__version__ = '0.5.2'

from .cobra.deletion import reaction_deletion, gene_deletion
from .cobra.essentiality import essential_genes, essential_reactions
from .cobra.phaseplane import PhPP
from .cobra.plotting import plot_flux_envelope, plot_flux_bounds
from .cobra.strain_design import combinatorial_gene_deletion, combinatorial_reaction_deletion, greedy_gene_deletion, greedy_reaction_deletion
from .cobra.variability import FVA, blocked_reactions, flux_envelope, production_envelope, flux_envelope_3d
from .cobra.simulation import FBA, pFBA, MOMA, lMOMA, ROOM
from .cobra.thermodynamics import TFA, TVA, looplessFBA, NET

from .io.plaintext import read_model_from_file, read_cbmodel_from_file, write_model_to_file
from .io.sbml import load_sbml_model, load_cbmodel, load_odemodel, save_cbmodel, save_sbml_model

from .kinetic.fitting import fit_from_metabolomics
from .kinetic.plotting import plot_timecourse, plot_flux_sampling
from .kinetic.sampling import sample_kinetic_model
from .kinetic.simulation import time_course, find_steady_state

from .omics.simulation import GIMME, eFlux

from .solvers import set_default_solver, solver_instance
from .solvers.solver import set_default_parameter, Parameter

from .model.model import Model, Metabolite, Compartment, Reaction
from .model.cbmodel import CBReaction, Gene, Protein, GPRAssociation, CBModel
from .model.environment import Environment
from .model.odemodel import ODEModel
from .model.transformation import simplify, make_irreversible

from .community.model import Community