M-x org-mode

simon

Jan. 24, 2019

Created: 2019-02-12 Tue 09:48

From where I talk ?

Who I am ?

Mainly a geek guy
Research Engineer at Univ. Paris 7 Diderot
- Post-Doc Católica (Chile)
- Post-Doc Univ. Liège (hi Berty!)
- PhD at ONERA Toulouse

simon.tournier@univ-paris-diderot.fr

https://github.com/zimoun

My life

2006-2010: Vim user… and happy!
2011 New Year Resolutions: Switch to Emacs (video)
2016: New Job with heavy context switch

Not able to Getting Things Done.

$\Rightarrow$ Switch to Org-mode

I am only an enthusiast user, not a guru

My typical use-cases

Organize my tasks and log them
Write docs for myself
Produce computational notebooks

(defun ask-at-point (&optional i-know)
  "Feel free to ask everything."
  (interactive "P")
  (if i-know (message "Quick Answer.")
   (browse-url
    (concat "https://www.ddg.gg/?q=org-mode+"
            (thing-at-point 'symbol)))))

What Org-mode is?

A major mode of Emacs
Markup language, help for:
- keeping notes
- maintenaing TODO lists
- planning projects
- authoring documents
- table editor
Killer feature of Emacs ;-)

What Emacs is ?

The Power to the people :-)

Explanations in previous info-math

https://zimoun.github.io/infomath-emacs/pres.html

(ok let quick recap in 3 slides)

Definition

Emacs is a User Interface (UI) to manipulate text

Decent editor
IDE for a lot of languages (CEDET, SLIME, Geiser, EIN)
Mail Reader, Mail Reader, RSS Reader, etc.
Extensible Lisp machine?
Windows Manager?
OS? :-)

Theorem / Corollary / Example

All what X is able, Emacs does it too.

Advice: give a try to the tutorial of Emacs: C-h t

Alternative Reality

How to configure

The Org-mode configuration is driven by

$HOME/.emacs.d/init.el

Configure what?

Nothing to do!

Org-mode is included in all recent Emacs

(since GNU Emacs 22 released in 2006)

But…

Specific features are in contrib

(require 'package)
(setq package-enable-at-startup nil)
(add-to-list 'package-archives
             ;; `use-package' is not in ELPA, as many more ;-)
             '("melpa" . "http://melpa.org/packages/"))
(add-to-list 'package-archives
               ;; Add org-plus-contrib
               '("org" . "http://orgmode.org/elpa/"))
(package-initialize)

M-x package-list-packages

Let's talk about Unicorn

org-mode is…

"Awesome!" – John Kitchin (video)

Org for beginners
A tutorial/blog
Google Tech Talk by Carsten Dominik (video)
Original Paper (2012)
Getting Started with Org-mode by New-York Emacs meetup (video)
An implementation: Org-mode + GTD
CEO explains his experience

Org is vast…

… start small!

"Don't try to set up the 'final' task managing system from the start. Because you have no idea yet what your system should look like. […] Start by creating and managing a small TODO list and then develop your own system as the needs arises." – Carsten Dominik (creator of org)

Where/How to start

2014-01-07-Map-for-learning-Org-Mode-for-Emacs-640x480.png

https://orgmode.org/orgcard.pdf

My experience

Learn a couple of its capabilities
Integrate them into your workflow
You’ll find yourself thinking, "Hum?, it would be nice if I could X"
Then browse the manual (C-h i m org)

… and, in fact, Org can do X

Show me the Unicorn!!

Markup languages

Basics

underline
bold
italic
verbatim
code
~~strike~~
list
section, link, etc.

Raw

* Level 1
** Level 2
*** Level 3
**** Level 4

   + _underline_
   + *bold*
   + /italic/

*** Other 3

   1) =verbatim=
   2) ~code~
   3) +strike+

** More 2

   - list
   - section, [[https://orgmode.org/][link]], etc.

Facilities to write

M-Enter creates new item
M-Left/Right changes the level
M-Up/Dow moves the item up/down
C-c C-n move next header (C-p previous)
C-c C-u move upper header (level 2->level 1)
S-Left/Right change list item kind (C-c -)
S-TAB cycles the visibility

Emacs power! ;-)

Equation (raw)

Let only consider $\pi^2$ or $\Pi_\infty$, considering
$$\cos(x) = \textrm{real}~ \sum_n \frac{ix}{n!}$$

\begin{array}{ccl}
u^{\prime\prime} + k^2 u &=& 0 \\
& \textrm{with} &
u(0) = 1 \\
& \textrm{and} &
u^\prime(1)=iku(1)
\end{array}

$\LaTeX$ support

The equations exported

Let only consider $\pi^2$ or $\Pi_\infty$, considering \[\cos(x) = \textrm{real}~ \sum_n \frac{ix}{n!}\]

\begin{array}{ccl} u^{\prime\prime} + k^2 u &=& 0 \\ & \textrm{with} & u(0) = 1 \\ & \textrm{and} & u^\prime(1)=iku(1) \end{array}

Exported?

Yes!

from .org to HTML or PDF (or .tex) or … Reveal.js etc.

—

C-c C-e opens the menu of exporters

More list: checkbox

* Stuff [2/4]

- [X] Read the Dautray-Lions
- [-] Write summary [75%]
  + [X] Tome 1
  + [X] Tome 2
  + [X] Tome 3
  + [ ] Les autres
- [ ] Present Chapter 2 in Seminar
- [X] Drink coffee

Validate: C-c C-c on the item
Automatic update

Wait!

Is not also a planner?

34909043-4ebd-4043-a6d5-c31b2f6cbbf4_1.8e2dea8a0fc20d8775352b09caca44ff.jpeg

Plan: TODO DONE (NEXT WAIT CANCELED) etc.

* TODO Presentation [1/4]
** TODO Collect ressources [50%]
*** DONE Read the manual
    CLOSED: [2019-01-22 Tue 17:12]
*** TODO Browse the web
** DONE Preparation
   DEADLINE: <2019-01-23 Wed>
   CLOSED: [2019-01-22 Tue 22:22]
** Free header
** TODO Lunch Bertrand
   SCHEDULED: <2019-01-24 Thu>
** TODO Fix bugs with Reveal.js
   DEADLINE: <2019-01-25 Fri>

C-c C-t cycles nothing->TODO->DONE->nothing
Automatic set date and hour when closing (see init.el)
S-Left/Right also works
C-c C-s schedules
C-c C-d assigns a deadline

Manipulation of dates

Cursor inside the brackets then S-Up/Down
C-c C-c updates the day
Use Emacs calendar M-x calendar

(C-h i g (emacs)Calendar Diary)

Agenda View

:bind ("\C-ca"  . org-agenda)

;; where to look for the agenda files
(setq org-agenda-files (directory-files-recursively "~/org/" "\.org$"))

demo

(C-c a a or M-x org-agenda)

Navigate: menu Agenda etc.
Search: C-a a s and e.g. web

@simon: v l to setup log on.

Tags / Priorities

** TODO Bertrand's idea
*** DONE Discuss                                                      :@meet:
    CLOSED: [2019-01-16 Wed 18:37]
*** TODO Proof-of-Concept with Julia                                   :code:
**** TODO [#B] Clean the geo file
**** TODO [#A] Read the mesh
**** TODO [#C] Update Petsc
**** TODO [#B] Implement decent Krylov
*** TODO Refresh the idea                                       :@meet:write:
    SCHEDULED: <2019-01-31 Thu 18:00>
*** TODO Sent the paper to Wave                                       :write:
    DEADLINE: <2019-02-01 Fri>
** DONE Calderon preconditioner                             :read:write:code:
   CLOSED: [2019-01-15 Tue 15:51]

demo

C-c a t shows the tasks sorted by priorities
C-c a m code shows the tasks corresponding to the tag code

Possible+Imposible = Possimpible?

or how to easily manage the table

M-x org-table-create

| Student | Algebra | Analysis |
|---------+---------+----------|
| Alice   |    12.5 |      15. |
| Bob     |     11. |      14. |
| John    |     10. |      10. |

