<gh_stars>0
"""
mfmodel module.  Contains the MFModel class

"""
import os, sys, inspect
import numpy as np
from .mfbase import PackageContainer, ExtFileAction, PackageContainerType, \
                    MFDataException, ReadAsArraysException, FlopyException, \
                    StructException
from .mfpackage import MFPackage
from .coordinates import modeldimensions
from .utils.reference import SpatialReference, StructuredSpatialReference, \
                             VertexSpatialReference
from .data import mfstructure, mfdatautil


class MFModel(PackageContainer):
    """
    MODFLOW Model Class.  Represents a single model in a simulation.

    Parameters
    ----------
    simulation_data : MFSimulationData
        simulation data object
    structure : MFModelStructure
        structure of this type of model
    modelname : string
        name of the model
    model_nam_file : string
        relative path to the model name file from model working folder
    version : string
        version of modflow
    exe_name : string
        model executable name
    model_ws : string
        model working folder path
    disfile : string
        relative path to dis file from model working folder
    grid_type : string
        type of grid the model will use (structured, unstructured, vertices)

    Attributes
    ----------
    model_name : string
        name of the model
    exe_name : string
        model executable name
    packages : OrderedDict(MFPackage)
        dictionary of model packages
    _name_file_io : MFNameFile
        name file

    Methods
    -------
    load : (simulation : MFSimulationData, model_name : string,
      namfile : string, type : string, version : string, exe_name : string,
      model_ws : string, strict : boolean) : MFSimulation
        a class method that loads a model from files
    write
        writes the simulation to files
    remove_package : (package_name : string)
        removes package from the model.  package_name can be the
        package's name, type, or package object to be removed from
        the model
    set_model_relative_path : (path : string)
        sets the file path to the model folder and updates all model file paths
    is_valid : () : boolean
        checks the validity of the model and all of its packages

    See Also
    --------

    Notes
    -----

    Examples
    --------

    """
    def __init__(self, simulation, model_type='gwf6', modelname='model',
                 model_nam_file=None, version='mf6',
                 exe_name='mf6.exe', add_to_simulation=True,
                 structure=None, model_rel_path='.', **kwargs):
        super(MFModel, self).__init__(simulation.simulation_data, modelname)
        self.simulation = simulation
        self.simulation_data = simulation.simulation_data
        self.name = modelname
        self.name_file = None
        self.version = version
        self.type = 'Model'

        if model_nam_file is None:
            model_nam_file = '{}.nam'.format(modelname)

        self.set_model_relative_path(model_rel_path)
        if add_to_simulation:
            self.structure = simulation.register_model(self, model_type,
                                                       modelname,
                                                       model_nam_file)
        else:
            self.structure = structure
        self.exe_name = exe_name
        self.dimensions = modeldimensions.ModelDimensions(self.name,
                                                          self.simulation_data)
        self.simulation_data.model_dimensions[modelname] = self.dimensions
        self._ftype_num_dict = {}
        self._package_paths = {}

        if model_nam_file is None:
            self.model_nam_file = '{}.nam'.format(modelname)
        else:
            self.model_nam_file = model_nam_file

        # check for spatial reference info in kwargs
        xul = kwargs.pop("xul", None)
        yul = kwargs.pop("yul", None)
        rotation = kwargs.pop("rotation", 0.)
        proj4_str = kwargs.pop("proj4_str", "EPSG:4326")
        self.sr = SpatialReference(xul=xul, yul=yul, rotation=rotation,
                                   proj4_str=proj4_str)

        # check for extraneous kwargs
        if len(kwargs) > 0:
            kwargs_str = ', '.join(kwargs.keys())
            excpt_str = 'ERROR: Extraneous kwargs "{}" provided to ' \
                        'MFModel.'.format(kwargs_str)
            raise FlopyException(excpt_str)

        # build model name file
        # create name file based on model type - support different model types
        package_obj = self.package_factory('nam', model_type[0:3])
        if not package_obj:
            excpt_str = 'Name file could not be found for model' \
                        '{}.'.format(model_type[0:3])
            print(excpt_str)
            raise StructException(excpt_str)

        self.name_file = package_obj(self, fname=self.model_nam_file,
                                     pname=self.name)
        self.verbose = simulation.verbose

    def __getattr__(self, item):
        """
        __getattr__ - used to allow for getting packages as if they are
                      attributes

        Parameters
        ----------
        item : str
            3 character package name (case insensitive)


        Returns
        -------
        pp : Package object
            Package object of type :class:`flopy.pakbase.Package`

        """
        return self.get_package(item)

    def __setattr__(self, key, value):
        if key == "sr":
            assert isinstance(value, SpatialReference) or \
                   isinstance(value, StructuredSpatialReference) or \
                   isinstance(value, VertexSpatialReference)
        super(MFModel, self).__setattr__(key, value)

    @classmethod
    def load_base(cls, simulation, structure, modelname='NewModel',
                  model_nam_file='modflowtest.nam', type='gwf', version='mf6',
                  exe_name='mf6.exe', strict=True, model_rel_path='.'):
        """
        Load an existing model.

