Albrja/mic-6483/Update log level (#663)

Albrja/mic-6483/Update log level

Update log level to info for step log message
- *Category*: Other
- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-6483

Author: albrja

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**3.5.5 - 10/14/25**
+
+  - Update simulation step log message to info level
+
 **3.5.4 - 10/8/25**
 
   - Sphinx nitpick typing.Union

docs/source/tutorials/boids.rst

@@ -195,6 +195,7 @@ we can set up our simulation with the following code:
    sim = InteractiveContext(
       components=[Population()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
    # Peek at the population table
@@ -210,6 +211,7 @@ we can set up our simulation with the following code:
    sim = InteractiveContext(
       components=[Population()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
 ::
@@ -316,6 +318,7 @@ Let's run the simulation with our new component and look again at the population
    sim = InteractiveContext(
       components=[Population(), Movement()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
    # Peek at the population table
@@ -330,16 +333,21 @@ Let's run the simulation with our new component and look again at the population
    sim = InteractiveContext(
       components=[Population(), Movement()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
-::
+   # Peek at the population table
+   print(sim.get_population().head()[["color", "x", "y", "vx", "vy"]])
+
+.. testoutput::
+
+     color           x           y        vx        vy
+   0   red  274.256447  907.889319 -0.396940  0.270696
+   1   red  388.784077   82.116094  0.392572 -1.693871
+   2   red  661.272905  303.481468 -0.102927  1.194465
+   3   red  758.825839  806.284468  0.709814  0.932636
+   4  blue  574.989313  159.504556 -1.487996  1.428098
 
-      tracked color entrance_time        vy        vx           x           y
-   0     True   red    2005-07-01 -1.492285 -1.546289  786.157545  686.064077
-   1     True  blue    2005-07-01  0.360843  1.662424  530.867936  545.621217
-   2     True   red    2005-07-01 -0.369045 -1.747372  779.830506  286.461394
-   3     True   red    2005-07-01 -1.479211  0.659691  373.141406  740.640070
-   4     True   red    2005-07-01  1.143885  0.258908   20.787001  878.792517
 
 Our population now has initial position and velocity!
 Now, we can take a step forward with ``sim.step()`` and "see" our boids' positions change,
@@ -361,18 +369,22 @@ but their velocity stay the same.
    sim = InteractiveContext(
       components=[Population(), Movement()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
    sim.step()
 
-::
+   # Peek at the population table
+   print(sim.get_population().head()[["color", "x", "y", "vx", "vy"]])
 
-      tracked color entrance_time        vy        vx           x           y
-   0     True   red    2005-07-01 -1.388859 -1.439121  784.718424  684.675217
-   1     True  blue    2005-07-01  0.360843  1.662424  532.530360  545.982060
-   2     True   red    2005-07-01 -0.369045 -1.747372  778.083134  286.092349
-   3     True   red    2005-07-01 -1.479211  0.659691  373.801097  739.160859
-   4     True   red    2005-07-01  1.143885  0.258908   21.045909  879.936402
+.. testoutput::
 
+     color           x           y        vx        vy
+   0   red  273.859507  908.160016 -0.396940  0.270696
+   1   red  389.176649   80.422223  0.392572 -1.693871
+   2   red  661.169977  304.675933 -0.102927  1.194465
+   3   red  759.535654  807.217104  0.709814  0.932636
+   4  blue  573.546355  160.889428 -1.442958  1.384873
+   
 
 Visualizing our population
 --------------------------
@@ -406,6 +418,7 @@ We can then visualize our flock with
    sim = InteractiveContext(
       components=[Population(), Movement()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
    plot_boids(sim, plot_velocity=True)
@@ -418,6 +431,7 @@ We can then visualize our flock with
    sim = InteractiveContext(
       components=[Population(), Movement()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
    plot_boids(sim, plot_velocity=True)
 
