Command line scripts

emsarray provides a set of tools to make it easy to write your own command line scripts that interact with emsarray, while promoting robustness and best practice. These scripts can be used to automate any repetitive process using emsarray.

Build from the following template to get started. A full copy of this scriptcan be downloaded for easier reading: sea_surface_temperature.py. Run this script as python3 sea_surface_temperature.py –help to see it in action.

#!/usr/bin/env python3
import argparse
import logging
import pathlib

import emsarray
import xarray
from emsarray.cli import console_entrypoint
from emsarray.cli.utils import geometry_argument
from shapely.geometry.base import BaseGeometry

# Log progress messages using `logger.info(...)`,
# debug messages using `logger.debug(...)`,
# and warning messages using `logger.warn(...)` or `logger.error(...)`.
# Print regular output using `print()`.
logger = logging.getLogger(__name__)


def command_line_flags(parser: argparse.ArgumentParser) -> None:
    """
    Specify all command line arguments here. These can be datasets to
    work with, or names of variables, date ranges, polygons and other
    geometries....

    See https://docs.python.org/3/library/argparse.html
    """
    parser.add_argument(
        "dataset", type=pathlib.Path,
        help="Path to a dataset")
    parser.add_argument(
        "geometry", type=geometry_argument,
        help="The region in which to calculate mean sea surface temperature")
    parser.add_argument(
        "-t", "--temperature-variable",
        type=str, default="temp", metavar="temp",
        help=(
            "The name of the temperature variable in the dataset. "
            "Defaults to 'temp'"
        ))


@console_entrypoint(command_line_flags)
def main(options: argparse.Namespace) -> None:
    """
    This function is where the script will start. `options` will have an
    attribute for each command line flag defined. Access them as
    `options.dataset` or `options.geometry` etc.
    """

    # Log what we are about to do
    logger.info(
        "Calculating mean sea surface temperature for %r in region %s",
        str(options.dataset), options.geometry.wkt)

    # Open the dataset and do our calculations
    dataset = emsarray.open_dataset(options.dataset)
    mean_sea_surface_temperature = calculate_mean_sea_surface_temperature(
        dataset=dataset,
        temperature=dataset[options.temperature_variable],
        geometry=options.geometry)

    # Print the output
    print(mean_sea_surface_temperature)


def calculate_mean_sea_surface_temperature(
    dataset: xarray.Dataset,
    temperature: xarray.DataArray,
    geometry: BaseGeometry,
) -> float:
    """
    Calculate the mean sea surface temperature inside a region.
    """
    ...  # Implementation left as an exercise
    return 18.0


# This `if` needs to be the last thing in the script
if __name__ == '__main__':
    main()

This script will automatically gain the following features:

• Command line flags are clearly defined near the top of the file,

• It will generate useful output when run with --help or when provided invalid arguments,

• The logging output level can be set using -v,

• Errors are handled gracefully.