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

[Turaga, Nitesh]

Hi Diego,

This is a good question.

Please note, that when you do a 'git clone¹, you are getting the commit
history of every branch, and master(trunk) locally. Git stores the log of
the commit history(trees, commits and blobs) locally in the .git/object
directory. 

When you checkout an svn branch, you are checking out 1 specific branch,
i.e, trunk or RELEASE_X_Y. It also needs to connect to the server to get
the commit history of your files.

These are fundamental differences in the way these version control systems
work, and this difference is expected.

Best,

Nitesh



>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.
>
>Diego
>
>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
>>>>https://git.bioconductor.org/packages/SummarizedExperiment
>>>>
>>>>- Read-write (developer) access for each package is available via ssh,
>>>>e.g.,
>>>>
>>>>      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
>>>>https://git.bioconductor.org/packages/<package>
>>>>      (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
>>>>history,
>>>>files, folders and all Bioconductor components.
>>>>
>>>>If you are new to Git or Github, there are learning materials online
>>>>https://try.github.io
>>>>
>>>>We encourage pull-requests on documentation. Please post other
>>>>beta-test feedback from the experience with the new git server to this
>>>>mailing list.
>>>>
>>>>Transition
>>>>--------------
>>>>
>>>>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,
>>>>
>>>>Nitesh
>>>>Bioconductor Core Team
>>>
>>
>>
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