@@ -517,6 +531,7 @@ For a quick test of our swarming behavior, let's add in these forces and check i
    sim = InteractiveContext(
       components=[Population(), Movement(), Neighbors(), Separation(), Cohesion(), Alignment()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
    sim.take_steps(100)
@@ -531,6 +546,7 @@ For a quick test of our swarming behavior, let's add in these forces and check i
    sim = InteractiveContext(
       components=[Population(), Movement(), Neighbors(), Separation(), Cohesion(), Alignment()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
    sim.take_steps(100)
    plot_boids(sim, plot_velocity=True)
@@ -562,6 +578,7 @@ Then, try it out like so:
   sim = InteractiveContext(
       components=[Population(), Movement(), Neighbors(), Separation(), Cohesion(), Alignment()],
       configuration={'population': {'population_size': 500}},
+      logging_verbosity=0,
    )
 
   anim = plot_boids_animated(sim)

src/vivarium/examples/boids/movement.py

@@ -6,13 +6,14 @@
 from vivarium import Component
 from vivarium.framework.engine import Builder
 from vivarium.framework.population import SimulantData
+from vivarium.framework.resource.resource import Resource
 
 
 class Movement(Component):
     ##############
     # Properties #
     ##############
-    configuration_defaults = {
+    CONFIGURATION_DEFAULTS = {
         "field": {
             "width": 1000,
             "height": 1000,
@@ -22,7 +23,14 @@ class Movement(Component):
         },
     }
 
-    columns_created = ["x", "vx", "y", "vy"]
+    @property
+    def columns_created(self) -> list[str]:
+        return ["x", "y", "vx", "vy"]
+
+    @property
+    def initialization_requirements(self) -> list[str | Resource]:
+        return [self.randomness]
+
 
     #####################
     # Lifecycle methods #
@@ -34,6 +42,7 @@ def setup(self, builder: Builder) -> None:
         self.acceleration = builder.value.register_value_producer(
             "acceleration", source=self.base_acceleration
         )
+        self.randomness = builder.randomness.get_stream(self.name)
 
     ##################################
     # Pipeline sources and modifiers #
@@ -47,14 +56,13 @@ def base_acceleration(self, index: pd.Index[int]) -> pd.DataFrame:
     ########################
 
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
-        count = len(pop_data.index)
         # Start randomly distributed, with random velocities
         new_population = pd.DataFrame(
             {
-                "x": self.config.field.width * np.random.random(count),
-                "y": self.config.field.height * np.random.random(count),
-                "vx": ((2 * np.random.random(count)) - 1) * self.config.movement.max_speed,
-                "vy": ((2 * np.random.random(count)) - 1) * self.config.movement.max_speed,
+                "x": self.config.field.width * self.randomness.get_draw(pop_data.index, "x"),
+                "y": self.config.field.height * self.randomness.get_draw(pop_data.index, "y"),
+                "vx": ((2 * self.randomness.get_draw(pop_data.index, "vx")) - 1) * self.config.movement.max_speed,
+                "vy": ((2 * self.randomness.get_draw(pop_data.index, "vy")) - 1) * self.config.movement.max_speed,
             },
             index=pop_data.index,
         )

src/vivarium/examples/boids/population.py

@@ -4,25 +4,34 @@
 from vivarium import Component
 from vivarium.framework.engine import Builder
 from vivarium.framework.population import SimulantData
+from vivarium.framework.resource.resource import Resource
 
 
 class Population(Component):
     ##############
     # Properties #
     ##############
-    configuration_defaults = {
+    CONFIGURATION_DEFAULTS = {
         "population": {
             "colors": ["red", "blue"],
         }
     }
-    columns_created = ["color", "entrance_time"]
+
+    @property
+    def columns_created(self) -> list[str]:
+        return ["color", "entrance_time"]
+
+    @property
+    def initialization_requirements(self) -> list[str | Resource]:
+        return [self.randomness]
 
     #####################
     # Lifecycle methods #
     #####################
 
     def setup(self, builder: Builder) -> None:
         self.colors = builder.configuration.population.colors
+        self.randomness = builder.randomness.get_stream(self.name)
 
     ########################
     # Event-driven methods #
@@ -31,7 +40,7 @@ def setup(self, builder: Builder) -> None:
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         new_population = pd.DataFrame(
             {
-                "color": np.random.choice(self.colors, len(pop_data.index)),
+                "color": self.randomness.choice(pop_data.index, self.colors),
                 "entrance_time": pop_data.creation_time,
             },
             index=pop_data.index,

src/vivarium/framework/engine.py

@@ -281,7 +281,7 @@ def initialize_simulants(self) -> None:
         self._clock.step_forward(self.get_population().index)
 
     def step(self) -> None:
-        self._logger.debug(self.current_time)
+        self._logger.info(self.current_time)
         for event in self.time_step_events:
             self._logger.debug(f"Event: {event}")
             self._lifecycle.set_state(event)