scipy 1.16.2__cp313-cp313-win_arm64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scipy/__config__.py +161 -0
- scipy/__init__.py +150 -0
- scipy/_cyutility.cp313-win_arm64.lib +0 -0
- scipy/_cyutility.cp313-win_arm64.pyd +0 -0
- scipy/_distributor_init.py +18 -0
- scipy/_lib/__init__.py +14 -0
- scipy/_lib/_array_api.py +931 -0
- scipy/_lib/_array_api_compat_vendor.py +9 -0
- scipy/_lib/_array_api_no_0d.py +103 -0
- scipy/_lib/_bunch.py +229 -0
- scipy/_lib/_ccallback.py +251 -0
- scipy/_lib/_ccallback_c.cp313-win_arm64.lib +0 -0
- scipy/_lib/_ccallback_c.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_disjoint_set.py +254 -0
- scipy/_lib/_docscrape.py +761 -0
- scipy/_lib/_elementwise_iterative_method.py +346 -0
- scipy/_lib/_fpumode.cp313-win_arm64.lib +0 -0
- scipy/_lib/_fpumode.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_gcutils.py +105 -0
- scipy/_lib/_pep440.py +487 -0
- scipy/_lib/_sparse.py +41 -0
- scipy/_lib/_test_ccallback.cp313-win_arm64.lib +0 -0
- scipy/_lib/_test_ccallback.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_test_deprecation_call.cp313-win_arm64.lib +0 -0
- scipy/_lib/_test_deprecation_call.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_test_deprecation_def.cp313-win_arm64.lib +0 -0
- scipy/_lib/_test_deprecation_def.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_testutils.py +373 -0
- scipy/_lib/_threadsafety.py +58 -0
- scipy/_lib/_tmpdirs.py +86 -0
- scipy/_lib/_uarray/LICENSE +29 -0
- scipy/_lib/_uarray/__init__.py +116 -0
- scipy/_lib/_uarray/_backend.py +707 -0
- scipy/_lib/_uarray/_uarray.cp313-win_arm64.lib +0 -0
- scipy/_lib/_uarray/_uarray.cp313-win_arm64.pyd +0 -0
- scipy/_lib/_util.py +1283 -0
- scipy/_lib/array_api_compat/__init__.py +22 -0
- scipy/_lib/array_api_compat/_internal.py +59 -0
- scipy/_lib/array_api_compat/common/__init__.py +1 -0
- scipy/_lib/array_api_compat/common/_aliases.py +727 -0
- scipy/_lib/array_api_compat/common/_fft.py +213 -0
- scipy/_lib/array_api_compat/common/_helpers.py +1058 -0
- scipy/_lib/array_api_compat/common/_linalg.py +232 -0
- scipy/_lib/array_api_compat/common/_typing.py +192 -0
- scipy/_lib/array_api_compat/cupy/__init__.py +13 -0
- scipy/_lib/array_api_compat/cupy/_aliases.py +156 -0
- scipy/_lib/array_api_compat/cupy/_info.py +336 -0
- scipy/_lib/array_api_compat/cupy/_typing.py +31 -0
- scipy/_lib/array_api_compat/cupy/fft.py +36 -0
- scipy/_lib/array_api_compat/cupy/linalg.py +49 -0
- scipy/_lib/array_api_compat/dask/__init__.py +0 -0
- scipy/_lib/array_api_compat/dask/array/__init__.py +12 -0
- scipy/_lib/array_api_compat/dask/array/_aliases.py +376 -0
- scipy/_lib/array_api_compat/dask/array/_info.py +416 -0
- scipy/_lib/array_api_compat/dask/array/fft.py +21 -0
- scipy/_lib/array_api_compat/dask/array/linalg.py +72 -0
- scipy/_lib/array_api_compat/numpy/__init__.py +28 -0
- scipy/_lib/array_api_compat/numpy/_aliases.py +190 -0
- scipy/_lib/array_api_compat/numpy/_info.py +366 -0
- scipy/_lib/array_api_compat/numpy/_typing.py +30 -0
- scipy/_lib/array_api_compat/numpy/fft.py +35 -0
- scipy/_lib/array_api_compat/numpy/linalg.py +143 -0
- scipy/_lib/array_api_compat/torch/__init__.py +22 -0
- scipy/_lib/array_api_compat/torch/_aliases.py +855 -0
- scipy/_lib/array_api_compat/torch/_info.py +369 -0
- scipy/_lib/array_api_compat/torch/_typing.py +3 -0
- scipy/_lib/array_api_compat/torch/fft.py +85 -0
- scipy/_lib/array_api_compat/torch/linalg.py +121 -0
- scipy/_lib/array_api_extra/__init__.py +38 -0
- scipy/_lib/array_api_extra/_delegation.py +171 -0
- scipy/_lib/array_api_extra/_lib/__init__.py +1 -0
- scipy/_lib/array_api_extra/_lib/_at.py +463 -0
- scipy/_lib/array_api_extra/_lib/_backends.py +46 -0
- scipy/_lib/array_api_extra/_lib/_funcs.py +937 -0
- scipy/_lib/array_api_extra/_lib/_lazy.py +357 -0
- scipy/_lib/array_api_extra/_lib/_testing.py +278 -0
- scipy/_lib/array_api_extra/_lib/_utils/__init__.py +1 -0
- scipy/_lib/array_api_extra/_lib/_utils/_compat.py +74 -0
- scipy/_lib/array_api_extra/_lib/_utils/_compat.pyi +45 -0
- scipy/_lib/array_api_extra/_lib/_utils/_helpers.py +559 -0
- scipy/_lib/array_api_extra/_lib/_utils/_typing.py +10 -0
- scipy/_lib/array_api_extra/_lib/_utils/_typing.pyi +105 -0
- scipy/_lib/array_api_extra/testing.py +359 -0
- scipy/_lib/cobyqa/__init__.py +20 -0
- scipy/_lib/cobyqa/framework.py +1240 -0
- scipy/_lib/cobyqa/main.py +1506 -0
- scipy/_lib/cobyqa/models.py +1529 -0
- scipy/_lib/cobyqa/problem.py +1296 -0
- scipy/_lib/cobyqa/settings.py +132 -0
- scipy/_lib/cobyqa/subsolvers/__init__.py +14 -0
- scipy/_lib/cobyqa/subsolvers/geometry.py +387 -0
- scipy/_lib/cobyqa/subsolvers/optim.py +1203 -0
- scipy/_lib/cobyqa/utils/__init__.py +18 -0
- scipy/_lib/cobyqa/utils/exceptions.py +22 -0
- scipy/_lib/cobyqa/utils/math.py +77 -0
- scipy/_lib/cobyqa/utils/versions.py +67 -0
- scipy/_lib/decorator.py +399 -0
- scipy/_lib/deprecation.py +274 -0
- scipy/_lib/doccer.py +366 -0
- scipy/_lib/messagestream.cp313-win_arm64.lib +0 -0
- scipy/_lib/messagestream.cp313-win_arm64.pyd +0 -0
- scipy/_lib/pyprima/__init__.py +212 -0
- scipy/_lib/pyprima/cobyla/__init__.py +0 -0
- scipy/_lib/pyprima/cobyla/cobyla.py +559 -0
- scipy/_lib/pyprima/cobyla/cobylb.py +714 -0
- scipy/_lib/pyprima/cobyla/geometry.py +226 -0
- scipy/_lib/pyprima/cobyla/initialize.py +215 -0
- scipy/_lib/pyprima/cobyla/trustregion.py +492 -0
- scipy/_lib/pyprima/cobyla/update.py +289 -0
- scipy/_lib/pyprima/common/__init__.py +0 -0
- scipy/_lib/pyprima/common/_bounds.py +34 -0
- scipy/_lib/pyprima/common/_linear_constraints.py +46 -0
- scipy/_lib/pyprima/common/_nonlinear_constraints.py +54 -0
- scipy/_lib/pyprima/common/_project.py +173 -0
- scipy/_lib/pyprima/common/checkbreak.py +93 -0
- scipy/_lib/pyprima/common/consts.py +47 -0
- scipy/_lib/pyprima/common/evaluate.py +99 -0
- scipy/_lib/pyprima/common/history.py +38 -0
- scipy/_lib/pyprima/common/infos.py +30 -0
- scipy/_lib/pyprima/common/linalg.py +435 -0
- scipy/_lib/pyprima/common/message.py +290 -0
- scipy/_lib/pyprima/common/powalg.py +131 -0
- scipy/_lib/pyprima/common/preproc.py +277 -0
- scipy/_lib/pyprima/common/present.py +5 -0
- scipy/_lib/pyprima/common/ratio.py +54 -0
- scipy/_lib/pyprima/common/redrho.py +47 -0
- scipy/_lib/pyprima/common/selectx.py +296 -0
- scipy/_lib/tests/__init__.py +0 -0
- scipy/_lib/tests/test__gcutils.py +110 -0
- scipy/_lib/tests/test__pep440.py +67 -0
- scipy/_lib/tests/test__testutils.py +32 -0
- scipy/_lib/tests/test__threadsafety.py +51 -0
- scipy/_lib/tests/test__util.py +641 -0
- scipy/_lib/tests/test_array_api.py +322 -0
- scipy/_lib/tests/test_bunch.py +169 -0
- scipy/_lib/tests/test_ccallback.py +196 -0
- scipy/_lib/tests/test_config.py +45 -0
- scipy/_lib/tests/test_deprecation.py +10 -0
- scipy/_lib/tests/test_doccer.py +143 -0
- scipy/_lib/tests/test_import_cycles.py +18 -0
- scipy/_lib/tests/test_public_api.py +482 -0
- scipy/_lib/tests/test_scipy_version.py +28 -0
- scipy/_lib/tests/test_tmpdirs.py +48 -0
- scipy/_lib/tests/test_warnings.py +137 -0
- scipy/_lib/uarray.py +31 -0
- scipy/cluster/__init__.py +31 -0
- scipy/cluster/_hierarchy.cp313-win_arm64.lib +0 -0
- scipy/cluster/_hierarchy.cp313-win_arm64.pyd +0 -0
- scipy/cluster/_optimal_leaf_ordering.cp313-win_arm64.lib +0 -0
- scipy/cluster/_optimal_leaf_ordering.cp313-win_arm64.pyd +0 -0
- scipy/cluster/_vq.cp313-win_arm64.lib +0 -0
- scipy/cluster/_vq.cp313-win_arm64.pyd +0 -0
- scipy/cluster/hierarchy.py +4348 -0
- scipy/cluster/tests/__init__.py +0 -0
- scipy/cluster/tests/hierarchy_test_data.py +145 -0
- scipy/cluster/tests/test_disjoint_set.py +202 -0
- scipy/cluster/tests/test_hierarchy.py +1238 -0
- scipy/cluster/tests/test_vq.py +434 -0
- scipy/cluster/vq.py +832 -0
- scipy/conftest.py +683 -0
- scipy/constants/__init__.py +358 -0
- scipy/constants/_codata.py +2266 -0
- scipy/constants/_constants.py +369 -0
- scipy/constants/codata.py +21 -0
- scipy/constants/constants.py +53 -0
- scipy/constants/tests/__init__.py +0 -0
- scipy/constants/tests/test_codata.py +78 -0
- scipy/constants/tests/test_constants.py +83 -0
- scipy/datasets/__init__.py +90 -0
- scipy/datasets/_download_all.py +71 -0
- scipy/datasets/_fetchers.py +225 -0
- scipy/datasets/_registry.py +26 -0
- scipy/datasets/_utils.py +81 -0
- scipy/datasets/tests/__init__.py +0 -0
- scipy/datasets/tests/test_data.py +128 -0
- scipy/differentiate/__init__.py +27 -0
- scipy/differentiate/_differentiate.py +1129 -0
- scipy/differentiate/tests/__init__.py +0 -0
- scipy/differentiate/tests/test_differentiate.py +694 -0
- scipy/fft/__init__.py +114 -0
- scipy/fft/_backend.py +196 -0
- scipy/fft/_basic.py +1650 -0
- scipy/fft/_basic_backend.py +197 -0
- scipy/fft/_debug_backends.py +22 -0
- scipy/fft/_fftlog.py +223 -0
- scipy/fft/_fftlog_backend.py +200 -0
- scipy/fft/_helper.py +348 -0
- scipy/fft/_pocketfft/LICENSE.md +25 -0
- scipy/fft/_pocketfft/__init__.py +9 -0
- scipy/fft/_pocketfft/basic.py +251 -0
- scipy/fft/_pocketfft/helper.py +249 -0
- scipy/fft/_pocketfft/pypocketfft.cp313-win_arm64.lib +0 -0
- scipy/fft/_pocketfft/pypocketfft.cp313-win_arm64.pyd +0 -0
- scipy/fft/_pocketfft/realtransforms.py +109 -0
- scipy/fft/_pocketfft/tests/__init__.py +0 -0
- scipy/fft/_pocketfft/tests/test_basic.py +1011 -0
- scipy/fft/_pocketfft/tests/test_real_transforms.py +505 -0
- scipy/fft/_realtransforms.py +706 -0
- scipy/fft/_realtransforms_backend.py +63 -0
- scipy/fft/tests/__init__.py +0 -0
- scipy/fft/tests/mock_backend.py +96 -0
- scipy/fft/tests/test_backend.py +98 -0
- scipy/fft/tests/test_basic.py +504 -0
- scipy/fft/tests/test_fftlog.py +215 -0
- scipy/fft/tests/test_helper.py +558 -0
- scipy/fft/tests/test_multithreading.py +84 -0
- scipy/fft/tests/test_real_transforms.py +247 -0
- scipy/fftpack/__init__.py +103 -0
- scipy/fftpack/_basic.py +428 -0
- scipy/fftpack/_helper.py +115 -0
- scipy/fftpack/_pseudo_diffs.py +554 -0
- scipy/fftpack/_realtransforms.py +598 -0
- scipy/fftpack/basic.py +20 -0
- scipy/fftpack/convolve.cp313-win_arm64.lib +0 -0
- scipy/fftpack/convolve.cp313-win_arm64.pyd +0 -0
- scipy/fftpack/helper.py +19 -0
- scipy/fftpack/pseudo_diffs.py +22 -0
- scipy/fftpack/realtransforms.py +19 -0
- scipy/fftpack/tests/__init__.py +0 -0
- scipy/fftpack/tests/fftw_double_ref.npz +0 -0
- scipy/fftpack/tests/fftw_longdouble_ref.npz +0 -0
- scipy/fftpack/tests/fftw_single_ref.npz +0 -0
- scipy/fftpack/tests/test.npz +0 -0
- scipy/fftpack/tests/test_basic.py +877 -0
- scipy/fftpack/tests/test_helper.py +54 -0
