[Bioc-devel] Announcing newtest coverage shields

[Andrzej Oleś]

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.

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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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