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:[email protected]> Sent: Thursday, November 2, 2017 02:19 To: Arman Shahrisa<mailto:[email protected]> Cc: bioc-devel<mailto:[email protected]> 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]] >> >> _______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]]
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