import random
from scipy.stats import loguniform
import argparse
import numpy as np
from string import Template
import json
import os
import sys
from datetime import date
from datafed.CommandLib import API
import logging
from nufeb_tools import __version__
from pathlib import Path
from glob import glob



__author__ = "<NAME>"
__copyright__ = "<NAME>"
__license__ = "MIT"

_logger = logging.getLogger(__name__)

def parse_args(args):
    """Parse command line parameters

    Args:
        args (List[str]): command line parameters as list of strings
            (for example  ``["--help"]``).

    Returns:
        :obj:`argparse.Namespace`: command line parameters namespace
    """
    # arguments to modify the conditions of the simulation seeding
    parser = argparse.ArgumentParser(description='Create atom definition files')
    parser.add_argument('--n', dest='num', action='store',
                    default=1,
                    help='Create atom definition files for NUFEB with --n #files desired (default is 1)')
    parser.add_argument('--r', dest='reps', action='store',
                    default=1,
                    help='Number of replicates')
    parser.add_argument('--c',dest='culture_type',action='store',default='co',
                        help='Set culture conditions with --c (co-culture), --ax-c (cyano), --ax-e (e.coli)')
    parser.add_argument('--co2', dest='co2', action='store',
                    default=6.8e-1,
                    help='Set initial CO2 concentration (mM)')
    parser.add_argument('--d', dest='dims', action='store', type=str,
                    default='1e-4,1e-4,1e-5',
                    help='Set simulation box dimensions (m)')
    parser.add_argument('--t', dest='timesteps', action='store',
                    default=35000,
                    help='Number of timesteps to run')
    parser.add_argument('--suc', dest='sucrose', action='store',
                    default=1e-19,
                    help='Set initial sucrose concentration (mM)')
    parser.add_argument('--grid', dest='grid', action='store',
                    default=2,
                    help='Diffusion grid density (um/grid)')
    parser.add_argument('--mono', dest='monolayer', action='store',
                    default=True,
                    help='Set seed generation to monolayer of cells')
    parser.add_argument('--u', dest='user', action='store',
                    help='CADES/CNMS user ID')
    parser.add_argument('--datafed', dest='datafed', action = 'store', default=False,
                        help='DataFed Upload')
    parser.add_argument('--cells',dest='cells',action='store',default=None,
    help='Number of cyanobacteria and e.coli to initialize simulation with, `e.g., 100,100. ` Default is random number between 1 and 100.')
    parser.add_argument('--sucR',dest='SucRatio',action='store',default=None,
                    help='Set sucrose secretion ratio (0 to 1). Default is random.')   
    parser.add_argument('--iptg',dest='iptg',action='store',default=None,type=float,
                    help='Set IPTG induction for sucrose secretion (0 to 1). Default is random.') 
    parser.add_argument('--muecw',dest='mu_ecw',action='store',default=6.71e-5,type=float,
                    help='E. coli W maximum growth rate')  
    parser.add_argument('--mucya',dest='mu_cya',action='store',default=1.89e-5,type=float,
                    help='S. elongatus maximum growth rate')   
    parser.add_argument('--rhoecw',dest='rho_ecw',action='store',default=230,type=float,
        help='E. coli W cell density')  
    parser.add_argument('--rhocya',dest='rho_cya',action='store',default=370,type=float,
        help='S. elongatus cell density')  
    parser.add_argument('--ksuc',dest='ksuc',action='store',default=3.6,type=float,
        help='E. coli W Ksuc')  
    parser.add_argument('--maintecw',dest='maint_ecw',action='store',default=9.50e-7,type=float,
        help='E. coli W maintenance cost')  
    parser.add_argument('--mass',dest='mass_max',action='store',default=1.5e-11,type=float,
        help='Maximum biomass')  

    parser.add_argument('--vtk',dest='vtk',action='store',default=False,help='Output VTK files')
    parser.add_argument('--h5',dest='hdf5',action='store',default=True,help='Output HDF5 files')
    parser.add_argument('--lammps',dest='lammps',action='store',default=False,help='Output lammps files')
    parser.add_argument(
    "-v",
    "--verbose",
    dest="loglevel",
    help="set loglevel to INFO",
    action="store_const",
    const=logging.INFO,
)
    parser.add_argument(
    "-vv",
    "--very-verbose",
    dest="loglevel",
    help="set loglevel to DEBUG",
    action="store_const",
    const=logging.DEBUG,
)
    return parser.parse_args(args)
# TODO Change sucRatio to IPTG
def setup_logging(loglevel):
    """Setup basic logging

