Adding examples

MarkDown.md

@@ -9,7 +9,7 @@ footer: 02/06/2023 | Markdown and applications | PY Barriat
 _footer: ""
 paginate: true
 _paginate: false
-math: true
+#math: true
 ---
 
 Markdown and applications<!--fit-->
@@ -123,6 +123,7 @@ Open VS Code and install the following extensions
 
 - `Markdown All in One`
 - `Marp`
+- `Pandoc Markdown`
 
 ---
 
@@ -149,7 +150,7 @@ rm -rf pandoc-3.1.2 pandoc-3.1.2-linux-amd64.tar.gz pandoc-crossref-Linux.tar.xz
 
 ---
 
-## Tex distribution
+## TeX distribution
 
 **LaTeX** is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation.
 > free and available for [macOS](https://www.tug.org/mactex/), [Windows](https://miktex.org/download), and Linux
@@ -196,18 +197,112 @@ And :
 
 - `Modern Fortran`
 
+---
+
+# Markdown Basic Syntax
+
+https://www.markdownguide.org/basic-syntax/
+
+## My first example: README.md on a Git web server
+
+https://gogs.elic.ucl.ac.be/pbarriat/learning-markdown/src/master/example
+
+### How to convert it ?
+
+```bash
+pandoc -s README.md -o README.pdf
+
+pandoc -s README.md -o README.docx
+
+pandoc -s README.md -o README.html --metadata title="README for EcEARTH"
+```
+
+---
+
+### How to custom the target style ?
+
+Using HTML template (html file and/or css)
+
+```bash
+pandoc -s README.md -o README.html --metadata title="README for EcEARTH" \
+    --template=html_templates/easy_template.html --toc
+```
+
+> don't forget to add `--toc` if you want a table of contents
+
+> you can also use the **VS Code Pandoc extension** to export/preview in HTML
+
+Using Latex template (latex file)
+
+```bash
+pandoc -s README.md -o README.pdf --template tex_templates/eisvogel
+```
+
+---
+
+## My second example: a letter
+
+Using my **UCLouvain letter** template (latex file)
+
+```bash
+pandoc -s letter.md -o letter.pdf --pdf-engine=xelatex --template tex_templates/letter
+```
+
+> **pdflatex** and **xelatex** are two implementations for the same purpose.
+> One of the main differences is that **xelatex** has better support for fonts: in particular you can use system fonts instead of only TeX fonts. It also has better support for non-latin character encodings.
 
 ---
 
-# My first example: README.md
+# Markdown Extended Syntax
+
+https://www.markdownguide.org/extended-syntax/
+
+## A scientific report
+
+```bash
+pandoc -s report.md -o report.html --webtex -H html_templates/report.css \
+       --bibliography assets/MyLib.bib --citeproc
+
+pandoc -s report.md -o report.pdf --template tex_templates/eisvogel \
+       --bibliography assets/MyLib.bib --citeproc
+```
+
+> don't forget to add `--webtex` if you want TeX formula in HTML
+
+> here we integrate a TeX bibliography
+
+> don't forget to add `--citeproc` if you want a list of references
 
 ---
 
-# For my second example, I want slides
+## Extended syntax example
+
+```bash
+pandoc -s advanced.md -o advanced.html --webtex -H html_templates/report.css --citeproc
+
+pandoc -s advanced.md -o advanced.pdf --template tex_templates/eisvogel --citeproc
+```
+
+Compare the HTML ouput and the PDF output !
+
+Some features are rendered only for PDF or HTML :
+
+- depends on **CSS** or **HTML** template
+- depends on **LaTeX** template
 
 ---
 
-# Now I want a small document: a letter
+# Markdown slides: Marp
+
+Replace `pandoc` command with `marp`
+
+```bash
+marp slides.md -o slides.pdf
+
+marp --bespoke.progress slides.md -o slides.html
+```
+
+> don't forget to add `--bespoke.progress` if you want a progress status
 
 ---
 
@@ -217,3 +312,13 @@ And :
 
 # My last example: a scientific paper !
 
+#marp --allow-local-files --theme tum.css git_elic.md -o git_elic.pdf
+#marp --template bespoke --bespoke.progress --allow-local-files --theme tum.css git_elic.md -o git_elic.html
+
+https://jaantollander.com/post/scientific-writing-with-markdown/
+
+https://curvenote.com/blog/writing-a-scientific-paper-faster-myst-markdown
+
+https://github.com/MartinHeroux/pandoc_article_template
+
+https://phd.row1.ca/phd

example/README.md

@@ -0,0 +1,88 @@
+# Sine hic parva
+
+## Gramen oblivia quantum
+
+Lorem markdownum et erat gurgite ipsaque et gravitas corpus dubitatis nostris
+dicta, descendat. Idem sola loquentes via circa, successore vidisti vidit at
+iter numen, Phoronidos ignarus obiecit tegumenque, nisi Hippolytum? Quam ibis
+quid erat noctis: vacavit et, rima.
+
+## Purpureus Iuno insurgere rudi Aquilone equorum ut
+
+Quae sanesque gradu Aeneas per inscribit luco *terras* mendaci animus lustrantem
+quem. Iam coniuge erat corpora arbor hoc ingens nempe si ver explicat.
+
+> Carens urbs dato circum **fugit**. Iungere [et formae] patria abiit.
+
+## Fulmina status
+
+Canibus sanguis **stabantque Hecaten** utraque. Quantum oras mora adeste falsa,
+auro consueta bracchia [parentis], hoc haec alternare audita remis me rem quo.
+Erat quod pars, subitam tegit invida positaeque recordor postera cornua
+angustum; Italiam sicut. Fata quae iuvenes, quid forma patris, via neque.
+
+## Ego isto temptent suum
+
+Sit est tamen digna *cinis Athenae* cum gutture nec fuisses adicis abit in
+paterno Somnus et iuvenis victu [tardus] de. Arethusa cumque quaeritur tanta
+[revertentes] hi ante Buten et super vimque premebam, fere quondam. Tu tingui:
+non, Latinas, dat totis dixit lacrimis dedit. Ingreditur carmina inque magis,
+coniunctaque futura.
+
+```
+module load craype-x86-milan
+module load PrgEnv-intel/8.3.3
+module load Perl/.5.34.1-GCCcore-11.3.0
+module load netCDF-Fortran/4.6.0-iompi-2022.05
+module load imkl/2022.1.0 OpenJPEG/2.5.0-GCCcore-11.3.0
+```
+
+## Non sacra
+
+Nuda Thebas dum stillanti regis nocebit, nam est difficilis vetui redditque? Et
+qui iam pererrat ad inani et abest sole volentem, autumnalia geri et unus dextra
+[Iolen] vidit Thetis discidium. Lecti tigno et **aevum** cum ut gelidis Danae
+animi; venturi Aglauros sunt tamen fetum; sit verum auxilium? Domum gramineo
+Patareaque pars.
+
+Superis ipse ac sibi dantibus haec fruges vita sumere tabulas, portasque
+trepidare laudem easdem utile. Antiquam erat peregit in parere manus his ut
+sanguine famae novissima alba umeris, ultima tam arae aspergine, pia. Verba
+sequuntur credas carentia; parentem Ulixem, est alterius putes. Viae crines
+fores inter dabat incubuit pande.
+
+1. Satiantur quae
+2. Moenibus labefactum munus
+3. Thalamo negant qui auctor saxoque onus fugam
+4. Aiacem exstat
+5. Humo pascua aranea cognata ferebat palluit Aeas
+6. Dixerat subito quietis frondibus litora procubuit nunc
+
+Cum Europa nurus? Acie refert; sub *iunctus malignas* iacuit, luna, undae vox
+avitis satiata, Narcissum **tellus**. Ab villae, inspiratque, usus maximus fert
+et murmura emisit crimenque mirantur.
+
+Nullaque monstro, ad mihi undas quarum quos ego rorantia, colle alii virgam
+pontus Abantiades [pressum iudicis], sanguine. Numici vel in sanguine Phoebus
+tandem pectoris manerem: siqua quos et villos parte, et pectora fecit. Inducta
+in minus pressanda in formam aequi guttura, et per color piscosamque quaesita
+regesta et ullum.
+
+[Iolen]: http://patris.org/fera
+[et formae]: http://iam.io/an-quas.php
+[parentis]: http://rapiunt.net/omni-ut.php
+[pressum iudicis]: http://utferoque.io/illa.html
+[revertentes]: http://dolebat.net/
+[tardus]: http://crevit-thalami.io/memorant-generis
+
+### Very first try
+
+|  CC   |  XIOS  | NEMO | IFS | #NODES |  WTIME per YEAR        |
+| ----- | ------ | -------------- | ------ | ------- | -------------------- |
+| `EC00.sh` |  1  |   86  |   320    |     3      | **121min**       |
+| `EC01.sh` |  3  |  128  |   288   |    4       | **??min**       |
+| `EC02.sh` |  1  |  128  |   512   |    6       | **83min**       |
+
+## Contributors
+
+- ELIC members [@pbarriat](https://gogs.elic.ucl.ac.be/pbarriat)

example/advanced.md

@@ -0,0 +1,323 @@
+---
+toc-title: Contents
+lang: en
+title: Pandoc Markdown
+subtitle: A `VSCode` extension for wrinting Pandoc Markdown documents using Pandoc
+author: Dr Taz
+keywords: Markdown, Pandoc, VSCode
+bibliography: "assets/MyLib.bib"
+csl: "assets/journal-of-neurophysiology.csl"
+fontsize: 11.5pt
+mainfont: Palatino, Georgia, Times, Arial
+---
+
+### Abstract
+
+`Pandoc Markdown` allows writing Markdown documents using Pandoc for both typesetting and real-time preview, with no third party renderers nor CSS files, just Pandoc. As a bonus, a curated *Article* CSS is provided, which allows producing documents inspired by those produced by the `article` LaTeX class. This extension requires Pandoc to be available from the command line.
+
+
+## 1. Intro
+
+Please see [Pandoc's Markdown] for detailed documentation about basic and extended Pandoc Markdown.
+
+## 2 Pandoc Markdown
+
+
+### 2.1 Code
+
+Pre formatted:
+
+~~~
+Normal text
+Pre formatted
+~~~
+
+Source code:
+
+~~~python
+# Python
+import numpy as np
+x = np.linspace(0,np.pi)
+print("Hi from Python")
+~~~
+
+And:
+
+~~~js
+// javascript
+const changeColor = (newColor) => {
+    const element = document.getElementById('message');
+    element.style.color = newColor;
+}
+~~~
+
+### 2.2 Columns
+
+Columns are specified as a `<div>` of class `.columns`, which contains another `<divs>` of `<.column>` class. `<divs>` are specified in Pandoc Markdown using at least three colons as  `:::` . For example:
+
+	:::{[#label] .columns [attrs]}
+	
+	:::{.column width="45%"}
+	First column contents
+	:::
+	
+	:::{.column width="10%"}
+	:::
+	
+	:::{.column width="45%"}
+	Second Column contents
+	:::
+	
+	:::
+
+Which produces something as:
+
+:::{.columns}
+
+:::{.column width="48%;font-style: italic"}
+1st Column Lorem ipsum dolor sit amet, consectetur adipiscing elit
+:::
+
+:::{.column width="4%"}
+:::
+
+:::{.column width="48%;background-color:#eee"}
+2nd Column, Lorem ipsum dolor sit amet, consectetur adipiscing elit
+:::
+
+:::
+
+### 2.3 Tables
+
+#### i. Simple
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua (see [Table 1](#Table1)).
+
+    incididunt ut labore et dolore magna aliqua (see [Table 1](#Table1)).
+
+    : Tabla 1: Tabla simple []{#Table1}
+
+    | Syntax    | Description |
+    | --------- | ----------- |
+    | Header    | Title       |
+    | Paragraph | Text        |
+
+Which renders as:
+
+: Tabla 1: Tabla simple []{#Table1}
+
+| Syntax    | Description |
+| --------- | ----------- |
+| Header    | Title       |
+| Paragraph | Text        |
+
+
+#### ii. Aligned
+
+Column alignments are determined by the position of the header text relative to the dashed line below it
+
+    : Table 1.1:  Simple table syntax.
+
+    Right     Left     Center     Default
+    -------     ------ ----------   -------
+    12          12      12          12
+    123         123     123         123
+    1           1       1           1
+
+: Table 1.1:  Simple table syntax.
+
+  Right     Left     Center     Default
+-------     ------ ----------   -------
+12          12      12          12
+123         123     123         123
+1           1       1           1
+
+Tables using pipes: 
+
+    : Table 2: Using pipes and colons
+
+    | Left      | Centered | Right       |
+    |:--------- |:--------:| -----------:|
+    | Header    | Title    | Here's this |
+    | Paragraph | Text     | And more    |
+
+Which renders as:
+
+: Table 2: Using pipes and colons
+
+| Left      | Centered | Right       |
+|:--------- |:--------:| -----------:|
+| Header    | Title    | Here's this |
+| Paragraph | Text     | And more    |
+
+Or simply:
+
+    : Tabla 2.1: Pipe, simple
+
+    Fruit  | Price ($)  | Existence
+    -------|-----------:| :-------:
+    apple  | 2.05       | 3 box
+    pear   | 1.37       | 2 kg
+
+
+: Tabla 2.1: Pipe, simple
+
+Fruit  | Price ($)  | Existence
+-------|-----------:| :-------:
+apple  | 2.05       | 3 box
+pear   | 1.37       | 2 kg
+
+
+
+### 2.4 Small caps
+
+To write small caps, use the smallcaps class: 
+
+    This is a  [Small caps text]{.smallcaps} , got it?
+
+This is a  [Small caps text]{.smallcaps} , got it?
+
+
+### 2.5 Figuras
+
+#### i. Simple
+
+    See [Fig. 1](#fig1)
+
+See [Fig. 1](#fig1)
+
+
+    ![Figure 1: A math plot](assets/plot-3d-small.png){#fig1}
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. 
+
+![Figure 1: A math plot](assets/plot-3d-small.png){#fig1}
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. 
+
+#### ii. With attributes
+
+See [Fig. 2](#figattrs).
+
+    ![Fig. 2: Image (scaled to width=40% column)](assets/plot-3d-small.png){#figattrs width=40%}
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua (see [Fig Attrs](#figattrs)).
+
+![Fig. 2: Image (scaled to width=40% column)](assets/plot-3d-small.png){#figattrs width=40%}
+
+
+
+### 2.6 Aside figures and text
+
+    <aside>
+
+    ![Fig. 3: Aside figure](assets/plot-small.png)
+
+    </aside>
+
+<aside>
+
+![Fig. 3: Aside figure](assets/plot-small.png)
+
+</aside>
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Turpis cursus in hac habitasse platea dictumst quisque sagittis. In ornare quam viverra orci. Mauris rhoncus aenean vel elit. Fames ac turpis egestas maecenas pharetra convallis. Mauris nunc congue nisi vitae suscipit tellus mauris a diam. 
+
+    <aside>
+    This text should be located as an `<aside>` insert (right side).
+    </aside>
+
+<aside>
+This text should be located as an `<aside>` insert (right side).
+</aside>
+
+Fames ac turpis egestas integer eget aliquet nibh praesent tristique. Laoreet suspendisse interdum consectetur libero id faucibus nisl tincidunt. Ornare aenean euismod elementum nisi quis. Ipsum dolor sit amet consectetur adipiscing elit ut. Vitae congue mauris rhoncus aenean vel elit scelerisque.
+
+### 2.7 Math
+
+Use one og the math rendering options, such as `--katex` , `--mathjax`, etc.
+
+[]{#xfoo}
+Dictumst ac turpis egestas integer dictumst quisque sit amet. A paraghrah. See [ec. 2](#ec-2)
+
+
+The formula, $y=mx+c$, is displayed inline. Some symbols and equations (such as 
+$\sum{x}$ or $\frac{1}{2}$) are rescaled to prevent disruptions to the regular 
+line spacing.
+
+For example: []{#ec-2}
+
+$$  f(x)  = \sum_{n=0}^{\infty} \frac {f^{(n)}(a)} {n!} (x-a)^n $$
+
+where:
+  : $f^{(n)}(a)$ = the $k$-th derivative of $f$ evaluated at point $a$.
+
+### 2.8 Definitions
+
+    **Term 1:**
+    : Definition 1 
+
+    **Term 2:**  
+    : Definition 2
+    
+**Term 1:**
+  : Definition 1 
+
+**Term 2:**  
+  : Definition 2
+
+### 2.9 Footnotes
+
+
+Pandoc’s Markdown allows footnotes, using the following syntax:
+
+    Here is a footnote reference[^1], and another one [^longnote].
+
+    [^1]: Here is the footnote.
+
+    [^longnote]: Here's one with multiple blocks.
+
+
+Here is a footnote reference[^1], and another one [^longnote] .
+
+[^1]: Here is the footnote.
+
+[^longnote]: Here's one with multiple blocks.
+
+
+### 2.10 Citations
+
+To cite a bibliographic item with an identifier foo [@hoffmann_platon_1951], use the syntax `[@foo]`. Normal citations should be included in square brackets, with semicolons separating distinct items:
+
+    Blah blah [doe99; smith2000; smith2004].
+
+How this is rendered depends on the citation style [@temple_beginnings_1993]. In an author-date style. @temple_beginnings_1993 says good things.
+
+Citation items may optionally include a prefix, a locator, and a suffix. In
+
+    Blah blah [see @doe99, pp. 33-35 and *passim*; @smith04, chap. 1].
+
+The first item (`@doe99`) has prefix see, `locator pp. 33-35`, and suffix and *passim*. The second item (`@smith04`) has locator `chap. 1` and no prefix or suffix.
+
+You can also write an author-in-text citation, by omitting the square brackets:
+
+    @smith04 says blah.
+    @smith04 [p. 33] says blah.
+
+This [@hoffmann_platon_1951] will cause the author’s name to be rendered, followed by the bibliographical details. Use this form when you want to make the citation the subject of a sentence [@hoffmann_platon_1951;@temple_beginnings_1993].
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent quis tortor sit amet urna facilisis sollicitudin. Ut efficitur, enim vitae sodales aliquet, odio dui consectetur nisl, quis facilisis mauris est ut odio. Proin convallis erat sit amet arcu pellentesque blandit. Aliquam at turpis vestibulum, iaculis nibh nec, eleifend ex. Vestibulum porta nec dolor ac porttitor. Nullam maximus vitae lacus ac hendrerit. Pellentesque aliquet, est nec finibus pharetra, nulla arcu malesuada orci, eget consequat lacus sapien eget libero. Phasellus dapibus turpis sed euismod sodales. Proin rhoncus odio non magna finibus, quis mollis enim lacinia. In hac habitasse platea dictumst. In eget neque blandit, dapibus lacus euismod, varius ligula. Praesent at dui ut eros gravida mollis. Ut viverra lorem risus.
+
+Cras ut congue sem. Mauris ex nulla, dapibus eu varius et, commodo eget dolor. Nunc velit ligula, sagittis placerat feugiat a, tincidunt et purus. Quisque eu convallis massa. Curabitur in sollicitudin felis. Phasellus mattis tincidunt ultricies. Sed sodales semper lorem quis semper. Quisque sollicitudin cursus dolor, quis fringilla magna lacinia eu. Donec at sagittis metus. Ut et lectus justo. Vestibulum sollicitudin commodo iaculis. In in elit nunc. Ut eget laoreet lorem.
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent quis tortor sit amet urna facilisis sollicitudin. Ut efficitur, enim vitae sodales aliquet, odio dui consectetur nisl, quis facilisis mauris est ut odio. Proin convallis erat sit amet arcu pellentesque blandit. Aliquam at turpis vestibulum, iaculis nibh nec, eleifend ex. Vestibulum porta nec dolor ac porttitor. Nullam maximus vitae lacus ac hendrerit. Pellentesque aliquet, est nec finibus pharetra, nulla arcu malesuada orci, eget consequat lacus sapien eget libero. Phasellus dapibus turpis sed euismod sodales. Proin rhoncus odio non magna finibus, quis mollis enim lacinia. In hac habitasse platea dictumst. In eget neque blandit, dapibus lacus euismod, varius ligula. Praesent at dui ut eros gravida mollis. Ut viverra lorem risus.
+
+Cras ut congue sem. Mauris ex nulla, dapibus eu varius et, commodo eget dolor. Nunc velit ligula, sagittis placerat feugiat a, tincidunt et purus. Quisque eu convallis massa. Curabitur in sollicitudin felis. Phasellus mattis tincidunt ultricies. Sed sodales semper lorem quis semper. Quisque sollicitudin cursus dolor, quis fringilla magna lacinia eu. Donec at sagittis metus. Ut et lectus justo. Vestibulum sollicitudin commodo iaculis. In in elit nunc. Ut eget laoreet lorem.
+
+## References
+
+
+[Pandoc]: https://pandoc.org/
+[VSCode]: https://code.visualstudio.com
+[markdown-it]: https://github.com/markdown-it/markdown-it
+[Pandoc's Markdown]: https://pandoc.org/MANUAL.html#pandocs-markdown

example/article.md

@@ -0,0 +1,363 @@
+# HOW TO PREPARE A GENERIC SCIENTIFIC MANUSCRIPT FOR SUBMISSION USING MARKDOWN AND PANDOC
+
+First A. Author^1^, Second B. Author^2^, Third Author^3^, Last  Author^1,2,3^
+
+
+1. University of Pandoc, Randwick, NSW, Australia
+2. Markdown Institute, Ottawa, ON, Canada
+3. LaTeX Research Institute, Kingston, On, Canada
+
+\
+\
+
+<!---
+Lines can be added or deleted
+If adding line in middle, end line with a space and \
+-->
+**Corresponding author** \
+Dr. First A. Author \
+University of Pandoc \
+42 Printers Lane \
+2031, Randwick, NSW, Australia \
+email: fa.author@pandoc.au \
+ph: +61-1-2345-6789
+\
+\
+\
+<!---
+Lines can be added or deleted based on journal requirements
+If adding line in middle, end line with a space and \
+-->
+**Keywords:** Pandoc, Markdown, Latex \
+**Running title:** Markdown manuscript \
+**Wordcount:** 4,321
+
+\newpage
+
+# Abstract
+**Purpose.** If journal requires abstract sections, these can be included and made bold by including double asterisks `**section_name**` before and after each header. If these are not needed, simply do not include them, simple.
+**Methods.** Because of our selected font, we can easily include special characters directly into our markdown file and these will be rendered properly. This provides some motivation to find a text editor that has a good *character map* plugin. Personally, I have grown rather fond of the Atom editor, which has a `character-map` plugin that does the trick. by clicking on a hotkey, `Alt-l`, I can type the name of the symbol I am looking and it is inserted into my document.
+**Results.** So lets say I just pressed `Alt-l` and typed `plusminus`. The item at the top of the list would be `±`, as expected. I hit `Enter` and it is inserted into my document. This makes it easy to say that, on average, my level of frustration drafting a manuscript has decreased by 77% ± 4% since learning about Markdown and Pandoc. Also, scientific papers always sound fancier when you use Greek letters. So I will search for the letter `beta`, which gives me the special character β. Also, because Pandoc converts Markdown to PDF using LaTeX, it is amazing support for mathematical equations and the like. Most basic tutorials on LaTeX should cover the basics of math-mode (i.e. `$math stuff$`).
+**Conclusion.** This dummy manuscript and its accompanying files includes everything you need to generate a basic manuscript for submission. The rest of this paper will provide a brief overview of Markdown, Pandoc and the various parts that accompany this manuscript to generate the final result. I chose a simple approach and targeted generic formatting. Much more sophisticated manuscripts can be generated, but it is always a good idea to start small and simple.
+
+\newpage
+
+# Introduction
+A guiding principle of Pandoc and LaTeX is to separate content from style. While this can be achieved in LaTeX, the actual document in which you write can be rather intimidating for the uninitated. It is filled with commands, for example `\usepackage[margin=3cm]{geometry}`, and typing even a simple document can become cluttered with function calls to make text bold (`\textbf{my text}`) or italic (`\emph{my text}`), or just trying to write a percent sign (`\%`). While LaTeX is more powerful and is what is used by many publishers to typeset the journals we publish, it can be overwhelming for people who have any used Microsoft Office or Libre Office.
+
+Markdown is a simple markup language initially created to write content for the web. Pandoc, on the other hand, is a powerful Swiss Army knife of a tool that converts documents from one format to another. Importantly, Pandoc adds functionality that allows us, researchers and scientists, to generate professional looking manuscripts. And yes, Pandoc handles references and citations in a clean and efficient way; more on this later.
+
+This means that we can now focus on the content of our manuscripts when we are writing them. We will let Pandoc do the heavy lifting of creating a professional looking manuscript that we can share with co-authors and submit for review. And since we are using Markdown to write our manuscript, we can use a simple text editor, and the text that we write will be quite straight forward, free of LaTeX-style function calls.
+
+While we may use various formatting styles when writing notes, reports, letters, etc., things are rather straightforward when preparing scientific manuscripts [^1]. The main types of inline formatting I use are italics, super- and subscript. I also include tables and figures, and very occasionally use footnotes. For the footnote I just used, I typed `[^1]` in the spot where I want the superscript number 1 to appear, and then, somewhere else in the document (I chose immediately after the paragraph as this makes it easy to find if I need to change it) add `[^1]: At least for the type of papers I find myself writing.` This text has to be on its own line, with an empty line before and after. To make something italic, simply add an asterisks on either side. For example, typing this, `*this will be slanted*` will result it text that appears as *this will be slanted*. Superscript is achieved by surrounding the text with the carat symbol. For example, `sum^adults^` will generate sum^adults^. Similarly, the tilda symbol is used for subscript: `sum~chilren~` will appear as sum~children~ in the final document. We will cover tables and figures later in this document. The key thing here is that making these style changes can be done later, *en masse*. If you don't remember how to make something italic, bold or superscript, don't worry. Just leave yourself a note [TODO: make this text bold] and keep your writing flow going. Remember, we are trying to separate content from style. Stay in the flow and don't get distracted. I have included a brief review of key inline formatting (Table 1) and special characters (Table 2) at the end of this paper.
+
+[^1]: At least for the type of papers I find myself writing.
+
+# Methods
+
+It turns out we need to add and specify a few things to Pandoc in order to obtain a presentable manuscript. As you can see, these details are not included in this file, the `manuscript.md` file. That is because we are trying to separate content from style (and distractions). So this file is where we should write our manuscript. The details that specify things like the font, whether or not we want numbered sections, the addition of line numbers, etc are in small helpers files. Lets go over these now.
+
+## Participants
+
+To generate the PDF output, we simply need to run `pandoc -d header.yaml` on the command line. The content of this file could be placed in a `yaml` header at the top of this document, but that would be distracting to use and confusing to our co-authors who might not be familiar with Markdown and Pandoc. So, we extracted the `yaml` header and placed it in its own file: `header.yaml`. Note that `yaml` files need to be formatted based on some simple rules, so if you want to change anything, make sure you adhere to proper formatting style; a quick Google search will locate a quick tutorial if you need one.
+
+In `header.yaml`, we find two commands related to referencing. One  specifies the Bibtex file that contains our references the other specifies the referencing style we want to use to format our references (note that a line that starts with `#` is a comment and has no effect).
+
+``` yaml
+# References and Reference Style
+csl: journal-of-neurophysiology.csl
+bibliography: references.bib
+citeproc: true # required in pandoc 2.14
+```
+
+`csl` stands for Citation Style Language. As stated on its website:
+
+> "Welcome to the open source Citation Style Language (CSL) project! Our goal is to facilitate scholarly publishing by automating the formatting of citations and bibliographies. We develop the Citation Style Language and maintain a crowdsourced repository with over 10,000 free CSL citation styles."
+
+We will have more to say about references later in this article.
+
+The next part of the `header.yaml` file specifies the input and output files.
+
+``` yaml
+# Names of Input and Output Files
+input-file: manuscript.md
+output-file: manuscript.pdf
+```
+
+These will need to be changed if you decide to rename the base Markdown file, or if you want a specific name for the outputed PDF file.
+
+Then our `header.yaml` file has three difference 'include' statements. These allow us to include the content of specified files into the header, or preamble, of the LaTeX file that will generate our article, as well as before and after the actual content of our article, the stuff if `manuscript.md` is added to the LaTeX file. What these files contain will be described in the following sub-sections.
+
+``` yaml
+# Addition to LaTeX Template
+include-in-header: header.tex # Change margin and line spacing
+include-before-body: before_body.tex
+include-after-body: after_body.tex
+```
+
+The next section in the `header.yaml` file specifies some Pandoc variables that will control various aspects of how are article is generated. In order to properly process special characters typed directly into our text editor, rather than specifying a special LaTeX command, we are using the `xelatex` pdf-engine. To have these special characters appear in our This font was selected as it has good support for special characters.
+
+``` yaml
+# LaTeX Specifications
+pdf-engine: xelatex
+variables:
+  documentclass: article
+  mainfont: "DejaVu Serif"
+  sansfont: Arial
+  classoption:
+    - 10pt # 11pt, 12pt
+```
+
+The final part of `header.yaml` contains instructions and a commented out line related to adding numbered sections to our article.
+
+``` yaml
+# To have numbered sections, uncomment the following line.
+# But we don't want our Title or Abstract to be numbered,
+# so we will add {.unnumbered} next to our Title and Abstract
+# headers, separated by one space.
+# Example: # Abstract {.unnumbered}
+
+# number-sections: true
+```
+
+## Experimental set-up
+
+The file called `header.tex` contains LaTeX commands that Pandoc will insert in the preamble of the LaTeX it generates to make our manuscript.
+
+``` latex
+\usepackage[margin=3cm]{geometry}
+\usepackage{lineno}
+\usepackage{setspace}
+\doublespacing
+%\singlespacing
+%\onehalfspacing
+```
+
+If you want to change the margins of the PDF document that is generated, you can change the value passed to the `geometry` packaged. Next, we instruct LaTeX to use the `lineno` package, which will allow us to add line numbers to our document. Finally, we load the `setspace` package, which gives us access to three functions that we can use to specify the line spacing we want for our manuscript. The default is double line spacing, but by commenting out `\doublespacing` with a `%` and uncommenting one of the other lines we can use single line spacing or one and a half line spacing.
+
+## Protocol
+
+The next file we have is `before_body.tex`. The content of this file is inserted after the `\begin{document}` command in the LaTeX file, but before the actual content --the stuff in this file-- is added (by the way, I used two dashes in a row `--` to get the two emdashes in this sentence).
+
+``` latex
+\thispagestyle{empty}
+\vspace*{2 cm}
+\begin{linenumbers}
+```
+
+The first line tells LaTeX to not add a page number to the first page, our title page. The second line adds some vertical space, which allows the title of our article to not be at the very top of our title page. The final line tells LaTeX to start numbering the lines in our document.
+
+If you did not want numbered lines, you could delete or comment out `\begin{linenumbers}` in this file, as well as `\end{linenumbers}` that we add to the very end of our document via the `after_body.tex` file.
+
+## Statistical analysis
+
+The file `after_body.tex` includes a single LaTeX command: `\end{linenumbers}`. As mentioned above, delete or comment out this command if you do not want line numbers
+
+# Results
+
+## Effect of font on blood pressure
+
+Many researchers love to hate referencing in manuscripts. Many people default to proprietary software like Endnote or Reference Manager, but many good quality free alternatives are available such as Mendeley, JabRef, Zotero, etc. Regardless of what reference manager program you choose, the key functionality that we want if for the program to automatically generate and update a `.bib` file that contains our references.
+
+I often manually generate my `.bib` Bibtex files when I know they will be relatively small. However, I have recently (re)started using Zotero, and I am licking it. I can add references when I a browsing for articles, using the Zotero plugin for the Firefox web browser. I can also search for references from within the Zotero desktop application. Also, having an online accounts allows me to view and sync my library on any computer. I recommend the Better Bibtex plugin for Zotero, which adds additional functionality.
+
+The key things is that you have a Bibtex file that contains your references. Each reference has a key, which we use to refer to the reference. Below is an example of a reference in a Bibtex file:
+
+``` bibtex
+@Article{Diong2015,
+   Author="Diong, J.  and Herbert, R. D. ",
+   Title="{{I}s ankle contracture after stroke due to abnormal intermuscular force transmission?}",
+   Journal="J. Appl. Biomech.",
+   Year="2015",
+   Volume="31",
+   Pages="13--18",
+}
+```
+The key of this reference is `Diong2015`. Therefore, I can refer to this paper by preceding it's key with the `@` symbol. To include a reference to the article that will be included in parentheses, I would type `[@Diong2015]`; this would result in the following [@Diong2015]. If was to refer to the paper by @Diong2015 in a sentence, as I just did, I would omit the square brackets (i.e. `@Diong2015`). You can also include several reference keys in the square brackets. For example, typing `[@Diong2012a; @Diong2012b; @Diong2015; @Diong2019]` will generate [@Diong2012a; @Diong2012b; @Diong2015; @Diong2019]. Note the semi-colon and space between each reference key.
+
+Sometimes we want to add text in the parentheses with our reference. This can be achieved by simply including the desired text before or after the reference. As an example, lets look at the following line of text: `contractures are a major problem [see @Diong2015 for a review]`; it looks like this when processed by Pandoc: contractures are a major problem [see @Diong2015 for a review]. More complex examples are also possible, such as `[see @Huijing2003, Figure 1; also @Bojsen-Moller2010, Table 2]`, which results in the following [see @Huijing2003, Figure 1; also @Bojsen-Moller2010, Table 2]. Some of these styles of referencing will be depending on the referencing style you are using.
+
+Now, if you skip to the end of this manuscript, you will find a References section where all the references I just cited will be properly formatted according to the style that I specified in the `header.yaml` file.
+
+``` yaml
+# References and Reference Style
+csl: jneurophysiol.csl
+bibliography: references.bib
+```
+
+Here we are using a Citation Style Language file that formats our references for submission to the Journal of Neurophysiology. There are literally thousands of such files available for download, or you can generate your own. That means, if your paper gets rejected from one journal and the next journal you want to submit to use a different referencing style, simply find the appropriate `.csl` file, add it to the project folder and change the appropriate line in your `header.yaml` file.
+
+## The relationship between hyphens and cholesterol
+
+It is worth mentioning that no reference manager software is perfect. When references are downloaded from the web, the formatting is not always correct, or they may not include the abbreviated version of a journal title. Thus, it is up to the authors to ensure the content of the `.bib` file is correct. For example, the tile of the paper sometimes comes in title case, where each word is capitalised. This needs to be fixed in the Zotero and the `.bib` file updated.
+
+## Causal relationship between Markdown use and happiness
+
+In many text editors, you can split your screen and have two documents open. Thus, you could have your paper open on one side and your `.bib` file open on the other. And when you want to enter a reference, you could search the `.bib` file for the reference and identify its key. As you probably have already realised, this is less than ideal.
+
+A better way to work is to use the Atom editor and the `autocomplete-bibtex` plugin. By pointing this plugin to the `.bib` file that is generated and regularly updated by Zotero, we can add references without having to move our hands from the keyboard. All we have to do is type `@` and start typing and a list of possible references will appear. We can scroll through the available choices or we can keep on typing to narrow down our search. The, when we have found the reference we were looking for, we simply click on `Enter` and the reference key is added. We can see an example of this is action in Figure 1, where I am adding this reference [@Diong2015].
+
+# Discussion
+
+This group of files provides a relatively simple approach to drafting scientific articles. It can be adapted to suite various requirements, yet remains relatively simple and clutter-free. Because of this, it remains a simple article template and may not suite everyone's needs. In preparing this group of files, several other examples were reviewed; some were relatively simple while others were sophisticated and generated publication-quality PDF documents, some based on the official LaTeX packages provided by publishers. The benefit of this series of files is that it can easily be adapted to other types of documents, such as study notes, lab notebooks, blog posts, etc. The building blocks are simple and most key parts are explained in the present article.
+
+## Not using maketitle
+
+Many introductory tutorials on using Markdown and Pandoc to generate nice looking PDF add the title, authors, abstract and date in the `yaml` header. This way, these entries are passed to LaTeX and used as part of the `\maketitle` command.
+
+I tried several ways to get `maketitle` to generate something that would be acceptable as a manuscript title page. Using an additional `LaTeX` package I was able to specify more than one affiliation per author. However, allowing room to specify the details of the corresponding author and also various other items such as word count, running title, key words, etc was not straightforward. There were hacks that hijacked the `date` variable, but these were less than optimal. Also, I was aiming for a simple approach that did not require writing a new LaTeX template file with newly defined (or redefined) functions.
+
+Therefore, I opted to bypass `maketitle` completely. This allows for great flexibility as to what appears on the title page. The downside is that I had to use several manual line breaks (i.e. `\`) and a call to `\newpage` in this, the main Markdown document.
+
+## Tables
+
+Tables can be found at the end of the manuscript, and they are rather easy to prepare, especially if you use Pandoc-style tables (see `manuscript.md` for example of how to prepare tables). To add a table caption, simply allow for one empty line and start the caption with 'Table: '; this will be recognised by Pandoc as a table caption and will be properly formatted in LaTeX. To ensure LaTeX produces the table in the expected location, use `\clearpage` between each new table you add.
+
+## Figures
+
+Figure are also found at the end of the manuscript and they too are easy to add to the manuscript.
+
+```markdown
+![Caption_goes_here](figure.png){ width=10cm }
+![Caption_goes_here](assets/figure.png){ height=10cm }
+```
+
+Add the full caption to your figure in the square brackets, but unlike tables, there is no need to add 'Figure' or something similar at the start. Pandoc, via LaTeX, will automatically add 'Figure' and the appropriate figure number on the final PDF.
+
+The figure can be located in the same folder as the Markdown file where you are drafting your article, but it can also be located in a dedicated folder, such as `assets`. In this case, simply include the folder name before the figure name (the forward slash may need to be backslash for Windows users).
+
+Finally, if you did not make your figures to exact size you want them to appear in the figure published manuscript, you really should do this, you can specify the size of the figure by adding an additional entry. Note that the entry goes between curly braces, with no space between the closing parenthesis and the opening curly brace, and with spaces on either side of the size command. Various options are possible, but the most sensible for manuscripts are to specify either the width or height of the figure.
+
+## Writing with co-authors
+
+Now comes the $1M dollar question: how to write a paper using this template with co-authors who only know Microsoft Word? Well, there are a few options.
+
+The best way would be to have your co-authors work directly on the Markdown file (`manuscript.md`), where comments could be left in an agreed upon format, for example in `typewriter` font. In papers than do not contain references to software or code, it is uncommon to use such a font, thus it would be an easy way to leave comments `|MH: I was wondering if we could expand on this point a little, maybe providing an example of what such a comment would look like|`.
+
+Also, rather than emailing the files around, the manuscript could be version controlled using git and hosted on GitHub or an internal GitLab server. With several co-authors, the person who is likely to give you the best and detailed feedback should go first, and then other co-authors could add their changes and comments after a few initial rounds between you and the other key authors (often your supervisor). It would also be possible to have each co-authors create a branch in the git repository, do their work their, and then make a pull-request. This allows for a nice, civilised conversation between the two parties. A workflow around git is definitely not common in many fields, including my own, but it makes total sense to have a lasting history of the manuscript in all its forms, and this without having dozens of files with co-author initials appended at the end or `v1`, `v2`, `v3final`, `v3finalfinal` appended at the end.
+
+An alternative to having your co-authors use git is to email them the Markdown file and have them email back their changes and comments. You can incorporate these changes yourself on a git branch, and then merge them in to the main document. This will likely be needed for co-authors not familiar with git.
+
+Another less-than-optimal alternative is to use Pandoc to output a Microsoft Word `.docx` file. While the formatting is not perfect, it is surprisingly good; definitely enough to have your co-authors revise the manuscript. But what do you do when the document is sent back to you?
+
+We can use Pandoc to convert our document back into a Markdown file. If you co-author used tracked-changes, you have to option to `accept` them all or `reject` them all. You will likely want to accept them all and add the modified file to a dedicated git branch, where you will be able to merge these changes (accepting and rejecting the changes individually). One thing to not is that any comment you co-authors left for you as Word comments will be lost.
+
+```bash
+% Example where all changes are accepted
+pandoc --from=docx manuscript.docx --track-changes=accept -o revised_manuscript.md
+
+% Example where all changes are rejected
+pandoc --from=docx manuscript.docx --track-changes=reject -o revised_manuscript.md
+```
+
+Another option is to accept all changes, including comments, by using `--track-changes=all`. This is likely not you want to do, as it actually embeds detailed notes about each change and comment made in the document. Here is an example:
+
+```markdown
+If [I added stuff.]{.insertion author="Martin Heroux" date="2021-07-08T15:22:24Z"}
+
+This means that we can now focus on the content of our manuscripts when we are writing them.
+[A comment.]{.comment-start id="0" author="Martin Heroux" date="2021-07-08T15:25:08Z"}
+[[]{.comment-end id="0"}]{.insertion author="Martin Heroux" date="2021-07-08T15:25:08Z"}
+```
+
+## Workflow in Atom
+If you are new to all of this and don't have a preferred writing environment, you might be curious about my current tooling. Well, as you can see in Figure 1, I use the Atom editor. This is an open-source editor that to which you can add plugins (from the folks at Atom or the Atom community). You can use Atom to do your actual coding (if you code), but you can also use it to write your papers! As you can see, I have my files and folders visible on the left side, my main `manuscript.md` file open in one window, a rendered PDF in another window, and, along the bottom, a command-line terminal.
+
+When I am in the flow of writing, I don't have the PDF visible, as it is distracting. It is too tempting to compile our cool document and see what it looks like. However, when you are in the final phase of preparing your manuscript, or when you are learning Markdown and Pandoc, it can be useful to see what the PDF output looks like.
+
+As explained above, I run `pandoc -d header.yaml` on the command line to generate my PDF manuscript. With the PDF viewer plugin that I use (see Table 3) for details, the PDF auto-updates.
+
+## Submitting your revised, final manuscript
+While you can usually submit a single PDF document to journals when first submitting your paper, they usually want your paper in a different format, including individual, high-quality figures. Oddly enough, publishers almost all use LaTeX to typeset journals, yet many journals do not accept LaTeX files to be submitted, or simply text file or Markdown files. Rather, they prefer Microsoft Word `.docx` files, a complex file type that mixes formatting and content, where the formatting will be stripped away by the typesetters.
+
+So, what to do after you have received reviewer feedback on your first submission and the editor new demands the source files? You are lucky if you are allowed to submit a LaTeX file. Then, you can use Pandoc to output a `.tex` file. The next easiest thing to do is to use Pandoc to convert your Markdown manuscript file into a Word file. The formatting should be good enough, but you might have to tweak your tables a little (see Figure 2 for an example). While this seems like an unnecessary and somewhat tedious step, you should only have to do it once per manuscript. And make sure you do it at the very end, when you and your colleagues have make all the required changes.
+
+Someday, we may actually be able to provide Markdown or text files as the final product. But we should not let a journal or publisher, and their idiosyncratic choice of preferred final file, influence how we spend the vast majority of our time working on our manuscript. We will spend countless hours writing and revising our paper; I would much prefer work in a simple, clean format like Markdown for those hours, and then spend a somewhat painful 5-10 min tweaking a Word document if my manuscript has passed a first round of reviews and I have been asked to submit a revised version.
+
+## Marked-up version of your manuscript
+
+When submitting a revised version of your manuscript, journals often ask for a marked-up version, to show the various additions and deletions that have been made. How do we do this in the current workflow?
+
+There is a wonderful LaTeX package called `latexdiff` that does a great job when you have two versions of the same `.tex` file. A call to this program would look like this:
+
+```
+latexdiff manuscript.tex revised_manuscript.tex > diff.tex
+```
+
+Thus, we could have Pandoc output two `.tex` files, one from our original submission and one from our revised version, and get the marked-up version that can be processed using `pdflatex` (or `xelatex`) to get a nice looking PDF. An example of what such a PDF document looks like is shown in Figure 3.
+
+Another option that is in theory simpler is to use ~~strikeout text for the things that you want to delete~~ and **bold text for any additions.** This is can be achieved using basic Pandoc Markdown: `~~strikeout text for the things that you want to delete~~ and **bold text for any additions.** ` While this approach may seem simpler because it does not require running files through `latex-diff` and recompiling a PDF document, it is actually much more work. Consider a document that has been through multiple rounds of revisions by you and your co-authors, how will you know what has been added and what has been deleted? The only way for this to work is for you and your co-authors to agree on the convention to manually strikeout text using `~~text~~` and manually bold new next with `**text**`. It could work, but because it is not common practice, it is quite likely that someone will forget to do it. Best to learn to work with `latex-diff` if you ask me.
+
+
+## Conclusion
+
+The approach presented here is somewhat simplistic. However, it provides a nice introduction to Pandoc and Markdown for academic writing that does not use much or any mathematical notation or formulas, or embedded code. A slightly different flavour of Markdown, called R-Markdown is popular amongst users of the R programming language. When combined with `knitr`, it can be used to write papers in various journal-specific styles. It can even work with Python code. However, my approach is generally to start simple and use more sophisticated tools when I need them. The current approach will do me just fine for the majority of my papers.
+
+\newpage
+
+# Acknowledgements
+I would like to thank the participants of the study, and to Dr. Honeycut for his wisdom and guidance.
+
+# Funding
+The present work was supported by the two gold coins I found the other day when I was cleaning between the sofa cushions.
+
+# Author Contributions
+Authors agree to attest that they have contributed sufficiently to be listed as an author.
+
+\clearpage
+
+Inline formatting    Pandoc Markdown command   Result
+------------------   ------------------------  ---------------
+Bold                 `**bold**`                **bold**
+Italic               `*italic*`                *italic*
+Superscript          `x^2^`                    x^2^
+Subscript            `x~2~`                    x~2~
+Emdash               `--`                      --
+
+Table: Fundamental inline formatting in Pandoc-flavoured Markdown
+
+\clearpage
+
+Character name       output
+---------------      -------
+Degree symbol        °
+Greek letters        β α
+plus-minus           ±
+Sumamtion            ∑
+Trademark            ™
+Copyright            ©
+Money                ¢ £ €
+
+Table: Example of special characters that can be typed directly into a text editor and are properly rendered by Pandoc, without using the LaTeX math-mode or other packages.
+
+\clearpage
+
+Atom plugins                 Functionality
+---------------              --------------
+`autocomplete-bibtex`        Amazing plugin that simplifies entering reference key
+`character-table`            For insert special characters
+`language-markdown`          To allow language highlighting for Markdown
+`pdf-view`                   Provides in-editor PDF reviewer
+`platformio-ide-termial`     An embedded terminal window to run your Pandoc commands
+`tool-bar-markdown-writer`   Helpful when first learning Markdown and its commands
+`markdown-preview`           Provides real-time HTML rendered view of Markdown document
+`wordcount`                  Wordcount of current document
+`markdown-fold`              Can fold sections, and thus focus on parts of document
+
+Table: Atom plugins that make writing (Markdown) documents a joy.
+
+\clearpage
+
+![Autocomplete Bibtex in action. After typing the `@` symbol and typing the first letter of the reference we wanted to enter, a list of possible references popped up. We can continue typing to narrow down the choice of available references, or we can us the up and down key to scroll through the references. Note that at the bottom of the pop-up screen there is a formatted version of the currently selected reference.](assets/autocomplete_bibtex.png){ width=16cm }
+
+\clearpage
+
+![Word document. What the first page of the current document looks like when it is converted to `.docx` using Pandoc. Much of the formatting is correct, including the references list.](assets/docx.png){ width=14cm }
+
+\clearpage
+
+![latex-diff. An example of generating a PDF document of the differences between two documents.](assets/diff.png){ width=14cm }
+
+\clearpage
+
+# References

