Code

The code for running experiments and analysing data is all stored on gitlab.

Introduction

To run experiments in a lab, you will need particular Matlab files that are stored in a Git repository

For bachelor/master/PhD students:

• Ask for an administrator (Marc van Wanrooij, Günter Windau) to create a new User Account.
• Login to Gitlab
• Ask for a Git Master (Marc van Wanrooij, Günter Windau) to give you access to the Git repository to add you as a Developer (this will allow you to change things without affecting the main repository).
• install Atlassian SourceTree by going to Windows/ProgramFiles/Atlassian and double clicking on sourcetree.exe (this will be your interface with the repository instead of the default terminal/command prompt).
• Clone the experiment-repository by clicking on Clone in SourceTree to MATLAB/experiment in your User account Documents folder (all required m-files will now be copied to your folder, i.e. you will own your own local repository)
• Create a new branch of this repository by clicking on Branch in SourceTree, and give it a meaningful name, such as your own first name (this will enable you to edit the m-files and upload/push it to the remote repository, without affecting the main repository).
• Add the local repository to Matlab's path (via ...)
• Start an experiment

At the end of a student's internship (or when relevant), request for a merge (to incorporate all the useful changes you made into the main repository)

How can I access Gitlab?

Login to gitlab with your Science Faculty account. Then ask Marc to gain access to biophysics and biophysics_labs

How can I get (clone) the code from the repository?

You can get the code from the repository in several ways, all with their own advantages.

Click

• Instal the GitHUB client for Windows or for Mac, and add the repository via Command line instructions:
  • Git global setup
    • git config --global user.name "Your Name"
    • git config --global user.email "your.e@mail.adress"
  • Create a new repository
    • git clone https://gitlab.science.ru.nl/username/projectname.git
    • cd test
    • touch README.md
    • git add README.md
    • git commit -m "add README"
    • git push -u origin master
  • Existing folder or Git repository
    • cd existing_folder
    • git init
    • git remote add origin https://gitlab.science.ru.nl/username/projectname.git
    • git push -u origin master

• Install the Git client Atlassian Sourcetree, and Clone the repository via a button press

How can I get the changes others have made (fetch/pull)?

• In Github for Windows: the Sync button
• In Atlassian Sourcetree: the Pull button

How can I put my changes of the code in the repository (commit/push)?

You should have Master rights to be able to upload your changes to the remote repository. If you do not have own, you should work in a branch.

• In Github for Windows and in Atlassian Source Tree: push the Branch button, and give it a meaningful name (i.e. your first name)

Then you can upload

• In Github for Windows: Sync
• In Atlassian SourceTree: stage files - commit - push when commit

Which repositories exist, and what are they for?

Biophysics

For running experiments in the Sphere_lab, to analyse fast eye and head movements, to do bayesian data anaysis, and some other utilities