Friday, 19 May 2017

Bioconductor histories with git-svn

If you are developing a software you might be using a version control (If not do it :). Bioconductor until 05/2017 is using svn. However it is migrating to git, meanwhile a hybrid system is provided, where one submits the project through GitHub using git control version system and internally it uses svn. Here are some experiences developing in for Bioconductor in this configuration.

After following the recommendations of the configuration .git/config ends up with:

[core]
    repositoryformatversion = 0
    filemode = true
    bare = false
    logallrefupdates = true
[remote "origin"]
    url = https://github.com/llrs/BioCor.git
    fetch = +refs/heads/*:refs/remotes/origin/*
[branch "master"]
    remote = origin
    merge = refs/heads/master
[remote "bioc"]
    url = https://github.com/Bioconductor-mirror/BioCor.git
    fetch = +refs/heads/*:refs/remotes/bioc/*
[svn-remote "devel"]
    url = https://hedgehog.fhcrc.org/bioconductor//trunk/madman/Rpacks/BioCor
    fetch = :refs/remotes/git-svn-devel
[svn-remote "release-3.5"]
    url = https://hedgehog.fhcrc.org/bioconductor//branches/RELEASE_3_5/madman/Rpacks/BioCor
    fetch = :refs/remotes/git-svn-release-3.5
[branch "release-3.5"]
    remote = bioc
    merge = refs/heads/release-3.5
[branch "devel"]
    remote = bioc
    merge = refs/heads/master

This configuration creates a devel branch forked from Github Bioconductor's mirror, which is equivalent to the devel trunk in svn.
However when I develop my package I do so in master branch which creates the hassle to bring (merge or cherry-pick) the changes (commits) from master to devel branch for later release on Bioconductor or for hot fix in a release-* branch.

Also make sure to try if you have the permissions to write on the repository in Bioconductor







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