    Args:
      loglevel (int): minimum loglevel for emitting messages
    """
    logformat = "[%(asctime)s] %(levelname)s:%(name)s:%(message)s"
    logging.basicConfig(
        level=loglevel, stream=sys.stdout, format=logformat, datefmt="%Y-%m-%d %H:%M:%S"
    )

def clean():
    """Remove old NUFEB runs
    """
    if os.path.isdir('runs'):
        import shutil
        try:
            shutil.rmtree('runs')
        except OSError as e:
            print("Error: %s : %s" % ('runs', e.strerror))
    slurm_path = glob('*.slurm')
    if slurm_path:
        for file in slurm_path:
            os.remove(file)

def main(args):
    """Wrapper function to generate new NUFEB simulation conditions

    Args:
      args (List[str]): command line parameters as list of strings
          
    """
    args = parse_args(args)
    setup_logging(args.loglevel)
    _logger.info("Generating NUFEB simulation files")
    # maximum growth rates, mu
    #$mu_cyanos = round(0.06/3600,7)
    #mu_ecw = 2.7e-04 for 37C only
    #mu_ecw = 6.71e-5
    # molecular weights of co2 and sucrose for unit conversions
    CO2MW = 44.01
    SucMW = 342.3
    TEMPLATES_DIR = (Path(__file__).parent) / 'templates'
    # check for runs folder
    if not os.path.isdir('runs'):
        os.mkdir('runs')
    today = str(date.today())
    for n in range(1,int(args.num)+1):
        if args.iptg is not None:
            IPTG = float(args.iptg)
            SucRatio = IPTG
        else:
            IPTG = np.round(loguniform.rvs(1e-3, 1e0, size=1)[0],5)
            SucRatio = IPTG
        #if args.SucRatio is not None:
        #    SucRatio = float(args.SucRatio)

        SucPct = int(SucRatio*100)
        if args.culture_type == 'co':
            cell_types = ['cyano','ecw']
            if args.cells is not None:
                n_cyanos = int(args.cells.split(',')[0])
                n_ecw = int(args.cells.split(',')[1])
            else:
                n_cyanos = int(random.uniform(1,100))
                n_ecw = int(random.uniform(1,100))
            n_cells = n_cyanos + n_ecw
            cyGroup = 'group CYANO type 1'
            ecwGroup = 'group ECW type 2'
            cyDiv = f'fix d1 CYANO divide 100 v_EPSdens v_divDia1 {random.randint(1,1e6)}'
            ecwDiv = f'fix d2 ECW divide 100 v_EPSdens v_divDia2 {random.randint(1,1e6)}'
            masses = 'c_myMass[1]+c_myMass[2]'

        elif args.culture_type == 'ax-c':
            cell_types = ['cyano']
            if args.cells is not None:
                n_cyanos = int(args.cells.split(',')[0])
            else:
                n_cyanos = int(random.uniform(1,100))
            n_ecw = 0
            n_cells = n_cyanos
            cyGroup = 'group CYANO type 1'
            ecwGroup = ''
            cyDiv = f'fix d1 CYANO divide 100 v_EPSdens v_divDia1 {random.randint(1,1e6)}'
            ecwDiv = ''
            masses = 'c_myMass[1]'
        elif args.culture_type == 'ax-e':
            cell_types = ['ecw']
            if args.cells is not None:
                n_ecw = int(args.cells.split(',')[1])
            else:
                n_ecw = int(random.uniform(1,100))
            n_cyanos=0
            n_cells = n_ecw
            cyGroup = ''
            ecwGroup = 'group ECW type 1'
            cyDiv = ''
            ecwDiv = f'fix d2 ECW divide 100 v_EPSdens v_divDia2 {random.randint(1,1e6)}'
            masses = 'c_myMass[1]'
        RUN_DIR = Path(f'runs/Run_{n_cyanos}_{n_ecw}_{IPTG:.2e}_{args.reps}_{today}_{random.randint(1,1e6)}')
        if not os.path.isdir(RUN_DIR):
            os.mkdir(RUN_DIR)
        # TODO embed cell type into metadata file and generate cell type programmatically
        InitialConditions = {'cyano': {'StartingCells' : n_cyanos,'GrowthRate' : args.mu_cya,
            'min_size' : 1.37e-6, 'max_size' : 1.94e-6, 'Density' : args.rho_cya,
                'K_s' : {'sub' : 3.5e-4,'o2' : 2e-4, 'suc' : 1e-2,'co2' : 1.38e-4},
                'GrowthParams' : {'Yield' : 0.55,'Maintenance' : 0,'Decay' : 0}},
                'ecw': {'StartingCells' : n_ecw,'GrowthRate' : args.mu_ecw,
            'min_size' : 8.8e-7, 'max_size' : 1.39e-6, 'Density' : args.rho_ecw,
                'K_s' : {'sub' : 0,'o2' : 1e-3, 'suc' : args.ksuc,'co2' : 5e-2},
                'GrowthParams' : {'Yield' : 0.43,'Maintenance' : args.maint_ecw,'Decay' : 0}},
                'Nutrients' : {'Concentration' :  {'sub' : 1e-1,'o2' : 9e-3, 'suc' : float(args.sucrose)*SucMW*1e-3, 'co2' : float(args.co2)*CO2MW*1e-3},
                'State' : {'sub' : 'g','o2' : 'l', 'suc' : 'l', 'co2' : 'l'},
                'xbc' : {'sub' : 'nn','o2' : 'nn', 'suc' : 'nn', 'co2' : 'nn'},
                'ybc' : {'sub' : 'nn','o2' : 'nn', 'suc' : 'nn', 'co2' : 'nn'},
                'zbc' : {'sub' : 'nn','o2' : 'nd', 'suc' : 'nn', 'co2' : 'nd'}},
                'Diff_c' : {'sub' : 0,'o2' : 2.30e-9, 'suc' : 5.2e-10,'co2' : 1.9e-09},
                'Dimensions' : [float(x) for x in args.dims.split(',')],'SucRatio' : SucRatio,'Replicates' : int(args.reps)

                }
        grids = int(args.grid)
        while True:
            if InitialConditions["Dimensions"][0]*1e6 % grids == 0 and InitialConditions["Dimensions"][1]*1e6 % grids == 0 and InitialConditions["Dimensions"][2]*1e6 % grids == 0:
                Mesh = f'{int(InitialConditions["Dimensions"][0]*1e6/grids)} {int(InitialConditions["Dimensions"][1]*1e6/grids)} {int(InitialConditions["Dimensions"][2]*1e6/grids)}'
                break
            else:
                grids +=1

        NutesNum = len(InitialConditions['Nutrients']['Concentration'])
        for r in range(1,int(args.reps)+1):
            L = [' NUFEB Simulation\r\n\n',f'     {n_cells} atoms \n',
                f'     {len(cell_types)} atom types \n',f'     {NutesNum} nutrients \n\n',
                f'  0.0e-4   {InitialConditions["Dimensions"][0] :.2e}  xlo xhi \n',f'  0.0e-4   {InitialConditions["Dimensions"][1] :.2e}  ylo yhi \n',
                f'  0.0e-4   {InitialConditions["Dimensions"][2] :.2e}  zlo zhi \n\n', ' Atoms \n\n'
                ]

            j = 1
            for c, CellType in enumerate(cell_types,start=1):
                for i in range(j,InitialConditions[CellType]['StartingCells']+j):
                    size = random.uniform(InitialConditions[CellType]['min_size'],
                                        InitialConditions[CellType]['max_size'])
                    x = random.uniform(0+size,InitialConditions['Dimensions'][0]-size)
                    y = random.uniform(0+size,InitialConditions['Dimensions'][1]-size)
                    z = random.uniform(0+size,InitialConditions['Dimensions'][2]-size)
                    L.append(f'     %d {c} {size :.2e}  {InitialConditions[CellType]["Density"]} {x :.2e} {y :.2e} {z :.2e} {size :.2e} \n'% (i))
                    j += 1

            L.append('\n')
            L.append(' Nutrients \n\n')
            for i,nute in enumerate(InitialConditions['Nutrients']['Concentration'].keys()):
                L.append(f'     %d {nute} {InitialConditions["Nutrients"]["State"][nute]} {InitialConditions["Nutrients"]["xbc"][nute]} {InitialConditions["Nutrients"]["ybc"][nute]} {InitialConditions["Nutrients"]["zbc"][nute]} {InitialConditions["Nutrients"]["Concentration"][nute] :.2e} {InitialConditions["Nutrients"]["Concentration"][nute] :.2e} \n'% (i+1))

            L.append('\n')
            L.append(' Type Name \n\n')
            for c, CellType in enumerate(cell_types,start=1):
                L.append(f'     {c} {CellType}  \n')
            L.append('\n')
            L.append(' Diffusion Coeffs \n\n')
            for key in InitialConditions['Diff_c'].keys():
                L.append(f'     {key} {InitialConditions["Diff_c"][key]} \n')
            L.append('\n')
            L.append(' Growth Rate \n\n')
            for CellType in cell_types:
                L.append(f'     {CellType} {InitialConditions[CellType]["GrowthRate"]} \n')
            L.append('\n')
            L.append(' Ks \n\n')
            for CellType in cell_types:
                k = f'     {CellType}'
                for key in InitialConditions[CellType]['K_s'].keys():
                    k = k + ' ' + str(InitialConditions[CellType]['K_s'][key])
                k = k + f' \n'
                L.append(k)
            L.append('\n')
            for key in InitialConditions["cyano"]['GrowthParams'].keys():
                L.append(' ' + key + f' \n\n')
                for CellType in cell_types:
                    L.append(f'     {CellType} {InitialConditions[CellType]["GrowthParams"][key]} \n')
                L.append('\n')


            L.append('\n\n')

