Utilities for Developers (`skbio.util`)#

This package provides general exception/warning definitions used throughout scikit-bio, as well as various utility functionality, including I/O and unit-testing convenience functions.

Testing utilities#

Common functionality to support testing in skbio.

`get_data_path`(fn[, subfolder])	Return path to filename `fn` in the data folder.
`assert_ordination_results_equal`(left, right)	Assert that ordination results objects are equal.
`assert_data_frame_almost_equal`(left, right)	Raise AssertionError if `pd.DataFrame` objects are not "almost equal".

Plotting utilities#

PlottableMixin()

A plottable object.

Miscellaneous utilities#

Generally useful functionality that doesn’t fit in more specific locations.

`get_rng`([seed])	Get a random generator.
`cardinal_to_ordinal`(n)	Return ordinal string version of cardinal int n.
`find_duplicates`(iterable)	Find duplicate elements in an iterable.
`safe_md5`(open_file[, block_size])	Compute an md5 sum without loading the file into memory.
`classproperty`(func)	Decorator for class-level properties.

Developer warnings#

EfficiencyWarning

Warn about potentially accidental use of inefficient code.

Details#

exception skbio.util.EfficiencyWarning[source]#