[Bioc-devel] GitHub and svn

S Manimaran manimaran_1975 at hotmail.com
Sat Oct 15 18:19:22 CEST 2016


I never understood the github mirror setup and the instructions below look unnecessarily complicated to me. I see that the current package submission process with the automatic hook added to github is the most easiest of all with every commit to github automatically triggering a build at Bioconductor. Now, my question is: Can't this same procedure be carried over once the Bioconductor 3.4 is released as well i.e commits to github automatically resulting in triggering a build at Bioconductor? The main use case that I am looking for is an easy way to commit directly from inside R-Studio. With R-Studio setup for GitHub project, it directly commits to GitHub, but now for having to commit to BioConductor, if the automatic trigger works well as is the case with the new package submission process, all is well and good. But if I have to do as what the page in git-mirror says, then it looks like that I have to get out of R-Studio to do some overly complicated process to achieve the same. It will be really helpful if I can continue to use the automatic trigger to automatically build after Bioconductor 3.4 release as well.


Scenario 2: Set Up Your Own GitHub Repository
If you do not already have a public git repository for package REPO the simplest thing to do is navigate to https://github.com/Bioconductor-mirror/REPO and click the Fork button in the upper right. This will create a copy of the repository on your personal account. You may want to re-enable issue tracking in your repository (it's disabled in the read-only mirrors and forks inherit this setting). To do this, go to Settings and then click the Issues checkbox. Then perform the following steps in your terminal.

  1.  git clone https://github.com/USER/REPO to clone the repository to your machine.
  2.  cd REPO to switch to the REPO directory.
  3.  bash /path/to/update_remotes.sh to setup the git remotes.
  4.  Commit to git and push to GitHub as you normally would.
  5.  Each time you want to push git commits to svn:
     *   git checkout devel to switch to the devel branch. (use release-X.X for release branches)
     *   git svn rebase to get the latest SVN changes.
     *   git merge master --log to merge your changes from the master branch or skip this step and work directly on the current branch.
     *   git svn dcommit --add-author-from to sync and commit your changes to svn. You may be prompted here for your SVN username and password.
When you're done, be sure and merge any changes from svn back into the git master branch:
git checkout master
git merge devel


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