minor code cleanup

tumor_tcell/composites/dendritic_agent.py

@@ -139,10 +139,13 @@ def generate_topology(self, config):
 # tests
 def test_dendritic_agent(
         total_time=1000,
-        agent_ids=['0'],
+        agent_ids=None,
         agent_timeline=None,
         initial_agent_state='PD1n',
 ):
+    """run a test on dendritic cell agents"""
+    if agent_ids is None:
+        agent_ids = ['0']
     composite = Composite()
     for agent_id in agent_ids:
         parameters = {'agent_id': agent_id}
@@ -191,6 +194,7 @@ def test_dendritic_agent(
 
 
 def run_agent(out_dir='out'):
+    """run one agent and plot results"""
     agent_ids = ['0', '1']
     agent_timeline = []
     data = test_dendritic_agent(

tumor_tcell/composites/t_cell_agent.py

@@ -147,10 +147,13 @@ def generate_topology(self, config):
 # tests
 def test_tcell_agent(
         total_time=1000,
-        agent_ids=['0'],
+        agent_ids=None,
         agent_timeline=None,
         initial_agent_state='PD1n',
 ):
+    """run a test on t cell agents"""
+    if agent_ids is None:
+        agent_ids = ['0']
     composite = Composite()
     for agent_id in agent_ids:
         parameters = {
@@ -217,7 +220,9 @@ def test_tcell_agent(
 
     return output
 
+
 def run_agent(out_dir='out'):
+    """run one agent and plot results"""
     agent_ids = ['0', '1']
     agent_timeline = [
         (500, {

tumor_tcell/composites/tumor_agent.py

@@ -147,10 +147,13 @@ def generate_topology(self, config):
 # tests
 def test_tumor_agent(
         total_time=1000,
-        agent_ids=['0'],
+        agent_ids=None,
         agent_timeline=None,
         initial_agent_state='PDL1n',
 ):
+    """run a test on tumor agents"""
+    if agent_ids is None:
+        agent_ids = ['0']
     composite = Composite()
     for agent_id in agent_ids:
         parameters = {
@@ -217,6 +220,7 @@ def test_tumor_agent(
 
 
 def run_agent(out_dir='out'):
+    """run one agent and plot results"""
     agent_ids = ['0', '1']
     agent_timeline = []
     data = test_tumor_agent(

tumor_tcell/processes/dendritic_cell.py

@@ -14,7 +14,7 @@
 from vivarium.library.units import units
 from vivarium.processes.timeline import TimelineProcess
 
-from tumor_tcell.processes.fields import DIFFUSION_RATES  # , CONCENTRATION_UNIT
+from tumor_tcell.processes.fields import DIFFUSION_RATES
 from tumor_tcell.processes.tumor import get_probability_timestep
 
 TIMESTEP = 60  # seconds
@@ -102,11 +102,6 @@ def ports_schema(self):
                 'cell_state_count': {
                     '_default': 0,
                     '_updater': 'accumulate'},  # counts how many total cell in a given time. Might not be needed.
-                # 'lymph_node_timer': {
-                #     # counts how long in lymph node, high value increases chance of migration back to tumor
-                #     '_default': 0,  # TODO -- does the LN time this, or do the cells?
-                #     '_emit': True,
-                #     '_updater': 'accumulate'},
             },
             'boundary': {
                 'cell_type': {

tumor_tcell/processes/lymph_node.py

@@ -7,7 +7,6 @@
 from vivarium.core.process import Process
 from vivarium.core.engine import pp, Engine
 from tumor_tcell.processes.t_cell import get_probability_timestep, TIMESTEP
-from vivarium.library.units import remove_units
 from tumor_tcell.library.location import random_location, DEFAULT_BOUNDS
 from tumor_tcell.processes.local_field import LENGTH_UNIT
 from tumor_tcell.processes.neighbors import DEFAULT_MASS_UNIT, DEFAULT_VELOCITY_UNIT
@@ -258,6 +257,7 @@ def next_update(self, timestep, states):
 
 
 def test_lymph_node():
+    """run a test for moving cells between the lymph node and tumor environment"""
     simtime = 1000000
     init_state = {
         'cells': {

tumor_tcell/processes/neighbors.py

@@ -39,7 +39,6 @@
 # directories
 from tumor_tcell import PROCESS_OUT_DIR
 
-
 NAME = 'neighbors'
 DEFAULT_MASS_UNIT = units.ng
 DEFAULT_VELOCITY_UNIT = units.um / units.s
@@ -56,22 +55,26 @@ def daughter_locations(mother_location, state):
     mother_y = mother_location[1]
     locations = []
     for daughter in range(2):
-        location = [mother_x + random.gauss(0, 0.1)*mother_diameter, mother_y + random.gauss(0, 0.1)*mother_diameter]
+        location = [mother_x + random.gauss(0, 0.1) * mother_diameter,
+                    mother_y + random.gauss(0, 0.1) * mother_diameter]
         locations.append(location)
     return locations
 
