To create a new repository on GitHub go to: https://github.com/new
Sign up for the academic/student pack on GitHub as all lab projects should be private (until publication, of course) and non-academics do not get unlimited free private ones. Sign up here — they only need your academic (ucl.ac.uk) email address to associate it with your account: https://education.github.com/pack
Cloning means getting something for the first time. So to download a whole repository for the first time (e.g., Olivia's gini repo):
git clone git@github.com:oliviaguest/gini.git
This command makes a new directory called in this case: gini.
So you would need to change directory in order to see your newly downloaded files, i.e., cd, like so:
cd gini
Then you can ls and ls -a to see all your files.
Feel free to actually clone my Gini repository as you cannot break it on GitHub since you do not have push rights.
Adding a file means asking version control to start watching it, but it is not yet in the history of your repository.
Just adding is not enough! All add does is say add this file to queue of files to be committed (the next section).
You can be explicit and name the files you want to add (all other files will not be added):
git add filename_1 filename_2... filename_n
Alternatively, you can add everything (except the things in your .gitignore file):
git add -A
If you just add a file, it is not safe yet!
It needs to be committed (next section) to be safely under version control!
Committing is adding all the files to version control, although not to the server (the next section).
To commit everything you have just added:
git commit -m "I've just made some very dramatic changes"
For your files to be 100% safe make you must also push them (the next section).
Only committing makes files be under version control on your local machine, e.g., your laptop, but they will not be accessible from another computer.
Pushing commits, and therefore files, makes your changes enter into the version control system on the server as well as your local machine, so on GitHub (or Overleaf, or GitLab, or whatever server you are using).
So pushing is the superior form of backup and version control because it means that there are at least two copies of your work and its history: one local copy (the stuff you were just working on) and one server-side copy (what you just pushed).
Once everything you need is added and committed, it is time to push.
Many adds may be in one commit, many commits may be in one push.
But there is no reason to limit yourself to pushing once a day.
Push as often as possible pretty much, is my advice.
Unsurprisingly, as you might guess, to push you type:
git push
To check what is going on, what changes have been made, compare your local repository's status with that of the server, etc., type:
git status
This command will often tell you what you need to do given the current changes you have made, e.g., tell you you need to push your commits.
If you are unsure of anything, running git status should give you a hint about what the next command you want to run is.
Importantly, if you have made server-side changes, i.e., you did some work on machine A and pushed all that work to the server and now you are on a completely different machine B and need to get back to working on your repo, you need to tell the repo on this different machine B to check the server for changes.
This can be done by asking your local git, on B, to fetch the changes from the server:
git fetch
Bear in mind that fetch does not download any files, it merely updates what your local git knows about the changes you did on machine A which you then pushed to the server.
After fetching, you may run git status as then the information on the differences between your local files and those on the server will be correct.
Otherwise, if you just run git status you risk getting the wrong information about what is on the server versus your local repo.
If you made some local changes and you do not want them around at all — you just want what is on the server, you can run:
git stash
This discards all your local changes that have not been added or committed.
