diff --git a/README.md b/README.md index 3d52f27d0745820b4d4a6089cf25ebbee5652900..3caa35440ab7de4199a14e9068356e9ac1028dc8 100644 --- a/README.md +++ b/README.md @@ -24,36 +24,13 @@ installed. ## For attendees -To run these notebooks in the `fslpython` environment, you must first install -jupyter: - - -``` -# If your FSL installation requires administrative privileges to modify, then -# you MUST run these commands as root - don't just prefix each individual -# command with sudo, or you will probably install jupyter into the wrong -# location! -# -# One further complication - once you have become root, $FSLDIR may not be set, -# so either set it as we have done below, or make sure that it is set, before -# proceeding. -sudo su -export FSLDIR=/usr/local/fsl -source $FSLDIR/fslpython/bin/activate fslpython -conda install jupyter -source deactivate -ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter -``` - - -Then, clone this repository on your local machine, and run -`fsljupyter notebook`: +These notebooks can be run in the `fslpython` environment using: ``` git clone git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git cd pytreat-2018-practicals -fsljupyter notebook +fslpython -m notebook ``` @@ -110,17 +87,14 @@ To contribute to the practicals: repository. -When you install `jupyter` above, you may also wish to install +You may also wish to install [`notedown`](https://github.com/aaren/notedown): ``` -# . -# see instructions above -# . -conda install jupyter +source $FSLDIR/fslpython/bin/activate fslpython pip install notedown source deactivate -ln -s $FSLDIR/fslpython/envs/fslpython/bin/jupyter $FSLDIR/bin/fsljupyter +fslpython -m notedown ln -s $FSLDIR/fslpython/envs/fslpython/bin/notedown $FSLDIR/bin/fslnotedown ```