[Bioc-devel] Bioconductor Git/GitHub Mirrors

Hi,


This sounds great! Not having to setup all those bridges everytime a
new BioC version is released should be a great feature, plus keeping
the commit history tidy. And we can still use Travis or other things
like Slack notifications on our own bridges.

to remind users to pull new content from the bioc remote before trying
to commit to svn.

Anyhow, great work!




I'm having a few problems with this new setup which hopefully are easy
to iron out. Basically, I am stuck at the "git svn rebase && git svn
dcommit --add-author-from" step. See 2b) below.


1) My git was pointing to an older version even after updated with
brew. This was because I still had MacPorts around.
How to diagnose:
$ which git
Wrong version was pointing to /opt/local/bin/git instead of
/usr/local/bin/git Can also see by running
$ git --version ## if it doesn't match the version number you
installed from brew
Solution:
* Uninstall all of MacPorts following instructions from
https://guide.macports.org/chunked/installing.macports.uninstalling.html
* Follow part of
http://stackoverflow.com/questions/20648235/error-linking-git-to-homebrew
$ sudo brew prune
$ brew update
$ brew install git
$ brew unlink git && brew link git

You might want to update subversion.
http://blog.victorquinn.com/fix-git-svn-in-mountain-lion might be
relevant for you.

2) Test case: derfinderHelper.

Smallest and simplest package I have, which won't matter much if
things break because it's stable.

a) You might want to delete update_remotes.sh after using it.
* I deleted the git-svn bridges to both
https://github.com/leekgroup/derfinderHelper and
https://github.com/leekgroup/derfinderHelper-release
* On https://github.com/leekgroup/derfinderHelper I removed bioc as a
collaborator and deleted the push-hook since it seems like we don't
need this anymore
* Download and ran update_remotes.sh as instructed. It doesn't seem
like we need it anymore after that point. If you leave it there, it
seems to give problems.
Easy to solve, but might want to clarify in the instructions.

b) Following the section "Use Git Locally And Publicly" I get stuck on
the "git svn rebase && git svn dcommit --add-author-from" step as
shown at https://gist.github.com/lcolladotor/ac8838b25955caeebcf1. The
"CONFLICT (add/add): Merge conflict" message lead me to
http://stackoverflow.com/questions/19475387/how-to-handle-fix-git-add-add-conflicts
from where I could resolve the initial problem that I saw using "git
diff". But was basically the changes between the very first version of
README.md and the very latest version of it.
There must be a way to not have to go through every single commit
and/or file one by one. Using "git rebase --continue" doesn't help.

c) Given the issue with b, the devel branch already has a merge
commit. Using http://stackoverflow.com/questions/927358/how-to-undo-the-last-commit
I cleaned things up. I don't think it's needed, but I don't want to
run into more issues.
$ git rebase --abort
$ git reset HEAD~1


As you can tell, I'm no "git rebase" expert. From
http://git-scm.com/docs/git-rebase it seems like the "ours" option
might be useful. But right now I prefer to get some pointers on how to
proceed before playing around further :P

Thanks,
Leo


PS At the "Unable to determine upstream SVN information" section, I
believe that there is a typo. "git svn dcomit" should be "git svn
dcommit"

On Tue, Jun 16, 2015 at 3:20 PM, Ryan C. Thompson <rct at thompsonclan.org> wrote:

This is great to hear. I sometimes want to delve into the source code of a
package's internals, but doing so through the SVN web interface is clunky.
Being able to use Github's repo browsing functionality for Bioc packages is
great.


On 06/16/2015 12:00 PM, Dan Tenenbaum 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