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

[Kern, Lori]

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.

Cheers,




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
<https://secure-web.cisco.com/1AzdS1tYYrXwytNGlxGn5nIQ5S2QFgiNKa39kg1ntO1bOB5u9JUp7IizCi7ASSnIVetgr7EQpJPq3_zJ6QdXsaE668iBtBjMi1eInSMgAl_JvGcXNmPQsNdNxEewtIAnfBi9Bl14uqTUTCrf2N4GY78l4RwrvYGJlYkbav2SHK7YZBoFYp_v9aPHTSD_ocy4v43iAeiFSM7e6PJepjToPX4pep_YPNHYnbg5It_4kmncK5CqEPKGfs8ZDz3dX5G52fM0VmO5o12qJ-VcLwme833YXeBdgQ7p2woFpz2Mkm_b7I6q6HQEduRNF_PN7GW3E/https%3A%2F%2Fcontributions.bioconductor.org%2Fpackage-maintenance.html>.
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
<https://secure-web.cisco.com/1z3BvjE0AI5Q308KS2qvolcXl0zd2jWgz_mTfjFZwSl1Tg-0e0l_RYYMphlFTnqwVGqsKyzoVa3rvWw1gHZxoTxqYi1Sa1BHMkm5R6-uy4jddc0SglMgeF4eo4xSl7xMmfZG1x-HH6dspf1_fsAAcvOwcC8LV77Xb2IuXWMPyRxC9Gc2INA4-F0jlwl1-VzLvisb0vIbJ8n8IHTR5Y2-q9F5frZhYEv375txPaNpqa0ttvcjY0MjxIPFwOq__9PKMIeMNZi6ew0JAiN3hJszSon3CT5ETAgUPAzj3mceVeNEWAE3yD0eO-T2NVyVVcO7r/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F>
freely.
(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
troubles)
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)

Thanks.



--
*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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