- scipy/fftpack/tests/test_import.py +33 -0
- scipy/fftpack/tests/test_pseudo_diffs.py +388 -0
- scipy/fftpack/tests/test_real_transforms.py +836 -0
- scipy/integrate/__init__.py +122 -0
- scipy/integrate/_bvp.py +1160 -0
- scipy/integrate/_cubature.py +729 -0
- scipy/integrate/_dop.cp313-win_arm64.lib +0 -0
- scipy/integrate/_dop.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_ivp/__init__.py +8 -0
- scipy/integrate/_ivp/base.py +290 -0
- scipy/integrate/_ivp/bdf.py +478 -0
- scipy/integrate/_ivp/common.py +451 -0
- scipy/integrate/_ivp/dop853_coefficients.py +193 -0
- scipy/integrate/_ivp/ivp.py +755 -0
- scipy/integrate/_ivp/lsoda.py +224 -0
- scipy/integrate/_ivp/radau.py +572 -0
- scipy/integrate/_ivp/rk.py +601 -0
- scipy/integrate/_ivp/tests/__init__.py +0 -0
- scipy/integrate/_ivp/tests/test_ivp.py +1287 -0
- scipy/integrate/_ivp/tests/test_rk.py +37 -0
- scipy/integrate/_lebedev.py +5450 -0
- scipy/integrate/_lsoda.cp313-win_arm64.lib +0 -0
- scipy/integrate/_lsoda.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_ode.py +1395 -0
- scipy/integrate/_odepack.cp313-win_arm64.lib +0 -0
- scipy/integrate/_odepack.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_odepack_py.py +273 -0
- scipy/integrate/_quad_vec.py +674 -0
- scipy/integrate/_quadpack.cp313-win_arm64.lib +0 -0
- scipy/integrate/_quadpack.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_quadpack_py.py +1283 -0
- scipy/integrate/_quadrature.py +1336 -0
- scipy/integrate/_rules/__init__.py +12 -0
- scipy/integrate/_rules/_base.py +518 -0
- scipy/integrate/_rules/_gauss_kronrod.py +202 -0
- scipy/integrate/_rules/_gauss_legendre.py +62 -0
- scipy/integrate/_rules/_genz_malik.py +210 -0
- scipy/integrate/_tanhsinh.py +1385 -0
- scipy/integrate/_test_multivariate.cp313-win_arm64.lib +0 -0
- scipy/integrate/_test_multivariate.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_test_odeint_banded.cp313-win_arm64.lib +0 -0
- scipy/integrate/_test_odeint_banded.cp313-win_arm64.pyd +0 -0
- scipy/integrate/_vode.cp313-win_arm64.lib +0 -0
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- scipy/integrate/lsoda.py +15 -0
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- scipy/integrate/quadpack.py +23 -0
- scipy/integrate/tests/__init__.py +0 -0
- scipy/integrate/tests/test__quad_vec.py +211 -0
- scipy/integrate/tests/test_banded_ode_solvers.py +305 -0
- scipy/integrate/tests/test_bvp.py +714 -0
- scipy/integrate/tests/test_cubature.py +1375 -0
- scipy/integrate/tests/test_integrate.py +840 -0
- scipy/integrate/tests/test_odeint_jac.py +74 -0
- scipy/integrate/tests/test_quadpack.py +680 -0
- scipy/integrate/tests/test_quadrature.py +730 -0
- scipy/integrate/tests/test_tanhsinh.py +1171 -0
- scipy/integrate/vode.py +15 -0
- scipy/interpolate/__init__.py +228 -0
- scipy/interpolate/_bary_rational.py +715 -0
- scipy/interpolate/_bsplines.py +2469 -0
- scipy/interpolate/_cubic.py +973 -0
- scipy/interpolate/_dfitpack.cp313-win_arm64.lib +0 -0
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- scipy/io/_fast_matrix_market/__init__.py +600 -0
- scipy/io/_fast_matrix_market/_fmm_core.cp313-win_arm64.lib +0 -0
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- scipy/io/_harwell_boeing/__init__.py +7 -0
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import threading
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import pickle
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import pytest
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from copy import deepcopy
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import platform
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import sys
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import math
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import numpy as np
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from numpy.testing import assert_allclose, assert_equal, suppress_warnings
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from scipy.stats.sampling import (
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TransformedDensityRejection,
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DiscreteAliasUrn,
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DiscreteGuideTable,
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NumericalInversePolynomial,
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NumericalInverseHermite,
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RatioUniforms,
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SimpleRatioUniforms,
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UNURANError
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)
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from pytest import raises as assert_raises
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from scipy import stats
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from scipy import special
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from scipy.stats import chisquare, cramervonmises
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from scipy.stats._distr_params import distdiscrete, distcont
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("DiscreteGuideTable", {"dist": [0.02, 0.18, 0.8]}),
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(lambda x: -x, UNURANError, r"..."),
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(lambda x: [], TypeError, floaterr),
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(lambda x: foo, NameError, r"name 'foo' is not defined"), # type: ignore[name-defined] # noqa: F821, E501
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# Infinite value returned => Overflow error.
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(lambda x: np.inf, UNURANError, r"..."),
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(lambda x: np.nan, UNURANError, r"..."),
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(lambda x: np.inf, UNURANError, r"..."),
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(lambda x: np.nan, UNURANError, r"..."),
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# Returning wrong type
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(lambda x: [], TypeError, floaterr),
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# Undefined name inside the function
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(lambda x: foo, NameError, r"name 'foo' is not defined"), # type: ignore[name-defined] # noqa: F821, E501
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(lambda: 1.0, TypeError, r"takes 0 positional arguments but 1 was given")
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(lambda x: [], TypeError, floaterr),
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(lambda x: foo, NameError, r"name 'foo' is not defined"), # type: ignore[name-defined] # noqa: F821, E501
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# Infinite value returned => Overflow error.
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(lambda x: np.inf, UNURANError, r"..."),
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# NaN value => internal error in UNU.RAN
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(lambda x: np.nan, UNURANError, r"..."),
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(lambda: 1.0, TypeError, r"takes 0 positional arguments but 1 was given")
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([[1.0, 0.0]], r"wrong number of dimensions \(expected 1, got 2\)"),
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([0.2, 0.4, np.nan, 0.8], r"must contain only finite / non-nan values"),
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([0.2, 0.4, np.inf, 0.8], r"must contain only finite / non-nan values"),
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]
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# size of the domains is incorrect
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((1, 2, 3), ValueError, r"must be a length 2 tuple"),
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# empty domain
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((), ValueError, r"must be a length 2 tuple")
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# domain values are incorrect
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bad_domains = [
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((2, 1), UNURANError, r"left >= right"),
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((1, 1), UNURANError, r"left >= right"),
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]
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# infinite and nan values present in domain.
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inf_nan_domains = [
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# left >= right
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((10, 10), UNURANError, r"left >= right"),
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((np.inf, np.inf), UNURANError, r"left >= right"),
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((-np.inf, -np.inf), UNURANError, r"left >= right"),
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((np.inf, -np.inf), UNURANError, r"left >= right"),
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# Also include nans in some of the domains.
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((-np.inf, np.nan), ValueError, r"only non-nan values"),
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((np.nan, np.inf), ValueError, r"only non-nan values")
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]
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# `nan` values present in domain. Some distributions don't support
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# infinite tails, so don't mix the nan values with infinities.
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nan_domains = [
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((0, np.nan), ValueError, r"only non-nan values"),
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+
((np.nan, np.nan), ValueError, r"only non-nan values")
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+
]
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+
|
150
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+
|
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+
# all the methods should throw errors for nan, bad sized, and bad valued
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# domains.
