arviz 0.18.0__py3-none-any.whl → 0.19.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- arviz/__init__.py +2 -1
- arviz/data/io_cmdstan.py +4 -0
- arviz/data/io_numpyro.py +1 -1
- arviz/plots/backends/bokeh/ecdfplot.py +1 -2
- arviz/plots/backends/bokeh/khatplot.py +8 -3
- arviz/plots/backends/bokeh/pairplot.py +2 -6
- arviz/plots/backends/matplotlib/ecdfplot.py +1 -2
- arviz/plots/backends/matplotlib/khatplot.py +7 -3
- arviz/plots/backends/matplotlib/traceplot.py +1 -1
- arviz/plots/bpvplot.py +2 -2
- arviz/plots/densityplot.py +1 -1
- arviz/plots/dotplot.py +2 -2
- arviz/plots/ecdfplot.py +205 -89
- arviz/plots/essplot.py +2 -2
- arviz/plots/forestplot.py +1 -1
- arviz/plots/hdiplot.py +2 -2
- arviz/plots/khatplot.py +23 -6
- arviz/plots/loopitplot.py +2 -2
- arviz/plots/mcseplot.py +3 -1
- arviz/plots/plot_utils.py +2 -4
- arviz/plots/posteriorplot.py +1 -1
- arviz/plots/rankplot.py +2 -2
- arviz/plots/violinplot.py +1 -1
- arviz/preview.py +17 -0
- arviz/rcparams.py +27 -2
- arviz/stats/diagnostics.py +13 -9
- arviz/stats/ecdf_utils.py +11 -8
- arviz/stats/stats.py +31 -16
- arviz/stats/stats_utils.py +8 -6
- arviz/tests/base_tests/test_data.py +1 -2
- arviz/tests/base_tests/test_data_zarr.py +0 -1
- arviz/tests/base_tests/test_diagnostics_numba.py +2 -7
- arviz/tests/base_tests/test_helpers.py +2 -2
- arviz/tests/base_tests/test_plot_utils.py +5 -13
- arviz/tests/base_tests/test_plots_matplotlib.py +92 -2
- arviz/tests/base_tests/test_rcparams.py +12 -0
- arviz/tests/base_tests/test_stats.py +1 -1
- arviz/tests/base_tests/test_stats_numba.py +2 -7
- arviz/tests/base_tests/test_utils_numba.py +2 -5
- arviz/tests/external_tests/test_data_pystan.py +5 -5
- arviz/tests/helpers.py +17 -9
- arviz/utils.py +4 -0
- {arviz-0.18.0.dist-info → arviz-0.19.0.dist-info}/METADATA +8 -4
- {arviz-0.18.0.dist-info → arviz-0.19.0.dist-info}/RECORD +47 -46
- {arviz-0.18.0.dist-info → arviz-0.19.0.dist-info}/LICENSE +0 -0
- {arviz-0.18.0.dist-info → arviz-0.19.0.dist-info}/WHEEL +0 -0
- {arviz-0.18.0.dist-info → arviz-0.19.0.dist-info}/top_level.txt +0 -0
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@@ -46,12 +46,13 @@ from ...plots import (
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from ...rcparams import rc_context, rcParams
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from ...stats import compare, hdi, loo, waic
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from ...stats.density_utils import kde as _kde
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from ...utils import _cov
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from ...utils import _cov, BehaviourChangeWarning
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from ...plots.plot_utils import plot_point_interval
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from ...plots.dotplot import wilkinson_algorithm
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from ..helpers import ( # pylint: disable=unused-import
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create_model,
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create_multidimensional_model,
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does_not_warn,
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eight_schools_params,
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models,
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multidim_models,
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@@ -261,7 +262,7 @@ def test_plot_trace_legend(compact, combined):
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axes = plot_trace(
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idata, var_names=["home", "atts_star"], compact=compact, combined=combined, legend=True
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)
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assert axes[0,
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assert axes[0, 1].get_legend()
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compact_legend = axes[1, 0].get_legend()
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if compact:
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assert axes.shape == (2, 2)
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@@ -1272,6 +1273,26 @@ def test_plot_ecdf_basic():
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assert axes is not None
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def test_plot_ecdf_eval_points():
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"""Check that BehaviourChangeWarning is raised if eval_points is not specified."""
