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

arviz/plots/backends/bokeh/khatplot.py

@@ -1,4 +1,5 @@
 """Bokeh pareto shape plot."""
+
 from collections.abc import Iterable
 
 from matplotlib import cm
@@ -20,6 +21,7 @@ def plot_khat(
     figsize,
     xdata,
     khats,
+    good_k,
     kwargs,
     threshold,
     coord_labels,
@@ -52,7 +54,11 @@ def plot_khat(
 
     if hlines_kwargs is None:
         hlines_kwargs = {}
-    hlines_kwargs.setdefault("hlines", [0, 0.5, 0.7, 1])
+
+    if good_k is None:
+        good_k = 0.7
+
+    hlines_kwargs.setdefault("hlines", [0, good_k, 1])
 
     cmap = None
     if isinstance(color, str):
@@ -74,7 +80,7 @@ def plot_khat(
             rgba_c = cmap(color)
 
     khats = khats if isinstance(khats, np.ndarray) else khats.values.flatten()
-    alphas = 0.5 + 0.2 * (khats > 0.5) + 0.3 * (khats > 1)
+    alphas = 0.5 + 0.2 * (khats > good_k) + 0.3 * (khats > 1)
 
     rgba_c = vectorized_to_hex(rgba_c)
 
@@ -129,7 +135,7 @@ def plot_khat(
     xmax = len(khats)
 
     if show_bins:
-        bin_edges = np.array([ymin, 0.5, 0.7, 1, ymax])
+        bin_edges = np.array([ymin, good_k, 1, ymax])
         bin_edges = bin_edges[(bin_edges >= ymin) & (bin_edges <= ymax)]
         hist, _, _ = histogram(khats, bin_edges)
         for idx, count in enumerate(hist):

arviz/plots/backends/bokeh/lmplot.py

@@ -1,4 +1,5 @@
 """Bokeh linear regression plot."""
+
 import numpy as np
 from bokeh.models.annotations import Legend
 

arviz/plots/backends/bokeh/loopitplot.py

@@ -1,4 +1,5 @@
 """Bokeh loopitplot."""
+
 import numpy as np
 from bokeh.models import BoxAnnotation
 from matplotlib.colors import hsv_to_rgb, rgb_to_hsv, to_hex, to_rgb

arviz/plots/backends/bokeh/mcseplot.py

@@ -1,4 +1,5 @@
 """Bokeh mcseplot."""
+
 import numpy as np
 from bokeh.models import ColumnDataSource, Span
 from bokeh.models.glyphs import Scatter

arviz/plots/backends/bokeh/pairplot.py

@@ -1,4 +1,5 @@
 """Bokeh pairplot."""
+
 import warnings
 from copy import deepcopy
 from uuid import uuid4
@@ -173,12 +174,8 @@ def plot_pair(
     source = ColumnDataSource(data=source_dict)
 
     if divergences:
-        source_nondiv = CDSView(
-            source=source, filters=[GroupFilter(column_name=divergenve_name, group="0")]
-        )
-        source_div = CDSView(
-            source=source, filters=[GroupFilter(column_name=divergenve_name, group="1")]
-        )
+        source_nondiv = CDSView(filter=GroupFilter(column_name=divergenve_name, group="0"))
+        source_div = CDSView(filter=GroupFilter(column_name=divergenve_name, group="1"))
 
     def get_width_and_height(jointplot, rotate):
         """Compute subplots dimensions for two or more variables."""

arviz/plots/backends/bokeh/parallelplot.py

@@ -1,4 +1,5 @@
 """Bokeh Parallel coordinates plot."""
+
 import numpy as np
 from bokeh.models import DataRange1d
 from bokeh.models.tickers import FixedTicker

arviz/plots/backends/bokeh/posteriorplot.py

@@ -1,4 +1,5 @@
 """Bokeh Plot posterior densities."""
+
 from numbers import Number
 from typing import Optional
 

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
 
@@ -12,7 +13,6 @@ def plot_ecdf(
     x_bands,
     lower,
     higher,
-    confidence_bands,
     plot_kwargs,
     fill_kwargs,
     plot_outline_kwargs,
@@ -58,7 +58,7 @@ def plot_ecdf(
 
     ax.step(x_coord, y_coord, **plot_kwargs)
 
-    if confidence_bands:
+    if x_bands is not None:
         if fill_band:
             ax.fill_between(x_bands, lower, higher, **fill_kwargs)
         else:

