fix interactive path diagram

Author: Naikless

environment.yml

@@ -11,3 +11,4 @@ dependencies:
   - seaborn
   - coolprop
   - scikits.odes
+  - python-graphviz

reactors/interactive_path_diagram.ipynb

@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 16,
    "metadata": {
     "tags": []
    },
@@ -20,7 +20,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Using Cantera version: 2.6.0a4\n"
+      "Using Cantera version: 2.6.0\n"
      ]
     }
    ],
@@ -29,6 +29,7 @@
     "from ipywidgets import widgets, interact\n",
     "import cantera as ct\n",
     "import numpy as np\n",
+    "import graphviz\n",
     "\n",
     "%matplotlib inline\n",
     "%config InlineBackend.figure_formats = [\"svg\"]\n",
@@ -50,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 5,
    "metadata": {
     "tags": []
    },
@@ -73,7 +74,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "metadata": {
     "tags": []
    },
@@ -91,7 +92,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 7,
    "metadata": {
     "tags": []
    },
@@ -109,7 +110,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 8,
    "metadata": {
     "tags": []
    },
@@ -130,7 +131,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 9,
    "metadata": {
     "tags": []
    },
@@ -158,18 +159,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e73efe770a6a424aab889d76a70ea2d4",
+       "model_id": "e9eb8420e3d1441d8dacca916d65ccea",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "interactive(children=(IntSlider(value=100, description='plot_step', max=1510, step=10), FloatSlider(value=0.1,…"
+       "interactive(children=(IntSlider(value=100, description='plot_step', max=1730, step=10), FloatSlider(value=0.1,…"
       ]
      },
      "metadata": {},
@@ -200,12 +201,8 @@
     "    diagram.threshold = threshold\n",
     "\n",
     "    diagram.show_details = details\n",
-    "    dot_file = \"reaction_paths.dot\"\n",
-    "    png_file = \"reaction_paths.png\"\n",
-    "    diagram.write_dot(dot_file)\n",
-    "    subprocess.run(f\"dot {dot_file} -Tpng -o{png_file} -Gdpi=100\".split())\n",
-    "    img = Image(filename=png_file)\n",
-    "    display(img)"
+    "    graph = graphviz.Source(diagram.get_dot())\n",
+    "    display(graph)"
    ]
   },
   {
@@ -218,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -240,7 +237,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -274,24 +271,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f389251a70744d52b493b85eae3e909f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "interactive(children=(FloatSlider(value=0.01, description='annotation_cutoff', max=4.0, min=0.01), Output()), …"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "@interact(\n",
     "    annotation_cutoff=widgets.FloatSlider(value=1e-2, min=1e-2, max=4, steps=10),\n",
@@ -348,7 +330,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -374,24 +356,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8a6a58db99d7422790a30e3f448189c2",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "interactive(children=(FloatLogSlider(value=1e-05, description='annotation_cutoff', max=-4.0, min=-5.0), Output…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "@interact(\n",
     "    annotation_cutoff=widgets.FloatLogSlider(\n",
@@ -437,7 +404,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.8.12"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
@@ -528,9 +495,9 @@
        "description": "annotation_cutoff",
        "layout": "IPY_MODEL_b31e0f2f2acb403b83a084fb18495310",
        "max": 0.0001,
-       "min": 1e-06,
+       "min": 0.000001,
        "step": 0.1,
-       "value": 1e-06
+       "value": 0.000001
       }
      },
      "11d4490fa73f470fa12134bdbe95172f": {
@@ -791,9 +758,9 @@
        "description": "annotation_cutoff",
        "layout": "IPY_MODEL_cebcfa314a17448385e00d23be4e1132",
        "max": 0.0001,
-       "min": 1e-06,
+       "min": 0.000001,
        "step": 0.1,
-       "value": 1e-06
+       "value": 0.000001
       }
      },
      "549874ce98c54398bdb34b108c543913": {
@@ -941,9 +908,9 @@
        "description": "annotation_cutoff",
        "layout": "IPY_MODEL_410cc700779545278ab29d6bdb515078",
        "max": 0.0001,
-       "min": 1e-06,
+       "min": 0.000001,
        "step": 0.1,
-       "value": 1e-06
+       "value": 0.000001
       }
      },
      "6c48772d2156460e98f2d2e53d19ce7d": {
@@ -956,9 +923,9 @@
        "description": "annotation_cutoff",
        "layout": "IPY_MODEL_d46402fffd6243a58b1eab788b948adc",
        "max": 0.1,
-       "min": 1e-05,
+       "min": 0.00001,
        "step": 0.1,
-       "value": 1e-05
+       "value": 0.00001
       }
      },
      "6db5fd30b2f7461ca1cc5547b1330a98": {
@@ -1527,9 +1494,9 @@
        "description": "annotation_cutoff",
        "layout": "IPY_MODEL_466f3c1486704068ac57d20e554de8cf",
        "max": 0.1,
-       "min": 1e-05,
+       "min": 0.00001,
        "step": 0.1,
-       "value": 1e-05
+       "value": 0.00001
       }
      },
      "ce95d34031c1420abab17b1f372f6edc": {