#+TITLE: Doom Emacs Configuration
:DRAWER:
#+STARTUP: overview

#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas

#+HTML_LINK_HOME: ./index.html
#+HTML_LINK_UP: ./index.html

#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="./css/htmlize.css"/>
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="./css/readtheorg.css"/>
#+HTML_HEAD: <script type="text/javascript" src="./js/jquery.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="./js/bootstrap.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="./js/jquery.stickytableheaders.min.js"></script>
#+HTML_HEAD: <script type="text/javascript" src="./js/readtheorg.js"></script>

#+PROPERTY: header-args :comments none :eval no :mkdir yes :results none :padline no
:END:

* LaTeX
** Coordinate
#+begin_src conf :tangle ~/.config/doom/snippets/latex/coordinate
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :coordinate
# --
\coordinate[${1:->}] (${2:name}) at (${3:pointcoordinate});
$0
#+end_src

** Draw
#+begin_src conf :tangle ~/.config/doom/snippets/latex/draw
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :draw
# --
\draw[${1:->}] (${2:point1}) -- (${3:point2});
$0
#+end_src

** Node
#+begin_src conf :tangle ~/.config/doom/snippets/latex/node
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :node
# --
node[${1:below right}] (${2:name}) {${3:label}};
$0
#+end_src

** Path
#+begin_src conf :tangle ~/.config/doom/snippets/latex/path
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :path
# --
\path[${1}] (${2:point1}) -- (${3:point2});
$0
#+end_src

* Matlab
** Clear
#+begin_src conf :tangle ~/.config/doom/snippets/matlab/clear
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :clear and close all
# --
clear; close all; clc;
$0
#+end_src

** Function
#+begin_src conf :tangle ~/.config/doom/snippets/matlab/function
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :function
# --
function [${4:outputs}] = ${1:functionName}(${2:inputs}, ${3:opts_param})
% $1 - Description
%
% Syntax: $1($2, $3)
%
% Inputs:
%    - $2 -
%    - $3 - Optionals parameters: structure with the following fields:
%        -
%
% Outputs:
%    - $4 -

%% Default value for opts
opts = struct(...
    '${5:outputs}', ${6:default_value} ...
);

if exist('opts_param','var')
    for opt = fieldnames($3)'
        if sum(strcmp(fieldnames(opts), opt{1})) == 1
            opts.(opt{1}) = $3.(opt{1});
        else
            warning(sprintf('%s is not a valid option.', opt{1}));
        end
    end
end

$0
#+end_src

* Org Mode
** Begin
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/begin
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :LaTeX Environment
# --
\begin{${1:equation}}
  $0
\end{$1}
#+end_src

** Caption
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/caption
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Caption
# --
#+caption: $0
#+end_src

** Block
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/block
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Org-Mode Block
#key: block
# --
#+begin_${1:$$(let ((type (yas-choose-value '("src" "example" "quote" "verse" "center" "latex" "html" "ascii"))))
               (if type (concat type (if (equal type "src")
                                         (concat " " (yas-choose-value '("emacs-lisp" "latex" "python" "sh" "matlab")))))))}
$0
#+end_${1:$(car (split-string yas-text))}
#+end_src

** Custom Box
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/cbox
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Custom Box
# --
#+attr_latex: :options [$1]{${2:blue}}{${3:ams nodisplayskip}}
#+begin_cbox
$0
#+end_cbox
#+end_src

** Latex Class
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/latex-class
#name: latex-class
#key: lc
#expand-env: ((classes (mapcar 'car org-latex-classes)))
# --
#+latex_class: ${1:$$(yas-choose-value classes)}
$0
#+end_src

** Bibliography with completion
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/bib
#name: bibliography with completion
#key: bib
# --
bibliography:${1:$$(yas-choose-value (org-ref-find-bibliography))}
#+end_src

** Cite
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/cite
#name: org-ref cite link
#key: cite
# --
cite:${1:$$(completing-read
       "bibtex key: "
       (let ((bibtex-files (org-ref-find-bibliography)))(bibtex-global-key-alist)))}
#+end_src

