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.
Clone the repo.
git config --system core.longpaths true
with administrator rights.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.
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.
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
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