Outline

1. Markdown basics

2. Pandoc

3. Web page

4. Presentation

5. Publication

6. Extras

Markdown

• lightweight markup language

• designed for HTML

• possible to generate many other formats: LaTeX, pdf, Beamer...

Markdown - headers

# Header

## Subheader

### Subsubheader

#### Subsubsubheader

Markdown - text formatting

A blank line - new paragraph.

*Text encapsulated in stars*

**Text encapsulated in double stars**

<font color=red>
HTML tags can be used directly.
</font>

Markdown - bullet list

Bullet list:

* one can use stars
- or dash
* it really does not matter

Markdown - numbered list

Numbered list:

1. one can use any number
9. it really does not matter
4. the list will be well ordered

Markdown - math

$$E = \frac{1}{2}\int\limits_0^c mx dx$$

Markdown - tables

| family I | family II | family III | 
|:---------|:---------:|-----------:|
| $e$      | $\mu$     | $\tau$     |
| $\nu_e$  | $\nu_\mu$ | $\nu_\tau$ |

Markdown - code

 ```

 some code

 ```

#include <iostream>

int main() {
    std::cout << "Hello World!\n";

    return 0;
}

Markdown - misc

Horizontal rule

---

[Link](http://neutrino.ift.uni.wroc.pl/)

---

![Picture](../img/andy.gif)

Horizontal rule

---

Link

---

Pandoc

• Pandoc is a universal document converter

• markdown, HTML, LaTeX, Beamer, ODT, ...

• more info: pandoc website

Pandoc - demo

Pandoc - examples

Standalone HTML:

pandoc -s input.md -o output.html

PDF:

pandoc input.md -o output.pdf

Beamer:

pandoc -t beamer input.md -o output.pdf

Beamer with template:

pandoc -t beamer -H template.tex input.md -o output.pdf

LaTeX:

pandoc -s input.md -o output.tex

Web page src

## Contact

* email: <tomasz.golan@uwr.edu.pl>
* room@ift: 438
* phone: +48 71 375-9405

## Research interests

* neutrino interactions
* nuclear effects in neutrino scattering off nuclei
* Monte Carlo generators
* machine learning in event reconstruction

## Teaching
...

src

Web page - pandoc

pandoc -s index.md -o index.html

Web page - markdown-styles

generate-md --layout src/mixu-radar-mod --input src/index.md --output www

Web page - preview example

Presentation src

% Golden Ratio
% Tomasz Golan
% Neutrino Seminar

# Outline

* Introduction
* Methods
* Solution

# Introduction

* $a$ and $b$ are in the golden ratio if:

$$\frac{a+b}{a} = \frac{a}{b}$$

* The solution of the following quadratic equation:

$$x^2 - x - 1 = 0$$

is found to represents the golden ratio:

$$\phi = 1.618...$$

# Methods

* The discriminant of quadratic equation is given by the following formula:

$$\Delta = b^2 - 4*a*c$$

* And the solutions are given by:

$$x = \frac{-b \pm \sqrt{\Delta}}{2a}$$

# Solution

* The following solution can be found:

$$x_1 = 1.618033988749895$$
$$x_2 = -0.6180339887498949$$

* The first one is the golden ratio

Presentation - preview

Presentation - PDF

Use -t beamer option to get the PDF presentation

pandoc -t beamer example.md -o example.pdf

One can include custom options, e.g. header.tex:

\setbeamertemplate{footline}[frame number]

Use -H [tex file] to include the file:

pandoc -t beamer -H header.tex example.md -o example.pdf

The output PDF file: result

Presentation - LaTeX src

pandoc -t beamer example.md -o example.tex

\begin{frame}{Outline}

\begin{itemize}
\tightlist
\item
  Introduction
\item
  Methods
\item
  Solution
\end{itemize}

\end{frame}

\begin{frame}{Introduction}

\begin{itemize}
\tightlist
\item
  \(a\) and \(b\) are in the golden ratio if:
\end{itemize}

\[\frac{a+b}{a} = \frac{a}{b}\]

\begin{itemize}
\tightlist
\item
  The solution of the following quadratic equation:
\end{itemize}

\[x^2 - x - 1 = 0\]

is found to represents the golden ratio:

\[\phi = 1.618...\]

\end{frame}

\begin{frame}{Methods}

\begin{itemize}
\tightlist
\item
  The discriminant of quadratic equation is given by the following
  formula:
\end{itemize}

\[\Delta = b^2 - 4*a*c\]

\begin{itemize}
\tightlist
\item
  And the solutions are given by:
\end{itemize}

\[x = \frac{-b \pm \sqrt{\Delta}}{2a}\]

\end{frame}

\begin{frame}{Solution}

\begin{itemize}
\tightlist
\item
  The following solution can be found:
\end{itemize}

\[x_1 = 1.618033988749895\] \[x_2 = -0.6180339887498949\]

\begin{itemize}
\tightlist
\item
  The first one is the golden ratio
\end{itemize}

\end{frame}

Publication src

% Tomasz Golan
% The study of nothing

# Introduction

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Praesent feugiat rutrum consectetur. Praesent volutpat mi ac consequat vehicula. Sed vitae faucibus lacus, sed semper turpis. Aliquam pulvinar est porttitor mollis malesuada. Phasellus vel sodales lectus. Vestibulum gravida malesuada feugiat. Duis ullamcorper, lectus pretium dignissim porttitor, odio nisi pretium ante, eget suscipit lectus tortor sit amet enim. Nam eleifend scelerisque lacus nec gravida.

$$\sum\limits_{i=1}^N |c_i|^2 = 1$$

# Lorep ipsum

Proin hendrerit erat ac lacus dapibus interdum. Vivamus sed tellus semper, pellentesque enim vel, scelerisque nibh. Curabitur eget feugiat enim. Praesent eu fermentum leo. Curabitur tempor bibendum lobortis. Maecenas eget nunc eget eros venenatis sollicitudin et in metus. Aliquam imperdiet tortor nec vehicula iaculis. Duis odio enim, auctor id massa in, aliquet ultricies elit. Ut sit amet turpis eu nibh aliquet ultrices aliquet ac nibh. In ullamcorper nibh nec arcu venenatis, eget bibendum tellus semper. Curabitur tortor libero, porta in hendrerit eu, sollicitudin eu sapien. Integer rutrum quam eget cursus sollicitudin. Proin at augue rhoncus lorem iaculis fringilla et in neque. Donec sollicitudin elit at nisl tristique, et laoreet dolor tempor. Nam sodales orci eget neque viverra pharetra. Suspendisse et volutpat lorem.

![My plot](plot.png)

## Subsection

Sed in iaculis ipsum. Morbi sollicitudin id ex eu aliquam. Nam lobortis bibendum elit, sed hendrerit turpis aliquam vitae. Nam lobortis ut mi et scelerisque. Aliquam porttitor eget arcu eu molestie. Ut condimentum sollicitudin elit accumsan pulvinar. Ut placerat iaculis risus ut aliquam. Aliquam erat volutpat. Phasellus sit amet euismod mi. Quisque dictum suscipit mauris sed mattis. Nunc ac aliquam lacus. Duis sed turpis in nunc tristique bibendum. Quisque elit diam, tristique et arcu in, suscipit tempus orci. Mauris accumsan tincidunt sem ut placerat. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin aliquet ligula sit amet turpis cursus, id sollicitudin arcu feugiat.

