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.
TestRunner(filename) Simple wrapper class around nosetests functionality.
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.

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]) Computes an md5 sum without loading the file into memory
classproperty(func) Decorator for class-level properties.


EfficiencyWarning Warn about potentially accidental use of inefficient code.
RepresentationWarning Warn about assumptions made for the successful completion of a process.