Tracking changes in markdown

Using markdown to write papers is an insanely great experience, because it is a concise yet powerful markup language, that pandoc can export to almost anything you like (and Word). Some journals, though, require that you upload a document with all changes highlighted in addition to the revised manuscript. As a reviewer, I find this helpful, but as an author, I’m always trying to find a way not to do it because it is not really straightforward.

Well, as it turns out, this is not true. I decided that it was time to stop being lazy, and I found a very simple way to get a good-looking marked copy with all changes.

Here is my originally submitted manuscript, in a file called orig.md:

# My cool project

This is a really cool paper written in markdown. It has equations like
$(1-x)^\rho$ and, also some references to *really* cool papers [@fra92].

I hope it will be accepted!


I can compile that using pandoc, and get the PDF file that I send for review. The referees, being referees, required some changes, so I made the revisions in a file called revised.md.

# My cool revised project

This is a really cool paper written in markdown. It has equations like
$(1-x)^\alpha$ because $\rho$ was not a good parameter name. Also there are
some references to *really* cool papers [@fra92; and references therein].

I hope it will be accepted *now*!

# References


Producing the marked-up copy is relatively easy. The first step is to convert both documents to latex, then use latexdiff. This is best done with a simple makefile, which I reproduce here:

OPTS= --bibliography=/home/tp/.pandoc/default.json --csl=/home/tp/vrac/styles/ecology.csl --template=template.tex

all: orig.pdf revised.pdf diff.pdf

orig.pdf: orig.md
pandoc $< -o$@ $(OPTS) revised.pdf: revised.md pandoc$< -o $@$(OPTS)

diff.pdf: orig.md revised.md
pandoc orig.md -o orig.tex $(OPTS) pandoc revised.md -o revised.tex$(OPTS)
latexdiff orig.tex revised.tex > diff.tex
pdflatex diff
rm {revised,orig,diff}.tex


The OPTS variable can be changed to whatever you like (and the whole file should be made nicer, but hey…), and once this is done, you just need to do make diff.pdf in the directory where your two files (orig.md and revised.md) are. The resulting PDF file will look like this:

This is what I really like with markdown and pandoc – you can have a whole make-based production workflow. Which means that automating tasks is easy, and once you spend 10 minutes figuring out a solution once, it will take you seconds to apply it every time the situation arises. If we compiled all of the dirty little hacks like this one in a single makefile specifically to make editing with markdown easier, we could have a really good do-it-yourself manuscript preparation system. Just sayin’…!