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data = np.random.randn(4, 1000)
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eval_points = np.linspace(-3, 3, 100)
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with pytest.warns(BehaviourChangeWarning):
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axes = plot_ecdf(data)
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assert axes is not None
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with does_not_warn(BehaviourChangeWarning):
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axes = plot_ecdf(data, eval_points=eval_points)
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assert axes is not None
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@pytest.mark.parametrize("confidence_bands", [True, "pointwise", "simulated"])
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def test_plot_ecdf_confidence_bands(confidence_bands):
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"""Check that all confidence_bands values correctly accepted"""
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data = np.random.randn(4, 1000)
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axes = plot_ecdf(data, confidence_bands=confidence_bands, cdf=norm(0, 1).cdf)
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assert axes is not None
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def test_plot_ecdf_values2():
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data = np.random.randn(4, 1000)
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data2 = np.random.randn(4, 1000)
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assert axes is not None
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def test_plot_ecdf_error():
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"""Check that all error conditions are correctly raised."""
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dist = norm(0, 1)
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data = dist.rvs(1000)
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# cdf not specified
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with pytest.raises(ValueError):
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plot_ecdf(data, confidence_bands=True)
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plot_ecdf(data, confidence_bands=True, cdf=dist.cdf)
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with pytest.raises(ValueError):
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plot_ecdf(data, difference=True)
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plot_ecdf(data, difference=True, cdf=dist.cdf)
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with pytest.raises(ValueError):
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plot_ecdf(data, pit=True)
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plot_ecdf(data, pit=True, cdf=dist.cdf)
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# contradictory confidence band types
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with pytest.raises(ValueError):
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plot_ecdf(data, cdf=dist.cdf, confidence_bands="simulated", pointwise=True)
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plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, pointwise=True)
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plot_ecdf(data, cdf=dist.cdf, confidence_bands="pointwise")
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# contradictory band probabilities
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with pytest.raises(ValueError):
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plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, ci_prob=0.9, fpr=0.1)
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plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, ci_prob=0.9)
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plot_ecdf(data, cdf=dist.cdf, confidence_bands=True, fpr=0.1)
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# contradictory reference
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data2 = dist.rvs(200)
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with pytest.raises(ValueError):
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plot_ecdf(data, data2, cdf=dist.cdf, difference=True)
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plot_ecdf(data, data2, difference=True)
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plot_ecdf(data, cdf=dist.cdf, difference=True)
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def test_plot_ecdf_deprecations():
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"""Check that deprecations are raised correctly."""
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dist = norm(0, 1)
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data = dist.rvs(1000)
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# base case, no deprecations
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with does_not_warn(FutureWarning):
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axes = plot_ecdf(data, cdf=dist.cdf, confidence_bands=True)
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assert axes is not None
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# values2 is deprecated
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data2 = dist.rvs(200)
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with pytest.warns(FutureWarning):
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axes = plot_ecdf(data, values2=data2, difference=True)
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# pit is deprecated
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with pytest.warns(FutureWarning):
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axes = plot_ecdf(data, cdf=dist.cdf, pit=True)
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assert axes is not None
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with does_not_warn(FutureWarning):
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axes = plot_ecdf(data, cdf=dist.cdf, ci_prob=0.9)
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@pytest.mark.parametrize(
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@pytest.mark.parametrize("args", [("stats.hdi_prob", "stats.ci_prob", 0.7, 0.7)])
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def test_deprecated_param(args):
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"""Test value and warning message correctly set for deprecated rcparams."""
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param_old, param_new, val_old, val_new = args
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assert param_new in rcParams
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assert not np.isclose(rcParams[param_new], val_new)
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msg = f"{param_old} is deprecated since .*, use {param_new} instead"
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with pytest.warns(FutureWarning, match=msg):
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with rc_context(rc={param_old: val_old}):
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assert np.isclose(rcParams[param_new], val_new)
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@pytest.mark.parametrize("allow_none", (True, False))
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@pytest.mark.parametrize("typeof", (str, int))
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def data(self, eight_schools_params, draws, chains):
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arviz/tests/helpers.py
CHANGED
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def does_not_warn(warning=Warning):
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warnings.simplefilter("always")
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return os.environ.get("ARVIZ_CI_MACHINE") is not None
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def importorskip(
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638
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) -> Any:
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Example::
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653
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docutils = pytest.importorskip("docutils")
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"""
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#
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if not
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# Unless ARVIZ_REQUIRE_ALL_DEPS is defined, tests that require a missing dependency are skipped
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# if set, missing optional dependencies trigger failed tests.
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if "ARVIZ_REQUIRE_ALL_DEPS" not in os.environ:
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import warnings
|
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|
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arviz/utils.py
CHANGED
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STATIC_FILES = ("static/html/icons-svg-inline.html", "static/css/style.css")
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class BehaviourChangeWarning(Warning):
|
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"""Custom warning to ease filtering it."""
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1
1
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Metadata-Version: 2.1
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2
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Name: arviz
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-
Version: 0.
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3
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+
Version: 0.19.0
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Summary: Exploratory analysis of Bayesian models
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5
5
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Home-page: http://github.com/arviz-devs/arviz
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6
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Author: ArviZ Developers
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@@ -23,7 +23,7 @@ Description-Content-Type: text/markdown
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License-File: LICENSE
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24
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Requires-Dist: setuptools >=60.0.0
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Requires-Dist: matplotlib >=3.5
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Requires-Dist: numpy
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+
Requires-Dist: numpy >=1.23.0
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Requires-Dist: scipy >=1.9.0
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Requires-Dist: packaging
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Requires-Dist: bokeh
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Requires-Dist: bokeh >=3 ; extra == 'all'
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Requires-Dist: zarr
|
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Requires-Dist: zarr <3,>=2.5.0 ; extra == 'all'
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|
Requires-Dist: xarray-datatree ; extra == 'all'
|
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Provides-Extra: preview
|
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+
Requires-Dist: arviz-base[h5netcdf] ; extra == 'preview'
|
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+
Requires-Dist: arviz-stats[xarray] ; extra == 'preview'
|
|
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|
+
Requires-Dist: arviz-plots ; extra == 'preview'
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|
<img src="https://raw.githubusercontent.com/arviz-devs/arviz-project/main/arviz_logos/ArviZ.png#gh-light-mode-only" width=200></img>
|
|
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50
|
<img src="https://raw.githubusercontent.com/arviz-devs/arviz-project/main/arviz_logos/ArviZ_white.png#gh-dark-mode-only" width=200></img>
|
|
@@ -1,23 +1,24 @@
|
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1
|
-
arviz/__init__.py,sha256=
|
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1
|
+
arviz/__init__.py,sha256=kcqBQn8wiV7gkzQvnJTezqtgI1IqPWYylkiz6Uvg9YQ,10397
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2
2
|
arviz/labels.py,sha256=w4-t0qdJzjKrqRyhzbtk6ucoMIAxle1HpHYlH7up06Q,6828
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3
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+
arviz/preview.py,sha256=5HwHycvbSAkWsAEYHBfd3Crwmeq8T06ysSgB528iQnA,375
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4