            #write atom definition file
            f= open(RUN_DIR / f"atom_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{r}_{today}.in","w+")
            f.writelines(L)

        #write initial conditions json file
        dumpfile = open(RUN_DIR / 'metadata.json','w')
        json.dump(InitialConditions, dumpfile, indent = 6)
        dumpfile.close()
        #write Inputscript
        #open the file


        if args.lammps ==True:
            lammps = 'dump    id all custom 100 output.lammmps id type diameter x y z'
        else: 
            lammps = ''
        if args.hdf5 == True:
            hdf5 = 'dump    traj all bio/hdf5 100 trajectory.h5 id type radius x y z con'
        else:
            hdf5 = ''
        if args.vtk == True:
            vtk = 'dump    du1 all vtk 100 atom_*.vtu id type diameter x y z'
            grid = 'dump    du2 all grid 100 grid_%_*.vti con'
            vtk_tarball = 'true'
        else:
            vtk = ''
            grid = ''
            vtk_tarball = 'false'
        filein = open( TEMPLATES_DIR / 'inputscript.txt' )
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'n' : n, 'SucRatio' : SucRatio, 'SucPct' : SucPct,
                                    'n_cyanos' : n_cyanos, 'n_ecw' : n_ecw,
                                    'Replicates' : args.reps,'IPTG' : f'{IPTG:.0e}','Timesteps' : args.timesteps,
                                    'date' : today,
                                    'CYANOGroup' : cyGroup,
                                    'ECWGroup' : ecwGroup,
                                    'Zheight' : InitialConditions["Dimensions"][2],
                                    'CYANODiv'  : cyDiv, 'ECWDiv' : ecwDiv,
                                    'GridMesh' : f'{int(InitialConditions["Dimensions"][0]*1e6/int(args.grid))} {int(InitialConditions["Dimensions"][1]*1e6/int(args.grid))} {int(InitialConditions["Dimensions"][2]*1e6/int(args.grid))}',
                                    'lammps' : lammps,
                                    'hdf5' : hdf5,
                                    'vtk' : vtk,
                                    'grid' : grid,
                                    'masses':masses,
                                    'mass_max':f'{args.mass_max:.2e}'
                                    })
        f= open(RUN_DIR / f"Inputscript_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{today}.lammps","w+")
        f.writelines(result)



        x = int(InitialConditions['Dimensions'][0]*1e6)
        y = int(InitialConditions['Dimensions'][1]*1e6)
        z = int(InitialConditions['Dimensions'][2]*1e6)
        if args.datafed is True or args.datafed == 'True':
        #create DataFed collection to hold the results
        # TODO actually make this work
            df_api = API()
            df_api.setContext('p/eng107')
            collectionName = f'NUFEB_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{today}_{x}_{y}_{z}'
            parent_collection = df_api.getAuthUser().split('/')[1]
            coll_msg = df_api.collectionCreate(collectionName,
                                            parent_id=parent_collection)
            global_coll_id = coll_msg[0].coll[0].id
        else:
            global_coll_id = None

        #write slurm script
        #open the file
        filein = open( TEMPLATES_DIR / 'slurm.txt' )
        
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'job' : f"NUFEB_{n}",
                                        'USER' : args.user,
                                        'VTK' : vtk_tarball})
        f= open(f"NUFEB_{today}.slurm","w+")
        f.writelines(result)
        #write local run script
        #open the file
        filein = open( TEMPLATES_DIR / 'local.txt' )
        
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'n' : n, 'SucRatio' : SucRatio, 'SucPct' : SucPct,
                                    'n_cyanos' : n_cyanos, 'n_ecw' : n_ecw,
                                    'Reps' : args.reps,'id': global_coll_id})
        f= open(RUN_DIR / f"local_{n_cyanos}_{n_ecw}_{SucPct}.sh","w+")
        f.writelines(result)

        _logger.info("Script ends here")

def run():
    """Calls :func:`main` passing the CLI arguments extracted from :obj:`sys.argv`

    This function can be used as entry point to create console scripts with setuptools.
    """
    main(sys.argv[1:])


if __name__ == "__main__":

    run()


import random
from scipy.stats import loguniform
import argparse
import numpy as np
from string import Template
import json
import os
import sys
from datetime import date
from datafed.CommandLib import API
import logging
from nufeb_tools import __version__
from pathlib import Path
from glob import glob



__author__ = "<NAME>"
__copyright__ = "<NAME>"
__license__ = "MIT"

_logger = logging.getLogger(__name__)

def parse_args(args):
    """Parse command line parameters

    Args:
        args (List[str]): command line parameters as list of strings
            (for example  ``["--help"]``).

    Returns:
        :obj:`argparse.Namespace`: command line parameters namespace
    """
    # arguments to modify the conditions of the simulation seeding
    parser = argparse.ArgumentParser(description='Create atom definition files')
    parser.add_argument('--n', dest='num', action='store',
                    default=1,
                    help='Create atom definition files for NUFEB with --n #files desired (default is 1)')
    parser.add_argument('--r', dest='reps', action='store',
                    default=1,
                    help='Number of replicates')
    parser.add_argument('--c',dest='culture_type',action='store',default='co',
                        help='Set culture conditions with --c (co-culture), --ax-c (cyano), --ax-e (e.coli)')
    parser.add_argument('--co2', dest='co2', action='store',
                    default=6.8e-1,
                    help='Set initial CO2 concentration (mM)')
    parser.add_argument('--d', dest='dims', action='store', type=str,
                    default='1e-4,1e-4,1e-5',
                    help='Set simulation box dimensions (m)')
    parser.add_argument('--t', dest='timesteps', action='store',
                    default=35000,
                    help='Number of timesteps to run')
    parser.add_argument('--suc', dest='sucrose', action='store',
                    default=1e-19,
                    help='Set initial sucrose concentration (mM)')
    parser.add_argument('--grid', dest='grid', action='store',
                    default=2,
                    help='Diffusion grid density (um/grid)')
    parser.add_argument('--mono', dest='monolayer', action='store',
                    default=True,
                    help='Set seed generation to monolayer of cells')
    parser.add_argument('--u', dest='user', action='store',
                    help='CADES/CNMS user ID')
    parser.add_argument('--datafed', dest='datafed', action = 'store', default=False,
                        help='DataFed Upload')
    parser.add_argument('--cells',dest='cells',action='store',default=None,
    help='Number of cyanobacteria and e.coli to initialize simulation with, `e.g., 100,100. ` Default is random number between 1 and 100.')
    parser.add_argument('--sucR',dest='SucRatio',action='store',default=None,
                    help='Set sucrose secretion ratio (0 to 1). Default is random.')   
    parser.add_argument('--iptg',dest='iptg',action='store',default=None,type=float,
                    help='Set IPTG induction for sucrose secretion (0 to 1). Default is random.') 
    parser.add_argument('--muecw',dest='mu_ecw',action='store',default=6.71e-5,type=float,
                    help='E. coli W maximum growth rate')  
    parser.add_argument('--mucya',dest='mu_cya',action='store',default=1.89e-5,type=float,
                    help='S. elongatus maximum growth rate')   
    parser.add_argument('--rhoecw',dest='rho_ecw',action='store',default=230,type=float,
        help='E. coli W cell density')  
    parser.add_argument('--rhocya',dest='rho_cya',action='store',default=370,type=float,
        help='S. elongatus cell density')  
    parser.add_argument('--ksuc',dest='ksuc',action='store',default=3.6,type=float,
        help='E. coli W Ksuc')  
    parser.add_argument('--maintecw',dest='maint_ecw',action='store',default=9.50e-7,type=float,
        help='E. coli W maintenance cost')  
    parser.add_argument('--mass',dest='mass_max',action='store',default=1.5e-11,type=float,
        help='Maximum biomass')  

    parser.add_argument('--vtk',dest='vtk',action='store',default=False,help='Output VTK files')
    parser.add_argument('--h5',dest='hdf5',action='store',default=True,help='Output HDF5 files')
    parser.add_argument('--lammps',dest='lammps',action='store',default=False,help='Output lammps files')
    parser.add_argument(
    "-v",
    "--verbose",
    dest="loglevel",
    help="set loglevel to INFO",
    action="store_const",
    const=logging.INFO,
)
    parser.add_argument(
    "-vv",
    "--very-verbose",
    dest="loglevel",
    help="set loglevel to DEBUG",
    action="store_const",
    const=logging.DEBUG,
)
    return parser.parse_args(args)
# TODO Change sucRatio to IPTG
def setup_logging(loglevel):
    """Setup basic logging

    Args:
      loglevel (int): minimum loglevel for emitting messages
    """
    logformat = "[%(asctime)s] %(levelname)s:%(name)s:%(message)s"
    logging.basicConfig(
        level=loglevel, stream=sys.stdout, format=logformat, datefmt="%Y-%m-%d %H:%M:%S"
    )

def clean():
    """Remove old NUFEB runs
    """
    if os.path.isdir('runs'):
        import shutil
        try:
            shutil.rmtree('runs')
        except OSError as e:
            print("Error: %s : %s" % ('runs', e.strerror))
    slurm_path = glob('*.slurm')
    if slurm_path:
        for file in slurm_path:
            os.remove(file)

def main(args):
    """Wrapper function to generate new NUFEB simulation conditions

