9.2.6. Utils¶

General utilities and helpers.

class junifer.utils.ConfigManager(*args, **kwargs)¶

Manage configuration parameters.

Attributes:

_configdict: Configuration parameters.

Initialize the class.

delete(key)¶

Delete configuration parameter.

Parameters:

keystr: The configuration key to delete.

get(key, default=None)¶

Get configuration parameter.

Parameters:

keystr: The configuration key to get.
defaultbool or int or float or None, optional: The default value to return if the key is not found (default None).

Returns:

bool or int or float: The configuration value.

set(key, val)¶

Set configuration parameter.

Parameters:

keystr: The configuration key to set.
valbool or int or float: The value to set key to.

junifer.utils.check_standardize(value)¶

Check the value of a standardize parameter.

Booleans were replaced by the strategy names used by nilearn, so they raise an error explaining the change instead of a generic validation error.

Parameters:

valueAny: The value of the parameter.

Returns:

Any: The value of the parameter.

Raises:

ValueError: If value is a boolean.

junifer.utils.configure_logging(level='WARNING', level_datalad=None)¶

Configure the logging functionality.

Parameters:

levelint or {“DEBUG”, “INFO”, “WARNING”, “ERROR”}: The level of the messages to print. If string, it will be interpreted as elements of logging (default “WARNING”).
level_dataladint or {“DEBUG”, “INFO”, “WARNING”, “ERROR”}, optional: The level of the messages to print for datalad. If string, it will be interpreted as elements of logging. If None, it will be set as the level parameter (default None).

junifer.utils.deep_update(d, u)¶

Deep update d with u.

From: “https://stackoverflow.com/questions/3232943/update-value-of-a-nested -dictionary-of-varying-depth”

Parameters:

ddict: The dictionary to deep-update.
udict: The dictionary to deep-update d with.

Returns:

dict: The updated dictionary.

junifer.utils.ensure_list(value)¶

Ensure list.

junifer.utils.ensure_list_or_none(value)¶

Ensure list or None.

junifer.utils.make_executable(path)¶

Make path executable.

Parameters:

pathpathlib.Path: The path to make executable.

junifer.utils.raise_error(msg, klass=<class 'ValueError'>, exception=None)¶

Raise error, but first log it.

Parameters:

msgstr: The message for the exception.
klasssubclass of Exception, optional: The subclass of Exception to raise using (default ValueError).
exceptionException, optional: The original exception to follow up on (default None).

junifer.utils.run_ext_cmd(name, cmd, cwd=None)¶

Run external command via subprocess.

Parameters:

namestr: The name of the command.
cmdlist of str: The command to run as list of string.
cwdpathlib.Path or None, optional: The directory to run the command in, e.g., for commands that write extra files in the current directory. If None, the current directory is used (default None).

Raises:

RuntimeError: If command fails.

junifer.utils.warn_with_log(msg, category=<class 'RuntimeWarning'>)¶

Warn, but first log it.

Parameters:

msgstr: Warning message.
categorysubclass of Warning, optional: The warning subclass (default RuntimeWarning).