        Parameters
        ----------
        simulation : MFSimulation
            simulation object that this model is a part of
        simulation_data : MFSimulationData
            simulation data object
        structure : MFModelStructure
            structure of this type of model
        model_name : string
            name of the model
        model_nam_file : string
            relative path to the model name file from model working folder
        version : string
            version of modflow
        exe_name : string
            model executable name
        model_ws : string
            model working folder relative to simulation working folder
        strict : boolean
            strict mode when loading files
        model_rel_path : string
            relative path of model folder to simulation folder
        Returns
        -------
        model : MFModel

        Examples
        --------
        """

        instance = cls(simulation, type, modelname,
                       model_nam_file=model_nam_file,
                       version=version, exe_name=exe_name,
                       add_to_simulation=False, structure=structure,
                       model_rel_path=model_rel_path)
        # load name file
        instance.name_file.load(strict)

        # order packages
        vnum = mfstructure.MFStructure().get_version_string()
        # FIX: Transport - Priority packages maybe should not be hard coded
        priority_packages = {'dis{}'.format(vnum): 1,'disv{}'.format(vnum): 1,
                             'disu{}'.format(vnum): 1}
        packages_ordered = []
        package_recarray = instance.simulation_data.mfdata[(modelname, 'nam',
                                                            'packages',
                                                            'packages')]
        for item in package_recarray.get_data():
            if item[0] in priority_packages:
                packages_ordered.insert(0, (item[0], item[1], item[2]))
            else:
                packages_ordered.append((item[0], item[1], item[2]))

        # load packages
        sim_struct = mfstructure.MFStructure().sim_struct
        instance._ftype_num_dict = {}
        for ftype, fname, pname in packages_ordered:
            ftype = ftype[0:-1].lower()
            if ftype in structure.package_struct_objs or ftype in \
              sim_struct.utl_struct_objs:
                if model_rel_path and model_rel_path != '.':
                    # strip off model relative path from the file path
                    filemgr = simulation.simulation_data.mfpath
                    fname = filemgr.strip_model_relative_path(modelname,
                                                              fname)
                print('loading {}...'.format(fname))
                # load package
                instance.load_package(ftype, fname, pname, strict, None)

        # load referenced packages
        if modelname in instance.simulation_data.referenced_files:
            for index, ref_file in \
              instance.simulation_data.referenced_files[modelname].items():
                if (ref_file.file_type in structure.package_struct_objs or
                  ref_file.file_type in sim_struct.utl_struct_objs) and \
                  not ref_file.loaded:
                    instance.load_package(ref_file.file_type,
                                          ref_file.file_name, None, strict,
                                          ref_file.reference_path)
                    ref_file.loaded = True

        # TODO: fix jagged lists where appropriate

        return instance

    def write(self, ext_file_action=ExtFileAction.copy_relative_paths):
        """
        write model to model files

        Parameters
        ----------
        ext_file_action : ExtFileAction
            defines what to do with external files when the simulation path has
            changed.  defaults to copy_relative_paths which copies only files
            with relative paths, leaving files defined by absolute paths fixed.

        Returns
        -------

        Examples
        --------
        """

        # write name file
        self.name_file.write(ext_file_action=ext_file_action)

        # write packages
        for pp in self.packages:
            pp.write(ext_file_action=ext_file_action)

    def is_valid(self):
        """
        checks the validity of the model and all of its packages

        Parameters
        ----------

        Returns
        -------
        valid : boolean

        Examples
        --------
        """

        # valid name file
        if not self.name_file.is_valid():
            return False

        # valid packages
        for pp in self.packages:
            if not pp.is_valid():
                return False

        # required packages exist
        for key, package_struct in self.structure.package_struct_objs.items():
            if not package_struct.optional and not package_struct.file_type \
              in self.package_type_dict:
                return False

        return True

    def set_model_relative_path(self, model_ws):
        """
        sets the file path to the model folder relative to the simulation
        folder and updates all model file paths, placing them in the model
        folder

        Parameters
        ----------
        model_ws : string
            model working folder relative to simulation working folder

        Returns
        -------

        Examples
        --------
        """
        # update path in the file manager
        file_mgr = self.simulation_data.mfpath
        file_mgr.set_last_accessed_model_path()
        path = file_mgr.string_to_file_path(model_ws)
        file_mgr.model_relative_path[self.name] = path

        if model_ws and model_ws != '.' and self.simulation.name_file is not \
                None:
            # update model name file location in simulation name file
            models = self.simulation.name_file.models
            models_data = models.get_data()
            for index, entry in enumerate(models_data):
                old_model_path, old_model_file_name = os.path.split(entry[1])
                old_model_base_name = os.path.splitext(old_model_file_name)[0]
                if old_model_base_name.lower() == self.name.lower() or \
                        self.name == entry[2]:
                    models_data[index][1] = os.path.join(path,
                                                         old_model_file_name)
                    break
            models.set_data(models_data)

            if self.name_file is not None:
                # update listing file location in model name file
                list_file = self.name_file.list.get_data()
                if list_file:
                    path, list_file_name = os.path.split(list_file)
                    try:
                        self.name_file.list.set_data(os.path.join(
                            path, list_file_name))
                    except MFDataException as mfde:
                        message = 'Error occurred while setting relative ' \
                                  'path "{}" in model '\
                                  '"{}".'.format(os.path.join(path,
                                                              list_file_name),
                                                 self.name)
                        raise MFDataException(mfdata_except=mfde,
                                              model=self.model_name,
                                              package=self.name_file.
                                              _get_pname(),
                                              message=message)
                # update package file locations in model name file
                packages = self.name_file.packages
                packages_data = packages.get_data()
                for index, entry in enumerate(packages_data):
                    old_package_path, \
                    old_package_name = os.path.split(entry[1])
                    packages_data[index][1] = os.path.join(path,
                                                           old_package_name)
                packages.set_data(packages_data)

