Merge branch 'master' into 'master'

More details in readme

See merge request fsl/pytreat-2018-practicals!2

README.md

@@ -4,24 +4,45 @@
 This repository contains Jupyter notebooks and data for the 2018 WIN PyTreat.
 
 
-The master repository can be found at:
+The upstream repository can be found at:
 
 https://git.fmrib.ox.ac.uk/fsl/pytreat-2018-practicals
 
 
 To contribute to the practicals:
 
-1. Fork the master repository on gitlab
+1. Fork the upstream repository on gitlab
 
-2. Make your changes on your fork
+2. Make a local clone of your fork:
 
-3. Submit a merge request back to the master repository
+    ```
+    git clone git@git.fmrib.ox.ac.uk:<username>/pytreat-2018-practicals
+    ```
 
+3. Add the upstream repository as a remote:
+
+    ```
+    git remote add upstream git@git.fmrib.ox.ac.uk:fsl/pytreat-2018-practicals.git
+    ```
+
+4. Make your changes on your local repository
+
+5. Rebase onto the upstream repository, and push your changes to your fork:
+
+    ```
+    git fetch --all
+    git rebase upstream/master
+    git push --force origin master
+    ```
+
+6. In gitlab, submit a merge request from your fork back to the upstream
+   repository.
 
 
 To run these notebooks in the `fslpython` environment, you must first install
 jupyter:
 
+
 ```
 source $FSLDIR/fslpython/bin/activate fslpython
 conda install jupyter
@@ -33,10 +54,15 @@ 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`)
+> you to convert a markdown (`.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.
+> browser interface. If you install notedown as suggested in the code block
+> above, you can run it on a markdown file like so:
+>
+> ```
+> notedown my_markdown_file.md > my_notebook.ipynb
+> ```
 
 
 Now you can start the notebook server from the repository root: