[Bioc-devel] Maintaining package with already modified fork repository from github.

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Nov 28 13:42:12 CET 2022

I'm not a git expert by any means and someone may have better advice but my plan of attack would be the following:

If the repository with the changes is a fork, they should be able to request a Pull Request to your original repo. I would start there. You can access the changes on a separate branch of the original repository that is closest in sync with Bioconductor.

Then before merging that branch/PR request,

I would clone the original repo, make sure the remotes are set with an upstream for Bioconductor. do a git fetch --all and a git pull upstream to merge any Bioconductor changes.  Resolve any conflicts with that.

Then I would switch/checkout to the PR branch, merge the main/master branch into the PR branch, and resolve any merge conflicts there.
Then checkout/switch back to the main/master branch and merge the PR branch.

Do the version bump separate and lastly after all merge conflicts are resolved.  If its a major release, you can not bump the x of version x.y.z yourself.  If you would like it to be 2.0.0 in the april release,  please bump the y to 99 and then continue to do routine maintenance by bumping z as normal.
eg.  if the version was 1.23.0, you would bump to 1.99.0 or 1.99.1 -- .

And as you described, you would only do all of this on the master branch that is associated with devel and have the changes in the april release.


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jean-Philippe Villemin <jpvillemin using gmail.com>
Sent: Friday, November 25, 2022 3:40 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Maintaining package with already modified fork repository from github.

I have a few questions about managing a bioconductor package. Of course I
have been through the doc for package maintenance here
I Just want to check that my forklow is ok.

We have a bioconductor package.
We want to move its github source account to our github account lab. I'm
not sure what should be my starting point.

One collaborator did somes changes on a fork from the github (not
bioconductor) in its github account . He shared access with us  (~100
commits without bumbling x.y.z+1 each commit). I want to reuse that but I
don't know if i still need to fetch also from Bioconductor (before/after)

1 - Access and modify BiocCredientials
(I'm not a maintainer, a colleague is, so he will add me. I need that to
fetch from biocond right ?)
2 - On local, clone the fork from my colleague. (or bioconductor first ? )
3 - Should I fetch from Bioconductor ? (pretty sure this part will create
4 - Create an empty remote with the same name as on bioconductor, push the
cloned repo

5 - Configure upstream bioconductor...
6 - git push to remote bioconductor.
7 - In April changes will be added to release.

Specific question for 3 : How do we handle the bumble version thing ?
For the push, it will be a major release . (S4 code refactoring) (so should
I push something like 2.0.0)


*Jean-Philippe Villemin   *- Bioinformatics, PhD -

Cancer Bioinformatics and Systems Biology

Institut de Recherche en Canc�rologie de Montpellier

Inserm U1194

*jpvillemin using gmail.com <jpvillemin using gmail.com>*

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