Git

Git is a distributed, fast and secure source code management tool. The official Git website is git-scm.com. Git was created by Linus Torvalds for the Linux project and is currently maintained by Junio Hamano.

Operating principle¶

Contrary to older source code management tools, Git works in a distributed way. This means that developers do not depend on a central repository to commit their changes. Each Git repository contains the full history of the project. Each Git object (changeset, file, directory) is the leaf of a tree with multiple branches. Developing a project with Git is based on a model in which one branch corresponds to one feature. Many revisions of the feature may be archived before the branch gets merged with the main trunk. For a detailed explanation of branch development, we recommend reading this page.

One especially interesting technique is cherry-picking, which is essentially taking part of a branch and merging it with another one.

Basic usage¶

Generally, a project developer will:

configure the global Git environment;
clone or create a repository;
make changes;
commit changes;
push changes to another repository.

Since Git is distributed, there may not be an authoritative repository.

Summary of commands¶

Command	Description
`git config`	Configure git
`git init`	Create a new repository
`git clone`	Clone an existing repository
`git add`	Add a file or directory to a repository
`git rm`	Delete a file or directory from the repository
`git commit`	Commit changes to the repository
`git push`	Push changes to another repository
`git pull`	Pull changes from another repository and merge them with your own repository
`git fetch`	Fetch changes from another repository without merging them with yours
`git merge`	Merge changes to the repository

Command	Description
`git blame`	Show which authors last modified a file
`git log`	Show the commit history
`git diff`	Compare two versions
`git status`	Display the status of the current files
`git show`	Display various git objects
`git cat-file`	Display the content, type or size of objects

Command	Description
`git branch`	Manage development branches
`git tag`	Manage version tags
`git remote`	Manage remote repositories
`git checkout`	Check out a branch or a path
`git reset`	Change the head of a branch

Command	Description
`git format-patch`	Create a patch
`git am`	Apply a patch
`git send-email`	Send a patch by email

Command	Description
`git bisect`	Used to diagnose problems
`git gc`	Collect garbage objects
`git rebase`	Rebase history of the repository
`git grep`	Search for content

Configuring the global Git environment¶

This section is based on the Software Carpentry - Version Control with Git lesson. When you start developing on a new system, you want to configure:

Your name and email address, which will be associated with every commit. Note: this information will become public if you push your revisions to a public repository.
```
git config --global user.name "First-name Last-name"
git config --global user.email "email@address.ca"
```
Limit yourself to only four threads, otherwise, your git clone commands may fail if they are using too many threads.
```
git config --global pack.threads 4
```
If you are not used to vi, you can set a different text editor for your commit messages.
```
git config --global core.editor "nano -w"
```
Finally, you may want to redefine the default name for the initial branch name. For example, main.
```
git config --global init.defaultBranch main
```

To list all options set in the global environment, run the following command.

git config --list --global

Creating or cloning a repository¶

The first step is usually to create your own repository, or to clone an existing one.

To create a repository:

git init my-project

To clone a repository:

git clone git://github.com/git/git.git

Committing a change¶

When the repository is ready, you change directory and edit the file.

cd my-project
nano file.txt

When work is done, you add the file

git add file.txt

then commit the change

git commit

If the repository was cloned, it is now possible to push your changes to the original repository with

git push origin main

In the above command, origin is the remote repository and main is the current branch that will be pushed.

You might have to use git push origin master for older git repositories.

Hosting Git repositories¶

GitHub and Bitbucket are two of the main Git repository hosting services. They are both available for commercial projects as well as free projects.

Troubleshooting¶

Unable to create thread¶

If you see:

fatal: unable to create thread: Resource temporarily unavailable
fatal: fetch-pack: invalid index-pack output

This is caused by resource limitations on the cluster login nodes. The solution is to limit the number of threads to 2. Use the following command on each cluster:

```bash git config --global pack.threads "2"