fix: make tests pass

jaxley/modules/base.py

@@ -2116,10 +2116,11 @@ def vis(
             type: The type of plot. One of ["line", "scatter", "comp", "morph"].
             kwargs: Keyword arguments passed to the plotting function.
         """
+        res = 100 if "resolution" not in kwargs else kwargs.pop("resolution")
         if "comp" in type.lower():
-            return plot_comps(self, dims=dims, ax=ax, color=color, **kwargs)
+            return plot_comps(self, dims=dims, ax=ax, color=color, resolution=res, **kwargs)
         if "morph" in type.lower():
-            return plot_morph(self, dims=dims, ax=ax, color=color, **kwargs)
+            return plot_morph(self, dims=dims, ax=ax, color=color, resolution=res, **kwargs)
 
         assert not np.any(
             [np.isnan(xyzr[:, dims]).all() for xyzr in self.xyzr]

jaxley/modules/network.py

@@ -485,6 +485,7 @@ def vis(
                 cell = nodes.loc[comp, "global_cell_index"]
                 branch_xyz = self.xyzr[branch]
 
+                xyz_loc = branch_xyz
                 if detail == "point":
                     xyz_loc = np.mean(self.cell(cell).xyzr[0], axis=0)
                 elif len(branch_xyz) == 2:

tests/test_plotting_api.py

@@ -28,8 +28,8 @@ def test_cell(SimpleMorphCell):
     # Plot 1.
     _, ax = plt.subplots(1, 1, figsize=(3, 3))
     ax = cell.vis(ax=ax)
-    ax = cell.branch([0, 1, 2]).vis(ax=ax, col="r")
-    ax = cell.branch(1).loc(0.9).vis(ax=ax, col="b")
+    ax = cell.branch([0, 1, 2]).vis(ax=ax, color="r")
+    ax = cell.branch(1).loc(0.9).vis(ax=ax, color="b")
 
     # Plot 2.
     cell.branch(0).add_to_group("soma")
@@ -59,9 +59,9 @@ def test_network(SimpleMorphCell):
     # Plot 1.
     _, ax = plt.subplots(1, 1, figsize=(3, 3))
     ax = net.cell([0, 1]).vis(ax=ax)
-    ax = net.cell(2).vis(ax=ax, col="r", type="line")
-    ax = net.cell(2).vis(ax=ax, col="r", type="scatter")
-    ax = net.cell(0).branch(np.arange(10).tolist()).vis(ax=ax, col="b")
+    ax = net.cell(2).vis(ax=ax, color="r", type="line")
+    ax = net.cell(2).vis(ax=ax, color="r", type="scatter")
+    ax = net.cell(0).branch(np.arange(10).tolist()).vis(ax=ax, color="b")
 
     # Plot 2.
     ax = net.vis(detail="full", type="line")
@@ -71,10 +71,12 @@ def test_network(SimpleMorphCell):
     net.vis(detail="point")
 
     # Plot 4.
-    net.vis(detail="point", layers=[2, 1])
+    net.arrange_in_layers([2, 1])
+    net.vis(detail="point")
 
     # Plot 5.
-    net.vis(detail="full", layers=[2, 1])
+    net.arrange_in_layers([2, 1])
+    net.vis(detail="full")
 
     # Plot 5.
     net.cell(0).add_to_group("excitatory")
@@ -174,18 +176,20 @@ def test_volume_plotting(
     morph_cell = SimpleMorphCell(fname, ncomp=1)
 
     fig, ax = plt.subplots()
-    for module in [comp, branch, cell, net, morph_cell]:
-        module.vis(type="comp", ax=ax, morph_plot_kwargs={"resolution": 6})
+    for module in [comp, branch, cell, morph_cell]:
+        module.vis(type="comp", ax=ax, resolution=6)
+    net.vis(type="comp", ax=ax, cell_plot_kwargs={"resolution": 6})
     plt.close(fig)
 
     # test 3D plotting
-    for module in [comp, branch, cell, net, morph_cell]:
-        module.vis(type="comp", dims=[0, 1, 2], morph_plot_kwargs={"resolution": 6})
+    for module in [comp, branch, cell, morph_cell]:
+        module.vis(type="comp", dims=[0, 1, 2], resolution=6)
+    net.vis(type="comp", dims=[0, 1, 2], cell_plot_kwargs={"resolution": 6})
     plt.close()
 
     # test morph plotting (does not work if no radii in xyzr)
     morph_cell.branch(1).vis(type="morph")
     morph_cell.branch(1).vis(
-        type="morph", dims=[0, 1, 2], morph_plot_kwargs={"resolution": 6}
+        type="morph", dims=[0, 1, 2], resolution=6
     )  # plotting whole thing takes too long
     plt.close()