[Biopython-dev] Coverage metrics

[Peter Cock]

On Mon, May 25, 2015 at 3:00 AM, Tiago Rodrigues Antao <tra at popgen.net> wrote:
> Dear all,
>
> I have been playing with metrics of test coverage with Biopython.
>
> There is this free service, called coveralls.io that allows to extract
> test coverage metrics from travis-ci runs.
>
> You can seen an example run here:
> https://coveralls.io/builds/2640315
> Check build 4.4:
> https://coveralls.io/jobs/6189201
> (the file name resolution is configured for Python 3.4 now - which is
> reprenseted by build 4.4)
> And, for example, a file report on the state of test coverage:
> https://coveralls.io/files/772119763
> Where you can get the coverage per line of code (number of times passed
> or none).
>
> This can be implemented with a trivial change to the travis file:
> https://github.com/tiagoantao/biopython/blob/coverage/.travis.yml
>
> As it stands this still has a few rough edges, but I think it is quite
> interesting and promising
>
> Tiago

I agree - should we apply this to the master branch?

One minor issue is that this shows the coverage statistics of
the offline tests only, so all the web API code appears to
have zero coverage. Similarly some of the TravisCI tests
are skipped due to missing dependencies (usually command
line tools or slow to install libraries).

Perhaps we need consider having one "online" target
in the TravisCI build matrix (and use that for coveralls)?

Peter