Gitlab

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

How can I access Gitlab?

Ask Marc to gain access to biophysics and biophysics_labs.

There are several ways to access a Gitlab repository.

• Login to gitlab with your Science Faculty account.
• Use command line instructions.
• Use a git client like Sourcetree.
• Use <Git Gui Here> from the popup menu in the Windows File Explorer.
• Open command line with <Git Bash Here> from the popup menu in the Windows File Explorer.
• Use the <source control> options from the popup menu in the folder browser in MATLAB.

For more info about installing the biofysica repository see: README.md

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.

Download zip-file

• Open the Gitlab Dashbord in your browser.
• In the left panel "Your work" select the "Projects" page.
• Select a project (=repository) e.g. "Marc van Wanrooij/biofysica"
• Press the button "Code" (at the top-right of your screen)
• Select "zip" under "Download Source Code"
• A zip-file with the code will appear in you download directory
• Open the zip-file and copy the code to the folder of your choice

Command Line Instructions

• 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

Use SourceTree

• 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?

Biofysica

Contains software for experiments with sound localization, for analyzing fast eye and head movements, for Bayesian data analysis, for interfacing with TDT devices, LSL devices, Led controllers, BIOX and other utilities.

• Biofysica

Matrix

Contains MATLAB code for the program Matrixtest, which is a program for word recognition experiments with noise and vocoder options.

• Matrix

fNIRS

For analysis of NIRS measurements.

• fNIRS