fix docs right sidebar and bokeh deprecation warning (#2405)

arviz/plots/backends/bokeh/densityplot.py

@@ -225,7 +225,11 @@ def _d_helper(
 
     if point_estimate is not None:
         est = calculate_point_estimate(point_estimate, vec, bw, circular)
-        plotted.append(ax.circle(est, 0, fill_color=color, line_color="black", size=markersize))
+        plotted.append(
+            ax.scatter(
+                est, 0, marker="circle", fill_color=color, line_color="black", size=markersize
+            )
+        )
 
     _title = Title()
     _title.text = vname

arviz/plots/backends/bokeh/dotplot.py

@@ -47,7 +47,10 @@ def plot_dot(
 
     if plot_kwargs is None:
         plot_kwargs = {}
-        plot_kwargs.setdefault("color", dotcolor)
+    else:
+        plot_kwargs = plot_kwargs.copy()
+    plot_kwargs.setdefault("color", dotcolor)
+    plot_kwargs.setdefault("marker", "circle")
 
     if linewidth is None:
         linewidth = auto_linewidth
@@ -95,7 +98,7 @@ def plot_dot(
     stack_locs, stack_count = wilkinson_algorithm(values, binwidth)
     x, y = layout_stacks(stack_locs, stack_count, binwidth, stackratio, rotated)
 
-    ax.circle(x, y, radius=dotsize * (binwidth / 2), **plot_kwargs, radius_dimension="y")
+    ax.scatter(x, y, radius=dotsize * (binwidth / 2), **plot_kwargs, radius_dimension="y")
     if rotated:
         ax.xaxis.major_tick_line_color = None
         ax.xaxis.minor_tick_line_color = None

arviz/plots/backends/bokeh/essplot.py

@@ -73,12 +73,14 @@ def plot_ess(
     for (var_name, selection, isel, x), ax_ in zip(
         plotters, (item for item in ax.flatten() if item is not None)
     ):
-        bulk_points = ax_.circle(np.asarray(xdata), np.asarray(x), size=6)
+        bulk_points = ax_.scatter(np.asarray(xdata), np.asarray(x), marker="circle", size=6)
         if kind == "evolution":
             bulk_line = ax_.line(np.asarray(xdata), np.asarray(x))
             ess_tail = ess_tail_dataset[var_name].sel(**selection)
             tail_points = ax_.line(np.asarray(xdata), np.asarray(ess_tail), color="orange")
-            tail_line = ax_.circle(np.asarray(xdata), np.asarray(ess_tail), size=6, color="orange")
+            tail_line = ax_.scatter(
+                np.asarray(xdata), np.asarray(ess_tail), marker="circle", size=6, color="orange"
+            )
         elif rug:
             if rug_kwargs is None:
                 rug_kwargs = {}

arviz/plots/backends/bokeh/forestplot.py

@@ -535,9 +535,10 @@ def forestplot(self, hdi_prob, quartiles, linewidth, markersize, ax, rope, plott
                         )
                     )
                 plotted[model_name].append(
-                    ax.circle(
+                    ax.scatter(
                         x=values[mid],
                         y=y,
+                        marker="circle",
                         size=markersize * 0.75,
                         fill_color=color,
                     )
@@ -555,9 +556,10 @@ def plot_neff(self, ax, markersize, plotted):
             for y, ess, color, model_name in plotter.ess():
                 if ess is not None:
                     plotted[model_name].append(
-                        ax.circle(
+                        ax.scatter(
                             x=ess,
                             y=y,
+                            marker="circle",
                             fill_color=color,
                             size=markersize,
                             line_color="black",
@@ -582,8 +584,13 @@ def plot_rhat(self, ax, markersize, plotted):
             for y, r_hat, color, model_name in plotter.r_hat():
                 if r_hat is not None:
                     plotted[model_name].append(
-                        ax.circle(
-                            x=r_hat, y=y, fill_color=color, size=markersize, line_color="black"
+                        ax.scatter(
+                            x=r_hat,
+                            y=y,
+                            marker="circle",
+                            fill_color=color,
+                            size=markersize,
+                            line_color="black",
                         )
                     )
         ax.x_range._property_values["start"] = 0.9  # pylint: disable=protected-access

