arviz 0.17.1__py3-none-any.whl → 0.19.0__py3-none-any.whl

arviz/tests/base_tests/test_plots_matplotlib.py

@@ -1,4 +1,5 @@
 """Tests use the default backend."""
+
 # pylint: disable=redefined-outer-name,too-many-lines
 import os
 from copy import deepcopy
@@ -45,16 +46,17 @@ from ...plots import (
 from ...rcparams import rc_context, rcParams
 from ...stats import compare, hdi, loo, waic
 from ...stats.density_utils import kde as _kde
-from ...utils import _cov
+from ...utils import _cov, BehaviourChangeWarning
 from ...plots.plot_utils import plot_point_interval
 from ...plots.dotplot import wilkinson_algorithm
 from ..helpers import (  # pylint: disable=unused-import
     create_model,
     create_multidimensional_model,
+    does_not_warn,
     eight_schools_params,
     models,
     multidim_models,
-    TestRandomVariable,
+    RandomVariableTestClass,
 )
 
 rcParams["data.load"] = "eager"
@@ -168,9 +170,9 @@ def test_plot_density_no_subset():
 
 def test_plot_density_nonstring_varnames():
     """Test plot_density works when variables are not strings."""
-    rv1 = TestRandomVariable("a")
-    rv2 = TestRandomVariable("b")
-    rv3 = TestRandomVariable("c")
+    rv1 = RandomVariableTestClass("a")
+    rv2 = RandomVariableTestClass("b")
+    rv3 = RandomVariableTestClass("c")
     model_ab = from_dict(
         {
             rv1: np.random.normal(size=200),
@@ -260,7 +262,7 @@ def test_plot_trace_legend(compact, combined):
     axes = plot_trace(
         idata, var_names=["home", "atts_star"], compact=compact, combined=combined, legend=True
     )
-    assert axes[0, 0].get_legend()
+    assert axes[0, 1].get_legend()
     compact_legend = axes[1, 0].get_legend()
     if compact:
         assert axes.shape == (2, 2)
@@ -752,7 +754,7 @@ def test_plot_ppc_transposed():
     )
     x, y = ax.get_lines()[2].get_data()
     assert not np.isclose(y[0], 0)
-    assert np.all(np.array([40, 43, 10, 9]) == x)
+    assert np.all(np.array([47, 44, 15, 11]) == x)
 
 
 @pytest.mark.parametrize("kind", ["kde", "cumulative", "scatter"])
@@ -1271,6 +1273,26 @@ def test_plot_ecdf_basic():
     assert axes is not None
 
 
+def test_plot_ecdf_eval_points():
+    """Check that BehaviourChangeWarning is raised if eval_points is not specified."""
+    data = np.random.randn(4, 1000)
+    eval_points = np.linspace(-3, 3, 100)
+    with pytest.warns(BehaviourChangeWarning):
+        axes = plot_ecdf(data)
+    assert axes is not None
+    with does_not_warn(BehaviourChangeWarning):
+        axes = plot_ecdf(data, eval_points=eval_points)
+    assert axes is not None
+
+
+@pytest.mark.parametrize("confidence_bands", [True, "pointwise", "simulated"])
+def test_plot_ecdf_confidence_bands(confidence_bands):
+    """Check that all confidence_bands values correctly accepted"""
+    data = np.random.randn(4, 1000)
+    axes = plot_ecdf(data, confidence_bands=confidence_bands, cdf=norm(0, 1).cdf)
+    assert axes is not None
+
+
 def test_plot_ecdf_values2():
     data = np.random.randn(4, 1000)
     data2 = np.random.randn(4, 1000)
@@ -1285,6 +1307,75 @@ def test_plot_ecdf_cdf():
     assert axes is not None
 
 
+def test_plot_ecdf_error():
+    """Check that all error conditions are correctly raised."""
+    dist = norm(0, 1)
+    data = dist.rvs(1000)
+
+    # cdf not specified
+    with pytest.raises(ValueError):
+        plot_ecdf(data, confidence_bands=True)
+    plot_ecdf(data, confidence_bands=True, cdf=dist.cdf)
+    with pytest.raises(ValueError):
+        plot_ecdf(data, difference=True)
+    plot_ecdf(data, difference=True, cdf=dist.cdf)
+    with pytest.raises(ValueError):
+        plot_ecdf(data, pit=True)
+    plot_ecdf(data, pit=True, cdf=dist.cdf)
+
+    # contradictory confidence band types
+    with pytest.raises(ValueError):
+        plot_ecdf(data, cdf=dist.cdf, confidence_bands="simulated", pointwise=True)
+    plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, pointwise=True)
+    plot_ecdf(data, cdf=dist.cdf, confidence_bands="pointwise")
+
+    # contradictory band probabilities
+    with pytest.raises(ValueError):
+        plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, ci_prob=0.9, fpr=0.1)
+    plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, ci_prob=0.9)
+    plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, fpr=0.1)
+
+    # contradictory reference
+    data2 = dist.rvs(200)
+    with pytest.raises(ValueError):
+        plot_ecdf(data, data2, cdf=dist.cdf, difference=True)
+    plot_ecdf(data, data2, difference=True)
+    plot_ecdf(data, cdf=dist.cdf, difference=True)
+
+
+def test_plot_ecdf_deprecations():
+    """Check that deprecations are raised correctly."""
+    dist = norm(0, 1)
+    data = dist.rvs(1000)
+    # base case, no deprecations
+    with does_not_warn(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, confidence_bands=True)
+    assert axes is not None
+
+    # values2 is deprecated
+    data2 = dist.rvs(200)
+    with pytest.warns(FutureWarning):
+        axes = plot_ecdf(data, values2=data2, difference=True)
+
+    # pit is deprecated
+    with pytest.warns(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, pit=True)
+    assert axes is not None
+
+    # fpr is deprecated
+    with does_not_warn(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, ci_prob=0.9)
+    with pytest.warns(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, fpr=0.1)
+    assert axes is not None
+
+    # pointwise is deprecated
+    with does_not_warn(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, confidence_bands="pointwise")
+    with pytest.warns(FutureWarning):
+        axes = plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, pointwise=True)
+
+
 @pytest.mark.parametrize(
     "kwargs",
     [

arviz/tests/base_tests/test_rcparams.py

@@ -127,6 +127,18 @@ def test_choice_bad_values(param):
         rcParams[param] = "bad_value"
 
 
+@pytest.mark.parametrize("args", [("stats.hdi_prob", "stats.ci_prob", 0.7, 0.7)])
+def test_deprecated_param(args):
+    """Test value and warning message correctly set for deprecated rcparams."""
+    param_old, param_new, val_old, val_new = args
+    assert param_new in rcParams
+    assert not np.isclose(rcParams[param_new], val_new)
+    msg = f"{param_old} is deprecated since .*, use {param_new} instead"
+    with pytest.warns(FutureWarning, match=msg):
+        with rc_context(rc={param_old: val_old}):
+            assert np.isclose(rcParams[param_new], val_new)
+
+
 @pytest.mark.parametrize("allow_none", (True, False))
 @pytest.mark.parametrize("typeof", (str, int))
 @pytest.mark.parametrize("args", [("not one", 10), (False, None), (False, 4)])

arviz/tests/base_tests/test_stats.py

@@ -89,25 +89,25 @@ def test_hdi_idata(centered_eight):
     data = centered_eight.posterior
     result = hdi(data)
     assert isinstance(result, Dataset)
-    assert dict(result.dims) == {"school": 8, "hdi": 2}
+    assert dict(result.sizes) == {"school": 8, "hdi": 2}
 
     result = hdi(data, input_core_dims=[["chain"]])
     assert isinstance(result, Dataset)
-    assert result.dims == {"draw": 500, "hdi": 2, "school": 8}
+    assert result.sizes == {"draw": 500, "hdi": 2, "school": 8}
 
 
 def test_hdi_idata_varnames(centered_eight):
     data = centered_eight.posterior
     result = hdi(data, var_names=["mu", "theta"])
     assert isinstance(result, Dataset)
-    assert result.dims == {"hdi": 2, "school": 8}
+    assert result.sizes == {"hdi": 2, "school": 8}
     assert list(result.data_vars.keys()) == ["mu", "theta"]
 
 
 def test_hdi_idata_group(centered_eight):
     result_posterior = hdi(centered_eight, group="posterior", var_names="mu")
     result_prior = hdi(centered_eight, group="prior", var_names="mu")
-    assert result_prior.dims == {"hdi": 2}
+    assert result_prior.sizes == {"hdi": 2}
     range_posterior = result_posterior.mu.values[1] - result_posterior.mu.values[0]
     range_prior = result_prior.mu.values[1] - result_prior.mu.values[0]
     assert range_posterior < range_prior
@@ -179,7 +179,7 @@ def test_compare_same(centered_eight, multidim_models, method, multidim):
     else:
         data_dict = {"first": centered_eight, "second": centered_eight}
 
-    weight = compare(data_dict, method=method)["weight"]
+    weight = compare(data_dict, method=method)["weight"].to_numpy()
     assert_allclose(weight[0], weight[1])
     assert_allclose(np.sum(weight), 1.0)
 

arviz/tests/base_tests/test_stats_numba.py

@@ -1,6 +1,4 @@
 # pylint: disable=redefined-outer-name, no-member
-import importlib
-
 import numpy as np
 import pytest
 
