Move executable code in separate scripts and add argparse option for …

.gitignore

@@ -159,3 +159,4 @@ profiler_stats
 .vscode
 .pylintrc
 myvenv/
+test.ipynb

README.md

@@ -29,15 +29,15 @@ pip install -e .
 Use the following command :
 
 ```bash
-python3 vivarium/simulator/grpc_server/simulator_server.py
+python3 scripts/run_server.py
 ```
 
 ### Interact with it from a web interface
 
 And launch the web interface from another terminal :
 
 ```bash
-panel serve vivarium/interface/panel_app.py --autoreload
+panel serve scrits/run_interface.py --autoreload
 ```
 
 Once this command will have completed, it will output a URL looking like `http://localhost:5006/panel_app`, that you can open in your browser.

scripts/run_interface.py

@@ -0,0 +1,5 @@
+from vivarium.interface.panel_app import WindowManager
+
+# Serve the app
+wm = WindowManager()
+wm.app.servable(title="Vivarium")

scripts/run_server.py

@@ -0,0 +1,69 @@
+import logging
+import argparse
+
+import numpy as np
+
+import vivarium.simulator.behaviors as behaviors
+from vivarium.controllers.config import SimulatorConfig, AgentConfig, ObjectConfig
+from vivarium.simulator.sim_computation import StateType
+from vivarium.simulator.simulator import Simulator
+from vivarium.simulator.sim_computation import dynamics_rigid
+from vivarium.controllers.converters import set_state_from_config_dict
+from vivarium.simulator.grpc_server.simulator_server import serve
+
+lg = logging.getLogger(__name__)
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Simulator Configuration')
+    parser.add_argument('--box_size', type=float, default=100.0, help='Size of the simulation box')
+    parser.add_argument('--n_agents', type=int, default=10, help='Number of agents')
+    parser.add_argument('--n_objects', type=int, default=2, help='Number of objects')
+    parser.add_argument('--num_steps-lax', type=int, default=4, help='Number of lax steps per loop')
+    parser.add_argument('--dt', type=float, default=0.1, help='Time step size')
+    parser.add_argument('--freq', type=float, default=40.0, help='Frequency parameter')
+    parser.add_argument('--neighbor_radius', type=float, default=100.0, help='Radius for neighbor calculations')
+    # By default jit compile the code and use normal python loops
+    parser.add_argument('--to_jit', action='store_false', help='Whether to use JIT compilation')
+    parser.add_argument('--use_fori_loop', action='store_true', help='Whether to use fori loop')
+    parser.add_argument('--log_level', type=str, default='INFO', help='Logging level')
+
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+    args = parse_args()
+
+    logging.basicConfig(level=args.log_level.upper())
+
+    simulator_config = SimulatorConfig(
+        box_size=args.box_size,
+        n_agents=args.n_agents,
+        n_objects=args.n_objects,
+        num_steps_lax=args.num_steps_lax,
+        dt=args.dt,
+        freq=args.freq,
+        neighbor_radius=args.neighbor_radius,
+        to_jit=args.to_jit,
+        use_fori_loop=args.use_fori_loop
+    )
+
+    agent_configs = [AgentConfig(idx=i,
+                                 x_position=np.random.rand() * simulator_config.box_size,
+                                 y_position=np.random.rand() * simulator_config.box_size,
+                                 orientation=np.random.rand() * 2. * np.pi)
+                     for i in range(simulator_config.n_agents)]
+
+    object_configs = [ObjectConfig(idx=simulator_config.n_agents + i,
+                                   x_position=np.random.rand() * simulator_config.box_size,
+                                   y_position=np.random.rand() * simulator_config.box_size,
+                                   orientation=np.random.rand() * 2. * np.pi)
+                      for i in range(simulator_config.n_objects)]
+
+    state = set_state_from_config_dict({StateType.AGENT: agent_configs,
+                                        StateType.OBJECT: object_configs,
+                                        StateType.SIMULATOR: [simulator_config]
+                                        })
+
+    simulator = Simulator(state, behaviors.behavior_bank, dynamics_rigid)
+    lg.info('Simulator server started')
+    serve(simulator)

