Git and GitLab

Installing Git
- Linux (Debian, Ubuntu)
- Mac OSX and Windows
Configuring Git
Using Git through the command line to synchronize your local files with Gitlab

This document is particularly important if you follow the RStudio or the Org-Mode path. If you follow the Jupyter path, it can be ignored at first as we have closely integrated Jupyter and GitLab in the context of this MOOC.

So far, you only used git via the web interface from the GitLab we deployed for the MOOC: https://app-learninglab.inria.fr/gitlab/

If you access this link from the FUN platform, you do not have to authenticate and you can readily read and modify all your files. This is very convenient but in most cases, you will want to have your own local copy of the repository and you will have to synchronize your local copy with the remote GitLab one. To propagate your modifications, you will obviously have to authenticate yourself on GitLab.

This document describes the software you need to have installed on your machine and how to handle authentication. The "Configuring Git" section is illustrated in a video tutorial (in French).

Please read all these instructions carefully, in particular the one on "Configuring your password on GitLab".

Installing Git

Linux (Debian, Ubuntu)

We provide here only instructions for Debian-based distributions. Feel free to contribute to this document to provide up-to-date information for other distributions (e.g., RedHat, Fedora).

Run (as root):

apt-get update ; apt-get install git

Mac OSX and Windows

Download and install Git from the Git website.
Optional Git clients (should not be needed if you work within RStudio):
- SourceTree
- GitHub Desktop
  
  Apparently, this works with GitLab and https.

Configuring Git

Telling Git who you are: Name and Email

Open terminal.

Set a Git username and email:

git config --global user.name "Mona Lisa"
git config --global user.email "email@example.com"

Confirm that you have set the Git username correctly:

git config --global user.name
git config --global user.email

Mona Lisa
email@example.com

Dealing with proxies

You may be behind a proxy, in which case you may have trouble cloning or fetching from a remote repository or you may get an error like unable to access ... Couldn't resolve host ...

In such case, consider something like this:

git config --global http.proxy http://proxyUsername:proxyPassword@proxy.server.com:port

The proxyPassword will be stored in plain text (unencrypted) in your .gitconfig file, which you may not want. In that case, remove it from the URL and you will be prompted for it every time it is needed.

Getting your default password on GitLab (and possibly changing it)

Warning (Jupyter users) : changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your ~/.git-credentials in the Jupyter environment (possibly several times).

Get your default password using the Gitlab credentials retrieval tool as described on the corresponding resource.

The first long and ugly character sequence is your GitLab login/id. It is easy to find once you are logged on gitlab. The second one however is your password and this webpage is the only place where you can find it. We used the FUN authentification mechanism to propagate your credentials so only you can have access to it. You'll need to use this password when trying to propagate some modifications from your computer to GitLab.

Note: You have to access this webpage from the FUN platform otherwise you may get a 405 error when trying to direcly open https://app-learninglab.inria.fr/jupyterhub/services/password.
Access GitLab.

Note: Again, you have to access Gitlab from the FUN platform otherwise you may get a 405 error when trying to direcly open https://app-learninglab.inria.fr/gitlab/users/sign_in.
Click on the first Sign in button (alternatively, you can the login/password you just retrieved and use the second Sign in button).
If you wish to modify your password, you should go to Account > Settings > Password and define your password using the default password you just retrieved. Again, if you use the Jupyter notebooks we have deployed for the MOOC, remember that changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your Jupyter ~/.git-credentials through a Jupyter console (see next section).

Remembering your password locally

If you clone your repository by simply pasting the GitLab URL, you will be prompted for your login and your password every time you want to propagate your local modifications, which is tedious. This is why you should ask git to remember your login and password as follows

git config --global credential.helper cache                  # remember my password
git config --global credential.helper "cache --timeout=3600" # for one hour at most

With this setup, you will be prompted for your password but it will be cached in memory and they will not be asked again before an hour. You may want to read these instructions to better understand how all this works.

If you want your password to be permanently remembered, you should use this command

git config credential.helper store

Your password will be then stored in a .git-credentials file in plain text. On a perfectly secured machine, it may be fine… or not… ;) Use it at your own risk.

Optional: authenticating through SSH

There are two ways of authenticating and synchronizing your local repository with GitLab: through HTTPS or through SSH. The first one is what was just described and does not require any particular software installation on your machine so this is what I recommend for this MOOC. Yet, I like the second one better (although is may seem a bit more technical), which is why I describe it here. It consists in installing SSH, creating a pair or private/public keys, and uploading your SSH public key on GitLab. This section provides with information on how to do this.

Installing SSH

Linux (Debian, Ubuntu)
We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information for other distributions (e.g., RedHat, Fedora).

Run (as root):
```
apt-get update ; apt-get install openssh-client
```
macOS

You do not have anything to do as it is installed by default.
Windows

You should install the Putty client. Once it is installed, look for the section on generating an SSH key.

Setting up SSH on GitLab

Here are all the official explanations on how to set up your SSH key on GitLab. Alternatively, you may also want to have a look at this video:

Using Git through the command line to synchronize your local files with Gitlab

This section describes a generic (through the command line) way to synchronize your local files with Gitlab. You will not need this if you follow the Jupyter path. If you follow the RStudio path, all these operations can be done through RStudio and you may want to read the corresponding instructions. If you follow the Org-Mode path, all these operations can be done through Magit and you may want to read the corresponding instructions.

Here are other ways to learn Git through the command line:

The Software Carpentry git tutorial
The (freely available) Pro Git book (in English or in French). Reading the first two chapters is enough to get a good start.
Learn Git Branching will allow to interactively learn Git and to understand with branches.

Now, let's start!

Obtain the repository URL
Cloning the repository
```
cd /the/directory/where/you/want/to/clone/your/repository
git clone https://app-learninglab.inria.fr/gitlab/xxx/mooc-rr.git
```
Alternatively, you may want to indicate now your login although I rather suggest you follow the Remembering your password locally instructions:
```
git clone https://xxx@app-learninglab.inria.fr/gitlab/xxx/mooc-rr.git
```
Now a directory mooc-rr has been created on your computer.
Inspect the repository
```
cd mooc-rr
ls # (Unix)
dir # (Windows)
```
Synchronizing to GitLab

You should indicate which files to track (git add) and commit them locally (git commit) before they can be transfered (git push) to GitLab. The git status will indicate you whether files are tracked/modified/committed/…

Let's assume you just created a `fichier.txt` file on the top of the mooc-rr directory.
```
git status
```
```
git add fichier.txt
git status
```
```
git commit -m "message commit"
```
```
git status
```
The file can then be transfered to GitLab:
```
git push
```
At this point, git will as you about your login/password unless you followed the previous Remembering your password locally instructions.

N.B.: you will not be allowed to propagate your modifications to GitLab if other modifications (e.g., from someone else) have been propagated in between
Synchronizing from Gitlab: to avoid the previous problem, you need to fetch the remote GitLab modifications first and apply them locally.
```
git pull
```
Only then will you be able to git push.