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arviz/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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4
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-
arviz/rcparams.py,sha256=
|
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5
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+
arviz/rcparams.py,sha256=lQnBprbDihEcsP5FujoJetGna4T8nc20JnuVf1Wn-1k,21031
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|
5
6
|
arviz/sel_utils.py,sha256=xvAYENhGXDTrhaT4Itlk1SJQUUGZ6BGcR04fPFgvzdM,6951
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6
|
-
arviz/utils.py,sha256=
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7
|
+
arviz/utils.py,sha256=sOUIkqmWtwY3PM-rQpN6arW9MsPt-MfvzdwAe78rT8U,26425
|
|
7
8
|
arviz/data/__init__.py,sha256=SG2umdZ8uVNYKVBoVYPy5tNxJnzLdyw0spPMjMTae5k,1558
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8
9
|
arviz/data/base.py,sha256=7GhA20dlU2t4J2VfAPavfHT_ZyF_fU8gQMsvHnWed6g,21026
|
|
9
10
|
arviz/data/converters.py,sha256=vyzQWlEnuBiCRQNiLe7sXWfE6po1USnMNChtJ0VG48A,7831
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|
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11
|
arviz/data/datasets.py,sha256=wPi23KZI-w4HrhjmY1LUg0Rj0aJobSJ4WO3LBrjfZQc,5392
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11
12
|
arviz/data/inference_data.py,sha256=ZUR-GgxWJ-mGPr9PvhS2mKT5j0U6ZkhxsUIkJTJ4loY,92455
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|
arviz/data/io_beanmachine.py,sha256=QQVBD6rftvs6_kLIb4Vm1QzQ6BsS0J9DTrzw2Jj4ob8,3745
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13
|
-
arviz/data/io_cmdstan.py,sha256=
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|
14
|
+
arviz/data/io_cmdstan.py,sha256=8YX9Nfkx4LqjfKms4s4GTOkOjZNelb6SukvRZRHY6iM,38994
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|
arviz/data/io_cmdstanpy.py,sha256=iSr8ciKBFoIa1tJGHEX-2JKkUJRyaTXzRXf-5mu8q5U,42991
|
|
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16
|
arviz/data/io_datatree.py,sha256=Ag_7LHAejqt0Zxbu350u8WBY44nGsFY7eyhKa0Wi7FE,502
|
|
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17
|
arviz/data/io_dict.py,sha256=HM4ke-NuopsPnIdU-UGMtppAnj3vcbkBti8eROpMRTs,17698
|
|
17
18
|
arviz/data/io_emcee.py,sha256=zsJJqwlyXLN_TfI6hgKz97p4N30NYTVvQSrIIpiLmB0,11844
|
|
18
19
|
arviz/data/io_json.py,sha256=lrSP_9abfUW_5E8TwnG4hsS5HNHzAHZQCJTynl_tXKY,1256
|
|
19
20
|
arviz/data/io_netcdf.py,sha256=cCxVnXSCTzWP3SU7cM4SqBiRRK9txFOsm-MchzNUzM4,2336
|
|
20
|
-
arviz/data/io_numpyro.py,sha256=
|
|
21
|
+
arviz/data/io_numpyro.py,sha256=_U6owmsY5hrQU7C5NPw43s76Swmy_YqXw4UZYfZwzU4,14241
|
|
21
22
|
arviz/data/io_pyjags.py,sha256=AG2ckAuygSxbjULVFQCJQSM72GnUoTMi3T94aQRJYKQ,13271
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|
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23
|
arviz/data/io_pyro.py,sha256=JYywUGUU1Qil_ahLuDYhYFafQAKB-y1kIipXdfH_vnQ,12740
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24
|
arviz/data/io_pystan.py,sha256=nRTU6yujilQCKERxzN7LIVwZplfvFNb-Y9Jk9YVJQLk,41700
|
|
@@ -31,33 +32,33 @@ arviz/data/example_data/data/non_centered_eight.nc,sha256=r7kyd10HyJTTRQs4OlSCXP
|
|
|
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arviz/plots/__init__.py,sha256=atWhfLXHAD6zaTjbdWdTaJrPTNBl3XpcSCY4etgw_cY,1514
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arviz/plots/autocorrplot.py,sha256=f-rYtnZtxgOns5sIT6pdw-EdU74lAVmAeV9b6rKLsgw,5666
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arviz/plots/bfplot.py,sha256=s8bizLCkF5uZnz66UKmuUJs_AXuMVrgGObTa2ofUF-Q,5124
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arviz/plots/bpvplot.py,sha256=
|
|
35
|
+
arviz/plots/bpvplot.py,sha256=QR4znezjiSLMyMagvnJLb9Y1SIlT99gJ52o4FnX5tZg,12098
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|
arviz/plots/compareplot.py,sha256=DQ1ebXSHGnP9A5y5iABq6PB8hO7Pn_ZlUH0ujNY_dc8,6074
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|
-
arviz/plots/densityplot.py,sha256=
|
|
37
|
+
arviz/plots/densityplot.py,sha256=6477ZljpBCcZRw0SUwcTO4FYjxqw_qYsJupWNo-jCok,10895
|
|
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38
