Code structure help

[Martin De Kauwe]

Hi,

I have been working on re-writing a model in python and have been
trying to adopt some of the advise offered on here to recent
questions. However I am not sure how easy on the eye my final
structure is and would appreciate any constructive comments/
suggestions. So broadly the model estimates plant growth using a
number of related sub functions which I have grouped into classes and
they all live in separate files. My main issue at the moment is I
think I have a lot of verbose class instances but I really can't see a
better way to do it. I have left some of the bones of the code out but
this is basically what would it looks like.

thanks.


import constants as const
from file_parser import ConfigFileParser
from plant_growth import PlantGrowth
from print_outputs import PrintOutput
from litter import LitterFlows
from decomp import DecompFactors
from soil_cnflows import CarbonFlows, NitrogenFlows
from nmineralisation import Mineralisation
from update_pools import CarbonPools, NitrogenPools
...etc...

class ModelName(object):
    def __init__(self, cfg_fname=None):
        """ Set everything up

        Read meterological forcing file, any user adjusted files. If
there
        is anything in the user file then adjust the model parameters,
control
        or initial state attributes that are used within the code.
        """

        # sweep the cmd line
        options, args = cmdline_parser()

        # quit if asked only to dump default paramater files
        if options.DUMP_INPUT == True:
            ...call some stuff...

        # read in user defined variables (stored in dictionaries)
        pars = ConfigFileParser(cfg_fname=cfg_fname)
        (control, params, state, files, fluxes, met_data) =
pars.main()

        # objects holding model state, fluxes, parameters and control
flags
        self.met_data = met_data
        self.control = control
        self.params = params
        self.state = state
        self.fluxes = fluxes

        # instances of other model parts..
        self.pr = PrintOutput(self.params, self.state, self.fluxes,
                                self.control, self.files, dump=False)

        # start date of simulation
        self.date = self.simulation_start_date()


        ...etc....

    def run_sim(self):

        mi = Mineralisation(self.control, self.params, self.state,
self.fluxes)
        cf = CarbonFlows(self.control, self.params, self.state,
self.fluxes)
        nf = NitrogenFlows(self.control, self.params, self.state,
self.fluxes)
        de = Derive(self.control, self.params, self.state,
self.fluxes)
        dc = DecompFactors(self.control, self.params, self.state,
self.fluxes)
        lf = LitterFlows(self.control, self.params, self.state,
self.fluxes)
        pg = PlantGrowth(self.control, self.params, self.state,
self.fluxes,
                            self.met_data)
        cpl = CarbonPools(self.control, self.params, self.state,
self.fluxes)
        npl = NitrogenPools(self.control, self.params, self.state,
self.fluxes)

        for i in self.met_data.doy:
            project_day = i - 1

            # N:C ratios
            leafnc, rootnc = self.leaf_root_ncratio()

            # litterfall rate: C and N fluxes
            lf.flows(leafnc, rootnc)

            # plant growth
            pg.grow(project_day, self.date, leafnc)

            # calculate model decay rates
            dc.decay_rates()

            # soil model fluxes
            cf.calculate_cflows()
            nf.calculate_nflows()

            # N uptake and loss
            mi.calculate_mineralisation()

            # carbon sink or source?
            self.fluxes.nep = (self.fluxes.npp -
self.fluxes.hetero_resp -
                                self.fluxes.ceaten *
                                (1. - self.params.fracfaeces))

            # soil model - update pools
            cact, cslo, cpas = cpl.calculate_cpools()
            npl.calculate_npools(cact, cslo, cpas)

            if self.control.print_options == 1:
                self.pr.print_state()
                self.pr.print_fluxes()

            self.increment_date()

        if self.control.print_options == 2:
            self.pr.print_state()
            self.pr.print_fluxes()

        # house cleaning, close ouput files
        self.pr.tidy_up()