test_sampling.py

#   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.

from itertools import combinations
from typing import Tuple
import numpy as np

try:
    import unittest.mock as mock  # py3
except ImportError:
    import mock

import numpy.testing as npt
import arviz as az
import pymc3 as pm
import theano.tensor as tt
from theano import shared
import theano
from pymc3.tests.models import simple_init
from pymc3.tests.helpers import SeededTest
from pymc3.exceptions import IncorrectArgumentsError
from scipy import stats
import pytest


@pytest.mark.xfail(
    condition=(theano.config.floatX == "float32"), reason="Fails on float32"
)
@pytest.mark.xfail(condition=(theano.config.floatX == "float32"), reason="Fails on float32")
class TestSample(SeededTest):
    def setup_method(self):
        super().setup_method()
        self.model, self.start, self.step, _ = simple_init()

    def test_sample_does_not_set_seed(self):
        random_numbers = []
        for _ in range(2):
            np.random.seed(1)
            with self.model:
                pm.sample(1, tune=0, chains=1)
                random_numbers.append(np.random.random())
        assert random_numbers[0] == random_numbers[1]

    def test_parallel_sample_does_not_reuse_seed(self):
        cores = 4
        random_numbers = []
        draws = []
        for _ in range(2):
            np.random.seed(1)  # seeds in other processes don't effect main process
            with self.model:
                trace = pm.sample(100, tune=0, cores=cores)
            # numpy thread mentioned race condition.  might as well check none are equal
            for first, second in combinations(range(cores), 2):
                first_chain = trace.get_values("x", chains=first)
                second_chain = trace.get_values("x", chains=second)
                assert not (first_chain == second_chain).all()
            draws.append(trace.get_values("x"))
            random_numbers.append(np.random.random())

        # Make sure future random processes aren't effected by this
        assert random_numbers[0] == random_numbers[1]
        assert (draws[0] == draws[1]).all()

    def test_sample(self):
        test_cores = [1]
        with self.model:
            for cores in test_cores:
                for steps in [1, 10, 300]:
                    pm.sample(
                        steps,
                        tune=0,
                        step=self.step,
                        cores=cores,
                        random_seed=self.random_seed,
                    )

    def test_sample_init(self):
        with self.model:
            for init in ("advi", "advi_map", "map"):
                pm.sample(
                    init=init,
                    tune=0,
                    n_init=1000,
                    draws=50,
                    random_seed=self.random_seed,
                )

    def test_sample_args(self):
        with self.model:
            with pytest.raises(ValueError) as excinfo:
                pm.sample(50, tune=0, init=None, foo=1)
            assert "'foo'" in str(excinfo.value)

            with pytest.raises(ValueError) as excinfo:
                pm.sample(50, tune=0, init=None, foo={})
            assert "foo" in str(excinfo.value)

            with pytest.raises(ValueError) as excinfo:
                pm.sample(10, tune=0, init=None, target_accept=0.9)
            assert "target_accept" in str(excinfo.value)

    def test_iter_sample(self):
        with self.model:
            samps = pm.sampling.iter_sample(
                draws=5,
                step=self.step,
                start=self.start,
                tune=0,
                random_seed=self.random_seed,
            )
            for i, trace in enumerate(samps):
                assert i == len(trace) - 1, "Trace does not have correct length."

    def test_parallel_start(self):
        with self.model:
            tr = pm.sample(
                0,
                tune=5,
                cores=2,
                discard_tuned_samples=False,
                start=[{"x": [10, 10]}, {"x": [-10, -10]}],
                random_seed=self.random_seed,
            )
        assert tr.get_values("x", chains=0)[0][0] > 0
        assert tr.get_values("x", chains=1)[0][0] < 0

    def test_sample_tune_len(self):
        with self.model:
            trace = pm.sample(draws=100, tune=50, cores=1)
            assert len(trace) == 100
            trace = pm.sample(draws=100, tune=50, cores=1, discard_tuned_samples=False)
            assert len(trace) == 150
            trace = pm.sample(draws=100, tune=50, cores=4)
            assert len(trace) == 100

