[Bioc-devel] Bioconductor-mirror permanently removed August 25th

[Jim Hester]

I understand the fragmentation concerns, just felt the mirrors should have
been maintained at least until a reasonable alternative exists.

The diverging history issues should be resolvable by resetting the state to
the canonical bioconductor repository and force pushing necessary changes
to their repository. Issues for the mirrors were disabled, and the
repositories had a pull request webhook setup to automatically close pull
requests with an informative message. You could potentially have similar
issues with the CRAN mirror (https://github.com/cran), but that seems to be
a valuable resource to the community.

Also FWIW the CERN root project repos are also on GitHub (
https://github.com/root-project), it is instructive to contrast the landing
page for the same repository on each
  - https://root.cern.ch/gitweb/?p=cling.gi
  - https://github.com/root-project/cling

I personally find repository interfaces that put commit messages up front
such as sourceforge and gitweb challenging to navigate. Generally if I am
looking at a repository it is because I want to see the source code, not
the latest commit messages. For self hosting solutions I would encourage
use of something like Gitea (https://gitea.io/en-US/), which has a richer
interface with easier access to source code / rendered READMEs etc.
(example repo https://try.gitea.io/klud/graphql-docker-api). I think
similarity concerns to GitHub are somewhat overblown and could be addressed
with some Bioconductor specific CSS if needed. There are performance
concerns with a richer interface, but I believe Gitea has much lower
resource requirements than other similar alternatives like GitLab and at
least their demo server seems to have no trouble with ~1300 repositories.

I feel the real value in having Bioconductor mirrors on GitHub is the
ability to easily search for code across all of the published R ecosystem
in one query. This is useful for deprecating functions, gauging usage
popularity etc. and becomes harder to do without a mirror.

Thank you to everyone for the replies and you are of course free to do what
you feel is in the best interest of the project!

Jim

On Wed, Sep 6, 2017 at 11:21 AM, Turaga, Nitesh <
Nitesh.Turaga at roswellpark.org> wrote:

> Hi Jim
>
> We are more worried about the confusion it creates among the users.
>
> Users have tried to push their commits to the bioconductor-mirror instead
> of the bioconductor git server. Another source of confusion is, some
> maintainers have forked their packages from the Bioconductor-mirror, and
> have started developing from that point on GitHub. This creates a unique
> issue of duplicate commits, when they merge updates from the bioc-git
> server. People also send in pull requests/issues to this mirror
> repositories where they are unmaintained, causing a new kind of problem to
> both users and maintainers.
>
> We realize the importance of a browsable source repository, and are
> looking into gitweb on the bioc-git server directly. Having a GitHub based
> mirror also prevents us from hosting data-packages on Github. The idea of a
> browsable source should be to view all Bioconductor packages( software /
> data / workflows). My vote is to remove this, only because of the amount of
> confusion it causes on the regular.
>
> I’ll let others chime in as well, and would love to hear your thoughts
> about Gitweb(https://git-scm.com/docs/gitweb) or other such software.
>
>
> Best,
>
> Nitesh
>
> > On Sep 6, 2017, at 11:07 AM, Jim Hester <james.f.hester at gmail.com>
> wrote:
> >
> > This mirror could be relatively simply supported by setting up an
> additional remote in the server side repositories and adding a post-receive
> hook to each repository that simply pushes to the GitHub mirror remote
> after commits are received.
> >
> > https://git-scm.com/book/gr/v2/Customizing-Git-Git-Hooks
> > https://help.github.com/articles/about-github-mirrors/
> >
> > Having an easily browsable source repository online is a pretty valuable
> thing, it is a shame to lose this.
> >
> > Jim
> >
> > On Thu, Aug 17, 2017 at 3:53 PM, Turaga, Nitesh <
> Nitesh.Turaga at roswellpark.org> wrote:
> > Hi Maintainers,
> >
> > The https://github.com/Bioconductor-mirror is now stale after
> Bioconductor’s git transition. We are no longer going to support it, and
> will be taking it offline permanently on August 25th (next Friday).
> >
> > If you have “forked” a repository from the Bioconductor-mirror, you will
> be fine. It will not have any consequence on your repository, the only
> change will be the “forked from bioconductor-mirror” tag will be removed.
> >
> >
> > Best,
> >
> > Nitesh
> >
> >
> >
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