@@ -9,15 +7,12 @@ from ...stats import r2_score, summary
 from ...utils import Numba
 from ..helpers import (  # pylint: disable=unused-import
     check_multiple_attrs,
+    importorskip,
     multidim_models,
-    running_on_ci,
 )
 from .test_stats import centered_eight, non_centered_eight  # pylint: disable=unused-import
 
-pytestmark = pytest.mark.skipif(  # pylint: disable=invalid-name
-    (importlib.util.find_spec("numba") is None) and not running_on_ci(),
-    reason="test requires numba which is not installed",
-)
+numba = importorskip("numba")
 
 rcParams["data.load"] = "eager"
 

arviz/tests/base_tests/test_stats_utils.py

@@ -1,4 +1,5 @@
 """Tests for stats_utils."""
+
 #  pylint: disable=no-member
 import numpy as np
 import pytest

arviz/tests/base_tests/test_utils.py

@@ -1,4 +1,5 @@
 """Tests for arviz.utils."""
+
 # pylint: disable=redefined-outer-name, no-member
 from unittest.mock import Mock
 
@@ -17,7 +18,7 @@ from ...utils import (
     one_de,
     two_de,
 )
-from ..helpers import TestRandomVariable
+from ..helpers import RandomVariableTestClass
 
 
 @pytest.fixture(scope="session")
@@ -123,7 +124,7 @@ def test_var_names_filter(var_args):
 
 def test_nonstring_var_names():
     """Check that non-string variables are preserved"""
-    mu = TestRandomVariable("mu")
+    mu = RandomVariableTestClass("mu")
     samples = np.random.randn(10)
     data = dict_to_dataset({mu: samples})
     assert _var_names([mu], data) == [mu]

arviz/tests/base_tests/test_utils_numba.py

@@ -8,13 +8,10 @@ import pytest
 
 from ...stats.stats_utils import stats_variance_2d as svar
 from ...utils import Numba, _numba_var, numba_check
-from ..helpers import running_on_ci
+from ..helpers import importorskip
 from .test_utils import utils_with_numba_import_fail  # pylint: disable=unused-import
 
-pytestmark = pytest.mark.skipif(  # pylint: disable=invalid-name
-    (importlib.util.find_spec("numba") is None) and not running_on_ci(),
-    reason="test requires numba which is not installed",
-)
+importorskip("numba")
 
 
 def test_utils_fixture(utils_with_numba_import_fail):

arviz/tests/external_tests/test_data_pystan.py

@@ -1,6 +1,7 @@
 # pylint: disable=no-member, invalid-name, redefined-outer-name, too-many-function-args
 import importlib
 from collections import OrderedDict
+import os
 
 import numpy as np
 import pytest
@@ -16,19 +17,18 @@ from ..helpers import (  # pylint: disable=unused-import
     importorskip,
     load_cached_models,
     pystan_version,
-    running_on_ci,
 )
 
 # Check if either pystan or pystan3 is installed
 pystan_installed = (importlib.util.find_spec("pystan") is not None) or (
     importlib.util.find_spec("stan") is not None
 )
-pytestmark = pytest.mark.skipif(
-    not (pystan_installed | running_on_ci()),
-    reason="test requires pystan/pystan3 which is not installed",
-)
 
 
+@pytest.mark.skipif(
+    not (pystan_installed or "ARVIZ_REQUIRE_ALL_DEPS" in os.environ),
+    reason="test requires pystan/pystan3 which is not installed",
+)
 class TestDataPyStan:
     @pytest.fixture(scope="class")
     def data(self, eight_schools_params, draws, chains):

arviz/tests/helpers.py

@@ -6,6 +6,8 @@ import logging
 import os
 import sys
 from typing import Any, Dict, List, Optional, Tuple, Union
+import warnings
+from contextlib import contextmanager
 
 import cloudpickle
 import numpy as np
@@ -18,7 +20,7 @@ from ..data import InferenceData, from_dict
 _log = logging.getLogger(__name__)
 
 
-class TestRandomVariable:
+class RandomVariableTestClass:
     """Example class for random variables."""
 
     def __init__(self, name):
@@ -29,6 +31,18 @@ class TestRandomVariable:
         return self.name
 
 
+@contextmanager
+def does_not_warn(warning=Warning):
+    with warnings.catch_warnings(record=True) as caught_warnings:
+        warnings.simplefilter("always")
+        yield
+        for w in caught_warnings:
+            if issubclass(w.category, warning):
+                raise AssertionError(
+                    f"Expected no {warning.__name__} but caught warning with message: {w.message}"
+                )
+
+
 @pytest.fixture(scope="module")
 def eight_schools_params():
     """Share setup for eight schools."""
@@ -620,11 +634,6 @@ def test_precompile_models(eight_schools_params, draws, chains):
     load_cached_models(eight_schools_params, draws, chains)
 