example/article.yaml

@@ -0,0 +1,32 @@
+---
+# References and Reference Style
+csl: assets/journal-of-neurophysiology.csl
+bibliography: assets/references.bib
+citeproc: true # required in pandoc 2.14
+
+# Names of Input and Output Files
+input-file: article.md
+output-file: article.pdf  # Change to .docx to make a Word file
+
+# Addition to LaTeX Template
+include-in-header: tex_templates/header.tex # Change margin and line spacing
+include-before-body: tex_templates/before_body.tex
+include-after-body: tex_templates/after_body.tex
+
+# LaTeX Specifications
+pdf-engine: xelatex
+variables:
+  documentclass: article
+  mainfont: "DejaVu Serif"
+  sansfont: Ubuntu
+  classoption:
+    - 10pt # 11pt, 12pt
+
+# To have numbered sections, uncomment the following line.
+# But we don't want our Title or Abstract to be numbered,
+# so we will add {.unnumbered} next to our Title and Abstract
+# headers, separated by one space.
+# Example: # Abstract {.unnumbered}
+
+# number-sections: true
+...

example/assets/MyLib.bib

@@ -0,0 +1,18 @@
+
+@article{hoffmann_platon_1951,
+	title = {Platon},
+	volume = {48},
+	number = {20},
+	journal = {Journal of Philosophy},
+	author = {Hoffmann, Ernst},
+	year = {1951},
+	file = {Snapshot:/Users/rsolano/Zotero/storage/54ZWU4MZ/KP-6.html:text/html},
+}
+
+@book{temple_beginnings_1993,
+	title = {The beginnings of writing},
+	publisher = {ERIC},
+	author = {Temple, Charles},
+	year = {1993},
+	file = {Snapshot:/Users/rsolano/Zotero/storage/K76FDZQR/eric.ed.gov.html:text/html},
+}

example/assets/journal-of-neurophysiology.csl

@@ -0,0 +1,232 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+  <info>
+    <title>Journal of Neurophysiology</title>
+    <id>http://www.zotero.org/styles/journal-of-neurophysiology</id>
+    <link href="http://www.zotero.org/styles/journal-of-neurophysiology" rel="self"/>
+    <link href="http://www.zotero.org/styles/american-physics-society" rel="template"/>
+    <link href="http://www.the-aps.org/publications/authorinfo/fullinfo.htm#references" rel="documentation"/>
+    <author>
+      <name>Michael Pesavento</name>
+      <email>mpesaven@gmail.com</email>
+    </author>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <category field="medicine"/>
+    <issn>0022-3077</issn>
+    <eissn>1522-1598</eissn>
+    <summary>The Journal of Neurophysiology style</summary>
+    <updated>2012-09-27T22:06:38+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <locale xml:lang="en">
+    <terms>
+      <term name="no date" form="long">date unknown</term>
+    </terms>
+  </locale>
+  <macro name="anon">
+    <text term="anonymous" form="short" text-case="capitalize-first" strip-periods="true"/>
+  </macro>
+  <macro name="author-bib">
+    <names variable="author" suffix=". ">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " font-weight="bold" delimiter-precedes-last="always"/>
+      <label form="long" prefix=", " suffix="."/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text macro="anon"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-cit">
+    <names variable="author">
+      <name form="short" and="text" delimiter=" " initialize-with=""/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text macro="anon"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="editor">
+    <names variable="editor" prefix="edited by ">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+    </names>
+  </macro>
+  <macro name="publisher">
+    <choose>
+      <if variable="URL">
+        <text variable="publisher"/>
+      </if>
+      <else>
+        <text variable="publisher-place" suffix=": "/>
+        <text variable="publisher" suffix=", "/>
+        <text macro="date"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="date">
+    <choose>
+      <if variable="issued">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else>
+        <text term="no date"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="DOI"/>
+      <!--don't use if there is a DOI-->
+      <else>
+        <choose>
+          <if variable="URL">
+            <group delimiter=" " prefix=" ">
+              <group>
+                <text variable="URL"/>
+              </group>
+              <group prefix="[" suffix="]" delimiter=" ">
+                <date variable="accessed">
+                  <date-part name="day"/>
+                  <date-part name="month" prefix=" " suffix=". " form="short" strip-periods="true"/>
+                  <date-part name="year"/>
+                </date>
+              </group>
+            </group>
+          </if>
+        </choose>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <!--this macro adds [online] to the end of an online ressource, but only when no DOI is given-->
+    <choose>
+      <if variable="DOI">
+        <text variable="title"/>
+      </if>
+      <else>
+        <group delimiter=" ">
+          <choose>
+            <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+              <choose>
+                <if variable="URL">
+                  <text variable="title"/>
+                </if>
+                <else>
+                  <text variable="title" font-style="italic"/>
+                </else>
+              </choose>
+            </if>
+            <else>
+              <text variable="title"/>
+            </else>
+          </choose>
+          <choose>
+            <if variable="URL">
+              <text term="online" prefix="[" suffix="]" text-case="capitalize-first"/>
+            </if>
+          </choose>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <!--   formatting citation      -->
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year">
+    <sort>
+      <key macro="date"/>
+      <key macro="author-bib"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=" ">
+        <group delimiter=", ">
+          <text macro="author-cit"/>
+          <text macro="date"/>
+        </group>
+        <!-- <text variable="locator" prefix="p."/> -->
+      </group>
+    </layout>
+  </citation>
+  <!--   formatting bibliography      -->
+  <bibliography>
+    <sort>
+      <key macro="author-bib"/>
+      <key macro="date"/>
+    </sort>
+    <layout suffix=".">
+      <text macro="author-bib"/>
+      <text macro="title" suffix=". "/>
+      <choose>
+        <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+          <group delimiter=" " suffix=".">
+            <text macro="edition"/>
+            <text macro="publisher"/>
+          </group>
+        </if>
+        <else-if type="chapter paper-conference" match="any">
+          <group delimiter=". ">
+            <group>
+              <text term="in" suffix=": " text-case="capitalize-first"/>
+              <text variable="container-title" font-style="italic"/>
+              <text macro="editor" prefix=", "/>
+            </group>
+            <text variable="event"/>
+            <text macro="publisher"/>
+          </group>
+          <text variable="page" prefix=", p. " suffix="."/>
+        </else-if>
+        <else-if type="article-journal">
+          <choose>
+            <if variable="issue volume" match="any">
+              <text variable="container-title" suffix=" " form="short" font-style="italic"/>
+              <text variable="volume"/>
+              <text variable="page" prefix=": "/>
+              <text macro="date" prefix=", " suffix="."/>
+            </if>
+            <else>
+              <choose>
+                <if variable="DOI">
+                  <text variable="container-title" suffix=" " form="short" font-style="italic"/>
+                  <group prefix="(" suffix=").">
+                    <date variable="issued">
+                      <date-part name="month" prefix=" " suffix=" "/>
+                      <date-part name="day" suffix=", "/>
+                      <date-part name="year"/>
+                    </date>
+                  </group>
+                  <text variable="DOI" prefix=" doi: "/>
+                </if>
+                <else>
+                  <text variable="container-title" suffix=". " form="short" font-style="italic"/>
+                </else>
+              </choose>
+            </else>
+          </choose>
+        </else-if>
+        <else>
+          <text variable="container-title" suffix=" " form="short" font-style="italic"/>
+          <text variable="volume"/>
+          <text variable="publisher" suffix="."/>
+          <text variable="page" prefix=": " suffix=", "/>
+          <text macro="date" prefix=" " suffix="."/>
+        </else>
+      </choose>
+      <text macro="access"/>
+    </layout>
+  </bibliography>
+</style>

