[Bioc-devel] Git Transition Plan

Turaga, Nitesh Nitesh.Turaga at roswellpark.org
Wed Mar 29 18:51:20 CEST 2017

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/>.


Nitesh Turaga
Bioconductor Core Team

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