Roadmap to v2.0, v3.0, v4.0


To make the khmer project easier to use and easier to build upon several fundamental changes need to happen. This document outlines our plan to do so while minimizing the impact of these changes on our existing users.

The discussion that lead to this document can be read at

Remainder of v1.x series

Start of transition to a single entrypoint named oxli. This will be exempt from the project’s semantic versioning and will be advertised as experimental and unstable.

Migration of Python script functionality to a Python module named oxli. As the code moves over there will be no change to external script functionality or their command line interfaces.

v2.x series

oxli command is now under semantic versioning. Scripts are still the advertised and preferred entry point for users. Developers and workflow systems can start to trial oxli but need not switch until 3.0. New functionality is added to both the scripts and the oxli command.

v3.0 and project renaming

Project renamed to ‘oxli’; all references to ‘khmer’ removed from the code and documentation except for a single note in the docs. All scripts dropped as their functionality has been moved to the oxli command. Websites that we maintain that have ‘khmer’ in the URL will have redirects installed.

Refinement of the Python API continues, however it is not part of the semantic versioning of the project.


The semantic versioning now extends to the Python API.

Python API wishlist

Python 3.0 support

API for multiple container types and implementation of the same.

Cleanup of Python/C++ class hierarchy to cut down on boilerplate glue code.

Switch to new-style Python objects (see LabelHash & Hashbits)

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