example/assets/references.bib

@@ -0,0 +1,659 @@
+%Huijing2011 
+@Article{Huijing2011,
+   Author="Huijing, P. A.  and Yaman, A.  and Ozturk, C.  and Yucesoy, C. A. ",
+   Title="{{E}ffects of knee joint angle on global and local strains within human triceps surae muscle: {M}{R}{I} analysis indicating in vivo myofascial force transmission between synergistic muscles}",
+   Journal="Surg. Radiol. Anat.",
+   Year="2011",
+   Volume="33",
+   Pages="869--879",
+}
+
+%Yaman2013
+@Article{Yaman2013,
+   Author="Yaman, A.  and Ozturk, C.  and Huijing, P. A.  and Yucesoy, C. A. ",
+   Title="{{M}agnetic resonance imaging assessment of mechanical interactions between human lower leg muscles in vivo}",
+   Journal="J Biomech Eng",
+   Year="2013",
+   Volume="135",
+   Number="9",
+   Pages="91003",
+   Month="Sep"
+}
+
+%Kaya2018
+@Article{Kaya2018,
+   Author="Kaya, C. S.  and Temelli, Y.  and Ates, F.  and Yucesoy, C. A. ",
+   Title="{{E}ffects of inter-synergistic mechanical interactions on the mechanical behaviour of activated spastic semitendinosus muscle of patients with cerebral palsy}",
+   Journal="J Mech Behav Biomed Mater",
+   Year="2018",
+   Volume="77",
+   Pages="78--84",
+   Month="01"
+}
+
+%Ates2014
+@Article{Ates2014,
+   Author="Ates, F.  and Temelli, Y.  and Yucesoy, C. A. ",
+   Title="{{I}ntraoperative experiments show relevance of inter-antagonistic mechanical interaction for spastic muscle's contribution to joint movement disorder}",
+   Journal="Clin Biomech (Bristol, Avon)",
+   Year="2014",
+   Volume="29",
+   Number="8",
+   Pages="943--949",
+   Month="Sep"
+}
+
+%Wilke2018 
+@Article{Wilke2018,
+   Author="Wilke, J.  and Schleip, R.  and Yucesoy, C. A.  and Banzer, W. ",
+   Title="{{N}ot merely a protective packing organ? {A} review of fascia and its force transmission capacity}",
+   Journal="J. Appl. Physiol.",
+   Year="2018",
+   Volume="124",
+   Pages="234--244",
+}
+
+%Bojsen-Moller2010 
+@Article{Bojsen-Moller2010,
+   Author="Bojsen-Moller, J.  and Schwartz, S.  and Kalliokoski, K. K.  and Finni, T.  and Magnusson, S. P. ",
+   Title="{{I}ntermuscular force transmission between human plantarflexor muscles in vivo}",
+   Journal="J. Appl. Physiol.",
+   Year="2010",
+   Volume="109",
+   Number="6",
+   Pages="1608--1618",
+   Month="Dec"
+}
+
+% Creze2018
+@Article{Creze2018,
+   Author="Creze, M.  and Nordez, A.  and Soubeyrand, M.  and Rocher, L.  and Ma\^{i}tre, X.  and Bellin, M. F. ",
+   Title="{{S}hear wave sonoelastography of skeletal muscle: basic principles, biomechanical concepts, clinical applications, and future perspectives}",
+   Journal="Skeletal. Radiol.",
+   Year="2018",
+   Volume="47",
+   Pages="457--471",
+}
+
+% Becker2010
+@Article{Becker2010,
+   Author="Becker, I.  and Baxter, G. D.  and Woodley, S. J. ",
+   Title="{{T}he vastus lateralis muscle: an anatomical investigation}",
+   Journal="Clin. Anat.",
+   Year="2010",
+   Volume="23",
+   Pages="575--585",
+}
+% Becker2009
+@Article{Becker2009,
+   Author="Becker, I.  and Woodley, S. J.  and Baxter, G. D. ",
+   Title="{{G}ross morphology of the vastus lateralis muscle: {A}n anatomical review}",
+   Journal="Clin. Anat.",
+   Year="2009",
+   Volume="22",
+   Pages="436--450",
+}
+
+% Bernabei2016
+@Article{Bernabei2016,
+   Author="Bernabei, M.  and Maas, H.  and van Die\'{e}n, J. H. ",
+   Title="{{A} lumped stiffness model of intermuscular and extramuscular myofascial pathways of force transmission}",
+   Journal="Biomech. Model Mechanobiol.",
+   Year="2016",
+   Volume="15",
+   Pages="1747--1763",
+}
+
+%Bernabei2015 
+@Article{Bernabei2015,
+   Author="Bernabei, M.  and van Die\'{e}n, J. H.  and Baan, G. C.  and Maas, H. ",
+   Title="{{S}ignificant mechanical interactions at physiological lengths and relative positions of rat plantar flexors}",
+   Journal="J. Appl. Physiol.",
+   Year="2015",
+   Volume="118",
+   Pages="427--436",
+}
+
+%Huijing2009 
+@Article{Huijing2009,
+   Author="Huijing, P. A. ",
+   Title="{{E}pimuscular myofascial force transmission: a historical review and implications for new research.}",
+   Journal="J. Biomech.",
+   Year="2009",
+   Volume="42",
+   Pages="9--21",
+}
+
+%Tijs2016
+@Article{Tijs2016,
+   Author="Tijs, C.  and van Dieen, J. H.  and Baan, G. C.  and Maas, H. ",
+   Title="{{S}ynergistic co-activation increases the extent of mechanical interaction between rat ankle plantar-flexors}",
+   Journal="Front. Physiol.",
+   Year="2016",
+   Volume="7",
+   Pages="414"
+}
+
+% Diong2015
+@Article{Diong2015,
+   Author="Diong, J.  and Herbert, R. D. ",
+   Title="{{I}s ankle contracture after stroke due to abnormal intermuscular force transmission?}",
+   Journal="J. Appl. Biomech.",
+   Year="2015",
+   Volume="31",
+   Pages="13--18",
+}
+
+% Diong2012a
+@Article{Diong2012a,
+   Author="Diong, J.  and Herbert, R. D.  and Kwah, L. K.  and Clarke, J. L.  and Harvey, L. A. ",
+   Title="{{M}echanisms of increased passive compliance of hamstring muscle-tendon units after spinal cord injury}",
+   Journal="Clin. Biomech.",
+   Year="2012",
+   Volume="27",
+   Pages="893--898",
+}
+
+% Diong2012b 
+@Article{Diong2012b,
+   Author="Diong, J. H.  and Herbert, R. D.  and Harvey, L. A.  and Kwah, L. K.  and Clarke, J. L.  and Hoang, P. D.  and Martin, J. H.  and Clarke, E. C.  and Bilston, L. E.  and Gandevia, S. C. ",
+   Title="{{P}assive mechanical properties of the gastrocnemius after spinal cord injury}",
+   Journal="Muscle Nerve",
+   Year="2012",
+   Volume="46",
+   Pages="237--245",
+}
+
+% Finni2017a 
+@Article{Finni2017a,
+   Author="Finni, T.  and Cronin, N. J.  and Mayfield, D.  and Lichtwark, G. A.  and Cresswell, A. G. ",
+   Title="{{E}ffects of muscle activation on shear between human soleus and gastrocnemius muscles}",
+   Journal="Scand. J. Med. Sci. Sports",
+   Year="2017",
+   Volume="27",
+   Pages="26--34",
+}
+
+% Grob2016
+@Article{Grob2016,
+   Author="Grob, K.  and Manestar, M.  and Filgueira, L.  and Ackland, T.  and Gilbey, H.  and Kuster, M. S. ",
+   Title="{{N}ew insight in the architecture of the quadriceps tendon}",
+   Journal="J. Exp. Orthop.",
+   Year="2016",
+   Volume="3",
+   Pages="32",
+}
+
+% Herbert2011 
+@Article{Herbert2011,
+   Author="Herbert, R. D.  and Clarke, J.  and Kwah, L. K.  and Diong, J.  and Martin, J.  and Clarke, E. C.  and Bilston, L. E.  and Gandevia, S. C. ",
+   Title="{{I}n vivo passive mechanical behaviour of muscle fascicles and tendons in human gastrocnemius muscle-tendon units}",
+   Journal="J. Physiol.",
+   Year="2011",
+   Volume="589",
+   Pages="5257--5267",
+}
+
+% Herbert2015 
+@Article{Herbert2015,
+   Author="Herbert, R. D.  and H\'{e}roux, M. E.  and Diong, J.  and Bilston, L. E.  and Gandevia, S. C.  and Lichtwark, G. A. ",
+   Title="{{C}hanges in the length and three-dimensional orientation of muscle fascicles and aponeuroses with passive length changes in human gastrocnemius muscles}",
+   Journal="J. Physiol.",
+   Year="2015",
+   Volume="593",
+   Pages="441--455",
+}
+
+% Huijing2003
+@Article{Huijing2003,
+   Author="Huijing, P. A.  and Baan, G. C. ",
+   Title="{{M}yofascial force transmission: muscle relative position and length determine agonist and synergist muscle force}",
+   Journal="J. Appl. Physiol.",
+   Year="2003",
+   Volume="94",
+   Pages="1092--1107",
+}
+
+%Ates2018 
+@Article{Ates2018,
+   Author="Ates, F.  and Andrade, R. J.  and Freitas, S. R.  and Hug, F.  and Lacourpaille, L.  and Gross, R.  and Yucesoy, C. A.  and Nordez, A. ",
+   Title="{{P}assive stiffness of monoarticular lower leg muscles is influenced by knee joint angle}",
+   Journal="Eur. J. Appl. Physiol.",
+   Year="2018",
+   Volume="118",
+   Pages="585--593",
+}
+
+% Kaya2018 
+@Article{Kaya2018,
+   Author="Kaya, C. S.  and Temelli, Y.  and Ates, F.  and Yucesoy, C. A. ",
+   Title="{{E}ffects of inter-synergistic mechanical interactions on the mechanical behaviour of activated spastic semitendinosus muscle of patients with cerebral palsy}",
+   Journal="J. Mech. Behav. Biomed. Mater.",
+   Year="2018",
+   Volume="77",
+   Pages="78--84",
+}
+% Maas2019 
+@Article{Maas2019,
+   Author="Maas, H. ",
+   Title="{{S}ignificance of epimuscular myofascial force transmission under passive muscle conditions}",
+   Journal="J. Appl. Physiol.",
+   Year="2019",
+   Volume="126",
+   Pages="1465--1473",
+}
+
+% Maas2004 
+@Article{Maas2004,
+   Author="Maas, H.  and Baan, G. C.  and Huijing, P. A. ",
+   Title="{{M}uscle force is determined also by muscle relative position: isolated effects}",
+   Journal="J. Biomech.",
+   Year="2004",
+   Volume="37",
+   Pages="99--110",
+}
+% Mass2018 
+@Article{Mass2018,
+   Author="Maas, H.  and Finni, T. ",
+   Title="{{M}echanical coupling between muscle-tendon units reduces peak stresses}",
+   Journal="Exerc. Sport. Sci. Rev.",
+   Year="2018",
+   Volume="46",
+   Pages="26--33",
+}
+
+% Mass2009
+@Article{Mass2009,
+   Author="Maas, H.  and Huijing, P. A. ",
+   Title="{{S}ynergistic and antagonistic interactions in the rat forelimb: acute effects of coactivation}",
+   Journal="J. Appl. Physiol.",
+   Year="2009",
+   Volume="107",
+   Pages="1453--1462",
+}
+
+% Sandercock2009 
+@Article{Sandercock2009,
+   Author="Sandercock, T. G.  and Maas, H. ",
+   Title="{{F}orce summation between muscles: are muscles independent actuators?}",
+   Journal="Med. Sci. Sports. Exerc.",
+   Year="2009",
+   Volume="41",
+   Pages="184--190",
+}
+
+% Maas2008 
+@Article{Maas2008,
+   Author="Maas, H.  and Sandercock, T. G. ",
+   Title="{{A}re skeletal muscles independent actuators? {F}orce transmission from soleus muscle in the cat}",
+   Journal="J. Appl. Physiol.",
+   Year="2008",
+   Volume="104",
+   Pages="1557--1567",
+}
+
+% Pamuk2016 
+@Article{Pamuk2016,
+   Author="Pamuk, U.  and Karakuzu, A.  and Ozturk, C.  and Acar, B.  and Yucesoy, C. A. ",
+   Title="{{C}ombined magnetic resonance and diffusion tensor imaging analyses provide a powerful tool for in vivo assessment of deformation along human muscle fibers}",
+   Journal="J. Mech. Behav. Biomed. Mater.",
+   Year="2016",
+   Volume="63",
+   Pages="207--219",
+}
+
+% Stubbs2018 
+@Article{Stubbs2018,
+   Author="Stubbs, P. W.  and Walsh, L. D.  and D'Souza, A.  and H\'{e}roux, M. E.  and Bolsterlee, B.  and Gandevia, S. C.  and Herbert, R. D. ",
+   Title="{{H}istory-dependence of muscle slack length following contraction and stretch in the human vastus lateralis}",
+   Journal="J. Physiol.",
+   Year="2018",
+   Volume="596",
+   Pages="2121--2129",
+}
+
+% Heroux2020
+@Article{Heroux2020,
+   Author="Héroux, M. E.  and Anderman, I.  and Nykvist Vouis, S.  and Diong, J.  and Stubbs, P. W.  and Herbert, R. D. ",
+   Title="{{H}istory-dependence of muscle slack length in humans: effects of contraction intensity, stretch amplitude, and time}",
+   Journal="J Appl Physiol",
+   Year="2020",
+   Volume="129",
+   Number="4",
+   Pages="957--966",
+}
+
+% Tian2012 
+@Article{Tian2012,
+   Author="Tian, M.  and Herbert, R. D.  and Hoang, P.  and Gandevia, S. C.  and Bilston, L. E. ",
+   Title="{{M}yofascial force transmission between the human soleus and gastrocnemius muscles during passive knee motion}",
+   Journal="J. Appl. Physiol.",
+   Year="2012",
+   Volume="113",
+   Pages="517--523",
+}
+
+% Kwah2013 
+@Article{Kwah2013,
+    Author="Kwah, L. and Pinto, R. Z. and Diong, J. and Herbert, R. D. ",
+    Title="{{R}eliability and validity of ultrasound measurements of muscle fascicle length and pennation in humans: a systematic review}",
+    Journal="J. Appl. Physiol.",
+    Year="2013",
+    Volume="114",
+    Pages="769--769",
+}
+
+% Calin-Jagerman2019 
+@Article{Calin-Jagerman2019,
+    Author="Calin-Jageman, R. J. and Cumming, G. ",
+    Title="{{E}stimation for better inference in neuroscience}",
+    Journal="eNeuro",
+    Year="2019",
+    Volume=" ",
+    Pages="ENEURO.0205-19.2019",
+}
+
+% Tijs2018
+@Article{Tijs2018,
+   Author="Tijs, C.  and Bernabei, M.  and van Die?n, J. H.  and Maas, H. ",
+   Title="{{M}yofascial loads can occur without fascicle length changes}",
+   Journal="Integr. Comp. Biol.",
+   Year="2018",
+   Volume="58",
+   Pages="251--260",
+}
+
+% Tijs2014 
+@Article{Tijs2016,
+   Author="Tijs, C.  and van Dieen, J. H.  and Baan, G. C.  and Maas, H. ",
+   Title="{{S}ynergistic co-activation increases the extent of mechanical interaction between rat ankle plantar-flexors}",
+   Journal="Front. Physiol.",
+   Year="2016",
+   Volume="7",
+   Pages="414"
+}
+
+% Tijs2014 
+@Article{Tijs2014,
+   Author="Tijs, C.  and van Dieen, J. H.  and Baan, G. C.  and Maas, H. ",
+   Title="{{T}hree-dimensional ankle moments and nonlinear summation of rat triceps surae muscles}",
+   Journal="PLoS ONE",
+   Year="2014",
+   Volume="9",
+   Pages="e111595"
+}
+
+% Tijs2015 
+@Article{Tijs2015,
+   Author="Tijs, C.  and van Dieen, J. H.  and Maas, H. ",
+   Title="{{E}ffects of epimuscular myofascial force transmission on sarcomere length of passive muscles in the rat hindlimb}",
+   Journal="Physiol. Rep.",
+   Year="2015",
+   Volume="3",
+   Pages="e12608"
+}
+
+% Diong2019  
+@Article{Diong2019,
+   Author="Diong, J.  and H\'{e}roux, M. E.  and Gandevia, S. C.  and Herbert, R. D. ",
+   Title="{{M}inimal force transmission between human thumb and index finger muscles under passive conditions}",
+   Journal="PLoS ONE",
+   Year="2019",
+   Volume="14",
+   Pages="e0212496"
+}
+
+% Maas2019
+@Article{Maas2019,
+   Author="Maas, H. ",
+   Title="{{S}ignificance of epimuscular myofascial force transmission under passive muscle conditions}",
+   Journal="J. Appl. Physiol.",
+   Year="2019",
+   Volume="126",
+   Number="5",
+   Pages="1465--1473",
+   Month="05"
+}
+
+%Yoshitake2018 
+@Article{Yoshitake2018,
+   Author="Yoshitake, Y.  and Uchida, D.  and Hirata, K.  and Mayfield, D. L.  and Kanehisa, H. ",
+   Title="{{M}echanical interaction between neighboring muscles in human upper limb: {E}vidence for epimuscular myofascial force transmission in humans}",
+   Journal="J Biomech",
+   Year="2018",
+   Volume="74",
+   Pages="150--155",
+}
+
+%Bojsen-Moller2010 
+@Article{Bojsen-Moller2010,
+   Author="Bojsen-Moller, J.  and Schwartz, S.  and Kalliokoski, K. K.  and Finni, T.  and Magnusson, S. P. ",
+   Title="{{I}ntermuscular force transmission between human plantarflexor muscles in vivo}",
+   Journal="J. Appl. Physiol.",
+   Year="2010",
+   Volume="109",
+   Number="6",
+   Pages="1608--1618",
+   Month="Dec"
+}
+
+%Freitas2019 
+@Article{Freitas2019,
+   Author="Freitas, S. R.  and Antunes, A.  and Salmon, P.  and Mendes, B.  and Firmino, T.  and Cruz-Montecinos, C.  and Cerda, M.  and Vaz, J. R. ",
+   Title="{{D}oes epimuscular myofascial force transmission occur between the human quadriceps muscles in vivo during passive stretching?}",
+   Journal="J Biomech",
+   Year="2019",
+   Volume="83",
+   Pages="91--96",
+   Month="01"
+}
+
+%Huijing2011 
+@Article{Huijing2011,
+   Author="Huijing, P. A.  and Yaman, A.  and Ozturk, C.  and Yucesoy, C. A. ",
+   Title="{{E}ffects of knee joint angle on global and local strains within human triceps surae muscle: {M}{R}{I} analysis indicating in vivo myofascial force transmission between synergistic muscles}",
+   Journal="Surg Radiol Anat",
+   Year="2011",
+   Volume="33",
+   Number="10",
+   Pages="869--879",
+   Month="Dec"
+}
+
+%Carvalhais2013
+@Article{Carvalhais2013,
+   Author="Carvalhais, V. O.  and Ocarino, J. d. e.  M.  and Araujo, V. L.  and Souza, T. R.  and Silva, P. L.  and Fonseca, S. T. ",
+   Title="{{M}yofascial force transmission between the latissimus dorsi and gluteus maximus muscles: an in vivo experiment}",
+   Journal="J Biomech",
+   Year="2013",
+   Volume="46",
+   Number="5",
+   Pages="1003--1007",
+   Month="Mar"
+}
+
+%Maas2010 
+@Article{Maas2010,
+   Author="Maas, H.  and Sandercock, T. G. ",
+   Title="{{F}orce transmission between synergistic skeletal muscles through connective tissue linkages}",
+   Journal="J. Biomed. Biotechnol.",
+   Year="2010",
+   Volume="2010",
+   Pages="575672"
+}
+
+%Smilde2016 
+@Article{Smilde2016,
+   Author="Smilde, H. A.  and Vincent, J. A.  and Baan, G. C.  and Nardelli, P.  and Lodder, J. C.  and Mansvelder, H. D.  and Cope, T. C.  and Maas, H. ",
+   Title="{{C}hanges in muscle spindle firing in response to length changes of neighboring muscles}",
+   Journal="J. Neurophysiol.",
+   Year="2016",
+   Volume="115",
+   Number="6",
+   Pages="3146--3155",
+   Month="06"
+}
+
+%Smilde2016
+@Article{Smilde2016,
+   Author="Smilde, H. A.  and Vincent, J. A.  and Baan, G. C.  and Nardelli, P.  and Lodder, J. C.  and Mansvelder, H. D.  and Cope, T. C.  and Maas, H. ",
+   Title="{{C}hanges in muscle spindle firing in response to length changes of neighboring muscles}",
+   Journal="J. Neurophysiol.",
+   Year="2016",
+   Volume="115",
+   Number="6",
+   Pages="3146--3155",
+   Month="06"
+}
+
+%Heroux2020
+@Article{Heroux2020,
+   Author="H\'{e}eroux, M.E. and Anderman, I. and Nykvist Vouis, S. and Diong, J. and Stubbs, P.W. and Herbert, R.D.",
+   Title="{{H}istory-dependence of muscle slack length in humans: effects of contraction intensity, stretch amplitude and time}",
+   Journal="J. Appl. Physiol.",
+   Year="In Press",
+   Volume="https://doi.org/10.1152/japplphysiol.00106.2020",
+   Number="",
+   Pages="",
+}
+
+%Kozinc2020 
+@Article{Kozinc2020,
+   Author="Kozinc, Z.  and Sarabon, N. ",
+   Title="{{S}hear-wave elastography for assessment of trapezius muscle stiffness: {R}eliability and association with low-level muscle activity}",
+   Journal="PLoS ONE",
+   Year="2020",
+   Volume="15",
+   Number="6",
+   Pages="e0234359"
+}
+
+%Wang2020 
+@Article{Wang2020,
+   Author="Wang, X.  and Hu, Y.  and Zhu, J.  and Gao, J.  and Chen, S.  and Liu, F.  and Li, W.  and Liu, Y.  and Ariun, B. ",
+   Title="{{E}ffect of acquisition depth and precompression from probe and couplant on shear wave elastography in soft tissue: an in vitro and in vivo study}",
+   Journal="Quant Imaging Med Surg",
+   Year="2020",
+   Volume="10",
+   Number="3",
+   Pages="754--765",
+   Month="Mar"
+}
+
+% Sarabon2019 
+@Article{Sarabon2019,
+   Author="Sarabon, N.  and Kozinc, Z.  and Podrekar, N. ",
+   Title="{{U}sing shear-wave elastography in skeletal muscle: {A} repeatability and reproducibility study on biceps femoris muscle}",
+   Journal="PLoS ONE",
+   Year="2019",
+   Volume="14",
+   Number="8",
+   Pages="e0222008"
+}
+
+% Graham2021
+@Article{Graham2021,
+   Author="Graham, H. K.  and Thomason, P.  and Willoughby, K.  and Hastings-Ison, T.  and Stralen, R. V.  and Dala-Ali, B.  and Wong, P.  and Rutz, E. ",
+   Title="{{M}usculoskeletal {P}athology in {C}erebral {P}alsy: {A} {C}lassification {S}ystem and {R}eliability {S}tudy}",
+   Journal="Children (Basel)",
+   Year="2021",
+   Volume="8",
+   Number="3",
+}
+
+% Ruby2019 
+@Article{Ruby2019,
+   Author="Ruby, L.  and Mutschler, T.  and Martini, K.  and Klingmuller, V.  and Frauenfelder, T.  and Rominger, M. B.  and Sanabria, S. J. ",
+   Title="{{W}hich confounders have the largest impact in shear wave elastography of muscle and how can they be minimized? {A}n elasticity phantom, ex vivo porcine muscle and volunteer study using a commercially available system}",
+   Journal="Ultrasound Med Biol",
+   Year="2019",
+   Volume="45",
+   Number="10",
+   Pages="2591--2611",
+}
+
+%Hoang2007 
+@Article{Hoang2007,
+   Author="Hoang, P. D.  and Herbert, R. D.  and Todd, G.  and Gorman, R. B.  and Gandevia, S. C. ",
+   Title="{{P}assive mechanical properties of human gastrocnemius muscle tendon units, muscle fascicles and tendons in vivo}",
+   Journal="J. Exp. Biol.",
+   Year="2007",
+   Volume="210",
+   Number="Pt 23",
+   Pages="4159--4168",
+   Month="Dec"
+}
+
+% 11490120 
+@Article{Chleboun2001,
+   Author="Chleboun, G. S.  and France, A. R.  and Crill, M. T.  and Braddock, H. K.  and Howell, J. N. ",
+   Title="{{I}n vivo measurement of fascicle length and pennation angle of the human biceps femoris muscle}",
+   Journal="Cells Tissues Organs (Print)",
+   Year="2001",
+   Volume="169",
+   Number="4",
+   Pages="401--409"
+}
+
+%Button2013 
+@Article{Button2013,
+   Author="Button, K. S.  and Ioannidis, J. P.  and Mokrysz, C.  and Nosek, B. A.  and Flint, J.  and Robinson, E. S.  and Munafò, M. R. ",
+   Title="{{P}ower failure: why small sample size undermines the reliability of neuroscience}",
+   Journal="Nat Rev Neurosci",
+   Year="2013",
+   Volume="14",
+   Number="5",
+   Pages="365--376",
+}
+
+%Le Sant2019 
+@Article{LeSant2019,
+   Author="Le Sant, G.  and Gross, R.  and Hug, F.  and Nordez, A. ",
+   Title="{{I}nfluence of low muscle activation levels on the ankle torque and muscle shear modulus during plantar flexor stretching}",
+   Journal="J Biomech",
+   Year="2019",
+   Volume="93",
+   Pages="111--117",
+}
+
+%Ioannidis2005 
+@Article{Ioannidis2005,
+   Author="Ioannidis, J. P. ",
+   Title="{{W}hy most published research findings are false}",
+   Journal="PLoS Med",
+   Year="2005",
+   Volume="2",
+   Number="8",
+   Pages="e124",
+}
+
+%Halsey2015 
+@Article{Halsey2015,
+   Author="Halsey, L. G.  and Curran-Everett, D.  and Vowler, S. L.  and Drummond, G. B. ",
+   Title="{{T}he fickle {P} value generates irreproducible results}",
+   Journal="Nat Methods",
+   Year="2015",
+   Volume="12",
+   Number="3",
+   Pages="179--185",
+}
+
+% Yanase2021 
+@Article{Yanase2021,
+   Author="Yanase, K.  and Yagi, M.  and Nakao, S.  and Motomura, Y.  and Umehara, J.  and Hirono, T.  and Komamura, T.  and Miyakoshi, K.  and Ibuki, S.  and Ichihashi, N. ",
+   Title="{{E}pimuscular myofascial force transmission from biarticular rectus femoris elongation increases shear modulus of monoarticular quadriceps muscles}",
+   Journal="J Biomech",
+   Year="2021",
+   Volume="122",
+   Pages="110421",
+}
+
+%Diong2019
+@Article{Diong2019,
+   Author="Diong, J.  and Gandevia, S. C.  and Nguyen, D.  and Foo, Y.  and Kastre, C.  and Andersson, K.  and Butler, J. E.  and Héroux, M. E. ",
+   Title="{{S}mall amounts of involuntary muscle activity reduce passive joint range of motion}",
+   Journal="J Appl Physiol",
+   Year="2019",
+   Volume="127",
+   Pages="229--234",
+}

example/blank_article.md

@@ -0,0 +1,78 @@
+# TITLE OF PAPER
+
+First A. Author^1^, Second B. Author^2^, Third Author^3^, Last  Author^1,2,3^
+
+
+1. First affiliation
+2. Second affiliation
+3. Third affiliation
+
+\
+\
+
+**Corresponding author** \
+Dr. First A. Author \
+University of Pandoc \
+42 Printers Lane \
+2031, Randwick, NSW, Australia \
+email: fa.author@pandoc.au \
+ph: +61-1-2345-6789
+\
+\
+\
+**Keywords:** Add keywords \
+**Running title:** Running title \
+**Wordcount:** n. of words
+
+\newpage
+
+# Abstract
+Add abstract text here.
+
+\newpage
+
+# Introduction
+Add introduction text here.
+
+# Methods
+
+Add methods text here.
+
+# Results
+
+Add results text here.
+
+# Discussion
+
+Add discussion text here.
+
+\newpage
+
+# Acknowledgements
+Add acknowledgements here.
+
+# Funding
+Add funding details here.
+
+# Author Contributions
+Add author contributions here.
+
+\clearpage
+
+Outcome      Blue hair     Red hair
+----------   -----------   ------------
+force (N)    4 ± 2         6 ± 3
+distance (m) 552 ± 53      590 ± 43
+height (cm)  170 ± 29      154 ± 18
+speed (m/s)  0.9 ± 0.02    1.1 ± 0.01
+
+
+Table: A table legend; values are mean ± SD Markdown
+
+\clearpage
+
+![Figure caption.](img/figure1.png){ width=16cm }
+
+\clearpage
+
+# References

example/html_templates/easy_template.html

@@ -0,0 +1,124 @@
+<!doctype html>
+<html $if(lang)$ lang="$lang$" $endif$>
+<head>
+    
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+        <!--[if lt IE 9]>
+                <script src="http://css3-mediaqueries-js.googlecode.com/svn/trunk/css3-mediaqueries.js"></script>
+        <![endif]-->
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta http-equiv="Content-Style-Type" content="text/css" />
+
+    <!-- <link rel="stylesheet" type="text/css" href="template.css" /> -->
+    <link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/template.css" />
+
+    <link href="https://vjs.zencdn.net/5.4.4/video-js.css" rel="stylesheet" />
+
+    <script src="https://code.jquery.com/jquery-2.2.1.min.js"></script>
+    <!-- <script type='text/javascript' src='menu/js/jquery.cookie.js'></script> -->
+    <!-- <script type='text/javascript' src='menu/js/jquery.hoverIntent.minified.js'></script> -->
+    <!-- <script type='text/javascript' src='menu/js/jquery.dcjqaccordion.2.7.min.js'></script> -->
+
+    <!-- <link href="menu/css/skins/blue.css" rel="stylesheet" type="text/css" /> -->
+    <!-- <link href="menu/css/skins/graphite.css" rel="stylesheet" type="text/css" /> -->
+    <!-- <link href="menu/css/skins/grey.css" rel="stylesheet" type="text/css" /> -->
+  
+    <!-- <script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> -->
+        
+  
+    <!-- <script src="script.js"></script> -->
+  
+    <!-- <script src="jquery.sticky-kit.js "></script> -->
+    <script type='text/javascript' src='https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/js/jquery.cookie.js'></script>
+    <script type='text/javascript' src='https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/js/jquery.hoverIntent.minified.js'></script>
+    <script type='text/javascript' src='https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/js/jquery.dcjqaccordion.2.7.min.js'></script>
+
+    <link href="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/css/skins/blue.css" rel="stylesheet" type="text/css" />
+    <link href="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/css/skins/graphite.css" rel="stylesheet" type="text/css" />
+    <link href="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/menu/css/skins/grey.css" rel="stylesheet" type="text/css" />
+    <link href="https://cdn.jsdelivr.net/gh/ryangrose/easy-pandoc-templates@948e28e5/css/elegant_bootstrap.css" rel="stylesheet" type="text/css" />
+  
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.4/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+  
+    <script src="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/script.js"></script>
+  
+    <script src="https://cdn.jsdelivr.net/gh/diversen/pandoc-bootstrap-adaptive-template@959c3622/jquery.sticky-kit.js"></script>
+    <meta name="generator" content="pandoc" />
+$for(author-meta)$
+  <meta name="author" content="$author-meta$" />
+$endfor$
+$if(date-meta)$
+  <meta name="date" content="$date-meta$" />
+$endif$
+  <title>$if(title-prefix)$$title-prefix$ - $endif$$pagetitle$</title>
+  <style type="text/css">code{white-space: pre;}</style>
+$if(quotes)$
+  <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
+$endif$
+$if(highlighting-css)$
+  <style type="text/css">
+$highlighting-css$
+  </style>
+$endif$
+$for(css)$
+  <link rel="stylesheet" href="$css$" $if(html5)$$else$type="text/css" $endif$/>
+$endfor$
+$if(math)$
+  $math$
+$endif$
+$for(header-includes)$
+  $header-includes$
+$endfor$
+</head>
+<body>
+
+    
+  $if(title)$
+  <div class="navbar navbar-static-top">
+    <div class="navbar-inner">
+      <div class="container">
+        <span class="doc-title">$title$</span>
+        <ul class="nav pull-right doc-info">
+          $for(author)$
+          <li><p class="navbar-text">$author$</p></li>
+          $endfor$
+          $if(date)$
+          <li><p class="navbar-text">$date$</p></li>
+          $endif$
+        </ul>
+      </div>
+    </div>
+  </div>
+  $endif$
+  <div class="container">
+    <div class="row">
+      $if(toc)$
+      <div id="$idprefix$TOC" class="span3">
+        <div class="well toc">
+
+        $toc$
+
+        </div>
+      </div>
+      $endif$
+      <div class="span$if(toc)$9$else$12$endif$">
+
+      $if(abstract)$
+          <H1>$abstract-title$</H1>
+          $abstract$
+      $endif$
+
+      $for(include-before)$
+      $include-before$
+      $endfor$
+$body$
+      $for(include-after)$
+      $include-after$
+      $endfor$
+      </div>
+    </div>
+  </div>
+  <script src="https://vjs.zencdn.net/5.4.4/video.js"></script>
+
+</body>
+</html>

example/html_templates/elegant_bootstrap.css

@@ -0,0 +1,482 @@
+/*
+ * I add this to html files generated with pandoc.
+ */
+
+html {
+  font-size: 100%;
+  overflow-y: scroll;
+  -webkit-text-size-adjust: 100%;
+  -ms-text-size-adjust: 100%;
+}
+
+body {
+  color: #444;
+  font-family: Georgia, Palatino, 'Palatino Linotype', Times, 'Times New Roman', serif;
+  font-size: 12px;
+  line-height: 1.8;
+  background: #fefefe;
+}
+
+a {
+  color: #0645ad;
+  text-decoration: none;
+}
+
+a:visited {
+  color: #0b0080;
+}
+
+a:hover {
+  color: #06e;
+}
+
+a:active {
+  color: #faa700;
+}
+
+a:focus {
+  outline: thin dotted;
+}
+
+*::-moz-selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #000;
+}
+
+*::selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #000;
+}
+
+a::-moz-selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #0645ad;
+}
+
+a::selection {
+  background: rgba(255, 255, 0, 0.3);
+  color: #0645ad;
+}
+
+p {
+  margin: 1em 0;
+}
+
+img {
+  max-width: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+  color: #111;
+  line-height: 125%;
+  /* margin-top: 2em; */
+  font-weight: normal;
+}
+
+h4, h5, h6 {
+  font-weight: bold;
+}
+
+h1 {
+  font-size: 2.5em;
+}
+
+h2 {
+  font-size: 2em;
+}
+
+h3 {
+  font-size: 1.5em;
+}
+
+h4 {
+  font-size: 1.2em;
+}
+
+h5 {
+  font-size: 1em;
+}
+
+h6 {
+  font-size: 0.9em;
+}
+
+blockquote {
+  color: #666666;
+  margin: 0;
+  padding-left: 3em;
+  border-left: 0.5em #EEE solid;
+}
+
+hr {
+  display: block;
+  height: 2px;
+  border: 0;
+  border-top: 1px solid #aaa;
+  border-bottom: 1px solid #eee;
+  margin: 1em 0;
+  padding: 0;
+}
+
+pre, code, kbd, samp {
+  color: #000;
+  font-family: monospace, monospace;
+  _font-family: 'courier new', monospace;
+  font-size: 0.98em;
+}
+
+pre {
+  white-space: pre;
+  white-space: pre-wrap;
+  word-wrap: break-word;
+}
+
+b, strong {
+  font-weight: bold;
+}
+
+dfn {
+  font-style: italic;
+}
+
+ins {
+  background: #ff9;
+  color: #000;
+  text-decoration: none;
+}
+
+mark {
+  background: #ff0;
+  color: #000;
+  font-style: italic;
+  font-weight: bold;
+}
+
+sub, sup {
+  font-size: 75%;
+  line-height: 0;
+  position: relative;
+  vertical-align: baseline;
+}
+
+sup {
+  top: -0.5em;
+}
+
+sub {
+  bottom: -0.25em;
+}
+
+ul, ol {
+  margin: 1em 0;
+  padding: 0 0 0 2em;
+}
+
+li {
+  line-height: inherit;
+}
+
+li p:last-child {
+  margin-bottom: 0;
+}
+
+ul ul, ol ol {
+  margin: .3em 0;
+}
+
+dl {
+  margin-bottom: 1em;
+}
+
+dt {
+  font-weight: bold;
+  margin-bottom: .8em;
+}
+
+dd {
+  margin: 0 0 .8em 2em;
+}
+
+dd:last-child {
+  margin-bottom: 0;
+}
+
+img {
+  border: 0;
+  -ms-interpolation-mode: bicubic;
+  vertical-align: middle;
+}
+
+figure {
+  display: block;
+  text-align: center;
+  margin: 1em 0;
+}
+
+figure img {
+  border: none;
+  margin: 0 auto;
+}
+
+figcaption {
+  font-size: 0.8em;
+  font-style: italic;
+  margin: 0 0 .8em;
+}
+
+table {
+  margin-bottom: 2em;
+  border-bottom: 1px solid #ddd;
+  border-right: 1px solid #ddd;
+  border-spacing: 0;
+  border-collapse: collapse;
+}
+
+table th {
+  padding: .2em 1em;
+  background-color: #eee;
+  border-top: 1px solid #ddd;
+  border-left: 1px solid #ddd;
+}
+
+table td {
+  padding: .2em 1em;
+  border-top: 1px solid #ddd;
+  border-left: 1px solid #ddd;
+  vertical-align: top;
+}
+
+.author {
+  font-size: 1.2em;
+  text-align: center;
+}
+
+@media only screen and (min-width: 480px) {
+  body {
+    font-size: 14px;
+  }
+}
+@media only screen and (min-width: 768px) {
+  body {
+    font-size: 16px;
+  }
+}
+@media print {
+  * {
+    background: transparent !important;
+    color: black !important;
+    filter: none !important;
+    -ms-filter: none !important;
+  }
+
+  body {
+    font-size: 12pt;
+    max-width: 100%;
+  }
+
+  a, a:visited {
+    text-decoration: underline;
+  }
+
+  hr {
+    height: 1px;
+    border: 0;
+    border-bottom: 1px solid black;
+  }
+
+  a[href]:after {
+    content: " (" attr(href) ")";
+  }
+
+  abbr[title]:after {
+    content: " (" attr(title) ")";
+  }
+
+  .ir a:after, a[href^="javascript:"]:after, a[href^="#"]:after {
+    content: "";
+  }
+
+  pre, blockquote {
+    border: 1px solid #999;
+    padding-right: 1em;
+    page-break-inside: avoid;
+  }
+
+  tr, img {
+    page-break-inside: avoid;
+  }
+
+  img {
+    max-width: 100% !important;
+  }
+
+  @page :left {
+    margin: 15mm 20mm 15mm 10mm;
+}
+
+  @page :right {
+    margin: 15mm 10mm 15mm 20mm;
+}
+
+  p, h2, h3 {
+    orphans: 3;
+    widows: 3;
+  }
+
+  h2, h3 {
+    page-break-after: avoid;
+  }
+}
+
+
+
+.Alert,
+.Warning,
+.Error,
+.Success,
+.Note {
+  padding: 11px;
+  margin-bottom: 24px;
+  border-style: solid;
+  border-width: 1px;
+  border-radius: 4px;
+}
+.Alert p,
+.Warning p,
+.Error p,
+.Success p,
+.Note p {
+  margin-top: 0;
+}
+.Alert p:last-child,
+.Warning p:last-child,
+.Error p:last-child,
+.Success p:last-child,
+.Note p:last-child {
+  margin-bottom: 0;
+}
+
+.Alert {
+  color: #224466;
+  background-color: #E2EEF9;
+  border-color: #BAC6D3;
+}
+
+.Warning {
+  color: #4C4A42;
+  background-color: #FFF9EA;
+  border-color: #DFD8C2;
+}
+
+.Error {
+  color: #991111;
+  background-color: #FCDEDE;
+  border-color: #D2B2B2;
+}
+
+.Success {
+  color: #22662C;
+  background-color: #E2F9E5;
+  border-color: #BAD3BE;
+}
+
+.Note {
+  color: #2F363D;
+  background-color: #F6F8FA;
+  border-color: #D5D8DA;
+}
+
+.Alert h1,
+.Alert h2,
+.Alert h3,
+.Alert h4,
+.Alert h5,
+.Alert h6 {
+  color: #224466;
+  margin-bottom: 0;
+}
+
+.Warning h1,
+.Warning h2,
+.Warning h3,
+.Warning h4,
+.Warning h5,
+.Warning h6 {
+  color: #4C4A42;
+  margin-bottom: 0;
+}
+
+.Error h1,
+.Error h2,
+.Error h3,
+.Error h4,
+.Error h5,
+.Error h6 {
+  color: #991111;
+  margin-bottom: 0;
+}
+
+.Success h1,
+.Success h2,
+.Success h3,
+.Success h4,
+.Success h5,
+.Success h6 {
+  color: #22662C;
+  margin-bottom: 0;
+}
+
+.Note h1,
+.Note h2,
+.Note h3,
+.Note h4,
+.Note h5,
+.Note h6 {
+  color: #2F363D;
+  margin-bottom: 0;
+}
+
+.Alert h1:first-child,
+.Alert h2:first-child,
+.Alert h3:first-child,
+.Alert h4:first-child,
+.Alert h5:first-child,
+.Alert h6:first-child {
+  margin-top: 0;
+}
+
+.Warning h1:first-child,
+.Warning h2:first-child,
+.Warning h3:first-child,
+.Warning h4:first-child,
+.Warning h5:first-child,
+.Warning h6:first-child {
+  margin-top: 0;
+}
+
+.Error h1:first-child,
+.Error h2:first-child,
+.Error h3:first-child,
+.Error h4:first-child,
+.Error h5:first-child,
+.Error h6:first-child {
+  margin-top: 0;
+}
+
+.Success h1:first-child,
+.Success h2:first-child,
+.Success h3:first-child,
+.Success h4:first-child,
+.Success h5:first-child,
+.Success h6:first-child {
+  margin-top: 0;
+}
+
+.Note h1:first-child,
+.Note h2:first-child,
+.Note h3:first-child,
+.Note h4:first-child,
+.Note h5:first-child,
+.Note h6:first-child {
+  margin-top: 0;
+}

