Notes on git

BioShell code is versioned by git

To checkout the newest source, run the following:

git clone git@bitbucket.org:dgront/bioshell.git

This will create a local directory named bioshell containing the source. Note, that you need bitbucket account to do this. Also, SSH key of the local machine must be registered at bitbucket.

Working in branches

  • Creating a local branch

git checkout -b name_of_branch The new branch will hold all the changes you’ve intoduced to the branch you diverged from (which most likely is origin/master)

  • Uploading a local branch

To push a local branch to bitbucket for the very first time, do the following: git push -u origin name_of_branch

  • Merging changes from master branch to a current branch feature

git checkout feature
git merge master

  • Cleaning up old branches

    First chech which branches are already merged in master and can be easily removed:
    git checkout master
    git branch --merged
    Then remove a merged branch locally and on the remote:
    git branch -d obsolete-branch
    git push origin --delete obsolete-branch

Moving around the repository

  • Check history of a particular subdirectory (10 last commits)

git log --name-status -10 path/to/dir

  • Looking up a file that has been deleted in the past

    git log --all --full-history -- **/Simulation*Settings.cc

    where SimulationSettings.cc is the actually deleted file; If you are not sure about spelling the name of the file, use ‘*’ as in this example