[Bioc-devel] Announcing newtest coverage shields

[Dan Tenenbaum]

Hi Andrzej,


----- Original Message -----
> From: "Andrzej Oleś" <andrzej.oles at gmail.com>
> Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at 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.bengtsson at ucsf.edu > wrote:
> 
> 
> On Wed, Jun 24, 2015 at 5:42 PM, Dan Tenenbaum <
> dtenenba at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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