.. This file is part of khmer, https://github.com/dib-lab/khmer/, and is Copyright (C) 2014-2015 Michigan State University Copyright (C) 2015 The Regents of the University of California. It is licensed under the three-clause BSD license; see LICENSE. Contact: khmer-project@idyll.org Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Michigan State University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Contact: khmer-project@idyll.org *************************** Roadmap to v3.0, v4.0, v5.0 *************************** Background ========== 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 https://github.com/dib-lab/khmer/issues/389 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. v5.0 ==== 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)