|
arviz/plots/distcomparisonplot.py,sha256=gVNQUN0VX7hC527fcUk1oxtQRdIl5mrltU95c0Nra9k,7184
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|
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|
arviz/plots/distplot.py,sha256=xWXOsN-pPBwhHrEjC6lbIJdn-17DtpMueSnj6YzWlX4,8472
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|
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arviz/plots/dotplot.py,sha256=
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|
-
arviz/plots/ecdfplot.py,sha256=
|
|
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|
+
arviz/plots/dotplot.py,sha256=9HTMeT1ZuZ4Vauxvg4TjsvvNnwORG8WWO2HistJwHiU,7736
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|
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|
+
arviz/plots/ecdfplot.py,sha256=BkukbyDUGMCW72b9ZFBCK9zrkavgGHwkcxRv76kQrzk,12734
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arviz/plots/elpdplot.py,sha256=NKqPkwTj9BWDzwMnG0cPeLmYBGMX_meP9F6bqvTwLKY,6433
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arviz/plots/energyplot.py,sha256=znEDPYpWaTIX0XpdVoyhXOITJ4A8BYkI9t1TVhJq4Qo,4797
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arviz/plots/essplot.py,sha256=
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arviz/plots/forestplot.py,sha256=
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arviz/plots/hdiplot.py,sha256
|
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arviz/plots/essplot.py,sha256=ch0DjUQDILk4ohpSUR-9VHejGFb6Xmelly-qa-fKb9E,11741
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arviz/plots/forestplot.py,sha256=WRgW6pg1kO4xrd412qKgbY8QAaFyALfJsNzmQIXMwTc,11896
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arviz/plots/hdiplot.py,sha256=cNj2r0dPxtquZNoChgjFO-wmqgU-W-dq_ed1kWJ2vHI,7589
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arviz/plots/kdeplot.py,sha256=eQze22vHcZdjJT_Z6P8IJweNMWJMXRM6Ei5S4vx0m54,11749
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arviz/plots/khatplot.py,sha256=
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arviz/plots/khatplot.py,sha256=u03gmBG1xwxG07ASLZEJB-GsRhRHtUCtbglpC1N0aIg,8086
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arviz/plots/lmplot.py,sha256=LxR7RXkaAi5J8076isebVrtdk6UwbcTRekEymM9S6cY,11726
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arviz/plots/loopitplot.py,sha256=
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arviz/plots/mcseplot.py,sha256=
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arviz/plots/loopitplot.py,sha256=bFUO_Fy4z6u6E39GdaF4rIvc-COWNwF4A0n2kcmZBfA,8321
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arviz/plots/mcseplot.py,sha256=rsiz4E9M9p58YetAaF75gbenGIj4M0hapWnh9UJOXzY,6829
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arviz/plots/pairplot.py,sha256=yVxyLC7ms0SKpTunifacUyOblH8BW9CsQqE2Hv0ARP4,10407
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arviz/plots/parallelplot.py,sha256=ZBEsHvnlmSXLRpSwP-KUwzgWBC2S4siKXFGJnLf7uAE,7125
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arviz/plots/plot_utils.py,sha256=
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arviz/plots/posteriorplot.py,sha256=
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arviz/plots/plot_utils.py,sha256=mawuYnwb9AfdLQ9HAerTOGT9iKNjXrQraXvtDd9tFco,18243
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arviz/plots/posteriorplot.py,sha256=pC-5SQZOGq1F4opM_sQLxn4ZG2we4Y9ULV8yhxjGVdo,10952
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arviz/plots/ppcplot.py,sha256=UPTtXDWHf3wFAb-apNPGcz8qw9CQwINGml_2YkYI-iM,13967
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arviz/plots/rankplot.py,sha256=
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arviz/plots/rankplot.py,sha256=lz0swHs6EBe-gXn4udP1Um3RS-EatsOAmguYqGMlIjU,8648
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arviz/plots/separationplot.py,sha256=Fx_QVeFUcF45fm7nn06pt0qubOzvH8QMU1cw5RLyaik,5491
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arviz/plots/traceplot.py,sha256=dwcF7rsjMAIxZ_LPv7Z8os01uQZHXTkDFWEBtsbzI9k,10216
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arviz/plots/tsplot.py,sha256=haTyvfGX5fA8Zle9bzllybG5n307BUJIxGywNAnOsU0,15925
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arviz/plots/violinplot.py,sha256=
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arviz/plots/violinplot.py,sha256=yxoEMGTIt4CDinZaNHPYI5MqFvXB2J2gyKdKJ47PKdk,7129
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arviz/plots/backends/__init__.py,sha256=LZxXo7ogt7ZVrdUea0xkxpx5YV0wpV20MHwdItgk3oU,7752
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arviz/plots/backends/bokeh/__init__.py,sha256=e2wfZNdGTFU5GjsLokCLpknweaNgjZ5v3k7NB0gry6g,4877
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arviz/plots/backends/bokeh/autocorrplot.py,sha256=9CruVndfMnqsi4waav7Gcr7pn0nmUB0mkJxkzOjtGtw,2463
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arviz/plots/backends/bokeh/distcomparisonplot.py,sha256=o8FHMb1ZzKPpt7fXhwBr6HGhqpclO1Qk9o6aTGypgv0,431
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arviz/plots/backends/bokeh/distplot.py,sha256=a2yY4waIPdwGhDpUtYi87Ra-TJiAA67oQumIiU-nXiA,4851
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arviz/plots/backends/bokeh/dotplot.py,sha256=qy8B4QL6B_ZfoVtDDA6c7HcsQofQLlE1tTnkcJO1mPA,2828
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arviz/plots/backends/bokeh/ecdfplot.py,sha256=
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arviz/plots/backends/bokeh/ecdfplot.py,sha256=Zrinhu6ViG3BbClxnRFZ_zIZm7S1nARiydHi-l1_i-g,1680
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arviz/plots/backends/bokeh/elpdplot.py,sha256=5bn_rH1Aixm0--BArAP4m4kuZMjWxR8ox-8T-xK_GMY,6487
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arviz/plots/backends/bokeh/energyplot.py,sha256=FKPYRaWwM32Vw0AHE0MIWBn9wZQeoYdP_YpYZGijIq0,4571
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arviz/plots/backends/bokeh/essplot.py,sha256=zghMEYUH3bAljqNt72-dRa8IFom27F7dMklHNQOrzBM,5494
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arviz/plots/backends/bokeh/forestplot.py,sha256=DIoGzSIAMA9vmKwpoNxVoNKFpDBwpfjdGd6KTl9u_OY,27219
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arviz/plots/backends/bokeh/hdiplot.py,sha256=bAhTPi9D7cw2ytSvjSIRD3g-PqpB9OFwusrQAnmKCYY,1538
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arviz/plots/backends/bokeh/kdeplot.py,sha256=nKEgJfnP7NK2Y2cipF_RglEC6GpowaagH5wZP3iZq-U,9329
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arviz/plots/backends/bokeh/khatplot.py,sha256=
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arviz/plots/backends/bokeh/khatplot.py,sha256=J5m9vugSzpi9sE-T_2PRzI8pA100Hf8rUMhpmkTP8n4,4599
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arviz/plots/backends/bokeh/loopitplot.py,sha256=FWjcsSWGJNy4wM63_N2qpg5oECb3Cq-uLy3xDS5x6j4,7172
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arviz/plots/backends/bokeh/mcseplot.py,sha256=teyAG-A4vIHor_Qr4iB3l5nLJ--EzvPvw1x44hUOVSI,5924
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arviz/plots/backends/bokeh/pairplot.py,sha256=
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arviz/plots/backends/bokeh/pairplot.py,sha256=2sByGaDuDT_ebyhPLIP3jRO1i43DLVDTPKWCpjd9MXc,13146
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arviz/plots/backends/bokeh/parallelplot.py,sha256=SNChOLWvcKxXuuJsIfWs9CNj7qDuVb95UZyp4CP1BQE,2230
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arviz/plots/backends/bokeh/posteriorplot.py,sha256=yBAlGo3lQpFBVro724eZtKnOHgVkY7LXupa-8_VtE7c,9380
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arviz/plots/backends/bokeh/ppcplot.py,sha256=mfDzTXxJU26CcK8ZKno3Y_yK_y3VYeUT3vaJqUoGEq4,13269
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@@ -96,14 +97,14 @@ arviz/plots/backends/matplotlib/densityplot.py,sha256=zlqzYvH3VXWPiiIvL--fxtMp3h
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arviz/plots/backends/matplotlib/distcomparisonplot.py,sha256=XZY2jITNKtcIMsg5tl_lzuwI-2DcdUdCWqrK7bsdvWE,3568
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arviz/plots/backends/matplotlib/distplot.py,sha256=V0CeyAPah5RzHXW9I5tssVXlZgj2NHPkg-k15ayEdVw,4581
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