Template for writing a PhD thesis in Markdown

This repository provides a framework for writing a PhD thesis in Markdown. I used the template for my PhD submission to University College London (UCL), but it should be straightforward to adapt suit other universities too.

Citing the template

If you have used this template in your work, please cite the following publication:

Tom Pollard et al. (2016). Template for writing a PhD thesis in Markdown. Zenodo. http://dx.doi.org/10.5281/zenodo.58490

Installation

Install pandoc. This repository requires pandoc 3.1+, so if you install pandoc using a package manager (e.g. apt), check that it meets the version requirement. Otherwise, install by following the link.
Install pandoc-crossref, a pandoc filter for numbering and cross-referencing figures, tables, sections and code blocks.
Install the required TeX packages to enable compilation to PDF.

Quickstart for Mac Users

If you're a Mac user and you have conda and brew installed, run the following in your terminal to install pandoc and TeX packages (steps 1 & 3):

# get texlive
brew install --cask mactex

# update tlmgr and packages
sudo tlmgr update --self

# make python venv and install pandoc
conda create -n phd -y python=3.7 pandoc
conda activate phd

# Install required python and texlive packages
make install

Notes for Linux Users

There are several ways to install TeXLive. This guide (written for Ubuntu) may be useful. In short, you can:

Install TeXLive from repositories (for Ubuntu, autocomplete apt install texlive to see all available packages), or;
Install TeXLive manually and use the package manager (tlmgr) to install required packages. If you go down this route, you can run make install to install required TeXLive packages.

Handy references

pandoc User Guide for Markdown syntax for figures, tables, lists, etc., as well as information on flags that can be used when calling pandoc
pandoc-crossref manual which outlines syntax and customisation options for cross-referencing (e.g. should the figure prefix be "fig,", "Fig." or "Figure")
This README for pandoc-crossref-compatible syntax to have shorter captions for figures in the List of Figures (PDF/LaTeX output only)
This README for pandoc-crossref-compatible syntax to have shorter captions for tables in the List of Tables (PDF/LaTeX output only)

Should I use this template?

Why write my thesis in Markdown?

Markdown is a super-friendly plain text format that can be easily converted to a bunch of other formats like PDF, Word and LaTeX. You'll enjoy working in Markdown because:

it is a clean, plain-text format...
...but you can use LaTeX when you need it (for example, in laying out mathematical formula).
it doesn't suffer from the freezes and crashes that some of us experience when working with large, image-heavy Word documents.
it automatically handles the table of contents, bibliography etc with pandoc.
comments, drafts of text, etc can be added to the document by wrapping them in
it works well with Git, so keeping backups is straightforward. Just commit the changes and then push them to your repository.
it is able to take advantage of autocompletion capabilities for figures and citations in several text editors (VSCode, Sublime, etc.)
there is no lock-in. If you decide that Markdown isn't for you, then just output to Word, or whatever, and continue working in the new format.

Are there any reasons not to use Markdown?

There are some minor annoyances:

if you haven't worked with Markdown before then you'll find yourself referring to the style-guide (pandoc User Guide) fairly often at first.
Some niche and more complicated requirements will require writing raw LaTeX, which won't appear in other output formats. In the worst case, it will require diving into Haskell or Lua filters for pandoc
the style documents in this framework could be improved. The PDF and HTML (thanks @ArcoMul) outputs are acceptable, but ~~HTML and~~ Word needs work if you plan to output to this format.
... if there are more, please add them here.

Detailed template information

How is the template organised?

README.md => these instructions.
License.md => terms of reuse (MIT license).
Makefile => contains instructions for using pandoc to produce the final thesis.
output/ => directory to hold the final version.
source/ => directory to hold the thesis content. Includes the references.bib file.
scratch/ => directory to hold tables which can be converted between different formats.
source/figures/ => directory to hold the figures.
style/ => directory to hold the style documents.

How do I get started?

Install the software outlined above, as well as:
- A text editor, like Sublime, which is what you'll use write the thesis.
- Git, for version control.
Fork the repository on Github
Clone the repository onto your local computer (or download the Zip file).
(Skip this step to use default UCL style) Configure style for your institution. See instructions below
Navigate to the directory that contains the Makefile and type "make pdf" (or "make html") at the command line to update the PDF (or HTML) in the output directory.
In case of an error (e.g. make: *** [pdf] Error 43), consult this article for possible fixes. Most importantly, make sure tlmgr is properly installed, then run ```install.sh``
Edit the files in the 'source' directory, then goto step 5.

