anat-processing-book

Notebook that describes processing of anatomical data for the Courtois-Neuromod Project.

To visualize the notebook click here.

Data and processing pipeline

The data are located here: https://github.com/courtois-neuromod/anat

The processing code is located here: https://github.com/courtois-neuromod/anat-processing

GitHub Action for automatic Jupyter-Book GitHub page builds

A GitHub Action is responsible for bulding jupyter-book from the source directory, then pushing built html files to the gh-pages branch.

1. Please ensure that the notebooks under the source directory are pushed to the main with the outputs saved.

• GitHub actions will not re-execute the notebooks, only the html outputs will be built based on what's saved in the notebooks (e.g. interactive figures).

2. Please be careful with pushing changes to the following lines of the source/_config.yml if requirements.txt:

execute:
  execute_notebooks: 'off'

• Setting this to auto or on will enforce book build to re-execute the notebooks during GitHub Actions build, which may fail if there are dependencies additional to those listed by requirements.txt.

Build the Notebook locally

Dependencies: Python 3.8 and higher

Option 1: Using miniconda

Install miniconda

Create and activate virtual environment:

conda create -n notebook_docs pip
conda activate notebook_docs

Option 2: Using virtualenv

virtualenv venv
source venv/bin/activate

Install package

Install required packages

pip install -r requirements.txt

Build the notebook

jupyter-book build source