[Bioc-devel] Confusion with how to maintain release/devel files on local computer.

Vincent Carey stvjc at channing.harvard.edu
Thu Nov 2 01:54:51 CET 2017 

As I plan to "fix a bug" in release version of BiocSklearn, I tried

%vjcair> git checkout remotes/upstream/RELEASE_3_6

Here is the result; what would I do to make some changes, alter DESCRIPTION
version to 1.0.1, commit and push so that the build system

has 1.0.1?

Note: checking out 'remotes/upstream/RELEASE_3_6'.


You are in 'detached HEAD' state. You can look around, make experimental

changes and commit them, and you can discard any commits you make in this

state without impacting any branches by performing another checkout.


If you want to create a new branch to retain commits you create, you may

do so (now or later) by using -b with the checkout command again. Example:


  git checkout -b <new-branch-name>


HEAD is now at 98fabcd... bump x.y.z versions to even y prior to creation
of RELEASE_3_6 branch

On Wed, Nov 1, 2017 at 8:19 PM, Arman Shahrisa <shahrisa.arman at hotmail.com>
wrote:

> I found how I can create another remote with GitHub using Rstudio. How can
> I merge master and GitHub?
>
> Best regards,
> Arman
>
> From: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>
> Sent: Thursday, November 2, 2017 03:23
> To: Stephanie M. Gogarten<mailto:sdmorris at uw.edu>; bioc-devel<mailto:
> bioc-devel at r-project.org>
> Subject: RE: [Bioc-devel] Confusion with how to maintain release/devel
> files on local computer.
>
> I cloned the package into a clean directory. Then I followed “New package
> workflow” strategy. By checking Description file while switching between
> branches, I can easily see the version change which is correct. If I
> understand it correctly, GitHub can only contain changes I make to master
> branch. If I want to push changes to GitHub as well, what should I do?
>
> Best regards,
> Arman
>
>
> From: Stephanie M. Gogarten<mailto:sdmorris at uw.edu>
> Sent: Thursday, November 2, 2017 02:19
> To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>
> Cc: bioc-devel<mailto:bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] Confusion with how to maintain release/devel
> files on local computer.
>
> One possible point of confusion: Laurent's workflow includes maintaining
> separate branches "master" and "devel", which he syncs to his own Github
> repo and Bioconductor's git repo respectively. However, the
> documentation on the bioc website
> (https://bioconductor.org/developers/how-to/git/) assumes that you have
> only one "master" branch that you push to both remotes.
>
> On 11/1/17 2:33 PM, Laurent Gatto wrote:
> >
> > On  1 November 2017 20:36, Arman Shahrisa wrote:
> >
> >> I'm confused with development process.
> >>
> >> At first, I need to have a folder with accepted packaged. Then I need
> to pull
> >> origion RELEASE_3_6?
> >>
> >> Then in another folder, I need to pull origion master?
> >
> > No, it all happens in the same folder, but switching between branches
> > using git. Here's an example of one of my own packages. The first
> > command list all available branches (all, using -a, means also
> > remote-only branches). My current branch is noted with an *, and I also
> > have a feature branch called writeMSData, which also lives on GitHub
> > (https://github.com/lgatto/MSnbase/, but that's optional).
> >
> > $ git branch -a
> >    devel
> > * master
> >    writeMSData
> >    remotes/origin/HEAD -> origin/master
> >    remotes/origin/centroiding
> >    remotes/origin/fixBracketSubset
> >    remotes/origin/issue82
> >    remotes/origin/master
> >    remotes/origin/orbifilter
> >    remotes/origin/processingData
> >    remotes/origin/removePrecMz
> >    remotes/origin/writeMSData
> >    remotes/upstream/RELEASE_2_10
> >    remotes/upstream/RELEASE_2_11
> >    remotes/upstream/RELEASE_2_12
> >    remotes/upstream/RELEASE_2_13
> >    remotes/upstream/RELEASE_2_14
> >    remotes/upstream/RELEASE_2_8
> >    remotes/upstream/RELEASE_2_9
> >    remotes/upstream/RELEASE_3_0
> >    remotes/upstream/RELEASE_3_1
> >    remotes/upstream/RELEASE_3_2
> >    remotes/upstream/RELEASE_3_3
> >    remotes/upstream/RELEASE_3_4
> >    remotes/upstream/RELEASE_3_5
> >    remotes/upstream/master
> >
> > As you can see (and as specified by Gabe in his earlier reply), I
> > haven't have pulled all Bioconductor releases. master points to GitHub's
> > origin/master branch, and devel points to Bioconductor's
> > upstream/master. As you can see above, I haven't got the latest release
> > references yet. I can do this with
> >
> > $ git fetch --all
> > Fetching origin
> > Fetching upstream
> > remote: Counting objects: 6, done.
> > remote: Compressing objects: 100% (6/6), done.
> > remote: Total 6 (delta 4), reused 0 (delta 0)
> > Unpacking objects: 100% (6/6), done.
> >  From git.bioconductor.org:packages/MSnbase
> >   * [new branch]      RELEASE_3_6 -> upstream/RELEASE_3_6
> >     b680678..a98138c  master     -> upstream/master
> >
> > And now
> >
> > $ git branch -a
> >    devel
> > * master
> >    writeMSData
> >    remotes/origin/HEAD -> origin/master
> >    remotes/origin/centroiding
> >    remotes/origin/fixBracketSubset
> >    remotes/origin/issue82
> >    remotes/origin/master
> >    remotes/origin/orbifilter
> >    remotes/origin/processingData
> >    remotes/origin/removePrecMz
> >    remotes/origin/writeMSData
> >    remotes/upstream/RELEASE_2_10
> >    remotes/upstream/RELEASE_2_11
> >    remotes/upstream/RELEASE_2_12
> >    remotes/upstream/RELEASE_2_13
> >    remotes/upstream/RELEASE_2_14
> >    remotes/upstream/RELEASE_2_8
> >    remotes/upstream/RELEASE_2_9
> >    remotes/upstream/RELEASE_3_0
> >    remotes/upstream/RELEASE_3_1
> >    remotes/upstream/RELEASE_3_2
> >    remotes/upstream/RELEASE_3_3
> >    remotes/upstream/RELEASE_3_4
> >    remotes/upstream/RELEASE_3_5
> >    remotes/upstream/RELEASE_3_6
> >    remotes/upstream/master
> >
> > If I want to modify the development branch (i.e. Bioconductor's
> > upstreams/master), then I checkout devel (that's how I named it
> > locally), do changes and push.
> >
> > $ git checkout devel
> > ## do stuff
> > $ git push
> >
> > Same principle for other branches.
> >
> >> So that by opening each folder, I know what I'm editing.
> >> Also during push, I need to be careful about where I'm pushing changes.
> >> Origion is bioc's git address of my package whereas master is the
> package directory in GitHub?
> >
> > No - I suggest you read a bit about git (GitHub is a web interface using
> > git) to familiarise yourself with the concepts and vocabulary.
> >
> >> Am I getting it correct?
> >> Is there anywhere that contains whole the process and codes in steps?
> >
> > All the setup and more details are provided in
> >
> >    https://github.com/bioconductor/bioc_git_transition/
> >
> > in particular the FAQ and all the scenarios at the bottom
> >
> >    https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/
> faq.md
> >
> > Best wishes,
> >
> > Laurent
> >
> >> Best regards,
> >> Arman
> >>
> >>
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
>
>
>         [[alternative HTML version deleted]]
>
>
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