** Ref
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/ref
#name: org-ref ref link with completion
#key: ref
# --
ref:${1:$$(completing-read "label: " (org-ref-get-labels))}
#+end_src

** Beamer - CBOX
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/bcbox
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Beamer Custom Box
# --
,*** ${1:@@latex:@@}           :B_cbox:
,:PROPERTIES:
:BEAMER_env: cbox
:BEAMER_opt: {${2:blue}}{${3:ams nodisplayskip}}
:END:

$0
#+end_src

** Code
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/code
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Code
# --
#+caption: ${1:Listing Caption}
#+label: lst:${2:listing_name}
,#+begin_src ${3:listing_language}
$0
,#+end_src
#+end_src

** Equation
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/equation
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Equation
# --
#+name: eq:${1:equation_name}
\begin{equation}
$0
\end{equation}
#+end_src

** Figure
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/figure
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Figure
# --
#+name: fig:${1:figure_name}
#+caption: ${2:Figure caption}
[[file:${3:figs/}$1.${4:pdf}]]
$0
#+end_src

** Frac
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/frac
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :LaTeX Fraction
# --
\frac{$1}{$2} $0
#+end_src

** Left
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/left
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Left Right mathematical delimitations
# --
\left$1 $0 \right$2
#+end_src

** Minipage
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minipage
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :minipage
# --
#+BEGIN_EXPORT latex
\begin{figure}[htbp]
\centering
\begin{minipage}[t]{0.49\linewidth}
#+END_EXPORT
#+attr_latex: :float nil :width 0.95\linewidth
$0
#+BEGIN_EXPORT latex
\end{minipage}%
\hfill%
\begin{minipage}[t]{0.49\linewidth}
#+END_EXPORT
#+attr_latex: :float nil :width 0.95\linewidth

#+BEGIN_EXPORT latex
\end{minipage}
\end{figure}
#+END_EXPORT
#+end_src

** Multicolumn
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/multicolumn
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Multcolumn
# --
#+attr_latex: :float multicolumn
$0
#+end_src

** Subfigure
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/subfigure
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Subfigure
# --
#+name: fig:${1:figure_name}
#+caption: ${2:figure caption}
#+attr_latex: :environment subfigure :width 0.49\linewidth :align c
| file:${3:sub_fig_name}.${4:pdf}       | file:${5:sub_fig_name}.${6:pdf} |
| <<fig:$3>> ${7:sub figure caption}    | <<fig:$5>> ${8:sub figure caption}    |
$0
#+end_src

** Table
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/table
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Table
# --
#+name: tab:${1:table_name}
#+caption: ${2:Table caption}
#+attr_latex: :environment tabularx :width ${3:\linewidth} :align ${4:lXX}
#+attr_latex: :center t :booktabs t :float t
| $0  |   |   |
|---+---+---|
|   |   |   |
#+end_src

** Tikz
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/tikz
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz figure
# --
,#+begin_src latex :file ${1:figure_name}.pdf :post pdf2svg(file=*this*, ext="png") :exports both
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src
#+end_src

** Tikzfig
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/tikzfig
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz Figure
# --
#+NAME: fig:${1:figure_name}
#+HEADER: :headers '("\\\\usepackage{tikz}" "\\\\usepackage{import}" "\\\\import{$HOME/Cloud/thesis/LaTeX/}{config.tex}")
#+HEADER: :imagemagick t :fit yes :iminoptions -scale 100% -density 150 :imoutoptions -quality 100
#+HEADER: :results raw replace :buffer no :eval no-export :exports both :mkdirp yes
#+HEADER: :output-dir ${2:figs}
,#+begin_src latex :file $1.pdf :post pdf2svg(file=*this*, ext="png") :exports both
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src

#+NAME: fig:$1
#+CAPTION: ${3:Caption}
#+RESULTS: fig:$1
#+end_src

** Tikzheader
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/tikzheader
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz Header
# --
,* ${1:Title/Description of the figure}
,#+begin_src latex :file ${2:figure_name}.pdf :tangle figs/$2.tex :exports ${3:both}
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src