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+
@pytest.mark.parametrize("domain, err, msg",
|
154
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+
bad_domains + bad_sized_domains +
|
155
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+
nan_domains) # type: ignore[operator]
|
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+
@pytest.mark.parametrize("method, kwargs", all_methods)
|
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|
+
def test_bad_domain(domain, err, msg, method, kwargs):
|
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+
Method = getattr(stats.sampling, method)
|
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+
with pytest.raises(err, match=msg):
|
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+
Method(**kwargs, domain=domain)
|
161
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+
|
162
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+
|
163
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+
@pytest.mark.parametrize("method, kwargs", all_methods)
|
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+
def test_random_state(method, kwargs):
|
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+
Method = getattr(stats.sampling, method)
|
166
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+
|
167
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+
# simple seed that works for any version of NumPy
|
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+
seed = 123
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+
rng1 = Method(**kwargs, random_state=seed)
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+
rng2 = Method(**kwargs, random_state=seed)
|
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+
assert_equal(rng1.rvs(100), rng2.rvs(100))
|
172
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+
|
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+
# global seed
|
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+
rng = np.random.RandomState(123)
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175
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+
rng1 = Method(**kwargs)
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176
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+
rvs1 = rng1.rvs(100, random_state=rng)
|
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+
np.random.seed(None)
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+
rng2 = Method(**kwargs, random_state=123)
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+
rvs2 = rng2.rvs(100)
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+
assert_equal(rvs1, rvs2)
|
181
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+
|
182
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+
# Generator seed for new NumPy
|
183
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+
# when a RandomState is given, it should take the bitgen_t
|
184
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+
# member of the class and create a Generator instance.
|
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+
seed1 = np.random.RandomState(np.random.MT19937(123))
|
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+
seed2 = np.random.Generator(np.random.MT19937(123))
|
187
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+
rng1 = Method(**kwargs, random_state=seed1)
|
188
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+
rng2 = Method(**kwargs, random_state=seed2)
|
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|
+
assert_equal(rng1.rvs(100), rng2.rvs(100))
|
190
|
+
|
191
|
+
|
192
|
+
def test_set_random_state():
|
193
|
+
rng1 = TransformedDensityRejection(StandardNormal(), random_state=123)
|
194
|
+
rng2 = TransformedDensityRejection(StandardNormal())
|
195
|
+
rng2.set_random_state(123)
|
196
|
+
assert_equal(rng1.rvs(100), rng2.rvs(100))
|
197
|
+
rng = TransformedDensityRejection(StandardNormal(), random_state=123)
|
198
|
+
rvs1 = rng.rvs(100)
|
199
|
+
rng.set_random_state(123)
|
200
|
+
rvs2 = rng.rvs(100)
|
201
|
+
assert_equal(rvs1, rvs2)
|
202
|
+
|
203
|
+
|
204
|
+
def test_threading_behaviour():
|
205
|
+
# Test if the API is thread-safe.
|
206
|
+
# This verifies if the lock mechanism and the use of `PyErr_Occurred`
|
207
|
+
# is correct.
|
208
|
+
errors = {"err1": None, "err2": None}
|
209
|
+
|
210
|
+
class Distribution:
|
211
|
+
def __init__(self, pdf_msg):
|
212
|
+
self.pdf_msg = pdf_msg
|
213
|
+
|
214
|
+
def pdf(self, x):
|
215
|
+
if 49.9 < x < 50.0:
|
216
|
+
raise ValueError(self.pdf_msg)
|
217
|
+
return x
|
218
|
+
|
219
|
+
def dpdf(self, x):
|
220
|
+
return 1
|
221
|
+
|
222
|
+
def func1():
|
223
|
+
dist = Distribution('foo')
|
224
|
+
rng = TransformedDensityRejection(dist, domain=(10, 100),
|
225
|
+
random_state=12)
|
226
|
+
try:
|
227
|
+
rng.rvs(100000)
|
228
|
+
except ValueError as e:
|
229
|
+
errors['err1'] = e.args[0]
|
230
|
+
|
231
|
+
def func2():
|
232
|
+
dist = Distribution('bar')
|
233
|
+
rng = TransformedDensityRejection(dist, domain=(10, 100),
|
234
|
+
random_state=2)
|
235
|
+
try:
|
236
|
+
rng.rvs(100000)
|
237
|
+
except ValueError as e:
|
238
|
+
errors['err2'] = e.args[0]
|
239
|
+
|
240
|
+
t1 = threading.Thread(target=func1)
|
241
|
+
t2 = threading.Thread(target=func2)
|
242
|
+
|
243
|
+
t1.start()
|
244
|
+
t2.start()
|
245
|
+
|
246
|
+
t1.join()
|
247
|
+
t2.join()
|
248
|
+
|
249
|
+
assert errors['err1'] == 'foo'
|
250
|
+
assert errors['err2'] == 'bar'
|
251
|
+
|
252
|
+
|
253
|
+
@pytest.mark.parametrize("method, kwargs", all_methods)
|
254
|
+
def test_pickle(method, kwargs):
|
255
|
+
Method = getattr(stats.sampling, method)
|
256
|
+
rng1 = Method(**kwargs, random_state=123)
|
257
|
+
obj = pickle.dumps(rng1)
|
258
|
+
rng2 = pickle.loads(obj)
|
259
|
+
assert_equal(rng1.rvs(100), rng2.rvs(100))
|
260
|
+
|
261
|
+
|
262
|
+
@pytest.mark.parametrize("size", [None, 0, (0, ), 1, (10, 3), (2, 3, 4, 5),
|
263
|
+
(0, 0), (0, 1)])
|
264
|
+
def test_rvs_size(size):
|
265
|
+
# As the `rvs` method is present in the base class and shared between
|
266
|
+
# all the classes, we can just test with one of the methods.
|
267
|
+
rng = TransformedDensityRejection(StandardNormal())
|
268
|
+
if size is None:
|
269
|
+
assert np.isscalar(rng.rvs(size))
|
270
|
+
else:
|
271
|
+
if np.isscalar(size):
|
272
|
+
size = (size, )
|
273
|
+
assert rng.rvs(size).shape == size
|
274
|
+
|
275
|
+
|
276
|
+
def test_with_scipy_distribution():
|
277
|
+
# test if the setup works with SciPy's rv_frozen distributions
|
278
|
+
dist = stats.norm()
|
279
|
+
urng = np.random.default_rng(0)
|
280
|
+
rng = NumericalInverseHermite(dist, random_state=urng)
|
281
|
+
u = np.linspace(0, 1, num=100)
|
282
|
+
check_cont_samples(rng, dist, dist.stats())
|
283
|
+
assert_allclose(dist.ppf(u), rng.ppf(u))
|
284
|
+
# test if it works with `loc` and `scale`
|
285
|
+
dist = stats.norm(loc=10., scale=5.)
|
286
|
+
rng = NumericalInverseHermite(dist, random_state=urng)
|
287
|
+
check_cont_samples(rng, dist, dist.stats())
|
288
|
+
assert_allclose(dist.ppf(u), rng.ppf(u))
|
289
|
+
# check for discrete distributions
|
290
|
+
dist = stats.binom(10, 0.2)
|
291
|
+
rng = DiscreteAliasUrn(dist, random_state=urng)
|
292
|
+
domain = dist.support()
|
293
|
+
pv = dist.pmf(np.arange(domain[0], domain[1]+1))
|
294
|
+
check_discr_samples(rng, pv, dist.stats())
|
295
|
+
|
296
|
+
|
297
|
+
def check_cont_samples(rng, dist, mv_ex, rtol=1e-7, atol=1e-1):
|
298
|
+
rvs = rng.rvs(100000)
|
299
|
+
mv = rvs.mean(), rvs.var()
|
300
|
+
# test the moments only if the variance is finite
|
301
|
+
if np.isfinite(mv_ex[1]):
|
302
|
+
assert_allclose(mv, mv_ex, rtol=rtol, atol=atol)
|
303
|
+
# Cramer Von Mises test for goodness-of-fit
|
304
|
+
rvs = rng.rvs(500)
|
305
|
+
dist.cdf = np.vectorize(dist.cdf)
|
306
|
+
pval = cramervonmises(rvs, dist.cdf).pvalue
|
307
|
+
assert pval > 0.1
|
308
|
+
|
309
|
+
|
310
|
+
def check_discr_samples(rng, pv, mv_ex, rtol=1e-3, atol=1e-1):
|
311
|
+
rvs = rng.rvs(100000)
|
312
|
+
# test if the first few moments match
|
313
|
+
mv = rvs.mean(), rvs.var()
|
314
|
+
assert_allclose(mv, mv_ex, rtol=rtol, atol=atol)
|
315
|
+
# normalize
|
316
|
+
pv = pv / pv.sum()
|
317
|
+
# chi-squared test for goodness-of-fit
|
318
|
+
obs_freqs = np.zeros_like(pv)
|
319
|
+
_, freqs = np.unique(rvs, return_counts=True)
|
320
|
+
freqs = freqs / freqs.sum()
|
321
|
+
obs_freqs[:freqs.size] = freqs
|
322
|
+
pval = chisquare(obs_freqs, pv).pvalue
|
323
|
+
assert pval > 0.1
|
324
|
+
|
325
|
+
|
326
|
+
def test_warning_center_not_in_domain():
|
327
|
+
# UNURAN will warn if the center provided or the one computed w/o the
|
328
|
+
# domain is outside of the domain
|
329
|
+
msg = "102 : center moved into domain of distribution"
|
330
|
+
with pytest.warns(RuntimeWarning, match=msg):
|
331
|
+
NumericalInversePolynomial(StandardNormal(), center=0, domain=(3, 5))
|
332
|
+
with pytest.warns(RuntimeWarning, match=msg):
|
333
|
+
NumericalInversePolynomial(StandardNormal(), domain=(3, 5))
|
334
|
+
|
335
|
+
|
336
|
+
@pytest.mark.parametrize('method', ["SimpleRatioUniforms",
|
337
|
+
"NumericalInversePolynomial",
|
338
|
+
"TransformedDensityRejection"])
|
339
|
+
def test_error_mode_not_in_domain(method):
|
340
|
+
# UNURAN raises an error if the mode is not in the domain
|
341
|
+
# the behavior is different compared to the case that center is not in the
|
342
|
+
# domain. mode is supposed to be the exact value, center can be an
|
343
|
+
# approximate value
|
344
|
+
Method = getattr(stats.sampling, method)
|
345
|
+
msg = "17 : mode not in domain"
|
346
|
+
with pytest.raises(UNURANError, match=msg):
|
347
|
+
Method(StandardNormal(), mode=0, domain=(3, 5))
|
348
|
+
|
349
|
+
|
350
|
+
@pytest.mark.parametrize('method', ["NumericalInverseHermite",
|
351
|
+
"NumericalInversePolynomial"])
|
352
|
+
class TestQRVS:
|
353
|
+
def test_input_validation(self, method):
|
354
|
+
match = "`qmc_engine` must be an instance of..."
|
355
|
+
with pytest.raises(ValueError, match=match):
|
356
|
+
Method = getattr(stats.sampling, method)
|
357
|
+
gen = Method(StandardNormal())
|
358
|
+
gen.qrvs(qmc_engine=0)
|
359
|
+
|
360
|
+
# issues with QMCEngines and old NumPy
|
361
|
+
Method = getattr(stats.sampling, method)
|
362
|
+
gen = Method(StandardNormal())
|
363
|
+
|
364
|
+
match = "`d` must be consistent with dimension of `qmc_engine`."
|
365
|
+
with pytest.raises(ValueError, match=match):
|
366
|
+
gen.qrvs(d=3, qmc_engine=stats.qmc.Halton(2))
|
367
|
+
|
368
|
+
qrngs = [None, stats.qmc.Sobol(1, seed=0), stats.qmc.Halton(3, seed=0)]
|
369
|
+
# `size=None` should not add anything to the shape, `size=1` should
|
370
|
+
sizes = [(None, tuple()), (1, (1,)), (4, (4,)),
|
371
|
+
((4,), (4,)), ((2, 4), (2, 4))] # type: ignore
|
372
|
+
# Neither `d=None` nor `d=1` should add anything to the shape
|
373
|
+
ds = [(None, tuple()), (1, tuple()), (3, (3,))]
|
374
|
+
|
375
|
+
@pytest.mark.parametrize('qrng', qrngs)
|
376
|
+
@pytest.mark.parametrize('size_in, size_out', sizes)
|
377
|
+
@pytest.mark.parametrize('d_in, d_out', ds)
|
378
|
+
@pytest.mark.thread_unsafe
|
379
|
+
def test_QRVS_shape_consistency(self, qrng, size_in, size_out,
|
380
|
+
d_in, d_out, method):
|
381
|
+
w32 = sys.platform == "win32" and platform.architecture()[0] == "32bit"
|
382
|
+
if w32 and method == "NumericalInversePolynomial":
|
383
|
+
pytest.xfail("NumericalInversePolynomial.qrvs fails for Win "
|
384
|
+
"32-bit")
|
385
|
+
|
386
|
+
dist = StandardNormal()
|
387
|
+
Method = getattr(stats.sampling, method)
|
388
|
+
gen = Method(dist)
|
389
|
+
|
390
|
+
# If d and qrng.d are inconsistent, an error is raised
|
391
|
+
if d_in is not None and qrng is not None and qrng.d != d_in:
|
392
|
+
match = "`d` must be consistent with dimension of `qmc_engine`."
