Added pandoc xnos compatibility

Makefile

@@ -6,6 +6,7 @@ INPUTDIR=$(BASEDIR)/source
 OUTPUTDIR=$(BASEDIR)/output
 TEMPLATEDIR=$(INPUTDIR)/templates
 STYLEDIR=$(BASEDIR)/style
+SCRATCHDIR=$(BASEDIR)/scratch
 
 BIBFILE=$(INPUTDIR)/references.bib
 
@@ -35,7 +36,7 @@ pdf:
  -V fontsize=12pt \
  -V papersize=a4paper \
  -V documentclass=report \
- -N \
+ --pdf-engine=xelatex \
  --verbose
 
 tex:
@@ -71,21 +72,5 @@ html:
  mkdir "$(OUTPUTDIR)/source"
  cp -r "$(INPUTDIR)/figures" "$(OUTPUTDIR)/source/figures"
 
-pdf_from_html:
- pandoc \
- --filter=pandoc-xnos \
- "$(INPUTDIR)"/*.md \
- -t html \
- --standalone \
- --template="$(STYLEDIR)/template.html" \
- --bibliography="$(BIBFILE)" \
- --csl="$(STYLEDIR)/ref_format.csl" \
- --include-in-header="$(STYLEDIR)/style.css" \
- --toc \
- --pdf-engine=wkhtmltopdf \
- -o "$(OUTPUTDIR)/thesis.pdf" \
- --number-sections
- rm -rf "$(OUTPUTDIR)/source"
- mkdir "$(OUTPUTDIR)/source"
 
-.PHONY: help pdf docx html tex pdf_from_html
+.PHONY: help pdf docx html tex 

source/01_title_page.md

@@ -9,7 +9,6 @@ and add the centred logo
 
  % Delete the following line
  % to remove the UCL header logo
- \ThisULCornerWallPaper{1.0}{style/univ_logo.eps}
   
   \vspace*{2.5cm}
   

source/06_list_of_figures.md

@@ -1,8 +1,3 @@
-# List of figures
-
-<!--
-For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
--->
 
 \listoffigures
 

source/07_list_of_tables.md

@@ -1,12 +1,9 @@
-# List of tables {.unnumbered}
+\listoftables
 
-<!-- 
-For me, this was the only drawback of writing in Markdown: it is not possible to add a short caption to figures and tables. This means that the \listoftables and \listoffigures commands will generate lists using the full titles, which is probably isn't what you want. For now, the solution is to create the lists manually, when everything else is finished.
--->
-
-Table 5.1 This is an example table . . . \hfill{pp} 
-Table x.x Short title of the figure . . . \hfill{pp} 
+\pagenumbering{roman}
+\setcounter{page}{4}
 
+\newpage
 
 
 

source/11_chapter_3.md

@@ -20,11 +20,6 @@ if mood == 'happy':
  print("I am a happy robot")
 ```
 
-Alternatively, you can also use LaTeX to create a code block as shown in the Java example below:
-\lstinputlisting[style=javaCodeStyle, caption=Main.java]{source/code/HelloWorld.java}
-
-If you use `javaCodeStyle` as defined in the `preamble.tex`, it is best to keep the maximum line length in the source code at 80 characters.
-
 ### Subsection 2
 
 This is the second part of the methodology. Proin tincidunt odio non sem mollis tristique. Fusce pharetra accumsan volutpat. In nec mauris vel orci rutrum dapibus nec ac nibh. Praesent malesuada sagittis nulla, eget commodo mauris ultricies eget. Suspendisse iaculis finibus ligula.

source/12_chapter_4.md

@@ -1,3 +1,8 @@
+---
+lof: True
+
+---
+
 # Research containing a figure
 
 ## Introduction
@@ -35,13 +40,13 @@ to **Fig. number: mylabel** by prefixing with @ for mid-sentence references and
 
 <!-- 
 Figures can be added with the following syntax:
-![my_caption ](source/figures/my_image.pdf){#fig:mylabel}{ width=50% }
+![main_text_caption](source/figures/my_image.pdf, "short_caption(optional)"){#fig:mylabel}{ width=50% }
 
 For details on setting attributes like width and height, see:
 http://pandoc.org/MANUAL.html#extension-link_attributes
 --> 
 
-![RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research.](source/figures/example_figure.pdf){ width=100% }{#fig:my_fig}
+![RV Calypso is a former British Royal Navy minesweeper converted into a research vessel for the oceanographic researcher Jacques-Yves Cousteau. It was equipped with a mobile laboratory for underwater field research.](source/figures/example_figure.pdf "It's a boat"){ width=100% }{#fig:my_fig}
 
 ## Conclusion
 

source/13_chapter_5.md

@@ -43,7 +43,7 @@ Row 4 0.5 0.6
 
 ---------------------------------------------------------------------------
 
-Table: This is the table caption. Suspendisse blandit dolor sed tellus venenatis, venenatis fringilla turpis pretium. {#tbl:my_table}
+Table: This is the table caption. {#tbl:my_table}
 
 
 ## Discussion