    @pytest.mark.parametrize("step_cls", [pm.NUTS, pm.Metropolis, pm.Slice])
    @pytest.mark.parametrize("discard", [True, False])
    def test_trace_report(self, step_cls, discard):
        with self.model:
            # add more variables, because stats are 2D with CompoundStep!
            pm.Uniform('uni')
            trace = pm.sample(
                draws=100, tune=50, cores=1,
                discard_tuned_samples=discard,
                step=step_cls()
            )
            assert trace.report.n_tune == 50
            assert trace.report.n_draws == 100
            assert isinstance(trace.report.t_sampling, float)
        pass

    @pytest.mark.parametrize('cores', [1, 2])
    def test_sampler_stat_tune(self, cores):
        with self.model:
            tune_stat = pm.sample(
                tune=5, draws=7, cores=cores,
                discard_tuned_samples=False,
                step=pm.Metropolis()
            ).get_sampler_stats('tune', chains=1)
            assert list(tune_stat).count(True) == 5
            assert list(tune_stat).count(False) == 7
        pass

    @pytest.mark.parametrize(
        "start, error",
        [
            ([1, 2], TypeError),
            ({"x": 1}, ValueError),
            ({"x": [1, 2, 3]}, ValueError),
            ({"x": np.array([[1, 1], [1, 1]])}, ValueError),
        ],
    )
    def test_sample_start_bad_shape(self, start, error):
        with pytest.raises(error):
            pm.sampling._check_start_shape(self.model, start)

    @pytest.mark.parametrize(
        "start", [{"x": np.array([1, 1])}, {"x": [10, 10]}, {"x": [-10, -10]}]
    )
    def test_sample_start_good_shape(self, start):
        pm.sampling._check_start_shape(self.model, start)

    def test_sample_callback(self):
        callback = mock.Mock()
        test_cores = [1, 2]
        test_chains = [1, 2]
        with self.model:
            for cores in test_cores:
                for chain in test_chains:
                    pm.sample(
                        10, tune=0, chains=chain, step=self.step, cores=cores, random_seed=self.random_seed,
                        callback=callback
                    )
                    assert callback.called

    def test_callback_can_cancel(self):
        trace_cancel_length = 5

        def callback(trace, draw):
            if len(trace) >= trace_cancel_length:
                raise KeyboardInterrupt()

        with self.model:
            trace = pm.sample(
                        10, tune=0, chains=1, step=self.step, cores=1, random_seed=self.random_seed,
                        callback=callback
                    )
            assert len(trace) == trace_cancel_length


def test_empty_model():
    with pm.Model():
        pm.Normal("a", observed=1)
        with pytest.raises(ValueError) as error:
            pm.sample()
        error.match("any free variables")


def test_partial_trace_sample():
    with pm.Model() as model:
        a = pm.Normal("a", mu=0, sigma=1)
        b = pm.Normal("b", mu=0, sigma=1)
        trace = pm.sample(trace=[a])


@pytest.mark.xfail(
    condition=(theano.config.floatX == "float32"), reason="Fails on float32"
)
class TestNamedSampling(SeededTest):
    def test_shared_named(self):
        G_var = shared(value=np.atleast_2d(1.0), broadcastable=(True, False), name="G")

        with pm.Model():
            theta0 = pm.Normal(
                "theta0",
                mu=np.atleast_2d(0),
                tau=np.atleast_2d(1e20),
                shape=(1, 1),
                testval=np.atleast_2d(0),
            )
            theta = pm.Normal(
                "theta", mu=tt.dot(G_var, theta0), tau=np.atleast_2d(1e20), shape=(1, 1)
            )
            res = theta.random()
            assert np.isclose(res, 0.0)

    def test_shared_unnamed(self):
        G_var = shared(value=np.atleast_2d(1.0), broadcastable=(True, False))
        with pm.Model():
            theta0 = pm.Normal(
                "theta0",
                mu=np.atleast_2d(0),
                tau=np.atleast_2d(1e20),
                shape=(1, 1),
                testval=np.atleast_2d(0),
            )
            theta = pm.Normal(
                "theta", mu=tt.dot(G_var, theta0), tau=np.atleast_2d(1e20), shape=(1, 1)
            )
            res = theta.random()
            assert np.isclose(res, 0.0)

    def test_constant_named(self):
        G_var = tt.constant(np.atleast_2d(1.0), name="G")
        with pm.Model():
            theta0 = pm.Normal(
                "theta0",
                mu=np.atleast_2d(0),
                tau=np.atleast_2d(1e20),
                shape=(1, 1),
                testval=np.atleast_2d(0),
            )
            theta = pm.Normal(
                "theta", mu=tt.dot(G_var, theta0), tau=np.atleast_2d(1e20), shape=(1, 1)
            )

            res = theta.random()
            assert np.isclose(res, 0.0)


class TestChooseBackend:
    def test_choose_backend_none(self):
        with mock.patch("pymc3.sampling.NDArray") as nd:
            pm.sampling._choose_backend(None, "chain")
        assert nd.called

    def test_choose_backend_list_of_variables(self):
        with mock.patch("pymc3.sampling.NDArray") as nd:
            pm.sampling._choose_backend(["var1", "var2"], "chain")
        nd.assert_called_with(vars=["var1", "var2"])

    def test_choose_backend_invalid(self):
        with pytest.raises(ValueError):
            pm.sampling._choose_backend("invalid", "chain")

    def test_choose_backend_shortcut(self):
        backend = mock.Mock()
        shortcuts = {"test_backend": {"backend": backend, "name": None}}
        pm.sampling._choose_backend("test_backend", "chain", shortcuts=shortcuts)
        assert backend.called


class TestSamplePPC(SeededTest):
    def test_normal_scalar(self):
        nchains = 2
        ndraws = 500
        with pm.Model() as model:
            mu = pm.Normal("mu", 0.0, 1.0)
            a = pm.Normal("a", mu=mu, sigma=1, observed=0.0)
            trace = pm.sample(draws=ndraws, chains=nchains)

        with model:
            # test list input
            ppc0 = pm.sample_posterior_predictive([model.test_point], samples=10)
            ppc0 = pm.fast_sample_posterior_predictive([model.test_point], samples=10)
            # deprecated argument is not introduced to fast version [2019/08/20:rpg]
            with pytest.warns(DeprecationWarning):
                ppc = pm.sample_posterior_predictive(trace, vars=[a])
            # test empty ppc
            ppc = pm.sample_posterior_predictive(trace, var_names=[])
            assert len(ppc) == 0
            ppc = pm.fast_sample_posterior_predictive(trace, var_names=[])
            assert len(ppc) == 0

            # test keep_size parameter
            ppc = pm.sample_posterior_predictive(trace, keep_size=True)
            assert ppc["a"].shape == (nchains, ndraws)
            ppc = pm.fast_sample_posterior_predictive(trace, keep_size=True)
            assert ppc["a"].shape == (nchains, ndraws)

            # test default case
            ppc = pm.sample_posterior_predictive(trace, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (nchains * ndraws,)
            # mu's standard deviation may have changed thanks to a's observed
            _, pval = stats.kstest(ppc["a"] - trace["mu"], stats.norm(loc=0, scale=1).cdf)
            assert pval > 0.001

            # test default case
            ppc = pm.fast_sample_posterior_predictive(trace, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (nchains * ndraws,)
            # mu's standard deviation may have changed thanks to a's observed
            _, pval = stats.kstest(ppc["a"] - trace["mu"], stats.norm(loc=0, scale=1).cdf)
            assert pval > 0.001


        # size argument not introduced to fast version [2019/08/20:rpg]
        with model:
            ppc = pm.sample_posterior_predictive(trace, size=5, var_names=["a"])
            assert ppc["a"].shape == (nchains * ndraws, 5)

    def test_normal_vector(self, caplog):
        with pm.Model() as model:
            mu = pm.Normal("mu", 0.0, 1.0)
            a = pm.Normal("a", mu=mu, sigma=1, observed=np.array([0.5, 0.2]))
            trace = pm.sample()

        with model:
            # test list input
            ppc0 = pm.sample_posterior_predictive([model.test_point], samples=10)
            ppc = pm.sample_posterior_predictive(trace, samples=12, var_names=[])
            assert len(ppc) == 0

            # test list input
            ppc0 = pm.fast_sample_posterior_predictive([model.test_point], samples=10)
            ppc = pm.fast_sample_posterior_predictive(trace, samples=12, var_names=[])
            assert len(ppc) == 0

            # test keep_size parameter
            ppc = pm.sample_posterior_predictive(trace, keep_size=True)
            assert ppc["a"].shape == (trace.nchains, len(trace), 2)
            with pytest.warns(UserWarning):
                ppc = pm.sample_posterior_predictive(trace, samples=12, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (12, 2)

            # test keep_size parameter
            ppc = pm.fast_sample_posterior_predictive(trace, keep_size=True)
            assert ppc["a"].shape == (trace.nchains, len(trace), 2)
            with pytest.warns(UserWarning):
                ppc = pm.fast_sample_posterior_predictive(trace, samples=12, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (12, 2)


            # size unsupported by fast_ version  argument. [2019/08/19:rpg]
            ppc = pm.sample_posterior_predictive(trace, samples=10, var_names=["a"], size=4)
            assert "a" in ppc
            assert ppc["a"].shape == (10, 4, 2)

    def test_exceptions(self, caplog):
        with pm.Model() as model:
            mu = pm.Normal("mu", 0.0, 1.0)
            a = pm.Normal("a", mu=mu, sigma=1, observed=np.array([0.5, 0.2]))
            trace = pm.sample()

        with model:
            with pytest.raises(IncorrectArgumentsError):
                ppc = pm.sample_posterior_predictive(trace, samples=10, keep_size=True)
            with pytest.raises(IncorrectArgumentsError):
                ppc = pm.fast_sample_posterior_predictive(trace, samples=10, keep_size=True)

            # Not for fast_sample_posterior_predictive
            with pytest.raises(IncorrectArgumentsError):
                ppc = pm.sample_posterior_predictive(trace, size=4, keep_size=True)
            with pytest.raises(IncorrectArgumentsError):
                ppc = pm.sample_posterior_predictive(trace, vars=[a], var_names=["a"])

    def test_vector_observed(self):
        with pm.Model() as model:
            mu = pm.Normal("mu", mu=0, sigma=1)
            a = pm.Normal("a", mu=mu, sigma=1, observed=np.array([0.0, 1.0]))
            trace = pm.sample()

        with model:
            # test list input
            ppc0 = pm.sample_posterior_predictive([model.test_point], samples=10)
            ppc = pm.sample_posterior_predictive(trace, samples=12, var_names=[])
            assert len(ppc) == 0
            ppc = pm.sample_posterior_predictive(trace, samples=12, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (12, 2)

            ppc = pm.sample_posterior_predictive(trace, samples=10, var_names=["a"], size=4)
            assert "a" in ppc
            assert ppc["a"].shape == (10, 4, 2)

            # now with fast version
            # test list input
            ppc0 = pm.fast_sample_posterior_predictive([model.test_point], samples=10)
            ppc = pm.fast_sample_posterior_predictive(trace, samples=12, var_names=[])
            assert len(ppc) == 0
            ppc = pm.fast_sample_posterior_predictive(trace, samples=12, var_names=["a"])
            assert "a" in ppc
            assert ppc["a"].shape == (12, 2)


    def test_sum_normal(self):
        with pm.Model() as model:
            a = pm.Normal("a", sigma=0.2)
            b = pm.Normal("b", mu=a)
            trace = pm.sample()

        with model:
            # test list input
            ppc0 = pm.sample_posterior_predictive([model.test_point], samples=10)
            assert ppc0 == {}
            ppc = pm.sample_posterior_predictive(trace, samples=1000, var_names=["b"])
            assert len(ppc) == 1
            assert ppc["b"].shape == (1000,)
            scale = np.sqrt(1 + 0.2 ** 2)
            _, pval = stats.kstest(ppc["b"], stats.norm(scale=scale).cdf)
            assert pval > 0.001

            # test list input
            ppc0 = pm.fast_sample_posterior_predictive([model.test_point], samples=10)
            assert ppc0 == {}
            ppc = pm.fast_sample_posterior_predictive(trace, samples=1000, var_names=["b"])
            assert len(ppc) == 1
            assert ppc["b"].shape == (1000,)
            scale = np.sqrt(1 + 0.2 ** 2)
            _, pval = stats.kstest(ppc["b"], stats.norm(scale=scale).cdf)
            assert pval > 0.001



    def test_model_not_drawable_prior(self):
        data = np.random.poisson(lam=10, size=200)
        model = pm.Model()
        with model:
            mu = pm.HalfFlat("sigma")
            pm.Poisson("foo", mu=mu, observed=data)
            trace = pm.sample(tune=1000)

