[Bioc-devel] GitHub and svn

Thanks, Gabe and Kasper, for the info.



Following up on Gabe's reply: That means, I need to setup two projects in
R-Studio with one for the release pointing to the release repository in SVN
and another for the development version pointing to the development
repository in SVN, right? Now, suppose I make a bug fix and commit to the
release repository and I want the same fix in the development repository as
well, how exactly do I go about this: Do I just manually copy those files
with the changes to the other development version project and commit it
there as well? (Personally, I also like to keep the original GitHub
repository in sync with the latest in BioConductor development, which would
mean I need to maintain three projects in R-Studio, right?) Or is there any
other way about this?



Thanks,

Mani




From: Gabe Becker [mailto:becker.gabe at gene.com]
Sent: Saturday, October 15, 2016 4:35 PM
To: Kasper Daniel Hansen
Cc: S Manimaran; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] GitHub and svn


Mani,

Related to what Kasper said, one thing you can do is commit directly to
the canonical repo for your package (which again is not on github once the
package is accepted) from rstudio. It supports svn.

~G

On Oct 15, 2016 11:38 AM, "Kasper Daniel Hansen" <
kasperdanielhansen at gmail.com<mailto:kasperdanielhansen at gmail.com>> wrote:
Not at the moment.  We are in the (long) process of changing this, but
there is no ETA for it.

The complications we currently have, as soon as a package is accepted in
Bioconductor, is that the "true" repository then becomes Bioconductor SVN
and your Github repository is just a way for you to develop.  This is not
the case during package submission.

Best,
Kasper


On Sat, Oct 15, 2016 at 12:19 PM, S Manimaran <manimaran_1975 at hotmail.com<
mailto:manimaran_1975 at hotmail.com>>
wrote:

Hi,

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 s!
 ame. It will be really helpful if I can continue to use the automatic
trigger to automatically build after Bioconductor 3.4 release as well.


http://bioconductor.org/developers/how-to/git-mirror/

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

Thanks,
Mani

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