Utility#

This module bundles mostly technical utilities that might not be all this interesting for users.

Interface#

Utils for the command line interface (CLI).

clusterking.util.cli.yn_prompt(question: str, yes=None, no=None) → bool[source]#

Ask yes-no question.

Parameters

  • question – Description of the prompt

  • yes – List of strings interpreted as yes

  • no – List of strings interpreted as no

Returns

True if yes, False if no.

clusterking.util.cli.handle_overwrite(paths, behavior, log)[source]#

Do we want to overwrite a file that exists?

Parameters

  • paths – List of pathlib.Paths

  • behavior – How to proceed if output file already exists: ‘ask’, ‘overwrite’, ‘raise’

  • log – logging.Logger instance

Returns

True if overwrite will occur, False otherwise.

Log#

Defines an easy function to set up a logger.

clusterking.util.log.get_logger(name='Logger', level=30, sh_level=30)[source]#

Sets up a logging.Logger.

If the colorlog module is available, the logger will use colors, otherwise it will be in b/w. The colorlog module is available at https://github.com/borntyping/python-colorlog but can also easily be installed with e.g. ‘sudo pip3 colorlog’ or similar commands.

Parameters

  • name – name of the logger

  • level – General logging level

  • sh_level – Logging level of stream handler

Returns

Logger

clusterking.util.log.set_global_log_level(level=20)[source]#

Metadata#

Miscellaneous utilities

clusterking.util.metadata.nested_dict()[source]#

This is very clever and stolen from https://stackoverflow.com/questions/16724788/ Use it to initialize a dictionary-like object which automatically adds levels. E.g.

a = nested_dict()
a['test']['this']['is']['working'] = "yaaay"
clusterking.util.metadata.turn_into_nested_dict(nested)[source]#

Turn a dictionary of dictionaries into a nested_dict default dict.

clusterking.util.metadata.version_info(log=None, path=None) → Dict[str, str][source]#
clusterking.util.metadata.get_git_info(log=None, path=None)[source]#

Return dictionary containing status of the git repository (commit hash, date etc.

Parameters

  • log – logging.Logger object (optional)

  • path – path to .git subfolder or search path (optional)

Returns

dictionary

clusterking.util.metadata.save_git_info(output_path=None, *args, **kwargs) → Dict[str, str][source]#

Save output of git_info to a file.

Parameters

  • output_path – Output path. If None, the default will be bclustering/git_info.json

  • *args – Passed on to git_info

  • **kwargs – Passed on to git_info

Returns

Output of git_info

clusterking.util.metadata.load_git_info(input_path=None) → Dict[str, str][source]#

Load previously saved output of git_info from a json file.

Parameters

input_path – Input path to json file. If None, the default will be bclustering/git_info.json

Returns

Parsed json file (should be identical to saved output of version_info).

clusterking.util.metadata.failsafe_serialize(obj)[source]#
clusterking.util.metadata.get_version()[source]#

Return ClusterKinG version.

Testing#