Using Git to Code, Collaborate and Share: Summary of Commands

Key Points

Why use a Version Control System?
  • Version control software refers to a type of program that records sets of changes made to files

  • VCS is a ubiquitous tool for software development

  • Tracking changes makes it easier to maintain neat and functional code

  • Tracking changes aids scientific reproducibility by providing a mechanism to recreate a particular state of your code base

  • VCS provides a viable mechanism for 100’s of people to work on the same set of files

  • VCS lets you undo mistakes and restore a code base to a previous working state

  • Git is the most widely used version control software

  • Using Git allows access to online tools for publication and collaboration

Committing and History
  • Setup Git with your details using git config –global “FIRST_NAME LAST_NAME” and git config –global “”

  • A git repository is the record of the history of a project and can be created with git init

  • Git records changes to files as commits

  • Git must be explicitly told which changes to include as part of commit (known as staging changes) with git add [file]…

  • Staged changes can be stored in a commit with git commit -m “commit message”

  • You can check which files have been changed and/or staged with git status

  • You can see the full changes made to files with git diff for unstaged files and git diff –cached

  • The commit history of a repository can be checked with git log

  • The command git revert commit_ref creates a new commit which undoes the changes of the specified commit

  • The command git reset –soft HEAD^ removes the previous commit from the history

Branching and Merging
  • Git allows non-linear commit histories called branches

  • A branch can be thought of as a label that applies to set of commits

  • Branches can and should be used to carry out development of new features

  • Branches in a project can be listed with git branch and created with git branch branch_name

  • The HEAD refers to the current position of the project in its commit history

  • The current branch can be changed using git checkout branch_name

  • Once a branch is complete the changes made can be integrated into the project using git merge branch_name

  • Merging creates a new commit in the target branch incorporating all of the changes made in a branch

  • Conflicts arise when two branches contain incompatible sets of changes and must be resolved before a merge can complete

  • Identify the details of merge conflicts using git diff and/or git status

  • A merge conflict can be resolved by manual editing followed by git add [conflicted file]… and git commit -m “commit_message”

Sharing your code
  • Public repositories are open to anyone to use and contribute.

  • Private repositories are just for yourself or a reduced set of contributors.

  • README contains a description of the software and, often, some simplified installation instructions.

  • The LICENSE describes how the software must be distributed and used.

  • Using one of the OSI (open source initiative) licenses is recommended if the repository is public.

  • CONTRIBUTING describes how other users can help developing the software.

  • CITATION helps others to cite your software in their own papers.

  • GitHub can be used to setup a software repository, share your code and manage who and how can access it.

Remote repositories
  • origin is typically the name of the remote repository used by git.

  • Local and remote repositories are not identical, in general.

  • Local and remote repositories are not synchronized automatically.

  • push and pull commands only affect the branch currently checked out.

  • Only changes to a branch that are committed are pushed to the remote.

  • Local branches need to be explicitly pushed to a new remote one in order to share them.

  • Forks and pull requests are GitHub concepts, not git.

  • Pull request can be opened to branches on your own repository or any other fork.

  • Some branches are restricted, meaning that PR cannot be open against them.

  • Merging a PR does not delete the original branch, just modifies the target one.

  • PR are often created to solve specific issues.

Summary of Commands

Action Command
Create a new repository git init


A widely used implementation of a Version Control System