                # update files referenced from within packages
                for package in self.packages:
                    package.set_model_relative_path(model_ws)

    def _remove_package_from_dictionaries(self, package):
        # remove package from local dictionaries and lists
        if package.path in self._package_paths:
            del self._package_paths[package.path]
        self._remove_package(package)

    def remove_package(self, package_name):
        """
        removes a package and all child packages from the model

        Parameters
        ----------
        package_name : str
            package name, package type, or package object to be removed from
            the model

        Returns
        -------

        Examples
        --------
        """
        if isinstance(package_name, MFPackage):
            packages = [package_name]
        else:
            packages = self.get_package(package_name)
            if not isinstance(packages, list):
                packages = [packages]
        for package in packages:
            if package._model_or_sim.name != self.name:
                except_text = 'ERROR: Package can not be removed from model {} ' \
                              'since it is ' \
                              'not part of '
                print(except_text)
                raise mfstructure.FlopyException(except_text)

            self._remove_package_from_dictionaries(package)

            try:
                # remove package from name file
                package_data = self.name_file.packages.get_data()
            except MFDataException as mfde:
                message = 'Error occurred while reading package names ' \
                          'from name file in model ' \
                          '"{}".'.format(self.name)
                raise MFDataException(mfdata_except=mfde,
                                      model=self.model_name,
                                      package=self.name_file._get_pname(),
                                      message=message)
            try:
                new_rec_array = None
                for item in package_data:
                    if item[1] != package.filename:
                        if new_rec_array is None:
                            new_rec_array = np.rec.array(item, package_data.dtype)
                        else:
                            new_rec_array = np.hstack((item, new_rec_array))
            except:
                type_, value_, traceback_ = sys.exc_info()
                raise MFDataException(self.structure.get_model(),
                                      self.structure.get_package(),
                                      self._path,
                                      'building package recarray',
                                      self.structure.name,
                                      inspect.stack()[0][3],
                                      type_, value_, traceback_, None,
                                      self._simulation_data.debug)
            try:
                self.name_file.packages.set_data(new_rec_array)
            except MFDataException as mfde:
                message = 'Error occurred while setting package names ' \
                          'from name file in model "{}".  Package name ' \
                          'data:\n{}'.format(self.name, new_rec_array)
                raise MFDataException(mfdata_except=mfde,
                                      model=self.model_name,
                                      package=self.name_file._get_pname(),
                                      message=message)

            # build list of child packages
            child_package_list = []
            for pkg in self.packages:
                if pkg.parent_file is not None and pkg.parent_file.path == \
                        package.path:
                    child_package_list.append(pkg)
            # remove child packages
            for child_package in child_package_list:
                self._remove_package_from_dictionaries(child_package)

    def register_package(self, package, add_to_package_list=True,
                         set_package_name=True, set_package_filename=True):
        """
        registers a package with the model

        Parameters
        ----------
        package : MFPackage
            package to register
        add_to_package_list : bool
            add package to lookup list
        set_package_name : bool
            produce a package name for this package
        set_package_filename : bool
            produce a filename for this package

        Returns
        -------
        (path : tuple, package structure : MFPackageStructure)

        Examples
        --------
        """
        package.container_type = [PackageContainerType.model]
        if package.parent_file is not None:
            path = package.parent_file.path + (package.package_type,)
        else:
            path = (self.name, package.package_type)

        if add_to_package_list and path in self._package_paths and not \
                set_package_name and package.package_name in \
                self.package_name_dict:
            # package of this type with this name already exists, replace it
            print('WARNING: Package with name {} already exists. '
                  'Replacing existing package.'.format(package.package_name))
            self.remove_package(self.package_name_dict[package.package_name])

        # make sure path is unique
        if path in self._package_paths:
            path_iter = mfdatautil.PathIter(path)
            for new_path in path_iter:
                if new_path not in self._package_paths:
                    path = new_path
                    break
        self._package_paths[path] = 1

        if package.package_type.lower() == 'nam':
            return path, self.structure.name_file_struct_obj

        package_struct = \
          self.structure.get_package_struct(package.package_type)
        if set_package_name:
            # produce a default package name
            if package_struct is not None and \
              package_struct.multi_package_support:
                # check for other registered packages of this type
                name_iter = mfdatautil.NameIter(package.package_type, False)
                for package_name in name_iter:
                    if package_name not in self.package_name_dict:
                        package.package_name = package_name
                        break
            else:
                package.package_name = package.package_type

        if set_package_filename:
            package.filename = '{}.{}'.format(self.name, package.package_type)

        if add_to_package_list:
            self._add_package(package, path)

            # add obs file to name file if it does not have a parent
            if package.package_type in self.structure.package_struct_objs or \
              (package.package_type == 'obs' and package.parent_file is None):
                # update model name file
                pkg_type = package.package_type.upper()
                if len(pkg_type) > 3 and pkg_type[-1] == 'A':
                    pkg_type = pkg_type[0:-1]
                # Model Assumption - assuming all name files have a package
                # rec array
                self.name_file.packages.\
                  update_record(['{}6'.format(pkg_type), package.filename,
                  package.package_name], 0)
        if package_struct is not None:
            return (path, package_struct)
        else:
            print('WARNING: Unable to register unsupported file type {} for '
                  'model {}.'.format(package.package_type, self.name))
        return (None, None)

    def load_package(self, ftype, fname, pname, strict, ref_path,
                     dict_package_name=None, parent_package=None):
        """
        loads a package from a file

        Parameters
        ----------
        ftype : string
            the file type
        fname : string
            the name of the file containing the package input
        pname : string
            the user-defined name for the package
        strict : bool
            strict mode when loading the file
        ref_path : string
            path to the file. uses local path if set to None
        dict_package_name : string
            package name for dictionary lookup
        parent_package : MFPackage
            parent package

        Examples
        --------
        """
        sim_struct = mfstructure.MFStructure().sim_struct
        if (ftype in self.structure.package_struct_objs and
          self.structure.package_struct_objs[ftype].multi_package_support) or \
          (ftype in sim_struct.utl_struct_objs and
          sim_struct.utl_struct_objs[ftype].multi_package_support):
            # resolve dictionary name for package
            if dict_package_name is not None:
                if parent_package is not None:
                    dict_package_name = '{}_{}'.format(parent_package.path[-1],
                                                       ftype)
                else:
                    # use dict_package_name as the base name
                    if ftype in self._ftype_num_dict:
                        self._ftype_num_dict[dict_package_name] += 1
                    else:
                        self._ftype_num_dict[dict_package_name] = 0
                    dict_package_name = '{}_{}'.format(dict_package_name,
                                                       self._ftype_num_dict[
                                                         dict_package_name])
            else:
                # use ftype as the base name
                if ftype in self._ftype_num_dict:
                    self._ftype_num_dict[ftype] += 1
                else:
                    self._ftype_num_dict[ftype] = 0
                if pname is not None:
                    dict_package_name = pname
                else:
                    dict_package_name = '{}_{}'.format(ftype,
                                                       self._ftype_num_dict[
                                                       ftype])
        else:
            dict_package_name = ftype

        # clean up model type text
        model_type = self.structure.model_type
        while mfdatautil.DatumUtil.is_int(model_type[-1]):
            model_type = model_type[0:-1]

        # create package
        package_obj = self.package_factory(ftype, model_type)
        package = package_obj(self, fname=fname, pname=dict_package_name,
                              loading_package=True,
                              parent_file=parent_package)
        try:
            package.load(strict)
        except ReadAsArraysException:
            #  create ReadAsArrays package and load it instead
            package_obj = self.package_factory('{}a'.format(ftype), model_type)
            package = package_obj(self, fname=fname, pname=dict_package_name,
                                  loading_package=True,
                                  parent_file=parent_package)
            package.load(strict)

        # register child package with the model
        self._add_package(package, package.path)
        if parent_package is not None:
            # register child package with the parent package
            parent_package._add_package(package, package.path)
"""
mfmodel module.  Contains the MFModel class

"""
import os, sys, inspect
import numpy as np
from .mfbase import PackageContainer, ExtFileAction, PackageContainerType, \
                    MFDataException, ReadAsArraysException, FlopyException, \
                    StructException
from .mfpackage import MFPackage
from .coordinates import modeldimensions
from .utils.reference import SpatialReference, StructuredSpatialReference, \
                             VertexSpatialReference
from .data import mfstructure, mfdatautil


class MFModel(PackageContainer):
    """
    MODFLOW Model Class.  Represents a single model in a simulation.

    Parameters
    ----------
    simulation_data : MFSimulationData
        simulation data object
    structure : MFModelStructure
        structure of this type of model
    modelname : string
        name of the model
    model_nam_file : string
        relative path to the model name file from model working folder
    version : string
        version of modflow
    exe_name : string
        model executable name
    model_ws : string
        model working folder path
    disfile : string
        relative path to dis file from model working folder
    grid_type : string
        type of grid the model will use (structured, unstructured, vertices)

    Attributes
    ----------
    model_name : string
        name of the model
    exe_name : string
        model executable name
    packages : OrderedDict(MFPackage)
        dictionary of model packages
    _name_file_io : MFNameFile
        name file

    Methods
    -------
    load : (simulation : MFSimulationData, model_name : string,
      namfile : string, type : string, version : string, exe_name : string,
      model_ws : string, strict : boolean) : MFSimulation
        a class method that loads a model from files
    write
        writes the simulation to files
    remove_package : (package_name : string)
        removes package from the model.  package_name can be the
        package's name, type, or package object to be removed from
        the model
    set_model_relative_path : (path : string)
        sets the file path to the model folder and updates all model file paths
    is_valid : () : boolean
        checks the validity of the model and all of its packages

    See Also
    --------

    Notes
    -----

    Examples
    --------

    """
    def __init__(self, simulation, model_type='gwf6', modelname='model',
                 model_nam_file=None, version='mf6',
                 exe_name='mf6.exe', add_to_simulation=True,
                 structure=None, model_rel_path='.', **kwargs):
        super(MFModel, self).__init__(simulation.simulation_data, modelname)
        self.simulation = simulation
        self.simulation_data = simulation.simulation_data
        self.name = modelname
        self.name_file = None
        self.version = version
        self.type = 'Model'

        if model_nam_file is None:
            model_nam_file = '{}.nam'.format(modelname)

        self.set_model_relative_path(model_rel_path)
        if add_to_simulation:
            self.structure = simulation.register_model(self, model_type,
                                                       modelname,
                                                       model_nam_file)
        else:
            self.structure = structure
        self.exe_name = exe_name
        self.dimensions = modeldimensions.ModelDimensions(self.name,
                                                          self.simulation_data)
        self.simulation_data.model_dimensions[modelname] = self.dimensions
        self._ftype_num_dict = {}
        self._package_paths = {}

        if model_nam_file is None:
            self.model_nam_file = '{}.nam'.format(modelname)
        else:
            self.model_nam_file = model_nam_file

        # check for spatial reference info in kwargs
        xul = kwargs.pop("xul", None)
        yul = kwargs.pop("yul", None)
        rotation = kwargs.pop("rotation", 0.)
        proj4_str = kwargs.pop("proj4_str", "EPSG:4326")
        self.sr = SpatialReference(xul=xul, yul=yul, rotation=rotation,
                                   proj4_str=proj4_str)

        # check for extraneous kwargs
        if len(kwargs) > 0:
            kwargs_str = ', '.join(kwargs.keys())
            excpt_str = 'ERROR: Extraneous kwargs "{}" provided to ' \
                        'MFModel.'.format(kwargs_str)
            raise FlopyException(excpt_str)

        # build model name file
        # create name file based on model type - support different model types
        package_obj = self.package_factory('nam', model_type[0:3])
        if not package_obj:
            excpt_str = 'Name file could not be found for model' \
                        '{}.'.format(model_type[0:3])
            print(excpt_str)
            raise StructException(excpt_str)

        self.name_file = package_obj(self, fname=self.model_nam_file,
                                     pname=self.name)
        self.verbose = simulation.verbose

    def __getattr__(self, item):
        """
        __getattr__ - used to allow for getting packages as if they are
                      attributes

        Parameters
        ----------
        item : str
            3 character package name (case insensitive)


        Returns
        -------
        pp : Package object
            Package object of type :class:`flopy.pakbase.Package`

        """
        return self.get_package(item)

    def __setattr__(self, key, value):
        if key == "sr":
            assert isinstance(value, SpatialReference) or \
                   isinstance(value, StructuredSpatialReference) or \
                   isinstance(value, VertexSpatialReference)
        super(MFModel, self).__setattr__(key, value)

    @classmethod
    def load_base(cls, simulation, structure, modelname='NewModel',
                  model_nam_file='modflowtest.nam', type='gwf', version='mf6',
                  exe_name='mf6.exe', strict=True, model_rel_path='.'):
        """
        Load an existing model.

        Parameters
        ----------
        simulation : MFSimulation
            simulation object that this model is a part of
        simulation_data : MFSimulationData
            simulation data object
        structure : MFModelStructure
            structure of this type of model
        model_name : string
            name of the model
        model_nam_file : string
            relative path to the model name file from model working folder
        version : string
            version of modflow
        exe_name : string
            model executable name
        model_ws : string
            model working folder relative to simulation working folder
        strict : boolean
            strict mode when loading files
        model_rel_path : string
            relative path of model folder to simulation folder
        Returns
        -------
        model : MFModel

        Examples
        --------
        """

        instance = cls(simulation, type, modelname,
                       model_nam_file=model_nam_file,
                       version=version, exe_name=exe_name,
                       add_to_simulation=False, structure=structure,
                       model_rel_path=model_rel_path)
        # load name file
        instance.name_file.load(strict)

        # order packages
        vnum = mfstructure.MFStructure().get_version_string()
        # FIX: Transport - Priority packages maybe should not be hard coded
        priority_packages = {'dis{}'.format(vnum): 1,'disv{}'.format(vnum): 1,
                             'disu{}'.format(vnum): 1}
        packages_ordered = []
        package_recarray = instance.simulation_data.mfdata[(modelname, 'nam',
                                                            'packages',
                                                            'packages')]
        for item in package_recarray.get_data():
            if item[0] in priority_packages:
                packages_ordered.insert(0, (item[0], item[1], item[2]))
            else:
                packages_ordered.append((item[0], item[1], item[2]))

        # load packages
        sim_struct = mfstructure.MFStructure().sim_struct
        instance._ftype_num_dict = {}
        for ftype, fname, pname in packages_ordered:
            ftype = ftype[0:-1].lower()
            if ftype in structure.package_struct_objs or ftype in \
              sim_struct.utl_struct_objs:
                if model_rel_path and model_rel_path != '.':
                    # strip off model relative path from the file path
                    filemgr = simulation.simulation_data.mfpath
                    fname = filemgr.strip_model_relative_path(modelname,
                                                              fname)
                print('loading {}...'.format(fname))
                # load package
                instance.load_package(ftype, fname, pname, strict, None)

        # load referenced packages
        if modelname in instance.simulation_data.referenced_files:
            for index, ref_file in \
              instance.simulation_data.referenced_files[modelname].items():
                if (ref_file.file_type in structure.package_struct_objs or
                  ref_file.file_type in sim_struct.utl_struct_objs) and \
                  not ref_file.loaded:
                    instance.load_package(ref_file.file_type,
                                          ref_file.file_name, None, strict,
                                          ref_file.reference_path)
                    ref_file.loaded = True

        # TODO: fix jagged lists where appropriate

        return instance

    def write(self, ext_file_action=ExtFileAction.copy_relative_paths):
        """
        write model to model files

        Parameters
        ----------
        ext_file_action : ExtFileAction
            defines what to do with external files when the simulation path has
            changed.  defaults to copy_relative_paths which copies only files
            with relative paths, leaving files defined by absolute paths fixed.

        Returns
        -------

        Examples
        --------
        """

        # write name file
        self.name_file.write(ext_file_action=ext_file_action)

        # write packages
        for pp in self.packages:
            pp.write(ext_file_action=ext_file_action)

    def is_valid(self):
        """
        checks the validity of the model and all of its packages

        Parameters
        ----------

        Returns
        -------
        valid : boolean

        Examples
        --------
        """

        # valid name file
        if not self.name_file.is_valid():
            return False

        # valid packages
        for pp in self.packages:
            if not pp.is_valid():
                return False

        # required packages exist
        for key, package_struct in self.structure.package_struct_objs.items():
            if not package_struct.optional and not package_struct.file_type \
              in self.package_type_dict:
                return False

        return True

    def set_model_relative_path(self, model_ws):
        """
        sets the file path to the model folder relative to the simulation
        folder and updates all model file paths, placing them in the model
        folder

        Parameters
        ----------
        model_ws : string
            model working folder relative to simulation working folder

        Returns
        -------

        Examples
        --------
        """
        # update path in the file manager
        file_mgr = self.simulation_data.mfpath
        file_mgr.set_last_accessed_model_path()
        path = file_mgr.string_to_file_path(model_ws)
        file_mgr.model_relative_path[self.name] = path

        if model_ws and model_ws != '.' and self.simulation.name_file is not \
                None:
            # update model name file location in simulation name file
            models = self.simulation.name_file.models
            models_data = models.get_data()
            for index, entry in enumerate(models_data):
                old_model_path, old_model_file_name = os.path.split(entry[1])
                old_model_base_name = os.path.splitext(old_model_file_name)[0]
                if old_model_base_name.lower() == self.name.lower() or \
                        self.name == entry[2]:
                    models_data[index][1] = os.path.join(path,
                                                         old_model_file_name)
                    break
            models.set_data(models_data)

            if self.name_file is not None:
                # update listing file location in model name file
                list_file = self.name_file.list.get_data()
                if list_file:
                    path, list_file_name = os.path.split(list_file)
                    try:
                        self.name_file.list.set_data(os.path.join(
                            path, list_file_name))
                    except MFDataException as mfde:
                        message = 'Error occurred while setting relative ' \
                                  'path "{}" in model '\
                                  '"{}".'.format(os.path.join(path,
                                                              list_file_name),
                                                 self.name)
                        raise MFDataException(mfdata_except=mfde,
                                              model=self.model_name,
                                              package=self.name_file.
                                              _get_pname(),
                                              message=message)
                # update package file locations in model name file
                packages = self.name_file.packages
                packages_data = packages.get_data()
                for index, entry in enumerate(packages_data):
                    old_package_path, \
                    old_package_name = os.path.split(entry[1])
                    packages_data[index][1] = os.path.join(path,
                                                           old_package_name)
                packages.set_data(packages_data)

                # update files referenced from within packages
                for package in self.packages:
                    package.set_model_relative_path(model_ws)

    def _remove_package_from_dictionaries(self, package):
        # remove package from local dictionaries and lists
        if package.path in self._package_paths:
            del self._package_paths[package.path]
        self._remove_package(package)

    def remove_package(self, package_name):
        """
        removes a package and all child packages from the model

        Parameters
        ----------
        package_name : str
            package name, package type, or package object to be removed from
            the model

        Returns
        -------

        Examples
        --------
        """
        if isinstance(package_name, MFPackage):
            packages = [package_name]
        else:
            packages = self.get_package(package_name)
            if not isinstance(packages, list):
                packages = [packages]
        for package in packages:
            if package._model_or_sim.name != self.name:
                except_text = 'ERROR: Package can not be removed from model {} ' \
                              'since it is ' \
                              'not part of '
                print(except_text)
                raise mfstructure.FlopyException(except_text)

            self._remove_package_from_dictionaries(package)

            try:
                # remove package from name file
                package_data = self.name_file.packages.get_data()
            except MFDataException as mfde:
                message = 'Error occurred while reading package names ' \
                          'from name file in model ' \
                          '"{}".'.format(self.name)
                raise MFDataException(mfdata_except=mfde,
                                      model=self.model_name,
                                      package=self.name_file._get_pname(),
                                      message=message)
            try:
                new_rec_array = None
                for item in package_data:
                    if item[1] != package.filename:
                        if new_rec_array is None:
                            new_rec_array = np.rec.array(item, package_data.dtype)
                        else:
                            new_rec_array = np.hstack((item, new_rec_array))
            except:
                type_, value_, traceback_ = sys.exc_info()
                raise MFDataException(self.structure.get_model(),
                                      self.structure.get_package(),
                                      self._path,
                                      'building package recarray',
                                      self.structure.name,
                                      inspect.stack()[0][3],
                                      type_, value_, traceback_, None,
                                      self._simulation_data.debug)
            try:
                self.name_file.packages.set_data(new_rec_array)
            except MFDataException as mfde:
                message = 'Error occurred while setting package names ' \
                          'from name file in model "{}".  Package name ' \
                          'data:\n{}'.format(self.name, new_rec_array)
                raise MFDataException(mfdata_except=mfde,
                                      model=self.model_name,
                                      package=self.name_file._get_pname(),
                                      message=message)

            # build list of child packages
            child_package_list = []
            for pkg in self.packages:
                if pkg.parent_file is not None and pkg.parent_file.path == \
                        package.path:
                    child_package_list.append(pkg)
            # remove child packages
            for child_package in child_package_list:
                self._remove_package_from_dictionaries(child_package)

    def register_package(self, package, add_to_package_list=True,
                         set_package_name=True, set_package_filename=True):
        """
        registers a package with the model

        Parameters
        ----------
        package : MFPackage
            package to register
        add_to_package_list : bool
            add package to lookup list
        set_package_name : bool
            produce a package name for this package
        set_package_filename : bool
            produce a filename for this package

        Returns
        -------
        (path : tuple, package structure : MFPackageStructure)

        Examples
        --------
        """
        package.container_type = [PackageContainerType.model]
        if package.parent_file is not None:
            path = package.parent_file.path + (package.package_type,)
        else:
            path = (self.name, package.package_type)

        if add_to_package_list and path in self._package_paths and not \
                set_package_name and package.package_name in \
                self.package_name_dict:
            # package of this type with this name already exists, replace it
            print('WARNING: Package with name {} already exists. '
                  'Replacing existing package.'.format(package.package_name))
            self.remove_package(self.package_name_dict[package.package_name])

        # make sure path is unique
        if path in self._package_paths:
            path_iter = mfdatautil.PathIter(path)
            for new_path in path_iter:
                if new_path not in self._package_paths:
                    path = new_path
                    break
        self._package_paths[path] = 1

        if package.package_type.lower() == 'nam':
            return path, self.structure.name_file_struct_obj

        package_struct = \
          self.structure.get_package_struct(package.package_type)
        if set_package_name:
            # produce a default package name
            if package_struct is not None and \
              package_struct.multi_package_support:
                # check for other registered packages of this type
                name_iter = mfdatautil.NameIter(package.package_type, False)
                for package_name in name_iter:
                    if package_name not in self.package_name_dict:
                        package.package_name = package_name
                        break
            else:
                package.package_name = package.package_type

        if set_package_filename:
            package.filename = '{}.{}'.format(self.name, package.package_type)

        if add_to_package_list:
            self._add_package(package, path)

            # add obs file to name file if it does not have a parent
            if package.package_type in self.structure.package_struct_objs or \
              (package.package_type == 'obs' and package.parent_file is None):
                # update model name file
                pkg_type = package.package_type.upper()
                if len(pkg_type) > 3 and pkg_type[-1] == 'A':
                    pkg_type = pkg_type[0:-1]
                # Model Assumption - assuming all name files have a package
                # rec array
                self.name_file.packages.\
                  update_record(['{}6'.format(pkg_type), package.filename,
                  package.package_name], 0)
        if package_struct is not None:
            return (path, package_struct)
        else:
            print('WARNING: Unable to register unsupported file type {} for '
                  'model {}.'.format(package.package_type, self.name))
        return (None, None)

    def load_package(self, ftype, fname, pname, strict, ref_path,
                     dict_package_name=None, parent_package=None):
        """
        loads a package from a file

        Parameters
        ----------
        ftype : string
            the file type
        fname : string
            the name of the file containing the package input
        pname : string
            the user-defined name for the package
        strict : bool
            strict mode when loading the file
        ref_path : string
            path to the file. uses local path if set to None
        dict_package_name : string
            package name for dictionary lookup
        parent_package : MFPackage
            parent package

        Examples
        --------
        """
        sim_struct = mfstructure.MFStructure().sim_struct
        if (ftype in self.structure.package_struct_objs and
          self.structure.package_struct_objs[ftype].multi_package_support) or \
          (ftype in sim_struct.utl_struct_objs and
          sim_struct.utl_struct_objs[ftype].multi_package_support):
            # resolve dictionary name for package
            if dict_package_name is not None:
                if parent_package is not None:
                    dict_package_name = '{}_{}'.format(parent_package.path[-1],
                                                       ftype)
                else:
                    # use dict_package_name as the base name
                    if ftype in self._ftype_num_dict:
                        self._ftype_num_dict[dict_package_name] += 1
                    else:
                        self._ftype_num_dict[dict_package_name] = 0
                    dict_package_name = '{}_{}'.format(dict_package_name,
                                                       self._ftype_num_dict[
                                                         dict_package_name])
            else:
                # use ftype as the base name
                if ftype in self._ftype_num_dict:
                    self._ftype_num_dict[ftype] += 1
                else:
                    self._ftype_num_dict[ftype] = 0
                if pname is not None:
                    dict_package_name = pname
                else:
                    dict_package_name = '{}_{}'.format(ftype,
                                                       self._ftype_num_dict[
                                                       ftype])
        else:
            dict_package_name = ftype

        # clean up model type text
        model_type = self.structure.model_type
        while mfdatautil.DatumUtil.is_int(model_type[-1]):
            model_type = model_type[0:-1]

        # create package
        package_obj = self.package_factory(ftype, model_type)
        package = package_obj(self, fname=fname, pname=dict_package_name,
                              loading_package=True,
                              parent_file=parent_package)
        try:
            package.load(strict)
        except ReadAsArraysException:
            #  create ReadAsArrays package and load it instead
            package_obj = self.package_factory('{}a'.format(ftype), model_type)
            package = package_obj(self, fname=fname, pname=dict_package_name,
                                  loading_package=True,
                                  parent_file=parent_package)
            package.load(strict)

        # register child package with the model
        self._add_package(package, package.path)
        if parent_package is not None:
            # register child package with the parent package
            parent_package._add_package(package, package.path)
mfmodel module.  Contains the MFModel class MODFLOW Model Class.  Represents a single model in a simulation.
 