|
393
|
+
with pytest.raises(ValueError, match=match):
|
394
|
+
gen.qrvs(size_in, d=d_in, qmc_engine=qrng)
|
395
|
+
return
|
396
|
+
|
397
|
+
# Sometimes d is really determined by qrng
|
398
|
+
if d_in is None and qrng is not None and qrng.d != 1:
|
399
|
+
d_out = (qrng.d,)
|
400
|
+
|
401
|
+
shape_expected = size_out + d_out
|
402
|
+
|
403
|
+
qrng2 = deepcopy(qrng)
|
404
|
+
qrvs = gen.qrvs(size=size_in, d=d_in, qmc_engine=qrng)
|
405
|
+
if size_in is not None:
|
406
|
+
assert qrvs.shape == shape_expected
|
407
|
+
|
408
|
+
if qrng2 is not None:
|
409
|
+
uniform = qrng2.random(np.prod(size_in) or 1)
|
410
|
+
qrvs2 = stats.norm.ppf(uniform).reshape(shape_expected)
|
411
|
+
assert_allclose(qrvs, qrvs2, atol=1e-12)
|
412
|
+
|
413
|
+
def test_QRVS_size_tuple(self, method):
|
414
|
+
# QMCEngine samples are always of shape (n, d). When `size` is a tuple,
|
415
|
+
# we set `n = prod(size)` in the call to qmc_engine.random, transform
|
416
|
+
# the sample, and reshape it to the final dimensions. When we reshape,
|
417
|
+
# we need to be careful, because the _columns_ of the sample returned
|
418
|
+
# by a QMCEngine are "independent"-ish, but the elements within the
|
419
|
+
# columns are not. We need to make sure that this doesn't get mixed up
|
420
|
+
# by reshaping: qrvs[..., i] should remain "independent"-ish of
|
421
|
+
# qrvs[..., i+1], but the elements within qrvs[..., i] should be
|
422
|
+
# transformed from the same low-discrepancy sequence.
|
423
|
+
|
424
|
+
dist = StandardNormal()
|
425
|
+
Method = getattr(stats.sampling, method)
|
426
|
+
gen = Method(dist)
|
427
|
+
|
428
|
+
size = (3, 4)
|
429
|
+
d = 5
|
430
|
+
qrng = stats.qmc.Halton(d, seed=0)
|
431
|
+
qrng2 = stats.qmc.Halton(d, seed=0)
|
432
|
+
|
433
|
+
uniform = qrng2.random(np.prod(size))
|
434
|
+
|
435
|
+
qrvs = gen.qrvs(size=size, d=d, qmc_engine=qrng)
|
436
|
+
qrvs2 = stats.norm.ppf(uniform)
|
437
|
+
|
438
|
+
for i in range(d):
|
439
|
+
sample = qrvs[..., i]
|
440
|
+
sample2 = qrvs2[:, i].reshape(size)
|
441
|
+
assert_allclose(sample, sample2, atol=1e-12)
|
442
|
+
|
443
|
+
|
444
|
+
class TestTransformedDensityRejection:
|
445
|
+
# Simple Custom Distribution
|
446
|
+
class dist0:
|
447
|
+
def pdf(self, x):
|
448
|
+
return 3/4 * (1-x*x)
|
449
|
+
|
450
|
+
def dpdf(self, x):
|
451
|
+
return 3/4 * (-2*x)
|
452
|
+
|
453
|
+
def cdf(self, x):
|
454
|
+
return 3/4 * (x - x**3/3 + 2/3)
|
455
|
+
|
456
|
+
def support(self):
|
457
|
+
return -1, 1
|
458
|
+
|
459
|
+
# Standard Normal Distribution
|
460
|
+
class dist1:
|
461
|
+
def pdf(self, x):
|
462
|
+
return stats.norm._pdf(x / 0.1)
|
463
|
+
|
464
|
+
def dpdf(self, x):
|
465
|
+
return -x / 0.01 * stats.norm._pdf(x / 0.1)
|
466
|
+
|
467
|
+
def cdf(self, x):
|
468
|
+
return stats.norm._cdf(x / 0.1)
|
469
|
+
|
470
|
+
# pdf with piecewise linear function as transformed density
|
471
|
+
# with T = -1/sqrt with shift. Taken from UNU.RAN test suite
|
472
|
+
# (from file t_tdr_ps.c)
|
473
|
+
class dist2:
|
474
|
+
def __init__(self, shift):
|
475
|
+
self.shift = shift
|
476
|
+
|
477
|
+
def pdf(self, x):
|
478
|
+
x -= self.shift
|
479
|
+
y = 1. / (abs(x) + 1.)
|
480
|
+
return 0.5 * y * y
|
481
|
+
|
482
|
+
def dpdf(self, x):
|
483
|
+
x -= self.shift
|
484
|
+
y = 1. / (abs(x) + 1.)
|
485
|
+
y = y * y * y
|
486
|
+
return y if (x < 0.) else -y
|
487
|
+
|
488
|
+
def cdf(self, x):
|
489
|
+
x -= self.shift
|
490
|
+
if x <= 0.:
|
491
|
+
return 0.5 / (1. - x)
|
492
|
+
else:
|
493
|
+
return 1. - 0.5 / (1. + x)
|
494
|
+
|
495
|
+
dists = [dist0(), dist1(), dist2(0.), dist2(10000.)]
|
496
|
+
|
497
|
+
# exact mean and variance of the distributions in the list dists
|
498
|
+
mv0 = [0., 4./15.]
|
499
|
+
mv1 = [0., 0.01]
|
500
|
+
mv2 = [0., np.inf]
|
501
|
+
mv3 = [10000., np.inf]
|
502
|
+
mvs = [mv0, mv1, mv2, mv3]
|
503
|
+
|
504
|
+
@pytest.mark.parametrize("dist, mv_ex",
|
505
|
+
zip(dists, mvs))
|
506
|
+
@pytest.mark.thread_unsafe
|
507
|
+
def test_basic(self, dist, mv_ex):
|
508
|
+
with suppress_warnings() as sup:
|
509
|
+
# filter the warnings thrown by UNU.RAN
|
510
|
+
sup.filter(RuntimeWarning)
|
511
|
+
rng = TransformedDensityRejection(dist, random_state=42)
|
512
|
+
check_cont_samples(rng, dist, mv_ex)
|
513
|
+
|
514
|
+
# PDF 0 everywhere => bad construction points
|
515
|
+
bad_pdfs = [(lambda x: 0, UNURANError, r"50 : bad construction points.")]
|
516
|
+
bad_pdfs += bad_pdfs_common # type: ignore[arg-type]
|
517
|
+
|
518
|
+
@pytest.mark.parametrize("pdf, err, msg", bad_pdfs)
|
519
|
+
def test_bad_pdf(self, pdf, err, msg):
|
520
|
+
class dist:
|
521
|
+
pass
|
522
|
+
dist.pdf = pdf
|
523
|
+
dist.dpdf = lambda x: 1 # an arbitrary dPDF
|
524
|
+
with pytest.raises(err, match=msg):
|
525
|
+
TransformedDensityRejection(dist)
|
526
|
+
|
527
|
+
@pytest.mark.parametrize("dpdf, err, msg", bad_dpdf_common)
|
528
|
+
def test_bad_dpdf(self, dpdf, err, msg):
|
529
|
+
class dist:
|
530
|
+
pass
|
531
|
+
dist.pdf = lambda x: x
|
532
|
+
dist.dpdf = dpdf
|
533
|
+
with pytest.raises(err, match=msg):
|
534
|
+
TransformedDensityRejection(dist, domain=(1, 10))
|
535
|
+
|
536
|
+
# test domains with inf + nan in them. need to write a custom test for
|
537
|
+
# this because not all methods support infinite tails.
|
538
|
+
@pytest.mark.parametrize("domain, err, msg", inf_nan_domains)
|
539
|
+
def test_inf_nan_domains(self, domain, err, msg):
|
540
|
+
with pytest.raises(err, match=msg):
|
541
|
+
TransformedDensityRejection(StandardNormal(), domain=domain)
|
542
|
+
|
543
|
+
@pytest.mark.parametrize("construction_points", [-1, 0, 0.1])
|
544
|
+
def test_bad_construction_points_scalar(self, construction_points):
|
545
|
+
with pytest.raises(ValueError, match=r"`construction_points` must be "
|
546
|
+
r"a positive integer."):
|
547
|
+
TransformedDensityRejection(
|
548
|
+
StandardNormal(), construction_points=construction_points
|
549
|
+
)
|
550
|
+
|
551
|
+
def test_bad_construction_points_array(self):
|
552
|
+
# empty array
|
553
|
+
construction_points = []
|
554
|
+
with pytest.raises(ValueError, match=r"`construction_points` must "
|
555
|
+
r"either be a "
|
556
|
+
r"scalar or a non-empty array."):
|
557
|
+
TransformedDensityRejection(
|
558
|
+
StandardNormal(), construction_points=construction_points
|
559
|
+
)
|
560
|
+
|
561
|
+
# construction_points not monotonically increasing
|
562
|
+
construction_points = [1, 1, 1, 1, 1, 1]
|
563
|
+
with pytest.warns(RuntimeWarning, match=r"33 : starting points not "
|
564
|
+
r"strictly monotonically "
|
565
|
+
r"increasing"):
|
566
|
+
TransformedDensityRejection(
|
567
|
+
StandardNormal(), construction_points=construction_points
|
568
|
+
)
|
569
|
+
|
570
|
+
# construction_points containing nans
|
571
|
+
construction_points = [np.nan, np.nan, np.nan]
|
572
|
+
with pytest.raises(UNURANError, match=r"50 : bad construction "
|
573
|
+
r"points."):
|
574
|
+
TransformedDensityRejection(
|
575
|
+
StandardNormal(), construction_points=construction_points
|
576
|
+
)
|
577
|
+
|
578
|
+
# construction_points out of domain
|
579
|
+
construction_points = [-10, 10]
|
580
|
+
with pytest.warns(RuntimeWarning, match=r"50 : starting point out of "
|
581
|
+
r"domain"):
|
582
|
+
TransformedDensityRejection(
|
583
|
+
StandardNormal(), domain=(-3, 3),
|
584
|
+
construction_points=construction_points
|
585
|
+
)
|
586
|
+
|
587
|
+
@pytest.mark.parametrize("c", [-1., np.nan, np.inf, 0.1, 1.])
|
588
|
+
def test_bad_c(self, c):
|
589
|
+
msg = r"`c` must either be -0.5 or 0."
|
590
|
+
with pytest.raises(ValueError, match=msg):
|
591
|
+
TransformedDensityRejection(StandardNormal(), c=-1.)
|
592
|
+
|
593
|
+
u = [np.linspace(0, 1, num=1000), [], [[]], [np.nan],
|
594
|
+
[-np.inf, np.nan, np.inf], 0,
|
595
|
+
[[np.nan, 0.5, 0.1], [0.2, 0.4, np.inf], [-2, 3, 4]]]
|
596
|
+
|
597
|
+
@pytest.mark.parametrize("u", u)
|
598
|
+
def test_ppf_hat(self, u):
|
599
|
+
# Increase the `max_squeeze_hat_ratio` so the ppf_hat is more
|
600
|
+
# accurate.
|
601
|
+
rng = TransformedDensityRejection(StandardNormal(),
|
602
|
+
max_squeeze_hat_ratio=0.9999)
|
603
|
+
# Older versions of NumPy throw RuntimeWarnings for comparisons
|
604
|
+
# with nan.
|
605
|
+
with suppress_warnings() as sup:
|
606
|
+
sup.filter(RuntimeWarning, "invalid value encountered in greater")
|
607
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
608
|
+
"greater_equal")
|
609
|
+
sup.filter(RuntimeWarning, "invalid value encountered in less")
|
610
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
611
|
+
"less_equal")
|
612
|
+
res = rng.ppf_hat(u)
|
613
|
+
expected = stats.norm.ppf(u)
|
614
|
+
assert_allclose(res, expected, rtol=1e-3, atol=1e-5)
|
615
|
+
assert res.shape == expected.shape
|
616
|
+
|
617
|
+
def test_bad_dist(self):
|
618
|
+
# Empty distribution
|
619
|
+
class dist:
|
620
|
+
...