 
-def running_on_ci() -> bool:
-    """Return True if running on CI machine."""
-    return os.environ.get("ARVIZ_CI_MACHINE") is not None
-
-
 def importorskip(
     modname: str, minversion: Optional[str] = None, reason: Optional[str] = None
 ) -> Any:
@@ -643,11 +652,10 @@ def importorskip(
     Example::
         docutils = pytest.importorskip("docutils")
     """
-    # ARVIZ_CI_MACHINE is True if tests run on CI, where ARVIZ_CI_MACHINE env variable exists
-    ARVIZ_CI_MACHINE = running_on_ci()
-    if not ARVIZ_CI_MACHINE:
+    # Unless ARVIZ_REQUIRE_ALL_DEPS is defined, tests that require a missing dependency are skipped
+    # if set, missing optional dependencies trigger failed tests.
+    if "ARVIZ_REQUIRE_ALL_DEPS" not in os.environ:
         return pytest.importorskip(modname=modname, minversion=minversion, reason=reason)
-    import warnings
 
     compile(modname, "", "eval")  # to catch syntaxerrors
 

arviz/utils.py

@@ -17,6 +17,10 @@ from .rcparams import rcParams
 STATIC_FILES = ("static/html/icons-svg-inline.html", "static/css/style.css")
 
 
+class BehaviourChangeWarning(Warning):
+    """Custom warning to ease filtering it."""
+
+
 def _check_tilde_start(x):
     return bool(isinstance(x, str) and x.startswith("~"))
 

arviz/wrappers/__init__.py

@@ -1,4 +1,5 @@
 """Sampling wrappers."""
+
 from .base import SamplingWrapper
 from .wrap_stan import PyStan2SamplingWrapper, PyStanSamplingWrapper, CmdStanPySamplingWrapper
 from .wrap_pymc import PyMCSamplingWrapper

{arviz-0.17.1.dist-info → arviz-0.19.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arviz
-Version: 0.17.1
+Version: 0.19.0
 Summary: Exploratory analysis of Bayesian models
 Home-page: http://github.com/arviz-devs/arviz
 Author: ArviZ Developers
@@ -12,35 +12,39 @@ Classifier: Intended Audience :: Education
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: Scientific/Engineering :: Mathematics
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: setuptools >=60.0.0
 Requires-Dist: matplotlib >=3.5
-Requires-Dist: numpy <2.0,>=1.22.0
-Requires-Dist: scipy >=1.8.0
+Requires-Dist: numpy >=1.23.0
+Requires-Dist: scipy >=1.9.0
 Requires-Dist: packaging
-Requires-Dist: pandas >=1.4.0
-Requires-Dist: xarray >=0.21.0
+Requires-Dist: pandas >=1.5.0
+Requires-Dist: dm-tree >=0.1.8
+Requires-Dist: xarray >=2022.6.0
 Requires-Dist: h5netcdf >=1.0.2
 Requires-Dist: typing-extensions >=4.1.0
 Requires-Dist: xarray-einstats >=0.3
 Provides-Extra: all
 Requires-Dist: numba ; extra == 'all'
 Requires-Dist: netcdf4 ; extra == 'all'
-Requires-Dist: bokeh <3.0,>=1.4.0 ; extra == 'all'
+Requires-Dist: bokeh >=3 ; extra == 'all'
 Requires-Dist: contourpy ; extra == 'all'
 Requires-Dist: ujson ; extra == 'all'
 Requires-Dist: dask[distributed] ; extra == 'all'
-Requires-Dist: zarr >=2.5.0 ; extra == 'all'
+Requires-Dist: zarr <3,>=2.5.0 ; extra == 'all'
 Requires-Dist: xarray-datatree ; extra == 'all'
+Provides-Extra: preview
+Requires-Dist: arviz-base[h5netcdf] ; extra == 'preview'
+Requires-Dist: arviz-stats[xarray] ; extra == 'preview'
+Requires-Dist: arviz-plots ; extra == 'preview'
 
 <img src="https://raw.githubusercontent.com/arviz-devs/arviz-project/main/arviz_logos/ArviZ.png#gh-light-mode-only" width=200></img>
 <img src="https://raw.githubusercontent.com/arviz-devs/arviz-project/main/arviz_logos/ArviZ_white.png#gh-dark-mode-only" width=200></img>

arviz-0.19.0.dist-info/RECORD

@@ -0,0 +1,183 @@
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+arviz/sel_utils.py,sha256=xvAYENhGXDTrhaT4Itlk1SJQUUGZ6BGcR04fPFgvzdM,6951
+arviz/utils.py,sha256=sOUIkqmWtwY3PM-rQpN6arW9MsPt-MfvzdwAe78rT8U,26425
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