Thank you Dan! The codecov.io mirror seems to be up-to-date now. It's great to see Bioconductor's and individual packages' code coverage increasing!
Cheers, Andrzej On Thu, Sep 10, 2015 at 10:59 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > Hi Andrzej, > > > ----- Original Message ----- > > From: "Andrzej Oleś" <andrzej.o...@gmail.com> > > Cc: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" < > bioc-devel@r-project.org> > > Sent: Thursday, September 10, 2015 12:35:19 AM > > Subject: Re: [Bioc-devel] Announcing newtest coverage shields > > > > > > > > > > > > > > Hi Dan, > > > > I find that the coverage shields are an extremely useful metrics for > > both end-users and package developers, as they reflect code quality > > and motivate to improve package test coverage. > > > > I've noticed that the badges are not updated as frequently as I would > > expect. Most of the packages on > > https://codecov.io/github/Bioconductor-mirror haven't been updated > > for 3 weeks now, and the badges on BioC landing pages seem to > > reflect this state. For example, see > > > > http://www.bioconductor.org/packages/devel/bioc/html/EBImage.html > > > > which has been updated a couple of times in the last 3 weeks, last > > time on 4 September. > > > > > > It would be great if the badges would show up-to-date coverage, as > > suggested in the announcement post. > > > > > > This is fixed now for EBImage; other packages will get updated tomorrow. > > This had to do with moving the build machines to the cloud; in doing so, > we needed a different way to map svn revision numbers to git commit ids, > also it appears that the codecov.io API changed slightly. > > Good work increasing the test coverage in EBImage! > > Dan > > > > > Cheers, > > > > Andrzej > > > > > > > > On Thu, Jun 25, 2015 at 3:21 AM, Henrik Bengtsson < > > henrik.bengts...@ucsf.edu > wrote: > > > > > > On Wed, Jun 24, 2015 at 5:42 PM, Dan Tenenbaum < > > dtene...@fredhutch.org > wrote: > > > Hello Bioconductors, > > > > > > We're pleased to announce a new shield to join the ones we rolled > > > out in May. > > > > > > The new shield measures test coverage of a package, as determined > > > by Jim Hester's covr package. > > > > > > Coverage is a measure of the degree to which package code is tested > > > by your unit tests ( https://en.wikipedia.org/wiki/Code_coverage > > > ). If you don't know what unit tests are, read our guidelines at > > > http://bioconductor.org/developers/how-to/unitTesting-guidelines/ > > > . > > > > > > These shields are on all package landing pages for software > > > packages in release and devel. An example shield can be seen at > > > > > > http://bioconductor.org/packages//Biobase/ > > > > > > It links to a detailed coverage report at https://codecov.io/ . > > > > > > If package coverage cannot be determined (shield value is > > > 'unknown'), the shield links to a section of > > > > http://bioconductor.org/developers/how-to/unitTesting-guidelines/#coverage > > > explaining why > > > this might be. > > > > > > Note that the coverage calculation happens on our linux build > > > machines only and is not run as part of the nightly builds, but it > > > is run several times a week. Only packages whose code has changed > > > since the last calculation are run through covr. > > > > > > We hope this shield motivates package developers to add unit tests > > > (if they don't have them already) and improve their package's unit > > > test coverage. Refer to the covr > > > documentation ( > > > http://cran.r-project.org/web/packages/covr/README.html ) for more > > > information on how to do this. > > > > > > Questions and comments are welcome as always on the bioc-devel > > > list. > > > > [snare drums] ... hi-hat! > > > > Thank you very much for adding this. For folks who yet haven't looked > > into code coverage - it's extremely useful: > > > > * You get line-by-line coverage estimates for your R code, e.g. > > https://codecov.io/github/Bioconductor-mirror/DNAcopy/R/segment.R > > > > * Also for your native code, e.g. > > > https://codecov.io/github/Bioconductor-mirror/DNAcopy/src/changepoints.f?ref=master > > > > * The line-to-line reports makes it very easy to design new tests. > > > > My experience from turning uncovered ("red") code lines into covered > > ("green") is that you are quite likely to discover a few more bugs > > along the way. I'd say it's one of the most efficient ways to find > > unknown bugs that I ever used. A useful rule of thumb is to always > > make sure that the code coverage never decreases whenever a new > > version is released. > > > > /Henrik > > > > > > > > > > > > Thanks, > > > Dan > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel