Extend simulation to run until some minimal budget is depleted.

biobalm/_sd_attractors/attractor_candidates.py

@@ -345,8 +345,9 @@ def compute_attractor_candidates(
 
         # Here, we gradually increase the iteration count while
         # the candidate set is being actively reduced. If the simulation
-        # cannot reduce any further states, we are done.
-        iterations = 1024
+        # cannot reduce any further states and exceeds the proposed budget,
+        # we are done.
+        iterations = 2 ** 10
         while len(candidate_states) > 0:
             if sd.config["debug"]:
                 print(
@@ -362,7 +363,7 @@ def compute_attractor_candidates(
                 simulation_seed=123,
             )
 
-            if len(reduced) == len(candidate_states):
+            if len(reduced) == len(candidate_states) and (iterations * len(candidate_states)) > sd.config["minimum_simulation_budget"]:
                 candidate_states = reduced
                 break
 

biobalm/succession_diagram.py

@@ -175,6 +175,7 @@ def default_config() -> SuccessionDiagramConfiguration:
             "pint_goal_size_limit": 8_192,
             "attractor_candidates_limit": 100_000,
             "retained_set_optimization_threshold": 1_000,
+            "minimum_simulation_budget": 1_000_000,
         }
 
     @staticmethod

biobalm/types.py

@@ -228,3 +228,15 @@ class SuccessionDiagramConfiguration(TypedDict):
     If there are more than this amount of attractor candidates, the attractor
     detection process will try to optimize the retained set using ASP (if enabled).
     """
+
+    minimum_simulation_budget: int
+    """
+    The minimum number of simulation steps that is guaranteed to be spent on eliminating
+    attractor candidate states.
+
+    Note that this is a budget that applies to all candidates collectively. So if the number
+    of candidates is larger, the number of steps per candidate is proportionally smaller. 
+    However, this budget only applies when simulation has not been able to make progress
+    in the recent round. That is, if simulation has actively eliminated some candidates in 
+    the recent round, it will still continue regardless of the budget limit.
+    """