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

Mon Jul 10 16:13:45 CEST 2017

Hi Nitesh,

Thank you for the explanation. Now everything is clear.

Best,
Diego

On Mon, Jul 10, 2017 at 10:55 PM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:
> 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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>
>
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