[Bioc-devel] Bioconductor git server beta testing begins now.

Diego Diez diego10ruiz at gmail.com
Sun Jul 9 11:13:07 CEST 2017

Dear all,

Great to know that the git transition is moving forward. I tested
cloning (https) several packages and I noticed a significant
difference in the repository size between svn and git. Two examples
showing the output (svn/git) of du -k:

Biobase: 4968 / 8720
limma: 6284 / 20296

Looking briefly at the .git folder inside the repositories it seems
the .pack file inside .git/objects/pack takes most of the overweight.
I wonder if this is expected?

Thank you.


PS: commands used to obtain the repositories:

git clone https://git.bioconductor.org/packages/limma
svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/limma
--username readonly

On Fri, Jul 7, 2017 at 9:42 PM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:
> Dear Maintainers,
> For those of you who have submitted your public github id instead of your
> public SSH key,  please make sure that the link
> `www.github.com/<username>.keys` is valid and shows your SSH key.
> If that is not valid, we are not able to add your SSH key to the
> bioconductor server.
> Thanks,
> Nitesh
>>>Dear Maintainers
>>>As announced earlier this year, Bioconductor is moving version control
>>>systems from SVN to Git.
>>>The plan
>>>- Software, experiment data, and workflow packages will be maintained
>>>  as git repositories created to capture the full commit history of
>>>  each package. (the commit history of the 'data_store' portion of
>>>  data experiment packages will unfortunately not carry forward to
>>>  git).
>>>- Read-only (user) access for each package is available via https,
>>>  e.g.,
>>>      git clone
>>>- Read-write (developer) access for each package is available via ssh,
>>>      git clone git at git.bioconductor.org:packages/SummarizedExperiment
>>>  Developers MUST SHARE public key(s) with Bioconductor. The process
>>>  for this during the beta phase is outlined below.
>>>- The build system and other core infrastructure will use
>>>  git.bioconductor.org as the canonical source after the transition.
>>>- Developers may wish to independently clone and maintain github or
>>>  other repositories to support their package. Developers are
>>>  responsible for pushing changes from these cloned repositories to
>>>  the canonical source.
>>>- https://github.com/Bioconductor-mirror will be removed after the
>>>  transition.
>>>Beta testers
>>>We are starting Beta testing now. We encourage as many people as
>>>possible to become beta-testers, either as users (via git clone
>>>https://...) or maintainers (via git clone git at ...).
>>>All software, data experiment, and workflow packages are available at
>>>      (read-only) git clone
>>>      (read / write) git clone
>>>git at git.bioconductor.org:packages/<package>
>>>These are STATIC SNAPSHOTS of SVN. Developers are encouraged to commit
>>>to these repositories, but the commits are not propagated to svn and
>>>will be lost at the end of the beta phase.
>>>For maintainers, Bioconductor needs your SSH public key. We have
>>>prepared a Google form for this
>>>    https://goo.gl/forms/eg36vcBkIUjfZfLe2
>>>The form requires your Bioconductor provided SVN username, and your
>>>Github user name (to retrieve your public keys from
>>>https://github.com/<your-github-id>.keys) OR SSH key. Currently, the
>>>form is processed on an approximately daily basis, so there is a delay
>>>between credential submission and developer access.
>>>(IMPORTANT) As a beta tester, we ask that you work through the
>>>'scenarios' at
>>>    https://github.com/Bioconductor/bioc_git_transition/tree/master/doc
>>>Package authors and maintainers, please take the extra measure to
>>>check that your package history is complete to July 4th, i.e commit
>>>files, folders and all Bioconductor components.
>>>If you are new to Git or Github, there are learning materials online
>>>We encourage pull-requests on documentation. Please post other
>>>beta-test feedback from the experience with the new git server to this
>>>mailing list.
>>>Important Dates:
>>>Transition: on date T, tentatively July 31st.
>>>Until July 30th 2017:
>>>    Beta testing phase.
>>>July 26th 2017:
>>>    Developer day demo session on Bioconductor's GIT transition/usage
>>>    going forward. (30-45 mins) Be sure to attend if you are at
>>>    Bioc2017, Boston. Slides will be made public.
>>>T - 2: Final SVN snapshot of data experiment packages
>>>    No more SVN commits to Data Experiment packages.
>>>T: Day of transition.
>>>    All SVN commits to software, experiment data, and workflow
>>>    repositories are stopped, forever.
>>>   Git repositories are updated to most recent svn version on day T.
>>>    (We estimate that this will take about 6 hours; no commits
>>>    possible on either svn or git).
>>>    Git commits resume. Please make sure to commit to
>>>    git at git.bioconductor.org.
>>>    Only git sever commits moving forward.
>>>This is an important step for the infrastructure of the project. If
>>>you have questions please reply to this email, i.e. to the bioc-devel
>>>mailing list. If there are any issues with individual packages, make
>>>sure to list them out.
>>>Best Regards,
>>>Bioconductor Core Team
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