arviz 0.21.0__py3-none-any.whl → 0.22.0__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 +8 -3
- arviz/data/inference_data.py +37 -19
- arviz/data/io_datatree.py +2 -2
- arviz/data/io_numpyro.py +112 -4
- arviz/plots/autocorrplot.py +12 -2
- arviz/plots/backends/bokeh/hdiplot.py +7 -6
- arviz/plots/backends/bokeh/lmplot.py +19 -3
- arviz/plots/backends/bokeh/pairplot.py +18 -48
- arviz/plots/backends/matplotlib/khatplot.py +8 -1
- arviz/plots/backends/matplotlib/lmplot.py +13 -7
- arviz/plots/backends/matplotlib/pairplot.py +14 -22
- arviz/plots/kdeplot.py +4 -4
- arviz/plots/lmplot.py +41 -14
- arviz/plots/pairplot.py +10 -3
- arviz/stats/density_utils.py +1 -1
- arviz/stats/stats.py +19 -7
- arviz/tests/base_tests/test_data.py +0 -4
- arviz/tests/base_tests/test_plots_bokeh.py +60 -2
- arviz/tests/base_tests/test_plots_matplotlib.py +77 -1
- arviz/tests/base_tests/test_stats.py +42 -1
- arviz/tests/external_tests/test_data_numpyro.py +130 -3
- arviz/wrappers/base.py +1 -1
- arviz/wrappers/wrap_stan.py +1 -1
- {arviz-0.21.0.dist-info → arviz-0.22.0.dist-info}/METADATA +7 -7
- {arviz-0.21.0.dist-info → arviz-0.22.0.dist-info}/RECORD +28 -28
- {arviz-0.21.0.dist-info → arviz-0.22.0.dist-info}/LICENSE +0 -0
- {arviz-0.21.0.dist-info → arviz-0.22.0.dist-info}/WHEEL +0 -0
- {arviz-0.21.0.dist-info → arviz-0.22.0.dist-info}/top_level.txt +0 -0
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@@ -46,7 +46,9 @@ class TestDataNumPyro:
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)
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return predictions
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def get_inference_data(
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def get_inference_data(
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self, data, eight_schools_params, predictions_data, predictions_params, infer_dims=False
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):
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posterior_samples = data.obj.get_samples()
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model = data.obj.sampler.model
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posterior_predictive = Predictive(model, posterior_samples)(
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@@ -55,6 +57,12 @@ class TestDataNumPyro:
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prior = Predictive(model, num_samples=500)(
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PRNGKey(2), eight_schools_params["J"], eight_schools_params["sigma"]
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)
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dims = {"theta": ["school"], "eta": ["school"], "obs": ["school"]}
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pred_dims = {"theta": ["school_pred"], "eta": ["school_pred"], "obs": ["school_pred"]}
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if infer_dims:
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dims = None
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pred_dims = None
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predictions = predictions_data
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return from_numpyro(
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posterior=data.obj,
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@@ -65,8 +73,8 @@ class TestDataNumPyro:
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"school": np.arange(eight_schools_params["J"]),
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"school_pred": np.arange(predictions_params["J"]),
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},
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dims=
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pred_dims=
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dims=dims,
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pred_dims=pred_dims,
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)
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def test_inference_data_namedtuple(self, data):
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@@ -77,6 +85,7 @@ class TestDataNumPyro:
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data.obj.get_samples = lambda *args, **kwargs: data_namedtuple
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inference_data = from_numpyro(
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posterior=data.obj,
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dims={}, # This mock test needs to turn off autodims like so or mock group_by_chain
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)
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assert isinstance(data.obj.get_samples(), Samples)
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data.obj.get_samples = _old_fn
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@@ -282,3 +291,121 @@ class TestDataNumPyro:
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(mcmc)
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assert inference_data.observed_data
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def test_mcmc_infer_dims(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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def model():
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# note: group2 gets assigned dim=-1 and group1 is assigned dim=-2
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with numpyro.plate("group2", 5), numpyro.plate("group1", 10):
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_ = numpyro.sample("param", dist.Normal(0, 1))
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(
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mcmc, coords={"group1": np.arange(10), "group2": np.arange(5)}
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)
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assert inference_data.posterior.param.dims == ("chain", "draw", "group1", "group2")
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assert all(dim in inference_data.posterior.param.coords for dim in ("group1", "group2"))
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def test_mcmc_infer_unsorted_dims(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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def model():
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group1_plate = numpyro.plate("group1", 10, dim=-1)
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group2_plate = numpyro.plate("group2", 5, dim=-2)
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# the plate contexts are entered in a different order than the pre-defined dims
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# we should make sure this still works because the trace has all of the info it needs
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with group2_plate, group1_plate:
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_ = numpyro.sample("param", dist.Normal(0, 1))
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(
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mcmc, coords={"group1": np.arange(10), "group2": np.arange(5)}
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)
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assert inference_data.posterior.param.dims == ("chain", "draw", "group2", "group1")
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assert all(dim in inference_data.posterior.param.coords for dim in ("group1", "group2"))
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def test_mcmc_infer_dims_no_coords(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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def model():
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with numpyro.plate("group", 5):
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_ = numpyro.sample("param", dist.Normal(0, 1))
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(mcmc)
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assert inference_data.posterior.param.dims == ("chain", "draw", "group")
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def test_mcmc_event_dims(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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def model():
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_ = numpyro.sample(
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"gamma", dist.ZeroSumNormal(1, event_shape=(10,)), infer={"event_dims": ["groups"]}
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)
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(mcmc, coords={"groups": np.arange(10)})