     Parameters
     ----------
     simulation_data : MFSimulationData
         simulation data object
     structure : MFModelStructure
         structure of this type of model
     modelname : string
         name of the model
     model_nam_file : string
         relative path to the model name file from model working folder
     version : string
         version of modflow
     exe_name : string
         model executable name
     model_ws : string
         model working folder path
     disfile : string
         relative path to dis file from model working folder
     grid_type : string
         type of grid the model will use (structured, unstructured, vertices)
 
     Attributes
     ----------
     model_name : string
         name of the model
     exe_name : string
         model executable name
     packages : OrderedDict(MFPackage)
         dictionary of model packages
     _name_file_io : MFNameFile
         name file
 
     Methods
     -------
     load : (simulation : MFSimulationData, model_name : string,
       namfile : string, type : string, version : string, exe_name : string,
       model_ws : string, strict : boolean) : MFSimulation
         a class method that loads a model from files
     write
         writes the simulation to files
     remove_package : (package_name : string)
         removes package from the model.  package_name can be the
         package's name, type, or package object to be removed from
         the model
     set_model_relative_path : (path : string)
         sets the file path to the model folder and updates all model file paths
     is_valid : () : boolean
         checks the validity of the model and all of its packages
 
     See Also
     --------
 
     Notes
     -----
 
     Examples
     -------- # check for spatial reference info in kwargs # check for extraneous kwargs # build model name file # create name file based on model type - support different model types __getattr__ - used to allow for getting packages as if they are
                       attributes
 
         Parameters
         ----------
         item : str
             3 character package name (case insensitive)
 
 
         Returns
         -------
         pp : Package object
             Package object of type :class:`flopy.pakbase.Package` Load an existing model.
 
         Parameters
         ----------
         simulation : MFSimulation
             simulation object that this model is a part of
         simulation_data : MFSimulationData
             simulation data object
         structure : MFModelStructure
             structure of this type of model
         model_name : string
             name of the model
         model_nam_file : string
             relative path to the model name file from model working folder
         version : string
             version of modflow
         exe_name : string
             model executable name
         model_ws : string
             model working folder relative to simulation working folder
         strict : boolean
             strict mode when loading files
         model_rel_path : string
             relative path of model folder to simulation folder
         Returns
         -------
         model : MFModel
 
         Examples
         -------- # load name file # order packages # FIX: Transport - Priority packages maybe should not be hard coded # load packages # strip off model relative path from the file path # load package # load referenced packages # TODO: fix jagged lists where appropriate write model to model files
 
         Parameters
         ----------
         ext_file_action : ExtFileAction
             defines what to do with external files when the simulation path has
             changed.  defaults to copy_relative_paths which copies only files
             with relative paths, leaving files defined by absolute paths fixed.
 
         Returns
         -------
 
         Examples
         -------- # write name file # write packages checks the validity of the model and all of its packages
 
         Parameters
         ----------
 
         Returns
         -------
         valid : boolean
 
         Examples
         -------- # valid name file # valid packages # required packages exist sets the file path to the model folder relative to the simulation
         folder and updates all model file paths, placing them in the model
         folder
 
         Parameters
         ----------
         model_ws : string
             model working folder relative to simulation working folder
 
         Returns
         -------
 
         Examples
         -------- # update path in the file manager # update model name file location in simulation name file # update listing file location in model name file # update package file locations in model name file # update files referenced from within packages # remove package from local dictionaries and lists removes a package and all child packages from the model
 
         Parameters
         ----------
         package_name : str
             package name, package type, or package object to be removed from
             the model
 
         Returns
         -------
 
         Examples
         -------- # remove package from name file # build list of child packages # remove child packages registers a package with the model
 
         Parameters
         ----------
         package : MFPackage
             package to register
         add_to_package_list : bool
             add package to lookup list
         set_package_name : bool
             produce a package name for this package
         set_package_filename : bool
             produce a filename for this package
 
         Returns
         -------
         (path : tuple, package structure : MFPackageStructure)
 
         Examples
         -------- # package of this type with this name already exists, replace it # make sure path is unique # produce a default package name # check for other registered packages of this type # add obs file to name file if it does not have a parent # update model name file # Model Assumption - assuming all name files have a package # rec array loads a package from a file
 
         Parameters
         ----------
         ftype : string
             the file type
         fname : string
             the name of the file containing the package input
         pname : string
             the user-defined name for the package
         strict : bool
             strict mode when loading the file
         ref_path : string
             path to the file. uses local path if set to None
         dict_package_name : string
             package name for dictionary lookup
         parent_package : MFPackage
             parent package
 
         Examples
         -------- # resolve dictionary name for package # use dict_package_name as the base name # use ftype as the base name # clean up model type text # create package #  create ReadAsArrays package and load it instead # register child package with the model # register child package with the parent package