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

arviz/tests/base_tests/test_diagnostics_numba.py

@@ -1,87 +0,0 @@
-"""Test Diagnostic methods"""
-
-# pylint: disable=redefined-outer-name, no-member, too-many-public-methods
-import numpy as np
-import pytest
-
-from ...data import load_arviz_data
-from ...rcparams import rcParams
-from ...stats import bfmi, mcse, rhat
-from ...stats.diagnostics import _mc_error, ks_summary
-from ...utils import Numba
-from ..helpers import importorskip
-from .test_diagnostics import data  # pylint: disable=unused-import
-
-importorskip("numba")
-
-rcParams["data.load"] = "eager"
-
-
-def test_numba_bfmi():
-    """Numba test for bfmi."""
-    state = Numba.numba_flag
-    school = load_arviz_data("centered_eight")
-    data_md = np.random.rand(100, 100, 10)
-    Numba.disable_numba()
-    non_numba = bfmi(school.posterior["mu"].values)
-    non_numba_md = bfmi(data_md)
-    Numba.enable_numba()
-    with_numba = bfmi(school.posterior["mu"].values)
-    with_numba_md = bfmi(data_md)
-    assert np.allclose(non_numba_md, with_numba_md)
-    assert np.allclose(with_numba, non_numba)
-    assert state == Numba.numba_flag
-
-
-@pytest.mark.parametrize("method", ("rank", "split", "folded", "z_scale", "identity"))
-def test_numba_rhat(method):
-    """Numba test for mcse."""
-    state = Numba.numba_flag
-    school = np.random.rand(100, 100)
-    Numba.disable_numba()
-    non_numba = rhat(school, method=method)
-    Numba.enable_numba()
-    with_numba = rhat(school, method=method)
-    assert np.allclose(with_numba, non_numba)
-    assert Numba.numba_flag == state
-
-
-@pytest.mark.parametrize("method", ("mean", "sd", "quantile"))
-def test_numba_mcse(method, prob=None):
-    """Numba test for mcse."""
-    state = Numba.numba_flag
-    school = np.random.rand(100, 100)
-    if method == "quantile":
-        prob = 0.80
-    Numba.disable_numba()
-    non_numba = mcse(school, method=method, prob=prob)
-    Numba.enable_numba()
-    with_numba = mcse(school, method=method, prob=prob)
-    assert np.allclose(with_numba, non_numba)
-    assert Numba.numba_flag == state
-
-
-def test_ks_summary_numba():
-    """Numba test for ks_summary."""
-    state = Numba.numba_flag
-    data = np.random.randn(100, 100)
-    Numba.disable_numba()
-    non_numba = (ks_summary(data)["Count"]).values
-    Numba.enable_numba()
-    with_numba = (ks_summary(data)["Count"]).values
-    assert np.allclose(non_numba, with_numba)
-    assert Numba.numba_flag == state
-
-
-@pytest.mark.parametrize("batches", (1, 20))
-@pytest.mark.parametrize("circular", (True, False))
-def test_mcse_error_numba(batches, circular):
-    """Numba test for mcse_error."""
-    data = np.random.randn(100, 100)
-    state = Numba.numba_flag
-    Numba.disable_numba()
-    non_numba = _mc_error(data, batches=batches, circular=circular)
-    Numba.enable_numba()
-    with_numba = _mc_error(data, batches=batches, circular=circular)
-    assert np.allclose(non_numba, with_numba)
-    assert state == Numba.numba_flag

arviz/tests/base_tests/test_helpers.py

@@ -1,18 +0,0 @@
-import pytest
-from _pytest.outcomes import Skipped
-
-from ..helpers import importorskip
-
-
-def test_importorskip_local(monkeypatch):
-    """Test ``importorskip`` run on local machine with non-existent module, which should skip."""
-    monkeypatch.delenv("ARVIZ_REQUIRE_ALL_DEPS", raising=False)
-    with pytest.raises(Skipped):
-        importorskip("non-existent-function")
-
-
-def test_importorskip_ci(monkeypatch):
-    """Test ``importorskip`` run on CI machine with non-existent module, which should fail."""
-    monkeypatch.setenv("ARVIZ_REQUIRE_ALL_DEPS", 1)
-    with pytest.raises(ModuleNotFoundError):
-        importorskip("non-existent-function")

arviz/tests/base_tests/test_labels.py

@@ -1,69 +0,0 @@
-"""Tests for labeller classes."""
-
-import pytest
-
-from ...labels import (
-    BaseLabeller,
-    DimCoordLabeller,
-    DimIdxLabeller,
-    IdxLabeller,
-    MapLabeller,
-    NoModelLabeller,
-    NoVarLabeller,
-)
-
-
-class Data:
-    def __init__(self):
-        self.sel = {
-            "instrument": "a",
-            "experiment": 3,
-        }
-        self.isel = {
-            "instrument": 0,
-            "experiment": 4,
-        }
-
-
-@pytest.fixture
-def multidim_sels():
-    return Data()
-
-
-class Labellers:
-    def __init__(self):
-        self.labellers = {
-            "BaseLabeller": BaseLabeller(),
-            "DimCoordLabeller": DimCoordLabeller(),
-            "IdxLabeller": IdxLabeller(),
-            "DimIdxLabeller": DimIdxLabeller(),
-            "MapLabeller": MapLabeller(),
-            "NoVarLabeller": NoVarLabeller(),
-            "NoModelLabeller": NoModelLabeller(),
-        }
-
-
-@pytest.fixture
-def labellers():
-    return Labellers()
-
-
-@pytest.mark.parametrize(
-    "args",
-    [
-        ("BaseLabeller", "theta\na, 3"),
-        ("DimCoordLabeller", "theta\ninstrument: a, experiment: 3"),
-        ("IdxLabeller", "theta\n0, 4"),
-        ("DimIdxLabeller", "theta\ninstrument#0, experiment#4"),
-        ("MapLabeller", "theta\na, 3"),
-        ("NoVarLabeller", "a, 3"),
-        ("NoModelLabeller", "theta\na, 3"),
-    ],
-)
-class TestLabellers:
-    # pylint: disable=redefined-outer-name
-    def test_make_label_vert(self, args, multidim_sels, labellers):
-        name, expected_label = args
-        labeller_arg = labellers.labellers[name]
-        label = labeller_arg.make_label_vert("theta", multidim_sels.sel, multidim_sels.isel)
-        assert label == expected_label

arviz/tests/base_tests/test_plot_utils.py

@@ -1,342 +0,0 @@
-# pylint: disable=redefined-outer-name
-import importlib
-import os
-
-import numpy as np
-import pytest
-import xarray as xr
-
-from ...data import from_dict
-from ...plots.backends.matplotlib import dealiase_sel_kwargs, matplotlib_kwarg_dealiaser
-from ...plots.plot_utils import (
-    compute_ranks,
-    filter_plotters_list,
-    format_sig_figs,
-    get_plotting_function,
-    make_2d,
-    set_bokeh_circular_ticks_labels,
-    vectorized_to_hex,
-)
-from ...rcparams import rc_context
-from ...sel_utils import xarray_sel_iter, xarray_to_ndarray
-from ...stats.density_utils import get_bins
-from ...utils import get_coords
-
-# Check if Bokeh is installed
-bokeh_installed = importlib.util.find_spec("bokeh") is not None  # pylint: disable=invalid-name
-skip_tests = (not bokeh_installed) and ("ARVIZ_REQUIRE_ALL_DEPS" not in os.environ)
-
-
-@pytest.mark.parametrize(
-    "value, default, expected",
-    [
-        (123.456, 2, 3),
-        (-123.456, 3, 3),
-        (-123.456, 4, 4),
-        (12.3456, 2, 2),
-        (1.23456, 2, 2),
-        (0.123456, 2, 2),
-    ],
-)
-def test_format_sig_figs(value, default, expected):
-    assert format_sig_figs(value, default=default) == expected
-
-
-@pytest.fixture(scope="function")
-def sample_dataset():
-    mu = np.arange(1, 7).reshape(2, 3)
-    tau = np.arange(7, 13).reshape(2, 3)
-
-    chain = [0, 1]
-    draws = [0, 1, 2]
-
-    data = xr.Dataset(
-        {"mu": (["chain", "draw"], mu), "tau": (["chain", "draw"], tau)},
-        coords={"draw": draws, "chain": chain},
-    )
-
-    return mu, tau, data
-
-
-def test_make_2d():
-    """Touches code that is hard to reach."""
-    assert len(make_2d(np.array([2, 3, 4])).shape) == 2
-
-
-def test_get_bins():
-    """Touches code that is hard to reach."""
-    assert get_bins(np.array([1, 2, 3, 100])) is not None
-
-
-def test_dataset_to_numpy_not_combined(sample_dataset):  # pylint: disable=invalid-name
-    mu, tau, data = sample_dataset
-    var_names, data = xarray_to_ndarray(data, combined=False)
-
-    # 2 vars x 2 chains
-    assert len(var_names) == 4
-    mu_tau = np.concatenate((mu, tau), axis=0)
-    tau_mu = np.concatenate((tau, mu), axis=0)
-    deqmt = data == mu_tau
-    deqtm = data == tau_mu
-    assert deqmt.all() or deqtm.all()
-
-
-def test_dataset_to_numpy_combined(sample_dataset):
-    mu, tau, data = sample_dataset
-    var_names, data = xarray_to_ndarray(data, combined=True)
-
-    assert len(var_names) == 2
-    assert (data[var_names.index("mu")] == mu.reshape(1, 6)).all()
-    assert (data[var_names.index("tau")] == tau.reshape(1, 6)).all()
-
-
-def test_xarray_sel_iter_ordering():
-    """Assert that coordinate names stay the provided order"""
-    coords = list("dcba")
-    data = from_dict(  # pylint: disable=no-member
-        {"x": np.random.randn(1, 100, len(coords))},
-        coords={"in_order": coords},
-        dims={"x": ["in_order"]},
-    ).posterior
-
-    coord_names = [sel["in_order"] for _, sel, _ in xarray_sel_iter(data)]
-    assert coord_names == coords
-
-
-def test_xarray_sel_iter_ordering_combined(sample_dataset):  # pylint: disable=invalid-name
-    """Assert that varname order stays consistent when chains are combined"""
-    _, _, data = sample_dataset
-    var_names = [var for (var, _, _) in xarray_sel_iter(data, var_names=None, combined=True)]
-    assert set(var_names) == {"mu", "tau"}
-
-
-def test_xarray_sel_iter_ordering_uncombined(sample_dataset):  # pylint: disable=invalid-name
-    """Assert that varname order stays consistent when chains are not combined"""
-    _, _, data = sample_dataset
-    var_names = [(var, selection) for (var, selection, _) in xarray_sel_iter(data, var_names=None)]
-
-    assert len(var_names) == 4
-    for var_name in var_names:
-        assert var_name in [
-            ("mu", {"chain": 0}),
-            ("mu", {"chain": 1}),
-            ("tau", {"chain": 0}),
-            ("tau", {"chain": 1}),
-        ]
-
-
-def test_xarray_sel_data_array(sample_dataset):  # pylint: disable=invalid-name
-    """Assert that varname order stays consistent when chains are combined
-
-    Touches code that is hard to reach.
