[Bioc-devel] Bioconductor Git: Online interface

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Tue Feb 11 23:15:29 CET 2020

I wanna revive this old thread.

I've used Gitea for internal git/issue trackers at the UCSF for quite
a while now and it works really well.  I've also looked into how easy
it would be to use it for pure code exposure and it's pretty
straightforward.  Gitea even has built-in tools for automatically
synchronize toward an existing git server *and* keep it up-to-date,
which makes the process even easier(*).  An example what this looks
like is:


That took me literally 15 seconds to set up.  Note how this is almost
a bare bone *read-only* git code browser, e.g. there's no issue
tracker.  Right now, it would require a teeny hack on the Gitea server
to have the 'git clone' URL to map to the official Bioconductor URL
(or to hide it completely).  It's also possible to link the 'Issue
Tracker' to, say, GitHub issues based on what's in BugReports:, e.g.


Note that the above read-only approach completely avoids having to map
or maintain user accounts; it's a pure read-only online viewer of the
Bioconductor git repositories.  (Depending on your setup, it might
even be that you can expose the Gitea interface as
https://git.bioconductor.org/ and have
https://git.bioconductor.org/packages/<pkg> take you to the Gitea
package page.)  There's a Swagger API that makes it possible to
automate everything, e.g. creating new repositories for new Bioc

I'd classify this as a low risk and straightforward project to implement.


(*) Technical details: The most efficient approach would probably be
to link to the existing git repositories via the file system, rather
than going over ssh/https. Linking via the file system avoids any
duplication.  The storage load of running such a Gitea instance would
be very very small.  The Gitea instance don't need write permissions
to the repositories, so there is no risk of Gitea messing up existing
git repositories.

On Thu, Oct 26, 2017 at 1:51 AM Martin Morgan
<martin.morgan using roswellpark.org> wrote:
> There has been previous discussion about this.
>    https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011455.html
> It is not in our short-term plans to offer a full on-line solution, but
> not impossible in a longer context.
> Martin
> On 10/26/2017 03:01 AM, Stian Lågstad wrote:
> > I would very much appreciate this as well. Issue tracking and communicating
> > with users directly in the repository would be very nice, as well as the
> > ability to reference source code directly.
> >
> > On Thu, Oct 26, 2017 at 8:50 AM, Henrik Bengtsson <
> > henrik.bengtsson using gmail.com> wrote:
> >
> >> Are there any plans for an online interface to
> >> https://git.bioconductor.org/?
> >>
> >> I've recently looked into solutions for an open-source in-house
> >> "GitHub/GitLab"-ish, and I've found https://gitea.io/ to be really
> >> nice.  It is very easy to install. It has support for various common
> >> user authentication methods, it supports organizations and user teams,
> >> repositories may have issues and wikis, sets of code lines can be
> >> referenced, commits and code diffs are annotated, and so on.  Wikis
> >> and issue trackers can be disabled (also for individual repositories).
> >> That's all I've learned thus far - I'm impressed.
> >>
> >> Just a thought
> >>
> >> Henrik
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> >
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