Optimize

.gitignore

@@ -10,3 +10,4 @@ venv/
 .python-version
 __pycache__/
 dist/
+.ipynb_checkpoints/*

release.sh

@@ -23,13 +23,13 @@ if [ ! -z "$(git status --untracked-files=no --porcelain)" ]; then
     exit 1
 fi
 
-# Check that we are on master
-branch="$(git rev-parse --abbrev-ref HEAD)"
-if [ "$branch" != "master" ]; then
-    echo "You are on $branch but should be on master for releases."
-    echo "Aborting."
-    exit 1
-fi
+## Check that we are on master
+#branch="$(git rev-parse --abbrev-ref HEAD)"
+#if [ "$branch" != "master" ]; then
+#    echo "You are on $branch but should be on master for releases."
+#    echo "Aborting."
+#    exit 1
+#fi
 
 # Create and push git tag
 git tag -m "Version v$version" "v$version"

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name='tumor-tcell',
-    version='0.0.29',
+    version='0.0.46',
     packages=[
         'tumor_tcell',
         'tumor_tcell.composites',

tumor_tcell/composites/dendritic_agent.py

@@ -35,6 +35,7 @@
 class DendriticAgent(Composer):
     name = NAME
     defaults = {
+        'time_step': TIMESTEP,
         'reuse_processes': False,
         'boundary_path': ('boundary',),
         'agents_path': ('..', '..', 'agents',),
@@ -69,6 +70,7 @@ class DendriticAgent(Composer):
 
     def __init__(self, config):
         super().__init__(config)
+        self.config['dendritic_cell']['time_step'] = self.config['time_step']
         self.processes_initialized = False
 
     def initialize_processes(self, config):
@@ -137,10 +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}
@@ -189,6 +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

@@ -37,6 +37,7 @@ class TCellAgent(Composer):
 
     name = NAME
     defaults = {
+        'time_step': TIMESTEP,
         'reuse_processes': False,
         'boundary_path': ('boundary',),
         'agents_path': ('..', '..', 'agents',),
@@ -77,6 +78,7 @@ class TCellAgent(Composer):
 
     def __init__(self, config):
         super().__init__(config)
+        self.config['tcell']['time_step'] = self.config['time_step']
         self.processes_initialized = False
 
     def initialize_processes(self, config):
@@ -145,10 +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 = {
@@ -215,7 +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

@@ -22,7 +22,7 @@
 from vivarium.processes.meta_division import MetaDivision
 from vivarium.processes.remove import Remove
 from vivarium.processes.timeline import TimelineProcess
-from tumor_tcell.processes.tumor import TumorProcess, TIMESTEP
+from tumor_tcell.processes.tumor import TumorCellProcess, TIMESTEP
 from tumor_tcell.processes.local_field import LocalField
 
 # directories/libraries
@@ -36,6 +36,7 @@ class TumorAgent(Composer):
 
     name = NAME
     defaults = {
+        'time_step': TIMESTEP,
         'reuse_processes': False,
         'boundary_path': ('boundary',),
         'agents_path': ('..', '..', 'agents',),
@@ -73,14 +74,15 @@ class TumorAgent(Composer):
 
     def __init__(self, config):
         super().__init__(config)
+        self.config['tumor']['time_step'] = self.config['time_step']
         self.processes_initialized = False
 
     def initial_state(self, config=None):
-        process = TumorProcess()
+        process = TumorCellProcess()
         return process.initial_state(config)
 
     def initialize_processes(self, config):
-        self.tumor_process = TumorProcess(config['tumor'])
+        self.tumor_process = TumorCellProcess(config['tumor'])
         self.local_field = LocalField()
 
         if self.config['reuse_processes']:
@@ -145,10 +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 = {
@@ -215,6 +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/composites/tumor_microenvironment.py

@@ -40,6 +40,9 @@ class TumorMicroEnvironment(Composer):
     """
     name = NAME
     defaults = {
+        'tumor_env_id': 'tumor_environment',
+        'ln_id': 'lymph_node',
+        'in_transit_id': 'in_transit',
         'neighbors_multibody': {
             'name': 'neighbors_multibody',
             'bounds': DEFAULT_BOUNDS,
@@ -54,28 +57,44 @@ class TumorMicroEnvironment(Composer):
     def __init__(self, config=None):
         super().__init__(config)
 
-    def generate_processes(self, config):
+    def initial_state(self, config):
+        return {
+            config['tumor_env_id']: {},
+            config['ln_id']: {},
+            config['in_transit_id']: {},
+        }
 
+    def generate_processes(self, config):
         # initialize processes
         neighbors_multibody = Neighbors(config['neighbors_multibody'])
         diffusion_field = Fields(config['diffusion_field'])
 
