This repo still under construction ❗

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Contents

• Screenshots
• Installation
  • Manual
    • Dependencies
    • Emacs Packages
    • system
    • Files and Libraries
  • Docker
• Configuration
  • Emacs configuration
    • org
      • Babel
    • org ref
    • Latex
      • classes
      • minted
      • syntax highlighting, babel and other configs
    • functions
• Building
• Main structure of your org file

Screenshots

click to see the image in full size

Installation

Manual

Dependencies

Emacs packages

• you can use any Emacs package manager you want, but i prefer using straight.el.
  Straight.el config

  ;;-------------------------
  ;; MANDATORY PACKAGES
  ;;-------------------------
  
  ;; installing and configure STRAIGHT
  (defvar bootstrap-version)
  (let ((bootstrap-file
         (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
        (bootstrap-version 5))
    (unless (file-exists-p bootstrap-file)
      (with-current-buffer
          (url-retrieve-synchronously
           "https://raw.githubusercontent.com/raxod502/straight.el/develop/install.el"
           'silent 'inhibit-cookies)
        (goto-char (point-max))
        (eval-print-last-sexp)))
    (load bootstrap-file nil 'nomessage))
  ;; use use-package along with straight
  (straight-use-package 'use-package)
  ;; make `use-package` to automatically install all of your packages 
  ;; without the need for adding `:straight t`.
  (setq straight-use-package-by-default t)
      

• org
  org mode installation & configuration

  ;; Installing ORG
  (use-package org)
      

• org-contrib here we can see the usefulness of straight.el packages manager
  org contrib installation & configuration

  ;; Installing and configure ORG-CONTRIB 
  (use-package org-contrib
    :config
    (require 'ox-extra)
    (ox-extras-activate '(latex-header-blocks ignore-headlines)))
      

• org-ref: John Kitchin (i might replace it with org-cite or org-ref-cite “org-refv3” in the future)
  org-ref installation & configuration

  ;; Installing ORG-REF
  (use-package org-ref
    :after org
    :config
    (setq org-ref-default-bibliography '("<path/to/your/bibliography>")
          org-ref-bibliography-notes "<path/to/your/bibliography>"
          org-ref-pdf-directory "<path/to/your/papers/folder>"
          org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename-helm-bibtex
          bibtex-completion-pdf-field "file"
          bibtex-completion-pdf-symbol ""
          bibtex-completion-display-formats
          '((t . "${title:46} ${author:20} ${year:4} ${=type=:4}${=has-pdf=:1}${=has-note=:1}"))))
  
  (defun org-ref-open-in-scihub ()
    "Open the bibtex entry at point in a browser using the url field or doi field.
    Not for real use, just here for demonstration purposes."
    (interactive)
    (let ((doi (org-ref-get-doi-at-point)))
      (when doi
        (if (string-match "^http" doi)
            (browse-url doi)
          (browse-url (format "http://sci-hub.se/%s" doi)))
        (message "No url or doi found"))))
  #+end_src
      

• ox-latex

System

• Linux
  • Arch-based (Artix, Manjaro, Parabola): pacman -S texlive-most texlive-lang
  • Debian-based (Ubuntu/Linux Mint): apt-get install texlive-full
  • Some distros (like Void) use tlmgr to install TeX packages instead of the main package manager.
• Windows: Here. (Choose the net install to be able to install all packages.)
• MacOS: Here

Files and Libraries

• latex-mimosis

Configuration

1. follow the instruction on the latex-mimosis repo on how you can add this library and use it on your project
   • long story short, copy the files mimosis.cls and bibliography-mimosis.tex into your root project directory
2. call the setupfile using the #+SETUPFILE: keyword, in our case here:

   #+SETUPFILE: ./lib/thesis.setup
       

   • this file contain all the configuration i used in my org-master, you can modify it by yourself and add any extra configuration you see fit.
3. add org, org-ref and latex configuration to your init.el, (this is the emacs’s configuration file), you can use my own configuration
4. ./lib/code.inc: contain function for cleaning, exporting and building, i use them throughout my work using the keyword #+CALL
   • an example for that is when i used the init() function to clean my root directory.
   • first include the ./lib/code.inc file, then call whatever function you want.

     #+INCLUDE:          ./lib/code.inc
     #+CALL:             init()
             

Emacs configuration

org

Babel

(eval-after-load "org"
  (use-package ob-async
    :ensure t
    :init (require 'ob-async)))
(setq org-confirm-babel-evaluate nil
      org-src-fontify-natively t
      org-confirm-babel-evaluate nil
      org-src-tab-acts-natively t)
(org-babel-do-load-languages
 'org-babel-load-languages
 '((python . t)
   (shell . t)
   (emacs-lisp . t)
   (R . t)
   ))
  

org ref

(use-package org-ref
  :config
  (setq reftex-default-bibliography '("/path/to/your/bibliography"))
  ;; see org-ref for use of these variables
  (setq org-ref-bibliography-notes "/path/to/your/bib/notes"
        org-ref-default-bibliography '("/path/to/your/bibliography")
        org-ref-pdf-directory "/path/to/your/papers"
        bibtex-dialect                    'biblatex
        ;; Optimize for 80 character frame display
        bibtex-completion-display-formats
        '((t . "${title:46} ${author:20} ${year:4} ${=type=:3}${=has-pdf=:1}${=has-note=:1}"))
        bibtex-completion-bibliography   "/path/to/your/bibliography"
        bibtex-completion-library-path    "/path/to/your/bib/notes"
        bibtex-completion-pdf-symbol ""
        bibtex-completion-notes-symbol ""
        ))

