diff --git a/README.md b/README.md index 6abf670dbeabf271a0668193171ac8c4373b4a12..2ae521c705aa6a5dac3f9ce9558f4ac4bdc06dfa 100644 --- a/README.md +++ b/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: