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	Return path to filename fn in the data folder.
assert_ordination_results_equal	Assert that ordination results objects are equal.
assert_ordination_results_equal_np	NumPy version of testing ordination results.
assert_data_frame_almost_equal	Raise AssertionError if pd.DataFrame objects are not "almost equal".

Plotting utilities

PlottableMixin

A plottable object.

Randomization

get_rng

Get a random generator.

Decorators

overrides	Indicate that a member is being overridden from a specific parent class.
classproperty	Decorator for class-level properties.
classonlymethod	Just like classmethod, but it can't be called on an instance.
deprecated	Mark a function or a method as deprecated.
aliased	Create an alias for a function or method.
register_aliases	Register aliases of members of a module or class.
params_aliased	Create aliases for parameters of a function or method.

Miscellaneous utilities

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

cardinal_to_ordinal	Return ordinal string version of cardinal int n.
find_duplicates	Find duplicate elements in an iterable.
safe_md5	Compute an md5 sum without loading the file into memory.