C-c | creates with the convention line x col
M-S-Right creates new col (Left deletes)
M-a/e moves beginning/end cell
C-c - or C-c Enter inserts horizontal line
M-S-Up removes the current line
C-c ^ sorts the col

table and $\LaTeX$

Write table with Org-mode (easy!)
Export to .tex with C-c C-e C-b l l (body only)
Use \input{}

(or epxort to buffer C-c C-e C-b l L and copy/paste)

DEMO!

makefile

all: doc.tex table1.tex table2.tex
    pdflatex doc.tex

%.tex: %.org
     emacs -batch -q $< --eval="(org-latex-export-to-latex nil nil t t)"

clean:
    -rm table?.tex
    -rm doc.{aux,log}

The spreadsheet

| N | N^4 | ~Sqrt(N)~ | 1/N | Mean |
|---+-----+-----------+-----+------|
| 4 |     |           |     |      |
| 3 |     |           |     |      |
| 2 |     |           |     |      |
| 1 |     |           |     |      |
|   |     |           |     |      |
#+TBLFM: $2=$1^4::$3=sqrt($1)::$4=1/$1::$5=vmean($2..$4)::@6$1=vmean(@2$1..@4$1)

I do not use myself

C-c ? to get information the current cell
C-c } to enter in debbuging mode

Entry point: the tutorial :-)

Computational Document

Toward Reproducible workflow

"Buzzword – What'chu talkin' 'bout, Willis?" – Arnold

Org-Babel
An Effective Git And Org-Mode Based Workflow For Reproducible Research
Choosing your Workflow Applications
Scimax by John Kitchin
Emacs + Org-mode + Python = reproducible research (video)

Org-babel

The Babel Fish is small, yellow, and simultaneously translates from one spoken language to another.

The Hitchhiker's Guide to the Galaxy – Douglas Adams

Blocks

#+begin_src python
  def f(x):
    return x + x
#+end_src

#+begin_src r
  f <- function(x) {
  x + x
  }
#+end_src

#+begin_src julia
  function f(x)
      x + x
  end
#+end_src

Options with :tangle or :noweb or :export etc.
C-c C-, opens the menu of different blocks
Org 9.2 <s or <q … does not work anymore. Use Org Tempo.

Eval blocks

demo

C-c C-v t tangles i.e. writes to files the exposed blocks
C-c C-v e evals all the blocks

Remember!

Org-mode is:

Markdown on steroids
Jupyter notebook usable outside class (troll inside :-)

Start now!

galactic_explorer.en.png

Key of Success

Master a tool needs large amount of work

think all the maths you learn before complete non-trivial proofs
Master a tool is not easy; otherwise it is a lie

think nunchaku practise to be as efficient as Bruce Lee

Why computing tools should be different ?

Be good at something is long

My personal conclusion

Why flamewar tools ? :-)

Our daily life is interacting with computers
We are all differently wired
Cognition is not straightforward

Tools should be freedom, not constraint and pain.

Tools must help you to get things done
Org+Emacs pays off … for me

M-x org-mode

simon

Jan. 24, 2019

From where I talk ?

Who I am ?

My life

My typical use-cases

What Org-mode is?

What Emacs is ?

The Power to the people :-)

Explanations in previous info-math

Definition

Theorem / Corollary / Example

Alternative Reality

How to configure

Configure what?

But…

Let's talk about Unicorn

org-mode is…

Org is vast…

Where/How to start

My experience

Show me the Unicorn!!

Markup languages

Basics

Raw

Facilities to write

Equation (raw)

The equations exported

Exported?

More list: checkbox

Wait!

Plan: TODO DONE (NEXT WAIT CANCELED) etc.

Manipulation of dates

Agenda View

Tags / Priorities

Possible+Imposible = Possimpible?

M-x org-table-create

table and \(\LaTeX\)

makefile

The spreadsheet

Computational Document

Org-babel

Blocks

Eval blocks

Remember!

Start now!

Key of Success

My personal conclusion

Why flamewar tools ? :-)

Happy end?

Be productive in procrastination :-)