import os
import re
import argparse

# Natural sort
def natural_key(string_):
    return [int(s) if s.isdigit() else s for s in re.split(r'(\d+)', string_)]


# Return absolute path from relative or absolute path
def abs_path(path):
    abs_path = os.path.abspath(path)
    return abs_path


# Sanitize user input paths
def san_path(path):
    san_path = os.path.normpath(path)
    return san_path


# Argument parser for run_simulations.py
def sim_parser(defaults):
    # Use default settings from run_simulation.py to generate argument parser
    parser = argparse.ArgumentParser()
    for _arg, _val in defaults.items():
            parser.add_argument(f'--{_arg}', type=type(_val[0]), default=_val[0], help=_val[1])
    args_dict = vars(parser.parse_args())
    return args_dict


# Argument parser for run_analysis.py
def analysis_parser():
    parser = argparse.ArgumentParser()
    parser.add_argument('--steps', type=int,
                    help='Number of timesteps to run the simulation')
    parser.add_argument('--jobs_path', type=str, nargs='+', action='append',
                    help='Directory path containing the jobs to be run')
    parser.add_argument('--namd_params', type=str,
                    help='Optional parameters to send to namd')
    parser.add_argument('--ffs_path', type=str,
                    help='Location of the forcefield files')
    parser.add_argument('--namd2_bin', type=str,
                    help='Location of the namd2 executable')
    args = parser.parse_args()
    return args