Add support for Google Colab

README.md

@@ -2,6 +2,7 @@
 [![full_tests](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/OpenFreeEnergy/ExampleNotebooks/HEAD)
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/switch_to_colab/openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb)
 
 # OpenFE Notebooks
 

easyCampaign/Cli Demo.ipynb

@@ -0,0 +1,110 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "785f29f9-889f-43ea-93ed-824de546993b",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "!pip install -q condacolab\n",
+    "import condacolab\n",
+    "condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c23f5c0d-a36e-43f5-9f1e-1e3f3fba80ea",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "# If this check fails, re-run\n",
+    "import condacolab\n",
+    "condacolab.check()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4a9a49bd-4520-4ca6-96e1-378559248ac4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "from IPython.display import JSON\n",
+    "from google.colab import output\n",
+    "from subprocess import getoutput\n",
+    "import os\n",
+    "\n",
+    "def shell(command):\n",
+    "  if command.startswith('cd'):\n",
+    "    path = command.strip().split(maxsplit=1)[1]\n",
+    "    os.chdir(path)\n",
+    "    return JSON([''])\n",
+    "  return JSON([getoutput(command)])\n",
+    "output.register_callback('shell', shell)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cc0b6da8-b400-4795-8f31-10d00e941449",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "#@title Colab Shell\n",
+    "%%html\n",
+    "<div id=term_demo></div>\n",
+    "<script src=\"https://code.jquery.com/jquery-latest.js\"></script>\n",
+    "<script src=\"https://cdn.jsdelivr.net/npm/jquery.terminal/js/jquery.terminal.min.js\"></script>\n",
+    "<link href=\"https://cdn.jsdelivr.net/npm/jquery.terminal/css/jquery.terminal.min.css\" rel=\"stylesheet\"/>\n",
+    "<script>\n",
+    "  $('#term_demo').terminal(async function(command) {\n",
+    "      if (command !== '') {\n",
+    "          try {\n",
+    "              let res = await google.colab.kernel.invokeFunction('shell', [command])\n",
+    "              let out = res.data['application/json'][0]\n",
+    "              this.echo(new String(out))\n",
+    "          } catch(e) {\n",
+    "              this.error(new String(e));\n",
+    "          }\n",
+    "      } else {\n",
+    "          this.echo('');\n",
+    "      }\n",
+    "  }, {\n",
+    "      greetings: 'Welcome to Colab Shell',\n",
+    "      name: 'colab_demo',\n",
+    "      height: 500,\n",
+    "      prompt: 'colab > '\n",
+    "  });"
+   ]
+  }
+ ],
+ "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": "3.10.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

easyCampaign/cli-tutorial.md

@@ -1,5 +1,7 @@
 # Relative Free Energies with the OpenFE CLI
 
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/switch_to_colab/easyCampaign/Cli%20Demo.ipynb)
+
 This tutorial will show how to use the OpenFE command line interface to get
 free energies -- with no Python at all! This will work for simple setups, you
 may need to use the Python interface for more complicated setups.

openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

@@ -31,6 +31,34 @@
     "T4-lysozyme L99A."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cd224909-3596-4800-9154-0f04e43c50cf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "# Only run this cell if on google colab\n",
+    "!pip install -q condacolab\n",
+    "import condacolab\n",
+    "condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2023/OpenFEforge-0.7.4-Linux-x86_64.sh\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5ecffc3a-1b2a-4e8e-b3aa-74c145089ef8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "# Only run this cell if on google colab\n",
+    "# If this check fails, re-run\n",
+    "import condacolab\n",
+    "condacolab.check()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -854,27 +882,27 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Usage: openfe [OPTIONS] COMMAND [ARGS]...\r\n",
-      "\r\n",
-      "  This is the command line tool to provide easy access to functionality from\r\n",
-      "  the OpenFE Python library.\r\n",
-      "\r\n",
-      "Options:\r\n",
-      "  --version   Show the version and exit.\r\n",
-      "  --log PATH  logging configuration file\r\n",
-      "  -h, --help  Show this message and exit.\r\n",
-      "\r\n",
-      "Setup Commands:\r\n",
-      "  atommapping        Check the atom mapping of a given pair of ligands\r\n",
-      "  plan-rhfe-network  Plan a relative hydration free energy network, saved in a\r\n",
-      "                     dir with multiple JSON files\r\n",
-      "  plan-rbfe-network  Plan a relative binding free energy network, saved in a\r\n",
-      "                     dir with multiple JSON files.\r\n",
-      "\r\n",
-      "Simulation Commands:\r\n",
-      "  gather    Gather DAG result jsons for network of RFE results into single TSV\r\n",
-      "            file\r\n",
-      "  quickrun  Run a given transformation, saved as a JSON file\r\n"
+      "Usage: openfe [OPTIONS] COMMAND [ARGS]...\n",
+      "\n",
+      "  This is the command line tool to provide easy access to functionality from\n",
+      "  the OpenFE Python library.\n",
+      "\n",
+      "Options:\n",
+      "  --version   Show the version and exit.\n",
+      "  --log PATH  logging configuration file\n",
+      "  -h, --help  Show this message and exit.\n",
+      "\n",
+      "Setup Commands:\n",
+      "  atommapping        Check the atom mapping of a given pair of ligands\n",
+      "  plan-rhfe-network  Plan a relative hydration free energy network, saved in a\n",
+      "                     dir with multiple JSON files\n",
+      "  plan-rbfe-network  Plan a relative binding free energy network, saved in a\n",
+      "                     dir with multiple JSON files.\n",
+      "\n",
+      "Simulation Commands:\n",
+      "  gather    Gather DAG result jsons for network of RFE results into single TSV\n",
+      "            file\n",
+      "  quickrun  Run a given transformation, saved as a JSON file\n"
      ]
     }
    ],
@@ -893,7 +921,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{0: 5, 1: 6, 2: 7, 3: 8, 4: 9, 5: 10, 6: 11, 7: 12, 8: 13, 9: 14, 10: 4, 11: 15}\r\n"
+      "{0: 5, 1: 6, 2: 7, 3: 8, 4: 9, 5: 10, 6: 11, 7: 12, 8: 13, 9: 14, 10: 4, 11: 15}\n"
      ]
     }
    ],