hacky trackign of agents at patch level, will probably break or blow …

…up but related to previous issues with raster layer cell not having geometry yet

.github/workflows/todos_to_issues.yml

@@ -0,0 +1,30 @@
+### NOTE: Disabled for now, since we are not paying for the MongoDB Atlas cluster -
+### probably should just self-host it but not really necessary at the moment for just this repo
+
+name: "Run TODO to Issue"
+on: ["push"]
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: "actions/checkout@v4"
+      - name: "TODO to Issue"
+        uses: "alstr/todo-to-issue-action@v5"
+        with:
+          INSERT_ISSUE_URLS: "true"
+          CLOSE_ISSUES: "true"
+
+      - name: Set Git user
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Commit and Push Changes
+        run: |
+          git add -A
+          if [[ `git status --porcelain` ]]; then
+            git commit -m "Automatically added GitHub issue links to TODOs"
+            git push
+          else
+            echo "No changes to commit"
+          fi

vegetation/config/transitions.py

@@ -27,4 +27,4 @@ def get_jotr_survival_rate(life_stage, aridity, nurse_indicator):
     if nurse_indicator:
         rate = rate + 0.2
 
-    return rate
+    return rate

vegetation/patch/model.py

@@ -26,6 +26,7 @@ def __init__(self, model, geometry, crs, age=None):
         )
 
         self.age = age
+        self.life_stage = None
 
         pos = (np.float64(geometry.x), np.float64(geometry.y))
         self._pos = pos
@@ -51,6 +52,9 @@ def __init__(self, model, geometry, crs, age=None):
 
     def step(self):
 
+        if self.life_stage == 'dead':
+            return
+
         intersecting_cell_filter = self.model.space.raster_layer.iter_neighbors(
             self.indices,
             moore=False,
@@ -94,11 +98,18 @@ def step(self):
         self.age += 1
         self._update_life_stage()
 
+        # Update underlying patch
+        intersecting_cell.update_occupancy(self)
+
         # Disperse
         if self.life_stage == 'breeding':
             self.disperse_seeds()
 
     def _update_life_stage(self):
+
+        if self.life_stage == 'dead':
+            return
+
         age = self.age if self.age else 0
         if age == 0:
             life_stage = 'seed'
@@ -141,57 +152,42 @@ def __init__(self, bounds, export_data=False, num_steps=20, epsg=4326):
         self.agents.select(agent_type=JoshuaTreeAgent).do('_update_life_stage')
 
         self.space.add_agents(agents)
+        self.update_metrics()
 
         self.datacollector = mesa.DataCollector(
             {
-                "Mean Age": self.mean_age,
-                "N Agents": self.n_agents,
-                "N Seeds": self.n_seeds,
-                "N Seedlings": self.n_seedlings,
-                "N Juveniles": self.n_juveniles,
-                "N Adults": self.n_adults,
-                "N Breeding": self.n_breeding
+                "Mean Age": 'mean_age',
+                "N Agents": 'n_agents',
+                "N Seeds": 'n_seeds',
+                "N Seedlings": 'n_seedlings',
+                "N Juveniles": 'n_juveniles',
+                "N Adults": 'n_adults',
+                "N Breeding": 'n_breeding'
             }
         )
 
-    @property
-    def mean_age(self):
-        return self.agents.select(agent_type=JoshuaTreeAgent) \
+    # @property
+    def update_metrics(self):
+        # Mean age
+        mean_age = self.agents.select(agent_type=JoshuaTreeAgent) \
             .agg('age', np.mean)
+        self.mean_age = mean_age
 
-    @property
-    def n_agents(self):
-        return len(self.agents.select(agent_type=JoshuaTreeAgent))
+        # Number of agents (JoshuaTreeAgent)
+        n_agents = len(self.agents.select(agent_type=JoshuaTreeAgent))
+        self.n_agents = n_agents
 
-    @property
-    def n_seeds(self):
+        # Number of agents by life stage
         count_dict = self.agents.select(agent_type=JoshuaTreeAgent) \
             .groupby('life_stage').count()
-        return count_dict['seed'] if 'seed' in count_dict else 0
-
-    @property
-    def n_seedlings(self):
-        count_dict = self.agents.select(agent_type=JoshuaTreeAgent) \
-            .groupby('life_stage').count()
-        return count_dict['seedling'] if 'seedling' in count_dict else 0
-
-    @property
-    def n_juveniles(self):
-        count_dict = self.agents.select(agent_type=JoshuaTreeAgent) \
-            .groupby('life_stage').count()
-        return count_dict['juvenile'] if 'juvenile' in count_dict else 0
-
-    @property
-    def n_adults(self):
-        count_dict = self.agents.select(agent_type=JoshuaTreeAgent) \
-            .groupby('life_stage').count()
-        return count_dict['adult'] if 'adult' in count_dict else 0
-
-    @property
-    def n_breeding(self):
-        count_dict = self.agents.select(agent_type=JoshuaTreeAgent) \
-            .groupby('life_stage').count()
-        return count_dict['breeding'] if 'breeding' in count_dict else 0
+        self.n_seeds = count_dict.get('seed', 0)
+        self.n_seedlings = count_dict.get('seedling', 0)
+        self.n_juveniles = count_dict.get('juvenile', 0)
+        self.n_adults = count_dict.get('adult', 0)
+        self.n_breeding = count_dict.get('breeding', 0)
 
     def step(self):
         self.agents.shuffle_do("step")
+        self.update_metrics()
+
+        self.datacollector.collect(self)

vegetation/patch/space.py

@@ -11,6 +11,7 @@
 import hashlib
 import logging
 import time
+# from patch.model import JoshuaTreeAgent
 # import rioxarray as rxr
 
 DEM_STAC_PATH = "https://planetarycomputer.microsoft.com/api/stac/v1/"
@@ -30,10 +31,27 @@ def __init__(
         super().__init__(model, pos, indices)
         self.elevation = None
         self.aridity = None
+        self.joshua_tree_occupancy = 0
+
+
+        ## TODO: Improve patch level tracking of JOTR agents
+        ## For now, this is somewhat of a hack to track which agents are present within a patch cell
+        ## This is something I suspect is an offshoot of my question posed to the mesa-geo team
+        ## (https://github.com/projectmesa/mesa-geo/issues/267), where the cell does not have a geometry
+        ## and thus I can't use the various geometry based intersection methods to find agents. My guess 
+        ## is that this will either not work or be very slow, but itll get us started
+        self.joshua_tree_agents = []
 
     def step(self):
         pass
 
+    def update_occupancy(self, jotr_agent):
+        if jotr_agent.life_stage and jotr_agent.life_stage != 'dead':
+            self.joshua_tree_agents.append(jotr_agent)
+            if jotr_agent not in self.joshua_tree_agents:
+                self.model.joshua_tree_agents.append(jotr_agent.unique_id)
+                self.joshua_tree_occupancy += 1
+
 
 class StudyArea(mg.GeoSpace):
     def __init__(self, bounds, epsg, model):
@@ -176,4 +194,4 @@ def is_at_boundary(self, row_idx, col_idx):
             or row_idx == self.raster_layer.height
             or col_idx == 0
             or col_idx == self.raster_layer.width
-        )
+        )