Utility functionality (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 functionality

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”.

Miscellaneous functionality

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


Return ordinal string version of cardinal int n.


Find duplicate elements in an iterable.

safe_md5(open_file[, block_size])

Computes an md5 sum without loading the file into memory


Decorator for class-level properties.



Warn about potentially accidental use of inefficient code.


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