    Args:
      args (List[str]): command line parameters as list of strings
          
    """
    args = parse_args(args)
    setup_logging(args.loglevel)
    _logger.info("Generating NUFEB simulation files")
    # maximum growth rates, mu
    #$mu_cyanos = round(0.06/3600,7)
    #mu_ecw = 2.7e-04 for 37C only
    #mu_ecw = 6.71e-5
    # molecular weights of co2 and sucrose for unit conversions
    CO2MW = 44.01
    SucMW = 342.3
    TEMPLATES_DIR = (Path(__file__).parent) / 'templates'
    # check for runs folder
    if not os.path.isdir('runs'):
        os.mkdir('runs')
    today = str(date.today())
    for n in range(1,int(args.num)+1):
        if args.iptg is not None:
            IPTG = float(args.iptg)
            SucRatio = IPTG
        else:
            IPTG = np.round(loguniform.rvs(1e-3, 1e0, size=1)[0],5)
            SucRatio = IPTG
        #if args.SucRatio is not None:
        #    SucRatio = float(args.SucRatio)

        SucPct = int(SucRatio*100)
        if args.culture_type == 'co':
            cell_types = ['cyano','ecw']
            if args.cells is not None:
                n_cyanos = int(args.cells.split(',')[0])
                n_ecw = int(args.cells.split(',')[1])
            else:
                n_cyanos = int(random.uniform(1,100))
                n_ecw = int(random.uniform(1,100))
            n_cells = n_cyanos + n_ecw
            cyGroup = 'group CYANO type 1'
            ecwGroup = 'group ECW type 2'
            cyDiv = f'fix d1 CYANO divide 100 v_EPSdens v_divDia1 {random.randint(1,1e6)}'
            ecwDiv = f'fix d2 ECW divide 100 v_EPSdens v_divDia2 {random.randint(1,1e6)}'
            masses = 'c_myMass[1]+c_myMass[2]'

        elif args.culture_type == 'ax-c':
            cell_types = ['cyano']
            if args.cells is not None:
                n_cyanos = int(args.cells.split(',')[0])
            else:
                n_cyanos = int(random.uniform(1,100))
            n_ecw = 0
            n_cells = n_cyanos
            cyGroup = 'group CYANO type 1'
            ecwGroup = ''
            cyDiv = f'fix d1 CYANO divide 100 v_EPSdens v_divDia1 {random.randint(1,1e6)}'
            ecwDiv = ''
            masses = 'c_myMass[1]'
        elif args.culture_type == 'ax-e':
            cell_types = ['ecw']
            if args.cells is not None:
                n_ecw = int(args.cells.split(',')[1])
            else:
                n_ecw = int(random.uniform(1,100))
            n_cyanos=0
            n_cells = n_ecw
            cyGroup = ''
            ecwGroup = 'group ECW type 1'
            cyDiv = ''
            ecwDiv = f'fix d2 ECW divide 100 v_EPSdens v_divDia2 {random.randint(1,1e6)}'
            masses = 'c_myMass[1]'
        RUN_DIR = Path(f'runs/Run_{n_cyanos}_{n_ecw}_{IPTG:.2e}_{args.reps}_{today}_{random.randint(1,1e6)}')
        if not os.path.isdir(RUN_DIR):
            os.mkdir(RUN_DIR)
        # TODO embed cell type into metadata file and generate cell type programmatically
        InitialConditions = {'cyano': {'StartingCells' : n_cyanos,'GrowthRate' : args.mu_cya,
            'min_size' : 1.37e-6, 'max_size' : 1.94e-6, 'Density' : args.rho_cya,
                'K_s' : {'sub' : 3.5e-4,'o2' : 2e-4, 'suc' : 1e-2,'co2' : 1.38e-4},
                'GrowthParams' : {'Yield' : 0.55,'Maintenance' : 0,'Decay' : 0}},
                'ecw': {'StartingCells' : n_ecw,'GrowthRate' : args.mu_ecw,
            'min_size' : 8.8e-7, 'max_size' : 1.39e-6, 'Density' : args.rho_ecw,
                'K_s' : {'sub' : 0,'o2' : 1e-3, 'suc' : args.ksuc,'co2' : 5e-2},
                'GrowthParams' : {'Yield' : 0.43,'Maintenance' : args.maint_ecw,'Decay' : 0}},
                'Nutrients' : {'Concentration' :  {'sub' : 1e-1,'o2' : 9e-3, 'suc' : float(args.sucrose)*SucMW*1e-3, 'co2' : float(args.co2)*CO2MW*1e-3},
                'State' : {'sub' : 'g','o2' : 'l', 'suc' : 'l', 'co2' : 'l'},
                'xbc' : {'sub' : 'nn','o2' : 'nn', 'suc' : 'nn', 'co2' : 'nn'},
                'ybc' : {'sub' : 'nn','o2' : 'nn', 'suc' : 'nn', 'co2' : 'nn'},
                'zbc' : {'sub' : 'nn','o2' : 'nd', 'suc' : 'nn', 'co2' : 'nd'}},
                'Diff_c' : {'sub' : 0,'o2' : 2.30e-9, 'suc' : 5.2e-10,'co2' : 1.9e-09},
                'Dimensions' : [float(x) for x in args.dims.split(',')],'SucRatio' : SucRatio,'Replicates' : int(args.reps)