example/html_templates/fixDefault.css

@@ -0,0 +1,32 @@
+<style>
+
+/* ---
+ * fixDefault.css - A fix to default Pandoc's CSS to be 
+ *    correctly displayed on a VS Code preview window,
+ *    and nicely printed on [digital] paper
+ *
+ * Ramon Solano <ramon.solano@gmail.com>
+ *
+ * usage: 
+ *    pandoc ... -H fixDefault.css ...
+ *
+ * V 1.0, Jul/2021
+ * --- 
+ */
+
+body {
+	font-family: inherit;
+	font-size: inherit;
+	color: inherit;
+}
+
+@media print {
+	html,body {
+		font-size: 10pt;
+	}
+	@page  {  
+		size: auto;
+	} 
+}
+
+</style>

example/html_templates/report.css

@@ -0,0 +1,152 @@
+<style>
+
+/* ---
+ * article.css - A beautiful css to complement Pandoc's own
+ *
+ * Provides:
+ *    - Article-style title and headers
+ *    - Images and tables centered
+ *    - New `<aside>` env (right side)
+ *
+ * Ramon Solano <ramon.solano@gmail.com>
+ *
+ * usage: 
+ *    pandoc ... -H article.css ...
+ * 
+ * V1.0, Jul/2021
+ * ---
+ */
+
+body {
+	max-width: 40em;
+   word-wrap: break-word; 
+}
+
+header p {
+	text-align: center;
+}
+header p.subtitle {
+	font-size: 1.2em;
+	line-height: 1.1em;
+	margin: 0.5em 2em 2em;
+/* 
+	 margin-top: 0.5em;
+	 margin-bottom: 2em;
+ */
+}
+header p.author {
+	font-size: 1.1em;
+	line-height: 0.5em;
+	font-variant-caps: small-caps;
+}
+header p.date {
+	font-size: 0.95em;
+	margin: 3em;
+}
+
+header h1 {
+	 line-height: 1em;
+	 margin-bottom: 0em;
+}
+/* abstract header */
+h3:first-child, #abstract {
+	font-size: 1.2em;
+	text-align: center;
+	margin: 0.5em ;
+}
+
+/* abstract paragraph */
+h3:first-child + p, #abstract + p {
+	font-size: 0.9em;
+	margin: 0em 4em;
+	margin-bottom: 3em;
+}
+
+h1 {
+  font-size: 1.6em;
+}
+h2 {
+  font-size: 1.3em;
+}
+h3 {
+  font-size: 1.1em;
+  font-style: italic;
+}
+h1, h2, h3, h4 {
+  margin-top: 0.95em;
+  margin-bottom: 0.80em;
+}
+
+/* Justify and hyphenate all paragraphs */
+p {
+  text-align: justify;
+}
+    
+/* center tables */
+table {
+	display: table;
+	width: auto;
+	margin-left: auto;
+	margin-right: auto;
+}
+table caption {
+	font-size: 0.95em;
+}
+
+/* centered figures  */
+figure {
+  text-align: center;
+  margin-top: 1.5em;
+  margin-bottom: 1.5em;
+}
+figcaption {
+  font-size: 0.95em;
+}
+
+/* lists: increase left margins */
+ul, ol {
+  padding: 0 0 0 3em;
+}    
+
+/* new style: objects (figures, text) right side */
+aside {
+  font-size: 0.9em;
+  width: 33%;
+  padding: 0 0 0 .8em;
+  margin: 1em 0 1em 1em;
+  float: right;
+}
+aside > *:first-child {
+  margin-top: 0;
+}
+aside > *:last-child {
+  margin-bottom: 0;
+}
+
+pre {
+  font-size: 0.87em;
+  line-height: 1.2em;
+  border: 1px solid #cccccc;
+  background: #f5f2f0;
+  padding: .7em;   
+}
+
+:not(pre) > code[class*="sourceCode"],
+pre[class*="sourceCode"] {
+  background: #f5f2f0;
+}
+
+code {
+  color: #92000c;
+  font-size: .9em;
+}
+
+pre code {
+  color: unset;
+}
+
+a {
+  color: #0050a0;
+}
+
+</style>

example/letter.md

@@ -0,0 +1,35 @@
+---
+#Info
+author: Pierre-Yves Barriat
+subject: Lorem ipsum
+city: Louvain-la-Neuve
+from:
+- Place Louis Pasteur 3 - 1348 Louvain-la-Neuve
+affiliation1: Université catholique de Louvain - Earth and Life Institute
+affiliation2: Earth and Climate - ELIC
+#PerLetter Info
+to:
+- Lorem ipsum
+- Lorem ipsum dolor
+- sit amet, consectetur
+- adipiscing elit - 1348 Louvain-la-Neuve
+#Settings
+mainfont: Ubuntu
+altfont: Ubuntu
+monofont: Cairo
+lang: fr-FR
+fontsize: 10pt
+geometry: a4paper, left=25mm, right=25mm, top=50mm, bottom=25mm
+page-background: "assets/garde.pdf"
+page-background-opacity: "0.8"
+#customdate: 1838-8-9
+signature: assets/signature.png
+---
+
+## Neque porro quisquam est qui dolorem ipsum quia dolor sit amet
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent quis tortor sit amet urna facilisis sollicitudin. Ut efficitur, enim vitae sodales aliquet, odio dui consectetur nisl, quis facilisis mauris est ut odio. Proin convallis erat sit amet arcu pellentesque blandit. Aliquam at turpis vestibulum, iaculis nibh nec, eleifend ex. Vestibulum porta nec dolor ac porttitor. Nullam maximus vitae lacus ac hendrerit. Pellentesque aliquet, est nec finibus pharetra, nulla arcu malesuada orci, eget consequat lacus sapien eget libero. Phasellus dapibus turpis sed euismod sodales. Proin rhoncus odio non magna finibus, quis mollis enim lacinia. In hac habitasse platea dictumst. In eget neque blandit, dapibus lacus euismod, varius ligula. Praesent at dui ut eros gravida mollis. Ut viverra lorem risus.
+
+Cras ut congue sem. Mauris ex nulla, dapibus eu varius et, commodo eget dolor. Nunc velit ligula, sagittis placerat feugiat a, tincidunt et purus. Quisque eu convallis massa. Curabitur in sollicitudin felis. Phasellus mattis tincidunt ultricies. Sed sodales semper lorem quis semper. Quisque sollicitudin cursus dolor, quis fringilla magna lacinia eu. Donec at sagittis metus. Ut et lectus justo. Vestibulum sollicitudin commodo iaculis. In in elit nunc. Ut eget laoreet lorem.
+
+Your devoted friend,

example/makefile

@@ -0,0 +1,10 @@
+TEX = pandoc
+FLAGS = --pdf-engine=xelatex
+
+src1 = assets/letter.latex example_letter.md
+op1 = example_letter
+
+all : $(op1).pdf
+
+$(op1).pdf : $(src1)
+	$(TEX) $(filter-out $<,$^ ) -o $@ --template=$< $(FLAGS)

example/report.md

@@ -0,0 +1,64 @@
+---
+title: My Great Report
+subtitle: First finding of something extraordinary
+author: Pierre-Yves Barriat
+#date: "15 avril 2022"
+lang: "en"
+fontsize: 11pt
+bibliography: "assets/MyLib.bib"
+---
+
+### Abstract
+
+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nost commodo consequat.
+
+## 1. Introduction
+ 
+ Ullamco laboris nisi ut aliquip ex ea commodo consequat [@hoffmann_platon_1951]. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. 
+
+## 2. Tables
+
+Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas [@temple_beginnings_1993].
+
+: Table 1.1:  Demonstration of simple table syntax.
+
+Default		| Center	| Right 
+-----------	|:------:|-----:
+Tires			| Pc		| 12.50
+Petrol		| Br		| 456.10
+
+
+## 3. Figures
+
+Sed quia consequuntur magni dolores eos qui ratione voluptatem sequi nesciunt. Neque porro quisquam est, qui dolorem ipsum quia dolor sit.
+
+ ![Fig. 1 - A sample figure](http://www.butleranalytics.com/wp-content/uploads/2014/07/optimizationw.jpg){width=60%}
+
+
+## 4. Equations
+
+The 0-dimension Energy Balance Model (EBM) or global EBM:
+
+$$(1 - \alpha)\frac{S_0}{4} = \sigma T^4 \qquad (1)$$
+
+The one-dimension EBM or zonal EBM:
+
+$$T_{i} = \frac{{\ S}_{i}\left( 1 - \alpha(T_{i}) \right) + K\overline{T} - A}{B + K} \qquad (2)$$
+
+- $T_i =$ the surface temperature at latitude band $i$
+- $S_i =$ the mean annual solar radiation at latitude $i$
+- $K =$ the transport coefficient (here set to 3.81 $Wm^{-2 \ \circ}C^{-1}$)
+- $A$ and $B$ are constants governing the longwave radiation loss (here taking values $A = 204.0 \ Wm^{-2}$ and $B = 2.17 Wm^{-2 \ \circ} C^{-1}$)
+- $\overline{T} =$ the global mean surface temperature
+- $\alpha(T_{i}) =$ the albedo at latitude i, and it can be formulated by:
+
+$$
+\alpha (T_i)=
+\begin{cases}
+0.5 & \quad \text{if \ $T{i} \leq 270K$}\\
+0.5 - 0.25 * \frac{T-270}{20} & \quad \text{if \ $270K \leq T{i} \leq 290K$}\\
+0.25 & \quad \text{if \ $T{i} \geq 290K$}\\
+\end{cases}
+$$
+
+## References

example/slides.md

@@ -0,0 +1,346 @@
+---
+title: Marp slide deck
+description: An example slide deck created by Marp CLI
+author: Yuki Hattori
+keywords: marp,marp-cli,slide
+#backgroundImage: url('0.png')
+#_backgroundImage: url('4.png')
+footer: 25/04/2022
+_footer: ""
+
+#url: https://marp.app/
+#image: https://marp.app/og-image.jpg
+# default, gaia, uncover
+theme: default
+paginate: true
+_paginate: false
+
+# Light theme all slides
+# First slide, Dark theme for title slide, Title slide style
+#class: invert
+#_class:
+#  - invert
+#  - lead
+
+# Nice preview for the VS Code extension
+marp: true
+---
+
+Marp
+===
+
+![h:250](https://avatars1.githubusercontent.com/u/20685754?v=4)
+
+##### Markdown presentation ecosystem
+
+###### by Marp Team ([@marp-team][marp-team])
+
+[marp-team]: https://github.com/marp-team
+[marpit]: https://github.com/marp-team/marpit
+[marp-core]: https://github.com/marp-team/marp-core
+[marp-cli]: https://github.com/marp-team/marp-cli
+[marp-vscode]: https://github.com/marp-team/marp-vscode
+
+---
+
+# Features
+
+- :memo: **Write slide deck with plain Markdown** (CommonMark)
+- :factory: Built on [Marpit framework][marpit]: A brand-new skinny framework for creating slide deck
+- :gear: [Marp Core][marp-core]: Easy to start using the core engine and built-in themes via npm
+- :tv: [Marp CLI][marp-cli]: Convert Markdown into HTML, PDF, PPTX, and images
+* :vs: [Marp for VS Code][marp-vscode]: Live-preview your deck while editting
+* and more...
+
+---
+
+# How to write slides?
+
+Split pages by horizontal ruler (e.g. `---`). It's very simple.
+
+```markdown
+# Slide 1
+
+foobar
+
+---
+
+# Slide 2
+
+foobar
+```
+
+---
+
+# Directives
+
+Marp has extended syntax called **"Directives"** to support creating beautiful slides.
+
+Insert front-matter to the top of Markdown:
+
+```
+---
+theme: default
+---
+```
+
+or HTML comment to anywhere:
+
+```html
+<!-- theme: default -->
+```
+
+https://marpit.marp.app/directives
+
+---
+
+## [Global directives](https://marpit.marp.app/directives?id=global-directives)
+
+- `theme`: Choose theme
+- `size`: Choose slide size from `16:9` and `4:3` *(except Marpit framework)*
+- [`headingDivider`](https://marpit.marp.app/directives?id=heading-divider): Instruct to divide slide pages at before of specified heading levels
+
+```
+---
+theme: gaia
+size: 4:3
+---
+
+# Content
+```
+
+> Marp can use [built-in themes in Marp Core](https://github.com/marp-team/marp-core/tree/master/themes#readme): `default`, `gaia`, and `uncover`.
+
+---
+
+## [Local directives](https://marpit.marp.app/directives?id=local-directives)
+
+These are the setting value per slide pages.
+
+- `paginate`: Show pagination by set `true`
+- `header`: Specify the contents for header
+- `footer`: Specify the contents for footer
+- `class`: Set HTML class for current slide
+- `color`: Set text color
+- `backgroundColor`: Set background color
+
+---
+
+### Spot directives
+
+Local directives would apply to **defined page and following pages**.
+
+They can apply to single page by using underscore prefix such as `_class`.
+
+![bg right 95%](https://marpit.marp.app/assets/directives.png)
+
+---
+
+### Example
+
+This page is using invert color scheme [defined in Marp built-in theme](https://github.com/marp-team/marp-core/tree/master/themes#readme).
+
+<!-- _class: invert -->
+
+```html
+<!-- _class: invert -->
+```
+
+---
+
+# [Image syntax](https://marpit.marp.app/image-syntax)
+
+You can resize image size and apply filters through keywords: `width` (`w`), `height` (`h`), and filter CSS keywords.
+
+```markdown
+![width:100px height:100px](image.png)
+```
+
+```markdown
+![blur sepia:50%](filters.png)
+```
+
+Please refer [resizing image syntax](https://marpit.marp.app/image-syntax?id=resizing-image) and [a list of CSS filters](https://marpit.marp.app/image-syntax?id=image-filters).
+
+![w:100px h:100px](https://avatars1.githubusercontent.com/u/20685754?v=4) ![w:100 h:100 blur sepia:50%](https://avatars1.githubusercontent.com/u/20685754?v=4)
+
+---
+
+# [Background image](https://marpit.marp.app/image-syntax?id=slide-backgrounds)
+
+You can set background image for a slide by using `bg` keyword.
+
+```markdown
+![bg opacity](https://yhatt-marp-cli-example.netlify.com/assets/gradient.jpg)
+```
+
+![bg opacity](https://yhatt-marp-cli-example.netlify.com/assets/gradient.jpg)
+
+---
+
+## Multiple backgrounds ([Marpit's advanced backgrounds](https://marpit.marp.app/image-syntax?id=advanced-backgrounds))
+
+Marp can use multiple background images.
+
+```markdown
+![bg blur:3px](https://fakeimg.pl/800x600/fff/ccc/?text=A)
+![bg blur:3px](https://fakeimg.pl/800x600/eee/ccc/?text=B)
+![bg blur:3px](https://fakeimg.pl/800x600/ddd/ccc/?text=C)
+```
+
+Also can change alignment direction by including `vertical` keyword.
+
+![bg blur:3px](https://fakeimg.pl/800x600/fff/ccc/?text=A)
+![bg blur:3px](https://fakeimg.pl/800x600/eee/ccc/?text=B)
+![bg blur:3px](https://fakeimg.pl/800x600/ddd/ccc/?text=C)
+
+---
+
+## [Split background](https://marpit.marp.app/image-syntax?id=split-backgrounds)
+
+Marp can use [Deckset](https://docs.deckset.com/English.lproj/Media/01-background-images.html#split-slides) style split background(s).
+
+Make a space for background by `bg` + `left` / `right` keywords.
+
+```markdown
+![bg right](image.jpg)
+```
+
+![bg right](https://images.unsplash.com/photo-1568488789544-e37edf90eb67?crop=entropy&cs=tinysrgb&fit=crop&fm=jpg&h=720&ixlib=rb-1.2.1&q=80&w=640)
+
+<!-- _footer: "*Photo by [Mohamed Nohassi](https://unsplash.com/@coopery?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText) on [Unsplash](https://unsplash.com/?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText)*" -->
+
+---
+
+## [Fragmented list](https://marpit.marp.app/fragmented-list)
+
+Marp will parse a list with asterisk marker as the fragmented list for appearing contents one by one. (_**Only for exported HTML** by [Marp CLI][marp-cli] / [Marp for VS Code][marp-vscode]_)
+
+```markdown
+# Bullet list
+
+- One
+- Two
+- Three
+
+---
+
+# Fragmented list
+
+* One
+* Two
+* Three
+```
+
+---
+
+## Math typesetting (only for [Marp Core][marp-core])
+
+[KaTeX](https://katex.org/) math typesetting such as $ax^2+bc+c$ can use with [Pandoc's math syntax](https://pandoc.org/MANUAL.html#math).
+
+$$I_{xx}=\int\int_Ry^2f(x,y)\cdot{}dydx$$
+
+```tex
+$ax^2+bc+c$
+```
+```tex
+$$I_{xx}=\int\int_Ry^2f(x,y)\cdot{}dydx$$
+```
+
+---
+
+## Auto-scaling (only for [Marp Core][marp-core])
+
+*Several built-in themes* are supported auto-scaling for code blocks and math typesettings.
+
+```text
+Too long code block will be scaled-down automatically. ------------>
+```
+```text
+Too long code block will be scaled-down automatically. ------------------------>
+```
+```text
+Too long code block will be scaled-down automatically. ------------------------------------------------>
+```
+
+---
+
+##### <!--fit--> Auto-fitting header (only for [Marp Core][marp-core])
+##### <!--fit--> is available by annotating `<!--fit-->` in headings.
+
+<br />
+
+```html
+## <!--fit--> Auto-fitting header (only for Marp Core)
+```
+
+---
+
+## [Theme CSS](https://marpit.marp.app/theme-css)
+
+Marp uses `<section>` as the container of each slide. And others are same as styling for plain Markdown. The customized theme can use in [Marp CLI][marp-cli] and [Marp for VS Code][marp-vscode].
+
+```css
+/* @theme your-theme */
+@import 'default';
+section {
+  /* Specify slide size */
+  width: 960px;
+  height: 720px;
+}
+h1 {
+  font-size: 30px;
+  color: #c33;
+}
+```
+
+---
+
+## [Tweak style in Markdown](https://marpit.marp.app/theme-css?id=tweak-style-through-markdown)
+
+`<style>` tag in Markdown will work in the context of theme CSS.
+
+```markdown
+---
+theme: default
+---
+
+<style>
+section {
+  background: yellow;
+}
+</style>
+
+Re-painted yellow background, ha-ha.
+```
+
+> You can also add custom styling by class like `section.custom-class { ... }`.
+> Apply style through `<!-- _class: custom-class -->`.
+
+---
+
+## [Scoped style](https://marpit.marp.app/theme-css?id=scoped-style)
+
+If you want one-shot styling for current page, you can use `<style scoped>`.
+
+```markdown
+<style scoped>
+a {
+  color: green;
+}
+</style>
+
+![Green link!](https://marp.app/)
+```
+
+<style scoped>
+a { color: green; }
+</style>
+
+---
+
+# Enjoy writing slides! :v: <!--fit-->
+
+##### ![w:1em h:1em](https://avatars1.githubusercontent.com/u/20685754?v=4)  Marp: Markdown presentation ecosystem — https://marp.app/
+
+###### by Marp Team ([@marp-team][marp-team])

