SUURPh-summer-school

This is the web-page of the Simula Summer School in Computational Physiology

Add section to web-page

To add a notebook or markdown document to the web-page, please open _toc.yml, create a new section if needed and add the file-name (without file extension)

Hide input/output for students

If you want to hide a cell (input) or the data produce by a cell (output), you can use pre-commit to collapse these in the jupyter notebook. They will be collapsed on the jupyter-server (that uses jupyter-lab), and will be collapsed on the webpage. Simply add the tags hide-input and/or hide-output to the cell tag in the Jupyter notebook.

To enforce this you can run pre-commit in the repository:

python3 -m pip install pre-commit
pre-commit autoupdate
pre-commit run

This will update the appropriate meta-data in the files (which in turn can be commited). If you have any questions or issues with this, please contact Jørgen S. Dokken or make an issue.

Installing the environment

Pixi is used to manage dependencies. First install pixi (see above docs), for instance by calling

curl -fsSL https://pixi.sh/install.sh | sh

Pixi might ask you to modify your path, please do: For instance,

export PATH=/root/.pixi/bin:$PATH

then call

pixi install

To build the book call

pixi run python3 -m jupyter book build  .

Go to _build/html/index.html

You can run any dependency in the pixi environment with pixi run ....