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 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])

Compute an md5 sum without loading the file into memory.


Decorator for class-level properties.

Developer warnings#


Warn about potentially accidental use of inefficient code.


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