+
 def sphere_volume_from_diameter(diameter):
     """Given a diameter for a sphere, return the volume"""
     radius = diameter / 2
-    volume = 4 / 3 * (PI * radius**3)
+    volume = 4 / 3 * (PI * radius ** 3)
     return volume
 
+
 def make_random_position(bounds):
     """Return a random position with the [x, y] bounds"""
     return [
         np.random.uniform(0, bound.magnitude) * bound.units
         for bound in bounds]
 
+
 def add_to_dict(dict, added):
     for k, v in added.items():
         if k in dict:
@@ -80,6 +83,7 @@ def add_to_dict(dict, added):
             dict[k] = v
     return dict
 
+
 def remove_from_dict(dict, removed):
     for k, v in removed.items():
         if k in dict:
@@ -145,7 +149,7 @@ def __init__(self, parameters=None):
             'bounds': [
                 b.to(self.length_unit).magnitude
                 for b in parameters['bounds']],
-            'physics_dt': min(timestep/10, 0.1)}
+            'physics_dt': min(timestep / 10, 0.1)}
         self.physics = Pymunk(multibody_config)
 
         # interactive plot for visualization
@@ -271,7 +275,8 @@ def bodies_remove_units(self, bodies):
         """
         for bodies_id, specs in bodies.items():
             # convert location
-            bodies[bodies_id]['boundary']['location'] = [loc.to(self.length_unit).magnitude for loc in specs['boundary']['location']]
+            bodies[bodies_id]['boundary']['location'] = [loc.to(self.length_unit).magnitude for loc in
+                                                         specs['boundary']['location']]
             # convert diameter
             bodies[bodies_id]['boundary']['diameter'] = specs['boundary']['diameter'].to(self.length_unit).magnitude
             # convert mass
@@ -359,16 +364,18 @@ def animate_frame(self, cells):
 
         xl = self.remove_length_units(bounds[0])
         yl = self.remove_length_units(bounds[1])
-        plt.xlim([-xl, 2*xl])
-        plt.ylim([-yl, 2*yl])
+        plt.xlim([-xl, 2 * xl])
+        plt.ylim([-yl, 2 * yl])
         plt.draw()
         plt.pause(0.01)
 
 
 # configs
 DEFAULT_DIAMETER = 7.5 * DEFAULT_LENGTH_UNIT
 
+
 def single_cell_config(config):
+    """return config dict for a single cell"""
     # cell dimensions
     diameter = DEFAULT_DIAMETER
     volume = sphere_volume_from_diameter(diameter)
@@ -402,6 +409,7 @@ def cell_body_config(config):
 class InvokeUpdate(object):
     def __init__(self, update):
         self.update = update
+
     def get(self, timeout=0):
         return self.update
 
@@ -411,6 +419,7 @@ def get(self, timeout=0):
     'bounds': DEFAULT_BOUNDS,
     'cell_ids': ['1', '2']}))
 
+
 def test_growth_division(config=default_gd_config, settings={}):
     initial_cells_state = config['cells']
 
@@ -426,7 +435,7 @@ def test_growth_division(config=default_gd_config, settings={}):
                 'diameter': {
                     '_updater': 'set',
                     '_divider': 'split'},
-                }})
+            }})
     experiment.state._apply_subschemas()
 
     # get initial cell state
@@ -489,6 +498,7 @@ def test_growth_division(config=default_gd_config, settings={}):
     experiment.end()
     return experiment.emitter.get_data()
 
+
 def multibody_neighbors_workflow(
         config={}, out_dir='out', filename='neighbors'):
     n_cells = 2
@@ -514,7 +524,6 @@ def multibody_neighbors_workflow(
     gd_data = test_growth_division(gd_config, settings)
 
 
-
 if __name__ == '__main__':
     out_dir = os.path.join(PROCESS_OUT_DIR, NAME)
     if not os.path.exists(out_dir):