arviz/plots/backends/bokeh/khatplot.py

@@ -94,19 +94,21 @@ def plot_khat(
 
     if not isinstance(rgba_c, str) and isinstance(rgba_c, Iterable):
         for idx, (alpha, rgba_c_) in enumerate(zip(alphas, rgba_c)):
-            ax.cross(
+            ax.scatter(
                 xdata[idx],
                 khats[idx],
+                marker="cross",
                 line_color=rgba_c_,
                 fill_color=rgba_c_,
                 line_alpha=alpha,
                 fill_alpha=alpha,
                 size=10,
             )
     else:
-        ax.cross(
+        ax.scatter(
             xdata,
             khats,
+            marker="cross",
             line_color=rgba_c,
             fill_color=rgba_c,
             size=10,

arviz/plots/backends/bokeh/lmplot.py

@@ -51,12 +51,18 @@ def plot_lm(
 
     if y_kwargs is None:
         y_kwargs = {}
+    else:
+        y_kwargs = y_kwargs.copy()
+    y_kwargs.setdefault("marker", "circle")
     y_kwargs.setdefault("fill_color", "red")
     y_kwargs.setdefault("line_width", 0)
     y_kwargs.setdefault("size", 3)
 
     if y_hat_plot_kwargs is None:
         y_hat_plot_kwargs = {}
+    else:
+        y_hat_plot_kwargs = y_hat_plot_kwargs.copy()
+    y_hat_plot_kwargs.setdefault("marker", "circle")
     y_hat_plot_kwargs.setdefault("fill_color", "orange")
     y_hat_plot_kwargs.setdefault("line_width", 0)
 
@@ -84,7 +90,7 @@ def plot_lm(
         _, _, _, y_plotters = y[i]
         _, _, _, x_plotters = x[i]
         legend_it = []
-        observed_legend = ax_i.circle(x_plotters, y_plotters, **y_kwargs)
+        observed_legend = ax_i.scatter(x_plotters, y_plotters, **y_kwargs)
         legend_it.append(("Observed", [observed_legend]))
 
         if y_hat is not None:
@@ -98,14 +104,14 @@ def plot_lm(
                         x_plotters_jitter = x_plotters + np.random.uniform(
                             low=-scale_high, high=scale_high, size=len(x_plotters)
                         )
-                        posterior_circle = ax_i.circle(
+                        posterior_circle = ax_i.scatter(
                             x_plotters_jitter,
                             y_hat_plotters[..., j],
                             alpha=0.2,
                             **y_hat_plot_kwargs,
                         )
                     else:
-                        posterior_circle = ax_i.circle(
+                        posterior_circle = ax_i.scatter(
                             x_plotters, y_hat_plotters[..., j], alpha=0.2, **y_hat_plot_kwargs
                         )
                     posterior_legend.append(posterior_circle)

arviz/plots/backends/bokeh/mcseplot.py

@@ -71,13 +71,13 @@ def plot_mcse(
             values = data[var_name].sel(**selection).values.flatten()
         if errorbar:
             quantile_values = _quantile(values, probs)
-            ax_.dash(probs, quantile_values)
+            ax_.scatter(probs, quantile_values, marker="dash")
             ax_.multi_line(
                 list(zip(probs, probs)),
                 [(quant - err, quant + err) for quant, err in zip(quantile_values, x)],
             )
         else:
-            ax_.circle(probs, x)
+            ax_.scatter(probs, x, marker="circle")
             if extra_methods:
                 mean_mcse_i = mean_mcse[var_name].sel(**selection).values.item()
                 sd_mcse_i = sd_mcse[var_name].sel(**selection).values.item()