Latex

classes

(with-eval-after-load 'ox-latex
  (add-to-list 'org-latex-classes
               '("elsarticle"
                 "\\documentclass{elsarticle}
   [NO-DEFAULT-PACKAGES]
   [PACKAGES]
   [EXTRA]"
                 ("\\section{%s}" . "\\section*{%s}")
                 ("\\subsection{%s}" . "\\subsection*{%s}")
                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
  (add-to-list 'org-latex-classes
               '("mimosis"
                 "\\documentclass{mimosis}
   [NO-DEFAULT-PACKAGES]
   [PACKAGES]
   [EXTRA]
  \\newcommand{\\mboxparagraph}[1]{\\paragraph{#1}\\mbox{}\\\\}
  \\newcommand{\\mboxsubparagraph}[1]{\\subparagraph{#1}\\mbox{}\\\\}"
                 ("\\chapter{%s}" . "\\chapter*{%s}")
                 ("\\section{%s}" . "\\section*{%s}")
                 ("\\subsection{%s}" . "\\subsection*{%s}")
                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                 ("\\mboxparagraph{%s}" . "\\mboxparagraph*{%s}")
                 ("\\mboxsubparagraph{%s}" . "\\mboxsubparagraph*{%s}")))

  (add-to-list 'org-latex-classes
               '( "koma-article"
                  "\\documentclass{scrartcl}"
                  ( "\\section{%s}" . "\\section*{%s}" )
                  ( "\\subsection{%s}" . "\\subsection*{%s}" )
                  ( "\\subsubsection{%s}" . "\\subsubsection*{%s}" )
                  ( "\\paragraph{%s}" . "\\paragraph*{%s}" )
                  ( "\\subparagraph{%s}" . "\\subparagraph*{%s}" )))
  )
  

minted

;; Coloured LaTeX using Minted
(setq org-latex-listings 'minted
      org-latex-packages-alist '(("" "minted"))
      org-latex-pdf-process
      '("latexmk -pdflatex='xelatex -shell-escape -interaction nonstopmode' -pdf -bibtex -output-directory=%o -f %f"))

syntax highlighting, babel and other configs

;; syntex-highlighting
(use-package htmlize)
;;Don’t include a footer...etc in exported HTML document.
(setq org-html-postamble nil)
(setq org-src-window-setup 'current-window)

(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)
(add-hook 'org-mode-hook 'org-display-inline-images)
(custom-set-variables
 '(org-export-backends '(ascii beamed html calendar latex DOT)))

functions

• idea from “Automatically enabling multiple Emacs minor modes via a major mode hook - The…”

(defun enable-writing-minor-modes ()
  "Enable flyspell and visual line mode for calling from mode hooks"
  (visual-line-mode 1)
  (flyspell-mode 1))

(use-package org
  :hook (org-mode . enable-writing-minor-modes))

Getting Started

Usage

Building

• use make build to build the .pdf file, make clean to clean the temp files, make watch to sync your modification with the preview using your PDF viewer
  you can specify your PDF viewer application in the latexmkrc file

Main structure of your org file

Main file configuration

#+TITLE:            my org thesis
#+SUBTITLE:         it is great to use Emacs
#+LATEX_CLASS:      mimosis
#+latex_header:     \KOMAoptions{headings=small,fontsize=12,DIV=12}
#+SETUPFILE:        ./lib/thesis.setup
#+INCLUDE:          ./lib/gls_ac.setup
#+INCLUDE:          ./lib/code.inc
#+CALL:             init()
#+EXCLUDE_TAGS:     journal noexport ignore
#+EXPORT_FILE_NAME: org-master.pdf
# ---------------------------------------------------------------------
#+INCLUDE: "./title.org"
#+latex_header: \pagenumbering{arabic}

#+begin_export latex
 \listoffigures
 \listoftables
\printglossaries
\appendix
#+end_export
#+begin_export latex
 \bibliographystyle{unsrt}
 \bibliography{./lib/refs.bib}{}
#+end_export


* Build :noexport:

# Bind derivatives change variable values *locally* on export.

These two are here because I'm defining the title and toc manually using latex, so I don't want org-latex to take care of that.
#+BIND: org-latex-title-command ""
#+BIND: org-latex-toc-command ""
This is so that src code blocks get src highlighting from the minted package.
#+BIND: org-latex-listings minted
This beautifies table borders. It will only work if the booktabs package is loaded, which I do in the setup file.
#+BIND: org-latex-tables-booktabs t
And this configuration increases the default width of images, so that they are larger and more readable on print.
#+BIND: org-latex-image-default-width ".97\\linewidth"

Credits