|
621
|
+
|
622
|
+
msg = r"`pdf` required but not found."
|
623
|
+
with pytest.raises(ValueError, match=msg):
|
624
|
+
TransformedDensityRejection(dist)
|
625
|
+
|
626
|
+
# dPDF not present in dist
|
627
|
+
class dist:
|
628
|
+
pdf = lambda x: 1-x*x # noqa: E731
|
629
|
+
|
630
|
+
msg = r"`dpdf` required but not found."
|
631
|
+
with pytest.raises(ValueError, match=msg):
|
632
|
+
TransformedDensityRejection(dist)
|
633
|
+
|
634
|
+
|
635
|
+
class TestDiscreteAliasUrn:
|
636
|
+
# DAU fails on these probably because of large domains and small
|
637
|
+
# computation errors in PMF. Mean/SD match but chi-squared test fails.
|
638
|
+
basic_fail_dists = {
|
639
|
+
'nchypergeom_fisher', # numerical errors on tails
|
640
|
+
'nchypergeom_wallenius', # numerical errors on tails
|
641
|
+
'randint' # fails on 32-bit ubuntu
|
642
|
+
}
|
643
|
+
|
644
|
+
@pytest.mark.parametrize("distname, params", distdiscrete)
|
645
|
+
def test_basic(self, distname, params):
|
646
|
+
if distname in self.basic_fail_dists:
|
647
|
+
msg = ("DAU fails on these probably because of large domains "
|
648
|
+
"and small computation errors in PMF.")
|
649
|
+
pytest.skip(msg)
|
650
|
+
if not isinstance(distname, str):
|
651
|
+
dist = distname
|
652
|
+
else:
|
653
|
+
dist = getattr(stats, distname)
|
654
|
+
dist = dist(*params)
|
655
|
+
domain = dist.support()
|
656
|
+
if not np.isfinite(domain[1] - domain[0]):
|
657
|
+
# DAU only works with finite domain. So, skip the distributions
|
658
|
+
# with infinite tails.
|
659
|
+
pytest.skip("DAU only works with a finite domain.")
|
660
|
+
k = np.arange(domain[0], domain[1]+1)
|
661
|
+
pv = dist.pmf(k)
|
662
|
+
mv_ex = dist.stats('mv')
|
663
|
+
rng = DiscreteAliasUrn(dist, random_state=42)
|
664
|
+
check_discr_samples(rng, pv, mv_ex)
|
665
|
+
|
666
|
+
# Can't use bad_pmf_common here as we evaluate PMF early on to avoid
|
667
|
+
# unhelpful errors from UNU.RAN.
|
668
|
+
bad_pmf = [
|
669
|
+
# inf returned
|
670
|
+
(lambda x: np.inf, ValueError,
|
671
|
+
r"must contain only finite / non-nan values"),
|
672
|
+
# nan returned
|
673
|
+
(lambda x: np.nan, ValueError,
|
674
|
+
r"must contain only finite / non-nan values"),
|
675
|
+
# all zeros
|
676
|
+
(lambda x: 0.0, ValueError,
|
677
|
+
r"must contain at least one non-zero value"),
|
678
|
+
# Undefined name inside the function
|
679
|
+
(lambda x: foo, NameError, # type: ignore[name-defined] # noqa: F821
|
680
|
+
r"name 'foo' is not defined"),
|
681
|
+
# Returning wrong type.
|
682
|
+
(lambda x: [], ValueError,
|
683
|
+
r"setting an array element with a sequence."),
|
684
|
+
# probabilities < 0
|
685
|
+
(lambda x: -x, UNURANError,
|
686
|
+
r"50 : probability < 0"),
|
687
|
+
# signature of PMF wrong
|
688
|
+
(lambda: 1.0, TypeError,
|
689
|
+
r"takes 0 positional arguments but 1 was given")
|
690
|
+
]
|
691
|
+
|
692
|
+
@pytest.mark.parametrize("pmf, err, msg", bad_pmf)
|
693
|
+
def test_bad_pmf(self, pmf, err, msg):
|
694
|
+
class dist:
|
695
|
+
pass
|
696
|
+
dist.pmf = pmf
|
697
|
+
with pytest.raises(err, match=msg):
|
698
|
+
DiscreteAliasUrn(dist, domain=(1, 10))
|
699
|
+
|
700
|
+
@pytest.mark.parametrize("pv", [[0.18, 0.02, 0.8],
|
701
|
+
[1.0, 2.0, 3.0, 4.0, 5.0, 6.0]])
|
702
|
+
def test_sampling_with_pv(self, pv):
|
703
|
+
pv = np.asarray(pv, dtype=np.float64)
|
704
|
+
rng = DiscreteAliasUrn(pv, random_state=123)
|
705
|
+
rng.rvs(100_000)
|
706
|
+
pv = pv / pv.sum()
|
707
|
+
variates = np.arange(0, len(pv))
|
708
|
+
# test if the first few moments match
|
709
|
+
m_expected = np.average(variates, weights=pv)
|
710
|
+
v_expected = np.average((variates - m_expected) ** 2, weights=pv)
|
711
|
+
mv_expected = m_expected, v_expected
|
712
|
+
check_discr_samples(rng, pv, mv_expected)
|
713
|
+
|
714
|
+
@pytest.mark.parametrize("pv, msg", bad_pv_common)
|
715
|
+
def test_bad_pv(self, pv, msg):
|
716
|
+
with pytest.raises(ValueError, match=msg):
|
717
|
+
DiscreteAliasUrn(pv)
|
718
|
+
|
719
|
+
# DAU doesn't support infinite tails. So, it should throw an error when
|
720
|
+
# inf is present in the domain.
|
721
|
+
inf_domain = [(-np.inf, np.inf), (np.inf, np.inf), (-np.inf, -np.inf),
|
722
|
+
(0, np.inf), (-np.inf, 0)]
|
723
|
+
|
724
|
+
@pytest.mark.parametrize("domain", inf_domain)
|
725
|
+
def test_inf_domain(self, domain):
|
726
|
+
with pytest.raises(ValueError, match=r"must be finite"):
|
727
|
+
DiscreteAliasUrn(stats.binom(10, 0.2), domain=domain)
|
728
|
+
|
729
|
+
def test_bad_urn_factor(self):
|
730
|
+
with pytest.warns(RuntimeWarning, match=r"relative urn size < 1."):
|
731
|
+
DiscreteAliasUrn([0.5, 0.5], urn_factor=-1)
|
732
|
+
|
733
|
+
def test_bad_args(self):
|
734
|
+
msg = (r"`domain` must be provided when the "
|
735
|
+
r"probability vector is not available.")
|
736
|
+
|
737
|
+
class dist:
|
738
|
+
def pmf(self, x):
|
739
|
+
return x
|
740
|
+
|
741
|
+
with pytest.raises(ValueError, match=msg):
|
742
|
+
DiscreteAliasUrn(dist)
|
743
|
+
|
744
|
+
def test_gh19359(self):
|
745
|
+
pv = special.softmax(np.ones((1533,)))
|
746
|
+
rng = DiscreteAliasUrn(pv, random_state=42)
|
747
|
+
# check the correctness
|
748
|
+
check_discr_samples(rng, pv, (1532 / 2, (1532**2 - 1) / 12),
|
749
|
+
rtol=5e-3)
|
750
|
+
|
751
|
+
|
752
|
+
class TestNumericalInversePolynomial:
|
753
|
+
# Simple Custom Distribution
|
754
|
+
class dist0:
|
755
|
+
def pdf(self, x):
|
756
|
+
return 3/4 * (1-x*x)
|
757
|
+
|
758
|
+
def cdf(self, x):
|
759
|
+
return 3/4 * (x - x**3/3 + 2/3)
|
760
|
+
|
761
|
+
def support(self):
|
762
|
+
return -1, 1
|
763
|
+
|
764
|
+
# Standard Normal Distribution
|
765
|
+
class dist1:
|
766
|
+
def pdf(self, x):
|
767
|
+
return stats.norm._pdf(x / 0.1)
|
768
|
+
|
769
|
+
def cdf(self, x):
|
770
|
+
return stats.norm._cdf(x / 0.1)
|
771
|
+
|
772
|
+
# Sin 2 distribution
|
773
|
+
# / 0.05 + 0.45*(1 +sin(2 Pi x)) if |x| <= 1
|
774
|
+
# f(x) = <
|
775
|
+
# \ 0 otherwise
|
776
|
+
# Taken from UNU.RAN test suite (from file t_pinv.c)
|
777
|
+
class dist2:
|
778
|
+
def pdf(self, x):
|
779
|
+
return 0.05 + 0.45 * (1 + np.sin(2*np.pi*x))
|
780
|
+
|
781
|
+
def cdf(self, x):
|
782
|
+
return (0.05*(x + 1) +
|
783
|
+
0.9*(1. + 2.*np.pi*(1 + x) - np.cos(2.*np.pi*x)) /
|
784
|
+
(4.*np.pi))
|
785
|
+
|
786
|
+
def support(self):
|
787
|
+
return -1, 1
|
788
|
+
|
789
|
+
# Sin 10 distribution
|
790
|
+
# / 0.05 + 0.45*(1 +sin(2 Pi x)) if |x| <= 5
|
791
|
+
# f(x) = <
|
792
|
+
# \ 0 otherwise
|
793
|
+
# Taken from UNU.RAN test suite (from file t_pinv.c)
|
794
|
+
class dist3:
|
795
|
+
def pdf(self, x):
|
796
|
+
return 0.2 * (0.05 + 0.45 * (1 + np.sin(2*np.pi*x)))
|
797
|
+
|
798
|
+
def cdf(self, x):
|
799
|
+
return x/10. + 0.5 + 0.09/(2*np.pi) * (np.cos(10*np.pi) -
|
800
|
+
np.cos(2*np.pi*x))
|
801
|
+
|
802
|
+
def support(self):
|
803
|
+
return -5, 5
|
804
|
+
|
805
|
+
dists = [dist0(), dist1(), dist2(), dist3()]
|
806
|
+
|
807
|
+
# exact mean and variance of the distributions in the list dists
|
808
|
+
mv0 = [0., 4./15.]
