[Bioc-devel] Bioconductor Git/GitHub Mirrors

Robert M. Flight rflight79 at gmail.com
Fri Jun 19 17:25:24 CEST 2015 

Hmmm, ok. I kind of liked having the message about being a fork of the
Bioc-mirror, but the difference message makes it a little messy. Oh well.
Was an interesting experiment.

On Fri, Jun 19, 2015 at 11:19 AM Jim Hester <james.f.hester at gmail.com>
wrote:

> I think these are unavoidable artifacts with the current setup.  The
> commits from the Bioconductor-mirror are coming from SVN after being
> translated so they have extra metadata attached to the commit message,
> while your original commits do not have this.  Therefore GitHub cannot
> properly disambiguate the two commits, and you get this message.  You will
> also notice you get the same commit twice in your log (
> https://github.com/rmflight/categoryCompare/commits/master) due to the
> same reason.
>
> Using your own repo instead of forking Bioconductor-mirror will make the
> message go away and you should also not have the issue with double commits
> I believe.
>
> On Fri, Jun 19, 2015 at 10:23 AM, Robert M. Flight <rflight79 at gmail.com>
> wrote:
>
>> So this seems to work quite nicely. But in my own testing of committing
>> with my categoryCompare package, there is one interesting issue of Github
>> complaining about how many commits ahead / behind the fork is.
>>
>> So I moved my old github repo, and then made a fresh fork from the
>> Bioconductor mirror, and made a new clone of that fork on my local machine,
>> and ran update_remotes.sh.
>>
>> Made some changes to the readme (pointing to personal repo for issues)
>> and committed in *master
>>
>> git push origin master (push back up to my personal copy)
>> git checkout devel
>> git svn rebase
>> git merge master --no-edit
>> git svn rebase && git svn dcommit --add-author-from
>>
>> When I looked at my personal fork, it shows 1 commit ahead & behind the
>> original. So I pulled from *bioc* remote into master (and merge it), and
>> then pushed back up to master.
>>
>> I still have this message: This branch is 2 commits ahead of
>> Bioconductor-mirror:master, but there are no file differences.
>>
>> Does anyone know how to make this message go away? Should I just use my
>> own repo instead of a *fork* of the Bioconductor-mirror?
>>
>> -Robert
>>
>>
>> On Wed, Jun 17, 2015 at 10:10 AM Jim Hester <james.f.hester at gmail.com>
>> wrote:
>>
>>> I have (in the past couple of minutes) added a more detailed description
>>> to all of the GitHub pages.  If you have URL or BugReports fields in your
>>> package DESCRIPTION those are used to provide links to the project page and
>>> bug tracker if they are available, see Roberts
>>> https://github.com/Bioconductor-mirror/categoryCompare for an example.
>>>
>>> I would also recommend doing as Robert suggests and adding a link in a
>>> README.md file if you would like to direct users elsewhere.  These files
>>> are automatically rendered by GitHub and users are used to looking at them
>>> for project documentation.
>>>
>>> Thank you all for being patient as we roll out this functionality.
>>>
>>> Jim
>>>
>>> On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight <rflight79 at gmail.com>
>>> wrote:
>>>
>>>> Why not write your own *readme.md* file for the package and put the
>>>> link
>>>> there? There is nothing stopping the maintainer from having a README
>>>> file
>>>> in the package. Although it does not show up on the Bioconductor page,
>>>> it
>>>> shows up nicely on Github:
>>>>
>>>> My package:
>>>>
>>>> https://github.com/Bioconductor-mirror/categoryCompare
>>>> https://github.com/rmflight/categoryCompare
>>>>
>>>> -Robert
>>>>
>>>> On Wed, Jun 17, 2015 at 8:43 AM Michael Lawrence <
>>>> lawrence.michael at gene.com>
>>>> wrote:
>>>>
>>>> > It would be cool if we could somehow get the equivalent of the
>>>> > bioconductor package page to show up as the "readme" on the github
>>>> > page. Or at least, if there could be a very obvious link from the
>>>> > mirror repository to the maintainer repository, without having to
>>>> > click through to the Bioconductor package page, which might confuse
>>>> > new users a bit.
>>>> >
>>>> >
>>>> > On Tue, Jun 16, 2015 at 12:00 PM, Dan Tenenbaum <
>>>> dtenenba at fredhutch.org>
>>>> > wrote:
>>>> > > Dear Bioconductors,
>>>> > >
>>>> > > We're pleased to announce the availability of Bioconductor Git
>>>> Mirrors.
>>>> > > These are read-only GitHub repositories (available under
>>>> > https://github.com/Bioconductor-mirror)
>>>> > > for every Bioconductor software package. These repositories are
>>>> > synchronized with our
>>>> > > Subversion repository. Package maintainers (or anyone else) can fork
>>>> > these repositories
>>>> > > and do their development on the fork. Complete documentation of the
>>>> > mirrors is at
>>>> > >
>>>> > > http://bioconductor.org/developers/how-to/git-mirror/
>>>> > >
>>>> > > These mirrors supersede the Git-SVN bridge, which is now deprecated.
>>>> > > Creation of new bridges is disabled and maintainers who are using
>>>> the
>>>> > bridge
>>>> > > should migrate to the Git mirrors as soon as it's convenient, as the
>>>> > bridge
>>>> > > will eventually go away. Instructions for migrating can be found at
>>>> the
>>>> > above link.
>>>> > >
>>>> > > Some features of the new Git Mirrors, and why we feel they are a
>>>> better
>>>> > solution than the Git-SVN bridge:
>>>> > >
>>>> > >  - The mirrors contain complete commit history.
>>>> > >  - The mirrors contain release branches for Bioconductor 3.0 and
>>>> 3.1, and
>>>> > >    new releases will be added as they happen. You will no longer
>>>> need
>>>> > >    separate repositories for release and devel.
>>>> > >  - Setup is easy and you no longer have to grant any permissions on
>>>> your
>>>> > >    repository to other users. You can commit directly to Subversion
>>>> > >    using git-svn (https://git-scm.com/docs/git-svn).
>>>> > >  - Each git commit appears in the SVN log as a distinct SVN commit;
>>>> > commits
>>>> > >    are no longer grouped together as they were with the bridge.
>>>> Each git
>>>> > >    commit can be mapped to a specific svn commit, and vice versa.
>>>> > >  - The Git mirrors are much more reliable.
>>>> > >  - Use is flexible. You can use git locally (without GitHub) or you
>>>> > >    can use GitHub as well, to take advantage of all its social
>>>> coding
>>>> > features.
>>>> > >  - Using GitHub's code search, you can search the entire
>>>> Bioconductor
>>>> > codebase.
>>>> > >    Here's a sample search: https://goo.gl/jI92Ys
>>>> > >  - Subversion is fully supported and remains the cannonical
>>>> repository;
>>>> > use
>>>> > >    of Git and GitHub is optional.
>>>> > >
>>>> > > We are excited about these new mirrors (brought to you by the hard
>>>> > > work of Jim Hester) and we hope you are too. Questions and comments
>>>> are
>>>> > > welcome on the bioc-devel mailing list.
>>>> > >
>>>> > > Dan
>>>> > >
>>>> > > _______________________________________________
>>>> > > Bioc-devel at r-project.org mailing list
>>>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> >
>>>> > _______________________________________________
>>>> > Bioc-devel at r-project.org mailing list
>>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>> >
>>>>
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>>>
>>>
>>>>
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>>>
>

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