Git training

Nicolas Barrier

Witold Podlejski

Criscely Lujan-Paredes

Presentation of the Git Software

What is Git?

• Free and open source software
• Light and local use (without internet)
• The most popular Version Control Software (VCS)
• Manages and tracks versions of a project (code, manuscript, data)
• Can be linked with remote server (GitHub, Gitlab)

What is Git for?

• For a single user:
  • Track changes (commits) over time with information about when and what are the changes
  • Eventually go back in time
  • Synchronize the project in the cloud with git servers (GitHub, Gitlab)

What is Git for ?

• For a collaborative project:
  • Track changes (commits) with information about who, when and what are the changes
  • Resolve version conflict when simultaneous changes
  • Highlight a specific version of the project (tags)
  • New version of a software
  • Submitted, revised versions of a paper
  • Create derivates of a project (branches)
    • Production
    • Development
    • Feature
  • Publish the project (open science)

In short…

Figure 1: Without Git

Figure 2: With Git

Installation and configurations

Installing Git

Windows and Mac

Download and install Git from https://git-scm.com/downloads.

When done, open Git Bash

Linux

Open a Terminal window and type:

sudo apt install git git-lfs git-flow

Git configuration

On Git Bash or in the Terminal:

• Type git config --global user.name "Firstname Lastname"
• Type git config --global user.email "myadresse@ird.fr"

Note

These two lines identify you in the history of a project.

• Type git config --global --list to see the global git configuration.

Getting started with Git in local

Git architecture

flowchart LR
    idw(Workspace)
    idi(Index)
    idl(Local)

    idw -->|git add| idi
    idi -->|git commit| idl

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;

• Workspace: your working directory \(\rightarrow\) your computer
• Local: the local repository \(\rightarrow\) contains the history of your project
• Index: a buffer between Workspace and Local \(\rightarrow\) list of the files that will be sent from Workspace to Local
• git add : the command to add the file(s) in the Index
• git commit: the command to validate the changes (moves the files from Index to Local)

Getting started

• Create a folder called training-git by typing mkdir training-git
• Move to the folder by typing cd training-git
• Type ls -alrt
• Type git init
• Type again ls -alrt.

Note

A .git folder has appeared. It contains the full history of your project (Local repository)

• Type git status and git log

First commit

• Create a README.md file. Type git status \(\rightarrow\) README.md is now in Workspace but not in Index nor in Local

• Type git add README.md and git status

flowchart LR
  idw(Workspace) -->|git add| idi(Index)
classDef workspace fill:lightgray,stroke:black,color:black
classDef index fill:lightblue,stroke:black,color:black
classDef local fill:lightgreen,stroke:black,color:black
classDef remote fill:yellow,stroke:black,color:black

class idw workspace;
class idi index;

• Type git commit -m "First commit" and type git log

flowchart LR
  idw(Index) -->|git commit| idl(Local)
classDef workspace fill:lightgray,stroke:black,color:black
classDef index fill:lightblue,stroke:black,color:black
classDef local fill:lightgreen,stroke:black,color:black
classDef remote fill:yellow,stroke:black,color:black

class idw index;
class idl local;

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
   commit id: "0f0e96a"

Note

0f0e96a is a short version of the identifier of the commit

Second commit

• Open the README.md file, add # Git training and save
• Type git status
• Type git diff

flowchart LR
  idw(Local) -->|git diff| idl(Workspace)
classDef workspace fill:lightgray,stroke:black,color:black
classDef index fill:lightblue,stroke:black,color:black
classDef local fill:lightgreen,stroke:black,color:black
classDef remote fill:yellow,stroke:black,color:black

class idw workspace;
class idl local;

• Type git commit -m "Second commit"
• Type git log

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"

Creating tags

• Open the README.md file and add ## Version v1.0.0.
• Type git add README.md
• Type git commit -m "Third commit"
• Type git tag v1.0.0 and git log

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    commit id: "07e8835" tag: "v1.0.0"

• Type git tag to list all existing tags

Ignoring files

It is possible to tell Git to ignore some files by using a .gitignore file.

