add worker-based execution example notebook

Author: atravitz

environment.yaml

@@ -14,11 +14,14 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - python
-  - openfe==1.11.0
   - openff-interchange-base != 0.5.1  # https://github.com/openforcefield/openff-interchange/issues/1450
+  - openfe
+  # tmp for dev build
+  - zstandard
+  - msgpack-python
   - pip:
-    - git+https://github.com/OpenFreeEnergy/openfe_analysis@v0.5.0 # Use conda-forge v0.5 after new openfe release updates pins on openfe-analysis
-    - git+https://github.com/OpenFreeEnergy/cinnabar@0.6.0 # Use conda-forge v0.6.0 after new openfe release updates pins on cinnabar
-    - git+https://github.com/OpenFreeEnergy/kartograf@v2.0.0  # Use conda-forge v2.0 after new openfe release updates pins on kartogra
-    - git+https://github.com/OpenFreeEnergy/konnektor@v0.4.0  # use conda-forge v0.4.0 after openfe conda-forge release
-    - git+https://github.com/OpenFreeEnergy/Lomap@v3.3.0  # use conda-forge v3.3.0 after openfe conda-forge release
+    - git+https://github.com/OpenFreeEnergy/openfe@epic/execution_improvements
+    - git+https://github.com/OpenFreeEnergy/exorcist@main
+    - git+https://github.com/OpenFreeEnergy/gufe@main
+
+

execution/alchemicalNetwork_mc1_small.json

@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "dfffe446-14c0-4dea-92ea-0b9f862fdec6",
+   "metadata": {},
+   "source": [
+    "# Worker-Based Execution"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b600d427-abe5-418b-b4d1-a7cb23d7edf0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import openfe"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0a2035c9-8e0f-454e-9189-be3e41ae57f6",
+   "metadata": {},
+   "source": [
+    "load an AlchemicalNetwork to execute - this is a small example campaign with only two edges and pre-charged ligands"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "6b72c4a4-310b-498d-afab-78950d5242bc",
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "FileNotFoundError",
+     "evalue": "[Errno 2] No such file or directory: 'alchemicalNetwork_mc1_small.json'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mFileNotFoundError\u001b[39m                         Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[2]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m alchemical_network = openfe.AlchemicalNetwork.from_json(\u001b[33m\"alchemicalNetwork_mc1_small.json\"\u001b[39m)\n",
+      "\u001b[36mFile \u001b[39m\u001b[32m~/micromamba/envs/openfe-notebooks/lib/python3.13/site-packages/gufe/tokenization.py:750\u001b[39m, in \u001b[36mGufeTokenizable.from_json\u001b[39m\u001b[34m(cls, file, content)\u001b[39m\n\u001b[32m    746\u001b[39m         \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mcls\u001b[39m.from_dict(deserialized)\n\u001b[32m    748\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mgufe\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mutils\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m ensure_filelike\n\u001b[32m--> \u001b[39m\u001b[32m750\u001b[39m \u001b[30;43m\u001b[39;49m\u001b[30;43;01mwith\u001b[39;49;00m\u001b[30;43m \u001b[39;49m\u001b[30;43mensure_filelike\u001b[39;49m\u001b[30;43m(\u001b[39;49m\u001b[30;43mfile\u001b[39;49m\u001b[30;43m,\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43mmode\u001b[39;49m\u001b[30;43m=\u001b[39;49m\u001b[30;43m\"\u001b[39;49m\u001b[30;43mr\u001b[39;49m\u001b[30;43m\"\u001b[39;49m\u001b[30;43m)\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43;01mas\u001b[39;49;00m\u001b[30;43m \u001b[39;49m\u001b[30;43mf\u001b[39;49m\u001b[30;43m:\u001b[39;49m\n\u001b[32m    751\u001b[39m \u001b[30;43m    \u001b[39;49m\u001b[30;43mdeserialized\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43m=\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43mjson\u001b[39;49m\u001b[30;43m.\u001b[39;49m\u001b[30;43mload\u001b[39;49m\u001b[30;43m(\u001b[39;49m\u001b[30;43mf\u001b[39;49m\u001b[30;43m,\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43mcls\u001b[39;49m\u001b[30;43m=\u001b[39;49m\u001b[30;43mJSON_HANDLER\u001b[39;49m\u001b[30;43m.\u001b[39;49m\u001b[30;43mdecoder\u001b[39;49m\u001b[30;43m)\u001b[39;49m\n\u001b[32m    753\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n",
+      "\u001b[36mFile \u001b[39m\u001b[32m~/micromamba/envs/openfe-notebooks/lib/python3.13/site-packages/gufe/utils.py:212\u001b[39m, in \u001b[36mensure_filelike.__enter__\u001b[39m\u001b[34m(self)\u001b[39m\n\u001b[32m    210\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34m__enter__\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[32m    211\u001b[39m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m.to_open \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[32m--> \u001b[39m\u001b[32m212\u001b[39m         \u001b[38;5;28mself\u001b[39m.context = \u001b[30;43mopen\u001b[39;49m\u001b[30;43m(\u001b[39;49m\u001b[30;43mself\u001b[39;49m\u001b[30;43m.\u001b[39;49m\u001b[30;43mto_open\u001b[39;49m\u001b[30;43m,\u001b[39;49m\u001b[30;43m \u001b[39;49m\u001b[30;43mmode\u001b[39;49m\u001b[30;43m=\u001b[39;49m\u001b[30;43mself\u001b[39;49m\u001b[30;43m.\u001b[39;49m\u001b[30;43mmode\u001b[39;49m\u001b[30;43m)\u001b[39;49m\n\u001b[32m    214\u001b[39m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m.context\n",
+      "\u001b[31mFileNotFoundError\u001b[39m: [Errno 2] No such file or directory: 'alchemicalNetwork_mc1_small.json'"
+     ]
+    }
+   ],
+   "source": [
+    "alchemical_network = openfe.AlchemicalNetwork.from_json(\"alchemicalNetwork_mc1_small.json\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4080f228-4603-432b-b64f-c632f2c8e52c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}