pymc-extras 0.2.5__py3-none-any.whl → 0.2.7__py3-none-any.whl

pymc_extras-0.2.5.dist-info/RECORD

@@ -1,108 +0,0 @@
-pymc_extras/__init__.py,sha256=lYGf9TcwUHROIElkX7Epnb7-IppcmiSEYuxdtRzqS3s,1195
-pymc_extras/linearmodel.py,sha256=6eitl15Ec15mSZu7zoHZ7Wwy4U1DPwqfAgwEt6ILeIc,3920
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-pymc_extras/inference/pathfinder/lbfgs.py,sha256=GOoJBil5Kft_iFwGNUGKSeqzI5x_shA4KQWDwgGuQtQ,7110
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-pymc_extras/inference/smc/sampling.py,sha256=AYwmKqGoV6pBtKnh9SUbBKbN7VcoFgb3MmNWV7SivMA,15365
-pymc_extras/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-pymc_extras/model/marginal/distributions.py,sha256=iM1yT7_BmivgUSloQPKE2QXGPgjvLqDMY_OTBGsdAWg,15563
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-pymc_extras/model/transforms/autoreparam.py,sha256=_NltGWmNqi_X9sHCqAvWcBveLTPxVy11-wENFTcN6kk,12377
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-pymc_extras/preprocessing/standard_scaler.py,sha256=Vajp33ma6OkwlU54JYtSS8urHbMJ3CRiRFxZpvFNuus,600
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-pymc_extras/statespace/models/SARIMAX.py,sha256=SX0eiSK1pOt4dHBjWzBqVpRz67pBGLN5pQQgXcOiOgY,21607
-pymc_extras/statespace/models/VARMAX.py,sha256=xkIuftNc_5NHFpqZalExni99-1kovnzm5OjMIDNgaxY,15989
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-pymc_extras/statespace/models/structural.py,sha256=sep9pesJdRN4X8Bea6_RhO3112uWOZRuYRxO6ibl_OA,63943
-pymc_extras/statespace/models/utilities.py,sha256=G9GuHKsghmIYOlfkPtvxBWF-FZY5-5JI1fJQM8N7EnE,15373
-pymc_extras/statespace/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-pymc_extras/utils/spline.py,sha256=qGq0gcoMG5dpdazKFzG0RXkkCWP8ADPPXN-653-oFn4,4820
-pymc_extras-0.2.5.dist-info/licenses/LICENSE,sha256=WjiLhUKEysJvy5e9jk6WwFv9tmAPtnov1uJ6gcH1kIs,11720
-tests/__init__.py,sha256=-ree9OWVCyTeXLR944OWjrQX2os15HXrRNkhJ7QdRjc,603
-tests/test_blackjax_smc.py,sha256=jcNgcMBxaKyPg9UvHnWQtwoL79LXlSpZfALe3RGEZnQ,7233
-tests/test_find_map.py,sha256=B8ThnXNyfTQeem24QaLoTitFrsxKoq2VQINUdOwzna0,3379
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-tests/test_laplace.py,sha256=fArHjwMR7x98K-gZLvrvb3AwNZ7_fo7E0A4SJyt4EGU,9843
-tests/test_linearmodel.py,sha256=iB8ApNqIX9_nUHoo-Tm51xuPdrva5t4VLLut6qXB5Ao,6906
-tests/test_model_builder.py,sha256=QiINEihBR9rx8xM4Nqlg4urZKoyo58aTKDtxl9SJF1s,11249
-tests/test_pathfinder.py,sha256=vlMI1p2Ja5X4QIaSV4h6U41I303rEppfO0JqE3xe1Rs,10023
-tests/test_pivoted_cholesky.py,sha256=PuMdMSCzO4KdQWpUF4SEBeuH_qsINCIH8TYtmmJ1NKo,692
-tests/test_printing.py,sha256=HnvwwjrjBuxXFAJdyU0K_lvKGLgh4nzHAnhsIUpenbY,5211
-tests/test_prior_from_trace.py,sha256=HOzR3l98pl7TEJquo_kSugED4wBTgHo4-8lgnpmacs8,5516
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-tests/distributions/__init__.py,sha256=jt-oloszTLNFwi9AgU3M4m6xKQ8xpQE338rmmaMZcMs,795
-tests/distributions/test_continuous.py,sha256=1-bu-IP6RgLUJnuPYpOD8ZS1ahYbKtsJ9oflBfqCaFo,5477
-tests/distributions/test_discrete.py,sha256=CjjaUpppsvQ6zLzV15ZsbwNOKrDmEdz4VWcleoCXUi0,7776
-tests/distributions/test_discrete_markov_chain.py,sha256=8RCHZXSB8IWjniuKaGGlM_iTWGmdrcOqginxmrAeEJg,9212
-tests/distributions/test_multivariate.py,sha256=LBvBuoT_3rzi8rR38b8L441Y-9Ff0cIXeRBKiEn6kjs,10452
-tests/distributions/test_transform.py,sha256=QM9sSQ5eSbuT2pM76nUMWqb-tQa7DGZbT9uwFDqIRUk,2672
-tests/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-pymc_extras-0.2.5.dist-info/METADATA,sha256=02v5liTQQ55sV8xeFl5EjFpwbOKSYKG6g5lE_4htpBo,5227
-pymc_extras-0.2.5.dist-info/WHEEL,sha256=lTU6B6eIfYoiQJTZNc-fyaR6BpL6ehTzU3xGYxn2n8k,91
-pymc_extras-0.2.5.dist-info/top_level.txt,sha256=D6RkgBiXiZCel0nvsYg_zYEoT_VuwocyIY98EMaulj0,18
-pymc_extras-0.2.5.dist-info/RECORD,,

pymc_extras-0.2.5.dist-info/top_level.txt

@@ -1,2 +0,0 @@
-pymc_extras
-tests

tests/__init__.py

@@ -1,13 +0,0 @@
-#   Copyright 2020 The PyMC Developers
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.

tests/distributions/__init__.py

@@ -1,19 +0,0 @@
-#   Copyright 2022 The PyMC Developers
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-
-
-from pymc_extras.distributions import histogram_utils
-from pymc_extras.distributions.histogram_utils import histogram_approximation
-
-__all__ = ["histogram_utils", "histogram_approximation"]

tests/distributions/test_continuous.py

@@ -1,185 +0,0 @@
-#   Copyright 2020 The PyMC Developers
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-import numpy as np
-import pymc as pm
-
-# general imports
-import pytest
-import scipy.stats.distributions as sp
-
-
-# test support imports from pymc
-from pymc.testing import (
-    BaseTestDistributionRandom,
-    Domain,
-    R,
-    Rplus,
-    Rplusbig,
-    assert_support_point_is_expected,
-    check_logcdf,
-    check_logp,
-    seeded_scipy_distribution_builder,
-    select_by_precision,
-)
-
-# the distributions to be tested
-from pymc_extras.distributions import Chi, GenExtreme, Maxwell
-
-
-class TestGenExtremeClass:
-    """
-    Wrapper class so that tests of experimental additions can be dropped into
-    PyMC directly on adoption.
-
-    pm.logp(GenExtreme.dist(mu=0.,sigma=1.,xi=0.5),value=-0.01)
-    """
-
-    def test_logp(self):
-        def ref_logp(value, mu, sigma, xi):
-            if 1 + xi * (value - mu) / sigma > 0:
-                return sp.genextreme.logpdf(value, c=-xi, loc=mu, scale=sigma)
-            else:
-                return -np.inf
-
-        check_logp(
-            GenExtreme,
-            R,
-            {
-                "mu": R,
-                "sigma": Rplusbig,
-                "xi": Domain([-1, -0.99, -0.5, 0, 0.5, 0.99, 1]),
-            },
-            ref_logp,
-        )
-
-    def test_logcdf(self):
-        def ref_logcdf(value, mu, sigma, xi):
-            if 1 + xi * (value - mu) / sigma > 0:
-                return sp.genextreme.logcdf(value, c=-xi, loc=mu, scale=sigma)
-            else:
-                return -np.inf
-
-        check_logcdf(
-            GenExtreme,
-            R,
-            {
-                "mu": R,
-                "sigma": Rplusbig,
-                "xi": Domain([-1, -0.99, -0.5, 0, 0.5, 0.99, 1]),
-            },
-            ref_logcdf,
-            decimal=select_by_precision(float64=6, float32=2),
-        )
-
-    @pytest.mark.parametrize(
-        "mu, sigma, xi, size, expected",
-        [
-            (0, 1, 0, None, 0),
-            (1, np.arange(1, 4), 0.1, None, 1 + np.arange(1, 4) * (1.1**-0.1 - 1) / 0.1),
-            (np.arange(5), 1, 0.1, None, np.arange(5) + (1.1**-0.1 - 1) / 0.1),
-            (
-                0,
-                1,
-                np.linspace(-0.2, 0.2, 6),
-                None,
-                ((1 + np.linspace(-0.2, 0.2, 6)) ** -np.linspace(-0.2, 0.2, 6) - 1)
-                / np.linspace(-0.2, 0.2, 6),
-            ),
-            (1, 2, 0.1, 5, np.full(5, 1 + 2 * (1.1**-0.1 - 1) / 0.1)),
-            (
-                np.arange(6),
-                np.arange(1, 7),
-                np.linspace(-0.2, 0.2, 6),
-                (3, 6),
-                np.full(
-                    (3, 6),
-                    np.arange(6)
-                    + np.arange(1, 7)
-                    * ((1 + np.linspace(-0.2, 0.2, 6)) ** -np.linspace(-0.2, 0.2, 6) - 1)
-                    / np.linspace(-0.2, 0.2, 6),
-                ),
-            ),
-        ],
-    )
-    def test_genextreme_support_point(self, mu, sigma, xi, size, expected):
-        with pm.Model() as model:
-            GenExtreme("x", mu=mu, sigma=sigma, xi=xi, size=size)
-        assert_support_point_is_expected(model, expected)
-
-    def test_gen_extreme_scipy_kwarg(self):
-        dist = GenExtreme.dist(xi=1, scipy=False)
-        assert dist.owner.inputs[-1].eval() == 1
-
-        dist = GenExtreme.dist(xi=1, scipy=True)
-        assert dist.owner.inputs[-1].eval() == -1
-
-
-class TestGenExtreme(BaseTestDistributionRandom):
-    pymc_dist = GenExtreme
-    pymc_dist_params = {"mu": 0, "sigma": 1, "xi": -0.1}
-    expected_rv_op_params = {"mu": 0, "sigma": 1, "xi": -0.1}
-    # Notice, using different parametrization of xi sign to scipy
-    reference_dist_params = {"loc": 0, "scale": 1, "c": 0.1}
-    reference_dist = seeded_scipy_distribution_builder("genextreme")
-    tests_to_run = [
-        "check_pymc_params_match_rv_op",
-        "check_pymc_draws_match_reference",
-        "check_rv_size",
-    ]
-
-
-class TestChiClass:
-    """
-    Wrapper class so that tests of experimental additions can be dropped into
-    PyMC directly on adoption.
-    """
-
-    def test_logp(self):
-        check_logp(
-            Chi,
-            Rplus,
-            {"nu": Rplus},
-            lambda value, nu: sp.chi.logpdf(value, df=nu),
-        )
-
-    def test_logcdf(self):
-        check_logcdf(
-            Chi,
-            Rplus,
-            {"nu": Rplus},
-            lambda value, nu: sp.chi.logcdf(value, df=nu),
-        )
-
-
-class TestMaxwell:
-    """
-    Wrapper class so that tests of experimental additions can be dropped into
-    PyMC directly on adoption.
-    """
-
-    def test_logp(self):
-        check_logp(
-            Maxwell,
-            Rplus,
-            {"a": Rplus},
-            lambda value, a: sp.maxwell.logpdf(value, scale=a),
-        )
-
-    def test_logcdf(self):
-        check_logcdf(
-            Maxwell,
-            Rplus,
-            {"a": Rplus},
-            lambda value, a: sp.maxwell.logcdf(value, scale=a),
-        )

tests/distributions/test_discrete.py

@@ -1,210 +0,0 @@
-#   Copyright 2023 The PyMC Developers
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-#   See the License for the specific language governing permissions and
-#   limitations under the License.
-import numpy as np
-import pymc as pm
-import pytensor
-import pytensor.tensor as pt
-import pytest
-import scipy.stats
-
-from pymc.logprob.utils import ParameterValueError
-from pymc.testing import (
-    BaseTestDistributionRandom,
-    Domain,
-    I,
-    Rplus,
-    assert_support_point_is_expected,
-    check_logp,
-    discrete_random_tester,
-)
-from pytensor import config
-
-from pymc_extras.distributions import (
-    BetaNegativeBinomial,
-    GeneralizedPoisson,
-    Skellam,
-)
-
-
-class TestGeneralizedPoisson:
-    class TestRandomVariable(BaseTestDistributionRandom):
-        pymc_dist = GeneralizedPoisson
-        pymc_dist_params = {"mu": 4.0, "lam": 1.0}
-        expected_rv_op_params = {"mu": 4.0, "lam": 1.0}
-        tests_to_run = [
-            "check_pymc_params_match_rv_op",
-            "check_rv_size",
-        ]
-
-        def test_random_matches_poisson(self):
-            discrete_random_tester(
-                dist=self.pymc_dist,
-                paramdomains={"mu": Rplus, "lam": Domain([0], edges=(None, None))},
-                ref_rand=lambda mu, lam, size: scipy.stats.poisson.rvs(mu, size=size),
-            )
-
-        @pytest.mark.parametrize("mu", (2.5, 20, 50))
-        def test_random_lam_expected_moments(self, mu):
-            lam = np.array([-0.9, -0.7, -0.2, 0, 0.2, 0.7, 0.9])
-            dist = self.pymc_dist.dist(mu=mu, lam=lam, size=(10_000, len(lam)))
-            draws = dist.eval()
-
-            expected_mean = mu / (1 - lam)
-            np.testing.assert_allclose(draws.mean(0), expected_mean, rtol=1e-1)
-
-            expected_std = np.sqrt(mu / (1 - lam) ** 3)
-            np.testing.assert_allclose(draws.std(0), expected_std, rtol=1e-1)
-
-    def test_logp_matches_poisson(self):
-        # We are only checking this distribution for lambda=0 where it's equivalent to Poisson.
-        mu = pt.scalar("mu")
-        lam = pt.scalar("lam")
-        value = pt.vector("value", dtype="int64")
-
-        logp = pm.logp(GeneralizedPoisson.dist(mu, lam), value)
-        logp_fn = pytensor.function([value, mu, lam], logp)
-
-        test_value = np.array([0, 1, 2, 30])
-        for test_mu in (0.01, 0.1, 0.9, 1, 1.5, 20, 100):
-            np.testing.assert_allclose(
-                logp_fn(test_value, test_mu, lam=0),
-                scipy.stats.poisson.logpmf(test_value, test_mu),
-                rtol=1e-7 if config.floatX == "float64" else 1e-5,
-            )
-
-        # Check out-of-bounds values
-        value = pt.scalar("value")
-        logp = pm.logp(GeneralizedPoisson.dist(mu, lam), value)
-        logp_fn = pytensor.function([value, mu, lam], logp)
-
-        logp_fn(-1, mu=5, lam=0) == -np.inf
-        logp_fn(9, mu=5, lam=-1) == -np.inf
-
-        # Check mu/lam restrictions
-        with pytest.raises(ParameterValueError):
-            logp_fn(1, mu=1, lam=2)
-
-        with pytest.raises(ParameterValueError):
-            logp_fn(1, mu=0, lam=0)
-
-        with pytest.raises(ParameterValueError):
-            logp_fn(1, mu=1, lam=-1)
-
-    def test_logp_lam_expected_moments(self):
-        mu = 30
-        lam = np.array([-0.9, -0.7, -0.2, 0, 0.2, 0.7, 0.9])
-        with pm.Model():
-            x = GeneralizedPoisson("x", mu=mu, lam=lam)
-            trace = pm.sample(chains=1, draws=10_000, random_seed=96).posterior
-
-        expected_mean = mu / (1 - lam)
-        np.testing.assert_allclose(trace["x"].mean(("chain", "draw")), expected_mean, rtol=1e-1)
-
-        expected_std = np.sqrt(mu / (1 - lam) ** 3)