scripts/run_simulation.py

@@ -0,0 +1,82 @@
+import argparse
+import logging
+
+import numpy as np
+
+from vivarium.simulator import behaviors
+from vivarium.simulator.sim_computation import dynamics_rigid, StateType
+from vivarium.controllers.config import AgentConfig, ObjectConfig, SimulatorConfig
+from vivarium.controllers import converters
+from vivarium.simulator.simulator import Simulator
+
+lg = logging.getLogger(__name__)
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Simulator Configuration')
+    # Experiment run arguments
+    parser.add_argument('--num_loops', type=int, default=10, help='Number of simulation loops')
+    # Simulator config arguments
+    parser.add_argument('--box_size', type=float, default=100.0, help='Size of the simulation box')
+    parser.add_argument('--n_agents', type=int, default=10, help='Number of agents')
+    parser.add_argument('--n_objects', type=int, default=2, help='Number of objects')
+    parser.add_argument('--num_steps_lax', type=int, default=4, help='Number of lax steps per loop')
+    parser.add_argument('--dt', type=float, default=0.1, help='Time step size')
+    parser.add_argument('--freq', type=float, default=40.0, help='Frequency parameter')
+    parser.add_argument('--neighbor_radius', type=float, default=100.0, help='Radius for neighbor calculations')
+    # By default jit compile the code and use normal python loops
+    parser.add_argument('--to_jit', action='store_false', help='Whether to use JIT compilation')
+    parser.add_argument('--use_fori_loop', action='store_true', help='Whether to use fori loop')
+    parser.add_argument('--log_level', type=str, default='INFO', help='Logging level')
+
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    args = parse_args()
+
+    logging.basicConfig(level=args.log_level.upper())
+
+    simulator_config = SimulatorConfig(
+        box_size=args.box_size,
+        n_agents=args.n_agents,
+        n_objects=args.n_objects,
+        num_steps_lax=args.num_steps_lax,
+        dt=args.dt,
+        freq=args.freq,
+        neighbor_radius=args.neighbor_radius,
+        to_jit=args.to_jit,
+        use_fori_loop=args.use_fori_loop
+    )
+
+    agent_configs = [
+        AgentConfig(idx=i,
+                    x_position=np.random.rand() * simulator_config.box_size,
+                    y_position=np.random.rand() * simulator_config.box_size,
+                    orientation=np.random.rand() * 2. * np.pi)
+        for i in range(simulator_config.n_agents)
+        ]
+
+    object_configs = [
+        ObjectConfig(idx=simulator_config.n_agents + i,
+                    x_position=np.random.rand() * simulator_config.box_size,
+                    y_position=np.random.rand() * simulator_config.box_size,
+                    orientation=np.random.rand() * 2. * np.pi)
+        for i in range(simulator_config.n_objects)
+        ]
+
+    state = converters.set_state_from_config_dict(
+        {
+            StateType.AGENT: agent_configs,
+            StateType.OBJECT: object_configs,
+            StateType.SIMULATOR: [simulator_config]
+        }
+        )
+
+
+    simulator = Simulator(state, behaviors.behavior_bank, dynamics_rigid)
+
+    lg.info("Running simulation")
+
+    simulator.run(threaded=False, num_loops=10)
+
+    lg.info("Simulation complete")

vivarium/controllers/notebook_controller.py

@@ -7,7 +7,6 @@
 from vivarium.controllers.simulator_controller import SimulatorController
 from vivarium.simulator.sim_computation import StateType, EntityType
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 class Entity:

vivarium/controllers/panel_controller.py

@@ -10,7 +10,6 @@
 
 import logging
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 class PanelConfig(Config):

vivarium/controllers/simulator_controller.py

@@ -9,7 +9,6 @@
 from contextlib import contextmanager
 import logging
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 param.Dynamic.time_dependent = True

vivarium/interface/panel_app.py

@@ -279,6 +279,7 @@ def set_callbacks(self):
         self.update_switch.param.watch(self.update_switch_cb, "value")
         self.update_timestep.param.watch(self.update_timestep_cb, "value")
 
-# Serve the app
-wm = WindowManager()
-wm.app.servable(title="Vivarium")
+# if __name__ == "__main__":
+#     # Serve the app
+#     wm = WindowManager()
+#     wm.app.servable(title="Vivarium")

vivarium/simulator/behaviors.py

@@ -4,7 +4,6 @@
 from jax import vmap
 from functools import partial
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 linear_behavior_enum = Enum('matrices', ['FEAR', 'AGGRESSION', 'LOVE', 'SHY'])

vivarium/simulator/grpc_server/simulator_server.py

@@ -20,7 +20,6 @@
 from vivarium.simulator.grpc_server.converters import state_to_proto, nve_state_to_proto, agent_state_to_proto, object_state_to_proto
 from vivarium.controllers.converters import set_state_from_config_dict
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 Empty = simulator_pb2.google_dot_protobuf_dot_empty__pb2.Empty

vivarium/simulator/simulator.py

@@ -18,7 +18,6 @@
 import math
 import logging
 
-logging.basicConfig(level=logging.INFO)
 lg = logging.getLogger(__name__)
 
 class Simulator:
@@ -181,31 +180,3 @@ def get_change_time(self):
 
     def get_state(self):
         return self.state
-
-
-if __name__ == "__main__":
-
-    simulator_config = SimulatorConfig(to_jit=True)
-
-    agent_configs = [AgentConfig(idx=i,
-                                 x_position=np.random.rand() * simulator_config.box_size,
-                                 y_position=np.random.rand() * simulator_config.box_size,
-                                 orientation=np.random.rand() * 2. * np.pi)
-                     for i in range(simulator_config.n_agents)]
-
-    object_configs = [ObjectConfig(idx=simulator_config.n_agents + i,
-                                   x_position=np.random.rand() * simulator_config.box_size,
-                                   y_position=np.random.rand() * simulator_config.box_size,
-                                   orientation=np.random.rand() * 2. * np.pi)
-                      for i in range(simulator_config.n_objects)]
-
-    state = converters.set_state_from_config_dict({StateType.AGENT: agent_configs,
-                                                   StateType.OBJECT: object_configs,
-                                                   StateType.SIMULATOR: [simulator_config]
-                                                   })
-
-    simulator = Simulator(state, behaviors.behavior_bank, dynamics_rigid)
-
-    simulator.run(threaded=False, num_loops=10)
-
-