Fixed Matplotlib 3.8 compatibility issues (#1049)

* specify angle as kwarg

* try removing some maybe unnecessary code?

* fight with mypy

* black

* fix sorts

* try switch to explain

* fix intersphinx

* other instances of wrong tutorial intersphinx

graspologic/layouts/render.py

@@ -127,9 +127,9 @@ def _draw_graph(
     for source, target in graph.edges():
         edge_color_list.append(node_colors[source])
 
-    ax.set_xbound(x_domain)
+    ax.set_xbound(*x_domain)
     ax.set_xlim(x_domain)
-    ax.set_ybound(y_domain)
+    ax.set_ybound(*y_domain)
     ax.set_ylim(y_domain)
 
     nx.draw_networkx_edges(

graspologic/plot/plot.py

@@ -2,7 +2,7 @@
 # Licensed under the MIT License.
 
 import warnings
-from typing import Any, Collection, Optional, Union
+from typing import Any, Collection, Literal, Optional, Union
 
 import matplotlib as mpl
 import matplotlib.axes
@@ -442,7 +442,7 @@ def gridplot(
         Set of colors for mapping the ``hue`` variable. If a dict, keys should
         be values in the ``hue`` variable.
         For acceptable string arguments, see the palette options at
-        :doc:`Choosing Colormaps in Matplotlib <tutorials/colors/colormaps>`
+        :doc:`Choosing Colormaps in Matplotlib <users/explain/colors/colormaps>`
     alpha : float [0, 1], default : 0.7
         Alpha value of plotted gridplot points
     sizes : length 2 tuple, default: (10, 200)
@@ -607,7 +607,7 @@ def pairplot(
         Set of colors for mapping the ``hue`` variable. If a dict, keys should
         be values in the ``hue`` variable.
         For acceptable string arguments, see the palette options at
-        :doc:`Choosing Colormaps in Matplotlib <tutorials/colors/colormaps>`.
+        :doc:`Choosing Colormaps in Matplotlib <users/explain/colors/colormaps>`.
     alpha : float, optional, default: 0.7
         Opacity value of plotter markers between 0 and 1
     size : float or int, optional, default: 50
@@ -763,10 +763,10 @@ def _plot_ellipse_and_data(
         angle = np.arctan(u[1] / u[0])
         angle = 180.0 * angle / np.pi
         ell = mpl.patches.Ellipse(
-            [mean[j], mean[k]],
+            (mean[j], mean[k]),
             v[0],
             v[1],
-            180.0 + angle,
+            angle=180.0 + angle,
             color=cluster_palette[i],
         )
         ell.set_clip_box(ax.bbox)
@@ -984,7 +984,7 @@ def pairplot_with_gmm(
             handles, labels = axes[1].get_legend_handles_labels()
         fig.legend(
             handles,
-            labels,
+            labels,  # type: ignore
             loc="center right",
             title=legend_name,
         )
@@ -1069,7 +1069,7 @@ def degreeplot(
         Set of colors for mapping the ``hue`` variable. If a dict, keys should
         be values in the ``hue`` variable.
         For acceptable string arguments, see the palette options at
-        :doc:`Choosing Colormaps in Matplotlib <tutorials/colors/colormaps>`.
+        :doc:`Choosing Colormaps in Matplotlib <users/explain/colors/colormaps>`.
     figsize : tuple of length 2, default (10, 5)
         Size of the figure (width, height)
 
@@ -1138,7 +1138,7 @@ def edgeplot(
         Set of colors for mapping the ``hue`` variable. If a dict, keys should
         be values in the ``hue`` variable.
         For acceptable string arguments, see the palette options at
-        :doc:`Choosing Colormaps in Matplotlib <tutorials/colors/colormaps>`.
+        :doc:`Choosing Colormaps in Matplotlib <users/explain/colors/colormaps>`.
     figsize : tuple of length 2, default (10, 5)
         Size of the figure (width, height)
 
