Running a clean install of ubuntu (for demonstration purposes, you don't need to run this)

docker run -it -v ~/:/mnt/home ubuntu:latest

Installing git on Ubuntu for example

apt update -> installing in a regular computer, you will need to use sudo apt ...

apt install git

apt git --version

Configuring git

This step is needed every time you are running git on a new computer or user

git config --global user.name "Name" -> any Name you want

git config --global user.email "user@example.com" -> this has to be the email linked with your github account

Generating and copying a ssh key to git website

This step is needed every time you are running git on a new computer or user

First check if you already have a ssh key:

ls ~/.ssh/id_rsa.pub -> if this doesn't return any results, run ssh-keygen -t rsa, this will generate your ssh key. You can run the command and press enter twice to keep the default cofiguration

cat ~/.ssh/id_rsa.pub

copy the key to your github:

1. open www.github.com

2. click on your profile picure on the top-right corner

3. go to settings -> Ssh and GPG keys -> new SSH key

4. give a name for you key, for example 'home pc' and paste your ssh key on the 'key' field

Now you should be able to pull and push your files without the need of a password

Installing text editor for demonstration purposes

apt install nano

Edit a random file you want to initiate the git

mkdir test_folder

cd test_folder

git init

nano test.m

Create a brand new repository at github website and run this code in the folder of the files of the new repository

git status

git add test.m or git add .

git commit -m "first commit"

git branch -M master

git remote add origin git@github.com:tsantini/test.git

git remote add upstream git@github.com:tsantini/test.git

git push -u origin master

Cloning from a existing repository

git clone git@github.com:tsantini/test.git

Editing the existing repository

nano test.m

git diff

git add .

git commit -m 'adding a new comment to the file'

git push

Creating a development branch

nano test.m

git status -> checking the current branch

git checkout -b development

git add .

git commit -m 'editing in the development branch'

git push

Updating just one file from the remote repository

git fetch
git checkout origin/branch_name -- file_name

Other important tools:

• brancking and pull request in the master from the development branch, asking for revision

• Pull request, comments, request of modification, and approval; issue tracker

• Using the github on matlab

• Access control and blocking branches for edition

• Forking

• Wiki

Misc useful commands

.gitignore -> file that contains the name of the files to the ignored by git, for example *.o would ignore all files with .o extension

git mv -> moves a files

git rm -> removes a files

git pull -> updates the current repository with the content of the remote repository

git remote update -> updates the current repository with the content of the remote repository without automatically merging

git branch -r -> list all the branchs in the repository

git remote show origin -> shows information about the branches

git checkout <branch> <file> --> copy a file from another branch to the current branch

Conflicts

when there is a conflict, for example, you modified a piece of code that was also modified remotely, it will show up like this when you do git pull:

If you have questions, please
<<<<<<< HEAD
open an issue
=======
ask your question in IRC.
>>>>>>> branch-a

Reverting changes

git log

git revert [commit-ID]

Updating fork from the original repository

git fetch git@github.com:original_user/original_repository.git

git merge FETCH_HEAD

git push

When you made changes before git pull

git stash

git pull

git stash apply

Configuring git with Matlab on Windowns

1 - install git for windows: https://git-scm.com/download/win, check the options "checkout as-is, commit as-is" and use Windows' default console window

2 - on powershell, create a key compatible with windows: ssh-keygen -t rsa -b 4096 -m PEM (source https://www.mathworks.com/matlabcentral/answers/494543-why-do-i-receive-an-auth-fail-error-when-interacting-with-a-git-remote-over-ssh-in-matlab-or-why-d)

3 - create an enviroment variable called HOME pointing to your home folder, as shown here: https://www.mathworks.com/help/matlab/matlab_prog/set-up-git-source-control.html

When you want to reverse the master last commit and change the modifications in another brach

git branch newbranchname: creates a new branch and stores the current committ

git reset --hard HEAD^: reverse to the previous commit in the master branch

git push origin master --force: for pushing the last modifications

git checkout newbranchname: go to the newly created branch

git push --set-upstream origin nROIs: push the new branch

creating a comment to ignore a line in the code

• create a file <project root>/.gitattributes and add filters to this new file, for example *.m filter=gitignore
• add the filter to the git config: git config --global filter.gitignore.clean "sed '/gitignore/d'"
• do nothing when pulling git config --global filter.gitignore.smudge cat