[Bioc-devel] git clarifications

Turaga, Nitesh Nitesh.Turaga at RoswellPark.org
Tue Jul 25 12:03:57 CEST 2017

Hi Michael,

The Github webhook is only for you to submit your latest push to the build system during the package submission process. I don't think you will need this after, because once your package gets accepted there will be a nightly package build. So whatever you commit will get built from our new git server.

It will not be possible to configure the webhook after transition (once your package is accepted, before that it remains the same).

You can choose to sync, but we highly recommend that you sync both your Github repo, and the RITAN bioconductor git repo. We have made this process easier now. As you pointed out there is documentation for this in the docs/scenario-2 or docs/scenario-9.

There are ways to push to both Github and Bioconductor remotes in one command. You'd have to configure your git urls. (Check out your `git config --list`)



From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Zimmermann, Michael T., Ph.D. <Zimmermann.Michael at mayo.edu>
Sent: Monday, July 24, 2017 11:56 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] git clarifications

Dear BioC Devs,

As of release 3.5 I have a package in BioC, originating from github.com/MTZimmer/RITAN. During package submission, the webhook process from github into bioc was smooth. At this point, my commits to github no longer propagate into bioc. After the bioc transition to git, will a similar webhook system to the devel branch be possible? Being able to commit to github and automatically push/mirror to the development branch would be convenient.

As is, the recommended procedures (http://bioconductor.org/developers/how-to/git-mirrors/) seem indirect to me. Is it, or will it be, possible to configure the webhook to point to the devel version on bioc after the transition? From the bioc_git_transition docs (https://github.com/Bioconductor/bioc_git_transition/tree/master/doc) it looks like the plan is for us to sync as we choose - correct?

Finally, is there anything "official" to be done to start using the bioc git beta?

Your help in clarifying this process is appreciated.


Michael T. Zimmermann
Ph. D. in Bioinformatics | Health Sciences Research | Division of Biomedical Statistics and Informatics
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org<http://www.mayoclinic.org>

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