Hi Nitesh and all,
Can you give any status update on the SVN-to-git transition? I haven't
seen any news since this exchange in March -- is the announced public
beta in progress or ongoing? Are new package submissions going straight
into git at this point?
Or did I miss something?
Thanks,
Nathan
On 04/01/2017 09:14 AM, Martin Morgan wrote:
On 03/29/2017 03:55 PM, Henrik Bengtsson wrote:
Thanks. I have a few thoughts and questions in order to plan ahead:
- Our plan is to make a 'clean' transition from SVN to git,
approximately one month after the next Bioconductor release.
Developers or users will not have access to the SVN system after the
date of transition.
In order to preserve commit authorship, what's your plan for mapping
SVN username to Git 'user.email' and 'user.name'? The 'user.email' is
what GitHub uses to associate commits and contributions to GitHub
accounts.
The svn administrators kept a comprehensive (but not complete) record
of svn id, real user name, and contact email at the time the svn id
was create. We use this to map between svn commits and git user name
and email address.
The information is not entirely consistent, with some fields for some
records 'missing' (e.g., my record doesn't contain my real name) and
of course out of date (e.g., my email address).
Our intention is NOT to re-write history, but to map the information
that we have to the git repositories. So my svn commits appear without
a proper name, and with an outdated email address. Of course, new
commits after the transition will contain whatever info git provides.
BTW, using obsolete email addresses may prevent people from being
associated with those email addresses on GitHub and other online
services that require authentication of authorship claims (which go
out via those email addresses).
When I SVN-to-Git exported my Bioconductor packages a few years ago, I
could handle manually because there were not too many contributors in
the SVN logs and I reached out to each of them and asked what email
addresses they would prefer to have in the Git commits. That approach
is obviously not feasible to automate for all Bioconductor packages.
Maybe this can be handled optionally by each package maintainers by
adding a .gitauthors file to the package root (or possibly via a
global Bioc one that everyone can commit to), e.g.
```r
hb = Henrik Bengtsson <henr...@braju.com>
j...@foo.com = John Doe <j...@someone.org>
```
and then Bioc can use this mapping when exporting to Git?
Finally, will people like me who already done the SVN-to-Git migration
be able to use that instead of the Bioc generated one? (I assume not,
but worth asking)
No, we'll make a git snapshots of svn at the time of transition, and
these git repositories will be the cannonical version -- developers
will need to sync with these as they see fit.
Martin
Thanks,
Henrik
On Wed, Mar 29, 2017 at 9:51 AM, Turaga, Nitesh
<nitesh.tur...@roswellpark.org> wrote:
Dear Bioconductor Developers,
More news about the Git transition plan. We are coming close to our
transition date and have made significant progress in getting our
new server ready for the Bioconductor community.
1. Overall plan:
- Bioconductor hosts each package as a distinct repository at
git.bioconductor.org<http://git.bioconductor.org/>. From
Bioconductor's perspective, this is the canonical location. Nightly
builds will be based on these repositories, release branches will be
created in these repositories, etc. The naming convention for
branches remains the same.
- Developers clone or otherwise sync their code base to these
repositories. Each developer will be able to push to and pull from
(e.g., during branching and version bumps at package release) their
git.bioconductor.org<http://git.bioconductor.org/> repository.
Version bumps and new branches(during Bioconductor release) will be
handled by the core team.
- Developers are encouraged to host and develop their source code on
Github or other git-based social platforms. This promotes community
involvement, and empowers developers to adopt best practices related
to issue tracking, continuous integration, bug fixes, pull requests
from their community, etc.
- All bioconductor infrastructure code will also be available on
Github, through our organization
page(https://github.com/Bioconductor). Community members are
encouraged to send us pull requests for all our public repositories.
2. Timing:
- Our plan is to make a 'clean' transition from SVN to git,
approximately one month after the next Bioconductor release.
Developers or users will not have access to the SVN system after the
date of transition.
3. Repositories:
- The git repositories will be derived from a 'snapshot' of the
latest SVN repository at the time of the transition. After the date
of transition, further commits to SVN will not be reflected in the
new git repositories.
- Each repository will capture the full SVN commit history of the
package. Releases will be included as branches in the repository.
- We anticipate that software and experiment data packages will be
hosted at git.bioconductor.org<http://git.bioconductor.org/>.
Experiment data packages will use git-lfs to manage large data.
- The Github Bioconductor-mirror repository will be removed.
4. Test phases:
- We anticipate two test periods.
- A private 'alpha' test phase is starting shortly. Alpha testers
will initially have pull access to their repository, and will follow
tentative work flows for gaining push access, for maintaining clones
of their packages, for committing to the
git.bioconductor.org<http://git.bioconductor.org/> repositories, and
for pulling from (e.g., version bumps and release branches) the
repositories.
- A public 'beta' test phase will start after the next Bioconductor
release, and last for approximately four weeks. Beta testers will
have pull access to all Bioconductor package repositories, and push
access to packages that they maintain. Commits will be visible, but
NOT synced with SVN or incorporated into nightly builds.
- An essential activity during test periods is to verify that the
SVN commit history has been captured in the git repositories. This
will be available in your git log.
5. Resources:
- We will be developing resources to help developers in the transition.
- As an addition to the resources, we also recommend the excellent
tutorials provided at
gittutorial<https://git-scm.com/docs/gittutorial>,
try.github.io<https://try.github.io/>.
Best,
Nitesh Turaga
Bioconductor Core Team
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