arviz/plots/backends/bokeh/pairplot.py

@@ -121,12 +121,14 @@ def plot_pair(
             )
 
     reference_values_kwargs = _init_kwargs_dict(reference_values_kwargs)
+    reference_values_kwargs.setdefault("marker", "circle")
     reference_values_kwargs.setdefault("line_color", "black")
     reference_values_kwargs.setdefault("fill_color", vectorized_to_hex("C2"))
     reference_values_kwargs.setdefault("line_width", 1)
     reference_values_kwargs.setdefault("size", 10)
 
     divergences_kwargs = _init_kwargs_dict(divergences_kwargs)
+    divergences_kwargs.setdefault("marker", "circle")
     divergences_kwargs.setdefault("line_color", "black")
     divergences_kwargs.setdefault("fill_color", vectorized_to_hex("C1"))
     divergences_kwargs.setdefault("line_width", 1)
@@ -155,6 +157,7 @@ def plot_pair(
     )
 
     point_estimate_marker_kwargs = _init_kwargs_dict(point_estimate_marker_kwargs)
+    point_estimate_marker_kwargs.setdefault("marker", "square")
     point_estimate_marker_kwargs.setdefault("size", markersize)
     point_estimate_marker_kwargs.setdefault("color", "black")
     point_estimate_kwargs.setdefault("line_color", "black")
@@ -265,9 +268,11 @@ def get_width_and_height(jointplot, rotate):
             elif j + marginals_offset > i:
                 if "scatter" in kind:
                     if divergences:
-                        ax[j, i].circle(var1, var2, source=source, view=source_nondiv)
+                        ax[j, i].scatter(
+                            var1, var2, marker="circle", source=source, view=source_nondiv
+                        )
                     else:
-                        ax[j, i].circle(var1, var2, source=source)
+                        ax[j, i].scatter(var1, var2, marker="circle", source=source)
 
                 if "kde" in kind:
                     var1_kde = plotters[i][-1].flatten()
@@ -293,7 +298,7 @@ def get_width_and_height(jointplot, rotate):
                     )
 
                 if divergences:
-                    ax[j, i].circle(
+                    ax[j, i].scatter(
                         var1,
                         var2,
                         source=source,
@@ -306,7 +311,7 @@ def get_width_and_height(jointplot, rotate):
                     var2_pe = plotters[j][-1].flatten()
                     pe_x = calculate_point_estimate(point_estimate, var1_pe)
                     pe_y = calculate_point_estimate(point_estimate, var2_pe)
-                    ax[j, i].square(pe_x, pe_y, **point_estimate_marker_kwargs)
+                    ax[j, i].scatter(pe_x, pe_y, **point_estimate_marker_kwargs)
 
                     ax_hline = Span(
                         location=pe_y,
@@ -344,7 +349,7 @@ def get_width_and_height(jointplot, rotate):
                     x = reference_values_copy[flat_var_names[j + marginals_offset]]
                     y = reference_values_copy[flat_var_names[i]]
                     if x and y:
-                        ax[j, i].circle(y, x, **reference_values_kwargs)
+                        ax[j, i].scatter(y, x, **reference_values_kwargs)
                 ax[j, i].xaxis.axis_label = flat_var_names[i]
                 ax[j, i].yaxis.axis_label = flat_var_names[j + marginals_offset]
 

arviz/plots/backends/bokeh/ppcplot.py

@@ -313,9 +313,10 @@ def plot_ppc(
                     obs_yvals += np.random.uniform(
                         low=scale_low, high=scale_high, size=len(obs_vals)
                     )
-                glyph = ax_i.circle(
+                glyph = ax_i.scatter(
                     obs_vals,
                     obs_yvals,
+                    marker="circle",
                     line_color=colors[1],
                     fill_color=colors[1],
                     size=markersize,

arviz/plots/backends/bokeh/rankplot.py

@@ -49,6 +49,7 @@ def plot_rank(
 
     if marker_vlines_kwargs is None:
         marker_vlines_kwargs = {}
+    marker_vlines_kwargs.setdefault("marker", "circle")
 
