update

bio_compose/__init__.py

@@ -1,4 +1,5 @@
 import os
+import time
 
 
 current_dir = os.path.dirname(__file__)
@@ -8,9 +9,52 @@
     __version__ = f.read().strip()
 
 
-def run_simulation(*args, **kwargs):
-    # TODO: implement this
-    pass
+def run_simulation(*args):
+    """
+    Run a simulation with BioCompose
+
+    Args:
+        - args: Positional arguments
+            - 1 argument(**smoldyn simulation only**): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
+            - 3 arguments(**smoldyn simulation only**): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt
+            - 5 arguments(**sbml simulation only**): sbml filepath, simulation start, simulation end, simulation steps, simulator
+
+    """
+    from bio_compose.runner import SimulationRunner, SimulationResult
+
+    # set up submission
+    runner = SimulationRunner()
+    in_file = args[0]
+    n_args = len(args)
+    submission = None
+
+    if n_args == 1:
+        submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file)
+    elif n_args == 3:
+        dur = args[1]
+        dt = args[2]
+        submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file, duration=dur, dt=dt)
+    elif n_args == 5:
+        start = args[1]
+        end = args[2]
+        steps = args[3]
+        simulator = args[4]
+        submission = runner.run_utc_simulation(sbml_filepath=in_file, start=start, end=end, steps=steps, simulator=simulator)
+
+    # fetch results
+    job_id = submission.get('job_id')
+    output = None
+    if job_id is not None:
+        while True:
+            simulation_result = runner.get_output(job_id=job_id)
+            status = simulation_result['content']['status']
+            if not 'COMPLETED' in status:
+                time.sleep(1)
+            else:
+                output = simulation_result
+                break
+
+    return SimulationResult(data=output)
 
 
 def verify(*args, **kwargs):
@@ -28,9 +72,7 @@ def verify(*args, **kwargs):
     Returns:
         Verification result instance. See documentation for more details.
     """
-    import time
-    from bio_compose.verifier import Verifier
-    from bio_compose.verifier import VerificationResult
+    from bio_compose.verifier import Verifier, VerificationResult
 
     verifier = Verifier()
     simulators = kwargs.get('simulators')

bio_compose/data_model.py

@@ -147,7 +147,7 @@ def get_output(self, job_id: str, download_dest: str = None, filename: str = Non
         except:
             import traceback
             tb_str = traceback.format_exc()
-            return RequestError(error=error_message)
+            return RequestError(error=tb_str)
 
     def get_job_status(self, job_id: str):
         output = self.get_output(job_id=job_id)

bio_compose/runner.py

@@ -110,3 +110,12 @@ def generate_simularium_file(self, smoldyn_output_filepath: str, box_size: float
         headers = {'Content-Type': multidata.content_type}
 
         return self._execute_request(endpoint=endpoint, headers=headers, multidata=multidata, query_params=query_params)
+
+
+class SimulationResult(dict):
+    def __init__(self, data):
+        self.data = data
+        self.job_id = self.data.get('job_id')
+
+    def visualize(self):
+        pass

pyproject.toml

@@ -1,7 +1,7 @@
 # This project configuration should relate only to the high level notebook api (as primary deps).
 [tool.poetry]
 name = "bio-compose"
-version = "0.5.1"
+version = "0.5.2"
 description = "Create, execute, and introspect reproducible composite simulations of dynamic biological systems."
 authors = ["Alex Patrie <[email protected]>"]
 readme = "README.md"

tests/test.ipynb

@@ -137,8 +137,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "__init__.py     \u001b[34mfixtures\u001b[m\u001b[m        observables.pdf rmse.pdf\n",
-      "\u001b[34m__pycache__\u001b[m\u001b[m     main.py         plot.pdf        test.ipynb\n"
+      "__init__.py     \u001B[34mfixtures\u001B[m\u001B[m        observables.pdf rmse.pdf\n",
+      "\u001B[34m__pycache__\u001B[m\u001B[m     main.py         plot.pdf        test.ipynb\n"
      ]
     }
    ],
@@ -169,11 +169,82 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
    "id": "c9c91ddd-cb0f-414e-acd4-7e0a3536d302",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-09-06T15:17:04.630824Z",
+     "start_time": "2024-09-06T15:17:04.625194Z"
+    }
+   },
+   "source": [
+    "def f(*args):\n",
+    "    if len(args) == 1:\n",
+    "        return args[0] ** 2\n",
+    "    elif len(args) == 3:\n",
+    "        return args[0] + args[1] + args[2]\n",
+    "    \n",
+    "    \n",
+    "f(10, 10, 10)"
+   ],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "30"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "execution_count": 1
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "start_time": "2024-09-06T15:25:24.177897Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "from bio_compose import run_simulation\n",
+    "\n",
+    "\n",
+    "results = run_simulation('/Users/alexanderpatrie/Desktop/repos/bio-compose/tests/fixtures/smoldyn/MinE.txt')"
+   ],
+   "id": "9f65ea642fe5cfc5",
+   "outputs": [
+    {
+     "ename": "KeyboardInterrupt",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m                         Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[1], line 4\u001B[0m\n\u001B[1;32m      1\u001B[0m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01mbio_compose\u001B[39;00m \u001B[38;5;28;01mimport\u001B[39;00m run_simulation\n\u001B[0;32m----> 4\u001B[0m results \u001B[38;5;241m=\u001B[39m \u001B[43mrun_simulation\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[38;5;124;43m/Users/alexanderpatrie/Desktop/repos/bio-compose/tests/fixtures/smoldyn/MinE.txt\u001B[39;49m\u001B[38;5;124;43m'\u001B[39;49m\u001B[43m)\u001B[49m\n",
+      "File \u001B[0;32m~/Desktop/repos/bio-compose/bio_compose/__init__.py:52\u001B[0m, in \u001B[0;36mrun_simulation\u001B[0;34m(*args)\u001B[0m\n\u001B[1;32m     50\u001B[0m status \u001B[38;5;241m=\u001B[39m simulation_result[\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mcontent\u001B[39m\u001B[38;5;124m'\u001B[39m][\u001B[38;5;124m'\u001B[39m\u001B[38;5;124mstatus\u001B[39m\u001B[38;5;124m'\u001B[39m]\n\u001B[1;32m     51\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124mCOMPLETED\u001B[39m\u001B[38;5;124m'\u001B[39m \u001B[38;5;129;01min\u001B[39;00m status:\n\u001B[0;32m---> 52\u001B[0m     \u001B[43mtime\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msleep\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;241;43m1\u001B[39;49m\u001B[43m)\u001B[49m\n\u001B[1;32m     53\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m     54\u001B[0m     output \u001B[38;5;241m=\u001B[39m simulation_result\n",
+      "\u001B[0;31mKeyboardInterrupt\u001B[0m: "
+     ]
+    }
+   ],
+   "execution_count": 1
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": "results",
+   "id": "a2eb33fd435820b7"
+  },
+  {
    "metadata": {},
+   "cell_type": "code",
    "outputs": [],
-   "source": []
+   "execution_count": null,
+   "source": "",
+   "id": "791935b3397ac5d6"
   }
  ],
  "metadata": {