-        np.testing.assert_allclose(trace["x"].std(("chain", "draw")), expected_std, rtol=1e-1)
-
-    @pytest.mark.parametrize(
-        "mu, lam, size, expected",
-        [
-            (50, [-0.6, 0, 0.6], None, np.floor(50 / (1 - np.array([-0.6, 0, 0.6])))),
-            ([5, 50], -0.1, (4, 2), np.full((4, 2), np.floor(np.array([5, 50]) / 1.1))),
-        ],
-    )
-    def test_moment(self, mu, lam, size, expected):
-        with pm.Model() as model:
-            GeneralizedPoisson("x", mu=mu, lam=lam, size=size)
-        assert_support_point_is_expected(model, expected)
-
-
-class TestBetaNegativeBinomial:
-    """
-    Wrapper class so that tests of experimental additions can be dropped into
-    PyMC directly on adoption.
-    """
-
-    def test_logp(self):
-        """
-
-        Beta Negative Binomial logp function test values taken from R package as
-        there is currently no implementation in scipy.
-        https://github.com/scipy/scipy/issues/17330
-
-        The test values can be generated in R with the following code:
-
-        .. code-block:: r
-
-            library(extraDistr)
-
-            create.test.rows <- function(alpha, beta, r, x) {
-                logp <- dbnbinom(x, alpha, beta, r, log=TRUE)
-                paste0("(", paste(alpha, beta, r, x, logp, sep=", "), ")")
-            }
-
-            x <- c(0, 1, 250, 5000)
-            print(create.test.rows(1, 1, 1, x), quote=FALSE)
-            print(create.test.rows(1, 1, 10, x), quote=FALSE)
-            print(create.test.rows(1, 10, 1, x), quote=FALSE)
-            print(create.test.rows(10, 1, 1, x), quote=FALSE)
-            print(create.test.rows(10, 10, 10, x), quote=FALSE)
-
-        """
-        alpha, beta, r, value = pt.scalars("alpha", "beta", "r", "value")
-        logp = pm.logp(BetaNegativeBinomial.dist(alpha, beta, r), value)
-        logp_fn = pytensor.function([value, alpha, beta, r], logp)
-
-        tests = [
-            # 1, 1, 1
-            (1, 1, 1, 0, -0.693147180559945),
-            (1, 1, 1, 1, -1.79175946922805),
-            (1, 1, 1, 250, -11.0548820266432),
-            (1, 1, 1, 5000, -17.0349862828565),
-            # 1, 1, 10
-            (1, 1, 10, 0, -2.39789527279837),
-            (1, 1, 10, 1, -2.58021682959232),
-            (1, 1, 10, 250, -8.82261694534392),
-            (1, 1, 10, 5000, -14.7359968760473),
-            # 1, 10, 1
-            (1, 10, 1, 0, -2.39789527279837),
-            (1, 10, 1, 1, -2.58021682959232),
-            (1, 10, 1, 250, -8.82261694534418),
-            (1, 10, 1, 5000, -14.7359968760446),
-            # 10, 1, 1
-            (10, 1, 1, 0, -0.0953101798043248),
-            (10, 1, 1, 1, -2.58021682959232),
-            (10, 1, 1, 250, -43.5891148758123),
-            (10, 1, 1, 5000, -76.2953173311091),
-            # 10, 10, 10
-            (10, 10, 10, 0, -5.37909807285049),
-            (10, 10, 10, 1, -4.17512526852455),
-            (10, 10, 10, 250, -21.781591505836),
-            (10, 10, 10, 5000, -53.4836799634603),
-        ]
-        for test_alpha, test_beta, test_r, test_value, expected_logp in tests:
-            np.testing.assert_allclose(
-                logp_fn(test_value, test_alpha, test_beta, test_r), expected_logp
-            )
-
-
-class TestSkellam:
-    def test_logp(self):
-        # Scipy Skellam underflows to -inf earlier than PyMC
-        Rplus_small = Domain([0, 0.01, 0.1, 0.9, 0.99, 1, 1.5, 2, 10, np.inf])
-        # Suppress warnings coming from Scipy logpmf implementation
-        with np.errstate(divide="ignore", invalid="ignore"):
-            check_logp(
-                Skellam,
-                I,
-                {"mu1": Rplus_small, "mu2": Rplus_small},
-                lambda value, mu1, mu2: scipy.stats.skellam.logpmf(value, mu1, mu2),
-            )