arviz 0.23.1__py3-none-any.whl → 1.0.0rc0__py3-none-any.whl

arviz/tests/base_tests/test_utils.py

@@ -1,376 +0,0 @@
-"""Tests for arviz.utils."""
-
-# pylint: disable=redefined-outer-name, no-member
-from unittest.mock import Mock
-
-import numpy as np
-import pytest
-import scipy.stats as st
-
-from ...data import dict_to_dataset, from_dict, load_arviz_data
-from ...stats.density_utils import _circular_mean, _normalize_angle, _find_hdi_contours
-from ...utils import (
-    _stack,
-    _subset_list,
-    _var_names,
-    expand_dims,
-    flatten_inference_data_to_dict,
-    one_de,
-    two_de,
-)
-from ..helpers import RandomVariableTestClass
-
-
-@pytest.fixture(scope="session")
-def inference_data():
-    centered_eight = load_arviz_data("centered_eight")
-    return centered_eight
-
-
-@pytest.fixture(scope="session")
-def data():
-    centered_eight = load_arviz_data("centered_eight")
-    return centered_eight.posterior
-
-
-@pytest.mark.parametrize(
-    "var_names_expected",
-    [
-        ("mu", ["mu"]),
-        (None, None),
-        (["mu", "tau"], ["mu", "tau"]),
-        ("~mu", ["theta", "tau"]),
-        (["~mu"], ["theta", "tau"]),
-    ],
-)
-def test_var_names(var_names_expected, data):
-    """Test var_name handling"""
-    var_names, expected = var_names_expected
-    assert _var_names(var_names, data) == expected
-
-
-def test_var_names_warning():
-    """Test confusing var_name handling"""
-    data = from_dict(
-        posterior={
-            "~mu": np.random.randn(2, 10),
-            "mu": -np.random.randn(2, 10),  # pylint: disable=invalid-unary-operand-type
-            "theta": np.random.randn(2, 10, 8),
-        }
-    ).posterior
-    var_names = expected = ["~mu"]
-    with pytest.warns(UserWarning):
-        assert _var_names(var_names, data) == expected
-
-
-def test_var_names_key_error(data):
-    with pytest.raises(KeyError, match="bad_var_name"):
-        _var_names(("theta", "tau", "bad_var_name"), data)
-
-
-@pytest.mark.parametrize(
-    "var_args",
-    [
-        (["ta"], ["beta1", "beta2", "theta"], "like"),
-        (["~beta"], ["phi", "theta"], "like"),
-        (["beta[0-9]+"], ["beta1", "beta2"], "regex"),
-        (["^p"], ["phi"], "regex"),
-        (["~^t"], ["beta1", "beta2", "phi"], "regex"),
-    ],
-)
-def test_var_names_filter_multiple_input(var_args):
-    samples = np.random.randn(10)
-    data1 = dict_to_dataset({"beta1": samples, "beta2": samples, "phi": samples})
-    data2 = dict_to_dataset({"beta1": samples, "beta2": samples, "theta": samples})
-    data = [data1, data2]
-    var_names, expected, filter_vars = var_args
-    assert _var_names(var_names, data, filter_vars) == expected
-
-
-@pytest.mark.parametrize(
-    "var_args",
-    [
-        (["alpha", "beta"], ["alpha", "beta1", "beta2"], "like"),
-        (["~beta"], ["alpha", "p1", "p2", "phi", "theta", "theta_t"], "like"),
-        (["theta"], ["theta", "theta_t"], "like"),
-        (["~theta"], ["alpha", "beta1", "beta2", "p1", "p2", "phi"], "like"),
-        (["p"], ["alpha", "p1", "p2", "phi"], "like"),
-        (["~p"], ["beta1", "beta2", "theta", "theta_t"], "like"),
-        (["^bet"], ["beta1", "beta2"], "regex"),
-        (["^p"], ["p1", "p2", "phi"], "regex"),
-        (["~^p"], ["alpha", "beta1", "beta2", "theta", "theta_t"], "regex"),
-        (["p[0-9]+"], ["p1", "p2"], "regex"),
-        (["~p[0-9]+"], ["alpha", "beta1", "beta2", "phi", "theta", "theta_t"], "regex"),
-    ],
-)
-def test_var_names_filter(var_args):
-    """Test var_names filter with partial naming or regular expressions."""
-    samples = np.random.randn(10)
-    data = dict_to_dataset(
-        {
-            "alpha": samples,
-            "beta1": samples,
-            "beta2": samples,
-            "p1": samples,
-            "p2": samples,
-            "phi": samples,
-            "theta": samples,
-            "theta_t": samples,
-        }
-    )
-    var_names, expected, filter_vars = var_args
-    assert _var_names(var_names, data, filter_vars) == expected
-
-
-def test_nonstring_var_names():
-    """Check that non-string variables are preserved"""
-    mu = RandomVariableTestClass("mu")
-    samples = np.random.randn(10)
-    data = dict_to_dataset({mu: samples})
-    assert _var_names([mu], data) == [mu]
-
-
-def test_var_names_filter_invalid_argument():
-    """Check invalid argument raises."""
-    samples = np.random.randn(10)
-    data = dict_to_dataset({"alpha": samples})
-    msg = r"^\'filter_vars\' can only be None, \'like\', or \'regex\', got: 'foo'$"
-    with pytest.raises(ValueError, match=msg):
-        assert _var_names(["alpha"], data, filter_vars="foo")
-
-
-def test_subset_list_negation_not_found():
-    """Check there is a warning if negation pattern is ignored"""
-    names = ["mu", "theta"]
-    with pytest.warns(UserWarning, match=".+not.+found.+"):
-        assert _subset_list("~tau", names) == names
-
-
-@pytest.fixture(scope="function")
-def utils_with_numba_import_fail(monkeypatch):
-    """Patch numba in utils so when its imported it raises ImportError"""
-    failed_import = Mock()
-    failed_import.side_effect = ImportError
-
-    from ... import utils
-
-    monkeypatch.setattr(utils.importlib, "import_module", failed_import)
-    return utils
-
-
-def test_conditional_jit_decorator_no_numba(utils_with_numba_import_fail):
-    """Tests to see if Numba jit code block is skipped with Import Failure
-
-    Test can be distinguished from test_conditional_jit__numba_decorator
-    by use of debugger or coverage tool
-    """
-
-    @utils_with_numba_import_fail.conditional_jit
-    def func():
-        return "Numba not used"
-
-    assert func() == "Numba not used"
-
-
-def test_conditional_vect_decorator_no_numba(utils_with_numba_import_fail):
-    """Tests to see if Numba vectorize code block is skipped with Import Failure
-
-    Test can be distinguished from test_conditional_vect__numba_decorator
-    by use of debugger or coverage tool
-    """
-
-    @utils_with_numba_import_fail.conditional_vect
-    def func():
-        return "Numba not used"
-
-    assert func() == "Numba not used"
-
-
-def test_conditional_jit_numba_decorator():
-    """Tests to see if Numba is used.
-
-    Test can be distinguished from test_conditional_jit_decorator_no_numba
-    by use of debugger or coverage tool
-    """
-    from ... import utils
-
-    @utils.conditional_jit
-    def func():
-        return True
-
-    assert func()
-
-
-def test_conditional_vect_numba_decorator():
-    """Tests to see if Numba is used.
-
-    Test can be distinguished from test_conditional_jit_decorator_no_numba
-    by use of debugger or coverage tool
-    """
-    from ... import utils
-
-    @utils.conditional_vect
-    def func(a_a, b_b):
-        return a_a + b_b
-
-    value_one = np.random.randn(10)
-    value_two = np.random.randn(10)
-    assert np.allclose(func(value_one, value_two), value_one + value_two)
-
-
-def test_conditional_vect_numba_decorator_keyword(monkeypatch):
-    """Checks else statement and vect keyword argument"""
-    from ... import utils
-
-    # Mock import lib to return numba with hit method which returns a function that returns kwargs
-    numba_mock = Mock()
-    monkeypatch.setattr(utils.importlib, "import_module", lambda x: numba_mock)
-
-    def vectorize(**kwargs):
-        """overwrite numba.vectorize function"""
-        return lambda x: (x(), kwargs)
-
-    numba_mock.vectorize = vectorize
-
-    @utils.conditional_vect(keyword_argument="A keyword argument")
-    def placeholder_func():
-        """This function does nothing"""
-        return "output"
-
-    # pylint: disable=unpacking-non-sequence
-    function_results, wrapper_result = placeholder_func
-    assert wrapper_result == {"keyword_argument": "A keyword argument"}
-    assert function_results == "output"
-
-
-def test_stack():
-    x = np.random.randn(10, 4, 6)
-    y = np.random.randn(100, 4, 6)
-    assert x.shape[1:] == y.shape[1:]
-    assert np.allclose(np.vstack((x, y)), _stack(x, y))
-    assert _stack
-
-
-@pytest.mark.parametrize("data", [np.random.randn(1000), np.random.randn(1000).tolist()])
-def test_two_de(data):
-    """Test to check for custom atleast_2d. List added to test for a non ndarray case."""
-    assert np.allclose(two_de(data), np.atleast_2d(data))
-
-
-@pytest.mark.parametrize("data", [np.random.randn(100), np.random.randn(100).tolist()])
-def test_one_de(data):
-    """Test to check for custom atleast_1d. List added to test for a non ndarray case."""
-    assert np.allclose(one_de(data), np.atleast_1d(data))
-
-
-@pytest.mark.parametrize("data", [np.random.randn(100), np.random.randn(100).tolist()])