        with model:
            with pytest.raises(ValueError) as excinfo:
                pm.sample_prior_predictive(50)
            assert "Cannot sample" in str(excinfo.value)
            samples = pm.sample_posterior_predictive(trace, 40)
            assert samples["foo"].shape == (40, 200)

            samples = pm.fast_sample_posterior_predictive(trace, 40)
            assert samples["foo"].shape == (40, 200)


    def test_model_shared_variable(self):
        x = np.random.randn(100)
        y = x > 0
        x_shared = theano.shared(x)
        y_shared = theano.shared(y)
        with pm.Model() as model:
            coeff = pm.Normal("x", mu=0, sd=1)
            logistic = pm.Deterministic("p", pm.math.sigmoid(coeff * x_shared))

            obs = pm.Bernoulli("obs", p=logistic, observed=y_shared)
            trace = pm.sample(100)

        x_shared.set_value([-1, 0, 1.0])
        y_shared.set_value([0, 0, 0])

        samples = 100
        with model:
            post_pred = pm.sample_posterior_predictive(
                trace, samples=samples, var_names=["p", "obs"]
            )

        expected_p = np.array(
            [logistic.eval({coeff: val}) for val in trace["x"][:samples]]
        )
        assert post_pred["obs"].shape == (samples, 3)
        assert np.allclose(post_pred["p"], expected_p)


        # fast version
        samples = 100
        with model:
            post_pred = pm.fast_sample_posterior_predictive(
                trace, samples=samples, var_names=["p", "obs"]
            )

        expected_p = np.array(
            [logistic.eval({coeff: val}) for val in trace["x"][:samples]]
        )
        assert post_pred["obs"].shape == (samples, 3)
        assert np.allclose(post_pred["p"], expected_p)

    def test_deterministic_of_observed(self):
        meas_in_1 = pm.theanof.floatX(2 + 4 * np.random.randn(100))
        meas_in_2 = pm.theanof.floatX(5 + 4 * np.random.randn(100))
        with pm.Model() as model:
            mu_in_1 = pm.Normal("mu_in_1", 0, 1)
            sigma_in_1 = pm.HalfNormal("sd_in_1", 1)
            mu_in_2 = pm.Normal("mu_in_2", 0, 1)
            sigma_in_2 = pm.HalfNormal("sd__in_2", 1)

            in_1 = pm.Normal("in_1", mu_in_1, sigma_in_1, observed=meas_in_1)
            in_2 = pm.Normal("in_2", mu_in_2, sigma_in_2, observed=meas_in_2)
            out_diff = in_1 + in_2
            pm.Deterministic("out", out_diff)

            trace = pm.sample(100)
            ppc_trace = pm.trace_to_dataframe(
                trace, varnames=[n for n in trace.varnames if n != "out"]
            ).to_dict("records")
            with pytest.warns(DeprecationWarning):
                ppc = pm.sample_posterior_predictive(
                    model=model,
                    trace=ppc_trace,
                    samples=len(ppc_trace),
                    vars=(model.deterministics + model.basic_RVs),
                )

            rtol = 1e-5 if theano.config.floatX == "float64" else 1e-3
            assert np.allclose(ppc["in_1"] + ppc["in_2"], ppc["out"], rtol=rtol)

            ppc = pm.sample_posterior_predictive(
                model=model,
                trace=ppc_trace,
                samples=len(ppc_trace),
                var_names = [var.name for var in (model.deterministics + model.basic_RVs)]
            )

            rtol = 1e-5 if theano.config.floatX == "float64" else 1e-3
            assert np.allclose(ppc["in_1"] + ppc["in_2"], ppc["out"], rtol=rtol)


            ppc = pm.fast_sample_posterior_predictive(
                model=model,
                trace=ppc_trace,
                samples=len(ppc_trace),
                var_names = [var.name for var in (model.deterministics + model.basic_RVs)]
            )

            rtol = 1e-5 if theano.config.floatX == "float64" else 1e-3
            assert np.allclose(ppc["in_1"] + ppc["in_2"], ppc["out"], rtol=rtol)



