Config files

The primary documentation for the config parser is in the tranche documentation. Here, we include some specific details relevant to using the tranche.Tranche in polaris.

Here, we provide the polaris.config.PolarisConfigParser that has almost the same functionality but also ensures that certain relative paths are converted automatically to absolute paths. PolarisConfigParser also has attributes for a filepath where the config file will be written out and a list of symlinks that will point to filepath. It also has a polaris.config.PolarisConfigParser.setup() method that can be overridden to add config options (e.g. algorithmically from other config options) as part of setting up polaris tasks and steps. These features are included to accommodate sharing config options across shared steps and/or multiple tasks.

The tranche.Tranche.add_from_package() method can be used to add the contents of a config file within a package to the config options. Examples of this can be found in many tasks as well as in the polaris.setup module. Here is a typical example from polaris.tasks.ocean.inertial_gravity_wave.InertialGravityWave:

from polaris import Task


class InertialGravityWave(Task):
    def __init__(self, component):
        name = 'inertial_gravity_wave'
        subdir = f'planar/{name}'
        super().__init__(component=component, name=name, subdir=subdir)

        ...

        self.config.add_from_package(
            'polaris.tasks.ocean.inertial_gravity_wave',
            'inertial_gravity_wave.cfg')

The first and second arguments are the name of a package containing the config file and the name of the config file itself, respectively. You can see that the file is in the path polaris/ocean/tasks/baroclinic_channel (replacing the . in the module name with /). In this case, we know that the config file should always exist, so we would like the code to raise an exception (exception=True) if the file is not found. This is the default behavior. In some cases, you would like the code to add the config options if the config file exists and do nothing if it does not. In this example from polaris.setup.setup_task(), there may not be a config file for the particular machine we’re on, and that’s fine:

from polaris.config import PolarisConfigParser


def _get_basic_config(config_file, machine, component_path, component):
    config = PolarisConfigParser()
    if machine is not None:
        config.add_from_package('mache.machines', f'{machine}.cfg',
                                exception=False)

If there isn’t a config file for this machine, nothing will happen.

The MpasConfigParser class also includes methods for adding a user config file and other config files by file name, but these are largely intended for use by the framework rather than individual tasks.

Other methods for the MpasConfigParser are similar to those for configparser.ConfigParser. In addition to get(), getinteger(), getfloat() and getboolean() methods, this class implements tranche.Tranche.getlist(), which can be used to parse a config value separated by spaces and/or commas into a list of strings, floats, integers, booleans, etc. Other useful methods are tranche.Tranche.getexpression(), which can be used to get python dictionaries, lists, and tuples, and tranche.Tranche.getnumpy(), which also suppports a small set of functions (range(), numpy.linspace(), numpy.arange(), and numpy.array())

Shared config files

Often, it makes sense for many tasks and steps to share the same config options. The default behavior is for a task and its “owned” steps to share a config file in the task’s work directory called {task.name}.cfg and symlinks with that same name in each step’s work directory. The default for a shared step is to have its own {step.name}.cfg in its work directory.

Developers can create shared config parsers that define the location of the shared config file and add them to tasks and steps using polaris.Task.set_shared_config() and polaris.Step.set_shared_config(). The location of the shared config file should be intuitive to users but local symlinks will also make it easy to modify the shared config options from within any of the tasks and steps that use them.

As an example, the baroclinic channel tasks share a single baroclinic_channel.cfg config file for each resolution that resides in the resolution’s work directory:

from polaris.config import PolarisConfigParser
from polaris.resolution import resolution_to_string
from polaris.tasks.ocean.baroclinic_channel.default import Default
from polaris.tasks.ocean.baroclinic_channel.init import Init
from polaris.tasks.ocean.baroclinic_channel.rpe import Rpe


def add_baroclinic_channel_tasks(component):
    for resolution in [10., 4., 1.]:
        resdir = resolution_to_string(resolution)
        resdir = f'planar/baroclinic_channel/{resdir}'

        config_filename = 'baroclinic_channel.cfg'
        config = PolarisConfigParser(filepath=f'{resdir}/{config_filename}')
        config.add_from_package('polaris.tasks.ocean.baroclinic_channel',
                                'baroclinic_channel.cfg')

        init = Init(component=component, resolution=resolution, indir=resdir)
        init.set_shared_config(config, link=config_filename)

        default = Default(component=component, resolution=resolution,
                          indir=resdir, init=init)
        default.set_shared_config(config, link=config_filename)
        component.add_task(default)

        ...

        component.add_task(Rpe(component=component, resolution=resolution,
                               indir=resdir, init=init, config=config))

For most tasks and steps, it is convenient to call set_shared_config() after constructing the step or task and before adding it to the component. In the example of the Rpe task here, we need the shared config in the constructor so it has to be passed in. We call self.set_shared_config() in the constructor, and then use config options to determine the steps to be added as follows:

from polaris import Task
from polaris.tasks.ocean.baroclinic_channel.forward import Forward
from polaris.tasks.ocean.baroclinic_channel.rpe.analysis import Analysis


class Rpe(Task):
    def __init__(self, component, resolution, indir, init, config):
        super().__init__(component=component, name='rpe', indir=indir)
        self.resolution = resolution

        # this needs to be added before we can use the config options it
        # brings in to set up the steps
        self.set_shared_config(config, link='baroclinic_channel.cfg')
        self.add_step(init, symlink='init')
        self._add_rpe_and_analysis_steps()

    def _add_rpe_and_analysis_steps(self):
        """ Add the steps in the test case either at init or set-up """
        config = self.config
        component = self.component
        resolution = self.resolution

        nus = config.getlist('baroclinic_channel_rpe', 'viscosities',
                             dtype=float)
        for nu in nus:
            name = f'nu_{nu:g}'
            step = Forward(
                component=component, name=name, indir=self.subdir,
                ntasks=None, min_tasks=None, openmp_threads=1,
                resolution=resolution, nu=nu)

            step.add_yaml_file(
                'polaris.tasks.ocean.baroclinic_channel.rpe',
                'forward.yaml')
            self.add_step(step)

        self.add_step(
            Analysis(component=component, resolution=resolution, nus=nus,
                     indir=self.subdir))

Comments in config files

One of the main advantages of tranche.Tranche over configparser.ConfigParser is that it keeps track of comments that are associated with config sections and options.

Comments must begin with the # character. They must be placed before the config section or option in question (preferably without blank lines between). The comments can be any number of lines long.