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.
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Return path to filename |
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Assert that ordination results objects are equal. |
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Raise AssertionError if |
Plotting utilities#
A plottable object. |
Miscellaneous utilities#
Generally useful functionality that doesn’t fit in more specific locations.
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Get a random generator. |
Return ordinal string version of cardinal int n. |
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Find duplicate elements in an iterable. |
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Compute an md5 sum without loading the file into memory. |
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Decorator for class-level properties. |
Developer warnings#
Warn about potentially accidental use of inefficient code. |
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Warn about assumptions made for the successful completion of a process. |
Details#
- exception skbio.util.EfficiencyWarning[source]#
Warn about potentially accidental use of inefficient code.
For example, if a user doesn’t have an optimized version of a function/algorithm available in their scikit-bio installation, a slower, pure-Python implementation may be used instead. This warning can be used to let the user know they are using a version of the function that could be potentially orders of magnitude slower.
- exception skbio.util.RepresentationWarning[source]#
Warn about assumptions made for the successful completion of a process.
Warn about substitutions, assumptions, or particular alterations that were made for the successful completion of a process. For example, if a value that is required for a task is not present, a best guess or least deleterious value could be used, accompanied by this warning.