Using Tectonic + Pandoc + custom filters for scientific writing. This project is a docker image that contains various tools to write scientific papers in Markdown. All this is made for Pandoc v2.9.

This project is a Docker container. This means that Pancake runs in a containerized machine based on Alpine linux. Inside that container, tools needed to use Pandoc and Tectonic are installed. In order to launch Pancake on a project, you first need to install docker. Then to run the converter use the following command:

    docker run -d -v $PWD:/data -e PANDOC_OPTIONS="--listings --top-level-division=chapter --number-sections" -e PANDOC_OUTPUT="thesis.pdf" -e PANDOC_INPUT="*.md" --name pancake grea09/pancake

The following options may be of use:

• -v: volume mount. Use /data as the working directory.
• PANDOC_OPTIONS: options to give to pandoc
• PANDOC_INPUT: input files to be converted
• PANDOC_OUTPUT: output file
• PANDOC_FROM: input format, if unspecified it is inferred from input's extension.
• PANDOC_EXTENSIONS: additional pandoc extensions to add to the format (e.g. markdown+hard_line_breaks).
• PANDOC_TO: output format, if unspecified it is inferred from output's extension.
• PANCAKE_ONCE: if defined, will end the container after the first conversion attempt. Otherwise, pandoc will be invoked on every file change until the container is manually stopped.

Pancake will search for .yaml files in the working directory. For convenience, you may put them in a styles folder. All style files will be read in the alphabetical order. The YAML files can contain any Pandoc metadata variables (except for font specification).

To specify a font you need to define it either using Pandoc's fontfamily variable or using the following:

    fonts:
      timesnew: Times New Roman
      foo:
        font: Arial # Main font
        regular: Arial
        italic: Arial Italic
        bold: Arial Black
        bold-italic: Arial Bold Italic
        slanted: Verdana
        bold-slanted: Verdana Bold
        smallcaps: Times New Roman
        scale: 1.2
        options: #fontspec options as a string list

The name of the font will be the key suffixed with font (here \timesnewfont & \foofont respectively). To define default fonts, name your font one of the following:

    main:
    sans:
    mono:
    math:
    cjk:

Additional fonts will be loaded from the /data/fonts folder. To list the available fonts, execute the fc-list inside the container using docker exec while it is running.

In order to change the appearance of the different elements in the document one must use the following:

    elements:
      my-element:
        theorem: #or
        block: true
        koma: true #Koma element
        prefix:
         - singularForm
         - pluralForm
        ref: shortcode for refs
        preposition: of #Between prefix and name
        font: macroFontName
        color: Blue
        title:
          font: \anotherMacro
          background: Grey
        style:
        border:
        background:
        options: #latex options as a string list
        number: section

The following elements can be styled:

    quote: # Title is lettrine
    code: #verbatim code
    algorithm: #Enables algorithmx
    document: #Title is main title, number is page number and only box.background change the page color. Style is pagestyle.
    chapter:
    section:
    figure:
    table:
    equation:

For the document element, here is the list of handled options:

• style: documet class
• color: text color
• background: page color
• options: class options like a4paper and such.

This part will use tcolorbox to generate theorem like blocks. Please refer to the (package documentation)[http://www.texdoc.net/texmf-dist/doc/latex/tcolorbox/tcolorbox.pdf].

Will generate classical block LaTeX code using begin and end.

This setting allows to style default KOMA class elements like section or chapter. The style is applied as part of the \addtokomafont command. Don't forget the font prefix added when defining fonts in Pancake. The style element is passed as a latex command.

Several lists of elements can be used in each document. Lists are tables that enumerates elements of a certain type and some of their properties. For example list of figures with their caption or various table of content or glossary. To change their display, use the following:

    lists:
      my-list: #Enables the list
        title: Super List
        depth: 4
        level: chapter #Heading of the list
        columns: 3 #Requires multicol
        linkcolor: solarized-base1

Here is the list of lists:

    glossary:
    figures:
    content:
    tables:

In order to change the default link colors, one must use the following:

    colorlinks:
      link: solarized-blue
      file: solarized-magenta
      cite: solarized-green
      url: solarized-cyan

For convenience, a new latex command parameter has been added to define custom LaTeX command:

    macro:
      - name: raw LaTeX definition
      - bb: \mathbb
      …

Glossaries are used in two steps: definition and usage. The glossary is defined in a .yaml configuration file. It can be put in a separate file or defined in the main configuration file as follows :

    glossary:
      acronyms:
        - FOO: First On Observation
      symbols:
        - label: bar
          symbol: _
          description: An example symbol
      entries:
        - name: trivial
          description: Complicated word to say simple.

Once defined, you may use the following notation to reference a word/acronym/symbol in your text:

    A few <+trivialS> ways to express examples can be done when <+foo> using the <-bar> notation.

The behavior can be modified in a few ways:

• +/- at the start of the <> notation is used for the entry type:
  • • for linked reference
  • • for text only reference
• Capitalisation of the first letter of the reference to use the capitalized form
• Adding a upper case S at the end of the reference for plural form.

Also, one can use code blocks to write pseudocode using algpseudocode:

    ~~~ {.algorithm #alg:example name="A smart caption" startLine="1"}
    \Function{example}{Stuff $s$, Problem $\mathcal{P}$} \EndFunction
    ~~~