some cleanup

vivarium_tellurium/processes/tellurium_process.py

@@ -1,45 +1,38 @@
-'''
-Execute by running: ``python template/processes/template_process.py``
-'''
+"""
+Execute by running: ``python vivarium_tellurium/processes/tellurium_process.py`
+"""
 
 from vivarium.core.process import Process
 from vivarium.core.engine import Engine, pp
 import tellurium as te
 
 
 class TelluriumProcess(Process):
-    '''
-    Class which serves to be a Tellurium implementation of the `vivarium.core.processes.Process()` interface.
-    '''
-
-    defaults = {
-        'sbml_model_path': '',
-        'antimony_string': None,
-        'exposed_species': None,  # list of exposed species ids
-        'parameter1': 3.0,
-    }
+    """Vivarium Process interface for Tellurium.
+
+    Instantiates a `roadrunner` simulator instance using either `SBML`(default,`file`) or `antimony`(optional,`str`)
 
-    def __init__(self, config=None):
-        '''
-        A new instance of a `tellurium`-based implementation of the `vivarium.core.processes.Process() interface.
-        
-        Instantiates a `roadrunner` simulator instance using either `SBML`(default,`file`) or `antimony`(optional,`str`)
-        
         #### Parameters:
         ----------------
         parameters: `Dict`
             configurations of the simulator process parameters. Defaults to `defaults`:\n
                             `'sbml_model_file': ''`
                             `'antimony_string': None`
                             `'exposed_species': None`  # list of exposed species ids
-                            `'parameter1': 3.0`
-                            
+
         #### Returns:
         -------------
         `TelluriumProcess`
             A generic instance of a Tellurium simulator process.
-        '''
-
+    """
+
+    defaults = {
+        'sbml_model_path': '',
+        'antimony_string': None,
+        'exposed_species': None,  # list of exposed species ids
+    }
+
+    def __init__(self, config=None):
         super().__init__(config)
 
         # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony
@@ -49,21 +42,18 @@ def __init__(self, config=None):
             self.simulator = te.loadSBMLModel(self.parameters['sbml_model_path'])
 
         # extract the variables 
-        self.species = self.simulator.get_species() # PLACEHOLDER!!!!!!!!
-
+        self.species = self.simulator.get_species()  # PLACEHOLDER!!!!!!!!
 
     def ports_schema(self):
-        # TODO -- need to set the ports/variables according to self.config assignments. Similar to viv-biosimul
-        species_schema = {
-            species_id: {
+        # TODO -- set the ports/variables according to self.config assignments. Similar to viv-biosimul
+        return {
+            'species': {
+                species_id: {
                     '_default': 1.0,
                     '_updater': 'set',
                     '_emit': True,
                 } for species_id in self.config['exposed_species']
-        }
-
-        return {
-            'species': species_schema
+            }
         }
 
     def next_update(self, interval, states):
@@ -84,14 +74,9 @@ def next_update(self, interval, states):
 
 # functions to configure and run the process
 def test_tellurium_process():
-    '''
-    Run a test simulation process. Loaded using SBML.
-
-    Returns:
-        The simulation output.
-    '''
-    sbml_model_path = 'vivarium_tellurium/library/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/Caravagna2010.xml'
-    # 1.) Declare the initial state, mirroring the ports structure. May be passed as a parsable argument.
+    sbml_model_path = 'vivarium_tellurium/models/Caravagna2010.xml'
+
+    # 1. Declare the initial state, mirroring the ports structure. May be passed as a parsable argument.
     initial_state = {
         'internal': {
             'A': 0.0
@@ -101,22 +86,21 @@ def test_tellurium_process():
         },
     }
 
-    # 2.) Create the simulation run parameters for the simulator
+    # 2. Create the simulation run parameters for the simulator
     config = {
         'sbml_model_path': sbml_model_path,
-        'parameter1': 4.0,
-    } 
+    }
 
-    # 3.) Initialize the process by passing in a config dict
+    # 3. Initialize the process by passing in a config dict
     template_process = TelluriumProcess(config)
 
-    # 4.) Get the ports for the process
+    # 4. Get the ports for the process
     template_process_ports = template_process.ports_schema()
 
-    # 4a.) view the ports:
+    # 4a. view the ports:
     print(f'PORTS FOR {pp(template_process)}: {pp(template_process_ports)}')
 
-    #5.) Feed the Simulator Process instance you just created to the vivarium Engine
+    # 5. Feed the Simulator Process instance you just created to the vivarium Engine
     sim = Engine(
         processes={
             'template': template_process,
@@ -129,33 +113,33 @@ def test_tellurium_process():
         initial_state=initial_state
     )
 
-    #6.) Call update with that sim object, which calls the next_update method in the implementation you created above using total_time
+    # 6. Call update with that sim object, which calls the next_update method in the implementation you created above using total_time
     total_time = 3
     sim.update(
         interval=total_time
     )
 
-    #7.) Get the data which is emitted from the sim object.
+    # 7. Get the data which is emitted from the sim object.
     data = sim.emitter.get_timeseries()
 
-    #7a.) Observe the data which is return from running the process:
+    # 7a. Observe the data which is return from running the process:
     print(f'RESULTS: {pp(data)}')
     return data
 
 
 def test_load_from_antimony():
-    # 1.) Adding an antimony string to your config dict will allow for "antimony mode" to be turned on.
+    # 1. Adding an antimony string to your config dict will allow for "antimony mode" to be turned on.
     config = {
         'antimony_string': 'S1 -> S2; k1*S1'
     }
 
-    # 2.) Initialize the process by passing in a config dict
+    # 2. Initialize the process by passing in a config dict
     antimony_process = TelluriumProcess(config)
     print(antimony_process.simulator)
 
 
-# run module with python template/processes/template_process.py
+# run module with python vivarium_tellurium/processes/tellurium_process.py
 if __name__ == '__main__':
     test_tellurium_process()
-    test_load_from_antimony()
+    # test_load_from_antimony()