• Create an empty output.log file and type git status
• Create a .gitignore file and write *.log. Type again git status

The output.log file does not appear as an Untracked file anymore

• Type git add .gitignore and git status
• Type git commit -m "Fourth commit"

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    commit id: "07e8835" tag: "v1.0.0"
    commit id: "9670a59"

Tip

To list the ignored files, type git ls-files --others --ignored --exclude-from=.gitignore

Moving in the history

• Type git checkout v1.0.0 \(\rightarrow\) move to a tag

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    commit id: "07e8835" tag: "v1.0.0" type:HIGHLIGHT
    commit id: "9670a59"

• Type git checkout 0f0e96a \(\rightarrow\) move to a specific commit

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a" type:HIGHLIGHT
    commit id: "c6dc2bc"
    commit id: "07e8835" tag: "v1.0.0"
    commit id: "9670a59"

• Type git checkout main \(\rightarrow\) move at the latest commit (replace main by master if the latter is the name of the main branch)

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    commit id: "07e8835" tag: "v1.0.0"
    commit id: "9670a59" type:HIGHLIGHT

Tip

HEAD is a symbolic reference pointing to wherever you are in your commit history, as shown in git log

Display differences

• Type git diff 0f0e96a v1.0.0 \(\rightarrow\) compares a commit and a tag.

Warning

Order matters when using git diff. Differences are shown with the reference state considered to be the first argument.

flowchart LR
  id1(0f0e96a)-->|git diff| id2(v1.0.0)
classDef workspace fill:lightgray,stroke:black,color:black
classDef index fill:lightblue,stroke:black,color:black
classDef local fill:lightgreen,stroke:black,color:black
classDef remote fill:yellow,stroke:black,color:black

class id1,id2 local;

• Type git diff 0f0e96a c6dc2bc \(\rightarrow\) compares two commits.

• Type git diff 0f0e96a HEAD \(\rightarrow\) compares where you are in the history (HEAD) with a given commit.

Using Git with online server (GitHub)

Using remotes

In addition of saving the history, Git has other advantages. It allows to:

• Save a project remotely
  • Synchronization with different computers (laptop, HPCs)
• Share a project (codes, packages) with the community
  • Reproducible science

To do so, a \(4^{th}\) component in the Git architecture must be considered: the Remote repository. It contains a remote version of the history of your project

flowchart LR
    idw(Workspace)
    idi(Index)
    idl(Local)
    idr(Remote)

    idw -->|git add| idi
    idi -->|git commit| idl
    idl -->|git push| idr
    idr --->|git pull| idw
    idr --->|git fetch| idl

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

Remote hosts

There are several remote hosting possibilities:

Commercial hosts:

• GitHub: https://github.com/
• GitLab: https://gitlab.com/

Institutional hosts:

• GitLab IRD: https://forge.ird.fr/
• GitLab Ifremer https://gitlab.ifremer.fr/

In the following, we will use GitHub.

Tip

GitHub proposes extra-features for students, teachers and researchers. Visit https://education.github.com/benefits for more informations

Creation of a GitHub repository

• On your GitHub page, click on Repositories
• Click on the the green New button
• Set the name of your remote repository. Leave the other fields empty
• Click on Create repository

Creation of a personal access token

To authentificate, you need to create an authentification token (see GitHub authentification of details for details).

To do so, click on your profile photo and then on Settings:

Creation of a personal access token

• In the left sidebar, click on Developer settings.
• Under Personal access tokens, click Tokens (classic).
• Select Generate new token and Generate new token (classic).

Creation of a personal access token

• Add a description note and click on the “repo” box, as shown below:

• Click on the Generate token box button.

• Copy and save in a .txt file or in a Password manager tool (KeePassXC) the token: this is your password! It should look like something like this:

ghp_***************************************

Linking Git local and remote

• In Terminal or Git Bash, type the following line:

git remote add origin https://github.com/barriern/git-train.git

Warning

Replac barriern by your GitHub login and git-train by the name of your GitHub repository.

• It connects your Local repository with a remote one, called origin

flowchart LR

    idl(Local)
    idr("Remote\n(origin)")

    idl-->idr
    idr-->idl

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

• Type git remote -vv

Linking Git local and remote

Now that the local and remote repositories are linked, the same thing must be done with the branches.

• Type git branch -M main by replacing main by the name of the remote branch on GitHub. It will rename the local branch with the same name.
• Type git push -u origin main

It connects the local and remote main branches (-u option) and sends the commits to the remote branch

flowchart LR

    idl("Main\n(Local)")
    idr("Main\n(Remote)")

    idl-->idr
    idr-->idl

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

• Type git branch -vv

Linking Git local and remote

Have a look at your repository on GitHub. Tags are missing!

Type git push --tags and refresh the GitHub page.

flowchart LR

    idl(Local)
    idr("Remote")

    idl-->|git push|idr


    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

Note

No need to specify the -u origin main arguments since the two branches are already connected.

Navigate on the GitHub page to see what has been done.

Synchronization from the remote

• In GitHub, click on the README.md file and then on the edit button

• Add a Update from Github line and click on Commit changes

The Remote change of README.md is not yet visible in Workspace!

• In Git Bash or Terminal, type git pull

flowchart RL

    idr(Remote)
    idw(Workspace)

    idr -->|git pull| idw

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

• Look again at the README.md file on your computer. You should see the update.

Synchronization: conflicts

• On GitHub, add x = 1 at the end of the README.md file. Do not type pull!
• On your computer, edit the README.md and add x = 2.
• Type git add README.md
• Type git commit -m "Fifth commit"
• Type git push. An error occurs because changes in Remote have not been pulled in Local.
• Type git pull and git status. An error occurs because there is a conflict in the README.md file which cannot be solved by Git.

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch origin/main
    commit id: "x = 1"
    checkout main
    commit id: "x = 2"

Synchronization: conflicts

• Open the README.md file. You should see:

<<<<<<< HEAD
x = 2
=======
x = 1
>>>>>>> 70a4c105e377db282c0769606960f0afcccdd071

Warning

These are conflicts markers. Git does’t know whether to chose x = 1 or x = 2. This is your job

• Open the file, replace the above by x = 3. Commit and push the changes

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch origin/main
    commit id: "x = 1"
    checkout main
    commit id: "x = 2"
    merge origin/main tag: "x = 3"

Cloning an existing repository

• In Terminal or Git Bash, type cd ..
• Now type git clone https://github.com/umr-marbec/git-training

flowchart RL

    idr(Remote)
    idw(Workspace)

    idr -->|git clone| idw

    classDef workspace fill:lightgray,stroke:black,color:black
    classDef index fill:lightblue,stroke:black,color:black
    classDef local fill:lightgreen,stroke:black,color:black
    classDef remote fill:yellow,stroke:black,color:black

    class idw workspace;
    class idi index;
    class idl local;
    class idr remote;

• Type git log to see the full history.
• To update the project, type git pull

Warning

Do not clone or initialize a Git repository in another Git repository!

Create a repository the simple way

To create a new repo more simply than done here:

• Create a repo. on GitHub with a README.md file and eventually a LICENCE file.
• Clone the repo.
• You are all set!
  • The remote and local repositories are synchonized
  • The remote and local main branches are synchonized

Conclusion: good practice

• Before starting editing a project, do a git pull
• Commit very often using git commit extensively
• Push often as well using git push
• Use git status extensively to know what you have done

Git clients

Git clients: what is it?

Git Clients are softwares that facilitate the use of Git (see Git Guis for a list).

Beside, most code editors include Git functionalities

Git clients

Figure 3: VSCode

Git clients

Figure 4: RStudio

Git clients

Figure 5: Netbeans

Going further

Going further…

For those who want, extra slides are available on:

• Git with Large File Storage extension.
• Working with branches, i.e. derivates of a project

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch bugfix
    branch develop
    checkout develop
    commit id: "214e348"
    checkout main
    commit id: "69bbd79"
    merge develop
    checkout develop
    branch feature
    commit id: "0a9ba0c"
    checkout bugfix
    commit id: "d9d02608"

Large file storage

To version (reasonably) large files (images, data samples) \(\rightarrow\) Git with LFS extension.

Warning

Make sure that the remote host is compatible with LFS (GitHub is compatible)

• Type git lfs install to activate the extension
• Create a data.csv file and add Year,Size,Species
• Type git lfs track "*.csv"

A .gitattributes file has appeared, which list all the file extensions managed by Git LFS.

Large file storage

• Type git add .gitattributes data.csv
• Type git commit -m "Using LFS"
• Type git push
• On GitHub, click on your file data.csv file.

Creating aliases

To create Git aliases (i.e. shortcuts):

• Type git config --global alias.tree log --all --decorate --oneline --graph
• Type git config --global alias.br branch -vv
• Type git config --global alias.re remove -vv

You can now call the git tree, git br and git re commands.

