Introduction to using Git and GitHub for software development: Summary of Commands

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 facilitates access to online tools for publication and collaboration

Setup Git with your details using git config --global user.name "FIRST_NAME LAST_NAME" and git config --global user.email "email@example.com"

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 stage [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 --staged

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

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 develop the software.

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

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

origin is the default name used by Git to refer to a remote repository.

Local and remote repositories are not identical, in general, as synchronisation must be performed manually.

git fetch, followed by git status, shows whether there are any changes to synchronise.

git pull brings changes in the upstream branch to the local branch.

git push synchronises any committed changes in your local branch with the upstream branch.

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

Issues are a feature of GitHub which let you track work in a repository.

GitHub provides functionality for referencing issues in comments

Task lists can be created to keep track of a list of issues

Formatting syntaxes, templates, and subscribing to issues help with communication

Knowing how to use Git from the command-line is useful for understanding concepts and as a fallback

Text editors and IDEs often have built-in Git support

GUIs are particularly useful for viewing the graph-like structure of a repository

It is worth taking time to explore other tools for Git so you can find a workflow that suits you