arviz 0.17.1__py3-none-any.whl → 0.18.0__py3-none-any.whl

arviz/plots/backends/bokeh/ppcplot.py

@@ -1,4 +1,5 @@
 """Bokeh Posterior predictive plot."""
+
 import numpy as np
 from bokeh.models.annotations import Legend
 from bokeh.models.glyphs import Scatter

arviz/plots/backends/bokeh/rankplot.py

@@ -1,4 +1,5 @@
 """Bokeh rankplot."""
+
 import numpy as np
 
 from bokeh.models import Span

arviz/plots/backends/bokeh/separationplot.py

@@ -1,4 +1,5 @@
 """Bokeh separation plot."""
+
 import numpy as np
 
 from ...plot_utils import _scale_fig_size, vectorized_to_hex

arviz/plots/backends/bokeh/traceplot.py

@@ -1,4 +1,5 @@
 """Bokeh Traceplot."""
+
 import warnings
 from collections.abc import Iterable
 from itertools import cycle

arviz/plots/backends/bokeh/violinplot.py

@@ -1,4 +1,5 @@
 """Bokeh Violinplot."""
+
 import numpy as np
 from bokeh.models.annotations import Title
 

arviz/plots/backends/matplotlib/autocorrplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Autocorrplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/bpvplot.py

@@ -1,4 +1,5 @@
 """Matplotib Bayesian p-value Posterior predictive plot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy import stats

arviz/plots/backends/matplotlib/compareplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Compareplot."""
+
 import matplotlib.pyplot as plt
 
 from ...plot_utils import _scale_fig_size

arviz/plots/backends/matplotlib/densityplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Densityplot."""
+
 from itertools import cycle
 
 import matplotlib.pyplot as plt

arviz/plots/backends/matplotlib/distcomparisonplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Density Comparison plot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -88,9 +89,7 @@ def plot_dist_comparison(
         kwargs = (
             prior_kwargs
             if group.startswith("prior")
-            else posterior_kwargs
-            if group.startswith("posterior")
-            else observed_kwargs
+            else posterior_kwargs if group.startswith("posterior") else observed_kwargs
         )
         for idx2, (
             var_name,

arviz/plots/backends/matplotlib/distplot.py

@@ -1,4 +1,5 @@
 """Matplotlib distplot."""
+
 import matplotlib.pyplot as plt
 from matplotlib import _pylab_helpers
 import numpy as np

arviz/plots/backends/matplotlib/dotplot.py

@@ -1,4 +1,5 @@
 """Matplotlib dotplot."""
+
 import math
 import warnings
 import numpy as np

arviz/plots/backends/matplotlib/ecdfplot.py

@@ -1,4 +1,5 @@
 """Matplotlib ecdfplot."""
+
 import matplotlib.pyplot as plt
 from matplotlib.colors import to_hex
 

arviz/plots/backends/matplotlib/elpdplot.py

@@ -1,4 +1,5 @@
 """Matplotlib ELPDPlot."""
+
 import warnings
 
 from matplotlib import cm

arviz/plots/backends/matplotlib/energyplot.py

@@ -1,4 +1,5 @@
 """Matplotlib energyplot."""
+
 from itertools import cycle
 
 import matplotlib.pyplot as plt

arviz/plots/backends/matplotlib/essplot.py

@@ -1,4 +1,5 @@
 """Matplotlib energyplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy.stats import rankdata
@@ -127,11 +128,11 @@ def plot_ess(
             ax_.annotate(
                 "mean",
                 (text_x, mean_ess_i),
-                va=text_va
-                if text_va is not None
-                else "bottom"
-                if mean_ess_i >= sd_ess_i
-                else "top",
+                va=(
+                    text_va
+                    if text_va is not None
+                    else "bottom" if mean_ess_i >= sd_ess_i else "top"
+                ),
                 **text_kwargs,
             )
             ax_.axhline(sd_ess_i, **extra_kwargs)

arviz/plots/backends/matplotlib/forestplot.py

@@ -1,4 +1,5 @@
 """Matplotlib forestplot."""
+
 from collections import OrderedDict, defaultdict
 from itertools import tee
 

arviz/plots/backends/matplotlib/hdiplot.py

@@ -1,4 +1,5 @@
 """Matplotlib hdiplot."""
+
 import matplotlib.pyplot as plt
 from matplotlib import _pylab_helpers
 