                }
        grids = int(args.grid)
        while True:
            if InitialConditions["Dimensions"][0]*1e6 % grids == 0 and InitialConditions["Dimensions"][1]*1e6 % grids == 0 and InitialConditions["Dimensions"][2]*1e6 % grids == 0:
                Mesh = f'{int(InitialConditions["Dimensions"][0]*1e6/grids)} {int(InitialConditions["Dimensions"][1]*1e6/grids)} {int(InitialConditions["Dimensions"][2]*1e6/grids)}'
                break
            else:
                grids +=1

        NutesNum = len(InitialConditions['Nutrients']['Concentration'])
        for r in range(1,int(args.reps)+1):
            L = [' NUFEB Simulation\r\n\n',f'     {n_cells} atoms \n',
                f'     {len(cell_types)} atom types \n',f'     {NutesNum} nutrients \n\n',
                f'  0.0e-4   {InitialConditions["Dimensions"][0] :.2e}  xlo xhi \n',f'  0.0e-4   {InitialConditions["Dimensions"][1] :.2e}  ylo yhi \n',
                f'  0.0e-4   {InitialConditions["Dimensions"][2] :.2e}  zlo zhi \n\n', ' Atoms \n\n'
                ]

            j = 1
            for c, CellType in enumerate(cell_types,start=1):
                for i in range(j,InitialConditions[CellType]['StartingCells']+j):
                    size = random.uniform(InitialConditions[CellType]['min_size'],
                                        InitialConditions[CellType]['max_size'])
                    x = random.uniform(0+size,InitialConditions['Dimensions'][0]-size)
                    y = random.uniform(0+size,InitialConditions['Dimensions'][1]-size)
                    z = random.uniform(0+size,InitialConditions['Dimensions'][2]-size)
                    L.append(f'     %d {c} {size :.2e}  {InitialConditions[CellType]["Density"]} {x :.2e} {y :.2e} {z :.2e} {size :.2e} \n'% (i))
                    j += 1

            L.append('\n')
            L.append(' Nutrients \n\n')
            for i,nute in enumerate(InitialConditions['Nutrients']['Concentration'].keys()):
                L.append(f'     %d {nute} {InitialConditions["Nutrients"]["State"][nute]} {InitialConditions["Nutrients"]["xbc"][nute]} {InitialConditions["Nutrients"]["ybc"][nute]} {InitialConditions["Nutrients"]["zbc"][nute]} {InitialConditions["Nutrients"]["Concentration"][nute] :.2e} {InitialConditions["Nutrients"]["Concentration"][nute] :.2e} \n'% (i+1))

            L.append('\n')
            L.append(' Type Name \n\n')
            for c, CellType in enumerate(cell_types,start=1):
                L.append(f'     {c} {CellType}  \n')
            L.append('\n')
            L.append(' Diffusion Coeffs \n\n')
            for key in InitialConditions['Diff_c'].keys():
                L.append(f'     {key} {InitialConditions["Diff_c"][key]} \n')
            L.append('\n')
            L.append(' Growth Rate \n\n')
            for CellType in cell_types:
                L.append(f'     {CellType} {InitialConditions[CellType]["GrowthRate"]} \n')
            L.append('\n')
            L.append(' Ks \n\n')
            for CellType in cell_types:
                k = f'     {CellType}'
                for key in InitialConditions[CellType]['K_s'].keys():
                    k = k + ' ' + str(InitialConditions[CellType]['K_s'][key])
                k = k + f' \n'
                L.append(k)
            L.append('\n')
            for key in InitialConditions["cyano"]['GrowthParams'].keys():
                L.append(' ' + key + f' \n\n')
                for CellType in cell_types:
                    L.append(f'     {CellType} {InitialConditions[CellType]["GrowthParams"][key]} \n')
                L.append('\n')


            L.append('\n\n')

            #write atom definition file
            f= open(RUN_DIR / f"atom_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{r}_{today}.in","w+")
            f.writelines(L)

