Using Travis CI cron for network tests

[zmughal]

I have created some changes on top the PR at #223 that would allow the use of a specific branch for running network tests on a regular basis. The changes can be seen here. This tests whatever is currently on master, but makes the build appear as though it is coming from this specific branch. Thus, the coverage will appear separate from the coverage for all the other non-network tests, so there shouldn't be an issue of coverage fluctuation.

In order to enable the cron job, the branch must be created on the bioperl-live repository and then a cron job should be set up in the Travis CI settings for bioperl-live.

[zmughal]

Another useful thing to enable would be the Status API for Coveralls. This can show increases and decreases in code coverage. Go to the settings for the repo in Coveralls and tick off the "Use Status API" box then Save.

CC: @cjfields

[cjfields]

I'll mark this for the next milestone, I think we'll try to push a quick 1.7.2 release out to help @carandraug

[cjfields]

@zmughal BTW did you want to take this on?

[zmughal]

@cjfields, sure I could take on this issue, but I think I would need some level of admin access to make it apply to this repository. See the Travis CI documentation (emphasis mine):

Access rights on Travis CI is based on the access rights on GitHub:

• Users that have admin access to a repository on GitHub can change enable/disable it on Travis CI and change its settings.

I'm running the same cron job on a weekly basis under my own fork, so that can also be used as an indication of the current state of the network tests.

[carandraug]

Another useful thing to enable would be the Status API for Coveralls. This can show increases and decreases in code coverage. Go to the settings for the repo in Coveralls and tick off the "Use Status API" box then Save.

This is already checked by dizt zilla for the distributions that have been converted. It also runs of a bunch of other checks. The developers of said distributions should be running dzil test before push and it will fail unless a subroutine is marked as internal or documented.

[zmughal]

That is POD/documentation coverage (using Pod::Coverage) rather than just the code-related coverage. Code-related coverage (using Devel::Cover) measures if the tests actually call the functions and each branch condition is triggered. And that is only if the distribution uses dzil which bioperl-live doesn't, but other dists might.

An example of how that works with the Coveralls status API is like this: (from https://github.com/project-renard/curie/pull/209). The status API is what shows the

✘ coverage/coveralls Coverage decreased (-1.3%) to 97.544% 

part. The comments by the coveralls bot are extra and do not need to be enabled.

Enabling these notifications will allow information that the CI build is already creating to be easily seen on each PR.

[zmughal]

@carandraug , @cjfields , I noticed that Travis CI has been disabled so the badge in the README is showing the last build failure 7 months ago. I just checked to see if it would pass here and it does.

But this does not test the network because of the dependencies e.g., Bio::DB::GenBank. Is this because the split is a work-in-progress?

[cjfields]

Just a note but the reliance on Travis-CI will likely need to change in the long term, likely to Github Actions.