async default for sweep script

Author: codegithubka

.gitignore

@@ -8,4 +8,5 @@ results/
 # Jupyter Notebook checkpoints
 .ipynb_checkpoints/
 # Data files
-data/
+data/
+.pytest_cache/

docs/kimon_prompts.md

@@ -20,6 +20,8 @@
 
 1. Create a comprehensive testing suite for the CA and PP classes. Test initialization, async update changes, synchronous update changes, prey growth in isolation behavior, predator starvation, parameter evolution and long run dynamics. Also make sur ethe test_viz mehtod works as desired
 
+---
+
 ### Parameter Sweep and PP Class Analysis
 
 2. Create a skeletal version of a .py script that will be subimtted into Snellius for parameter analysis. The purpose of this script should be to identify power law distribution with the consideration of finite size scaling, the hydra effect, and suitable parameter configurtaions for time series analysis for model evolution. Compare the non-evo to the evo model.
@@ -31,3 +33,5 @@
 
 5. Create a minimal bash script for Snellius. Use the rome configiuration.
 
+6. Fix predator-prey analysis script so that the hydra effect focuses on the prey hydra effect as a result of the increasing prey death rate.
+

models/mean_field.py

@@ -182,10 +182,6 @@ def sweep_death_rate(
             "net_growth": self.birth - d_r_values,
         }
 
-
-# FIXME: Add plotting utilities
-
-
 if __name__ == "__main__":
     print("Mean-Field Model Module")
     mf = MeanFieldModel()

pp_analysis.py

@@ -110,7 +110,8 @@ class Config:
     # Parallel settings
     n_jobs: int = -1  # -1 = all available cores
 
-    synchronous: bool = True  # Use synchronous/async updates
+    # Update mode (False = asynchronous/random-sequential, matches Gillespie)
+    synchronous: bool = False
 
     def get_prey_births(self) -> np.ndarray:
         return np.linspace(self.prey_birth_min, self.prey_birth_max, self.n_prey_birth)
@@ -921,10 +922,10 @@ def main():
     )
 
     parser.add_argument(
-        "--async",
-        action="store_false",
+        "--sync",
+        action="store_true",
         dest="synchronous",
-        help="Run simulation in asynchronous (random-sequential) mode"
+        help="Run simulation in synchronous mode (default is asynchronous)"
     )
 
     args = parser.parse_args()
@@ -957,7 +958,7 @@ def main():
     logger.info(f"Mode: {args.mode}")
     logger.info(f"Output: {output_dir}")
     logger.info(f"Cores: {cfg.n_jobs}")
-    logger.info(f"Update mode: {'synchronous' if cfg.synchronous else 'asynchronous'}")
+    logger.info(f"Update rule: {'synchronous' if cfg.synchronous else 'asynchronous (random-sequential)'}")
     logger.info(f"Fixed predator_death: {cfg.predator_death}")
     logger.info(f"Evolving: prey_death (SD={cfg.evolve_sd}, bounds=[{cfg.evolve_min}, {cfg.evolve_max}])")