-def test_expand_dims(data):
-    """Test to check for custom expand_dims. List added to test for a non ndarray case."""
-    assert np.allclose(expand_dims(data), np.expand_dims(data, 0))
-
-
-@pytest.mark.parametrize("var_names", [None, "mu", ["mu", "tau"]])
-@pytest.mark.parametrize(
-    "groups", [None, "posterior_groups", "prior_groups", ["posterior", "sample_stats"]]
-)
-@pytest.mark.parametrize("dimensions", [None, "draw", ["chain", "draw"]])
-@pytest.mark.parametrize("group_info", [True, False])
-@pytest.mark.parametrize(
-    "var_name_format", [None, "brackets", "underscore", "cds", ((",", "[", "]"), ("_", ""))]
-)
-@pytest.mark.parametrize("index_origin", [None, 0, 1])
-def test_flatten_inference_data_to_dict(
-    inference_data, var_names, groups, dimensions, group_info, var_name_format, index_origin
-):
-    """Test flattening (stacking) inference data (subgroups) for dictionary."""
-    res_dict = flatten_inference_data_to_dict(
-        data=inference_data,
-        var_names=var_names,
-        groups=groups,
-        dimensions=dimensions,
-        group_info=group_info,
-        var_name_format=var_name_format,
-        index_origin=index_origin,
-    )
-    assert res_dict
-    assert "draw" in res_dict
-    assert any("mu" in item for item in res_dict)
-    if group_info:
-        if groups != "prior_groups":
-            assert any("posterior" in item for item in res_dict)
-            if var_names is None:
-                assert any("sample_stats" in item for item in res_dict)
-        else:
-            assert any("prior" in item for item in res_dict)
-    elif groups == "prior_groups":
-        assert all("prior" not in item for item in res_dict)
-
-    else:
-        assert all("posterior" not in item for item in res_dict)
-        if var_names is None:
-            assert all("sample_stats" not in item for item in res_dict)
-
-
-@pytest.mark.parametrize("mean", [0, np.pi, 4 * np.pi, -2 * np.pi, -10 * np.pi])
-def test_circular_mean_scipy(mean):
-    """Test our `_circular_mean()` function gives same result than Scipy version."""
-    rvs = st.vonmises.rvs(loc=mean, kappa=1, size=1000)
-    mean_az = _circular_mean(rvs)
-    mean_sp = st.circmean(rvs, low=-np.pi, high=np.pi)
-    np.testing.assert_almost_equal(mean_az, mean_sp)
-
-
-@pytest.mark.parametrize("mean", [0, np.pi, 4 * np.pi, -2 * np.pi, -10 * np.pi])
-def test_normalize_angle(mean):
-    """Testing _normalize_angles() return values between expected bounds"""
-    rvs = st.vonmises.rvs(loc=mean, kappa=1, size=1000)
-    values = _normalize_angle(rvs, zero_centered=True)
-    assert ((-np.pi <= values) & (values <= np.pi)).all()
-
-    values = _normalize_angle(rvs, zero_centered=False)
-    assert ((values >= 0) & (values <= 2 * np.pi)).all()
-
-
-@pytest.mark.parametrize("mean", [[0, 0], [1, 1]])
-@pytest.mark.parametrize(
-    "cov",
-    [
-        np.diag([1, 1]),
-        np.diag([0.5, 0.5]),
-        np.diag([0.25, 1]),
-        np.array([[0.4, 0.2], [0.2, 0.8]]),
-    ],
-)
-@pytest.mark.parametrize("contour_sigma", [np.array([1, 2, 3])])
-def test_find_hdi_contours(mean, cov, contour_sigma):
-    """Test `_find_hdi_contours()` against SciPy's multivariate normal distribution."""
-    # Set up scipy distribution
-    prob_dist = st.multivariate_normal(mean, cov)
-
-    # Find standard deviations and eigenvectors
-    eigenvals, eigenvecs = np.linalg.eig(cov)
-    eigenvecs = eigenvecs.T
-    stdevs = np.sqrt(eigenvals)
-
-    # Find min and max for grid at 7-sigma contour
-    extremes = np.empty((4, 2))
-    for i in range(4):
-        extremes[i] = mean + (-1) ** i * 7 * stdevs[i // 2] * eigenvecs[i // 2]
-    x_min, y_min = np.amin(extremes, axis=0)
-    x_max, y_max = np.amax(extremes, axis=0)
-
-    # Create 256x256 grid
-    x = np.linspace(x_min, x_max, 256)
-    y = np.linspace(y_min, y_max, 256)
-    grid = np.dstack(np.meshgrid(x, y))
-
-    density = prob_dist.pdf(grid)
-
-    contour_sp = np.empty(contour_sigma.shape)
-    for idx, sigma in enumerate(contour_sigma):
-        contour_sp[idx] = prob_dist.pdf(mean + sigma * stdevs[0] * eigenvecs[0])
-
-    hdi_probs = 1 - np.exp(-0.5 * contour_sigma**2)
-    contour_az = _find_hdi_contours(density, hdi_probs)
-
-    np.testing.assert_allclose(contour_sp, contour_az, rtol=1e-2, atol=1e-4)

