From cf44f643da67b55ac30e858fcd3c87fcaa6a2fbf Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Tue, 9 Jan 2024 17:02:02 -0700
Subject: [PATCH] Add deps to colab notebook (#32)

* this should work...

* fix colab bug

* add batteries included env file

* update notebook to use new env

* forgot rdkit

* oops made a mistake, rdkit is a dep for karto

* looks like we can't pass in `--no-deps`
---
 examples/environment.yaml        |  8 ++++
 examples/kartograf_example.ipynb | 79 ++++++++++++++++++++++++++------
 2 files changed, 74 insertions(+), 13 deletions(-)
 create mode 100644 examples/environment.yaml

diff --git a/examples/environment.yaml b/examples/environment.yaml
new file mode 100644
index 0000000..82d34c8
--- /dev/null
+++ b/examples/environment.yaml
@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+dependencies:
+  - kartograf >=1
+  - openfe >=0.15
+  - pip
+  - pip:
+    - git+https://github.com/OpenFreeEnergy/openfe-benchmarks.git
diff --git a/examples/kartograf_example.ipynb b/examples/kartograf_example.ipynb
index 8a51fb6..cfdd616 100644
--- a/examples/kartograf_example.ipynb
+++ b/examples/kartograf_example.ipynb
@@ -3,7 +3,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "source": [
     "# Example Notebook: Atom Mappings\n",
@@ -17,6 +20,25 @@
     "with well aligned conformations."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# NBVAL_SKIP\n",
+    "# Only run this cell if on google colab\n",
+    "import os\n",
+    "if \"COLAB_RELEASE_TAG\" in os.environ:\n",
+    "    !pip install -U https://github.com/conda-incubator/condacolab/archive/cuda-version-12.tar.gz\n",
+    "    import condacolab\n",
+    "    condacolab.install_mambaforge()\n",
+    "    !wget -q https://raw.githubusercontent.com/OpenFreeEnergy/kartograf/main/examples/environment.yaml\n",
+    "    !mamba env update -q --name=base --file=environment.yaml\n",
+    "    from google.colab import output\n",
+    "    output.enable_custom_widget_manager()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -36,10 +58,10 @@
       "  Cloning https://github.com/OpenFreeEnergy/openfe-benchmarks.git to /tmp/pip-req-build-dsih_khc\n",
       "  Running command git clone --filter=blob:none --quiet https://github.com/OpenFreeEnergy/openfe-benchmarks.git /tmp/pip-req-build-dsih_khc\n",
       "  Resolved https://github.com/OpenFreeEnergy/openfe-benchmarks.git to commit d81c79273b88f9b3baddd9886097789151e3df39\n",
-      "  Preparing metadata (setup.py) ... \u001B[?25ldone\n",
-      "\u001B[?25hBuilding wheels for collected packages: openfe-benchmarks\n",
-      "  Building wheel for openfe-benchmarks (setup.py) ... \u001B[?25ldone\n",
-      "\u001B[?25h  Created wheel for openfe-benchmarks: filename=openfe_benchmarks-0.0.0-py2.py3-none-any.whl size=1338664 sha256=156abe05cd092abb61d261190aa89c60dc9084f1ad2bb96e4ecba6eaf90e1c1e\n",
+      "  Preparing metadata (setup.py) ... \u001b[?25ldone\n",
+      "\u001b[?25hBuilding wheels for collected packages: openfe-benchmarks\n",
+      "  Building wheel for openfe-benchmarks (setup.py) ... \u001b[?25ldone\n",
+      "\u001b[?25h  Created wheel for openfe-benchmarks: filename=openfe_benchmarks-0.0.0-py2.py3-none-any.whl size=1338664 sha256=156abe05cd092abb61d261190aa89c60dc9084f1ad2bb96e4ecba6eaf90e1c1e\n",
       "  Stored in directory: /tmp/pip-ephem-wheel-cache-jp81fv_5/wheels/3d/2e/0d/a9d202ebefb2df685d9ab7255081f70a7ace5ff45bcdd698d2\n",
       "Successfully built openfe-benchmarks\n",
       "Installing collected packages: openfe-benchmarks\n",
@@ -78,10 +100,20 @@
     "Chem.Draw.MolsToGridImage([c.to_rdkit() for c in components])\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "source": [
     "## Generate Atom Mappings with Kartograf:\n",
@@ -98,6 +130,9 @@
      "start_time": "2023-11-06T00:01:55.473133240Z"
     },
     "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    },
     "scrolled": true
    },
    "outputs": [
@@ -284,7 +319,10 @@
      "end_time": "2023-11-06T00:01:55.817641995Z",
      "start_time": "2023-11-06T00:01:55.741239258Z"
     },
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
@@ -310,7 +348,10 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "source": [
     "## Scoring Metrics for Atom mappings:\n",
@@ -327,7 +368,10 @@
      "end_time": "2023-11-06T00:01:55.951440479Z",
      "start_time": "2023-11-06T00:01:55.813431246Z"
     },
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
@@ -434,7 +478,10 @@
      "end_time": "2023-11-06T00:01:56.139870575Z",
      "start_time": "2023-11-06T00:01:55.943210488Z"
     },
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
@@ -464,7 +511,10 @@
      "end_time": "2023-11-06T00:01:59.231030094Z",
      "start_time": "2023-11-06T00:01:56.163961283Z"
     },
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
@@ -522,7 +572,10 @@
      "end_time": "2023-11-06T00:01:59.231424281Z",
      "start_time": "2023-11-06T00:01:59.224933917Z"
     },
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": []
@@ -544,7 +597,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,