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

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)

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 occurr, False otherwise.

Log

Defines an easy function to set up a logger.

clusterking.util.log.get_logger(name='Logger', level=30, sh_level=30)

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)

Metadata

Miscellaneous utilities

clusterking.util.metadata.nested_dict()

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)

Turn a dictionary of dictionaries into a nested_dict default dict.

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

clusterking.util.metadata.get_git_info(log=None, path=None)

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]

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]

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)

clusterking.util.metadata.get_version()

Return ClusterKinG version.

Testing

clusterking.util.testing.set_testing_mode(testing_mode: bool) → None

Set an environment variable signalling if we are in testing mode.

Parameters:testing_mode (bool) – True if we are in testing mode Returns:None

clusterking.util.testing.is_testing_mode()

clusterking.util.testing.test_jupyter_notebook(path) → None

Runs jupyter notebook. A ValueError is raised if the file was not found.

class clusterking.util.testing.MyTestCase(*args, **kwargs)

Bases: unittest.case.TestCase

Implements an additional general testing methods.

__init__(*args, **kwargs)

assertAllClose(a, b)

Compares two numpy arrays