-    """
-    _, _, data = sample_dataset
-    var_names = [var for (var, _, _) in xarray_sel_iter(data.mu, var_names=None, combined=True)]
-    assert set(var_names) == {"mu"}
-
-
-class TestCoordsExceptions:
-    # test coord exceptions on datasets
-    def test_invalid_coord_name(self, sample_dataset):  # pylint: disable=invalid-name
-        """Assert that nicer exception appears when user enters wrong coords name"""
-        _, _, data = sample_dataset
-        coords = {"NOT_A_COORD_NAME": [1]}
-
-        with pytest.raises(
-            (KeyError, ValueError),
-            match=(
-                r"Coords "
-                r"({'NOT_A_COORD_NAME'} are invalid coordinate keys"
-                r"|should follow mapping format {coord_name:\[dim1, dim2\]})"
-            ),
-        ):
-            get_coords(data, coords)
-
-    def test_invalid_coord_value(self, sample_dataset):  # pylint: disable=invalid-name
-        """Assert that nicer exception appears when user enters wrong coords value"""
-        _, _, data = sample_dataset
-        coords = {"draw": [1234567]}
-
-        with pytest.raises(
-            KeyError, match=r"Coords should follow mapping format {coord_name:\[dim1, dim2\]}"
-        ):
-            get_coords(data, coords)
-
-    def test_invalid_coord_structure(self, sample_dataset):  # pylint: disable=invalid-name
-        """Assert that nicer exception appears when user enters wrong coords datatype"""
-        _, _, data = sample_dataset
-        coords = {"draw"}
-
-        with pytest.raises(TypeError):
-            get_coords(data, coords)
-
-    # test coord exceptions on dataset list
-    def test_invalid_coord_name_list(self, sample_dataset):  # pylint: disable=invalid-name
-        """Assert that nicer exception appears when user enters wrong coords name"""
-        _, _, data = sample_dataset
-        coords = {"NOT_A_COORD_NAME": [1]}
-
-        with pytest.raises(
-            (KeyError, ValueError),
-            match=(
-                r"data\[1\]:.+Coords "
-                r"({'NOT_A_COORD_NAME'} are invalid coordinate keys"
-                r"|should follow mapping format {coord_name:\[dim1, dim2\]})"
-            ),
-        ):
-            get_coords((data, data), ({"draw": [0, 1]}, coords))
-
-    def test_invalid_coord_value_list(self, sample_dataset):  # pylint: disable=invalid-name
-        """Assert that nicer exception appears when user enters wrong coords value"""
-        _, _, data = sample_dataset
-        coords = {"draw": [1234567]}
-
-        with pytest.raises(
-            KeyError,
-            match=r"data\[0\]:.+Coords should follow mapping format {coord_name:\[dim1, dim2\]}",
-        ):
-            get_coords((data, data), (coords, {"draw": [0, 1]}))
-
-
-def test_filter_plotter_list():
-    plotters = list(range(7))
-    with rc_context({"plot.max_subplots": 10}):
-        plotters_filtered = filter_plotters_list(plotters, "")
-    assert plotters == plotters_filtered
-
-
-def test_filter_plotter_list_warning():
-    plotters = list(range(7))
-    with rc_context({"plot.max_subplots": 5}):
-        with pytest.warns(UserWarning, match="test warning"):
-            plotters_filtered = filter_plotters_list(plotters, "test warning")
-    assert len(plotters_filtered) == 5
-
-
-@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
-def test_bokeh_import():
-    """Tests that correct method is returned on bokeh import"""
-    plot = get_plotting_function("plot_dist", "distplot", "bokeh")
-
-    from ...plots.backends.bokeh.distplot import plot_dist
-
-    assert plot is plot_dist
-
-
-@pytest.mark.parametrize(
-    "params",
-    [
-        {
-            "input": (
-                {
-                    "dashes": "-",
-                },
-                "scatter",
-            ),
-            "output": "linestyle",
-        },
-        {
-            "input": (
-                {"mfc": "blue", "c": "blue", "line_width": 2},
-                "plot",
-            ),
-            "output": ("markerfacecolor", "color", "line_width"),
-        },
-        {"input": ({"ec": "blue", "fc": "black"}, "hist"), "output": ("edgecolor", "facecolor")},
-        {
-            "input": ({"edgecolors": "blue", "lw": 3}, "hlines"),
-            "output": ("edgecolor", "linewidth"),
-        },
-    ],
-)
-def test_matplotlib_kwarg_dealiaser(params):
-    dealiased = matplotlib_kwarg_dealiaser(params["input"][0], kind=params["input"][1])
-    for returned in dealiased:
-        assert returned in params["output"]
-
-
-@pytest.mark.parametrize("c_values", ["#0000ff", "blue", [0, 0, 1]])
-def test_vectorized_to_hex_scalar(c_values):
-    output = vectorized_to_hex(c_values)
-    assert output == "#0000ff"
-
-
-@pytest.mark.parametrize(
-    "c_values", [["blue", "blue"], ["blue", "#0000ff"], np.array([[0, 0, 1], [0, 0, 1]])]
-)
-def test_vectorized_to_hex_array(c_values):
-    output = vectorized_to_hex(c_values)
-    assert np.all([item == "#0000ff" for item in output])
-
-
-def test_mpl_dealiase_sel_kwargs():
-    """Check mpl dealiase_sel_kwargs behaviour.
-
-    Makes sure kwargs are overwritten when necessary even with alias involved and that
-    they are not modified when not included in props.
-    """
-    kwargs = {"linewidth": 3, "alpha": 0.4, "line_color": "red"}
-    props = {"lw": [1, 2, 4, 5], "linestyle": ["-", "--", ":"]}
-    res = dealiase_sel_kwargs(kwargs, props, 2)
-    assert "linewidth" in res
-    assert res["linewidth"] == 4
-    assert "linestyle" in res
-    assert res["linestyle"] == ":"
-    assert "alpha" in res
-    assert res["alpha"] == 0.4
-    assert "line_color" in res
-    assert res["line_color"] == "red"
-
-
-@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
-def test_bokeh_dealiase_sel_kwargs():
-    """Check bokeh dealiase_sel_kwargs behaviour.
-
-    Makes sure kwargs are overwritten when necessary even with alias involved and that
-    they are not modified when not included in props.
-    """
-    from ...plots.backends.bokeh import dealiase_sel_kwargs
-
-    kwargs = {"line_width": 3, "line_alpha": 0.4, "line_color": "red"}
-    props = {"line_width": [1, 2, 4, 5], "line_dash": ["dashed", "dashed", "dashed"]}
-    res = dealiase_sel_kwargs(kwargs, props, 2)
-    assert "line_width" in res
-    assert res["line_width"] == 4
-    assert "line_dash" in res
-    assert res["line_dash"] == "dashed"
-    assert "line_alpha" in res
-    assert res["line_alpha"] == 0.4
-    assert "line_color" in res
-    assert res["line_color"] == "red"
-
-
-@pytest.mark.skipif(skip_tests, reason="test requires bokeh which is not installed")
-def test_set_bokeh_circular_ticks_labels():
-    """Assert the axes returned after placing ticks and tick labels for circular plots."""
-    import bokeh.plotting as bkp
-
-    ax = bkp.figure(x_axis_type=None, y_axis_type=None)
-    hist = np.linspace(0, 1, 10)
-    labels = ["0°", "45°", "90°", "135°", "180°", "225°", "270°", "315°"]
-    ax = set_bokeh_circular_ticks_labels(ax, hist, labels)
-    renderers = ax.renderers
-    assert len(renderers) == 3
-    assert renderers[2].data_source.data["text"] == labels
-    assert len(renderers[0].data_source.data["start_angle"]) == len(labels)
-
-
-def test_compute_ranks():
-    pois_data = np.array([[5, 4, 1, 4, 0], [2, 8, 2, 1, 1]])
-    expected = np.array([[9.0, 7.0, 3.0, 8.0, 1.0], [5.0, 10.0, 6.0, 2.0, 4.0]])
-    ranks = compute_ranks(pois_data)
-    np.testing.assert_equal(ranks, expected)
-
-    norm_data = np.array(
-        [
-            [0.2644187, -1.3004813, -0.80428456, 1.01319068, 0.62631143],
-            [1.34498018, -0.13428933, -0.69855487, -0.9498981, -0.34074092],
-        ]
-    )
-    expected = np.array([[7.0, 1.0, 3.0, 9.0, 8.0], [10.0, 6.0, 4.0, 2.0, 5.0]])
-    ranks = compute_ranks(norm_data)
-    np.testing.assert_equal(ranks, expected)