Merge pull request #229 from UCL/jupyter-cleanup

.gitignore

@@ -7,11 +7,32 @@ workflow/
 vendor/
 .sconsign.dblite
 html/index.html
-pdf
+*pdf
 *.pyc
+*.ipynb
 *.nbconvert.ipynb
 *.swp
+*.html
+*.mp4
 a.out
+ch00*/learning_git
+ch00*/somefile.md
+ch01*/fourteen.py
+ch01*/draw*
+ch02*/my*
+ch02*/maze*
+ch02*/*csv
+ch02*/*png
+ch02*/greengraph
+ch03*/DiffusionExample
+ch03*/commands
+ch03*/diffusion
+ch03*/saskatchewan
+ch03*/solutions*
+ch04*/greetings*
+ch04*/maze*
+ch08*/*png
+ch98*/*png
 html/reveal/.DS_Store
 html/reveal/assets/night-ucl-overlay.css
 html/reveal/assets/solarized-ucl-overlay.css

Makefile

@@ -5,11 +5,12 @@ ROOT=""
 PANDOCARGS=-t revealjs -s -V theme=night --css=http://lab.hakim.se/reveal-js/css/theme/night.css \
 					 --css=$(ROOT)/css/ucl_reveal.css --css=$(ROOT)/site-styles/reveal.css \
            --default-image-extension=png --highlight-style=zenburn --mathjax -V revealjs-url=http://lab.hakim.se/reveal-js
-
+PRENOTEBOOKS=$(wildcard ch*/*.ipynb.py)
+NOTEBOOKS_DONE=$(PRENOTEBOOKS:.ipynb.py=.ipynb)
 NOTEBOOKS=$(filter-out %.v2.ipynb %.nbconvert.ipynb,$(sort $(wildcard ch*/*.ipynb)))
 SVGS=$(wildcard ch*/*.svg)
 
-HTMLS=$(NOTEBOOKS:.ipynb=.html)
+HTMLS=$(PRENOTEBOOKS:.ipynb.py=.html)
 
 EXECUTED=$(NOTEBOOKS:.ipynb=.nbconvert.ipynb)
 PNGS=$(SVGS:.svg=.png)
@@ -41,6 +42,9 @@ default: _site
 %.v2.ipynb: %.nbconvert.ipynb
 	jupyter nbconvert --to notebook --nbformat 2 --stdout $< > $@
 
+%.ipynb: %.ipynb.py
+	jupytext --to ipynb $< -o - > $@
+
 %.nbconvert.ipynb: %.ipynb
 	jupyter nbconvert --to notebook --allow-errors --ExecutePreprocessor.timeout=120 --execute --stdout $< > $@
 
@@ -72,10 +76,14 @@ _site: ready
 preview: ready
 	jekyll serve --verbose
 
+worked: $(NOTEBOOKS_DONE)
+	find ./ -iname '*ipynb'
+
 clean:
 	rm -f ch*/generated/*.png
 	rm -rf ch*/*.html
 	rm -f ch*/*.pyc
+	rm -f ch*/*.ipynb
 	rm -f index.html
 	rm -rf _site
 	rm -rf images js css _includes _layouts favicon* master.zip indigo-jekyll-master

README.md

@@ -29,7 +29,7 @@ You are required to bring your own laptop to the course as the classrooms we are
 
 # Contributing to this repository
 
-This repository contains the course notes as jupyter notebooks. This makes it a bit difficult to contribute and to review contributions. Please, only include changes in the cells modified and not other metadata that changes when running them.
+This repository contains the course notes as Jupyter notebooks converted into `py:percent` format. This allows to edit the files as plain text as well as jupyter notebooks. To edit them as jupyter notebooks you'll need to have installed jupytext and open the `ipynb.py` files as notebooks via right-click and select "open with" and "notebook" on the Jupyter file browser.
 
 ⚠ Do not run `make` locally on your computer! ⚠ 
 
@@ -78,3 +78,16 @@ $ docker run --rm --volume="$PWD:/srv/jekyll" --volume="$PWD/vendor/bundle:/usr/
 
 and open http://localhost:4000/rsd-engineeringcourse (or the link provided).
 Note that this is mounting the `bundle` directory where `act` will create them.
+
+# Migration from jupyter notebooks to py:percent
+
+Using `jupytext` we've converted all the jupyter notebooks into plain text python files (py:percent) with:
+
+```bash
+# First cleaned all outputs and commited it
+nbstripout --extra-keys metadata.kernelspec ch*/*ipynb
+# convert them
+find ./ -iname '*ipynb' -exec jupytext --opt notebook_metadata_filter="kernelspec,jupytext,jekyll" --to py:percent {} -o {}.py \;
+# then deleted the ipynb
+find ./ -iname '*ipynb' -delete
+```