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🎛️ Use configuration files for the NARPS open pipelines project

Purpose

The package narps_open.utils.configuration allows to load configuration files at runtime. This is useful, especially while running pipelines in several environments.

The class Configuration of module narps_open.utils.configuration acts as a parser for configuration files that are installed with the package narps_open. Configuration is a singleton (see narps_open.utils.singleton), meaning that there is only one instance of this object per runtime. This makes sure only one configuration type is used at a time (avoiding mixing parameters from several configurations).

For now, two configuration types are available:

  • testing : used for testing purposes only (while running pytest)
  • default : the default configuration

Usage

from narps_open.utils.configuration import Configuration

configuration = Configuration(config_type = 'testing')
dir_dataset = configuration['directories']['dataset'] # gets the directory where the dataset is

You can also set a custom configuration file that better suits your needs.

from narps_open.utils.configuration import Configuration

configuration = Configuration(config_type = 'custom')
configuration.config_file = '/path/to/my/own/configuration/file.toml'

Writing configuration files

Configuration files must conform with the TOML format. See this article on Real Python to know more about configuration files with TOML.

For python versions below 3.11, we use tomli as a dependency for parsing TOML. Starting from python 3.11, tomllib is included in the Standard Library and would replace tomli.