example/tex_templates/after_body.tex

@@ -0,0 +1 @@
+\end{linenumbers}

example/tex_templates/before_body.tex

@@ -0,0 +1,3 @@
+\thispagestyle{empty}
+\vspace*{2 cm}
+\begin{linenumbers}

example/tex_templates/eisvogel.latex

@@ -0,0 +1,1088 @@
+%%
+% Copyright (c) 2017 - 2023, Pascal Wagler;
+% Copyright (c) 2014 - 2023, John MacFarlane
+%
+% All rights reserved.
+%
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+%
+% - Redistributions of source code must retain the above copyright
+% notice, this list of conditions and the following disclaimer.
+%
+% - Redistributions in binary form must reproduce the above copyright
+% notice, this list of conditions and the following disclaimer in the
+% documentation and/or other materials provided with the distribution.
+%
+% - Neither the name of John MacFarlane nor the names of other
+% contributors may be used to endorse or promote products derived
+% from this software without specific prior written permission.
+%
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+% "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+% LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+% FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+% COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+% INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+% BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+% LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+% LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+% ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+% POSSIBILITY OF SUCH DAMAGE.
+%%
+
+%%
+% This is the Eisvogel pandoc LaTeX template.
+%
+% For usage information and examples visit the official GitHub page:
+% https://github.com/Wandmalfarbe/pandoc-latex-template
+%%
+
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+\PassOptionsToPackage{dvipsnames,svgnames,x11names,table}{xcolor}
+$if(CJKmainfont)$
+\PassOptionsToPackage{space}{xeCJK}
+$endif$
+%
+\documentclass[
+$if(fontsize)$
+  $fontsize$,
+$endif$
+$if(papersize)$
+  $papersize$paper,
+$else$
+  paper=a4,
+$endif$
+$if(beamer)$
+  ignorenonframetext,
+$if(handout)$
+  handout,
+$endif$
+$if(aspectratio)$
+  aspectratio=$aspectratio$,
+$endif$
+$endif$
+$for(classoption)$
+  $classoption$$sep$,
+$endfor$
+  ,captions=tableheading
+]{$if(beamer)$$documentclass$$else$$if(book)$scrbook$else$scrartcl$endif$$endif$}
+$if(beamer)$
+$if(background-image)$
+\usebackgroundtemplate{%
+  \includegraphics[width=\paperwidth]{$background-image$}%
+}
+% In beamer background-image does not work well when other images are used, so this is the workaround
+\pgfdeclareimage[width=\paperwidth,height=\paperheight]{background}{$background-image$}
+\usebackgroundtemplate{\pgfuseimage{background}}
+$endif$
+\usepackage{pgfpages}
+\setbeamertemplate{caption}[numbered]
+\setbeamertemplate{caption label separator}{: }
+\setbeamercolor{caption name}{fg=normal text.fg}
+\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
+$for(beameroption)$
+\setbeameroption{$beameroption$}
+$endfor$
+% Prevent slide breaks in the middle of a paragraph
+\widowpenalties 1 10000
+\raggedbottom
+$if(section-titles)$
+\setbeamertemplate{part page}{
+  \centering
+  \begin{beamercolorbox}[sep=16pt,center]{part title}
+    \usebeamerfont{part title}\insertpart\par
+  \end{beamercolorbox}
+}
+\setbeamertemplate{section page}{
+  \centering
+  \begin{beamercolorbox}[sep=12pt,center]{part title}
+    \usebeamerfont{section title}\insertsection\par
+  \end{beamercolorbox}
+}
+\setbeamertemplate{subsection page}{
+  \centering
+  \begin{beamercolorbox}[sep=8pt,center]{part title}
+    \usebeamerfont{subsection title}\insertsubsection\par
+  \end{beamercolorbox}
+}
+\AtBeginPart{
+  \frame{\partpage}
+}
+\AtBeginSection{
+  \ifbibliography
+  \else
+    \frame{\sectionpage}
+  \fi
+}
+\AtBeginSubsection{
+  \frame{\subsectionpage}
+}
+$endif$
+$endif$
+$if(beamerarticle)$
+\usepackage{beamerarticle} % needs to be loaded first
+$endif$
+\usepackage{amsmath,amssymb}
+$if(linestretch)$
+\usepackage{setspace}
+$else$
+% Use setspace anyway because we change the default line spacing.
+% The spacing is changed early to affect the titlepage and the TOC.
+\usepackage{setspace}
+\setstretch{1.2}
+$endif$
+\usepackage{iftex}
+\ifPDFTeX
+  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
+  \usepackage[utf8]{inputenc}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+$if(mathspec)$
+  \ifXeTeX
+    \usepackage{mathspec} % this also loads fontspec
+  \else
+    \usepackage{unicode-math} % this also loads fontspec
+  \fi
+$else$
+  \usepackage{unicode-math} % this also loads fontspec
+$endif$
+  \defaultfontfeatures{Scale=MatchLowercase}$-- must come before Beamer theme
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
+\fi
+$if(fontfamily)$
+$else$
+$-- Set default font before Beamer theme so the theme can override it
+\usepackage{lmodern}
+$endif$
+$-- Set Beamer theme before user font settings so they can override theme
+$if(beamer)$
+$if(theme)$
+\usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$}
+$endif$
+$if(colortheme)$
+\usecolortheme{$colortheme$}
+$endif$
+$if(fonttheme)$
+\usefonttheme{$fonttheme$}
+$endif$
+$if(mainfont)$
+\usefonttheme{serif} % use mainfont rather than sansfont for slide text
+$endif$
+$if(innertheme)$
+\useinnertheme{$innertheme$}
+$endif$
+$if(outertheme)$
+\useoutertheme{$outertheme$}
+$endif$
+$endif$
+$-- User font settings (must come after default font and Beamer theme)
+$if(fontfamily)$
+\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
+$endif$
+\ifPDFTeX\else
+  % xetex/luatex font selection
+$if(mainfont)$
+  \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
+$endif$
+$if(sansfont)$
+  \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
+$endif$
+$if(monofont)$
+  \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$}
+$endif$
+$for(fontfamilies)$
+  \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
+$endfor$
+$if(mathfont)$
+$if(mathspec)$
+  \ifXeTeX
+    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+  \else
+    \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+  \fi
+$else$
+  \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
+$endif$
+$endif$
+$if(CJKmainfont)$
+  \ifXeTeX
+    \usepackage{xeCJK}
+    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
+    $if(CJKsansfont)$
+      \setCJKsansfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKsansfont$}
+    $endif$
+    $if(CJKmonofont)$
+      \setCJKmonofont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmonofont$}
+    $endif$
+  \fi
+$endif$
+$if(luatexjapresetoptions)$
+  \ifLuaTeX
+    \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
+  \fi
+$endif$
+$if(CJKmainfont)$
+  \ifLuaTeX
+    \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
+    \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
+  \fi
+$endif$
+\fi
+$if(zero-width-non-joiner)$
+%% Support for zero-width non-joiner characters.
+\makeatletter
+\def\zerowidthnonjoiner{%
+  % Prevent ligatures and adjust kerning, but still support hyphenating.
+  \texorpdfstring{%
+    \TextOrMath{\nobreak\discretionary{-}{}{\kern.03em}%
+      \ifvmode\else\nobreak\hskip\z@skip\fi}{}%
+  }{}%
+}
+\makeatother
+\ifPDFTeX
+  \DeclareUnicodeCharacter{200C}{\zerowidthnonjoiner}
+\else
+  \catcode`^^^^200c=\active
+  \protected\def ^^^^200c{\zerowidthnonjoiner}
+\fi
+%% End of ZWNJ support
+$endif$
+% Use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+\IfFileExists{microtype.sty}{% use microtype if available
+  \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
+  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+$if(indent)$
+$else$
+\makeatletter
+\@ifundefined{KOMAClassName}{% if non-KOMA class
+  \IfFileExists{parskip.sty}{%
+    \usepackage{parskip}
+  }{% else
+    \setlength{\parindent}{0pt}
+    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
+}{% if KOMA class
+  \KOMAoptions{parskip=half}}
+\makeatother
+$endif$
+$if(verbatim-in-note)$
+\usepackage{fancyvrb}
+$endif$
+\usepackage{xcolor}
+\definecolor{default-linkcolor}{HTML}{A50000}
+\definecolor{default-filecolor}{HTML}{A50000}
+\definecolor{default-citecolor}{HTML}{4077C0}
+\definecolor{default-urlcolor}{HTML}{4077C0}
+$if(footnotes-pretty)$
+% load footmisc in order to customize footnotes (footmisc has to be loaded before hyperref, cf. https://tex.stackexchange.com/a/169124/144087)
+\usepackage[hang,flushmargin,bottom,multiple]{footmisc}
+\setlength{\footnotemargin}{0.8em} % set space between footnote nr and text
+\setlength{\footnotesep}{\baselineskip} % set space between multiple footnotes
+\setlength{\skip\footins}{0.3cm} % set space between page content and footnote
+\setlength{\footskip}{0.9cm} % set space between footnote and page bottom
+$endif$
+$if(geometry)$
+$if(beamer)$
+\geometry{$for(geometry)$$geometry$$sep$,$endfor$}
+$else$
+\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$else$
+$if(beamer)$
+$else$
+\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering,$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
+$endif$
+$endif$
+$if(titlepage-logo)$
+\usepackage[export]{adjustbox}
+\usepackage{graphicx}
+$endif$
+$if(beamer)$
+\newif\ifbibliography
+$endif$
+$if(listings)$
+\usepackage{listings}
+\newcommand{\passthrough}[1]{#1}
+\lstset{defaultdialect=[5.3]Lua}
+\lstset{defaultdialect=[x86masm]Assembler}
+$endif$
+$if(listings-no-page-break)$
+\usepackage{etoolbox}
+\BeforeBeginEnvironment{lstlisting}{\par\noindent\begin{minipage}{\linewidth}}
+\AfterEndEnvironment{lstlisting}{\end{minipage}\par\addvspace{\topskip}}
+$endif$
+$if(lhs)$
+\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
+$endif$
+$if(highlighting-macros)$
+$highlighting-macros$
+
+% Workaround/bugfix from jannick0.
+% See https://github.com/jgm/pandoc/issues/4302#issuecomment-360669013)
+% or https://github.com/Wandmalfarbe/pandoc-latex-template/issues/2
+%
+% Redefine the verbatim environment 'Highlighting' to break long lines (with
+% the help of fvextra). Redefinition is necessary because it is unlikely that
+% pandoc includes fvextra in the default template.
+\usepackage{fvextra}
+\DefineVerbatimEnvironment{Highlighting}{Verbatim}{breaklines,fontsize=$if(code-block-font-size)$$code-block-font-size$$else$\small$endif$,commandchars=\\\{\}}
+
+$endif$
+$if(tables)$
+\usepackage{longtable,booktabs,array}
+$if(multirow)$
+\usepackage{multirow}
+$endif$
+\usepackage{calc} % for calculating minipage widths
+$if(beamer)$
+\usepackage{caption}
+% Make caption package work with longtable
+\makeatletter
+\def\fnum@table{\tablename~\thetable}
+\makeatother
+$else$
+% Correct order of tables after \paragraph or \subparagraph
+\usepackage{etoolbox}
+\makeatletter
+\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
+\makeatother
+% Allow footnotes in longtable head/foot
+\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
+\makesavenoteenv{longtable}
+$endif$
+$endif$
+% add backlinks to footnote references, cf. https://tex.stackexchange.com/questions/302266/make-footnote-clickable-both-ways
+$if(footnotes-disable-backlinks)$
+$else$
+\usepackage{footnotebackref}
+$endif$
+$if(graphics)$
+\usepackage{graphicx}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+% Make use of float-package and set default placement for figures to H.
+% The option H means 'PUT IT HERE' (as  opposed to the standard h option which means 'You may put it here if you like').
+\usepackage{float}
+\floatplacement{figure}{$if(float-placement-figure)$$float-placement-figure$$else$H$endif$}
+\makeatother
+$endif$
+$if(svg)$
+\usepackage{svg}
+$endif$
+$if(strikeout)$
+$-- also used for underline
+\ifLuaTeX
+  \usepackage{luacolor}
+  \usepackage[soul]{lua-ul}
+\else
+\usepackage{soul}
+\fi
+$endif$
+\setlength{\emergencystretch}{3em} % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+$if(numbersections)$
+\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
+$else$
+\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
+$endif$
+$if(subfigure)$
+\usepackage{subcaption}
+$endif$
+$if(beamer)$
+$else$
+$if(block-headings)$
+% Make \paragraph and \subparagraph free-standing
+\ifx\paragraph\undefined\else
+  \let\oldparagraph\paragraph
+  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+  \let\oldsubparagraph\subparagraph
+  \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+$endif$
+$endif$
+$if(pagestyle)$
+\pagestyle{$pagestyle$}
+$endif$
+$if(csl-refs)$
+\newlength{\cslhangindent}
+\setlength{\cslhangindent}{1.5em}
+\newlength{\csllabelwidth}
+\setlength{\csllabelwidth}{3em}
+\newlength{\cslentryspacingunit} % times entry-spacing
+\setlength{\cslentryspacingunit}{\parskip}
+\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
+ {% don't indent paragraphs
+  \setlength{\parindent}{0pt}
+  % turn on hanging indent if param 1 is 1
+  \ifodd #1
+  \let\oldpar\par
+  \def\par{\hangindent=\cslhangindent\oldpar}
+  \fi
+  % set entry spacing
+  \setlength{\parskip}{#2\cslentryspacingunit}
+ }%
+ {}
+\usepackage{calc}
+\newcommand{\CSLBlock}[1]{#1\hfill\break}
+\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
+\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
+\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
+$endif$
+$if(lang)$
+\ifLuaTeX
+\usepackage[bidi=basic]{babel}
+\else
+\usepackage[bidi=default]{babel}
+\fi
+$if(babel-lang)$
+\babelprovide[main,import]{$babel-lang$}
+$if(mainfont)$
+\ifPDFTeX
+\else
+\babelfont{rm}[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
+\fi
+$endif$
+$endif$
+$for(babel-otherlangs)$
+\babelprovide[import]{$babel-otherlangs$}
+$endfor$
+$for(babelfonts/pairs)$
+\babelfont[$babelfonts.key$]{rm}{$babelfonts.value$}
+$endfor$
+% get rid of language-specific shorthands (see #6817):
+\let\LanguageShortHands\languageshorthands
+\def\languageshorthands#1{}
+$endif$
+$for(header-includes)$
+$header-includes$
+$endfor$
+\ifLuaTeX
+  \usepackage{selnolig}  % disable illegal ligatures
+\fi
+$if(dir)$
+\ifPDFTeX
+  \TeXXeTstate=1
+  \newcommand{\RL}[1]{\beginR #1\endR}
+  \newcommand{\LR}[1]{\beginL #1\endL}
+  \newenvironment{RTL}{\beginR}{\endR}
+  \newenvironment{LTR}{\beginL}{\endL}
+\fi
+$endif$
+$if(natbib)$
+\usepackage[$natbiboptions$]{natbib}
+\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
+$endif$
+$if(biblatex)$
+\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
+$for(bibliography)$
+\addbibresource{$bibliography$}
+$endfor$
+$endif$
+$if(nocite-ids)$
+\nocite{$for(nocite-ids)$$it$$sep$, $endfor$}
+$endif$
+$if(csquotes)$
+\usepackage{csquotes}
+$endif$
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\urlstyle{$if(urlstyle)$$urlstyle$$else$same$endif$}
+$if(links-as-notes)$
+% Make links footnotes instead of hotlinks:
+\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
+$endif$
+$if(verbatim-in-note)$
+\VerbatimFootnotes % allow verbatim text in footnotes
+$endif$
+\hypersetup{
+$if(title-meta)$
+  pdftitle={$title-meta$},
+$endif$
+$if(author-meta)$
+  pdfauthor={$author-meta$},
+$endif$
+$if(lang)$
+  pdflang={$lang$},
+$endif$
+$if(subject)$
+  pdfsubject={$subject$},
+$endif$
+$if(keywords)$
+  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
+$endif$
+$if(colorlinks)$
+  colorlinks=true,
+  linkcolor={$if(linkcolor)$$linkcolor$$else$default-linkcolor$endif$},
+  filecolor={$if(filecolor)$$filecolor$$else$default-filecolor$endif$},
+  citecolor={$if(citecolor)$$citecolor$$else$default-citecolor$endif$},
+  urlcolor={$if(urlcolor)$$urlcolor$$else$default-urlcolor$endif$},
+$else$
+  hidelinks,
+$endif$
+  breaklinks=true,
+  pdfcreator={LaTeX via pandoc with the Eisvogel template}}
+$if(title)$
+\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
+$endif$
+$if(subtitle)$
+$if(beamer)$
+$else$
+\usepackage{etoolbox}
+\makeatletter
+\providecommand{\subtitle}[1]{% add subtitle to \maketitle
+  \apptocmd{\@title}{\par {\large #1 \par}}{}{}
+}
+\makeatother
+$endif$
+\subtitle{$subtitle$}
+$endif$
+\author{$for(author)$$author$$sep$ \and $endfor$}
+\date{$date$}
+$if(beamer)$
+$if(institute)$
+\institute{$for(institute)$$institute$$sep$ \and $endfor$}
+$endif$
+$if(titlegraphic)$
+\titlegraphic{\includegraphics{$titlegraphic$}}
+$endif$
+$if(logo)$
+\logo{\includegraphics{$logo$}}
+$endif$
+$endif$
+
+
+
+%%
+%% added
+%%
+
+$if(page-background)$
+\usepackage[pages=all]{background}
+$endif$
+
+%
+% for the background color of the title page
+%
+$if(titlepage)$
+\usepackage{pagecolor}
+\usepackage{afterpage}
+$if(titlepage-background)$
+\usepackage{tikz}
+$endif$
+$if(geometry)$
+$else$
+\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering]{geometry}
+$endif$
+$endif$
+
+%
+% break urls
+%
+\PassOptionsToPackage{hyphens}{url}
+
+%
+% When using babel or polyglossia with biblatex, loading csquotes is recommended
+% to ensure that quoted texts are typeset according to the rules of your main language.
+%
+\usepackage{csquotes}
+
+%
+% captions
+%
+\definecolor{caption-color}{HTML}{777777}
+$if(beamer)$
+$else$
+\usepackage[font={stretch=1.2}, textfont={color=caption-color}, position=top, skip=4mm, labelfont=bf, singlelinecheck=false, justification=$if(caption-justification)$$caption-justification$$else$raggedright$endif$]{caption}
+\setcapindent{0em}
+$endif$
+
+%
+% blockquote
+%
+\definecolor{blockquote-border}{RGB}{221,221,221}
+\definecolor{blockquote-text}{RGB}{119,119,119}
+\usepackage{mdframed}
+\newmdenv[rightline=false,bottomline=false,topline=false,linewidth=3pt,linecolor=blockquote-border,skipabove=\parskip]{customblockquote}
+\renewenvironment{quote}{\begin{customblockquote}\list{}{\rightmargin=0em\leftmargin=0em}%
+\item\relax\color{blockquote-text}\ignorespaces}{\unskip\unskip\endlist\end{customblockquote}}
+
+%
+% Source Sans Pro as the de­fault font fam­ily
+% Source Code Pro for monospace text
+%
+% 'default' option sets the default
+% font family to Source Sans Pro, not \sfdefault.
+%
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  $if(fontfamily)$
+  $else$
+  \usepackage[default]{sourcesanspro}
+  \usepackage{sourcecodepro}
+  $endif$
+\else % if not pdftex
+  $if(mainfont)$
+  $else$
+  \usepackage[default]{sourcesanspro}
+  \usepackage{sourcecodepro}
+
+  % XeLaTeX specific adjustments for straight quotes: https://tex.stackexchange.com/a/354887
+  % This issue is already fixed (see https://github.com/silkeh/latex-sourcecodepro/pull/5) but the
+  % fix is still unreleased.
+  % TODO: Remove this workaround when the new version of sourcecodepro is released on CTAN.
+  \ifxetex
+    \makeatletter
+    \defaultfontfeatures[\ttfamily]
+      { Numbers   = \sourcecodepro@figurestyle,
+        Scale     = \SourceCodePro@scale,
+        Extension = .otf }
+    \setmonofont
+      [ UprightFont    = *-\sourcecodepro@regstyle,
+        ItalicFont     = *-\sourcecodepro@regstyle It,
+        BoldFont       = *-\sourcecodepro@boldstyle,
+        BoldItalicFont = *-\sourcecodepro@boldstyle It ]
+      {SourceCodePro}
+    \makeatother
+  \fi
+  $endif$
+\fi
+
+%
+% heading color
+%
+\definecolor{heading-color}{RGB}{40,40,40}
+$if(beamer)$
+$else$
+\addtokomafont{section}{\color{heading-color}}
+$endif$
+% When using the classes report, scrreprt, book,
+% scrbook or memoir, uncomment the following line.
+%\addtokomafont{chapter}{\color{heading-color}}
+
+%
+% variables for title, author and date
+%
+$if(beamer)$
+$else$
+\usepackage{titling}
+\title{$title$}
+\author{$for(author)$$author$$sep$, $endfor$}
+\date{$date$}
+$endif$
+
+%
+% tables
+%
+$if(tables)$
+
+\definecolor{table-row-color}{HTML}{F5F5F5}
+\definecolor{table-rule-color}{HTML}{999999}
+
+%\arrayrulecolor{black!40}
+\arrayrulecolor{table-rule-color}     % color of \toprule, \midrule, \bottomrule
+\setlength\heavyrulewidth{0.3ex}      % thickness of \toprule, \bottomrule
+\renewcommand{\arraystretch}{1.3}     % spacing (padding)
+
+$if(table-use-row-colors)$
+% TODO: This doesn't work anymore. I don't know why.
+% Reset rownum counter so that each table
+% starts with the same row colors.
+% https://tex.stackexchange.com/questions/170637/restarting-rowcolors
+%
+% Unfortunately the colored cells extend beyond the edge of the
+% table because pandoc uses @-expressions (@{}) like so:
+%
+% \begin{longtable}[]{@{}ll@{}}
+% \end{longtable}
+%
+% https://en.wikibooks.org/wiki/LaTeX/Tables#.40-expressions
+\let\oldlongtable\longtable
+\let\endoldlongtable\endlongtable
+\renewenvironment{longtable}{
+\rowcolors{3}{}{table-row-color!100}  % row color
+\oldlongtable} {
+\endoldlongtable
+\global\rownum=0\relax}
+$endif$
+$endif$
+
+%
+% remove paragraph indention
+%
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+
+%
+%
+% Listings
+%
+%
+
+$if(listings)$
+
+%
+% general listing colors
+%
+\definecolor{listing-background}{HTML}{F7F7F7}
+\definecolor{listing-rule}{HTML}{B3B2B3}
+\definecolor{listing-numbers}{HTML}{B3B2B3}
+\definecolor{listing-text-color}{HTML}{000000}
+\definecolor{listing-keyword}{HTML}{435489}
+\definecolor{listing-keyword-2}{HTML}{1284CA} % additional keywords
+\definecolor{listing-keyword-3}{HTML}{9137CB} % additional keywords
+\definecolor{listing-identifier}{HTML}{435489}
+\definecolor{listing-string}{HTML}{00999A}
+\definecolor{listing-comment}{HTML}{8E8E8E}
+
+\lstdefinestyle{eisvogel_listing_style}{
+  language         = java,
+$if(listings-disable-line-numbers)$
+  xleftmargin      = 0.6em,
+  framexleftmargin = 0.4em,
+$else$
+  numbers          = left,
+  xleftmargin      = 2.7em,
+  framexleftmargin = 2.5em,
+$endif$
+  backgroundcolor  = \color{listing-background},
+  basicstyle       = \color{listing-text-color}\linespread{1.0}%
+                      \lst@ifdisplaystyle%
+                      $if(code-block-font-size)$$code-block-font-size$$else$\small$endif$%
+                      \fi\ttfamily{},
+  breaklines       = true,
+  frame            = single,
+  framesep         = 0.19em,
+  rulecolor        = \color{listing-rule},
+  frameround       = ffff,
+  tabsize          = 4,
+  numberstyle      = \color{listing-numbers},
+  aboveskip        = 1.0em,
+  belowskip        = 0.1em,
+  abovecaptionskip = 0em,
+  belowcaptionskip = 1.0em,
+  keywordstyle     = {\color{listing-keyword}\bfseries},
+  keywordstyle     = {[2]\color{listing-keyword-2}\bfseries},
+  keywordstyle     = {[3]\color{listing-keyword-3}\bfseries\itshape},
+  sensitive        = true,
+  identifierstyle  = \color{listing-identifier},
+  commentstyle     = \color{listing-comment},
+  stringstyle      = \color{listing-string},
+  showstringspaces = false,
+  escapeinside     = {/*@}{@*/}, % Allow LaTeX inside these special comments
+  literate         =
+  {á}{{\'a}}1 {é}{{\'e}}1 {í}{{\'i}}1 {ó}{{\'o}}1 {ú}{{\'u}}1
+  {Á}{{\'A}}1 {É}{{\'E}}1 {Í}{{\'I}}1 {Ó}{{\'O}}1 {Ú}{{\'U}}1
+  {à}{{\`a}}1 {è}{{\`e}}1 {ì}{{\`i}}1 {ò}{{\`o}}1 {ù}{{\`u}}1
+  {À}{{\`A}}1 {È}{{\`E}}1 {Ì}{{\`I}}1 {Ò}{{\`O}}1 {Ù}{{\`U}}1
+  {ä}{{\"a}}1 {ë}{{\"e}}1 {ï}{{\"i}}1 {ö}{{\"o}}1 {ü}{{\"u}}1
+  {Ä}{{\"A}}1 {Ë}{{\"E}}1 {Ï}{{\"I}}1 {Ö}{{\"O}}1 {Ü}{{\"U}}1
+  {â}{{\^a}}1 {ê}{{\^e}}1 {î}{{\^i}}1 {ô}{{\^o}}1 {û}{{\^u}}1
+  {Â}{{\^A}}1 {Ê}{{\^E}}1 {Î}{{\^I}}1 {Ô}{{\^O}}1 {Û}{{\^U}}1
+  {œ}{{\oe}}1 {Œ}{{\OE}}1 {æ}{{\ae}}1 {Æ}{{\AE}}1 {ß}{{\ss}}1
+  {ç}{{\c c}}1 {Ç}{{\c C}}1 {ø}{{\o}}1 {å}{{\r a}}1 {Å}{{\r A}}1
+  {€}{{\EUR}}1 {£}{{\pounds}}1 {«}{{\guillemotleft}}1
+  {»}{{\guillemotright}}1 {ñ}{{\~n}}1 {Ñ}{{\~N}}1 {¿}{{?`}}1
+  {…}{{\ldots}}1 {≥}{{>=}}1 {≤}{{<=}}1 {„}{{\glqq}}1 {“}{{\grqq}}1
+  {”}{{''}}1
+}
+\lstset{style=eisvogel_listing_style}
+
+%
+% Java (Java SE 12, 2019-06-22)
+%
+\lstdefinelanguage{Java}{
+  morekeywords={
+    % normal keywords (without data types)
+    abstract,assert,break,case,catch,class,continue,default,
+    do,else,enum,exports,extends,final,finally,for,if,implements,
+    import,instanceof,interface,module,native,new,package,private,
+    protected,public,requires,return,static,strictfp,super,switch,
+    synchronized,this,throw,throws,transient,try,volatile,while,
+    % var is an identifier
+    var
+  },
+  morekeywords={[2] % data types
+    % primitive data types
+    boolean,byte,char,double,float,int,long,short,
+    % String
+    String,
+    % primitive wrapper types
+    Boolean,Byte,Character,Double,Float,Integer,Long,Short
+    % number types
+    Number,AtomicInteger,AtomicLong,BigDecimal,BigInteger,DoubleAccumulator,DoubleAdder,LongAccumulator,LongAdder,Short,
+    % other
+    Object,Void,void
+  },
+  morekeywords={[3] % literals
+    % reserved words for literal values
+    null,true,false,
+  },
+  sensitive,
+  morecomment  = [l]//,
+  morecomment  = [s]{/*}{*/},
+  morecomment  = [s]{/**}{*/},
+  morestring   = [b]",
+  morestring   = [b]',
+}
+
+\lstdefinelanguage{XML}{
+  morestring      = [b]",
+  moredelim       = [s][\bfseries\color{listing-keyword}]{<}{\ },
+  moredelim       = [s][\bfseries\color{listing-keyword}]{</}{>},
+  moredelim       = [l][\bfseries\color{listing-keyword}]{/>},
+  moredelim       = [l][\bfseries\color{listing-keyword}]{>},
+  morecomment     = [s]{<?}{?>},
+  morecomment     = [s]{<!--}{-->},
+  commentstyle    = \color{listing-comment},
+  stringstyle     = \color{listing-string},
+  identifierstyle = \color{listing-identifier}
+}
+$endif$
+
+%
+% header and footer
+%
+$if(beamer)$
+$else$
+$if(disable-header-and-footer)$
+$else$
+\usepackage[headsepline,footsepline]{scrlayer-scrpage}
+
+\newpairofpagestyles{eisvogel-header-footer}{
+  \clearpairofpagestyles
+  \ihead*{$if(header-left)$$header-left$$else$$title$$endif$}
+  \chead*{$if(header-center)$$header-center$$else$$endif$}
+  \ohead*{$if(header-right)$$header-right$$else$$date$$endif$}
+  \ifoot*{$if(footer-left)$$footer-left$$else$$for(author)$$author$$sep$, $endfor$$endif$}
+  \cfoot*{$if(footer-center)$$footer-center$$else$$endif$}
+  \ofoot*{$if(footer-right)$$footer-right$$else$\thepage$endif$}
+  \addtokomafont{pageheadfoot}{\upshape}
+}
+\pagestyle{eisvogel-header-footer}
+
+$if(book)$
+\deftripstyle{ChapterStyle}{}{}{}{}{\pagemark}{}
+\renewcommand*{\chapterpagestyle}{ChapterStyle}
+$endif$
+
+$if(page-background)$
+\backgroundsetup{
+scale=1,
+color=black,
+opacity=$if(page-background-opacity)$$page-background-opacity$$else$0.2$endif$,
+angle=0,
+contents={%
+  \includegraphics[width=\paperwidth,height=\paperheight]{$page-background$}
+  }%
+}
+$endif$
+$endif$
+$endif$
+
+%%
+%% end added
+%%
+
+\begin{document}
+
+%%
+%% begin titlepage
+%%
+$if(beamer)$
+$else$
+$if(titlepage)$
+\begin{titlepage}
+$if(titlepage-background)$
+\newgeometry{top=2cm, right=4cm, bottom=3cm, left=4cm}
+$else$
+\newgeometry{left=6cm}
+$endif$
+$if(titlepage-color)$
+\definecolor{titlepage-color}{HTML}{$titlepage-color$}
+\newpagecolor{titlepage-color}\afterpage{\restorepagecolor}
+$endif$
+$if(titlepage-background)$
+\tikz[remember picture,overlay] \node[inner sep=0pt] at (current page.center){\includegraphics[width=\paperwidth,height=\paperheight]{$titlepage-background$}};
+$endif$
+\newcommand{\colorRule}[3][black]{\textcolor[HTML]{#1}{\rule{#2}{#3}}}
+\begin{flushleft}
+\noindent
+\\[-1em]
+\color[HTML]{$if(titlepage-text-color)$$titlepage-text-color$$else$5F5F5F$endif$}
+\makebox[0pt][l]{\colorRule[$if(titlepage-rule-color)$$titlepage-rule-color$$else$435488$endif$]{1.3\textwidth}{$if(titlepage-rule-height)$$titlepage-rule-height$$else$4$endif$pt}}
+\par
+\noindent
+
+$if(titlepage-background)$
+% The titlepage with a background image has other text spacing and text size
+{
+  \setstretch{2}
+  \vfill
+  \vskip -8em
+  \noindent {\huge \textbf{\textsf{$title$}}}
+  $if(subtitle)$
+  \vskip 1em
+  {\Large \textsf{$subtitle$}}
+  $endif$
+  \vskip 2em
+  \noindent {\Large \textsf{$for(author)$$author$$sep$, $endfor$} \vskip 0.6em \textsf{$date$}}
+  \vfill
+}
+$else$
+{
+  \setstretch{1.4}
+  \vfill
+  \noindent {\huge \textbf{\textsf{$title$}}}
+  $if(subtitle)$
+  \vskip 1em
+  {\Large \textsf{$subtitle$}}
+  $endif$
+  \vskip 2em
+  \noindent {\Large \textsf{$for(author)$$author$$sep$, $endfor$}}
+  \vfill
+}
+$endif$
+
+$if(titlepage-logo)$
+\noindent
+\includegraphics[width=$if(logo-width)$$logo-width$$else$35mm$endif$, left]{$titlepage-logo$}
+$endif$
+
+$if(titlepage-background)$
+$else$
+\textsf{$date$}
+$endif$
+\end{flushleft}
+\end{titlepage}
+\restoregeometry
+\pagenumbering{arabic} 
+$endif$
+$endif$
+
+%%
+%% end titlepage
+%%
+
+$if(has-frontmatter)$
+\frontmatter
+$endif$
+$if(title)$
+$if(beamer)$
+\frame{\titlepage}
+% don't generate the default title
+% $else$
+% \maketitle
+$endif$
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+$endif$
+
+$if(first-chapter)$
+\setcounter{chapter}{$first-chapter$}
+\addtocounter{chapter}{-1}
+$endif$
+
+$for(include-before)$
+$include-before$
+
+$endfor$
+$if(toc)$
+$if(toc-title)$
+\renewcommand*\contentsname{$toc-title$}
+$endif$
+$if(beamer)$
+\begin{frame}[allowframebreaks]
+$if(toc-title)$
+  \frametitle{$toc-title$}
+$endif$
+  \tableofcontents[hideallsubsections]
+\end{frame}
+$if(toc-own-page)$
+\newpage
+$endif$
+$else$
+{
+$if(colorlinks)$
+\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
+$endif$
+\setcounter{tocdepth}{$toc-depth$}
+\tableofcontents
+$if(toc-own-page)$
+\newpage
+$endif$
+}
+$endif$
+$endif$
+$if(lof)$
+\listoffigures
+$endif$
+$if(lot)$
+\listoftables
+$endif$
+$if(linestretch)$
+\setstretch{$linestretch$}
+$endif$
+$if(has-frontmatter)$
+\mainmatter
+$endif$
+$body$
+
+$if(has-frontmatter)$
+\backmatter
+$endif$
+$if(natbib)$
+$if(bibliography)$
+$if(biblio-title)$
+$if(has-chapters)$
+\renewcommand\bibname{$biblio-title$}
+$else$
+\renewcommand\refname{$biblio-title$}
+$endif$
+$endif$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+  \bibliographytrue
+$endif$
+  \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
+$if(beamer)$
+\end{frame}
+$endif$
+
+$endif$
+$endif$
+$if(biblatex)$
+$if(beamer)$
+\begin{frame}[allowframebreaks]{$biblio-title$}
+  \bibliographytrue
+  \printbibliography[heading=none]
+\end{frame}
+$else$
+\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
+$endif$
+
+$endif$
+$for(include-after)$
+$include-after$
+
+$endfor$
+\end{document}

example/tex_templates/header.tex

@@ -0,0 +1,6 @@
+\usepackage[margin=3cm]{geometry}
+\usepackage{lineno}
+\usepackage{setspace}
+\doublespacing
+%\singlespacing
+%\onehalfspacing

example/tex_templates/letter.latex

@@ -0,0 +1,162 @@
+%!TEX TS-program = xelatex
+%!TEX encoding = UTF-8 Unicode
+
+\documentclass[$fontsize$, a4paper]{article}
+\usepackage{fontspec}
+
+% LAYOUT
+%--------------------------------
+\usepackage{geometry}
+\geometry{$geometry$}
+
+% No page numbers
+\pagenumbering{gobble}
+
+% Left align
+\usepackage[document]{ragged2e}
+
+% Trim excessive whitespace before lists
+\usepackage{enumitem}
+\setlist{nolistsep}
+
+$if(page-background)$
+\usepackage[pages=all]{background}
+$endif$
+
+$if(letterhead)$
+\usepackage{wallpaper}
+\addtolength{\wpXoffset}{-5cm}
+\addtolength{\wpYoffset}{11cm}
+% \ThisULCornerWallPaper{1}{letterhead-front.pdf} % Uncomment to include a different letterhead on the first page
+\CenterWallPaper{0.2}{$letterhead$}
+$endif$
+
+\usepackage{fontawesome5}
+
+% LANGUAGE
+%--------------------------------
+$if(lang)$
+\usepackage{polyglossia}
+\setmainlanguage{$lang$}
+$endif$
+
+% TYPOGRAPHY
+%--------------------------------
+\usepackage{xunicode}
+\usepackage{xltxtra}
+\usepackage[protrusion=true,final]{microtype}
+
+% converts LaTeX specials (quotes, dashes etc.) to Unicode
+\defaultfontfeatures{Mapping=tex-text}
+\setromanfont [Ligatures={Common}, Numbers={OldStyle}]{$mainfont$}
+\setsansfont[Scale=0.9]{$altfont$}
+\setmonofont[Scale=0.8]{$monofont$}
+
+% Set paragraph break
+\setlength{\parskip}{1em}
+
+% Custom ampersand
+\newcommand{\amper}{{\fontspec[Scale=.95]{$mainfont$}\selectfont\itshape\&}}
+
+$if(mainfont)$
+    \setmainfont{$mainfont$}
+$endif$
+$if(altfont)$
+    \setsansfont{$altfont$}
+$endif$
+
+% Command required by how Pandoc handles the list conversion
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+% PDF SETUP
+%--------------------------------
+\usepackage[xetex, bookmarks, colorlinks, breaklinks]{hyperref}
+\hypersetup
+{
+  pdfauthor={$author$},
+  pdfsubject={$subject$},
+  pdftitle={$subject$},
+  colorlinks,breaklinks,
+  filecolor=black,
+  urlcolor=[rgb]{0.117,0.682,0.858},
+  linkcolor=[rgb]{0.117,0.682,0.858},
+  linkcolor=[rgb]{0.117,0.682,0.858},
+  citecolor=[rgb]{0.117,0.682,0.858}
+}
+
+% To display custom date in the example
+$if(customdate)$
+\usepackage[$lang$]{datetime2}
+\DTMsavedate{customdate}{$customdate$}
+$endif$
+
+$if(page-background)$
+\backgroundsetup{
+scale=1,
+color=black,
+opacity=$if(page-background-opacity)$$page-background-opacity$$else$0.2$endif$,
+angle=0,
+contents={%
+  \includegraphics[width=\paperwidth,height=\paperheight]{$page-background$}
+  }%
+}
+$endif$
+
+% remove section numbering
+\setcounter{secnumdepth}{-\maxdimen} 
+
+% DOCUMENT
+%--------------------------------
+\begin{document}
+\small
+
+\textsc{\textbf{$author$}\\$affiliation1$}\\ \textsc{$affiliation2$}\\ 
+$for(from)$
+\textsc{$from$}
+$endfor$
+
+%$for(contact)$
+%\textsc{$contact$}
+%$endfor$
+
+\vspace{2em}
+
+\normalsize \sffamily
+$for(to)$
+$to$\\
+$endfor$
+
+%\vspace{3em}
+
+\rmfamily
+\begin{flushright}
+  $city$ \textbullet{} $if(customdate)$\DTMusedate{customdate}$else$\today$endif$
+\end{flushright}
+
+%\vspace{1em}
+
+%$if(subject)$
+%\textbf{$subject$}
+%$endif$
+
+%\vspace{1em}
+
+%$salutation$ $toname$:
+
+$body$
+
+$if(signature)$
+  \begin{FlushRight}  
+    \IfFileExists{$signature$}
+    {
+      \includegraphics[height=5.5\baselineskip]{$signature$} \par
+    }
+    {
+      \vspace{5.5\baselineskip}
+    }
+    $author$  
+  \end{FlushRight}
+$endif$
+
+\end{document}