        #write initial conditions json file
        dumpfile = open(RUN_DIR / 'metadata.json','w')
        json.dump(InitialConditions, dumpfile, indent = 6)
        dumpfile.close()
        #write Inputscript
        #open the file


        if args.lammps ==True:
            lammps = 'dump    id all custom 100 output.lammmps id type diameter x y z'
        else: 
            lammps = ''
        if args.hdf5 == True:
            hdf5 = 'dump    traj all bio/hdf5 100 trajectory.h5 id type radius x y z con'
        else:
            hdf5 = ''
        if args.vtk == True:
            vtk = 'dump    du1 all vtk 100 atom_*.vtu id type diameter x y z'
            grid = 'dump    du2 all grid 100 grid_%_*.vti con'
            vtk_tarball = 'true'
        else:
            vtk = ''
            grid = ''
            vtk_tarball = 'false'
        filein = open( TEMPLATES_DIR / 'inputscript.txt' )
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'n' : n, 'SucRatio' : SucRatio, 'SucPct' : SucPct,
                                    'n_cyanos' : n_cyanos, 'n_ecw' : n_ecw,
                                    'Replicates' : args.reps,'IPTG' : f'{IPTG:.0e}','Timesteps' : args.timesteps,
                                    'date' : today,
                                    'CYANOGroup' : cyGroup,
                                    'ECWGroup' : ecwGroup,
                                    'Zheight' : InitialConditions["Dimensions"][2],
                                    'CYANODiv'  : cyDiv, 'ECWDiv' : ecwDiv,
                                    'GridMesh' : f'{int(InitialConditions["Dimensions"][0]*1e6/int(args.grid))} {int(InitialConditions["Dimensions"][1]*1e6/int(args.grid))} {int(InitialConditions["Dimensions"][2]*1e6/int(args.grid))}',
                                    'lammps' : lammps,
                                    'hdf5' : hdf5,
                                    'vtk' : vtk,
                                    'grid' : grid,
                                    'masses':masses,
                                    'mass_max':f'{args.mass_max:.2e}'
                                    })
        f= open(RUN_DIR / f"Inputscript_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{today}.lammps","w+")
        f.writelines(result)



        x = int(InitialConditions['Dimensions'][0]*1e6)
        y = int(InitialConditions['Dimensions'][1]*1e6)
        z = int(InitialConditions['Dimensions'][2]*1e6)
        if args.datafed is True or args.datafed == 'True':
        #create DataFed collection to hold the results
        # TODO actually make this work
            df_api = API()
            df_api.setContext('p/eng107')
            collectionName = f'NUFEB_{n_cyanos}_{n_ecw}_{IPTG:.0e}_{today}_{x}_{y}_{z}'
            parent_collection = df_api.getAuthUser().split('/')[1]
            coll_msg = df_api.collectionCreate(collectionName,
                                            parent_id=parent_collection)
            global_coll_id = coll_msg[0].coll[0].id
        else:
            global_coll_id = None

        #write slurm script
        #open the file
        filein = open( TEMPLATES_DIR / 'slurm.txt' )
        
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'job' : f"NUFEB_{n}",
                                        'USER' : args.user,
                                        'VTK' : vtk_tarball})
        f= open(f"NUFEB_{today}.slurm","w+")
        f.writelines(result)
        #write local run script
        #open the file
        filein = open( TEMPLATES_DIR / 'local.txt' )
        
        #read it
        src = Template( filein.read() )
        #do the substitution
        result = src.safe_substitute({'n' : n, 'SucRatio' : SucRatio, 'SucPct' : SucPct,
                                    'n_cyanos' : n_cyanos, 'n_ecw' : n_ecw,
                                    'Reps' : args.reps,'id': global_coll_id})
        f= open(RUN_DIR / f"local_{n_cyanos}_{n_ecw}_{SucPct}.sh","w+")
        f.writelines(result)

        _logger.info("Script ends here")

def run():
    """Calls :func:`main` passing the CLI arguments extracted from :obj:`sys.argv`

    This function can be used as entry point to create console scripts with setuptools.
    """
    main(sys.argv[1:])


if __name__ == "__main__":

    run()


Parse command line parameters      Args:         args (List[str]): command line parameters as list of strings             (for example  ``["--help"]``).      Returns:         :obj:`argparse.Namespace`: command line parameters namespace # arguments to modify the conditions of the simulation seeding #files desired (default is 1)') # TODO Change sucRatio to IPTG Setup basic logging      Args:       loglevel (int): minimum loglevel for emitting messages Remove old NUFEB runs Wrapper function to generate new NUFEB simulation conditions      Args:       args (List[str]): command line parameters as list of strings # maximum growth rates, mu #$mu_cyanos = round(0.06/3600,7) #mu_ecw = 2.7e-04 for 37C only #mu_ecw = 6.71e-5 # molecular weights of co2 and sucrose for unit conversions # check for runs folder #if args.SucRatio is not None: #    SucRatio = float(args.SucRatio) # TODO embed cell type into metadata file and generate cell type programmatically #write atom definition file #write initial conditions json file #write Inputscript #open the file #read it #do the substitution #create DataFed collection to hold the results # TODO actually make this work #write slurm script #open the file #read it #do the substitution #write local run script #open the file #read it #do the substitution Calls :func:`main` passing the CLI arguments extracted from :obj:`sys.argv`      This function can be used as entry point to create console scripts with setuptools.