|
809
|
+
mv1 = [0., 0.01]
|
810
|
+
mv2 = [-0.45/np.pi, 2/3*0.5 - 0.45**2/np.pi**2]
|
811
|
+
mv3 = [-0.45/np.pi, 0.2 * 250/3 * 0.5 - 0.45**2/np.pi**2]
|
812
|
+
mvs = [mv0, mv1, mv2, mv3]
|
813
|
+
|
814
|
+
@pytest.mark.parametrize("dist, mv_ex",
|
815
|
+
zip(dists, mvs))
|
816
|
+
def test_basic(self, dist, mv_ex):
|
817
|
+
rng = NumericalInversePolynomial(dist, random_state=42)
|
818
|
+
check_cont_samples(rng, dist, mv_ex)
|
819
|
+
|
820
|
+
@pytest.mark.xslow
|
821
|
+
@pytest.mark.parametrize("distname, params", distcont)
|
822
|
+
def test_basic_all_scipy_dists(self, distname, params):
|
823
|
+
|
824
|
+
very_slow_dists = ['anglit', 'gausshyper', 'kappa4',
|
825
|
+
'ksone', 'kstwo', 'levy_l',
|
826
|
+
'levy_stable', 'studentized_range',
|
827
|
+
'trapezoid', 'triang', 'vonmises']
|
828
|
+
# for these distributions, some assertions fail due to minor
|
829
|
+
# numerical differences. They can be avoided either by changing
|
830
|
+
# the seed or by increasing the u_resolution.
|
831
|
+
fail_dists = ['chi2', 'fatiguelife', 'gibrat',
|
832
|
+
'halfgennorm', 'lognorm', 'ncf',
|
833
|
+
'ncx2', 'pareto', 't']
|
834
|
+
# for these distributions, skip the check for agreement between sample
|
835
|
+
# moments and true moments. We cannot expect them to pass due to the
|
836
|
+
# high variance of sample moments.
|
837
|
+
skip_sample_moment_check = ['rel_breitwigner']
|
838
|
+
|
839
|
+
if distname in very_slow_dists:
|
840
|
+
pytest.skip(f"PINV too slow for {distname}")
|
841
|
+
if distname in fail_dists:
|
842
|
+
pytest.skip(f"PINV fails for {distname}")
|
843
|
+
dist = (getattr(stats, distname)
|
844
|
+
if isinstance(distname, str)
|
845
|
+
else distname)
|
846
|
+
dist = dist(*params)
|
847
|
+
with suppress_warnings() as sup:
|
848
|
+
sup.filter(RuntimeWarning)
|
849
|
+
rng = NumericalInversePolynomial(dist, random_state=42)
|
850
|
+
if distname in skip_sample_moment_check:
|
851
|
+
return
|
852
|
+
check_cont_samples(rng, dist, [dist.mean(), dist.var()])
|
853
|
+
|
854
|
+
@pytest.mark.parametrize("pdf, err, msg", bad_pdfs_common)
|
855
|
+
def test_bad_pdf(self, pdf, err, msg):
|
856
|
+
class dist:
|
857
|
+
pass
|
858
|
+
dist.pdf = pdf
|
859
|
+
with pytest.raises(err, match=msg):
|
860
|
+
NumericalInversePolynomial(dist, domain=[0, 5])
|
861
|
+
|
862
|
+
@pytest.mark.parametrize("logpdf, err, msg", bad_logpdfs_common)
|
863
|
+
def test_bad_logpdf(self, logpdf, err, msg):
|
864
|
+
class dist:
|
865
|
+
pass
|
866
|
+
dist.logpdf = logpdf
|
867
|
+
with pytest.raises(err, match=msg):
|
868
|
+
NumericalInversePolynomial(dist, domain=[0, 5])
|
869
|
+
|
870
|
+
# test domains with inf + nan in them. need to write a custom test for
|
871
|
+
# this because not all methods support infinite tails.
|
872
|
+
@pytest.mark.parametrize("domain, err, msg", inf_nan_domains)
|
873
|
+
def test_inf_nan_domains(self, domain, err, msg):
|
874
|
+
with pytest.raises(err, match=msg):
|
875
|
+
NumericalInversePolynomial(StandardNormal(), domain=domain)
|
876
|
+
|
877
|
+
u = [
|
878
|
+
# test if quantile 0 and 1 return -inf and inf respectively and check
|
879
|
+
# the correctness of the PPF for equidistant points between 0 and 1.
|
880
|
+
np.linspace(0, 1, num=10000),
|
881
|
+
# test the PPF method for empty arrays
|
882
|
+
[], [[]],
|
883
|
+
# test if nans and infs return nan result.
|
884
|
+
[np.nan], [-np.inf, np.nan, np.inf],
|
885
|
+
# test if a scalar is returned for a scalar input.
|
886
|
+
0,
|
887
|
+
# test for arrays with nans, values greater than 1 and less than 0,
|
888
|
+
# and some valid values.
|
889
|
+
[[np.nan, 0.5, 0.1], [0.2, 0.4, np.inf], [-2, 3, 4]]
|
890
|
+
]
|
891
|
+
|
892
|
+
@pytest.mark.parametrize("u", u)
|
893
|
+
def test_ppf(self, u):
|
894
|
+
dist = StandardNormal()
|
895
|
+
rng = NumericalInversePolynomial(dist, u_resolution=1e-14)
|
896
|
+
# Older versions of NumPy throw RuntimeWarnings for comparisons
|
897
|
+
# with nan.
|
898
|
+
with suppress_warnings() as sup:
|
899
|
+
sup.filter(RuntimeWarning, "invalid value encountered in greater")
|
900
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
901
|
+
"greater_equal")
|
902
|
+
sup.filter(RuntimeWarning, "invalid value encountered in less")
|
903
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
904
|
+
"less_equal")
|
905
|
+
res = rng.ppf(u)
|
906
|
+
expected = stats.norm.ppf(u)
|
907
|
+
assert_allclose(res, expected, rtol=1e-11, atol=1e-11)
|
908
|
+
assert res.shape == expected.shape
|
909
|
+
|
910
|
+
x = [np.linspace(-10, 10, num=10000), [], [[]], [np.nan],
|
911
|
+
[-np.inf, np.nan, np.inf], 0,
|
912
|
+
[[np.nan, 0.5, 0.1], [0.2, 0.4, np.inf], [-np.inf, 3, 4]]]
|
913
|
+
|
914
|
+
@pytest.mark.parametrize("x", x)
|
915
|
+
def test_cdf(self, x):
|
916
|
+
dist = StandardNormal()
|
917
|
+
rng = NumericalInversePolynomial(dist, u_resolution=1e-14)
|
918
|
+
# Older versions of NumPy throw RuntimeWarnings for comparisons
|
919
|
+
# with nan.
|
920
|
+
with suppress_warnings() as sup:
|
921
|
+
sup.filter(RuntimeWarning, "invalid value encountered in greater")
|
922
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
923
|
+
"greater_equal")
|
924
|
+
sup.filter(RuntimeWarning, "invalid value encountered in less")
|
925
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
926
|
+
"less_equal")
|
927
|
+
res = rng.cdf(x)
|
928
|
+
expected = stats.norm.cdf(x)
|
929
|
+
assert_allclose(res, expected, rtol=1e-11, atol=1e-11)
|
930
|
+
assert res.shape == expected.shape
|
931
|
+
|
932
|
+
@pytest.mark.slow
|
933
|
+
def test_u_error(self):
|
934
|
+
dist = StandardNormal()
|
935
|
+
rng = NumericalInversePolynomial(dist, u_resolution=1e-10)
|
936
|
+
max_error, mae = rng.u_error()
|
937
|
+
assert max_error < 1e-10
|
938
|
+
assert mae <= max_error
|
939
|
+
rng = NumericalInversePolynomial(dist, u_resolution=1e-14)
|
940
|
+
max_error, mae = rng.u_error()
|
941
|
+
assert max_error < 1e-14
|
942
|
+
assert mae <= max_error
|
943
|
+
|
944
|
+
bad_orders = [1, 4.5, 20, np.inf, np.nan]
|
945
|
+
bad_u_resolution = [1e-20, 1e-1, np.inf, np.nan]
|
946
|
+
|
947
|
+
@pytest.mark.parametrize("order", bad_orders)
|
948
|
+
def test_bad_orders(self, order):
|
949
|
+
dist = StandardNormal()
|
950
|
+
|
951
|
+
msg = r"`order` must be an integer in the range \[3, 17\]."
|
952
|
+
with pytest.raises(ValueError, match=msg):
|
953
|
+
NumericalInversePolynomial(dist, order=order)
|
954
|
+
|
955
|
+
@pytest.mark.parametrize("u_resolution", bad_u_resolution)
|
956
|
+
def test_bad_u_resolution(self, u_resolution):
|
957
|
+
msg = r"`u_resolution` must be between 1e-15 and 1e-5."
|
958
|
+
with pytest.raises(ValueError, match=msg):
|
959
|
+
NumericalInversePolynomial(StandardNormal(),
|
960
|
+
u_resolution=u_resolution)
|
961
|
+
|
962
|
+
def test_bad_args(self):
|
963
|
+
|
964
|
+
class BadDist:
|
965
|
+
def cdf(self, x):
|
966
|
+
return stats.norm._cdf(x)
|
967
|
+
|
968
|
+
dist = BadDist()
|
969
|
+
msg = r"Either of the methods `pdf` or `logpdf` must be specified"
|
970
|
+
with pytest.raises(ValueError, match=msg):
|
971
|
+
rng = NumericalInversePolynomial(dist)
|
972
|
+
|
973
|
+
dist = StandardNormal()
|
974
|
+
rng = NumericalInversePolynomial(dist)
|
975
|
+
msg = r"`sample_size` must be greater than or equal to 1000."
|
976
|
+
with pytest.raises(ValueError, match=msg):
|
977
|
+
rng.u_error(10)
|
978
|
+
|
979
|
+
class Distribution:
|
980
|
+
def pdf(self, x):
|
981
|
+
return np.exp(-0.5 * x*x)
|
982
|
+
|
983
|
+
dist = Distribution()
|
984
|
+
rng = NumericalInversePolynomial(dist)
|
985
|
+
msg = r"Exact CDF required but not found."
|
986
|
+
with pytest.raises(ValueError, match=msg):
|
987
|
+
rng.u_error()
|
988
|
+
|
989
|
+
def test_logpdf_pdf_consistency(self):
|
990
|
+
# 1. check that PINV works with pdf and logpdf only
|
991
|
+
# 2. check that generated ppf is the same (up to a small tolerance)
|
992
|
+
|
993
|
+
class MyDist:
|
994
|
+
pass
|
995
|
+
|
996
|
+
# create generator from dist with only pdf
|
997
|
+
dist_pdf = MyDist()
|
998
|
+
dist_pdf.pdf = lambda x: math.exp(-x*x/2)
|
999
|
+
rng1 = NumericalInversePolynomial(dist_pdf)
|
1000
|
+
|
1001
|
+
# create dist with only logpdf
|
1002
|
+
dist_logpdf = MyDist()
|
1003
|
+
dist_logpdf.logpdf = lambda x: -x*x/2
|
1004
|
+
rng2 = NumericalInversePolynomial(dist_logpdf)
|
1005
|
+
|
1006
|
+
q = np.linspace(1e-5, 1-1e-5, num=100)
|
1007
|
+
assert_allclose(rng1.ppf(q), rng2.ppf(q))
|
1008
|
+
|
1009
|
+
|
1010
|
+
class TestNumericalInverseHermite:
|
1011
|
+
# / (1 +sin(2 Pi x))/2 if |x| <= 1
|
1012
|
+
# f(x) = <
|
1013
|
+
# \ 0 otherwise
|
1014
|
+
# Taken from UNU.RAN test suite (from file t_hinv.c)
|
1015
|
+
class dist0:
|
1016
|
+
def pdf(self, x):
|
1017
|
+
return 0.5*(1. + np.sin(2.*np.pi*x))
|
1018
|
+
|
1019
|
+
def dpdf(self, x):
|
1020
|
+
return np.pi*np.cos(2.*np.pi*x)
|
1021
|
+
|
1022
|
+
def cdf(self, x):
|
1023
|
+
return (1. + 2.*np.pi*(1 + x) - np.cos(2.*np.pi*x)) / (4.*np.pi)
|
1024
|
+
|
1025
|
+
def support(self):
|
1026
|
+
return -1, 1
|
1027
|
+
|
1028
|
+
# / Max(sin(2 Pi x)),0)Pi/2 if -1 < x <0.5
|
1029
|
+
# f(x) = <
|
1030
|
+
# \ 0 otherwise
|
1031
|
+
# Taken from UNU.RAN test suite (from file t_hinv.c)
|
1032
|
+
class dist1:
|
1033
|
+
def pdf(self, x):
|
1034
|
+
if (x <= -0.5):
|
1035
|
+
return np.sin((2. * np.pi) * x) * 0.5 * np.pi
|
1036
|
+
if (x < 0.):
|
1037
|
+
return 0.
|
1038
|
+
if (x <= 0.5):
|
1039
|
+
return np.sin((2. * np.pi) * x) * 0.5 * np.pi
|
1040
|
+
|
1041
|
+
def dpdf(self, x):
|
1042
|
+
if (x <= -0.5):
|
1043
|
+
return np.cos((2. * np.pi) * x) * np.pi * np.pi
|
1044
|
+
if (x < 0.):
|
1045
|
+
return 0.