Creating branches

• Type git checkout -b develop
• Type git status, git br and git tree
• Open the README.md file, add some text and save.
• Type git add README.md
• Type git commit -m "3rd commit"
• Type git br and git tree

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch develop
    commit id: "214e348"

Switching branch

• Type git checkout main (or git checkout master)
• Type git br
• Open the LICENCE file and add some text in it
• Type git add LICENCE
• Type git commit -m "Third commit"
• Type git tree

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch develop
    checkout develop
    commit id: "214e348"
    checkout main
    commit id: "69bbd79"

Merging branches

• On the main branch, type git merge develop -m "merge-develop"
• Type git log and git tree

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch develop
    checkout develop
    commit id: "214e348"
    checkout main
    commit id: "69bbd79"
    merge develop

The merge command puts the commits from the argument branch (here develop) and puts them into the current branch (here main).

Note

During the merging process, another commit is created

Creating branch from another branch

• Type git checkout -b feature develop
• Create a script.R file
• Type git add script.R
• Type git commit -m "Fourth commit"

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch develop
    checkout develop
    commit id: "214e348"
    checkout main
    commit id: "69bbd79"
    merge develop
    checkout develop
    branch feature
    commit id: "0a9ba0c"

Creating branch from a commit

• Type git checkout -b feat-com 1831e4e replacing 1831e4e by an actual commit ID.
• Create a script.py file
• Type git add script.py and git commit -m "Sixth commit"

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    branch feat-com
    branch develop
    checkout develop
    commit id: "214e348"
    checkout main
    commit id: "69bbd79"
    merge develop
    checkout develop
    branch feature
    commit id: "0a9ba0c"
    checkout feat-com
    commit id: "d9d02608"

Differences between branches

• Type git diff develop main

You will see the text that has been added to the LICENCE file (69bbd79 commit)

Warning

Order matters: it shows what has been added to main branch compared to the develop branch

flowchart LR
  id1(Develop)-->|git diff| id2(Main)
classDef workspace fill:lightgray,stroke:black,color:black
classDef index fill:lightblue,stroke:black,color:black
classDef local fill:lightgreen,stroke:black,color:black
classDef remote fill:yellow,stroke:black,color:black

class id1,id2 local;

Deleting a branch

• Type git checkout main
• Type git branch -d develop
• Type git br
• Type git branch -d feat-com

An error occurs! The suppression of feat-com implies the loss of the d9d02608 commit. To force the suppression, use -D instead of -d.

• Type git branch -D feat-com

Note

The suppression of develop was ok because the content of commit 3rd is included in the merge.

Reverting a commit

• Type git revert c6dc2bc (replace c6dc2bc by your commit id)

%%{init: { 'logLevel': 'debug', 'theme': 'base', 'gitGraph': {'rotateCommitLabel': true}}}%%
gitGraph
    commit id: "0f0e96a"
    commit id: "c6dc2bc"
    commit id: "-c6dc2bc" type: REVERSE

Remainder

Basic commands

• git init: initialise a git project (create .git folder)
• git add [files]: add files to list of tracked files
• git commit -m ”message”: validate locally a version of the project
• git status: see the unvalidated and untracked changes
• git checkout [commit]: load the project version corresponding to the index
• git pull: import the changes from remote project to local
• git push: export the changes from local project to the remote server

Git configuration (mandatory)

• Configure your identity: git config --global user.name "Firstname Lastname"
• Configure your e-mail: git config --global user.email "myadresse@ird.fr"

Branch handling

• git branch [branch_name]: create a new branch (but you remain on the previous branch)
• git branch -b [branch_name]: create a new branch and move to this newly created branch
• git checkout [branch_name]: move to the corresponding branch
• git merge [branch_name1] [branch_name2]: merge two different branch, you may need to resolve version conflict.
• git branch -d [branch_name1]: delete a branch (safe mode)
• git branch -D [branch_name1]: delete a branch (unsafe mode)

Linking with remote

• git clone [URL]: Import an existing project from remote server.
• git remote add origin [URL]: link directly the local repository with a remote

Authentication of your computer and the remote server

• SSH key: easy way on Linux distributions
  • Tuto here: https://jdblischak.github.io/2014-09-18-chicago/novice/git/05-sshkeys.html
• Authentication Token
  • Tuto here: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token

Good practices

• Pull before any work on the project
• Commit as frequently as possible
• Write explicit commit message
• Push regularly

IDE (graphical user interface) with Git

• R
  • RStudio
  • Visual Studio Code
• Python
  • Spyder
  • Visual Studio Code
  • Pycharm (all JetBrain softwares)

Sources

• Plateau bioinformatique, Montpellier: Formation Git(Lab) (05/04/2018)
• UMR AMAP (Atelier MAIA P3M), Montpellier: Introduction à GIT (04/04/2019)