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Bioconductor/bioc_git_transition

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Bioconductor SVN to GIT transition

This package provides functionality to allow for SVN - Git transition for the Bioconductor Project.

Goals

  • Create a private git server with all Bioconductor packages, including commit history from each of the RELEASE branches and the devel branch.

Setup

Usage: clone, push, pull, etc.

  • ALPHA testing. Remember, repositories are static snapshots of svn; they are not current, changes commited here are not propagated to svn, and will not be retained.

  • Clone a package for read-only access

     git clone https://git.bioconductor.org/packages/<package>.git
    

    or for read / write (appropriate permissions required)

     git clone git@git.bioconductor.org:packages/<package>
    
  • See the branches available

     cd BiocGenerics
     git branch -a
    
  • Checkout branch and see if the commit history is correct

     git checkout RELEASE_3_0
     git log
    
  • Local commits

     ...
     git commit -m "alpha test" -a
    
  • Push commits to writeable repositories (commits will be lost after testing phases are complete)

     git push
    
  • (Non-core users): Fail to push changes on non-master or RELEASE_3_4 branch.

     git checkout RELEASE_3_3
     ...
     git commit -m "alpha test" -a
     git push # fail
    

Usage: exploration

  • Elementary browser interface available at

     https://git.bioconductor.org
    
  • View R(ead) / W(rite) privileges

     ssh git@git.bioconductor.org info # all packages
     ssh git@git.bioconductor.org info packages/BiocGenerics
    

Status

  • ssh-based read-only access to all repositories
  • ssh-based read-write access to selected repositories
  • public read-only access to all repositories
  • experiment-data packages

Troubleshooting

SSH

ssh may have to choose between multiple keys. Resolve this with an entry in the plain-text ~/.ssh/config file, where identityfile disambiguates the key you'd like to use.

 host git-bioc
 user git
 hostname git.bioconductor.org
 port 22
 identityfile ~/.ssh/id_rsa

Use as git clone git-bioc:packages/BiocGenerics.

About

This python package is for transitioning bioconductor from SVN to git

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