    def test_deterministic_of_observed_modified_interface(self):
        meas_in_1 = pm.theanof.floatX(2 + 4 * np.random.randn(100))
        meas_in_2 = pm.theanof.floatX(5 + 4 * np.random.randn(100))
        with pm.Model() as model:
            mu_in_1 = pm.Normal("mu_in_1", 0, 1)
            sigma_in_1 = pm.HalfNormal("sd_in_1", 1)
            mu_in_2 = pm.Normal("mu_in_2", 0, 1)
            sigma_in_2 = pm.HalfNormal("sd__in_2", 1)

            in_1 = pm.Normal("in_1", mu_in_1, sigma_in_1, observed=meas_in_1)
            in_2 = pm.Normal("in_2", mu_in_2, sigma_in_2, observed=meas_in_2)
            out_diff = in_1 + in_2
            pm.Deterministic("out", out_diff)

            trace = pm.sample(100)
            ppc_trace = pm.trace_to_dataframe(
                trace, varnames=[n for n in trace.varnames if n != "out"]
            ).to_dict("records")
            ppc = pm.sample_posterior_predictive(
                model=model,
                trace=ppc_trace,
                samples=len(ppc_trace),
                var_names=[x.name for x in (model.deterministics + model.basic_RVs)],
            )

            rtol = 1e-5 if theano.config.floatX == "float64" else 1e-3
            assert np.allclose(ppc["in_1"] + ppc["in_2"], ppc["out"], rtol=rtol)

            ppc = pm.fast_sample_posterior_predictive(
                model=model,
                trace=ppc_trace,
                samples=len(ppc_trace),
                var_names=[x.name for x in (model.deterministics + model.basic_RVs)],
            )

            rtol = 1e-5 if theano.config.floatX == "float64" else 1e-3
            assert np.allclose(ppc["in_1"] + ppc["in_2"], ppc["out"], rtol=rtol)


    def test_variable_type(self):
        with pm.Model() as model:
            mu = pm.HalfNormal("mu", 1)
            a = pm.Normal("a", mu=mu, sigma=2, observed=np.array([1, 2]))
            b = pm.Poisson("b", mu, observed=np.array([1, 2]))
            trace = pm.sample()

        with model:
            ppc = pm.sample_posterior_predictive(trace, samples=1)
            assert ppc["a"].dtype.kind == "f"
            assert ppc["b"].dtype.kind == "i"


class TestSamplePPCW(SeededTest):
    def test_sample_posterior_predictive_w(self):
        data0 = np.random.normal(0, 1, size=500)

        with pm.Model() as model_0:
            mu = pm.Normal("mu", mu=0, sigma=1)
            y = pm.Normal("y", mu=mu, sigma=1, observed=data0)
            trace_0 = pm.sample()

        with pm.Model() as model_1:
            mu = pm.Normal("mu", mu=0, sigma=1, shape=len(data0))
            y = pm.Normal("y", mu=mu, sigma=1, observed=data0)
            trace_1 = pm.sample()

        traces = [trace_0, trace_0]
        models = [model_0, model_0]
        ppc = pm.sample_posterior_predictive_w(traces, 100, models)
        assert ppc["y"].shape == (100, 500)

        traces = [trace_0, trace_1]
        models = [model_0, model_1]
        ppc = pm.sample_posterior_predictive_w(traces, 100, models)
        assert ppc["y"].shape == (100, 500)


@pytest.mark.parametrize(
    "method",
    [
        "jitter+adapt_diag",
        "adapt_diag",
        "advi",
        "ADVI+adapt_diag",
        "advi+adapt_diag_grad",
        "map",
        "advi_map",
        "adapt_full",
        "jitter+adapt_full",
    ],
)
def test_exec_nuts_init(method):
    with pm.Model() as model:
        pm.Normal("a", mu=0, sigma=1, shape=2)
        pm.HalfNormal("b", sigma=1)
    with model:
        start, _ = pm.init_nuts(init=method, n_init=10)
        assert isinstance(start, list)
        assert len(start) == 1
        assert isinstance(start[0], dict)
        assert "a" in start[0] and "b_log__" in start[0]
        start, _ = pm.init_nuts(init=method, n_init=10, chains=2)
        assert isinstance(start, list)
        assert len(start) == 2
        assert isinstance(start[0], dict)
        assert "a" in start[0] and "b_log__" in start[0]


@pytest.fixture(scope="class")
def point_list_arg_bug_fixture() -> Tuple[pm.Model, pm.backends.base.MultiTrace]:
    with pm.Model() as pmodel:
        n = pm.Normal('n')
        trace = pm.sample()

    with pmodel:
        d = pm.Deterministic('d', n * 4)
    return pmodel, trace

class TestSamplePriorPredictive(SeededTest):
    def test_ignores_observed(self):
        observed = np.random.normal(10, 1, size=200)
        with pm.Model():
            # Use a prior that's way off to show we're ignoring the observed variables
            observed_data = pm.Data("observed_data", observed)
            mu = pm.Normal("mu", mu=-100, sigma=1)
            positive_mu = pm.Deterministic("positive_mu", np.abs(mu))
            z = -1 - positive_mu
            pm.Normal("x_obs", mu=z, sigma=1, observed=observed_data)
            prior = pm.sample_prior_predictive()

        assert "observed_data" not in prior
        assert (prior["mu"] < 90).all()
        assert (prior["positive_mu"] > 90).all()
        assert (prior["x_obs"] < 90).all()
        assert prior["x_obs"].shape == (500, 200)
        npt.assert_array_almost_equal(
            prior["positive_mu"], np.abs(prior["mu"]), decimal=4
        )

    def test_respects_shape(self):
        for shape in (2, (2,), (10, 2), (10, 10)):
            with pm.Model():
                mu = pm.Gamma("mu", 3, 1, shape=1)
                goals = pm.Poisson("goals", mu, shape=shape)
                with pytest.warns(DeprecationWarning):
                    trace1 = pm.sample_prior_predictive(10, vars=["mu", "goals"])
                    trace2 = pm.sample_prior_predictive(10, var_names=["mu", "goals"])
            if shape == 2:  # want to test shape as an int
                shape = (2,)
            assert trace1["goals"].shape == (10,) + shape
            assert trace2["goals"].shape == (10,) + shape

    def test_multivariate(self):
        with pm.Model():
            m = pm.Multinomial("m", n=5, p=np.array([0.25, 0.25, 0.25, 0.25]), shape=4)
            trace = pm.sample_prior_predictive(10)

        assert m.random(size=10).shape == (10, 4)
        assert trace["m"].shape == (10, 4)

    def test_multivariate2(self):
        # Added test for issue #3271
        mn_data = np.random.multinomial(n=100, pvals=[1 / 6.0] * 6, size=10)
        with pm.Model() as dm_model:
            probs = pm.Dirichlet("probs", a=np.ones(6), shape=6)
            obs = pm.Multinomial("obs", n=100, p=probs, observed=mn_data)
            burned_trace = pm.sample(20, tune=10, cores=1)
        sim_priors = pm.sample_prior_predictive(samples=20,
                                                model=dm_model)
        sim_ppc = pm.sample_posterior_predictive(burned_trace,
                                                 samples=20,
                                                 model=dm_model)
        assert sim_priors['probs'].shape == (20, 6)
        assert sim_priors['obs'].shape == (20,) + obs.distribution.shape
        assert sim_ppc['obs'].shape == (20,) + obs.distribution.shape

        sim_ppc = pm.fast_sample_posterior_predictive(burned_trace,
                                                 samples=20,
                                                 model=dm_model)
        assert sim_ppc['obs'].shape == (20,) + obs.distribution.shape


    def test_layers(self):
        with pm.Model() as model:
            a = pm.Uniform("a", lower=0, upper=1, shape=10)
            b = pm.Binomial("b", n=1, p=a, shape=10)

        avg = b.random(size=10000).mean(axis=0)
        npt.assert_array_almost_equal(avg, 0.5 * np.ones_like(b), decimal=2)

    def test_transformed(self):
        n = 18
        at_bats = 45 * np.ones(n, dtype=int)
        hits = np.random.randint(1, 40, size=n, dtype=int)
        draws = 50

        with pm.Model() as model:
            phi = pm.Beta("phi", alpha=1.0, beta=1.0)

            kappa_log = pm.Exponential("logkappa", lam=5.0)
            kappa = pm.Deterministic("kappa", tt.exp(kappa_log))

            thetas = pm.Beta(
                "thetas", alpha=phi * kappa, beta=(1.0 - phi) * kappa, shape=n
            )