     if backend_kwargs is None:
         backend_kwargs = {}
@@ -109,7 +110,7 @@ def plot_rank(
         elif kind == "vlines":
             ymin = np.full(len(all_counts), all_counts.mean())
             for idx, counts in enumerate(all_counts):
-                ax.circle(
+                ax.scatter(
                     bin_ary,
                     counts,
                     fill_color=colors[idx],

arviz/plots/backends/bokeh/traceplot.py

@@ -385,9 +385,10 @@ def _plot_chains_bokeh(
                 **dealiase_sel_kwargs(trace_kwargs, chain_prop, chain_idx),
             )
             if marker:
-                ax_trace.circle(
+                ax_trace.scatter(
                     x=x_name,
                     y=y_name,
+                    marker="circle",
                     source=cds,
                     radius=0.30,
                     alpha=0.5,

arviz/plots/backends/bokeh/violinplot.py

@@ -81,9 +81,10 @@ def plot_violin(
                 [0, 0], per[:2], line_width=linewidth * 3, line_color="black", line_cap="round"
             )
         ax_.line([0, 0], hdi_probs, line_width=linewidth, line_color="black", line_cap="round")
-        ax_.circle(
+        ax_.scatter(
             0,
             per[-1],
+            marker="circle",
             line_color="white",
             fill_color="white",
             size=linewidth * 1.5,

arviz/plots/plot_utils.py

@@ -482,16 +482,18 @@ def plot_point_interval(
         if point_estimate:
             point_value = calculate_point_estimate(point_estimate, values)
             if rotated:
-                ax.circle(
+                ax.scatter(
                     x=0,
                     y=point_value,
+                    marker="circle",
                     size=markersize,
                     fill_color=markercolor,
                 )
             else:
-                ax.circle(
+                ax.scatter(
                     x=point_value,
                     y=0,
+                    marker="circle",
                     size=markersize,
                     fill_color=markercolor,
                 )
@@ -534,7 +536,7 @@ def set_bokeh_circular_ticks_labels(ax, hist, labels):
     )
 
     radii_circles = np.linspace(0, np.max(hist) * 1.1, 4)
-    ax.circle(0, 0, radius=radii_circles, fill_color=None, line_color="grey")
+    ax.scatter(0, 0, marker="circle", radius=radii_circles, fill_color=None, line_color="grey")
 
     offset = np.max(hist * 1.05) * 0.15
     ticks_labels_pos_1 = np.max(hist * 1.05)

doc/_templates/sourcelink.html

@@ -0,0 +1,8 @@
+{# Displays a link to the .rst source of the current page. #}
+{% if show_source and has_source and sourcename %}
+  <div class="tocsection sourcelink">
+    <a href="{{ pathto('_sources/' + sourcename, true)|e }}">
+      <i class="fa-solid fa-file-lines"></i> {{ _("Show Source") }}
+    </a>
+  </div>
+{% endif %}

doc/source/conf.py

@@ -205,7 +205,7 @@
     "navbar_start": ["navbar-logo", "navbar-version"],
     "navbar_align": "content",
     "header_links_before_dropdown": 5,
-    "secondary_sidebar_items": ["page-toc", "searchbox", "edit-this-page", "sourcelink", "donate"],
+    "secondary_sidebar_items": ["page-toc", "edit-this-page", "sourcelink", "donate"],
     "use_edit_page_button": True,
     "analytics": {"google_analytics_id": "G-W1G68W77YV"},
     "external_links": [
@@ -219,10 +219,7 @@
     "doc_path": "doc/source/",
     "default_mode": "light",
 }
-html_sidebars: Dict[str, Any] = {
-    "index": [],
-    "community": ["search-field.html", "sidebar-nav-bs.html", "twitter.html"],
-}
+html_sidebars: Dict[str, Any] = {"index": []}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,