Version control¶

All of khmer development is done at http://github.com/dib-lab/khmer/ using Git and GitHub.

Issue tracking¶

All issue tracking is done via github issues: https://github.com/dib-lab/khmer/issues

Note especially meta issues that discuss collections of issues.

Automated tests¶

All tests are under tests/.

We use py.test.

All tests can be run with ‘make test’.

You can run specific files with py.test <filename>.

Documentation¶

Documentation is written in reStructuredText.

Documentation is hosted at https://khmer.readthedocs.io/.

Literate resting¶

We keep our tutorials and recipes working with automated tests a la:

https://github.com/dib-lab/literate-resting

Benchmarking¶

See @jessicamizzi’s latest, https://github.com/jessicamizzi/ep-streaming/blob/master/Utilization-Figures.ipynb, and 2014 PyCon (http://ivory.idyll.org/blog/2014-pycon.html).

Communication¶

There are two mailing lists (khmer and khmer-announce); we have a gitter channel; and that’s about it.

Proposing changes and code review¶

We use GitHub Flow; basically, submit pull requests.

Docs for getting started: https://khmer.readthedocs.io/en/v2.0/dev/getting-started.html

We have coding guidelines and a code review checklist: https://khmer.readthedocs.io/en/v2.0/dev/coding-guidelines-and-review.html

Sandbox scripts¶

We have lots of scripts in sandbox/ that are not officially supported but may be useful - see README.

Release checklist¶

We have a release checklist:

https://khmer.readthedocs.io/en/v2.0/dev/release.html