Git and Github

Psicometria per le Neuroscienze Cognitive

Filippo Gambarota, PhD

Git and Github

Git and Github

  • The basic idea is to track changes within a folder, assign a message and eventually a tag to a specific version obtaining a version hystory. The version history is completely navigable, you can go back to a previous version of the code.
  • The are advanced features like branches for creating an independent version of the project to test new features and then merge into the main streamline.
  • The entire (local) Git project can be hosted on Github to improve collaboration. Other people or collaborators can clone the repository and push their changes to the project.

Veeeery basic Git workflow

Veeeery basic Git workflow

After installing Git, you can start a new repository opening a terminal on a folder and typing git init. The folder is now a git project you can notice by the hidden .git folder.

cd ~/some/folder
git init

Then you can add files to the staging area. Basically these files are ready to be committed i.e. “written” in the Git history.

git add file1.txt
# git add . # add everyting

Finally you can commit the modified version of the file using git commit -m message

git commit -m "my first amazing commit"

you can see the Git hystory with all your commits:

git log

Github

Imagine to put everyting into a server with nice viewing options and advanced features. Github is just an hosting service for your git folder.

You can create an empty repository on Github named git-test. Now my repo has the path git@github.com:filippogambarota/git-test.git.

git remote add origin git@github.com:filippogambarota/git-test.git
git push

Now our local repository is linked with the remote repository. Every time we do git push our local commits will be uploaded.

If you worked on the repository from another machine or a colleague add some changes, you can do git pull and your local machine will be updated.


The repository git-test is online and can be seen here filippogambarota/git-test.

Github

An now let’s see on Github the result:

More about Git and Github

There are a lot of resources online:

Open Science Framework

Open Science Framework

OSF is a free, open platform to support your research and enable collaboration.

Is a great tool to upload and share materials with others and collaborate on a project. Similarly to Github you can track the changes made to a project.

The great addition is having a DOI thus the project is persistently online and can be cited.

It is now common practice to create a OSF project supporting a research paper and put the link within the paper containing supplementary materials, raw data, scripts etc.

Open Science Framework

It’s very easy to create a new project, then you simply need to add files and share it.

The project can be accessed here (depending on the visibility) https://osf.io/yf9tg/.

Open Science Framework

OSF and Github

An interesting feature is linking a Github repository to OSF. Now all changes made on Github (easier to manage) are mirrored into OSF. You can easily work in Github for the coding part and use OSF to upload other data or information and to assign a DOI to the project.

Preprints

OSF is also linked to a popular service for preprints called PsyArXiv https://psyarxiv.com/ thus you can link a preprint to an OSF project.

More on OSF

  • https://help.osf.io/article/342-getting-started-on-the-osf
  • https://arca-dpss.github.io/manual-open-science/osf-chapter.html

More on reproducibility

In general, I highly suggest the online book The Open Science Manual https://arca-dpss.github.io/manual-open-science/ written by my friend Claudio Zandonella and Davide Massidda where these and other topics are explained in details: