Cleaned up for new stylings

.gitignore

@@ -21,3 +21,24 @@ html/reveal/assets/callgrind.png
 html/reveal/assets/coverage.png
 html/reveal/assets/jenkins.png
 tdd.png
+.ipynb_checkpoints
+session01/analyzer.py
+session01/eight
+session01/eight.py
+session01/module1/
+session01/pretty.py
+combined.ipynb
+combined_files/
+notebooks.zip
+notes.pdf
+notes.tex
+session04/greeter.py
+session04/map.png
+session04/midvals.yaml
+session05/anotherfile.py
+session05/config.yaml
+session05/context.py
+session06/fixed.png
+session07/datasource2.yaml
+session07/datasource3.yaml
+session07/example.yaml

Makefile

@@ -6,6 +6,14 @@ PANDOCARGS=-t revealjs -s -V theme=night --css=http://lab.hakim.se/reveal-js/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
 
+NOTEBOOKS=$(filter-out %.v2.ipynb %.nbconvert.ipynb,$(wildcard session*/*.ipynb))
+
+HTMLS=$(NOTEBOOKS:.ipynb=.html)
+
+EXECUTED=$(NOTEBOOKS:.ipynb=.nbconvert.ipynb)
+
+NBV2=$(NOTEBOOKS:.ipynb=.v2.ipynb)
+
 default: _site
 
 %/slides.html: %/*.md Makefile
@@ -21,18 +29,37 @@ default: _site
 	dot $< -T png -o $@
 
 %.png: %.uml Makefile
-	plantuml -p < $< > $@
+   java -Djava.awt.headless=true -jar plantuml.jar -p < $< > $@
+
+%.html: %.nbconvert.ipynb Makefile jekyll.tpl
+	ipython nbconvert --to html  --template jekyll.tpl --stdout $< > $@
+
+%.v2.ipynb: %.nbconvert.ipynb
+	ipython nbconvert --to notebook --nbformat 2 --stdout $< > $@
+
+%.nbconvert.ipynb: %.ipynb
+	ipython nbconvert --to notebook --ExecutePreprocessor.timeout=120 --execute --stdout $< > $@
 
-%.html: %.ipynb Makefile jekyll.tpl
-	ipython nbconvert --to html --template jekyll.tpl --execute --stdout $< > $@
+notes.pdf: combined.ipynb Makefile
+	ipython nbconvert --to pdf --template latex.tplx $<
+	mv combined.pdf notes.pdf
 
-%.html: %.ipyhtml Makefile
-	yamlheader 
+combined.ipynb: $(EXECUTED)
+	python nbmerge.py $^ $@
+
+notes.tex: combined.ipynb Makefile
+	ipython nbconvert --to latex --template latex.tplx $<
+	mv combined.tex notes.tex
+
+notebooks.zip: ${NBV2}
+	zip -r notebooks $^
 
 master.zip: Makefile
 	rm -f master.zip
 	wget https://github.com/UCL-RITS/indigo-jekyll/archive/master.zip
 
+ready: indigo $(HTMLS) notes.pdf notebooks.zip
+
 indigo-jekyll-master: Makefile master.zip
 	rm -rf indigo-jekyll-master
 	unzip master.zip
@@ -47,16 +74,41 @@ indigo: indigo-jekyll-master Makefile
 	cp -r indigo-jekyll-master/indigo/favicon* .
 	touch indigo
 
-_site: indigo \
-	     session01/01data.html session01/03control.html session01/04functions.html \
-			 session01/05modules.html session01/00pythons.html session01/02types.html \
-			 session01/06exercise.html
+plantuml.jar:
+	wget http://sourceforge.net/projects/plantuml/files/plantuml.jar/download -O plantuml.jar
+
+.PHONY: ready
+
+_site: ready
 	jekyll build	
 
+preview: ready
+	jekyll serve
+
 clean:
 	rm -f session*/generated/*.png
 	rm -rf session*/*.html
+	rm -f session*/*.pyc
 	rm -f index.html
 	rm -rf _site
 	rm -rf images js css _includes _layouts favicon* master.zip indigo-jekyll-master
-
+	rm -f indigo
+	rm -f session01/analyzer.py
+	rm -f session01/eight
+	rm -f session01/eight.py
+	rm -rf session01/module1/
+	rm -f session01/pretty.py
+	rm -f session*/*.nbconvert.ipynb
+	rm -rf session*/*.v2.ipynb
+	rm -rf combined*
+	rm -f notes.pdf
+	rm -f notes.tex
+	rm -f session04/greeter.py
+	rm -f session04/map.png
+	rm -f session05/anotherfile.py
+	rm -f session05/config.yaml
+	rm -f session05/context.py
+	rm -f session06/fixed.png
+	rm -f session07/datasource*.yaml
+	rm -f session07/example.yaml
+	rm -f notebooks.zip

jekyll.tpl

@@ -1,7 +1,8 @@
 {%- extends 'basic.tpl' -%}
 {%- block header -%}
 ---
-title: {{resources['metadata']['name']}}
+title: {% if 'jekyll' in nb['metadata'] %} {{nb['metadata']['jekyll']['display_name']}} {% endif %}
+nblink: True
 ---
 {{super()}}
 {%- endblock header -%}

latex.tplx

@@ -0,0 +1,33 @@
+
+% Default to the notebook output style
+((* if not cell_style is defined *))
+    ((* set cell_style = 'style_ipython.tplx' *))
+((* endif *))
+
+% Inherit from the specified cell style.
+((* extends cell_style *))
+
+((* block title *))
+\title{An introduction to Python Programming for Research}
+((* endblock title *))
+
+((* block author *))
+\author{James Hetherington}
+((* endblock author *))
+
+%===============================================================================
+% Latex Book
+%===============================================================================
+
+((* block predoc *))
+    ((( super() )))
+    ((* block tableofcontents *))\tableofcontents((* endblock tableofcontents *))
+((* endblock predoc *))
+
+((* block docclass *))
+\documentclass{report}
+((* endblock docclass *))
+
+((* block markdowncell scoped *))
+((( cell.source | citation2latex | strip_files_prefix | markdown2latex(extra_args=["--chapters"]) )))
+((* endblock markdowncell *))