arviz/tests/base_tests/test_utils_numba.py

@@ -1,87 +0,0 @@
-# pylint: disable=redefined-outer-name, no-member
-"""Tests for arviz.utils."""
-import importlib
-from unittest.mock import Mock
-
-import numpy as np
-import pytest
-
-from ...stats.stats_utils import stats_variance_2d as svar
-from ...utils import Numba, _numba_var, numba_check
-from ..helpers import importorskip
-from .test_utils import utils_with_numba_import_fail  # pylint: disable=unused-import
-
-importorskip("numba")
-
-
-def test_utils_fixture(utils_with_numba_import_fail):
-    """Test of utils fixture to ensure mock is applied correctly"""
-
-    # If Numba doesn't exist in dev environment this will raise an ImportError
-    import numba  # pylint: disable=unused-import,W0612
-
-    with pytest.raises(ImportError):
-        utils_with_numba_import_fail.importlib.import_module("numba")
-
-
-def test_conditional_jit_numba_decorator_keyword(monkeypatch):
-    """Checks else statement and JIT keyword argument"""
-    from ... import utils
-
-    # Mock import lib to return numba with hit method which returns a function that returns kwargs
-    numba_mock = Mock()
-    monkeypatch.setattr(utils.importlib, "import_module", lambda x: numba_mock)
-
-    def jit(**kwargs):
-        """overwrite numba.jit function"""
-        return lambda fn: lambda: (fn(), kwargs)
-
-    numba_mock.jit = jit
-
-    @utils.conditional_jit(keyword_argument="A keyword argument")
-    def placeholder_func():
-        """This function does nothing"""
-        return "output"
-
-    # pylint: disable=unpacking-non-sequence
-    function_results, wrapper_result = placeholder_func()
-    assert wrapper_result == {"keyword_argument": "A keyword argument", "nopython": True}
-    assert function_results == "output"
-
-
-def test_numba_check():
-    """Test for numba_check"""
-    numba = importlib.util.find_spec("numba")
-    flag = numba is not None
-    assert flag == numba_check()
-
-
-def test_numba_utils():
-    """Test for class Numba."""
-    flag = Numba.numba_flag
-    assert flag == numba_check()
-    Numba.disable_numba()
-    val = Numba.numba_flag
-    assert not val
-    Numba.enable_numba()
-    val = Numba.numba_flag
-    assert val
-    assert flag == Numba.numba_flag
-
-
-@pytest.mark.parametrize("axis", (0, 1))
-@pytest.mark.parametrize("ddof", (0, 1))
-def test_numba_var(axis, ddof):
-    """Method to test numba_var."""
-    flag = Numba.numba_flag
-    data_1 = np.random.randn(100, 100)
-    data_2 = np.random.rand(100)
-    with_numba_1 = _numba_var(svar, np.var, data_1, axis=axis, ddof=ddof)
-    with_numba_2 = _numba_var(svar, np.var, data_2, ddof=ddof)
-    Numba.disable_numba()
-    non_numba_1 = _numba_var(svar, np.var, data_1, axis=axis, ddof=ddof)
-    non_numba_2 = _numba_var(svar, np.var, data_2, ddof=ddof)
-    Numba.enable_numba()
-    assert flag == Numba.numba_flag
-    assert np.allclose(with_numba_1, non_numba_1)
-    assert np.allclose(with_numba_2, non_numba_2)

