[Bioc-devel] Bioconductor git server beta testing begins now.
Nitesh.Turaga at RoswellPark.org
Fri Jul 7 14:42:07 CEST 2017
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
>>As announced earlier this year, Bioconductor is moving version control
>>systems from SVN to Git.
>>- 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
>>- Read-only (user) access for each package is available via https,
>> 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
>>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
>>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
>>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
>>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.
>>Bioconductor Core Team
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
More information about the Bioc-devel