[Bioc-devel] Bioconductor Git: Online interface

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Feb 11 23:42:28 CET 2020

(sending again from / to an appropriate email address, sorry for the noise)

Henrik -- I appreciate the ease with which gitea can be deployed in this one-off solution but cynically think that a real deployment would introduce significant work, e.g., re-tooling our approach to new package addition, management of user credentials, and integration of the nightly build system.

If you'd like to work on a more complete (off-line, so as not to present a confusion of interfaces for the user and developer) implementation I'd be happy to provide some pointers to the major challenges.


On 2/11/20, 5:16 PM, "Bioc-devel on behalf of Henrik Bengtsson" <bioc-devel-bounces using r-project.org on behalf of henrik.bengtsson using gmail.com> wrote:

    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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