Save States Patches + Misc.

ecoli/composites/ecoli_engine_process.py

@@ -10,8 +10,8 @@
 
 from vivarium.core.composer import Composer
 from vivarium.core.engine import Engine
-from vivarium.core.process import Process
 from vivarium.core.serialize import serialize_value, deserialize_value
+from vivarium.core.store import Store
 from vivarium.library.dict_utils import deep_merge
 
 from ecoli.experiments.ecoli_master_sim import (
@@ -103,6 +103,7 @@ def colony_save_states(engine, config):
             raise ValueError(
                 f'Config contains save_time ({time}) > total '
                 f'time ({config["total_time"]})')
+
     for i in range(len(config["save_times"])):
         if i == 0:
             time_to_next_save = config["save_times"][i]
@@ -113,13 +114,19 @@ def colony_save_states(engine, config):
         time_elapsed = config["save_times"][i]
 
         # Save the full state of the super-simulation
-        def not_a_process(value):
-            return not isinstance(value, Process)
-        state = engine.state.get_value(condition=not_a_process)
+        def save_cell_processes(value):
+            """
+            Excludes every process in the state except for the cell processes.
+            """
+            return not (isinstance(value, Store) and value.topology and not isinstance(value.value, EngineProcess))
+        state = engine.state.get_value(condition=save_cell_processes)
         state_to_save = copy.deepcopy(state)
 
         del state_to_save['agents']  # Replace 'agents' with agent states
         state_to_save['agents'] = {}
+
+        def not_a_process(value):
+            return not (isinstance(value, Store) and value.topology)
         for agent_id in state['agents']:
             # Get internal state from the EngineProcess sub-simulation
             cell_state = state['agents'][agent_id]['cell_process'][0].sim.state.get_value(condition=not_a_process)
@@ -160,9 +167,8 @@ def run_simulation():
                 },
             },
         )
-
         diffusion_schema = environment_composite.processes[
-            'diffusion'].get_schema()
+            'reaction_diffusion'].get_schema()
         multibody_schema = environment_composite.processes[
             'multibody'].get_schema()
         tunnel_out_schemas['fields_tunnel'] = diffusion_schema['fields']

ecoli/experiments/ecoli_master_sim.py

@@ -18,8 +18,8 @@
 from typing import Optional, Dict, Any
 
 from vivarium.core.engine import Engine
-from vivarium.core.process import Process
 from vivarium.core.serialize import deserialize_value
+from vivarium.core.store import Store
 from vivarium.library.dict_utils import deep_merge, deep_merge_combine_lists
 from vivarium.library.topology import assoc_path
 from ecoli.library.logging import write_json
@@ -199,6 +199,9 @@ def merge_config_dicts(d1, d2):
         for key in LIST_KEYS_TO_MERGE:
             d2.setdefault(key, [])
             d2[key].extend(d1.get(key, []))
+            if key == 'save_times':
+                d2[key] = list(set(d2[key]))  # Ensures there are no duplicates in d2
+                d2[key].sort()
         deep_merge(d1, d2)
 
     def update_from_json(self, path):
@@ -454,20 +457,22 @@ def save_states(self):
                 raise ValueError(
                     f'Config contains save_time ({time}) > total '
                     f'time ({self.total_time})')
+
         for i in range(len(self.save_times)):
             if i == 0:
                 time_to_next_save = self.save_times[i]
             else:
                 time_to_next_save = self.save_times[i] - self.save_times[i - 1]
             self.ecoli_experiment.update(time_to_next_save)
             time_elapsed = self.save_times[i]
-            state = self.ecoli_experiment.state.get_value()
+
+            def not_a_process(value):
+                return not (isinstance(value, Store) and value.topology)
+            state = self.ecoli_experiment.state.get_value(condition=not_a_process)
             if self.divide:
                 state = state['agents'][self.agent_id]
-            state_to_save = {key: state[key] for key in state.keys() if
-                             not (isinstance(state[key], tuple) and isinstance(state[key][0], Process))}
-            write_json('data/vivecoli_t' + str(time_elapsed) + '.json', state_to_save)
-            print('Finished saving the state at t = ' + str(time_elapsed) + '\n')
+            write_json('data/vivecoli_t' + str(time_elapsed) + '.json', state)
+            print('Finished saving the state at t = ' + str(time_elapsed))
         time_remaining = self.total_time - self.save_times[-1]
         if time_remaining:
             self.ecoli_experiment.update(time_remaining)

ecoli/processes/environment/multibody_physics.py

@@ -149,7 +149,7 @@ def __init__(self, parameters=None):
             'jitter_force': jitter_force,
             'bounds': remove_units(self.bounds),
             'barriers': self.mother_machine,
-            'physics_dt': self.parameters['time_step'] / 10,
+            'physics_dt': self.parameters['timestep'] / 10,
         }
         self.physics = PymunkMultibody(multibody_config)
 

requirements.txt

@@ -128,7 +128,7 @@ typing_extensions==4.0.1
 Unum==4.1.4
 vivarium-bioscrape==0.0.0.7
 vivarium-convenience==0.0.3
-vivarium-core==1.2.4
+vivarium-core==1.2.8
 vivarium-multibody==0.0.16
 wcwidth==0.2.5
 webencodings==0.5.1