arviz/plots/backends/matplotlib/kdeplot.py

@@ -1,4 +1,5 @@
 """Matplotlib kdeplot."""
+
 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib import _pylab_helpers
@@ -162,10 +163,11 @@ def plot_kde(
         ax.grid(False)
         if contour:
             qcfs = ax.contourf(x_x, y_y, density, antialiased=True, **contourf_kwargs)
-            qcs = ax.contour(x_x, y_y, density, **contour_kwargs)
+            ax.contour(x_x, y_y, density, **contour_kwargs)
             if not fill_last:
-                qcfs.collections[0].set_alpha(0)
-                qcs.collections[0].set_alpha(0)
+                alpha = np.ones(len(qcfs.allsegs), dtype=float)
+                alpha[0] = 0
+                qcfs.set_alpha(alpha)
         else:
             ax.pcolormesh(x_x, y_y, density, **pcolormesh_kwargs)
 

arviz/plots/backends/matplotlib/khatplot.py

@@ -1,4 +1,5 @@
 """Matplotlib khatplot."""
+
 import warnings
 
 import matplotlib as mpl

arviz/plots/backends/matplotlib/lmplot.py

@@ -1,4 +1,5 @@
 """Matplotlib plot linear regression figure."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/loopitplot.py

@@ -1,4 +1,5 @@
 """Matplotlib loopitplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 from matplotlib.colors import hsv_to_rgb, rgb_to_hsv, to_hex, to_rgb

arviz/plots/backends/matplotlib/mcseplot.py

@@ -1,4 +1,5 @@
 """Matplotlib mcseplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy.stats import rankdata
@@ -94,22 +95,22 @@ def plot_mcse(
                 ax_.annotate(
                     "mean",
                     (text_x, mean_mcse_i),
-                    va=text_va
-                    if text_va is not None
-                    else "bottom"
-                    if mean_mcse_i > sd_mcse_i
-                    else "top",
+                    va=(
+                        text_va
+                        if text_va is not None
+                        else "bottom" if mean_mcse_i > sd_mcse_i else "top"
+                    ),
                     **text_kwargs,
                 )
                 ax_.axhline(sd_mcse_i, **extra_kwargs)
                 ax_.annotate(
                     "sd",
                     (text_x, sd_mcse_i),
-                    va=text_va
-                    if text_va is not None
-                    else "bottom"
-                    if sd_mcse_i >= mean_mcse_i
-                    else "top",
+                    va=(
+                        text_va
+                        if text_va is not None
+                        else "bottom" if sd_mcse_i >= mean_mcse_i else "top"
+                    ),
                     **text_kwargs,
                 )
         if rug:

arviz/plots/backends/matplotlib/pairplot.py

@@ -1,4 +1,5 @@
 """Matplotlib pairplot."""
+
 import warnings
 from copy import deepcopy
 
@@ -333,7 +334,7 @@ def plot_pair(
                     if reference_values:
                         x_name = flat_var_names[i]
                         y_name = flat_var_names[j + not_marginals]
-                        if x_name and y_name not in difference:
+                        if (x_name not in difference) and (y_name not in difference):
                             ax[j, i].plot(
                                 reference_values_copy[x_name],
                                 reference_values_copy[y_name],

arviz/plots/backends/matplotlib/parallelplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Parallel coordinates plot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/posteriorplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Plot posterior densities."""
+
 from numbers import Number
 
 import matplotlib.pyplot as plt

arviz/plots/backends/matplotlib/ppcplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Posterior predictive plot."""
+
 import logging
 import platform
 

arviz/plots/backends/matplotlib/rankplot.py

@@ -1,4 +1,5 @@
 """Matplotlib rankplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/separationplot.py

@@ -1,4 +1,5 @@
 """Matplotlib separation plot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/traceplot.py

@@ -1,4 +1,5 @@
 """Matplotlib traceplot."""
+
 import warnings
 from itertools import cycle
 

arviz/plots/backends/matplotlib/tsplot.py

@@ -1,4 +1,5 @@
 """Matplotlib plot time series figure."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 

arviz/plots/backends/matplotlib/violinplot.py

@@ -1,4 +1,5 @@
 """Matplotlib Violinplot."""
+
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -60,7 +61,7 @@ def plot_violin(
             cols,
             backend_kwargs=backend_kwargs,
         )
-        fig.set_constrained_layout(False)
+        fig.set_layout_engine("none")
         fig.subplots_adjust(wspace=0)
 
     ax = np.atleast_1d(ax)

arviz/plots/bpvplot.py

@@ -1,4 +1,5 @@
 """Bayesian p-value Posterior/Prior predictive plot."""
+
 import numpy as np
 
 from ..labels import BaseLabeller

arviz/plots/compareplot.py

@@ -1,4 +1,5 @@
 """Summary plot for model comparison."""
+
 import numpy as np
 
 from ..labels import BaseLabeller

arviz/plots/densityplot.py

@@ -1,4 +1,5 @@
 """KDE and histogram plots for multiple variables."""
+
 import warnings
 
