#!/usr/bin/env python3
import argparse
import os
import subprocess
from pathlib import Path
from importlib.resources import files
import configparser


# --- Core function ---
def innitialize_simulation_dir(directory: Path):
    os.chdir(directory)
    
    params = configparser.ConfigParser()
    params = params.read('params.ini')

    template_path = files("polyamorphism_optimization.templates") / f"topology_{params['model']}.top"
    TOPOLOGY = template_path.read_text()
    template_path = files("polyamorphism_optimization.templates") / "mdp_parameters.mdp"
    MDP_PARAMETERS = template_path.read_text()
    
    # Write files
    Path("mdp_parameters.mdp").write_text(MDP_PARAMETERS)
    Path("topology.top").write_text(TOPOLOGY)

    script_dir = Path(__file__).parent
    subprocess.run([script_dir / "create_emin.sh"], check=True)
    subprocess.run([script_dir / "create_annealing1.sh"], check=True)

    print(f"finished and simulation directory {directory} created and filled")
    for f in os.listdir(directory):
        print(f)

# --- CLI entry point ---
def main():
    parser = argparse.ArgumentParser(description="Create simulation input files.")
    parser.add_argument("-d", "--directory", default=".", help="Base directory")
    args = parser.parse_args()

    create_simulation_dir(Path(args.directory))

if __name__ == "__main__":
    main()