QIIME is now hosted on GitHub, and bug in compare_alpha_diversity.py

26 10 2012

Hello QIIME users,
As you may or may not have noticed, as of 16 October QIIME is now hosted on GitHub rather than Sourceforge. This includes our source code revision control (which is now in git rather than svn), as well as our website. As always, you should still access the QIIME website through www.qiime.org, which now points to our site on GitHub.

We also ported all feature requests and bug reports to GitHub Issues, and have additionally moved our trac system from a locally-hosted, controlled access system to a GitHub-hosted, publicly accessible system (that same GitHub Issues tracker), so users can now check in to see what we’re working on. All new feature requests and bug reports should be submitted though GitHub Issues.

The switch to GitHub was primarily motivated by its Pull Request system, which facilitates a more open development environment than we think is possible on Sourceforge. Developers outside of the QIIME group can now fork the repository and make changes (e.g., add a new feature, fix a bug, or update some documentation). When your changes are ready, you can then issue a pull request and the developers will review those changes and either merge the pull request or get back to you with requests for modifications. As you can see here and here, we’ve already had a few pull requests from developers outside of the core developer group. Thanks for these initial submissions, and keep those pull requests coming! If you want to find out if we’re interested in incorporating a new feature that you’d like to work on, just ask on the QIIME Forum.

We have also recently expanded the qiime_test_data repository, which contains example input and output for nearly all of the QIIME scripts (and the remaining few will have test data added shortly). This provides an additional source of documentation for users (you can see what valid input looks like for a script, for example, see here for the pick_otus_through_otu_table.py script), and is also used to help us keep our usage examples up-to-date. You’ll notice now that when you call a script with the -h parameter that the input and output data corresponds to data in the qiime_test_data repository. We test these usage examples using qiime_test_data on a nightly basis as part of our automated testing system, so we now know within 24 hours if we’ve made a change that broke one of our usage examples.

Thanks to all of the QIIME developers who participated in the 15-16 October code sprint where we implemented these changes and additions!

Finally, we recently noticed a bug in the compare_alpha_diversity.py code that would result in an incorrect t-statistic and p-value being generated. This bug made the test more conservative (i.e., an insignificant p-value was returned when it should have been significant). This has been fixed, but affects all versions of QIIME prior to commit d223376 (22 October 2012). Sorry for the inconvenience! Please get in touch on the QIIME forum if you have any questions about this.

Greg

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