added copasi process docs to utils

biosimulator_processes/utils.py

@@ -1,4 +1,6 @@
+from typing import Dict
 from basico import biomodels, load_model_from_string
+from process_bigraph import Composite, pf
 
 
 def fetch_biomodel_by_term(term: str, index: int = 0):
@@ -18,11 +20,30 @@ def fetch_biomodel_by_term(term: str, index: int = 0):
 
 
 def fetch_biomodel(model_id: str):
+    # TODO: make this generalizable
     sbml = biomodels.get_content_for_model(model_id)
     return load_model_from_string(sbml)
 
 
-def generate_copasi_process_instance(config: dict, instance_name: str):
+def play_composition(instance: dict, duration: int):
+    """Configure and run a Composite workflow"""
+    workflow = Composite({
+        'state': instance
+    })
+    workflow.run(duration)
+    results = workflow.gather_results()
+    print(f'RESULTS: {pf(results)}')
+    return results
+
+
+def generate_copasi_process_instance(instance_name: str, config: Dict) -> Dict:
+    """Generate an instance of a single copasi process which is named `instance_name`
+        and configured by `config` formatted to the process bigraph Composite API.
+
+        Args:
+            instance_name:`str`: name of the new instance referenced by PBG.
+            config:`Dict`: see `biosimulator_processes.processes.copasi_process.CopasiProcess`
+    """
     return {
         instance_name: {
             '_type': 'process',

notebooks/copasi_process_composer.ipynb

@@ -12,9 +12,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "initial_id",
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-02-28T21:35:30.970032Z",
+     "start_time": "2024-02-28T21:35:30.965409Z"
+    }
+   },
    "outputs": [],
    "source": [
     "import sys \n",
@@ -24,12 +29,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "c6c10dc5988e52d4",
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-28T21:35:36.900035Z",
+     "start_time": "2024-02-28T21:35:34.590082Z"
+    }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CobraProcess registered successfully.\n",
+      "CopasiProcess registered successfully.\n",
+      "SmoldynProcess registered successfully.\n",
+      "TelluriumProcess registered successfully.\n"
+     ]
+    }
+   ],
    "source": [
     "import os \n",
     "from basico import *\n",
@@ -41,16 +61,7 @@
   {
    "cell_type": "code",
    "outputs": [],
-   "source": [
-    "def play_composition(instance: dict, duration: int):\n",
-    "    workflow = Composite({\n",
-    "        'state': instance\n",
-    "    })\n",
-    "    workflow.run(duration)\n",
-    "    results = workflow.gather_results()\n",
-    "    print(f'RESULTS: {pf(results)}')\n",
-    "    return results"
-   ],
+   "source": [],
    "metadata": {
     "collapsed": false
    },
@@ -376,12 +387,12 @@
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
-     "end_time": "2024-02-28T21:21:05.924230Z",
-     "start_time": "2024-02-28T21:21:05.401040Z"
+     "end_time": "2024-02-28T21:35:19.452122Z",
+     "start_time": "2024-02-28T21:35:19.448652Z"
     }
    },
    "id": "56fe39f779b76c37",
-   "execution_count": 2
+   "execution_count": 3
   },
   {
    "cell_type": "code",