            y = pm.Binomial("y", n=at_bats, p=thetas, observed=hits)
            gen = pm.sample_prior_predictive(draws)

        assert gen["phi"].shape == (draws,)
        assert gen["y"].shape == (draws, n)
        assert "thetas_logodds__" in gen

    def test_shared(self):
        n1 = 10
        obs = shared(np.random.rand(n1) < 0.5)
        draws = 50

        with pm.Model() as m:
            p = pm.Beta("p", 1.0, 1.0)
            y = pm.Bernoulli("y", p, observed=obs)
            gen1 = pm.sample_prior_predictive(draws)

        assert gen1["y"].shape == (draws, n1)

        n2 = 20
        obs.set_value(np.random.rand(n2) < 0.5)
        with m:
            gen2 = pm.sample_prior_predictive(draws)

        assert gen2["y"].shape == (draws, n2)

    def test_density_dist(self):

        obs = np.random.normal(-1, 0.1, size=10)
        with pm.Model():
            mu = pm.Normal("mu", 0, 1)
            sd = pm.Gamma("sd", 1, 2)
            a = pm.DensityDist(
                "a",
                pm.Normal.dist(mu, sd).logp,
                random=pm.Normal.dist(mu, sd).random,
                observed=obs,
            )
            prior = pm.sample_prior_predictive()

        npt.assert_almost_equal(prior["a"].mean(), 0, decimal=1)

    def test_shape_edgecase(self):
        with pm.Model():
            mu = pm.Normal("mu", shape=5)
            sd = pm.Uniform("sd", lower=2, upper=3)
            x = pm.Normal("x", mu=mu, sigma=sd, shape=5)
            prior = pm.sample_prior_predictive(10)
        assert prior["mu"].shape == (10, 5)

    def test_zeroinflatedpoisson(self):
        with pm.Model():
            theta = pm.Beta("theta", alpha=1, beta=1)
            psi = pm.HalfNormal("psi", sd=1)
            pm.ZeroInflatedPoisson("suppliers", psi=psi, theta=theta, shape=20)
            gen_data = pm.sample_prior_predictive(samples=5000)
            assert gen_data["theta"].shape == (5000,)
            assert gen_data["psi"].shape == (5000,)
            assert gen_data["suppliers"].shape == (5000, 20)

    def test_bounded_dist(self):
        with pm.Model() as model:
            BoundedNormal = pm.Bound(pm.Normal, lower=0.0)
            x = BoundedNormal(
                "x", mu=tt.zeros((3, 1)), sd=1 * tt.ones((3, 1)), shape=(3, 1)
            )

        with model:
            prior_trace = pm.sample_prior_predictive(5)
            assert prior_trace["x"].shape == (5, 3, 1)

class TestSamplePosteriorPredictive:
    def test_point_list_arg_bug_fspp(self, point_list_arg_bug_fixture):
        pmodel, trace = point_list_arg_bug_fixture
        with pmodel:
            pp = pm.fast_sample_posterior_predictive(
                [trace[15]],
                var_names=['d']
            )

    def test_point_list_arg_bug_spp(self, point_list_arg_bug_fixture):
        pmodel, trace = point_list_arg_bug_fixture
        with pmodel:
            pp = pm.sample_posterior_predictive(
                [trace[15]],
                var_names=['d']
            )

    def test_sample_from_xarray_prior(self, point_list_arg_bug_fixture):
        pmodel, trace = point_list_arg_bug_fixture

        with pmodel:
            prior = pm.sample_prior_predictive(samples=20)
        idat = az.from_pymc3(trace, prior=prior)
        with pmodel:
            pp = pm.sample_posterior_predictive(
                idat.prior,
                var_names=['d']
            )

    def test_sample_from_xarray_posterior(self, point_list_arg_bug_fixture):
        pmodel, trace = point_list_arg_bug_fixture
        idat = az.from_pymc3(trace)
        with pmodel:
            pp = pm.sample_posterior_predictive(
                idat.posterior,
                var_names=['d']
            )

    def test_sample_from_xarray_posterior_fast(self, point_list_arg_bug_fixture):
        pmodel, trace = point_list_arg_bug_fixture
        idat = az.from_pymc3(trace)
        with pmodel:
            pp = pm.fast_sample_posterior_predictive(
                idat.posterior,
                var_names=['d']
            )