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.

Decorators

overrides(interface_class)	Indicate that a member is being overridden from a specific parent class.
classproperty(func)	Decorator for class-level properties.
classonlymethod(function, /)	Just like classmethod, but it can't be called on an instance.
deprecated(ver[, msg, append])	Mark a function or a method as deprecated.
aliased(name[, ver, warn])	Create an alias for a function or method.
register_aliases(cls)	Register aliases of members of a module or class.
params_aliased([params])	Create aliases for parameters of a function or method.

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.