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
@@ -19,6 +20,7 @@ def plot_khat(
     figsize,
     xdata,
     khats,
+    good_k,
     kwargs,
     threshold,
     coord_labels,
@@ -60,8 +62,11 @@ def plot_khat(
     backend_kwargs.setdefault("figsize", figsize)
     backend_kwargs["squeeze"] = True
 
+    if good_k is None:
+        good_k = 0.7
+
     hlines_kwargs = matplotlib_kwarg_dealiaser(hlines_kwargs, "hlines")
-    hlines_kwargs.setdefault("hlines", [0, 0.5, 0.7, 1])
+    hlines_kwargs.setdefault("hlines", [0, good_k, 1])
     hlines_kwargs.setdefault("linestyle", [":", "-.", "--", "-"])
     hlines_kwargs.setdefault("alpha", 0.7)
     hlines_kwargs.setdefault("zorder", -1)
@@ -101,7 +106,7 @@ def plot_khat(
                 rgba_c = cmap(norm_fun(color))
 
         khats = khats if isinstance(khats, np.ndarray) else khats.values.flatten()
-        alphas = 0.5 + 0.2 * (khats > 0.5) + 0.3 * (khats > 1)
+        alphas = 0.5 + 0.2 * (khats > good_k) + 0.3 * (khats > 1)
         rgba_c[:, 3] = alphas
         rgba_c = vectorized_to_hex(rgba_c)
         kwargs["c"] = rgba_c
@@ -150,7 +155,7 @@ def plot_khat(
         )
 
     if show_bins:
-        bin_edges = np.array([ymin, 0.5, 0.7, 1, ymax])
+        bin_edges = np.array([ymin, good_k, 1, ymax])
         bin_edges = bin_edges[(bin_edges >= ymin) & (bin_edges <= ymax)]
         hist, _, _ = histogram(khats, bin_edges)
         for idx, count in enumerate(hist):

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
 
@@ -439,7 +440,7 @@ def plot_trace(
                     [], [], label="combined", **dealiase_sel_kwargs(plot_kwargs, chain_prop, -1)
                 ),
             )
-        ax.figure.axes[0].legend(handles=handles, title="chain", loc="upper right")
+        ax.figure.axes[1].legend(handles=handles, title="chain", loc="upper right")
 
     if axes is None:
         axes = np.array(ax.figure.axes).reshape(-1, 2)

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
@@ -79,7 +80,7 @@ def plot_bpv(
     hdi_prob : float, optional
         Probability for the highest density interval for the analytical reference distribution when
         ``kind=u_values``. Should be in the interval (0, 1]. Defaults to the
-        rcParam ``stats.hdi_prob``. See :ref:`this section <common_hdi_prob>` for usage examples.
+        rcParam ``stats.ci_prob``. See :ref:`this section <common_hdi_prob>` for usage examples.
     color : str, optional
         Matplotlib color
     grid : tuple, optional
@@ -201,7 +202,7 @@ def plot_bpv(
         raise TypeError("`reference` argument must be either `analytical`, `samples`, or `None`")
 
     if hdi_prob is None:
-        hdi_prob = rcParams["stats.hdi_prob"]
+        hdi_prob = rcParams["stats.ci_prob"]
     elif not 1 >= hdi_prob > 0:
         raise ValueError("The value of hdi_prob should be in the interval (0, 1]")
 

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
@@ -208,7 +209,7 @@ def plot_density(
         )
 
     if hdi_prob is None:
-        hdi_prob = rcParams["stats.hdi_prob"]
+        hdi_prob = rcParams["stats.ci_prob"]
     elif not 1 >= hdi_prob > 0:
         raise ValueError("The value of hdi_prob should be in the interval (0, 1]")
 

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
@@ -66,7 +67,7 @@ def plot_dot(
         The shape of the marker. Valid for matplotlib backend.
     hdi_prob : float, optional
         Valid only when point_interval is True. Plots HDI for chosen percentage of density.
-        Defaults to ``stats.hdi_prob`` rcParam. See :ref:`this section <common_hdi_prob>`
+        Defaults to ``stats.ci_prob`` rcParam. See :ref:`this section <common_hdi_prob>`
         for usage examples.
     rotated : bool, default False
         Whether to rotate the dot plot by 90 degrees.
@@ -150,7 +151,7 @@ def plot_dot(
     values.sort()
 
     if hdi_prob is None:
-        hdi_prob = rcParams["stats.hdi_prob"]
+        hdi_prob = rcParams["stats.ci_prob"]
     elif not 1 >= hdi_prob > 0:
         raise ValueError("The value of hdi_prob should be in the interval (0, 1]")