#+name: fig:$2
#+caption: $1 ([[./figs/$2.png][png]], [[./figs/$2.pdf][pdf]], [[./figs/$2.tex][tex]]).
#+RESULTS:
[[file:./figs/$2.png]]
#+end_src

** User-config
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/user-config
# -*- mode: snippet -*-
# name: user-config
# key: uc
# --
,#+begin_src emacs-lisp :tangle user-config.el
$1
,#+end_src
#+end_src

** User-init
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/user-init
# -*- mode: snippet -*-
# name: user-init
# key: ui
# --
,#+begin_src emacs-lisp :tangle user-init.el
$1
,#+end_src
#+end_Sec

** Wrap
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/wrap
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Wrap
# --
#+attr_latex: :float wrap
$0
#+end_src

** Matlab Specific
*** Mconfig
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mconfig
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Configuration-Header
# --
#+PROPERTY: header-args:matlab  :session *MATLAB*
#+PROPERTY: header-args:matlab+ :tangle ${1:filename}.m
#+PROPERTY: header-args:matlab+ :comments org
#+PROPERTY: header-args:matlab+ :exports both
#+PROPERTY: header-args:matlab+ :results none
#+PROPERTY: header-args:matlab+ :eval no-export
#+PROPERTY: header-args:matlab+ :noweb yes
#+PROPERTY: header-args:matlab+ :mkdirp yes
#+PROPERTY: header-args:matlab+ :output-dir ${2:figs}
$0
#+end_src

*** Mdescription
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Measurement-Description
# --
,* Measurement description
,** Setup                                                             :ignore:
*Setup*:

,** Goal                                                              :ignore:
*Goal*:

,** Measurements                                                      :ignore:
*Measurements*:

Three measurements are done:
| Measurement File        | Description                  |
|-------------------------+------------------------------|
| =mat/data_${1:001}.mat= | $2                           |

Each of the measurement =mat= file contains one =data= array with 3 columns:
| Column number | Description       |
|---------------+-------------------|
|             1 | $3                |
|             2 | $4                |
|             3 | Time              |

$0
#+end_src

*** Mfigure
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Figure
# --
,#+begin_src matlab :tangle no :exports results :results file replace
   exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}');
,#+end_src

,#+name: fig:$1
,#+caption: $0
,#+RESULTS:
[[file:figs/$1.png]]
#+end_src

*** Mfunction
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfunction
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Function
# --
,* ${1:Function Name}
:PROPERTIES:
:header-args:matlab+: :tangle src/${2:matlab_file_name}.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:$2>>

This Matlab function is accessible [[file:src/$2.m][here]].

,#+begin_src matlab
  function [${4:in_data}] = $2(${3:in_data})
  % $2 - $0
  %
  % Syntax: [$4] = $2($3)
  %
  % Inputs:
  %    - $3 -
  %
  % Outputs:
  %    - $4 -

  end
,#+end_src
#+end_src

*** Mheader
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mheader
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Header
# --
,* ${1:Heading Name}
:PROPERTIES:
:header-args:matlab+: :tangle matlab/${2:matlab_file_name}.m
:header-args:matlab+: :comments org :mkdirp yes
:END:
<<sec:$2>>

,** ZIP file containing the data and matlab files                     :ignore:
,#+begin_src bash :exports none :results none
  if [ matlab/$2.m -nt data/$2.zip ]; then
    cp matlab/$2.m $2.m;
    zip data/$2 \
        mat/data.mat \
        $2.m
    rm $2.m;
  fi
,#+end_src

,#+begin_note
  All the files (data and Matlab scripts) are accessible [[file:data/$2.zip][here]].
,#+end_note

$0
#+end_src

*** Minit
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minit
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Init
# --
,** Matlab Init                                             :noexport:ignore:
,#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
  <<matlab-dir>>
,#+end_src

,#+begin_src matlab :exports none :results silent :noweb yes
  <<matlab-init>>
,#+end_src

$0
#+end_src

*** Mtable
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mtable
#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Table
# --
,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
  data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
,#+end_src
$0
#+end_src