arviz/tests/conftest.py

@@ -1,46 +0,0 @@
-# pylint: disable=redefined-outer-name
-"""Configuration for test suite."""
-import logging
-import os
-
-import numpy as np
-import pytest
-
-_log = logging.getLogger(__name__)
-
-
-@pytest.fixture(autouse=True)
-def random_seed():
-    """Reset numpy random seed generator."""
-    np.random.seed(0)
-
-
-def pytest_addoption(parser):
-    """Definition for command line option to save figures from tests."""
-    parser.addoption("--save", nargs="?", const="test_images", help="Save images rendered by plot")
-
-
-@pytest.fixture(scope="session")
-def save_figs(request):
-    """Enable command line switch for saving generation figures upon testing."""
-    fig_dir = request.config.getoption("--save")
-
-    if fig_dir is not None:
-        # Try creating directory if it doesn't exist
-        _log.info("Saving generated images in %s", fig_dir)
-
-        os.makedirs(fig_dir, exist_ok=True)
-        _log.info("Directory %s created", fig_dir)
-
-        # Clear all files from the directory
-        # Does not alter or delete directories
-        for file in os.listdir(fig_dir):
-            full_path = os.path.join(fig_dir, file)
-
-            try:
-                os.remove(full_path)
-
-            except OSError:
-                _log.info("Failed to remove %s", full_path)
-
-    return fig_dir

arviz/tests/external_tests/__init__.py

@@ -1 +0,0 @@
-"""Backend test suite."""

arviz/tests/external_tests/test_data_beanmachine.py

@@ -1,78 +0,0 @@
-# pylint: disable=no-member, invalid-name, redefined-outer-name
-import numpy as np
-import pytest
-
-from ...data.io_beanmachine import from_beanmachine  # pylint: disable=wrong-import-position
-from ..helpers import (  # pylint: disable=unused-import, wrong-import-position
-    chains,
-    draws,
-    eight_schools_params,
-    importorskip,
-    load_cached_models,
-)
-
-pytest.skip("Ignore beanmachine tests until it supports pytorch 2", allow_module_level=True)
-
-# Skip all tests if beanmachine or pytorch not installed
-torch = importorskip("torch")
-bm = importorskip("beanmachine.ppl")
-dist = torch.distributions
-
-
-class TestDataBeanMachine:
-    @pytest.fixture(scope="class")
-    def data(self, eight_schools_params, draws, chains):
-        class Data:
-            model, prior, obj = load_cached_models(
-                eight_schools_params,
-                draws,
-                chains,
-                "beanmachine",
-            )["beanmachine"]
-
-        return Data
-
-    @pytest.fixture(scope="class")
-    def predictions_data(self, data):
-        """Generate predictions for predictions_params"""
-        posterior_samples = data.obj
-        model = data.model
-        predictions = bm.inference.predictive.simulate([model.obs()], posterior_samples)
-        return predictions
-
-    def get_inference_data(self, eight_schools_params, predictions_data):
-        predictions = predictions_data
-        return from_beanmachine(
-            sampler=predictions,
-            coords={
-                "school": np.arange(eight_schools_params["J"]),
-                "school_pred": np.arange(eight_schools_params["J"]),
-            },
-        )
-
-    def test_inference_data(self, data, eight_schools_params, predictions_data):
-        inference_data = self.get_inference_data(eight_schools_params, predictions_data)
-        model = data.model
-        mu = model.mu()
-        tau = model.tau()
-        eta = model.eta()
-        obs = model.obs()
-
-        assert mu in inference_data.posterior
-        assert tau in inference_data.posterior
-        assert eta in inference_data.posterior
-        assert obs in inference_data.posterior_predictive
-
-    def test_inference_data_has_log_likelihood_and_observed_data(self, data):
-        idata = from_beanmachine(data.obj)
-        obs = data.model.obs()
-
-        assert obs in idata.log_likelihood
-        assert obs in idata.observed_data
-
-    def test_inference_data_no_posterior(self, data):
-        model = data.model
-        # only prior
-        inference_data = from_beanmachine(data.prior)
-        assert not model.obs() in inference_data.posterior
-        assert "observed_data" not in inference_data