How does it work?

The universal document converter pandoc does all the heavy lifting. For example:

make pdf (the code under pdf: ... in Makefile) runs pandoc which takes as input
1. the markdown files which contain the writing content: input/*.md
2. a yaml file with metadata: input/metadata.yml
3. a LaTeX template: style/template.tex
4. a LaTeX header: style/preamble.tex
5. a BibTeX file of your references: input/references.bib
6. a csl style file for citations: style/ref_format.csl
7. a bunch of options which change the output e.g. --number-sections

the output produced is:
1. the generated pdf: output/thesis.pdf
2. logs (which contain the .tex which was compiled): pandoc.pdf.log

Put simply, pandoc uses the latex template provided to create a .tex file, then compiles it. In detail, pandoc processes the input files in the following way (the file names in quotes aren't visible to you, but are named for the purpose of understanding):

Make replacements within the markdown files input/*.md e.g.:
- references to figures, captions, and sections are handled: @fig:my_fig -> \ref{fig:my_fig}
- equations are converted to LaTeX and numbered: $$f(x) = ax^3 + bx^2 + cx + d$$ {#eq:my_equation} -> \begin{equation}f(x) = ax^3 + bx^2 + cx + d\label{eq:my_equation}\end{equation}
- citations are handled: [@Cousteau1963] -> (Cousteau Jacques & Dugan James 1963)
- see input/*.md for more examples!
Create "body.tex" by:
- converting all the *.md files in the order that they were stated in the pandoc call
Create "main.tex" from style/template.tex by running code wrapped in $ signs. The important things to note are:
- this populates style/template.tex with metadata from input/metadata.yml and the arguments from the pandoc call
- "body.tex" is pasted in verbatim in place of $body$
Create "references.tex" by converting ./input/references.bib
Concatenate files together to create the final thesis.tex = style/preamble.tex + "main.tex" + "references.tex"
Compile thesis.tex (you can see the logs for this process, and what "thesis.tex" would look like in pandoc.pdf.log)
- TIP: You can also generate and view output/thesis.tex by running make tex - this follows all the above steps, bar the final compilation

What else do I need to know?

Some useful points, in a random order:

if you only care about generating thesis.pdf you can always fall back on writing LaTeX within the markdown files (but note that thesis.html and other outputs will not be able to render this)
the markdown files you write (i.e. your chapters) will be compiled in alphabetical order, so keep the filenames sorted in the order you want them to appear e.g. 01_chapter_1.md, 02_chapter_2.md, etc. This is required because of the way we have written make pdf. You can change this behaviour by writing a custom pandoc command instead of using make pdf.
each chapter must finish with at least one blank line, otherwise the header of the following chapter may not be picked up.
add two spaces at the end of a line to force a line break.
PDFs are generated using the LaTeX templates in the style directory. Fonts etc can be changed in the TeX templates.
To change the citation style, just overwrite ref_format.csl with the new style. Style files can be obtained from citationstyles.org/
For fellow web developers, there is a Grunt task file (Gruntfile.js) which can be used to 'watch' the markdown files. By running $ npm install and then $ npm run watch the PDF and HTML export is done automatically when saving a Markdown file.
You can automatically reload the HTML page on your browser using LiveReload with the command $ npm run livereload. The HTML page will automatically reload when saving a Markdown file after the export is done.

Troubleshooting

The first thing to try if the make * command fails is a simpler build, e.g. if make pdf failed, try make tex to see if that fails too.
If tex compilation is failing (i.e. make tex works but make pdf fails), try updating tex live and/or packages. For example, if you get the error make: *** [pdf] Error 43, have a look in pandoc.pdf.log for the error. If it is something like

`l3backend-xdvipdfmx.def' not found

then try:

sudo tlmgr update --self
sudo tlmgr l3backend
# Full nuclear option - update *all* the packages! (takes about 10m)
# sudo tlmgr update --all

Try reinstalling everything from scratch (tip: check out .travis.yml)
Search the github issues and pull requests in this repo

Contributing

Contributions to the template are encouraged! There are lots of things that could be improved, like:

cleaning up the LaTeX templates, which are messy at the moment.
improving the style of Word and TeX outputs.

Please fork and edit the project, then send a pull request.

tompollard / phd_thesis_markdown