Commit 4af93434 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Readme updates

parent 2ab0ed4f
......@@ -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
```
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