1.0, 2)/18.0/n # sf, cdf = mpmath.exp(logp), -mpmath.expm1(logp) # pdf = (6.0*n*x+1.0) * 2 * sf/3 # print(mpmath.nstr(sf, 20), mpmath.nstr(cdf, 20), mpmath.nstr(pdf, 20)) # # Tests use 1/n < x < 1-1/n and n > 1e6 to use the asymptotic computation. # Larger x has a smaller sf. @pytest.mark.parametrize('x,n,sf,cdf,pdf,rtol', [(2.0e-5, 1000000000, 0.44932297307934442379, 0.55067702692065557621, 35946.137394996276407, 5e-15), (2.0e-9, 1000000000, 0.99999999061111115519, 9.3888888448132728224e-9, 8.6666665852962971765, 5e-14), (5.0e-4, 1000000000, 7.1222019433090374624e-218, 1.0, 1.4244408634752704094e-211, 5e-14)]) def test_gh17775_regression(x, n, sf, cdf, pdf, rtol): # Regression test for gh-17775. In scipy 1.9.3 and earlier, # these test would fail. # # KS one asymptotic sf ~ e^(-(6nx+1)^2 / 18n) # Given a large 32-bit integer n, 6n will overflow in the c implementation. # Example of broken behaviour: # ksone.sf(2.0e-5, 1000000000) == 0.9374359693473666 ks = stats.ksone vals = np.array([ks.sf(x, n), ks.cdf(x, n), ks.pdf(x, n)]) expected = np.array([sf, cdf, pdf]) npt.assert_allclose(vals, expected, rtol=rtol) # The sf+cdf must sum to 1.0. npt.assert_equal(vals[0] + vals[1], 1.0) # Check inverting the (potentially very small) sf (uses a lower tolerance) npt.assert_allclose([ks.isf(sf, n)], [x], rtol=1e-8) def test_rvs_gh2069_regression(): # Regression tests for gh-2069. In scipy 0.17 and earlier, # these tests would fail. # # A typical example of the broken behavior: # >>> norm.rvs(loc=np.zeros(5), scale=np.ones(5)) # array([-2.49613705, -2.49613705, -2.49613705, -2.49613705, -2.49613705]) rng = np.random.RandomState(123) vals = stats.norm.rvs(loc=np.zeros(5), scale=1, random_state=rng) d = np.diff(vals) npt.assert_(np.all(d != 0), "All the values are equal, but they shouldn't be!") vals = stats.norm.rvs(loc=0, scale=np.ones(5), random_state=rng) d = np.diff(vals) npt.assert_(np.all(d != 0), "All the values are equal, but they shouldn't be!") vals = stats.norm.rvs(loc=np.zeros(5), scale=np.ones(5), random_state=rng) d = np.diff(vals) npt.assert_(np.all(d != 0), "All the values are equal, but they shouldn't be!") vals = stats.norm.rvs(loc=np.array([[0], [0]]), scale=np.ones(5), random_state=rng) d = np.diff(vals.ravel()) npt.assert_(np.all(d != 0), "All the values are equal, but they shouldn't be!") assert_raises(ValueError, stats.norm.rvs, [[0, 0], [0, 0]], [[1, 1], [1, 1]], 1) assert_raises(ValueError, stats.gamma.rvs, [2, 3, 4, 5], 0, 1, (2, 2)) assert_raises(ValueError, stats.gamma.rvs, [1, 1, 1, 1], [0, 0, 0, 0], [[1], [2]], (4,)) def test_nomodify_gh9900_regression(): # Regression test for gh-9990 # Prior to gh-9990, calls to stats.truncnorm._cdf() use what ever was # set inside the stats.truncnorm instance during stats.truncnorm.cdf(). # This could cause issues wth multi-threaded code. # Since then, the calls to cdf() are not permitted to modify the global # stats.truncnorm instance. tn = stats.truncnorm # Use the right-half truncated normal # Check that the cdf and _cdf return the same result. npt.assert_almost_equal(tn.cdf(1, 0, np.inf), 0.6826894921370859) npt.assert_almost_equal(tn._cdf([1], [0], [np.inf]), 0.6826894921370859) # Now use the left-half truncated normal npt.assert_almost_equal(tn.cdf(-1, -np.inf, 0), 0.31731050786291415) npt.assert_almost_equal(tn._cdf([-1], [-np.inf], [0]), 0.31731050786291415) # Check that the right-half truncated normal _cdf hasn't changed npt.assert_almost_equal(tn._cdf([1], [0], [np.inf]), 0.6826894921370859) # noqa, NOT 1.6826894921370859 npt.assert_almost_equal(tn.cdf(1, 0, np.inf), 0.6826894921370859) # Check that the left-half truncated normal _cdf hasn't changed npt.assert_almost_equal(tn._cdf([-1], [-np.inf], [0]), 0.31731050786291415) # noqa, Not -0.6826894921370859 npt.assert_almost_equal(tn.cdf(1, -np.inf, 0), 1) # Not 1.6826894921370859 npt.assert_almost_equal(tn.cdf(-1, -np.inf, 0), 0.31731050786291415) # Not -0.6826894921370859 def test_broadcast_gh9990_regression(): # Regression test for gh-9990 # The x-value 7 only lies within the support of 4 of the supplied # distributions. Prior to 9990, one array passed to # stats.reciprocal._cdf would have 4 elements, but an array # previously stored by stats.reciprocal_argcheck() would have 6, leading # to a broadcast error. a = np.array([1, 2, 3, 4, 5, 6]) b = np.array([8, 16, 1, 32, 1, 48]) ans = [stats.reciprocal.cdf(7, _a, _b) for _a, _b in zip(a,b)] npt.assert_array_almost_equal(stats.reciprocal.cdf(7, a, b), ans) ans = [stats.reciprocal.cdf(1, _a, _b) for _a, _b in zip(a,b)] npt.assert_array_almost_equal(stats.reciprocal.cdf(1, a, b), ans) ans = [stats.reciprocal.cdf(_a, _a, _b) for _a, _b in zip(a,b)] npt.assert_array_almost_equal(stats.reciprocal.cdf(a, a, b), ans) ans = [stats.reciprocal.cdf(_b, _a, _b) for _a, _b in zip(a,b)] npt.assert_array_almost_equal(stats.reciprocal.cdf(b, a, b), ans) def test_broadcast_gh7933_regression(): # Check broadcast works stats.truncnorm.logpdf( np.array([3.0, 2.0, 1.0]), a=(1.5 - np.array([6.0, 5.0, 4.0])) / 3.0, b=np.inf, loc=np.array([6.0, 5.0, 4.0]), scale=3.0 ) def test_gh2002_regression(): # Add a check that broadcast works in situations where only some # x-values are compatible with some of the shape arguments. x = np.r_[-2:2:101j] a = np.r_[-np.ones(50), np.ones(51)] expected = [stats.truncnorm.pdf(_x, _a, np.inf) for _x, _a in zip(x, a)] ans = stats.truncnorm.pdf(x, a, np.inf) npt.assert_array_almost_equal(ans, expected) def test_gh1320_regression(): # Check that the first example from gh-1320 now works. c = 2.62 stats.genextreme.ppf(0.5, np.array([[c], [c + 0.5]])) # The other examples in gh-1320 appear to have stopped working # some time ago. # ans = stats.genextreme.moment(2, np.array([c, c + 0.5])) # expected = np.array([25.50105963, 115.11191437]) # stats.genextreme.moment(5, np.array([[c], [c + 0.5]])) # stats.genextreme.moment(5, np.array([c, c + 0.5])) def test_method_of_moments(): # example from https://en.wikipedia.org/wiki/Method_of_moments_(statistics) np.random.seed(1234) x = [0, 0, 0, 0, 1] a = 1/5 - 2*np.sqrt(3)/5 b = 1/5 + 2*np.sqrt(3)/5 # force use of method of moments (uniform.fit is overriden) loc, scale = super(type(stats.uniform), stats.uniform).fit(x, method="MM") npt.assert_almost_equal(loc, a, decimal=4) npt.assert_almost_equal(loc+scale, b, decimal=4) def check_sample_meanvar_(popmean, popvar, sample): if np.isfinite(popmean): check_sample_mean(sample, popmean) if np.isfinite(popvar): check_sample_var(sample, popvar) def check_sample_mean(sample, popmean): # Checks for unlikely difference between sample mean and population mean prob = stats.ttest_1samp(sample, popmean).pvalue assert prob > 0.01 def check_sample_var(sample, popvar): # check that population mean lies within the CI bootstrapped from the # sample. This used to be a chi-squared test for variance, but there were # too many false positives res = stats.bootstrap( (sample,), lambda x, axis: x.var(ddof=1, axis=axis), confidence_level=0.995, ) conf = res.confidence_interval low, high = conf.low, conf.high assert low <= popvar <= high def check_cdf_ppf(distfn, arg, msg): values = [0.001, 0.5, 0.999] npt.assert_almost_equal(distfn.cdf(distfn.ppf(values, *arg), *arg), values, decimal=DECIMAL, err_msg=msg + ' - cdf-ppf roundtrip') def check_sf_isf(distfn, arg, msg): npt.assert_almost_equal(distfn.sf(distfn.isf([0.1, 0.5, 0.9], *arg), *arg), [0.1, 0.5, 0.9], decimal=DECIMAL, err_msg=msg + ' - sf-isf roundtrip') npt.assert_almost_equal(distfn.cdf([0.1, 0.9], *arg), 1.0 - distfn.sf([0.1, 0.9], *arg), decimal=DECIMAL, err_msg=msg + ' - cdf-sf relationship') def check_pdf(distfn, arg, msg): # compares pdf at median with numerical derivative of cdf median = distfn.ppf(0.5, *arg) eps = 1e-6 pdfv = distfn.pdf(median, *arg) if (pdfv < 1e-4) or (pdfv > 1e4): # avoid checking a case where pdf is close to zero or # huge (singularity) median = median + 0.1 pdfv = distfn.pdf(median, *arg) cdfdiff = (distfn.cdf(median + eps, *arg) - distfn.cdf(median - eps, *arg))/eps/2.0 # replace with better diff and better test (more points), # actually, this works pretty well msg += ' - cdf-pdf relationship' npt.assert_almost_equal(pdfv, cdfdiff, decimal=DECIMAL, err_msg=msg) def check_pdf_logpdf(distfn, args, msg): # compares pdf at several points with the log of the pdf points = np.array([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8]) vals = distfn.ppf(points, *args) vals = vals[np.isfinite(vals)] pdf = distfn.pdf(vals, *args) logpdf = distfn.logpdf(vals, *args) pdf = pdf[(pdf != 0) & np.isfinite(pdf)] logpdf = logpdf[np.isfinite(logpdf)] msg += " - logpdf-log(pdf) relationship" npt.assert_almost_equal(np.log(pdf), logpdf, decimal=7, err_msg=msg) def check_pdf_logpdf_at_endpoints(distfn, args, msg): # compares pdf with the log of the pdf at the (finite) end points points = np.array([0, 1]) vals = distfn.ppf(points, *args) vals = vals[np.isfinite(vals)] pdf = distfn.pdf(vals, *args) logpdf = distfn.logpdf(vals, *args) pdf = pdf[(pdf != 0) & np.isfinite(pdf)] logpdf = logpdf[np.isfinite(logpdf)] msg += " - logpdf-log(pdf) relationship" npt.assert_almost_equal(np.log(pdf), logpdf, decimal=7, err_msg=msg) def check_sf_logsf(distfn, args, msg): # compares sf at several points with the log of the sf points = np.array([0.0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 1.0]) vals = distfn.ppf(points, *args) vals = vals[np.isfinite(vals)] sf = distfn.sf(vals, *args) logsf = distfn.logsf(vals, *args) sf = sf[sf != 0] logsf = logsf[np.isfinite(logsf)] msg += " - logsf-log(sf) relationship" npt.assert_almost_equal(np.log(sf), logsf, decimal=7, err_msg=msg) def check_cdf_logcdf(distfn, args, msg): # compares cdf at several points with the log of the cdf points = np.array([0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 1.0]) vals = distfn.ppf(points, *args) vals = vals[np.isfinite(vals)] cdf = distfn.cdf(vals, *args) logcdf = distfn.logcdf(vals, *args) cdf = cdf[cdf != 0] logcdf = logcdf[np.isfinite(logcdf)] msg += " - logcdf-log(cdf) relationship" npt.assert_almost_equal(np.log(cdf), logcdf, decimal=7, err_msg=msg) def check_ppf_broadcast(distfn, arg, msg): # compares ppf for multiple argsets. num_repeats = 5 args = [] * num_repeats if arg: args = [np.array([_] * num_repeats) for _ in arg] median = distfn.ppf(0.5, *arg) medians = distfn.ppf(0.5, *args) msg += " - ppf multiple" npt.assert_almost_equal(medians, [median] * num_repeats, decimal=7, err_msg=msg) def check_distribution_rvs(dist, args, alpha, rvs): # dist is either a cdf function or name of a distribution in scipy.stats. # args are the args for scipy.stats.dist(*args) # alpha is a significance level, ~0.01 # rvs is array_like of random variables # test from scipy.stats.tests # this version reuses existing random variables D, pval = stats.kstest(rvs, dist, args=args, N=1000) if (pval < alpha): # The rvs passed in failed the K-S test, which _could_ happen # but is unlikely if alpha is small enough. # Repeat the test with a new sample of rvs. # Generate 1000 rvs, perform a K-S test that the new sample of rvs # are distributed according to the distribution. D, pval = stats.kstest(dist, dist, args=args, N=1000) npt.assert_(pval > alpha, "D = " + str(D) + "; pval = " + str(pval) + "; alpha = " + str(alpha) + "\nargs = " + str(args)) def check_vecentropy(distfn, args): npt.assert_equal(distfn.vecentropy(*args), distfn._entropy(*args)) def check_loc_scale(distfn, arg, m, v, msg): # Make `loc` and `scale` arrays to catch bugs like gh-13580 where # `loc` and `scale` arrays improperly broadcast with shapes. loc, scale = np.array([10.0, 20.0]), np.array([10.0, 20.0]) mt, vt = distfn.stats(loc=loc, scale=scale, *arg) npt.assert_allclose(m*scale + loc, mt) npt.assert_allclose(v*scale*scale, vt) def check_ppf_private(distfn, arg, msg): # fails by design for truncnorm self.nb not defined ppfs = distfn._ppf(np.array([0.1, 0.5, 0.9]), *arg) npt.assert_(not np.any(np.isnan(ppfs)), msg + 'ppf private is nan') def check_retrieving_support(distfn, args): loc, scale = 1, 2 supp = distfn.support(*args) supp_loc_scale = distfn.support(*args, loc=loc, scale=scale) npt.assert_almost_equal(np.array(supp)*scale + loc, np.array(supp_loc_scale)) def check_fit_args(distfn, arg, rvs, method): with np.errstate(all='ignore'), npt.suppress_warnings() as sup: sup.filter(category=RuntimeWarning, message="The shape parameter of the erlang") sup.filter(category=RuntimeWarning, message="floating point number truncated") vals = distfn.fit(rvs, method=method) vals2 = distfn.fit(rvs, optimizer='powell', method=method) # Only check the length of the return; accuracy tested in test_fit.py npt.assert_(len(vals) == 2+len(arg)) npt.assert_(len(vals2) == 2+len(arg)) def check_fit_args_fix(distfn, arg, rvs, method): with np.errstate(all='ignore'), npt.suppress_warnings() as sup: sup.filter(category=RuntimeWarning, message="The shape parameter of the erlang") vals = distfn.fit(rvs, floc=0, method=method) vals2 = distfn.fit(rvs, fscale=1, method=method) npt.assert_(len(vals) == 2+len(arg)) npt.assert_(vals[-2] == 0) npt.assert_(vals2[-1] == 1) npt.assert_(len(vals2) == 2+len(arg)) if len(arg) > 0: vals3 = distfn.fit(rvs, f0=arg[0], method=method) npt.assert_(len(vals3) == 2+len(arg)) npt.assert_(vals3[0] == arg[0]) if len(arg) > 1: vals4 = distfn.fit(rvs, f1=arg[1], method=method) npt.assert_(len(vals4) == 2+len(arg)) npt.assert_(vals4[1] == arg[1]) if len(arg) > 2: vals5 = distfn.fit(rvs, f2=arg[2], method=method) npt.assert_(len(vals5) == 2+len(arg)) npt.assert_(vals5[2] == arg[2]) @pytest.mark.filterwarnings('ignore::RuntimeWarning') @pytest.mark.parametrize('method', ['pdf', 'logpdf', 'cdf', 'logcdf', 'sf', 'logsf', 'ppf', 'isf']) @pytest.mark.parametrize('distname, args', distcont) def test_methods_with_lists(method, distname, args): # Test that the continuous distributions can accept Python lists # as arguments. dist = getattr(stats, distname) f = getattr(dist, method) if distname == 'invweibull' and method.startswith('log'): x = [1.5, 2] else: x = [0.1, 0.2] shape2 = [[a]*2 for a in args] loc = [0, 0.1] scale = [1, 1.01] result = f(x, *shape2, loc=loc, scale=scale) npt.assert_allclose(result, [f(*v) for v in zip(x, *shape2, loc, scale)], rtol=1e-14, atol=5e-14) @pytest.mark.parametrize('method', ['pdf', 'logpdf', 'cdf', 'logcdf', 'sf', 'logsf', 'ppf', 'isf']) def test_gilbrat_deprecation(method): expected = getattr(stats.gibrat, method)(1) with pytest.warns( DeprecationWarning, match=rf"\s*`gilbrat\.{method}` is deprecated,.*", ): result = getattr(stats.gilbrat, method)(1) assert result == expected @pytest.mark.parametrize('method', ['pdf', 'logpdf', 'cdf', 'logcdf', 'sf', 'logsf', 'ppf', 'isf']) def test_gilbrat_deprecation_frozen(method): expected = getattr(stats.gibrat, method)(1) with pytest.warns(DeprecationWarning, match=r"\s*`gilbrat` is deprecated"): # warn on instantiation of frozen distribution... g = stats.gilbrat() # ... not on its methods result = getattr(g, method)(1) assert result == expected def test_burr_fisk_moment_gh13234_regression(): vals0 = stats.burr.moment(1, 5, 4) assert isinstance(vals0, float) vals1 = stats.fisk.moment(1, 8) assert isinstance(vals1, float) def test_moments_with_array_gh12192_regression(): # array loc and scalar scale vals0 = stats.norm.moment(order=1, loc=np.array([1, 2, 3]), scale=1) expected0 = np.array([1., 2., 3.]) npt.assert_equal(vals0, expected0) # array loc and invalid scalar scale vals1 = stats.norm.moment(order=1, loc=np.array([1, 2, 3]), scale=-1) expected1 = np.array([np.nan, np.nan, np.nan]) npt.assert_equal(vals1, expected1) # array loc and array scale with invalid entries vals2 = stats.norm.moment(order=1, loc=np.array([1, 2, 3]), scale=[-3, 1, 0]) expected2 = np.array([np.nan, 2., np.nan]) npt.assert_equal(vals2, expected2) # (loc == 0) & (scale < 0) vals3 = stats.norm.moment(order=2, loc=0, scale=-4) expected3 = np.nan npt.assert_equal(vals3, expected3) assert isinstance(vals3, expected3.__class__) # array loc with 0 entries and scale with invalid entries vals4 = stats.norm.moment(order=2, loc=[1, 0, 2], scale=[3, -4, -5]) expected4 = np.array([10., np.nan, np.nan]) npt.assert_equal(vals4, expected4) # all(loc == 0) & (array scale with invalid entries) vals5 = stats.norm.moment(order=2, loc=[0, 0, 0], scale=[5., -2, 100.]) expected5 = np.array([25., np.nan, 10000.]) npt.assert_equal(vals5, expected5) # all( (loc == 0) & (scale < 0) ) vals6 = stats.norm.moment(order=2, loc=[0, 0, 0], scale=[-5., -2, -100.]) expected6 = np.array([np.nan, np.nan, np.nan]) npt.assert_equal(vals6, expected6) # scalar args, loc, and scale vals7 = stats.chi.moment(order=2, df=1, loc=0, scale=0) expected7 = np.nan npt.assert_equal(vals7, expected7) assert isinstance(vals7, expected7.__class__) # array args, scalar loc, and scalar scale vals8 = stats.chi.moment(order=2, df=[1, 2, 3], loc=0, scale=0) expected8 = np.array([np.nan, np.nan, np.nan]) npt.assert_equal(vals8, expected8) # array args, array loc, and array scale vals9 = stats.chi.moment(order=2, df=[1, 2, 3], loc=[1., 0., 2.], scale=[1., -3., 0.]) expected9 = np.array([3.59576912, np.nan, np.nan]) npt.assert_allclose(vals9, expected9, rtol=1e-8) # (n > 4), all(loc != 0), and all(scale != 0) vals10 = stats.norm.moment(5, [1., 2.], [1., 2.]) expected10 = np.array([26., 832.]) npt.assert_allclose(vals10, expected10, rtol=1e-13) # test broadcasting and more a = [-1.1, 0, 1, 2.2, np.pi] b = [-1.1, 0, 1, 2.2, np.pi] loc = [-1.1, 0, np.sqrt(2)] scale = [-2.1, 0, 1, 2.2, np.pi] a = np.array(a).reshape((-1, 1, 1, 1)) b = np.array(b).reshape((-1, 1, 1)) loc = np.array(loc).reshape((-1, 1)) scale = np.array(scale) vals11 = stats.beta.moment(order=2, a=a, b=b, loc=loc, scale=scale) a, b, loc, scale = np.broadcast_arrays(a, b, loc, scale) for i in np.ndenumerate(a): with np.errstate(invalid='ignore', divide='ignore'): i = i[0] # just get the index # check against same function with scalar input expected = stats.beta.moment(order=2, a=a[i], b=b[i], loc=loc[i], scale=scale[i]) np.testing.assert_equal(vals11[i], expected) def test_broadcasting_in_moments_gh12192_regression(): vals0 = stats.norm.moment(order=1, loc=np.array([1, 2, 3]), scale=[[1]]) expected0 = np.array([[1., 2., 3.]]) npt.assert_equal(vals0, expected0) assert vals0.shape == expected0.shape vals1 = stats.norm.moment(order=1, loc=np.array([[1], [2], [3]]), scale=[1, 2, 3]) expected1 = np.array([[1., 1., 1.], [2., 2., 2.], [3., 3., 3.]]) npt.assert_equal(vals1, expected1) assert vals1.shape == expected1.shape vals2 = stats.chi.moment(order=1, df=[1., 2., 3.], loc=0., scale=1.) expected2 = np.array([0.79788456, 1.25331414, 1.59576912]) npt.assert_allclose(vals2, expected2, rtol=1e-8) assert vals2.shape == expected2.shape vals3 = stats.chi.moment(order=1, df=[[1.], [2.], [3.]], loc=[0., 1., 2.], scale=[-1., 0., 3.]) expected3 = np.array([[np.nan, np.nan, 4.39365368], [np.nan, np.nan, 5.75994241], [np.nan, np.nan, 6.78730736]]) npt.assert_allclose(vals3, expected3, rtol=1e-8) assert vals3.shape == expected3.shape def test_kappa3_array_gh13582(): # https://github.com/scipy/scipy/pull/15140#issuecomment-994958241 shapes = [0.5, 1.5, 2.5, 3.5, 4.5] moments = 'mvsk' res = np.array([[stats.kappa3.stats(shape, moments=moment) for shape in shapes] for moment in moments]) res2 = np.array(stats.kappa3.stats(shapes, moments=moments)) npt.assert_allclose(res, res2) @pytest.mark.xslow def test_kappa4_array_gh13582(): h = np.array([-0.5, 2.5, 3.5, 4.5, -3]) k = np.array([-0.5, 1, -1.5, 0, 3.5]) moments = 'mvsk' res = np.array([[stats.kappa4.stats(h[i], k[i], moments=moment) for i in range(5)] for moment in moments]) res2 = np.array(stats.kappa4.stats(h, k, moments=moments)) npt.assert_allclose(res, res2) # https://github.com/scipy/scipy/pull/15250#discussion_r775112913 h = np.array([-1, -1/4, -1/4, 1, -1, 0]) k = np.array([1, 1, 1/2, -1/3, -1, 0]) res = np.array([[stats.kappa4.stats(h[i], k[i], moments=moment) for i in range(6)] for moment in moments]) res2 = np.array(stats.kappa4.stats(h, k, moments=moments)) npt.assert_allclose(res, res2) # https://github.com/scipy/scipy/pull/15250#discussion_r775115021 h = np.array([-1, -0.5, 1]) k = np.array([-1, -0.5, 0, 1])[:, None] res2 = np.array(stats.kappa4.stats(h, k, moments=moments)) assert res2.shape == (4, 4, 3) 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_continuous_frozen' object has no attribute" with pytest.raises(AttributeError, match=message): stats.norm().pmf with pytest.raises(AttributeError, match=message): stats.norm().logpmf stats.norm.pmf = "herring" frozen_norm = stats.norm() assert isinstance(frozen_norm, rv_continuous_frozen) delattr(stats.norm, 'pmf') def test_skewnorm_pdf_gh16038(): rng = np.random.default_rng(0) x, a = -np.inf, 0 npt.assert_equal(stats.skewnorm.pdf(x, a), stats.norm.pdf(x)) x, a = rng.random(size=(3, 3)), rng.random(size=(3, 3)) mask = rng.random(size=(3, 3)) < 0.5 a[mask] = 0 x_norm = x[mask] res = stats.skewnorm.pdf(x, a) npt.assert_equal(res[mask], stats.norm.pdf(x_norm)) npt.assert_equal(res[~mask], stats.skewnorm.pdf(x[~mask], a[~mask])) # for scalar input, these functions should return scalar output scalar_out = [['rvs', []], ['pdf', [0]], ['logpdf', [0]], ['cdf', [0]], ['logcdf', [0]], ['sf', [0]], ['logsf', [0]], ['ppf', [0]], ['isf', [0]], ['moment', [1]], ['entropy', []], ['expect', []], ['median', []], ['mean', []], ['std', []], ['var', []]] scalars_out = [['interval', [0.95]], ['support', []], ['stats', ['mv']]] @pytest.mark.parametrize('case', scalar_out + scalars_out) def test_scalar_for_scalar(case): # Some rv_continuous functions returned 0d array instead of NumPy scalar # Guard against regression method_name, args = case method = getattr(stats.norm(), method_name) res = method(*args) if case in scalar_out: assert isinstance(res, np.number) else: assert isinstance(res[0], np.number) assert isinstance(res[1], np.number) def test_scalar_for_scalar2(): # test methods that are not attributes of frozen distributions res = stats.norm.fit([1, 2, 3]) assert isinstance(res[0], np.number) assert isinstance(res[1], np.number) res = stats.norm.fit_loc_scale([1, 2, 3]) assert isinstance(res[0], np.number) assert isinstance(res[1], np.number) res = stats.norm.nnlf((0, 1), [1, 2, 3]) assert isinstance(res, np.number)