rerun create_alchemical_network

Author: atravitz

cookbook/create_alchemical_network.ipynb

@@ -36,16 +36,7 @@
    "execution_count": 1,
    "id": "ba6d0d2f-03df-463f-8976-c15a2bdf65e5",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/openmoltools/utils.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
-      "  from pkg_resources import resource_filename\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import openfe, rdkit.Chem\n",
     "from openff.units import unit\n",
@@ -262,7 +253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 7,
    "id": "2da4dafb-20d6-4ce7-ab83-4690528097d6",
    "metadata": {
     "slideshow": {
@@ -281,6 +272,14 @@
     "    transformation_name = transformation.name or transformation.key\n",
     "    transformation.to_json(transformations_dir / f\"{n}_{transformation_name}.json\")"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "86eeead8-7db5-4240-ba30-dbbc218d65b5",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -299,7 +298,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.11.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {