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

[Laurent Gatto]

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]]
>
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-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/