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

[Stephanie M. Gogarten]

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]]
>>
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> 
>