From 544e3414594d99eb26cc1c938c345338c030fdf4 Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Wed, 21 Feb 2024 10:58:30 -0500
Subject: [PATCH] added main notebook and updated docker runner

---
 main.ipynb            | 102 ++++++++++++++++++++++++++++++++++++++++++
 scripts/run-docker.sh |   2 +-
 2 files changed, 103 insertions(+), 1 deletion(-)
 create mode 100644 main.ipynb

diff --git a/main.ipynb b/main.ipynb
new file mode 100644
index 000000000..35aa00a5a
--- /dev/null
+++ b/main.ipynb
@@ -0,0 +1,102 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "initial_id",
+   "metadata": {
+    "collapsed": true,
+    "is_executing": true
+   },
+   "outputs": [],
+   "source": [
+    "import os \n",
+    "import smoldyn\n",
+    "import tellurium as te\n",
+    "import sed2.core \n",
+    "from process_bigraph import Composite\n",
+    "from biosimulator_processes.smoldyn_process import SmoldynProcess"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "instance = {\n",
+    "        'smoldyn': {\n",
+    "            '_type': 'process',\n",
+    "            'address': 'local:smoldyn',\n",
+    "            'config': {\n",
+    "                'model_filepath': 'biosimulator_processes/model_files/minE_model.txt',\n",
+    "                'animate': False},\n",
+    "            'inputs': {\n",
+    "                'species_counts': ['species_counts_store'],\n",
+    "                'molecules': ['molecules_store']},\n",
+    "            'outputs': {\n",
+    "                'species_counts': ['species_counts_store'],\n",
+    "                'molecules': ['molecules_store']}\n",
+    "        },\n",
+    "        'emitter': {\n",
+    "            '_type': 'step',\n",
+    "            'address': 'local:ram-emitter',\n",
+    "            'config': {\n",
+    "                'emit': {\n",
+    "                    'species_counts': 'tree[string]',\n",
+    "                    'molecules': 'tree[string]'}\n",
+    "            },\n",
+    "            'inputs': {\n",
+    "                'species_counts': ['species_counts_store'],\n",
+    "                'molecules': ['molecules_store']}\n",
+    "        }\n",
+    "    }"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "e379ea06228d2046"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "fp = instance.get('smoldyn').get('config').get('model_filepath')\n",
+    "\n",
+    "os.path.exists(fp)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "54541b0cc32e5940"
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   },
+   "id": "beca4cc35a69b69c"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/scripts/run-docker.sh b/scripts/run-docker.sh
index ea5b8e3f3..63934cfbb 100755
--- a/scripts/run-docker.sh
+++ b/scripts/run-docker.sh
@@ -2,7 +2,7 @@
 yes | docker system prune
 docker buildx create --name biosimbuilder --use
 docker buildx inspect --bootstrap
-docker buildx build --platform linux/amd64 -t biosimulator-processes . \
+docker buildx build --platform linux/amd64 -t biosimulators/biosimulator-processes:0.0.1 . \
   && docker run --platform linux/amd64 -it -p 8888:8888 biosimulator-processes