|
1046
|
+
if (x <= 0.5):
|
1047
|
+
return np.cos((2. * np.pi) * x) * np.pi * np.pi
|
1048
|
+
|
1049
|
+
def cdf(self, x):
|
1050
|
+
if (x <= -0.5):
|
1051
|
+
return 0.25 * (1 - np.cos((2. * np.pi) * x))
|
1052
|
+
if (x < 0.):
|
1053
|
+
return 0.5
|
1054
|
+
if (x <= 0.5):
|
1055
|
+
return 0.75 - 0.25 * np.cos((2. * np.pi) * x)
|
1056
|
+
|
1057
|
+
def support(self):
|
1058
|
+
return -1, 0.5
|
1059
|
+
|
1060
|
+
dists = [dist0(), dist1()]
|
1061
|
+
|
1062
|
+
# exact mean and variance of the distributions in the list dists
|
1063
|
+
mv0 = [-1/(2*np.pi), 1/3 - 1/(4*np.pi*np.pi)]
|
1064
|
+
mv1 = [-1/4, 3/8-1/(2*np.pi*np.pi) - 1/16]
|
1065
|
+
mvs = [mv0, mv1]
|
1066
|
+
|
1067
|
+
@pytest.mark.parametrize("dist, mv_ex",
|
1068
|
+
zip(dists, mvs))
|
1069
|
+
@pytest.mark.parametrize("order", [3, 5])
|
1070
|
+
@pytest.mark.thread_unsafe
|
1071
|
+
def test_basic(self, dist, mv_ex, order):
|
1072
|
+
rng = NumericalInverseHermite(dist, order=order, random_state=42)
|
1073
|
+
check_cont_samples(rng, dist, mv_ex)
|
1074
|
+
|
1075
|
+
# test domains with inf + nan in them. need to write a custom test for
|
1076
|
+
# this because not all methods support infinite tails.
|
1077
|
+
@pytest.mark.parametrize("domain, err, msg", inf_nan_domains)
|
1078
|
+
def test_inf_nan_domains(self, domain, err, msg):
|
1079
|
+
with pytest.raises(err, match=msg):
|
1080
|
+
NumericalInverseHermite(StandardNormal(), domain=domain)
|
1081
|
+
|
1082
|
+
def basic_test_all_scipy_dists(self, distname, shapes):
|
1083
|
+
slow_dists = {'ksone', 'kstwo', 'levy_stable', 'skewnorm'}
|
1084
|
+
fail_dists = {'beta', 'gausshyper', 'geninvgauss', 'ncf', 'nct',
|
1085
|
+
'norminvgauss', 'genhyperbolic', 'studentized_range',
|
1086
|
+
'vonmises', 'kappa4', 'invgauss', 'wald'}
|
1087
|
+
|
1088
|
+
if distname in slow_dists:
|
1089
|
+
pytest.skip("Distribution is too slow")
|
1090
|
+
if distname in fail_dists:
|
1091
|
+
# specific reasons documented in gh-13319
|
1092
|
+
# https://github.com/scipy/scipy/pull/13319#discussion_r626188955
|
1093
|
+
pytest.xfail("Fails - usually due to inaccurate CDF/PDF")
|
1094
|
+
|
1095
|
+
np.random.seed(0)
|
1096
|
+
|
1097
|
+
dist = getattr(stats, distname)(*shapes)
|
1098
|
+
fni = NumericalInverseHermite(dist)
|
1099
|
+
|
1100
|
+
x = np.random.rand(10)
|
1101
|
+
p_tol = np.max(np.abs(dist.ppf(x)-fni.ppf(x))/np.abs(dist.ppf(x)))
|
1102
|
+
u_tol = np.max(np.abs(dist.cdf(fni.ppf(x)) - x))
|
1103
|
+
|
1104
|
+
assert p_tol < 1e-8
|
1105
|
+
assert u_tol < 1e-12
|
1106
|
+
|
1107
|
+
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
|
1108
|
+
@pytest.mark.xslow
|
1109
|
+
@pytest.mark.parametrize(("distname", "shapes"), distcont)
|
1110
|
+
def test_basic_all_scipy_dists(self, distname, shapes):
|
1111
|
+
# if distname == "truncnorm":
|
1112
|
+
# pytest.skip("Tested separately")
|
1113
|
+
self.basic_test_all_scipy_dists(distname, shapes)
|
1114
|
+
|
1115
|
+
@pytest.mark.fail_slow(5)
|
1116
|
+
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
|
1117
|
+
def test_basic_truncnorm_gh17155(self):
|
1118
|
+
self.basic_test_all_scipy_dists("truncnorm", (0.1, 2))
|
1119
|
+
|
1120
|
+
def test_input_validation(self):
|
1121
|
+
match = r"`order` must be either 1, 3, or 5."
|
1122
|
+
with pytest.raises(ValueError, match=match):
|
1123
|
+
NumericalInverseHermite(StandardNormal(), order=2)
|
1124
|
+
|
1125
|
+
match = "`cdf` required but not found"
|
1126
|
+
with pytest.raises(ValueError, match=match):
|
1127
|
+
NumericalInverseHermite("norm")
|
1128
|
+
|
1129
|
+
match = "could not convert string to float"
|
1130
|
+
with pytest.raises(ValueError, match=match):
|
1131
|
+
NumericalInverseHermite(StandardNormal(),
|
1132
|
+
u_resolution='ekki')
|
1133
|
+
|
1134
|
+
rngs = [None, 0, np.random.RandomState(0)]
|
1135
|
+
rngs.append(np.random.default_rng(0)) # type: ignore
|
1136
|
+
sizes = [(None, tuple()), (8, (8,)), ((4, 5, 6), (4, 5, 6))]
|
1137
|
+
|
1138
|
+
@pytest.mark.parametrize('rng', rngs)
|
1139
|
+
@pytest.mark.parametrize('size_in, size_out', sizes)
|
1140
|
+
@pytest.mark.thread_unsafe
|
1141
|
+
def test_RVS(self, rng, size_in, size_out):
|
1142
|
+
dist = StandardNormal()
|
1143
|
+
fni = NumericalInverseHermite(dist)
|
1144
|
+
|
1145
|
+
rng2 = deepcopy(rng)
|
1146
|
+
rvs = fni.rvs(size=size_in, random_state=rng)
|
1147
|
+
if size_in is not None:
|
1148
|
+
assert rvs.shape == size_out
|
1149
|
+
|
1150
|
+
if rng2 is not None:
|
1151
|
+
rng2 = check_random_state(rng2)
|
1152
|
+
uniform = rng2.uniform(size=size_in)
|
1153
|
+
rvs2 = stats.norm.ppf(uniform)
|
1154
|
+
assert_allclose(rvs, rvs2)
|
1155
|
+
|
1156
|
+
def test_inaccurate_CDF(self):
|
1157
|
+
# CDF function with inaccurate tail cannot be inverted; see gh-13319
|
1158
|
+
# https://github.com/scipy/scipy/pull/13319#discussion_r626188955
|
1159
|
+
shapes = (2.3098496451481823, 0.6268795430096368)
|
1160
|
+
match = ("98 : one or more intervals very short; possibly due to "
|
1161
|
+
"numerical problems with a pole or very flat tail")
|
1162
|
+
|
1163
|
+
# fails with default tol
|
1164
|
+
with pytest.warns(RuntimeWarning, match=match):
|
1165
|
+
NumericalInverseHermite(stats.beta(*shapes))
|
1166
|
+
|
1167
|
+
# no error with coarser tol
|
1168
|
+
NumericalInverseHermite(stats.beta(*shapes), u_resolution=1e-8)
|
1169
|
+
|
1170
|
+
def test_custom_distribution(self):
|
1171
|
+
dist1 = StandardNormal()
|
1172
|
+
fni1 = NumericalInverseHermite(dist1)
|
1173
|
+
|
1174
|
+
dist2 = stats.norm()
|
1175
|
+
fni2 = NumericalInverseHermite(dist2)
|
1176
|
+
|
1177
|
+
assert_allclose(fni1.rvs(random_state=0), fni2.rvs(random_state=0))
|
1178
|
+
|
1179
|
+
u = [
|
1180
|
+
# check the correctness of the PPF for equidistant points between
|
1181
|
+
# 0.02 and 0.98.
|
1182
|
+
np.linspace(0., 1., num=10000),
|
1183
|
+
# test the PPF method for empty arrays
|
1184
|
+
[], [[]],
|
1185
|
+
# test if nans and infs return nan result.
|
1186
|
+
[np.nan], [-np.inf, np.nan, np.inf],
|
1187
|
+
# test if a scalar is returned for a scalar input.
|
1188
|
+
0,
|
1189
|
+
# test for arrays with nans, values greater than 1 and less than 0,
|
1190
|
+
# and some valid values.
|
1191
|
+
[[np.nan, 0.5, 0.1], [0.2, 0.4, np.inf], [-2, 3, 4]]
|
1192
|
+
]
|
1193
|
+
|
1194
|
+
@pytest.mark.parametrize("u", u)
|
1195
|
+
def test_ppf(self, u):
|
1196
|
+
dist = StandardNormal()
|
1197
|
+
rng = NumericalInverseHermite(dist, u_resolution=1e-12)
|
1198
|
+
# Older versions of NumPy throw RuntimeWarnings for comparisons
|
1199
|
+
# with nan.
|
1200
|
+
with suppress_warnings() as sup:
|
1201
|
+
sup.filter(RuntimeWarning, "invalid value encountered in greater")
|
1202
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
1203
|
+
"greater_equal")
|
1204
|
+
sup.filter(RuntimeWarning, "invalid value encountered in less")
|
1205
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
1206
|
+
"less_equal")
|
1207
|
+
res = rng.ppf(u)
|
1208
|
+
expected = stats.norm.ppf(u)
|
1209
|
+
assert_allclose(res, expected, rtol=1e-9, atol=3e-10)
|
1210
|
+
assert res.shape == expected.shape
|
1211
|
+
|
1212
|
+
@pytest.mark.slow
|
1213
|
+
def test_u_error(self):
|
1214
|
+
dist = StandardNormal()
|
1215
|
+
rng = NumericalInverseHermite(dist, u_resolution=1e-10)
|
1216
|
+
max_error, mae = rng.u_error()
|
1217
|
+
assert max_error < 1e-10
|
1218
|
+
assert mae <= max_error
|
1219
|
+
with suppress_warnings() as sup:
|
1220
|
+
# ignore warning about u-resolution being too small.
|
1221
|
+
sup.filter(RuntimeWarning)
|
1222
|
+
rng = NumericalInverseHermite(dist, u_resolution=1e-14)
|
1223
|
+
max_error, mae = rng.u_error()
|
1224
|
+
assert max_error < 1e-14
|
1225
|
+
assert mae <= max_error
|
1226
|
+
|
1227
|
+
|
1228
|
+
class TestDiscreteGuideTable:
|
1229
|
+
basic_fail_dists = {
|
1230
|
+
'nchypergeom_fisher', # numerical errors on tails
|
1231
|
+
'nchypergeom_wallenius', # numerical errors on tails
|
1232
|
+
'randint' # fails on 32-bit ubuntu
|
1233
|
+
}
|
1234
|
+
|
1235
|
+
def test_guide_factor_gt3_raises_warning(self):
|
1236
|
+
pv = [0.1, 0.3, 0.6]
|
1237
|
+
urng = np.random.default_rng()
|
1238
|
+
with pytest.warns(RuntimeWarning):
|
1239
|
+
DiscreteGuideTable(pv, random_state=urng, guide_factor=7)
|
1240
|
+
|
1241
|
+
def test_guide_factor_zero_raises_warning(self):
|
1242
|
+
pv = [0.1, 0.3, 0.6]
|
1243
|
+
urng = np.random.default_rng()
|
1244
|
+
with pytest.warns(RuntimeWarning):
|
1245
|
+
DiscreteGuideTable(pv, random_state=urng, guide_factor=0)
|
1246
|
+
|
1247
|
+
def test_negative_guide_factor_raises_warning(self):
|
1248
|
+
# This occurs from the UNU.RAN wrapper automatically.
|
1249
|
+
# however it already gives a useful warning
|
1250
|
+
# Here we just test that a warning is raised.
|
1251
|
+
pv = [0.1, 0.3, 0.6]
|
1252
|
+
urng = np.random.default_rng()
|
1253
|
+
with pytest.warns(RuntimeWarning):
|
1254
|
+
DiscreteGuideTable(pv, random_state=urng, guide_factor=-1)
|
1255
|
+
|
1256
|
+
@pytest.mark.parametrize("distname, params", distdiscrete)
|
1257
|
+
def test_basic(self, distname, params):
|
1258
|
+
if distname in self.basic_fail_dists:
|
1259
|
+
msg = ("DGT fails on these probably because of large domains "
|
1260
|
+
"and small computation errors in PMF.")
|
1261
|
+
pytest.skip(msg)
|
1262
|
+
|
1263
|
+
if not isinstance(distname, str):
|
1264
|
+
dist = distname
|
1265
|
+
else:
|
1266
|
+
dist = getattr(stats, distname)
|
1267
|
+
|
1268
|
+
dist = dist(*params)
|
1269
|
+
domain = dist.support()
|
1270
|
+
|
1271
|
+
if not np.isfinite(domain[1] - domain[0]):
|
1272
|
+
# DGT only works with finite domain. So, skip the distributions
|
1273
|
+
# with infinite tails.
|
1274
|
+
pytest.skip("DGT only works with a finite domain.")
|
1275
|
+
|
1276
|
+
k = np.arange(domain[0], domain[1]+1)
|
1277
|
+
pv = dist.pmf(k)
|
1278
|
+
mv_ex = dist.stats('mv')
|
1279
|
+
rng = DiscreteGuideTable(dist, random_state=42)
|
1280
|
+
check_discr_samples(rng, pv, mv_ex)
|
1281
|
+
|
1282
|
+
u = [
|
1283
|
+
# the correctness of the PPF for equidistant points between 0 and 1.
|
1284
|
+
np.linspace(0, 1, num=10000),
|
1285
|
+
# test the PPF method for empty arrays
|
1286
|
+
[], [[]],
|
1287
|
+
# test if nans and infs return nan result.
|
1288
|
+
[np.nan], [-np.inf, np.nan, np.inf],
|
1289
|
+
# test if a scalar is returned for a scalar input.
|
1290
|
+
0,
|
1291
|
+
# test for arrays with nans, values greater than 1 and less than 0,
|
1292
|
+
# and some valid values.
|
1293
|
+
[[np.nan, 0.5, 0.1], [0.2, 0.4, np.inf], [-2, 3, 4]]
|
1294
|
+
]
|
1295
|
+
|
1296
|
+
@pytest.mark.parametrize('u', u)
|
1297
|
+
def test_ppf(self, u):
|
1298
|
+
n, p = 4, 0.1
|
1299
|
+
dist = stats.binom(n, p)
|
1300
|
+
rng = DiscreteGuideTable(dist, random_state=42)
|
1301
|
+
|
1302
|
+
# Older versions of NumPy throw RuntimeWarnings for comparisons
|
1303
|
+
# with nan.
|
1304
|
+
with suppress_warnings() as sup:
|
1305
|
+
sup.filter(RuntimeWarning, "invalid value encountered in greater")
|
1306
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
1307
|
+
"greater_equal")
|
1308
|
+
sup.filter(RuntimeWarning, "invalid value encountered in less")
|
1309
|
+
sup.filter(RuntimeWarning, "invalid value encountered in "
|
1310
|
+
"less_equal")
|
1311
|
+
|
1312
|
+
res = rng.ppf(u)
|
1313
|
+
expected = stats.binom.ppf(u, n, p)
|
1314
|
+
assert_equal(res.shape, expected.shape)
|
1315
|
+
assert_equal(res, expected)
|
1316
|
+
|
1317
|
+
@pytest.mark.parametrize("pv, msg", bad_pv_common)
|
1318
|
+
def test_bad_pv(self, pv, msg):
|
1319
|
+
with pytest.raises(ValueError, match=msg):
|
1320
|
+
DiscreteGuideTable(pv)
|
1321
|
+
|
1322
|
+
# DGT doesn't support infinite tails. So, it should throw an error when
|
1323
|
+
# inf is present in the domain.
|
1324
|
+
inf_domain = [(-np.inf, np.inf), (np.inf, np.inf), (-np.inf, -np.inf),
|
1325
|
+
(0, np.inf), (-np.inf, 0)]
|
1326
|
+
|
1327
|
+
@pytest.mark.parametrize("domain", inf_domain)
|
1328
|
+
def test_inf_domain(self, domain):
|
1329
|
+
with pytest.raises(ValueError, match=r"must be finite"):
|
1330
|
+
DiscreteGuideTable(stats.binom(10, 0.2), domain=domain)
|
1331
|
+
|
1332
|
+
|
1333
|
+
class TestSimpleRatioUniforms:
|
1334
|
+
# pdf with piecewise linear function as transformed density
|
1335
|
+
# with T = -1/sqrt with shift. Taken from UNU.RAN test suite
|
1336
|
+
# (from file t_srou.c)
|
1337
|
+
class dist:
|
1338
|
+
def __init__(self, shift):
|
1339
|
+
self.shift = shift
|
1340
|
+
self.mode = shift
|
1341
|
+
|
1342
|
+
def pdf(self, x):
|
1343
|
+
x -= self.shift
|
1344
|
+
y = 1. / (abs(x) + 1.)
|
1345
|
+
return 0.5 * y * y
|
1346
|
+
|
1347
|
+
def cdf(self, x):
|
1348
|
+
x -= self.shift
|
1349
|
+
if x <= 0.:
|
1350
|
+
return 0.5 / (1. - x)
|
1351
|
+
else:
|
1352
|
+
return 1. - 0.5 / (1. + x)
|
1353
|
+
|
1354
|
+
dists = [dist(0.), dist(10000.)]
|
1355
|
+
|
1356
|
+
# exact mean and variance of the distributions in the list dists
|
1357
|
+
mv1 = [0., np.inf]
|
1358
|
+
mv2 = [10000., np.inf]
|
1359
|
+
mvs = [mv1, mv2]
|
1360
|
+
|
1361
|
+
@pytest.mark.parametrize("dist, mv_ex",
|
1362
|
+
zip(dists, mvs))
|
1363
|
+
@pytest.mark.thread_unsafe
|
1364
|
+
def test_basic(self, dist, mv_ex):
|
1365
|
+
rng = SimpleRatioUniforms(dist, mode=dist.mode, random_state=42)
|
1366
|
+
check_cont_samples(rng, dist, mv_ex)
|
1367
|
+
rng = SimpleRatioUniforms(dist, mode=dist.mode,
|
1368
|
+
cdf_at_mode=dist.cdf(dist.mode),
|
1369
|
+
random_state=42)
|
1370
|
+
check_cont_samples(rng, dist, mv_ex)
|
1371
|
+
|
1372
|
+
# test domains with inf + nan in them. need to write a custom test for
|
1373
|
+
# this because not all methods support infinite tails.
|
1374
|
+
@pytest.mark.parametrize("domain, err, msg", inf_nan_domains)
|
1375
|
+
def test_inf_nan_domains(self, domain, err, msg):
|
1376
|
+
with pytest.raises(err, match=msg):
|
1377
|
+
SimpleRatioUniforms(StandardNormal(), domain=domain)
|
1378
|
+
|
1379
|
+
def test_bad_args(self):
|
1380
|
+
# pdf_area < 0
|
1381
|
+
with pytest.raises(ValueError, match=r"`pdf_area` must be > 0"):
|
1382
|
+
SimpleRatioUniforms(StandardNormal(), mode=0, pdf_area=-1)
|
1383
|
+
|
1384
|
+
|
1385
|
+
class TestRatioUniforms:
|
1386
|
+
def test_rv_generation(self):
|
1387
|
+
# use KS test to check distribution of rvs
|
1388
|
+
# normal distribution
|
1389
|
+
f = stats.norm.pdf
|
1390
|
+
v = np.sqrt(f(np.sqrt(2))) * np.sqrt(2)
|
1391
|
+
u = np.sqrt(f(0))
|
1392
|
+
gen = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=12345)
|
1393
|
+
assert_equal(stats.kstest(gen.rvs(2500), 'norm')[1] > 0.25, True)
|
1394
|
+
|
1395
|
+
# exponential distribution
|
1396
|
+
gen = RatioUniforms(lambda x: np.exp(-x), umax=1,
|
1397
|
+
vmin=0, vmax=2*np.exp(-1), random_state=12345)
|
1398
|
+
assert_equal(stats.kstest(gen.rvs(1000), 'expon')[1] > 0.25, True)
|
1399
|
+
|
1400
|
+
def test_shape(self):
|
1401
|
+
# test shape of return value depending on size parameter
|
1402
|
+
f = stats.norm.pdf
|
1403
|
+
v = np.sqrt(f(np.sqrt(2))) * np.sqrt(2)
|
1404
|
+
u = np.sqrt(f(0))
|
1405
|
+
|
1406
|
+
gen1 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1407
|
+
gen2 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1408
|
+
gen3 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1409
|
+
r1, r2, r3 = gen1.rvs(3), gen2.rvs((3,)), gen3.rvs((3, 1))
|
1410
|
+
assert_equal(r1, r2)
|
1411
|
+
assert_equal(r2, r3.flatten())
|
1412
|
+
assert_equal(r1.shape, (3,))
|
1413
|
+
assert_equal(r3.shape, (3, 1))
|
1414
|
+
|
1415
|
+
gen4 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=12)
|
1416
|
+
gen5 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=12)
|
1417
|
+
r4, r5 = gen4.rvs(size=(3, 3, 3)), gen5.rvs(size=27)
|
1418
|
+
assert_equal(r4.flatten(), r5)
|
1419
|
+
assert_equal(r4.shape, (3, 3, 3))
|
1420
|
+
|
1421
|
+
gen6 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1422
|
+
gen7 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1423
|
+
gen8 = RatioUniforms(f, umax=u, vmin=-v, vmax=v, random_state=1234)
|
1424
|
+
r6, r7, r8 = gen6.rvs(), gen7.rvs(1), gen8.rvs((1,))
|
1425
|
+
assert_equal(r6, r7)
|
1426
|
+
assert_equal(r7, r8)
|
1427
|
+
|
1428
|
+
def test_random_state(self):
|
1429
|
+
f = stats.norm.pdf
|
1430
|
+
v = np.sqrt(f(np.sqrt(2))) * np.sqrt(2)
|
1431
|
+
umax = np.sqrt(f(0))
|
1432
|
+
gen1 = RatioUniforms(f, umax=umax, vmin=-v, vmax=v, random_state=1234)
|
1433
|
+
r1 = gen1.rvs(10)
|
1434
|
+
rng = np.random.RandomState(1234)
|
1435
|
+
gen2 = RatioUniforms(f, umax=umax, vmin=-v, vmax=v, random_state=rng)
|
1436
|
+
r2 = gen2.rvs(10)
|
1437
|
+
assert_equal(r1, r2)
|
1438
|
+
|
1439
|
+
def test_exceptions(self):
|
1440
|
+
f = stats.norm.pdf
|
1441
|
+
# need vmin < vmax
|
1442
|
+
with assert_raises(ValueError, match="vmin must be smaller than vmax"):
|
1443
|
+
RatioUniforms(pdf=f, umax=1, vmin=3, vmax=1)
|
1444
|
+
with assert_raises(ValueError, match="vmin must be smaller than vmax"):
|
1445
|
+
RatioUniforms(pdf=f, umax=1, vmin=1, vmax=1)
|
1446
|
+
# need umax > 0
|
1447
|
+
with assert_raises(ValueError, match="umax must be positive"):
|
1448
|
+
RatioUniforms(pdf=f, umax=-1, vmin=1, vmax=3)
|
1449
|
+
with assert_raises(ValueError, match="umax must be positive"):
|
1450
|
+
RatioUniforms(pdf=f, umax=0, vmin=1, vmax=3)
|