On org mode
Introduction
org mode is a markup language, initially designed for task management within emacs. Since then, it has evolved into a markdown alternative for general note taking purposes. It has also export functionalities.
org mode is great for writing short and simple texts. For example, these blog pages are written in org mode and exported to html. For scientific writing, native LaTeX has more advantages, because things like author's affiliations, reference management, and layout customisation work better. In my experience, advanced options become increasingly more difficult to achieve and you get diminishing returns. Your document won't be true plain text anymore and the main argument for using org mode, that is its simplicity, is gone. At this point, you should use LaTeX.
When writing an org document, it is good practice to declare the document type with:
#+mode: -*- mode: org
The general syntax of modifying an org documents default behaviour is
using #+<keyword>, followed by values.
Task management
Simple tasks require only two states, TODO and DONE. We can
also define our own states, although I currently don't use this
functionality:
#+todo: TODO WAIT IN-PROGRESS | DONE CANCELLED
The following creates a time stamp whenever a task is closed:
(setq org-log-done t)
The org-agenda view summarises tasks and can be used to scan across different files. In order to declare which files to scan, we use:
(setq org-agenda-files (list "~/org/scratch.org" "~/org/misc.org"))
The list of tasks can then be displayed via M-x org-agenda.
A good workflow is to couple this with orgzly, to get the tasks synced between your mobile phone and your personal computer.
In addition, I currently have in my init.el, which opens the
org-agenda view at start up:
(setq inhibit-splash-screen t)
(org-agenda-list)
(delete-other-windows)
Export
In general, org documents can contain metadata that will be used during export:
#+title: org mode #+author: ilhan özgen xian
Other possible metadata is #+date. If it's not defined, org mode
will use the system's clock.
html documents
By default, org mode creates html documents with javascript, whether it's needed or not. This behaviour can be modified as:
#+options: toc:nil html-scripts:nil num:nil
Here, toc:nil disables the table of contents, html-scripts:nil
disables javascript, and num:nil disables numbered headings.
LaTeX documents
My LaTeX preamble looks like this:
#+latex_class: article #+latex_class_options: [a4paper, draft]
Change draft to final once you are done. In general, I advise
against using org mode to generate complex manuscripts.
Interactive notebooks
An interesting application of org mode is literate programming, or
the ability to create notebooks that have executable code mixed
with exposition. This is done through Babel, which ships with org
mode. One advantage of using org mode is that it allows mixing
different programming languages in the same session. The syntax
for defining an active code block is:
#+begin_src python :session jupyter
The :session pde option specifies that the state of the workspace
is saved and can be used further if it is referenced. This is
useful for loading environment variables via bash. The list of
languages that are allowed to be executed within org are defined in
init.el as:
(org-babel-do-load-languages 'org-babel-load-languages '((shell . t) (python . t) (R . t)))
We can also control what gets exported:
#+begin_src python :session jupyter :exports both
The :exports option takes keywords both, none, and code.
org mode's default behaviour is to ask for permission before evaluating a code block. This is for security reasons, but it gets tedious if there are a lot of blocks to be evaluated. In these cases, use:
(setq org-html-validation-link nil)
org-tree-slide
org-tree-slide presents different sections of an org-file as
individual slides. Open an org-file and execute M-x
org-tree-slide-mode. Then, navigate through the slides using C->
(forward) and C-< (backward).