@@ -1620,17 +1620,17 @@ def _plot_groups(
     axline_kws = dict(linestyle="dashed", lw=0.9, alpha=0.3, zorder=3, color="grey")
     # draw lines
     for x in inner_freq_cumsum[1:-1]:
-        ax.vlines(x, 0, n_verts + 1, **axline_kws)
-        ax.hlines(x, 0, n_verts + 1, **axline_kws)
+        ax.vlines(x, 0, n_verts + 1, **axline_kws)  # type: ignore
+        ax.hlines(x, 0, n_verts + 1, **axline_kws)  # type: ignore
 
     # add specific lines for the borders of the plot
     pad = 0.001
     low = pad
     high = 1 - pad
-    ax.plot((low, low), (low, high), transform=ax.transAxes, **axline_kws)
-    ax.plot((low, high), (low, low), transform=ax.transAxes, **axline_kws)
-    ax.plot((high, high), (low, high), transform=ax.transAxes, **axline_kws)
-    ax.plot((low, high), (high, high), transform=ax.transAxes, **axline_kws)
+    ax.plot((low, low), (low, high), transform=ax.transAxes, **axline_kws)  # type: ignore
+    ax.plot((low, high), (low, low), transform=ax.transAxes, **axline_kws)  # type: ignore
+    ax.plot((high, high), (low, high), transform=ax.transAxes, **axline_kws)  # type: ignore
+    ax.plot((low, high), (high, high), transform=ax.transAxes, **axline_kws)  # type: ignore
 
     # generic curve that we will use for everything
     lx = np.linspace(-np.pi / 2.0 + 0.05, np.pi / 2.0 - 0.05, 500)
@@ -1648,7 +1648,7 @@ def _plot_groups(
 
     # top inner curves
     ax_x = divider.new_vertical(size="5%", pad=0.0, pack_start=False)
-    ax.figure.add_axes(ax_x)
+    ax.figure.add_axes(ax_x)  # type: ignore
     _plot_brackets(
         ax_x,
         np.tile(inner_unique, len(outer_unique)),
@@ -1662,7 +1662,7 @@ def _plot_groups(
     )
     # side inner curves
     ax_y = divider.new_horizontal(size="5%", pad=0.0, pack_start=True)
-    ax.figure.add_axes(ax_y)
+    ax.figure.add_axes(ax_y)  # type: ignore
     _plot_brackets(
         ax_y,
         np.tile(inner_unique, len(outer_unique)),
@@ -1679,7 +1679,7 @@ def _plot_groups(
         # top outer curves
         pad_scalar = 0.35 / 30 * fontsize
         ax_x2 = divider.new_vertical(size="5%", pad=pad_scalar, pack_start=False)
-        ax.figure.add_axes(ax_x2)
+        ax.figure.add_axes(ax_x2)  # type: ignore
         _plot_brackets(
             ax_x2,
             outer_unique,
@@ -1693,7 +1693,7 @@ def _plot_groups(
         )
         # side outer curves
         ax_y2 = divider.new_horizontal(size="5%", pad=pad_scalar, pack_start=True)
-        ax.figure.add_axes(ax_y2)
+        ax.figure.add_axes(ax_y2)  # type: ignore
         _plot_brackets(
             ax_y2,
             outer_unique,
@@ -1715,7 +1715,7 @@ def _plot_brackets(
     tick_width: np.ndarray,
     curve: np.ndarray,
     level: str,
-    axis: str,
+    axis: Literal["both", "x", "y"],
     max_size: int,
     fontsize: int,
 ) -> None:

graspologic/plot/plot_matrix.py

@@ -156,11 +156,11 @@ def _remove_shared_ax(ax):
     """
     Remove ax from its sharex and sharey
     """
-    # Remove ax from the Grouper object
-    shax = ax.get_shared_x_axes()
-    shay = ax.get_shared_y_axes()
-    shax.remove(ax)
-    shay.remove(ax)
+    # # Remove ax from the Grouper object
+    # shax = ax.get_shared_x_axes()
+    # shay = ax.get_shared_y_axes()
+    # shax.remove(ax)
+    # shay.remove(ax)
 
     # Set a new ticker with the respective new locator and formatter
     for axis in [ax.xaxis, ax.yaxis]: