Roadmap to v3.0, v4.0, v5.0


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 version numbers are approximate; there may be additional major number releases to support needed changes to the API along the way. This document has been updated for v2.0 onwards from the original roadmap.

The discussion that lead to this document can be read at

Remainder of v2.x series

Continue transition to a single entrypoint named oxli . This will be exempt from the project's semantic versioning and will not be advertised as it is experimental and unstable. (For the 2.0 version we removed the oxli script just prior to release and restored it afterwards to the development tree.)

The Python script functionality will continue to migrate 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 (except for new features).

v3.x series

The 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 4.0. New functionality is added to both the scripts and the oxli command.

v4.0 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

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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