rerun choose_protocol

Author: atravitz

cookbook/choose_protocol.ipynb

@@ -90,16 +90,7 @@
     },
     "tags": []
    },
-   "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": [
     "from openfe.protocols.openmm_rfe import (\n",
     "    RelativeHybridTopologyProtocol,\n",
@@ -261,7 +252,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/gufe/settings/models.py:30: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n",
+      "/Users/atravitz/micromamba/envs/openfe-conda/lib/python3.11/site-packages/gufe/settings/models.py:30: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n",
       "  pprint.pprint(self.dict())\n"
      ]
     }
@@ -493,6 +484,14 @@
    "source": [
     "Unlike `ProtocolSettings`, a `Protocol` instance is immutable. The only way to safely change the settings of a `Protocol` is to recreate it from the modified `ProtocolSettings` object."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "91e223bc-5dc7-4533-ba5d-da112809be9a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -511,7 +510,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.11.14"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {