arviz 0.17.0__py3-none-any.whl → 0.18.0__py3-none-any.whl

arviz/plots/backends/bokeh/dotplot.py

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

arviz/plots/backends/bokeh/ecdfplot.py

@@ -1,4 +1,5 @@
 """Bokeh ecdfplot."""
+
 from matplotlib.colors import to_hex
 
 from ...plot_utils import _scale_fig_size

arviz/plots/backends/bokeh/elpdplot.py

@@ -1,4 +1,5 @@
 """Bokeh ELPDPlot."""
+
 import warnings
 
 import bokeh.plotting as bkp

arviz/plots/backends/bokeh/energyplot.py

@@ -1,4 +1,5 @@
 """Bokeh energyplot."""
+
 from itertools import cycle
 
 import numpy as np

arviz/plots/backends/bokeh/forestplot.py

@@ -15,7 +15,6 @@ from ....rcparams import rcParams
 from ....stats import hdi
 from ....stats.density_utils import get_bins, histogram, kde
 from ....stats.diagnostics import _ess, _rhat
-from ....utils import conditional_jit
 from ...plot_utils import _scale_fig_size
 from .. import show_layout
 from . import backend_kwarg_defaults
@@ -277,7 +276,6 @@ class PlotHandler:
         """Collect labels and ticks from plotters."""
         val = self.plotters.values()
 
-        @conditional_jit(forceobj=True, nopython=False)
         def label_idxs():
             labels, idxs = [], []
             for plotter in val:
@@ -640,7 +638,7 @@ class VarHandler:
             grouped_data = [[(0, datum)] for datum in self.data]
             skip_dims = self.combine_dims.union({"chain"})
         else:
-            grouped_data = [datum.groupby("chain") for datum in self.data]
+            grouped_data = [datum.groupby("chain", squeeze=False) for datum in self.data]
             skip_dims = self.combine_dims
 
         label_dict = OrderedDict()
@@ -648,7 +646,7 @@ class VarHandler:
         for name, grouped_datum in zip(self.model_names, grouped_data):
             for _, sub_data in grouped_datum:
                 datum_iter = xarray_var_iter(
-                    sub_data,
+                    sub_data.squeeze(),
                     var_names=[self.var_name],
                     skip_dims=skip_dims,
                     reverse_selections=True,

arviz/plots/backends/bokeh/hdiplot.py

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

arviz/plots/backends/bokeh/kdeplot.py

@@ -6,7 +6,7 @@ from numbers import Integral
 import numpy as np
 from bokeh.models import ColumnDataSource
 from bokeh.models.glyphs import Scatter
-from matplotlib.cm import get_cmap
+from matplotlib import colormaps
 from matplotlib.colors import rgb2hex
 from matplotlib.pyplot import rcParams as mpl_rcParams
 
@@ -188,7 +188,7 @@ def plot_kde(
 
             cmap = contourf_kwargs.pop("cmap", "viridis")
             if isinstance(cmap, str):
-                cmap = get_cmap(cmap)
+                cmap = colormaps[cmap]
             if isinstance(cmap, Callable):
                 colors = [rgb2hex(item) for item in cmap(np.linspace(0, 1, len(levels_scaled) + 1))]
             else:
@@ -225,7 +225,7 @@ def plot_kde(
         else:
             cmap = pcolormesh_kwargs.pop("cmap", "viridis")
             if isinstance(cmap, str):
-                cmap = get_cmap(cmap)
+                cmap = colormaps[cmap]
             if isinstance(cmap, Callable):
                 colors = [rgb2hex(item) for item in cmap(np.linspace(0, 1, 256))]
             else:

arviz/plots/backends/bokeh/khatplot.py

@@ -1,4 +1,5 @@
 """Bokeh pareto shape plot."""
+
 from collections.abc import Iterable
 
 from matplotlib import cm

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

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
@@ -84,7 +85,7 @@ def plot_compare(
     else:
         ax.set_yticks(yticks_pos[::2])
 
-    scale = comp_df["scale"][0]
+    scale = comp_df["scale"].iloc[0]
 
     if insample_dev:
         p_ic = comp_df[f"p_{information_criterion.split('_')[1]}"]

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
 
@@ -11,7 +12,6 @@ from ....stats import hdi
 from ....stats.density_utils import get_bins, histogram, kde
 from ....stats.diagnostics import _ess, _rhat
 from ....sel_utils import xarray_var_iter
-from ....utils import conditional_jit
 from ...plot_utils import _scale_fig_size
 from . import backend_kwarg_defaults, backend_show
 
@@ -236,7 +236,6 @@ class PlotHandler:
         """Collect labels and ticks from plotters."""
         val = self.plotters.values()
 
-        @conditional_jit(forceobj=True, nopython=False)
         def label_idxs():
             labels, idxs = [], []
             for plotter in val:
@@ -536,7 +535,7 @@ class VarHandler:
             grouped_data = [[(0, datum)] for datum in self.data]
             skip_dims = self.combine_dims.union({"chain"})
         else:
-            grouped_data = [datum.groupby("chain") for datum in self.data]
+            grouped_data = [datum.groupby("chain", squeeze=False) for datum in self.data]
             skip_dims = self.combine_dims
 
         label_dict = OrderedDict()
@@ -544,7 +543,7 @@ class VarHandler:
         for name, grouped_datum in zip(self.model_names, grouped_data):
             for _, sub_data in grouped_datum:
                 datum_iter = xarray_var_iter(
-                    sub_data,
+                    sub_data.squeeze(),
                     var_names=[self.var_name],
                     skip_dims=skip_dims,
                     reverse_selections=True,

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
 
@@ -430,7 +431,7 @@ def plot_trace(
             Line2D(
                 [], [], label=chain_id, **dealiase_sel_kwargs(legend_kwargs, chain_prop, chain_id)
             )
-            for chain_id in range(data.dims["chain"])
+            for chain_id in range(data.sizes["chain"])
         ]
         if combined:
             handles.insert(

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/bfplot.py

@@ -38,7 +38,7 @@ def plot_bf(
     algorithm presented in [1]_.
 
     Parameters
-    -----------
+    ----------
     idata : InferenceData
         Any object that can be converted to an :class:`arviz.InferenceData` object
         Refer to documentation of :func:`arviz.convert_to_dataset` for details.
@@ -52,16 +52,16 @@ def plot_bf(
         Tuple of valid Matplotlib colors. First element for the prior, second for the posterior.
     figsize : (float, float), optional
         Figure size. If `None` it will be defined automatically.
-    textsize: float, optional
+    textsize : float, optional
         Text size scaling factor for labels, titles and lines. If `None` it will be auto
         scaled based on `figsize`.
-    plot_kwargs : dicts, optional
+    plot_kwargs : dict, optional
         Additional keywords passed to :func:`matplotlib.pyplot.plot`.
-    hist_kwargs : dicts, optional
+    hist_kwargs : dict, optional
         Additional keywords passed to :func:`arviz.plot_dist`. Only works for discrete variables.
     ax : axes, optional
         :class:`matplotlib.axes.Axes` or :class:`bokeh.plotting.Figure`.
-    backend :{"matplotlib", "bokeh"}, default "matplotlib"
+    backend : {"matplotlib", "bokeh"}, default "matplotlib"
         Select plotting backend.
     backend_kwargs : dict, optional
         These are kwargs specific to the backend being used, passed to
@@ -78,7 +78,7 @@ def plot_bf(
     References
     ----------
     .. [1] Heck, D., 2019. A caveat on the Savage-Dickey density ratio:
-    The case of computing Bayes factors for regression parameters.
+       The case of computing Bayes factors for regression parameters.
 
     Examples
     --------
@@ -92,6 +92,7 @@ def plot_bf(
         >>> idata = az.from_dict(posterior={"a":np.random.normal(1, 0.5, 5000)},
         ...     prior={"a":np.random.normal(0, 1, 5000)})
         >>> az.plot_bf(idata, var_name="a", ref_val=0)
+
     """
     posterior = extract(idata, var_names=var_name).values
 

arviz/plots/bpvplot.py

@@ -1,4 +1,5 @@
 """Bayesian p-value Posterior/Prior predictive plot."""
+
 import numpy as np
 
 from ..labels import BaseLabeller
@@ -230,11 +231,11 @@ def plot_bpv(
 
     if flatten_pp is None:
         if flatten is None:
-            flatten_pp = list(predictive_dataset.dims.keys())
+            flatten_pp = list(predictive_dataset.dims)
         else:
             flatten_pp = flatten
     if flatten is None:
-        flatten = list(observed.dims.keys())
+        flatten = list(observed.dims)
 
     if coords is None:
         coords = {}

arviz/plots/compareplot.py

@@ -1,4 +1,5 @@
 """Summary plot for model comparison."""
+
 import numpy as np
 
 from ..labels import BaseLabeller
@@ -90,10 +91,10 @@ def plot_compare(
     References
     ----------
     .. [1] Vehtari et al. (2016). Practical Bayesian model evaluation using leave-one-out
-    cross-validation and WAIC https://arxiv.org/abs/1507.04544
+       cross-validation and WAIC https://arxiv.org/abs/1507.04544
 
     .. [2] McElreath R. (2022). Statistical Rethinking A Bayesian Course with Examples in
-    R and Stan, Second edition, CRC Press.
+       R and Stan, Second edition, CRC Press.
 
     Examples
     --------

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