[Bioc-devel] GitHub and svn

Nathan Sheffield nathan at code.databio.org
Sun Oct 16 03:05:39 CEST 2016

Hi Kevin, Mani --

Isn't the git-svn bridge deprecated?

And this message:

----- Forwarded Message -----
From: "Dan Tenenbaum"<dtenenba at fredhutch.org>
To: "bioc-devel"<bioc-devel at r-project.org>
Sent: Monday, December 28, 2015 11:08:29 AM
Subject: [Bioc-devel] Git-Svn bridge will be removed permanently on January	29, 2016

Attention Bioconductor developers,

The deprecated Git-SVN bridge will be removed permanently on Friday, January 29th, 2016.

But anyway, Mani, I at least agree with you that the current system is 
"unnecessarily complicated" (git-svn, cherry-picking, credentials, 
mirrors and so forth) and I hope it will become much better after, as 
Kasper put it, "the (long) process of changing this" gets finished, 
which I hope means a system that is git-centered, since that seems to be 
the way the world has moved.

I, for one at least, have several ideas for new packages and maintenance 
of old ones that I continue to put off on the hopes that one day soon 
the update system will be as easy for an official Bioconductor repo as 
it is to simply push a git commit to my own repository on GitHub. But 
alas, it is not yet the case -- but I think when this gets "fixed" it 
will be a glorious future indeed.


On 10/15/2016 06:41 PM, Kevin RUE wrote:
> Dear Mani,
> That's actually where I think the git-svn bridge becomes useful.
> If you take the time once to synchronise the devel branch of your package
> from the Bioconductor-mirror to one of the branch on your GitHub repository
> (for me the master branch), you could then:
> 1) commit changes to your own repository first (does not affect the BioC
> code)
> 2) follow the BioC git-svn instructions that you mentioned to selectively
> push the changes to either or both the devel and release branche(s) of
> Bioconductor.
> I personally don't think that the current system is "unnecessarily
> complicated". That handful of commands is probably as simple as a system
> can be, to handle version control selectively applied to multiple branches
> (devel, 3.3, 3.2, master, ...) of multiple repositories (BioC, GitHub, ...)
> using multiple version control software (git, svn).
> The learning curve for version control can be quite steep beyond the basic
> commands, but one has to bear in mind that RStudio is not a version control
> software in itself. The GUI only provides buttons for the most common
> version controls commands (pull/push/update). For more advanced commands,
> you will have to open a shell anyway (the little wheel icon).
> I must admit that I was a bit scared/frustrated at first with the system,
> but after a few attempts to get it right, this little process to control
> the branches to synchronise can almost become enjoyable when proudly
> releasing new code :)
> All the best,
> Kevin
> On Sat, Oct 15, 2016 at 10:21 PM, S Manimaran <manimaran_1975 at hotmail.com>
> wrote:
>> 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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