[Bioc-devel] Announcing newtest coverage shields

[Andrzej Oleś]

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 <dtenenba at fredhutch.org>
wrote:

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

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