Python CLI arguments preference: CLI > Env Var > config file > default

click-config-file-example.py

import click
import click_config_file
import yaml


def myprovider(file_path, cmd_name):
    with open(file_path) as config_file:
        return yaml.safe_load(config_file)

@click.command()
@click.option("--opt", default="from-default")
@click_config_file.configuration_option(
    provider=myprovider, config_file_name="config.yaml", implicit=False
)
def main(opt):
    print("opt", opt)


if __name__ == "__main__":
    main(auto_envvar_prefix="FOO")

config.yaml

opt: from-file

configargparse-example.py

import configargparse
import yaml

p = configargparse.ArgumentParser(
    auto_env_var_prefix="FOO_", add_config_file_help=False, add_env_var_help=False,
)
p.add("-c", "--my-config", required=False, is_config_file=True, help="config file path")
p.add("--opt", required=False, help="path to genome file", default="from-default")

options = p.parse_args()
print("opt", options.opt)

$ python configargparse-example.py
opt from-default

$ python configargparse-example.py -c config.yaml
opt from-file

$ env FOO_OPT=FROM_ENV_VAR python configargparse-example.py -c config.yaml
opt FROM_ENV_VAR

$ env FOO_OPT=FROM_ENV_VAR python configargparse-example.py -c config.yaml --opt from-CLI
opt from-CLI