Struggling with scrivomatic output

Hi everyone,

I’m in the final days of preparing my thesis. I’ve been getting along fairly well writing in scrivener but it’s now time to compile the devil and I’m having trouble. I’m not particularly experienced with typesetting, I’ve done a few things in LaTeX over the years, but they were pretty simple and I would just grope around in the dark on a template until things looked right. With a document this big with crossreferences and loads of figures I didn’t think that was a good plan.

So, I’m using scrivomatic/pandocomatic. But, here’s the problem. When it compiles the two chapters I’m using to troubleshoot, the main text of the pdf is italicized, paragraphs are not indented, one of my figures is duplicated, and there is no table of figures. Well, except some sections don’t end italicized… and some text was duplicated.

When I look at the .md file, the first lines of a chapter look like this:

[code]## 1.3 Protein Stability ##

One of the themes…[/code]

And then the next paragraph is preceded by a blank line, and begins with another [code]

[/code] character.

And it the .tex file, I get this,

\subsubsection{1.3 Protein Stability}\label{protein-stability}}

One of the themes…[/code]
and then the subsection ends with,

[/code] and the \emph isn't taken care of (but it shouldn't be there to begin with).

So, here's my setup:
* The main text is written in the Paragraph setting from the style pane (which I tweaked to have 1.5 linespacing, size 12, and a font I like). 
* I defined superscript and subscript character-styles like in the instructions for scrivomatic, so that when compiled, ^ or ~ are added around characters. 
* Figure captions are written in the Captions style.
* At the end of each paragraph, I typed [space][space][return][return] (again, from the scrivomatic instructions)
* Figures are added in-text and referenced using the <$img:> and <$n:Chapter:X>.<$n:figure:namehere> 

And in terms of the compiling options... 
* The metadata file is compiled as-is, 
* The two section layouts I use are [b]Chapter number and text[/b] and [b]Text section with heading[/b]. 
* I have tried to set most other things like in the example compiling format from the scrivomatic instructions... e.g. the pandoc  arguments as [code]
-i "<$inputfile>" -l -v -B 2>&1 >>scrivomatic.log
  • I’m using the scrivomatic dotpandoc files and the included templates and stuff (added my own .csl style and adjusted references to the .bib file). Oh, and I tweaked the .yaml file too use the fonts with latex I want.
  • I’m trying to use the “latex-with-lof” and “pdf-refs” template while I get things working

I have something set wrong or I’ve overlooked something obvious and I’m losing my mind trying to figure things out. Help me Obi-Wan, you’re my only hope.

This would be better in the forum dedicated to MultiMarkdown and Latex.


Ah. Thank you. I’ll see about asking there.

Please send me your sample project in a private message or attach here and I can have a look, it is hard to trouble shoot from the description alone…