[Bioc-devel] EXTERNAL: Resolve mismatch between master and release branches

Mike Smith gr|mbough @end|ng |rom gm@||@com
Tue Mar 23 09:31:02 CET 2021

Hi Sarah,

Just to reiterate Marcel's point, if these are new features or tweaks to
your package, then they shouldn't be committed to the release branch at
all.  The Bioconductor ethos is that the release version of a package
should remain stable for a 6 month window (the release cycle), and changes
to that release version should only be made for critical bugs, patches to
fix errors introduced by an update to a CRAN package you depend on, etc.
This is to try and ensure that all Bioconductor packages within a release
present a stable interface; both for users and for packages that
interoperate.  There's an expectation that things in the release branch
will "just work" and will produce consistent results during a release
cycle.  On the other hand, in the devel branch you can make more dramatic
changes, add new features, update options or defaults arguments etc.  It's
still nice to inform users if the result of a function might change between
versions, but it's fine to introduce a change like that.

Assuming your changes are bug fixes, it's also perfectly reasonable to have
a divergence like "7 commits behind master and 3 commits ahead" between the
master and release branches.  The two branches should have
different package version numbers, and that's going to require a different
commit to each branch.  As soon as you've done that you'll see a message
like this, because there's now a commit in master that doesn't appear in
release, and likewise one that's in release that doesn't appear in master.
This doesn't mean anything has gone wrong, the Bioconductor versioning
guidelines have been followed, GitHub just likes to let you know the two
branches have both diverged from their common ancestor.


On Mon, 22 Mar 2021 at 23:59, Marcel Ramos <
marcel.ramosperez using roswellpark.org> wrote:

> Hi Sarah,
> The release branch is meant for bug fixes that ensure the stability of
> the code.
> It does not usually include 'updates' from the devel.
> The way to cleanly do this is to hard reset to a previous commit. The
> commit
> where your packages version was bumped for the 3.12 release. You
> can then force push the release branch to your GitHub repository
> RELEASE_3_12 branch.
> https://bioconductor.org/developers/how-to/git/abandon-changes/
> <https://bioconductor.org/developers/how-to/git/abandon-changes/>
> After emailing Nitesh and he would apply a force push to the Bioc git
> repo.
> You will then be able to apply your changes from the devel branch by
> cherry-picking those changes** onto the release branch.
> ** your changes in the devel branch should be atomic, meaning they do not
> include version bumps, so that cherry-picking is easier, if that is not
> the case
> you may have to apply a diff or manually update the version.
> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
> <
> https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
> >
> Hope that helps.
> Best,
> Marcel
> On 3/22/21 4:43 PM, Sarah Voisin wrote:
> > Hi,
> >
> > I have updated the master branch of my MEAT package yesterday (
> > https://github.com/sarah-voisin/MEAT), and I tried updating the release
> > branch as well (RELEASE_3_12), but I must have messed up since the
> release
> > branch is now 7 commits behind master and 3 commits ahead, and I am
> stuck.
> > How do I do this again cleanly so I can push all changes from the master
> > branch to the release branch without messing up further?
> >
> > Thank you for your help.
> >
> > Kind regards,
> >
> > *Sarah Voisin*
> > *Senior Lecturer*
> > Institute for Health and Sport (IHES)
> > Victoria University, Footscray Park Campus, VIC 3011 Australia
> > *Email*: sarah.voisin.aeris using gmail.com
> > *Office phone*: +61 3 9919 5744
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> ---
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
> This email message may contain legally privileged and/or...{{dropped:4}}
> _______________________________________________
> Bioc-devel using r-project.org mailing list
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