diff --git a/README.md b/README.md index f9d5f8c8f870f40a6e8e45654f70cee1315ce8ea..6abf670dbeabf271a0668193171ac8c4373b4a12 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,9 @@ This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat. -The master repository can be found at: https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals +The master repository can be found at: + +https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals To contribute to the practicals: @@ -14,3 +16,31 @@ To contribute to the practicals: 2. Make your changes on your fork 3. Submit a merge request back to the master repository + + + +To run these notebooks in the `fslpython` environment, you must first install +jupyter: + +``` +source $FSLDIR/fslpython/bin/activate fslpython +conda install jupyter +pip install notedown +source deactivate +ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter +ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown +``` + + +> [`notedown`](https://github.com/aaren/notedown) is a handy tool which allows +> you to convert a markdownd (`.md`) file to a Jupyter notebook (`.ipynb`) +> file. So you can write your practical in your text editor of choice, and +> then convert it into a notebook, instead of writing the practical in the web +> browser interface. + + +Now you can start the notebook server from the repository root: + +``` +fsljupyter notebook +```