GLaDOS: Graph Layout algorithm Datasets for Open Science

This paper is under submission to the the experimental track at JoVI.

Papers for this track are written in Quarto which is an open source publishing format that supports inline code, including languages like R, Python, Julia, and JavaScript (via Observable Notebook).

!  Only edit .qmd files! The other files are generated from this.

See https://osf.io/j7ucv/ for more details on the related publication and supplemental materials.

Setup instructions

1. Clone the repo.

   • On Windows, we currently have paths in the data directory that are too long for git to handle. This prevents cloning. To avoid this problem, run git config --system core.longpaths true with administrator rights.

2. CD to the repo directory. Create and activate a virtual environment for this project. You may need to modify the code you use depending on what Python you have installed and how your machine is configured.

3. Run the setup commands below.

   • On macOS, Linux, or Windows Subsystem for Linux, run these three commands separately in case there are errors:

     python3 -m venv env

     source env/bin/activate

     which python

     If you don't have venv installed on Ubuntu, you can run this to install it:

     apt-get install python3-virtualenv

   • On Windows, run these three commands separately in case there are errors:

     python -m venv env

     .\env\Scripts\activate.bat

     where.exe python

   Check the path(s) provided by which python or where.exe python—the first one listed should be inside the env folder you just created.

4. Install necessary packages.

   python -m pip install -r requirements-simple.txt

   If you want to install the exact versions used by the authors, run instead

   python -m pip install -r requirements-wsl-ubuntu.txt

   which containes the pinned package list generated by running python -m pip freeze > requirements-pinned.txt in the virtual environment.

   The install may take a few minutes.

   If you don't have Quarto installed, install it. On Ubuntu, you can do this by running:

   curl -s https://api.github.com/repos/quarto-dev/quarto-cli/releases/latest | grep "browser_download_url.*amd64.deb" | cut -d : -f 2,3 | tr -d \" | wget -qi -

   then:

   sudo dpkg -i *amd64.deb

Run instructions

Follow the instructions at https://quarto.org/docs/get-started/hello/. If you are using the VSCode Quarto extension and WSL, ensure you start VSCode from the repository directory by running code . at the WSL terminal.

For example, to preview the website run

quarto preview --no-browser --no-watch-inputs

and to publish it to GitHub pages use

quarto publish --no-prompt gh-pages

While you're editing, it is helpful to periodically delete the _site folder and regenerate it to ensure all changes are used and that warnings don't show up:

rm -rf _site