 from ..data import convert_to_dataset

arviz/plots/distcomparisonplot.py

@@ -1,4 +1,5 @@
 """Density Comparison plot."""
+
 import warnings
 from ..labels import BaseLabeller
 from ..rcparams import rcParams

arviz/plots/dotplot.py

@@ -1,4 +1,5 @@
 """Plot distribution as dot plot or quantile dot plot."""
+
 import numpy as np
 
 from ..rcparams import rcParams

arviz/plots/ecdfplot.py

@@ -1,4 +1,5 @@
 """Plot ecdf or ecdf-difference plot with confidence bands."""
+
 import numpy as np
 from scipy.stats import uniform
 

arviz/plots/elpdplot.py

@@ -1,4 +1,5 @@
 """Plot pointwise elpd estimations of inference data."""
+
 import numpy as np
 
 from ..rcparams import rcParams

arviz/plots/energyplot.py

@@ -1,4 +1,5 @@
 """Plot energy transition distribution in HMC inference."""
+
 import warnings
 
 from ..data import convert_to_dataset

arviz/plots/essplot.py

@@ -1,4 +1,5 @@
 """Plot quantile or local effective sample sizes."""
+
 import numpy as np
 import xarray as xr
 

arviz/plots/forestplot.py

@@ -1,4 +1,5 @@
 """Forest plot."""
+
 from ..data import convert_to_dataset
 from ..labels import BaseLabeller, NoModelLabeller
 from ..rcparams import rcParams

arviz/plots/hdiplot.py

@@ -1,4 +1,5 @@
 """Plot highest density intervals for regression data."""
+
 import warnings
 
 import numpy as np

arviz/plots/khatplot.py

@@ -1,4 +1,5 @@
 """Pareto tail indices plot."""
+
 import logging
 
 import numpy as np

arviz/plots/lmplot.py

@@ -1,4 +1,5 @@
 """Plot regression figure."""
+
 import warnings
 from numbers import Integral
 from itertools import repeat

arviz/plots/loopitplot.py

@@ -1,4 +1,5 @@
 """Plot LOO-PIT predictive checks of inference data."""
+
 import numpy as np
 from scipy import stats
 

arviz/plots/mcseplot.py

@@ -1,4 +1,5 @@
 """Plot quantile MC standard error."""
+
 import numpy as np
 import xarray as xr
 

arviz/plots/pairplot.py

@@ -1,4 +1,5 @@
 """Plot a scatter, kde and/or hexbin of sampled parameters."""
+
 import warnings
 from typing import List, Optional, Union
 

arviz/plots/parallelplot.py

@@ -1,4 +1,5 @@
 """Parallel coordinates plot showing posterior points with and without divergences marked."""
+
 import numpy as np
 from scipy.stats import rankdata
 

arviz/plots/plot_utils.py

@@ -1,4 +1,5 @@
 """Utilities for plotting."""
+
 import importlib
 import warnings
 from typing import Any, Dict

arviz/plots/posteriorplot.py

@@ -1,4 +1,5 @@
 """Plot posterior densities."""
+
 from ..data import convert_to_dataset
 from ..labels import BaseLabeller
 from ..sel_utils import xarray_var_iter

arviz/plots/ppcplot.py

@@ -1,4 +1,5 @@
 """Posterior/Prior predictive plot."""
+
 import logging
 import warnings
 from numbers import Integral

arviz/plots/rankplot.py

@@ -1,4 +1,5 @@
 """Histograms of ranked posterior draws, plotted for each chain."""
+
 from itertools import cycle
 
 import matplotlib.pyplot as plt

arviz/plots/separationplot.py

@@ -1,4 +1,5 @@
 """Separation plot for discrete outcome models."""
+
 import warnings
 
 import numpy as np

arviz/plots/traceplot.py

@@ -1,4 +1,5 @@
 """Plot kde or histograms and values from MCMC samples."""
+
 import warnings
 from typing import Any, Callable, List, Mapping, Optional, Tuple, Union, Sequence
 

arviz/plots/tsplot.py

@@ -1,4 +1,5 @@
 """Plot timeseries data."""
+
 import warnings
 import numpy as np
 

arviz/plots/violinplot.py

@@ -1,4 +1,5 @@
 """Plot posterior traces as violin plot."""
+
 from ..data import convert_to_dataset
 from ..labels import BaseLabeller
 from ..sel_utils import xarray_var_iter

arviz/rcparams.py

@@ -1,4 +1,5 @@
 """ArviZ rcparams. Based on matplotlib's implementation."""
+
 import locale
 import logging
 import os

arviz/sel_utils.py

@@ -1,4 +1,5 @@
 """Utilities for selecting and iterating on xarray objects."""
+
 from itertools import product, tee
 
 import numpy as np

arviz/static/css/style.css

@@ -302,7 +302,8 @@ dl.xr-attrs {
   grid-template-columns: 125px auto;
 }
 
-.xr-attrs dt, dd {
+.xr-attrs dt,
+.xr-attrs dd {
   padding: 0;
   margin: 0;
   float: left;

arviz/stats/density_utils.py

@@ -5,7 +5,8 @@ import warnings
 import numpy as np
 from scipy.fftpack import fft
 from scipy.optimize import brentq
-from scipy.signal import convolve, convolve2d, gaussian  # pylint: disable=no-name-in-module
+from scipy.signal import convolve, convolve2d
+from scipy.signal.windows import gaussian
 from scipy.sparse import coo_matrix
 from scipy.special import ive  # pylint: disable=no-name-in-module
 

arviz/stats/diagnostics.py

@@ -836,7 +836,7 @@ def _mcse_sd(ary):
         return np.nan
     ess = _ess_sd(ary)
     if _numba_flag:
-        sd = float(_sqrt(svar(np.ravel(ary), ddof=1), np.zeros(1)))
+        sd = float(_sqrt(svar(np.ravel(ary), ddof=1), np.zeros(1)).item())
     else:
         sd = np.std(ary, ddof=1)
     fac_mcse_sd = np.sqrt(np.exp(1) * (1 - 1 / ess) ** (ess - 1) - 1)
@@ -904,7 +904,7 @@ def _mc_error(ary, batches=5, circular=False):
                 else:
                     std = stats.circstd(ary, high=np.pi, low=-np.pi)
             elif _numba_flag:
-                std = float(_sqrt(svar(ary), np.zeros(1)))
+                std = float(_sqrt(svar(ary), np.zeros(1)).item())
             else:
                 std = np.std(ary)
             return std / np.sqrt(len(ary))

arviz/stats/ecdf_utils.py

@@ -1,4 +1,5 @@
 """Functions for evaluating ECDFs and their confidence bands."""
+
 from typing import Any, Callable, Optional, Tuple
 import warnings
 

arviz/stats/stats_refitting.py

@@ -1,4 +1,5 @@
 """Stats functions that require refitting the model."""
+
 import logging
 import warnings
 

arviz/stats/stats_utils.py

@@ -1,4 +1,5 @@
 """Stats-utility functions for ArviZ."""
+
 import warnings
 from collections.abc import Sequence
 from copy import copy as _copy
@@ -134,7 +135,10 @@ def make_ufunc(
                 raise TypeError(msg)
         for idx in np.ndindex(out.shape[:n_dims_out]):
             arys_idx = [ary[idx].ravel() if ravel else ary[idx] for ary in arys]
-            out[idx] = np.asarray(func(*arys_idx, *args[n_input:], **kwargs))[index]
+            out_idx = np.asarray(func(*arys_idx, *args[n_input:], **kwargs))[index]
+            if n_dims_out is None:
+                out_idx = out_idx.item()
+            out[idx] = out_idx
         return out
 
     def _multi_ufunc(*args, out=None, out_shape=None, **kwargs):

arviz/tests/base_tests/test_data.py

@@ -1077,6 +1077,20 @@ def test_dict_to_dataset():
     assert set(dataset.b.coords) == {"chain", "draw", "c"}
 
 
+def test_nested_dict_to_dataset():
+    datadict = {
+        "top": {"a": np.random.randn(100), "b": np.random.randn(1, 100, 10)},
+        "d": np.random.randn(100),
+    }
+    dataset = convert_to_dataset(datadict, coords={"c": np.arange(10)}, dims={("top", "b"): ["c"]})
+    assert set(dataset.data_vars) == {("top", "a"), ("top", "b"), "d"}
+    assert set(dataset.coords) == {"chain", "draw", "c"}
+
+    assert set(dataset[("top", "a")].coords) == {"chain", "draw"}
+    assert set(dataset[("top", "b")].coords) == {"chain", "draw", "c"}
+    assert set(dataset.d.coords) == {"chain", "draw"}
+
+
 def test_dict_to_dataset_event_dims_error():
     datadict = {"a": np.random.randn(1, 100, 10)}
     coords = {"b": np.arange(10), "c": ["x", "y", "z"]}

arviz/tests/base_tests/test_diagnostics.py

@@ -1,4 +1,5 @@
 """Test Diagnostic methods"""
+
 # pylint: disable=redefined-outer-name, no-member, too-many-public-methods
 import os
 

arviz/tests/base_tests/test_diagnostics_numba.py

@@ -1,4 +1,5 @@
 """Test Diagnostic methods"""
+
 import importlib
 
 # pylint: disable=redefined-outer-name, no-member, too-many-public-methods

arviz/tests/base_tests/test_labels.py

@@ -1,4 +1,5 @@
 """Tests for labeller classes."""
+
 import pytest
 
 from ...labels import (