better aggregations and updating on every step now, instead of just J…

…OTR step, which is obviously a poor choice as evidenced by my comment lol

vegetation/patch/model.py

@@ -123,7 +123,7 @@ def step(self):
             )
 
         # Update underlying patch
-        intersecting_cell.update_occupancy(self)
+        intersecting_cell.add_agent_link(self)
 
         # Disperse
         if self.life_stage == LifeStage.BREEDING:
@@ -264,10 +264,6 @@ def update_metrics(self):
         mean_age = self.agents.select(agent_type=JoshuaTreeAgent).agg("age", np.mean)
         self.mean_age = mean_age
 
-        # Number of agents (JoshuaTreeAgent)
-        n_agents = len(self.agents.select(agent_type=JoshuaTreeAgent))
-        self.n_agents = n_agents
-
         # Number of agents by life stage
         count_dict = (
             self.agents.select(agent_type=JoshuaTreeAgent).groupby("life_stage").count()
@@ -277,6 +273,11 @@ def update_metrics(self):
         self.n_juveniles = count_dict.get(LifeStage.JUVENILE, 0)
         self.n_adults = count_dict.get(LifeStage.ADULT, 0)
         self.n_breeding = count_dict.get(LifeStage.BREEDING, 0)
+        self.n_dead = count_dict.get(LifeStage.DEAD, 0)
+
+        # Number of agents (JoshuaTreeAgent)
+        n_agents = len(self.agents.select(agent_type=JoshuaTreeAgent))
+        self.n_agents = n_agents - self.n_dead
 
         # Number of refugia cells occupied by JoshuaTreeAgents
         count_dict = (
@@ -289,7 +290,7 @@ def update_metrics(self):
 
     def step(self):
         # Print timestep header
-        timestep_str = f"# {STD_INDENT*0}🕰️ Time passes. It is the year {self.steps} #"
+        timestep_str = f"# {STD_INDENT*0}🕰️  Time passes. It is the year {self.steps}. #"
         nchar_timestep_str = len(timestep_str)
         print("#" * (nchar_timestep_str - 1))
         print(timestep_str)

vegetation/patch/space.py

@@ -12,6 +12,8 @@
 import logging
 import time
 
+from config.stages import LifeStage
+
 # from patch.model import JoshuaTreeAgent
 # import rioxarray as rxr
 
@@ -47,15 +49,17 @@ def __init__(
 
     def step(self):
         # Right now, this cell is being updated by the JOTR agent step, but it probably shouldn't be
-        # self.update_occupancy()
+        self.update_occupancy()
         pass
+
+    def update_occupancy(self):
+            # Very clunky way to exclude dead agents
+            alive_jotr_agents = [agent for agent in self.jotr_agents if agent.life_stage != LifeStage.DEAD]
+            self.occupied_by_jotr_agents = True if len(alive_jotr_agents) > 0 else False
 
-
-    def update_occupancy(self, jotr_agent):
+    def add_agent_link(self, jotr_agent):
         if jotr_agent.life_stage and jotr_agent not in self.jotr_agents:
             self.jotr_agents.append(jotr_agent)
-            self.occupied_by_jotr_agents = True if len(self.jotr_agents) > 0 else False
-
 
 class StudyArea(mg.GeoSpace):
     def __init__(self, bounds, epsg, model):