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.
RepresentationWarning	Warn about assumptions made for the successful completion of a process.

Details

exception skbio.util.EfficiencyWarning

Warn about potentially accidental use of inefficient code.

For example, if a user doesn’t have an optimized version of a function/algorithm available in their scikit-bio installation, a slower, pure-Python implementation may be used instead. This warning can be used to let the user know they are using a version of the function that could be potentially orders of magnitude slower.

exception skbio.util.RepresentationWarning

Warn about assumptions made for the successful completion of a process.

Warn about substitutions, assumptions, or particular alterations that were made for the successful completion of a process. For example, if a value that is required for a task is not present, a best guess or least deleterious value could be used, accompanied by this warning.