[Bioc-devel] Confusion with how to maintain release/devel files on local computer.
I can see two branches master and releas_3_6. I created GMaster to connect it with GitHub. But as far as it looks like, it?s only a local directory. Also, I don?t know weather I can remove it or not. Should upsteam appear here? Best regards, Arman From: Martin Morgan<mailto:martin.morgan at roswellpark.org> Sent: Thursday, November 2, 2017 05:00 To: Arman Shahrisa<mailto:shahrisa.arman at hotmail.com>; 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.
On 11/01/2017 07:53 PM, Arman Shahrisa wrote:
I cloned the package into a clean directory.
It helps to be more precise here. Were did you clone the package from? In the simplest case it would be git clone git at git.bioconductor.org:packages/your-package and you'd have a single remote named 'origin' git remote -v You can add or rename remotes, e.g., git remote rename origin upstream git remote add origin git at github.com:your-name/your-package and you can pull (or fetch and then merge) from each git pull upstream # pull changes from 'upstream' remote git pull origin # pull changes from 'origin' Study the how-to documents for different scenarios, and be precise as possible with what you are trying to do. Also, when learning, it can be comforting to know that removing your local repository from your disk is not the end of the world, you can just start over with a new clone from git.bioconductor.org or from github.
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?
You can do whatever you want with your local clone, and with github. The Bioconductor git repository allows you to push only to 'master' and the current release, RELEASE_3_6. Suppose you'd made changes to master, and you named the remotes 'origin' (for github) and 'upstream' (for bioconductor). Then after after adding (git add ...) and committing (git commit ...) to the local repository, you'd push to bioconductor with git push upstream master and to github with git push origin master Martin
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
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