[Bioc-devel] Git Transition Plan

Wed Jul 5 19:30:35 CEST 2017

Hi Philipp,

The beta testing phase just started. I sent out an email to the bio-devel mailing list today.

We thank you for your enthusiasm to participate in this beta test phase.

Best Regards,

Nitesh

hi, do you know by now when the beta will start? i’m honestly a bit tired of SVN and would like to participate

________________________________
Von: "Turaga, Nitesh" <Nitesh.Turaga at RoswellPark.org<mailto:Nitesh.Turaga at RoswellPark.org>>
An: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Gesendet: Donnerstag, 1. Juni 2017 14:19:59
Betreff: Re: [Bioc-devel] Git Transition Plan

Hi Nathan,

We¹ve been working on a few things for the beta phase of the transition.

1. Getting the experiment data packages on board
2. Making sure manifests are in order along with their commit history.
3. Writing documentation for our new workflows for developers/maintainers.

The beta process has not started but, we expect it to be in play very
soon.

New package submissions are still going through SVN. We will make sure to
send out an email/ post in the support group NEWS, and inform all the
users as soon as that happens.

You did not miss anything.

Best,

Nitesh

>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 <henrikb at braju.com<mailto:henrikb at braju.com>>
>>> joe at foo.com<mailto:joe at foo.com> = John Doe <jd at someone.org<mailto:jd at 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.Turaga at roswellpark.org<mailto:Nitesh.Turaga at 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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