curl -o emacs_files/ob-julia.el https://code.orgmode.org/bzg/org-mode/raw/master/contrib/lisp/ob-julia.el
curl -o emacs_files/ox-bibtex.el https://code.orgmode.org/bzg/org-mode/raw/master/contrib/lisp/ox-bibtex.el

;; Use your own packages for classical stuff
(package-initialize)
;; requires Emacs speaks statistics, Org
(require 'ess-site)
(require 'org)

;; removes ugly horizontal lines in html-exported code 
;; (not mandatory)
(setq org-html-keep-old-src t)

;; As ob-julia.el and ox-bibtex are less common, 
;; we use a local repository.
;;
;; Usage: emacs -q --load emacs_files/init.el
;;
;; In a more usual setting one should use:
;; (require 'ob-julia.el)
;; (require 'ox-bibtex)
(load-file "emacs_files/ob-julia.el") ; works with ess-site, our notebook engine
(load-file "emacs_files/ox-bibtex.el"); used for bibliography HTML-export 

;; allows julia src block (requires ob-julia.el)
(setq org-confirm-babel-evaluate nil)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((julia . t)))

;; defines image width in the OrgMode buffer (this is not for html
;; exports, for this you must use #+HTML_ATTR: :width 900px for
;; instance)
;;
;; This is not mandatory, but useful when one uses the gr() Plots.jl
;; backend as it exports wide .png files. CAVEAT: use imagemagick for
;; image resizing.
;;
(setq org-image-actual-width (/ (display-pixel-width) 4))

;; uses the minted package instead of the listings one
(setq org-latex-listings 'minted)

;; defines how to generate the pdf file using lualatex + biber
(setq org-latex-pdf-process
      '("lualatex -shell-escape -interaction nonstopmode -output-directory %o %f"
        "biber %b"
        "lualatex -shell-escape -interaction nonstopmode -output-directory %o %f"
        "lualatex -shell-escape -interaction nonstopmode -output-directory %o %f"))

# uses minted package instead of listings 
#+LATEX_HEADER: \usepackage{minted}    

# uses fonts to support Greek letters etc...
#+LATEX_HEADER: \usepackage{fontspec}
#+LATEX_HEADER: \setmonofont{DejaVu Sans Mono}[Scale=MatchLowercase]

# defines the \begin{comment} \end{comment} environment, used to avoid
# conflict between bibtex and biblatex
#+LATEX_HEADER: \usepackage{verbatim} 

# uses the biblatex package (and not the old bibtex) 
#+LATEX_HEADER: \usepackage[backend=biber, bibencoding=utf8 ]{biblatex}
# our bibliography file
#+LATEX_HEADER: \addbibresource{my-bib.bib}

#+BEGIN_EXPORT latex
\definecolor{bg}{rgb}{0.95,0.95,0.95}
\setminted[julia]{
  bgcolor=bg,
  breaklines=true,
  mathescape,
  fontsize=\footnotesize}
#+END_EXPORT

#+TITLE: My title
#+AUTHOR: author

* Very simple demo

#+BEGIN_SRC julia  :eval no-export :session *demo_session* :exports none
using Plots
#+END_SRC 

** UTF8 support + escape math equation
Note that UTF8 is supported (the \alpha variable) :

#+BEGIN_SRC julia :eval no-export :session *demo_session* :exports both :results silent :wrap "SRC julia :eval never"
# Generate a matrix $a_{i,j}=\mathcal{U}([0,1[)$
α=rand(4,5)
#+END_SRC

** Long lines are wrapped

#+BEGIN_SRC julia :eval no-export :session *demo_session* :exports both :results output :wrap "SRC julia :eval never"
function ⊗(a::AbstractArray{T},b::AbstractArray{S}) where {T<:Number,S<:Number} kron(a,b) end;

β=rand(2,5);
γ = α ⊗ β
#+END_SRC

** Plot example

You can easily generate plots, one example from [[http://docs.juliaplots.org/latest/examples/pyplot/][Plots Julia package]],
 is used to generate Figure [[PolarPlot]].

#+BEGIN_SRC julia  :eval no-export :session *demo_session* :exports code :results silent
Θ = linspace(0,1.5π,100)
r = abs(0.1 * randn(100) + sin.(3Θ))
plot(Θ,r,proj=:polar,m=2)
#+END_SRC

#+BEGIN_SRC julia  :eval no-export :session *demo_session* :results graphics :file example.png :exports results
savefig("example.png")
#+END_SRC

#+CAPTION: A polar plot.
#+ATTR_HTML: :width 900px
#+NAME: PolarPlot
#+RESULTS:
[[file:example.png]]

** Org with bibliography

\begin{align}
\label{eq:one_eq}
{\frac {d}{dt}}\iint _{\Sigma (t)}\mathbf {F} (\mathbf {r} ,t)\cdot d\mathbf {A} = & \iint _{\Sigma (t)}\left(\mathbf {F} _{t}(\mathbf {r},t)+\left[\nabla \cdot \mathbf {F} (\mathbf {r} ,t)\right]\mathbf {v}
\right)\cdot d\mathbf {A} - \\
& \oint _{\partial \Sigma (t)}\left[\mathbf{v} \times \mathbf {F} (\mathbf {r} ,t)\right]\cdot d\mathbf {s} \nonumber
\end{align}

Eq. \ref{eq:one_eq} is demonstrated in cite:Flanders1973.

#+BEGIN_EXPORT latex
\printbibliography
#+END_EXPORT

#+BEGIN_EXPORT latex
\begin{comment}
#+END_EXPORT
#+BIBLIOGRAPHY: my-bib plain
#+BEGIN_EXPORT latex
\end{comment}
#+END_EXPORT

#+BIBLIOGRAPHY: my-bib plain

#+BEGIN_EXPORT latex
\begin{comment}
#+END_EXPORT
#+BIBLIOGRAPHY: my-bib plain
#+BEGIN_EXPORT latex
\end{comment}
#+END_EXPORT

#+BEGIN_EXPORT latex
\printbibliography
#+END_EXPORT

emacs -q --load emacs_files/init.el