added documentation

Author: AlexPatrie

README.md

@@ -12,7 +12,7 @@
 The primary method of user-facing interaction for this service is done through the use of a high-level "notebook" api called `bio_check`. 
 A convenient notebook demonstrating the functionality of this service is hosted on Google Colab and can be accessed by clicking the above "Open In Colab" badge.
 
-[View the template notebook as markdown](docs/verification_api_demo.md)
+[View the template notebook as markdown](documentation/verification_api_demo.md)
 
 
 Installation of this tooling can be performed using PyPI as such:

bio_compose/runner.py

@@ -14,22 +14,20 @@ class SimulationRunner(Api):
     submitted_jobs: List[Dict]
 
     def __init__(self):
-        """A new instance of the Verifier class. NOTE: this may clash with your record keeping in a notebook, so it is highly recommended that users
-            treat instances of this class as quasi-singletons, although not necessary for fundamental interaction.
+        """A new instance of the Verifier class. NOTE: this may clash with your record keeping in a notebook, so it is highly recommended that users treat instances of this class as quasi-singletons, although not necessary for fundamental interaction.
         """
         super().__init__()
 
     def run_smoldyn_simulation(self, smoldyn_configuration_filepath: str, duration: int = None, dt: float = None) -> Dict[str, Any]:
-        """Run a smoldyn simulation using a standard Smoldyn configuration file. Please see https://www.smoldyn.org/SmoldynManual.pdf for more information on running
-            simulations with Smoldyn.
+        """Run a smoldyn simulation using a standard Smoldyn configuration file. Please see https://www.smoldyn.org/SmoldynManual.pdf for more information on running simulations with Smoldyn.
 
-            Args:
-                smoldyn_configuration_filepath:`str`: The path to the Smoldyn configuration file for the given model simulation.
-                duration:`int`: The duration of the simulation. If `None` is passed, duration inference will be attempted using `time_stop` parameter within the Smoldyn configuration. Defaults to `None`.
-                dt:`float`: The timestep to use within the Smoldyn simulation. If `None` is passed, dt inference will be attempted using the `.dt` parameter of the loaded Smoldyn simulation. Defaults to `None`.
+        Args:
+        smoldyn_configuration_filepath:`str`: The path to the Smoldyn configuration file for the given model simulation.
+        duration:`int`: The duration of the simulation. If `None` is passed, duration inference will be attempted using `time_stop` parameter within the Smoldyn configuration. Defaults to `None`.
+        dt:`float`: The timestep to use within the Smoldyn simulation. If `None` is passed, dt inference will be attempted using the `.dt` parameter of the loaded Smoldyn simulation. Defaults to `None`.
 
-            Returns:
-                The response for the Smoldyn simulation submission request.
+        Returns:
+        The response for the Smoldyn simulation submission request.
 
         """
         endpoint = self._format_endpoint(f'run-smoldyn')
@@ -53,15 +51,15 @@ def run_smoldyn_simulation(self, smoldyn_configuration_filepath: str, duration:
     def run_utc_simulation(self, sbml_filepath: str, start: int, end: int, steps: int, simulator: str) -> Dict[str, Any]:
         """Run a uniform time course simulation of the model specified in `sbml_filepath` with a supported simulator.
 
-            Args:
-                sbml_filepath:`str`: The path to a valid SBML file.
-                start:`int`: The start time of the simulation.
-                end:`int`: The end time of the simulation.
-                steps:`int`: The number of steps to record within the ODE.
-                simulator:`str`: The simulator to use. Currently, simulator choices include: `'amici'`, `'copasi'`, or `'tellurium'`.
+        Args:
+        sbml_filepath:`str`: The path to a valid SBML file.
+        start:`int`: The start time of the simulation.
+        end:`int`: The end time of the simulation.
+        steps:`int`: The number of steps to record within the ODE.
+        simulator:`str`: The simulator to use. Currently, simulator choices include: `'amici'`, `'copasi'`, or `'tellurium'`.
 
-            Returns:
-                The response for the UTC simulation submission request.
+        Returns:
+        The response for the UTC simulation submission request.
         """
         endpoint = self._format_endpoint(f'run-utc')
 
@@ -84,14 +82,13 @@ def run_utc_simulation(self, sbml_filepath: str, start: int, end: int, steps: in
     def generate_simularium_file(self, smoldyn_output_filepath: str, box_size: float, filename: str = None) -> Dict[str, Any]:
         """Run a Smoldyn simulation and generate a Simularium trajectory from the aforementioned simulation's outputs.
 
-            Args:
-                smoldyn_output_filepath:`str`: The path to the Smoldyn output file for the given model simulation.
-                box_size:`float`: The box size to use for the Simularium trajectory.
-                filename:`str`: The name of the Simularium file that is generated. If `None` is passed, a general `'simulation.simularium'` filename will be used.
-                    Defaults to `None`.
+        Args:
+        smoldyn_output_filepath:`str`: The path to the Smoldyn output file for the given model simulation.
+        box_size:`float`: The box size to use for the Simularium trajectory.
+        filename:`str`: The name of the Simularium file that is generated. If `None` is passed, a general `'simulation.simularium'` filename will be used. Defaults to `None`.
 
-            Returns:
-                The response for the Simularium submission request.
+        Returns:
+        The response for the Simularium submission request.
         """
         endpoint = self._format_endpoint(f'generate-simularium-file')