Le Wed, Mar 19, 2014 at 10:20:33PM -0400, Yaroslav Halchenko a écrit : > > upon brief look: I have apt-get sourced cufflinks -- found no > unittests available > > the same for tophat
Hi Yaroslav, yes, unit tests are not always available, but I see more and more editorials in top journals advocating “reproducible research”, so I think that more and more bioinformaticians will be able to convince their managers to work on unit tests. It is very good that in Debian we have the autopkgtest infrastructure growing at the same time. For packages without upstream tests, in the meantime, even the most simple tests like running the command with the --help option, are potentially useful. My favorite example is T-COFFEE, where we were distributing a 100 % broken package on arm for years. With autopkgtest, we will have a better overview on what package works where (just a successful build is not enough), and this will help people to evaluate the feasiblity of projects based on Debian on amd64, and also on more rarely used platforms (such as the Raspberry Pi as we read on this list). Slightly more complex tests can often be built from the examples in the program's README. On my side, I am still on a learning phase with autopkgtest, but I hope that collectively we will have a clear vision on what to recommend Upstream so that they can write or accept user-contributed tests are trivially run by autopkgtest. I also like a lot the “litteral programming” side of the “reproducible research” trend. I am developing some tutorials based on real data analyses from my work, which are currently implemented in knitr (http://yihui.name/knitr/), and which I hope to iron out so that they can be used to test a Debian image in an integrated way. However, they currently still use programs that are not yet packaged. Work in progress but comments welcome ! https://github.com/charles-plessy/tutorial Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
