[Examples] Update reaction_path.py for Sphinx Gallery

doc/sphinx/conf.py

@@ -57,7 +57,7 @@ sphinx_gallery_conf = {
     'ignore_pattern': r'(__.*__\.py|test_examples\.m)',
     'image_srcset': ["2x"],
     'remove_config_comments': True,
-    'ignore_repr_types': r'matplotlib\.(text|axes|legend)',
+    'ignore_repr_types': r'(matplotlib\.(text|axes|legend)|graphviz\.(sources\.Source|graphs\.Graph|graphs\.Digraph))',
     'image_scrapers': ('matplotlib', ctutils.GraphvizScraper()),
     'examples_dirs': [
        '../samples/python/',

doc/sphinx/ctutils.py

@@ -41,9 +41,9 @@ class GraphvizScraper():
         # a path to a file name that adheres to Sphinx-Gallery naming convention.
         image_path_iterator = block_vars['image_path_iterator']
 
-        # Define a list of our already-created figure objects.
+        graph_types = (graphviz.Source, graphviz.graphs.Digraph, graphviz.graphs.Graph)
         for obj in block_vars["example_globals"].values():
-            if isinstance(obj, graphviz.Source) and id(obj) not in self.processed:
+            if isinstance(obj, graph_types) and id(obj) not in self.processed:
                 self.processed.add(id(obj))
                 image_path = Path(next(image_path_iterator)).with_suffix(".svg")
                 obj.format = "svg"

samples/python/kinetics/reaction_path.py

@@ -7,17 +7,21 @@ and the program 'dot' must be on your path for this example to work.
 Graphviz can be obtained from https://www.graphviz.org/ or (possibly) installed
 using your operating system's package manager.
 
-Requires: cantera >= 2.5.0
+Requires: cantera >= 2.5.0, graphviz
 
 .. tags:: Python, kinetics, reaction path analysis, pollutant formation
 """
 
 from subprocess import run
-import sys
 from pathlib import Path
+import graphviz
 
 import cantera as ct
 
+# %%
+# Generate a Solution with a state where reactions are occurring
+# --------------------------------------------------------------
+#
 # these lines can be replaced by any commands that generate
 # an object of a class derived from class Kinetics in some state.
 gas = ct.Solution('gri30.yaml')
@@ -29,12 +33,18 @@ while T < 1900:
     net.step()
     T = r.T
 
+# %%
+# Create a reaction path diagram following nitrogen
+# -------------------------------------------------
 element = 'N'
 
 diagram = ct.ReactionPathDiagram(gas, element)
 diagram.title = 'Reaction path diagram following {0}'.format(element)
 diagram.label_threshold = 0.01
 
+# %%
+# Save the reaction path diagram
+# ------------------------------
 dot_file = 'rxnpath.dot'
 img_file = 'rxnpath.png'
 img_path = Path.cwd().joinpath(img_file)
@@ -42,11 +52,12 @@ img_path = Path.cwd().joinpath(img_file)
 diagram.write_dot(dot_file)
 print(diagram.get_data())
 
-print("Wrote graphviz input file to '{0}'.".format(Path.cwd().joinpath(dot_file)))
+print(f"Wrote graphviz input file to '{Path.cwd().joinpath(dot_file)}'.")
 
-run('dot {0} -Tpng -o{1} -Gdpi=200'.format(dot_file, img_file).split())
-print("Wrote graphviz output file to '{0}'.".format(img_path))
+run(f"dot {dot_file} -Tpng -o{img_file} -Gdpi=200".split())
+print(f"Wrote graphviz output file to '{img_path}'.")
 
-if "-view" in sys.argv:
-    import webbrowser
-    webbrowser.open(f"file:///{img_path}")
+# %%
+# View the reaction path diagram
+# ------------------------------
+graphviz.Source(diagram.get_dot())