[Bioc-devel] Bioconductor Git: Online interface

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Wed Feb 12 00:06:10 CET 2020

On Tue, Feb 11, 2020 at 2:42 PM Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> (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.

Among those examples, the only thing I see would be the workload of
adding/removing packages from Gitea so that it reflects what's on the
Git server.  Since Gitea can automatically sync with a Git server via
an URL, I don't see how things such as nightly builds etc come into
play.  User credentials should also not matter.  There should be no
backup needs other than possible one admin account with Swagger API

> 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.

I proposed Gitea because I know it well now, it has GitHub like
features that people already knows about (e.g. linking to code
snippets https://gitea.com/hb/aroma.light/src/branch/master/R/iwpca.R#L147-L152),
and it has the more potentials/features if you choose to go down that
route. I know there are other Git-to-webpage tools out there, which
are purely designed for viewing. It might be that those are a safer
route to go down. Given how easy it is to set up Gitea for this, and
Gitea has much more features, I'd be surprise if it wouldn't be as
easy for those tools too.  It could be that they're zero-config, e.g.
point to the folder where the git repositories live and you're ready
to go live.

Feel free to forward discussions/ideas (better if already public
somewhere; there might be others who can pitch in too), but
unfortunately I don't have much spare cycles to work on this.

Being able to browse code and link to code when reaching out to
maintainers is something Bioconductor is really missing right now.
This would lower the friction for contributing to packages that you
don't work on on a regular basis, e.g. typos, bug fixes, etc.


> Martin
> 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:
>       https://gitea.com/hb/aroma.light
>     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.
>       https://gitea.com/hb/QDNAseq
>     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
>     packages.
>     I'd classify this as a low risk and straightforward project to implement.
>     /Henrik
>     (*) 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
>     > >>
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>     > >
>     > >
>     >
>     >
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