Merging dev onto release

.github/workflows/generate-docs.yml

@@ -27,7 +27,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          uv sync --group docs --group interactive
+          uv sync --group docs --group interactive --extra extras
 
       - name: Build the documentation
         run: |

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "openpnm"
-version = "3.6.1"
+version = "3.6.1-dev3"
 description = "A framework for conducting pore network modeling simulations of multiphase transport in porous materials"
 authors = [{ name = "OpenPNM Team", email = "jgostick@gmail.com" }]
 maintainers = [
@@ -220,7 +220,7 @@ path = "src/openpnm/__version__.py"
 packages = ["src/openpnm"]
 
 [tool.bumpversion]
-current_version = "3.6.1"
+current_version = "3.6.1-dev3"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

src/openpnm/_skgraph/queries/_funcs.py

@@ -168,7 +168,7 @@ def find_connected_nodes(network, inds, flatten=True, logic="or"):
             if len(inds):
                 temp = temp.astype(float)
                 temp[inds] = np.nan
-            temp = np.reshape(temp, newshape=[len(edges), 2], order="F")
+            temp = np.reshape(temp, [len(edges), 2], order="F")
             neighbors = temp
         else:
             neighbors = [np.array([], dtype=np.int64) for i in range(len(edges))]

src/openpnm/visualization/_plottools.py

@@ -148,23 +148,27 @@ class of matplotlib, so check their documentation for additional
     throat_pos = np.column_stack((xyz[P1], xyz[P2])).reshape((Ts.size, 2, dim.sum()))
 
     # Deal with optional style related arguments
-    if 'c' in kwargs.keys():
-        color = kwargs.pop('c')
-    color = mcolors.to_rgb(color) + tuple([alpha])
     if isinstance(cmap, str):
         try:
             cmap = plt.colormaps.get_cmap(cmap)
         except AttributeError:
             cmap = plt.cm.get_cmap(cmap)
+    kwargs['cmap'] = cmap
     # Override colors with color_by if given
-    if color_by is not None:
+    if color_by is None:
+        if 'c' in kwargs.keys():
+            color = kwargs.pop('c')
+        color = mcolors.to_rgb(color) + tuple([alpha])
+        kwargs['color'] = color
+        _ = kwargs.pop('cmap', None)
+    else:
         color_by = np.array(color_by)
         if len(color_by) != len(Ts):
             color_by = color_by[Ts]
         if not np.all(np.isfinite(color_by)):
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
-        color = color_by
+        kwargs['array'] = color_by
     if size_by is not None:
         if len(size_by) != len(Ts):
             size_by = size_by[Ts]
@@ -180,13 +184,22 @@ class of matplotlib, so check their documentation for additional
     vmax = kwargs.pop('vmax', None)
 
     if ThreeD:
-        lc = Line3DCollection(throat_pos, array=color, cmap=cmap, alpha=alpha,
-                              linestyles=linestyle, linewidths=linewidth,
-                              antialiaseds=np.ones_like(network.Ts), **kwargs)
+        lc = Line3DCollection(
+            throat_pos,
+            alpha=alpha,
+            linestyles=linestyle,
+            linewidths=linewidth,
+            antialiaseds=np.ones_like(network.Ts),
+            **kwargs,
+        )
     else:
-        lc = LineCollection(throat_pos, array=color, cmap=cmap, alpha=alpha,
-                            linestyles=linestyle, linewidths=linewidth,
-                            antialiaseds=np.ones_like(network.Ts), **kwargs)
+        lc = LineCollection(
+            throat_pos, alpha=alpha,
+            linestyles=linestyle,
+            linewidths=linewidth,
+            antialiaseds=np.ones_like(network.Ts),
+            **kwargs,
+        )
         if label_by is not None:
             for count, (P1, P2) in enumerate(network.conns[Ts, :]):
                 i, j, k = np.mean(network.coords[[P1, P2], :], axis=0)
@@ -332,23 +345,26 @@ def plot_coordinates(network,
     Xl, Yl, Zl = network['pore.coords'].T
 
     # Parse formatting kwargs
-    if 'c' in kwargs.keys():
-        color = kwargs.pop('c')
-    if 's' in kwargs.keys():
-        markersize = kwargs.pop('s')
     if isinstance(cmap, str):
         try:
             cmap = plt.colormaps.get_cmap(cmap)
         except AttributeError:
             cmap = plt.cm.get_cmap(cmap)
-    if color_by is not None:
+    kwargs['cmap'] = cmap
+    if color_by is None:
+        if 'c' in kwargs.keys():
+            color = kwargs.pop('c')
+        _ = kwargs.pop('cmap')
+    else:
         color_by = np.array(color_by)
         if len(color_by) != len(Ps):
             color_by = color_by[Ps]
         if not np.all(np.isfinite(color_by)):
             color_by[~np.isfinite(color_by)] = 0
             logger.warning('nans or infs found in color_by array, setting to 0')
         color = color_by
+    if 's' in kwargs.keys():
+        markersize = kwargs.pop('s')
     if size_by is not None:
         if len(size_by) != len(Ps):
             size_by = size_by[Ps]
@@ -375,7 +391,6 @@ def plot_coordinates(network,
                         s=markersize,
                         marker=marker,
                         alpha=alpha,
-                        cmap=cmap,
                         **kwargs)
         if label_by is not None:
             for count, (i, j, k) in enumerate(network.coords[Ps, :]):