Version Control with Git

Reference

Setting Up Git

Use git config to configure a user name, email address, editor, and other preferences once per machine.

Creating a Repository

git init initializes a repository.

Tracking Changes

git status shows the status of a repository.
Files can be stored in a project’s working directory (which users see), the staging area (where the next commit is being built up) and the local repository (where revisions are permanently recorded).
git add puts files in the staging area.
git commit saves the revisions in the staging area to the local repository.
Always write a log message when committing changes.

Exploring History

git diff displays differences between revisions.
git checkout recovers old versions of files.

Ignoring Things

The .gitignore file tells Git what files to ignore.

Branching

All work is performed on a branch. The default branch is master.
git branch lists the existing branches
git branch xxx creates a new branch called xxx, starting from the current branch.
git checkout xxx switches to the branch xxx
git merge xxx merges the changes from xxx into the current branch.

Remotes in GitHub

A local Git repository can be connected to one or more remote repositories.
Use the HTTPS protocol to connect to remote repositories until you have learned how to set up SSH.
git push copies changes from a local repository to a remote repository.
git pull copies changes from a remote repository to a local repository.

Collaborating

git clone copies a remote repository to create a local repository with a remote called origin automatically set up.

Conflicts

Conflicts occur when two or more people change the same file(s) at the same time.
The version control system does not allow people to blindly overwrite each other’s changes. Instead, it highlights conflicts so that they can be resolved.

Open Science

Open scientific work is more useful and more highly cited than closed.

Licensing

People who incorporate GPL’d software into their own software must make their software also open under the GPL license; most other open licenses do not require this.
The Creative Commons family of licenses allow people to mix and match requirements and restrictions on attribution, creation of derivative works, further sharing, and commercialization.
People who are not lawyers should not try to write licenses from scratch.

Hosting

Projects can be hosted on university servers, on personal domains, or on public forges.
Rules regarding intellectual property and storage of sensitive information apply no matter where code and data are hosted.

Glossary

change set: A group of changes to one or more files that are or will be added to a single commit in a version control repository.
commit: To record the current state of a set of files (a change set) in a version control repository. As a noun, the result of commiting, i.e. a recorded change set in a repository. If a commit contains changes to multiple files, all of the changes are recorded together.
conflict: A change made by one user of a version control system that is incompatible with changes made by other users. Helping users resolve conflicts is one of version control’s major tasks.
HTTP: The Hypertext Transfer Protocol used for sharing web pages and other data on the World Wide Web.
infective license: A license, such as the GPL, that legally requires people who incorporate material under the infective license into their own work to also release under the same infective license (eg. under the GPL license).
merge: (a repository): To reconcile two sets of changes to a repository.
protocol: A set of rules that define how one computer communicates with another. Common protocols on the Internet include HTTP and SSH.
remote: (of a repository) A version control repository connected to another, in such way that both can be kept in sync exchanging commits.
repository: A storage area where a version control system stores the full history of commits of a project and information about who changed what, when.
resolve: To eliminate the conflicts between two or more incompatible changes to a file or set of files being managed by a version control system.
revision: A recorded change set of a version control repository. The same as a commit.
SSH: The Secure Shell protocol used for secure communication between computers.
timestamp: A record of when a particular event occurred.
version control: A tool for managing changes to a set of files. Each set of changes creates a new commit of the files; the version control system allows users to recover old commits reliably, and helps manage conflicting changes made by different users.