# Summary

Integer a odio accumsan, sagittis erat vel, condimentum velit. Quisque ullamcorper ante turpis, non ultricies odio suscipit at. Morbi eget lectus eu ex mollis sodales a ut magna. Phasellus commodo consequat enim, sit amet rutrum dui congue eu. Vestibulum sit amet rutrum arcu. Curabitur viverra lacus sit amet nulla accumsan maximus. Donec fermentum eu nibh eget ornare. Aliquam in leo a elit gravida pretium. In urna elit, cursus a erat vitae, vehicula convallis velit. Mauris eget nisl at turpis tincidunt tincidunt non non purus. Praesent pharetra tempor augue at tempor. Cras risus lorem, dictum ut sapien a, sagittis mollis felis. Suspendisse commodo neque id nisi mattis consectetur ut sit amet urna. Praesent pretium, dolor sed malesuada gravida, nulla neque pellentesque dui, eget tempus arcu justo at odio. Pellentesque fermentum diam enim, sit amet eleifend nulla accumsan non.

Donec et consectetur mauris. Cras pulvinar arcu quis lobortis congue. Phasellus lobortis augue justo, eu auctor leo tempor vel. Mauris sit amet eros odio. Nam tellus arcu, scelerisque semper tristique vitae, tincidunt vestibulum sem. Duis augue nibh, ornare ac orci vitae, sollicitudin volutpat neque. Maecenas at erat dolor. Praesent convallis ornare tortor eu vestibulum. Maecenas luctus eget nibh sed pellentesque.

Publication - output

One can get PDF directly:

pandoc example_pub.md -o example_pub.pdf

result

Or one can get LaTeX source:

pandoc -s example_pub.md -o example_pub.tex

References

Nobody @my_ref says nothing.

# References

@article{my_ref,
author="Nobody",
title="Nothing",
year="2017"}

pandoc --filter=pandoc-citeproc --biblio=example.bib --csl example.csl \
       example_ref.md -o example_ref.pdf

Markdown-to-slides

# My first markdown-to-slides presentation

## Is is that simple?

1. first bullet point
.red[- important subbullet]
2. and some equation

$$x^2 = \int_0^x ydy$$

.footnote[.gray[*I like footnotes]]

## Two columns? Why not

.left-column[
You may want to use some colors, like .red[red], to highlight .blue[important stuff].
Or even .orange[**bold some part of text**]. And sometime you want to provide a link to your source:

Gif source = [link](http://theodysseyonline.com/portland-state/life-lessons-from-andy-dwyer/343455)

]
.right-column[
![](andy.gif)
]

## Some bash code

 ```bash
#!/bin/bash

cd $HOME
echo "I am at home!"
 ```

###Some C++ code

 ```cpp
#include <iostream>

using namespace std;

int main(int argc, char *argv[])
{
    cout << "Hello World!\n";

    return 0;
}
 ```

## References

- Introduction to *remark*: http://remarkjs.com/
- Introduction to *markdown-to-slides*: [md2slides](http://www.lendmeyourear.net/wp-content/uploads/markdown-remark-slides.html)
- *Markdown* wiki: [markdown](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)

MARP

src

Markdown Here

Markdown Here

Code documentation

• GitHub readme/wiki, e.g. NuWro wiki

• MkDocs

  • site generator that's geared towards building project documentation

  • a single YAML configuration file

  • documentation source files are written in Markdown

  • deploying gh-pages

MkDocs - configuration file

Configuration file:

site_name: Hello World
pages:
    - Home: index.md
    - Installation: install.md
    - More: more.md
theme: readthedocs

• mkdocs serve - local preview at http://127.0.0.1:8000/
• mkdocs build - create the web site

MkDocs - example

MkDocs - gh-pages

• What is special about another web site generator?

• Automatic gh-pages deploying: mkdocs gh-deploy

• Example: Hello World

MkDocs - nuwro-wiki

• the same amount of work as for GitHub wiki

• better organization / structure

• pictures / plots within the same repository (w/o polluting NuWro repository)

• suggested address: https://nuwro.github.io/user-guide

• Test@my account: NuWro - wiki

Summary

• Markdown syntax is trivial, and yet, it provides an easy way to generate:

  • HTML code

  • LaTeX code (including Beamer)

  • PDF (through LaTeX engine)

  • HTML presentations

  • Beamer presentations

  • Documenation

  • and... wait for it

Terminal presentations using Markdown

Yes, really. Not sure why you would want that, though.

src