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assert inference_data.posterior.gamma.dims == ("chain", "draw", "groups")
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assert "groups" in inference_data.posterior.gamma.coords
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@pytest.mark.xfail
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def test_mcmc_inferred_dims_univariate(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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import jax.numpy as jnp
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def model():
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alpha = numpyro.sample("alpha", dist.Normal(0, 1))
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sigma = numpyro.sample("sigma", dist.HalfNormal(1))
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with numpyro.plate("obs_idx", 3):
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# mu is plated by obs_idx, but isnt broadcasted to the plate shape
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# the expected behavior is that this should cause a failure
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mu = numpyro.deterministic("mu", alpha)
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return numpyro.sample("y", dist.Normal(mu, sigma), obs=jnp.array([-1, 0, 1]))
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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inference_data = from_numpyro(mcmc, coords={"obs_idx": np.arange(3)})
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assert inference_data.posterior.mu.dims == ("chain", "draw", "obs_idx")
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assert "obs_idx" in inference_data.posterior.mu.coords
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def test_mcmc_extra_event_dims(self):
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import numpyro
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import numpyro.distributions as dist
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from numpyro.infer import MCMC, NUTS
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def model():
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gamma = numpyro.sample("gamma", dist.ZeroSumNormal(1, event_shape=(10,)))
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_ = numpyro.deterministic("gamma_plus1", gamma + 1)
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mcmc = MCMC(NUTS(model), num_warmup=10, num_samples=10)
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mcmc.run(PRNGKey(0))
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mcmc, coords={"groups": np.arange(10)}, extra_event_dims={"gamma_plus1": ["groups"]}
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)
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assert inference_data.posterior.gamma_plus1.dims == ("chain", "draw", "groups")
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def test_mcmc_predictions_infer_dims(
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inference_data = self.get_inference_data(
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)
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assert inference_data.predictions.obs.dims == ("chain", "draw", "J")
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assert "J" in inference_data.predictions.obs.coords
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arviz/wrappers/base.py
CHANGED
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"""Check that all methods listed are implemented.
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Not all functions that require refitting need to have all the methods implemented in
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order to work properly. This function
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order to work properly. This function should be used before using the SamplingWrapper and
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its subclasses to get informative error messages.
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arviz/wrappers/wrap_stan.py
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Variable name containing the pointwise log likelihood data of the excluded
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data. As PyStan cannot call C++ functions and log_likelihood__i is already
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calculated *during* the
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calculated *during* the simulation, instead of the value on which to evaluate
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"""
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Metadata-Version: 2.1
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Name: arviz
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Version: 0.
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Version: 0.22.0
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Summary: Exploratory analysis of Bayesian models
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Home-page: http://github.com/arviz-devs/arviz
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Author: ArviZ Developers
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: setuptools>=60.0.0
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Requires-Dist: matplotlib>=3.
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Requires-Dist: numpy>=1.
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Requires-Dist: scipy>=1.
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Requires-Dist: matplotlib>=3.8
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Requires-Dist: numpy>=1.26.0
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Requires-Dist: scipy>=1.11.0
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Requires-Dist: pandas>=1.
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Requires-Dist: xarray>=
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Requires-Dist: pandas>=2.1.0
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Requires-Dist: xarray>=2023.7.0
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Requires-Dist: h5netcdf>=1.0.2
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Requires-Dist: ujson; extra == "all"
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Requires-Dist: zarr<3,>=2.5.0; extra == "all"
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Requires-Dist: xarray>=2024.11.0; extra == "all"
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Provides-Extra: preview
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Requires-Dist: arviz-base[h5netcdf]; extra == "preview"
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arviz/__init__.py,sha256=
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arviz/__init__.py,sha256=IOdU7uIJbHurf--mKztuR4Yq-fVHSLyU_neL4nK89KE,10590
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arviz/labels.py,sha256=w4-t0qdJzjKrqRyhzbtk6ucoMIAxle1HpHYlH7up06Q,6828
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arviz/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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arviz/data/base.py,sha256=PALdVidyCxJqje_za4XPwXH010qAMJt4VzzeOflUCC8,21365
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arviz/data/converters.py,sha256=4QU5_0OU84HV3gSXXY_N5bd6S9ft81lfpnCT-8E8qyc,7933
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arviz/data/datasets.py,sha256=wPi23KZI-w4HrhjmY1LUg0Rj0aJobSJ4WO3LBrjfZQc,5392
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arviz/data/inference_data.py,sha256=
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arviz/data/inference_data.py,sha256=BvZsTROxRIGc6c4Jg_NQrjnlfm_WquPyhJi88KBEkis,94545
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arviz/data/io_beanmachine.py,sha256=QQVBD6rftvs6_kLIb4Vm1QzQ6BsS0J9DTrzw2Jj4ob8,3745
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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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arviz/data/io_datatree.py,sha256=
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arviz/data/io_datatree.py,sha256=QNj6Fkbv9HiJbCMbQmwGNPkwhYD4BkeMN10syhV9-J0,498
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arviz/data/io_dict.py,sha256=HM4ke-NuopsPnIdU-UGMtppAnj3vcbkBti8eROpMRTs,17698
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arviz/data/io_emcee.py,sha256=zsJJqwlyXLN_TfI6hgKz97p4N30NYTVvQSrIIpiLmB0,11844
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arviz/data/io_json.py,sha256=lrSP_9abfUW_5E8TwnG4hsS5HNHzAHZQCJTynl_tXKY,1256
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