Building

The current build process is labrinthine and I regret it somewhat, but it works. It's broken down into a series of steps:

Jupyter Notebooks -> Markdown

Config files: dodo.py:task_markdown, pandoc/figure_to_markdown.py Uses NbConvert to convert notebooks to markdown. figure_to_markdown.py converts <figure> tags to markdown images and parses a bunch of metadata from the figure tags

<figure>
<img src="src" style="max-width:700px;" title="title">
<figcaption>
Caption
</figcaption>
</figure>

giving output in the form:

![alt_text](src)(href){#fig:label  width=100% short-caption="title"}

I use html <figure> tags in Jupyter rather than plain markdown image tags because it allows me to preview the captions and center them with css.

Markdown -> HTML

Config files: dodo.py:task_html, pandoc/markdown_to_html.yml pandoc/html_filter.py For a jekyll website version. html_filter fixes the relative image links.

Markdown -> Latex

Config files: dodo.py:task_latex, pandoc/markdown_to_latex.yml pandoc/latex_filter.py pandoc/latex_short_caption.lua For the PDF version latex_filter sorts out image paths and adds "Animated version online" to images that have a gif version. latex_short_caption.lua allows the title from markdown tags that look like [alt_text](src){short-caption="title" extra = metadata} to be incorporated into latex figures using \caption[title]{alt_text}

Doing compilation locally

Once:

# install texlive, mine was already installed so I'll skip this step, google it.
# make sure you have tlmgr, I think this comes with texlive

sudo tlmgr update --self #update tlmgr because it always complains
sudo tlmgr install latexmk # latexmk manages latex compilation with the latexmkrc file
sudo tlmgr install texliveonfly # this package can autoinstall dependencies

# auto install dependencies in thesis.tex
# this will install everything and then eventually fail but don't worry
sudo texliveonfly thesis.tex 

# actually compile
latexmk -pdf -shell-escape -interaction=nonstopmode thesis.tex

Getting it working in visual studio code

Install Latex Workshop Add the -shell-escape arg to the latexmk commandd invocation by adding this to settings.json:

    "latex-workshop.latex.recipes": [
        {
          "name": "latexmk 🔃",
          "tools": [
            "latexmk"
          ]
        }
      ],
    "latex-workshop.latex.tools": [
        {
          "name": "latexmk",
          "command": "latexmk",
          "args": [
            "-synctex=1",
            "-interaction=nonstopmode",
            "-file-line-error",
            "-pdf",
            "-outdir=%OUTDIR%",
            "-shell-escape", // The non default line for the minted package  to work
            "%DOC%"
          ],
          "env": {}
        }],

Reproducing overleaf compilation locally

Using a custom latexmkrc

How to put .sty files in a subfolder

Conda environment

To install

conda env create --file environment.yml

To update after changing environment.yml

conda env update --file environment.yml --prune