         # make dictionary of processes
         return {
-            'neighbors_multibody': neighbors_multibody,
-            'diffusion_field': diffusion_field,
+            config['tumor_env_id']: {
+                'neighbors_multibody': neighbors_multibody,
+                'diffusion_field': diffusion_field,
+                'agents': {},
+            },
+            config['ln_id']: {'agents': {}},
+            config['in_transit_id']: {'agents': {}},
         }
 
     def generate_topology(self, config):
         return {
-            'neighbors_multibody': {
-                'cells': ('agents',)
-            },
-            'diffusion_field': {
-                'cells': ('agents',),
-                'fields': ('fields',),
-                'dimensions': ('dimensions',),
+            config['tumor_env_id']: {
+                'neighbors_multibody': {
+                    'cells': ('agents',)
+                },
+                'diffusion_field': {
+                    'cells': ('agents',),
+                    'fields': ('fields',),
+                    'dimensions': ('dimensions',),
+                },
+                'agents': {}
             },
+            config['ln_id']: {'agents': {}},
+            config['in_transit_id']: {'agents': {}},
         }
 
 
@@ -85,6 +104,7 @@ class TumorAndLymphNodeEnvironment(Composer):
     defaults = {
         'tumor_env_id': 'tumor_environment',
         'ln_id': 'lymph_node',
+        'in_transit_id': 'in_transit',
         'neighbors_multibody': {
             'name': 'neighbors_multibody',
             'bounds': DEFAULT_BOUNDS,
@@ -102,6 +122,13 @@ class TumorAndLymphNodeEnvironment(Composer):
     def __init__(self, config=None):
         super().__init__(config)
 
+    def initial_state(self, config):
+        return {
+            config['tumor_env_id']: {},
+            config['ln_id']: {},
+            config['in_transit_id']: {},
+        }
+
     def generate_processes(self, config):
         # initialize processes
         neighbors_multibody = Neighbors(config['neighbors_multibody'])
@@ -111,9 +138,12 @@ def generate_processes(self, config):
         # make dictionary of processes
         return {
             config['tumor_env_id']: {
+                'agents': {},
                 'neighbors_multibody': neighbors_multibody,
                 'diffusion_field': diffusion_field,
             },
+            config['ln_id']: {'agents': {}},
+            config['in_transit_id']: {'agents': {}},
             'lymph_node_transfer': lymph_node_transfer_process
         }
 
@@ -128,7 +158,10 @@ def generate_topology(self, config):
                     'fields': ('fields',),
                     'dimensions': ('dimensions',),
                 },
+                'agents': {},
             },
+            config['ln_id']: {'agents': {}},
+            config['in_transit_id']: {'agents': {}},
             'lymph_node_transfer': {
                 'cells': (config['tumor_env_id'],),
                 'lymph_node': (config['ln_id'],),
@@ -192,6 +225,7 @@ def make_neighbors_config(
 
     return config
 
+
 def single_agent_config(config):
     bounds = config.get('bounds', DEFAULT_BOUNDS)
     location = config.get('location')
@@ -206,13 +240,15 @@ def single_agent_config(config):
         'mass': 1339 * units.fg,
     }}
 
+
 def agent_body_config(config):
     agent_ids = config['agent_ids']
     agent_config = {
         agent_id: single_agent_config(config)
         for agent_id in agent_ids}
     return agent_config
 
+
 def test_microenvironment(
         n_agents=1,
         bounds=[25 * units.um, 25 * units.um],
@@ -221,7 +257,6 @@ def test_microenvironment(
         diffusion=1e-1,
         end_time=10
 ):
-
     # configure the compartment
     config = make_neighbors_config(
         bounds=bounds,
@@ -235,15 +270,16 @@ def test_microenvironment(
     initial_field = np.zeros((n_bins[0], n_bins[1]))
     initial_field[:, -1] = 100
     initial_state = {
-        'fields': {'IFNg': initial_field},
-        'agents': {}}
+        'tumor_environment': {
+            'fields': {'IFNg': initial_field},
+            'agents': {}}}
     if n_agents:
         agent_ids = [str(agent_id) for agent_id in range(n_agents)]
         body_config = {'agent_ids': agent_ids}
         if 'neighbors_multibody' in config and 'bounds' in config['neighbors_multibody']:
             body_config.update({'bounds': config['neighbors_multibody']['bounds']})
         initial_agents_state = agent_body_config(body_config)
-        initial_state.update({'agents': initial_agents_state})
+        initial_state['tumor_environment'].update({'agents': initial_agents_state})
 
     # configure experiment
     composite = compartment.generate()
@@ -256,7 +292,7 @@ def test_microenvironment(
     data = experiment.emitter.get_data_deserialized()
 
     # assert that the agent remains in the simulation until the end
-    assert len(data[end_time]['agents']) == n_agents
+    assert len(data[end_time]['tumor_environment']['agents']) == n_agents
     return data