# -*- mode: org -*-
#+TITLE:      Emacs init file written in org-mode
#+AUTHOR:    Arnaud Legrand
#+EMAIL:     arnaud.legrand@imag.fr
#+STARTUP: indent
#+LANGUAGE:   en

This is a "minimal" =.emacs= configuration file. For this configuration
to work, you'll need:
- emacs25 (>25.2) (this way installing through elpa will save you some
  time) and emacs-goodies (e.g., for color themes)
- org-mode > 9.0 (there has been several major compatibility breakage
  so need to stay away from old versions)
- ess and R
- texlive and auctex

* Installation Instructions
Backup you own =.emacs= if you have one and replace it with [[file:init.el][the content
of this file]]. If you ever want to regenerate if from this org
document, simply =M-x org-babel-tangle=.

* Machine-dependent configuration
#+begin_src emacs-lisp :tangle init.el
;; Machine-dependent configuration - adapt as required for your computer!

;; There are two kinds of settings that might have to be adapted to the
;; specific environment of a computer:
;; 1. Telling Emacs which executables to use for Python and R
;; 2. Telling Emacs to use a Web proxy

;;
;; 1. Telling Emacs which executables to use for Python and R
;;
;; Default setting: Use "python3" under Linux and macOS, but "Python" under Windows.
;; The default for R is "R" for all platforms (predefined by Emacs).
(setq org-babel-python-command
      (if (memq system-type '(windows-nt ms-dos))
          "Python"
        "python3 -q"))

;; If the Python and R executables are on your system's search path,
;; you should not have to modify anything here. If Emacs does not find
;; Python or R, or if it uses a different version of Python or R than you
;; expect, you can uncomment these two lines (one for Python, one for R)
;; and modify them to point to the executables.

;; Python
;; Be careful if the path to your Python installation contains spaces. The path
;; must then be surrounded by backslash-escaped quotation marks, as in
;; (setq org-babel-python-command "\"C:/Program Files/Python/Python37/python.exe\"")

;; R
;; (setq inferior-R-program-name "C:/Program Files/R/R-3.5.1/bin/x64/Rterm.exe")

;;
;; 2. Telling Emacs to use a Web proxy
;;
;; If your local network imposes the use of a Web proxy, you must uncomment and adapt
;; the following lines. Emacs does NOT use system-wide proxy settings. In most
;; cases, only the first two lines (proxy-name and proxy-port) need to be changed,
;; but sometimes the fifth line (no_proxy) also requires modifications. If you are
;; unsure what the right settings are, ask your local network administrator for help.

;; (let* ((proxy-name "proxy.mynetwork.org")
;;        (proxy-port "8080")
;;        (proxy-name-port (concat proxy-name ":" proxy-port))
;;        (proxy-url (concat "http://" proxy-name-port "/")))
;;   (setq url-proxy-services (list (cons "no_proxy" "127.0.0.1")
;;                                  (cons "http"  proxy-name-port)
;;                                  (cons "https"  proxy-name-port)))
;;   (setenv "http_proxy"  proxy-url)
;;   (setenv "https_proxy" proxy-url)
;;   (setenv "JVM_OPTS" (concat "-Dhttp.proxyHost=" proxy-name
;;                              " -Dhttp.proxyPort=" proxy-port)))
#+end_src

* Package sources
** Use melpa-stable
#+BEGIN_SRC emacs-lisp :tangle init.el
(package-initialize)
(add-to-list 'package-archives
		 '("melpa-stable" . "http://stable.melpa.org/packages/"))
#+END_SRC
* Loading files:  
** Loading babel: 						     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(require 'org)
#+end_src
** Loading ESS (Emacs support for R)
This seems to be needed on some platforms.
#+begin_src emacs-lisp :tangle init.el
(require 'ess-site)
#+end_src
* Emacs aesthetics:
** Remove splash screen:						:WEB:
#+begin_src emacs-lisp :tangle init.el
(setq inhibit-splash-screen t)
#+end_src
** Change frame name of emacs:					   :LUKA:WEB:
#+begin_src emacs-lisp :tangle init.el
(setq frame-title-format
  '("Emacs - " (buffer-file-name "%f"
    (dired-directory dired-directory "%b"))))
#+end_src
** Text coloring						     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
  (global-font-lock-mode t)
  (custom-set-faces
    '(flyspell-incorrect ((t (:inverse-video t)))))
#+end_src
** Line and column numbering					     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(line-number-mode 1)
(column-number-mode 1)
#+end_src
** Parenthesis                                                       :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(load-library "paren")
(show-paren-mode 1)
(transient-mark-mode t)
(require 'paren)
#+end_src
** Asking for confirmation concisely: 					:WEB:
Link: http://org.ryuslash.org/dotfiles/emacs/init.html#sec-7-1 Being
asked to type in yes explicitly all the time gets very tedious. I
understand that it is safer since y is much easier to type in
accidentally than yes and so the potential to say yes to things you
don't want is there, but I haven't had any such problems yet.

#+begin_src emacs-lisp :tangle init.el
(defalias 'yes-or-no-p 'y-or-n-p)
#+end_src
* Shortcuts:
** UTF 8 by default                                                 :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(set-terminal-coding-system 'utf-8)
(set-keyboard-coding-system 'utf-8)
(prefer-coding-system 'utf-8)
#+end_src
** Keyboard fix for Mac OS X users...                               :ADRIEN:
Thanks to Adrien Lebre for providing me with this
=ns-use-mac-modifier-symbols= thing. Unfortunately, this is broken at
the moment (I tried to wrap the command around the cond but it should
fail on mac). 
#+begin_src emacs-lisp :tangle init.el
    (setq
     ns-command-modifier 'meta         ; Apple/Command key is Meta
	 ns-alternate-modifier nil         ; Option is the Mac Option key
	 ns-use-mac-modifier-symbols  nil  ; display standard Emacs (and not standard Mac) modifier symbols
	 )
#+end_src
** CUA mode a.k.a =C-x, C-c, C-v= 
Yuck! Many people like this but I hate it as it conflicts with some of
my other shortcuts (e.g., the ones for spelling a region).
#+begin_src emacs-lisp :tangle init.el
(cua-mode t)
#+end_src
** Navigate back in text                                   :ARNAUD:noexport:
#+begin_src emacs-lisp
(defun jump-mark ()
  (interactive)
  (set-mark-command (point)))
(defun beginning-of-defun-and-mark ()
  (interactive)
  (push-mark (point))
  (beginning-of-defun))
(defun end-of-defun-and-mark ()
  (interactive)
  (push-mark (point))
  (end-of-defun))

(global-set-key "\^c\^b" 'beginning-of-defun-and-mark)
(global-set-key "\^c\^e" 'end-of-defun-and-mark)
(global-set-key "\^c\^j" 'jump-mark)
(global-set-key [S-f6] 'jump-mark)		;; jump from mark to mark
#+end_src
** Goto line							     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(global-set-key "\M-g" 'goto-line)
#+end_src
** Increase/decrease text size in emacs                                :WEB:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-+") 'text-scale-increase)
(global-set-key (kbd "C--") 'text-scale-decrease)
;; C-x C-0 restores the default font size
#+end_src
[11:26:47; 18.04.2014]
** Add spell checker to the file                                       :WEB:
#+begin_src emacs-lisp :tangle init.el
;; Inspired from http://tex.stackexchange.com/questions/166681/changing-language-of-flyspell-emacs-with-a-shortcut
;; (defun spell (choice)
;;    "Switch between language dictionaries."
;;    (interactive "cChoose:  (a) American | (f) Francais")
;;     (cond ((eq choice ?1)
;;            (setq flyspell-default-dictionary "american")
;;            (setq ispell-dictionary "american")
;;            (ispell-kill-ispell))
;;           ((eq choice ?2)
;;            (setq flyspell-default-dictionary "francais")
;;            (setq ispell-dictionary "francais")
;;            (ispell-kill-ispell))
;;           (t (message "No changes have been made."))) )

(define-key global-map (kbd "C-c s a") (lambda () (interactive) (ispell-change-dictionary "american")))
(define-key global-map (kbd "C-c s f") (lambda () (interactive) (ispell-change-dictionary "francais")))
(define-key global-map (kbd "C-c s r") 'flyspell-region)
(define-key global-map (kbd "C-c s b") 'flyspell-buffer)
(define-key global-map (kbd "C-c s s") 'flyspell-mode)
#+end_src
** Reload buffer                                                     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(global-set-key [f5] '(lambda () (interactive) (revert-buffer nil t nil)))
#+end_src
** Invoke magit (for git)                                              :WEB:
From http://magit.vc/manual/magit.pdf

#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-x g") 'magit-status)
(global-set-key (kbd "C-x M-g") 'magit-dispatch-popup)
;; (global-magit-file-mode 1)
#+end_src
* Small fixes for LaTeX:
** PDF with LaTeX by default                                        :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(defun auto-fill-mode-on () (TeX-PDF-mode 1))
(add-hook 'tex-mode-hook 'TeX-PDF-mode-on)
(add-hook 'latex-mode-hook 'TeX-PDF-mode-on)
(setq TeX-PDF-mode t)
#+end_src
** Auto-fill-mode
#+begin_src emacs-lisp :tangle init.el
(defun auto-fill-mode-on () (auto-fill-mode 1))
(add-hook 'text-mode-hook 'auto-fill-mode-on)
(add-hook 'emacs-lisp-mode 'auto-fill-mode-on)
(add-hook 'tex-mode-hook 'auto-fill-mode-on)
(add-hook 'latex-mode-hook 'auto-fill-mode-on)
#+end_src
* Org-mode convenient configuration
** Default directory
#+begin_src emacs-lisp :tangle init.el
(setq org-directory "~/org/")
#+end_src
** Cosmetics
#+begin_src emacs-lisp :tangle init.el
(setq org-hide-leading-stars t)
(setq org-alphabetical-lists t)
(setq org-src-fontify-natively t)  ;; you want this to activate coloring in blocks
(setq org-src-tab-acts-natively t) ;; you want this to have completion in blocks
(setq org-hide-emphasis-markers t) ;; to hide the *,=, or / markers
(setq org-pretty-entities t)       ;; to have \alpha, \to and others display as utf8 http://orgmode.org/manual/Special-symbols.html
#+end_src
** Agenda
*** Add short cut keys for the org-agenda			     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-cc" 'org-capture)
(global-set-key (kbd "C-c a") 'org-agenda)
(define-key global-map "\C-cl" 'org-store-link)
(define-key global-map (kbd "C-c a") 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)
(setq org-default-notes-file "~/org/notes.org")
     (define-key global-map "\C-cd" 'org-capture)
(setq org-capture-templates (quote (("t" "Todo" entry (file+headline "~/org/liste.org" "Tasks") "* TODO %?
  %i
  %a" :prepend t) ("j" "Journal" entry (file+datetree "~/org/journal.org") "* %?
Entered on %U
  %i
  %a"))))
#+end_src

#+RESULTS:
| t | Todo    | entry | (file+headline ~/org/liste.org Tasks) | * TODO %?\n  %i\n  %a           | :prepend | t |
| j | Journal | entry | (file+datetree ~/org/journal.org)     | * %?\nEntered on %U\n  %i\n  %a |          |   |

*** Agenda config						     :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(setq org-agenda-include-all-todo t)
(setq org-agenda-include-diary t)
#+end_src
* Org-mode shortcuts
** Adding date with brackets with command "C-c d":		       :LUKA:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-c d") 'insert-date)
(defun insert-date (prefix)
    "Insert the current date. With prefix-argument, use ISO format. With
   two prefix arguments, write out the day and month name."
    (interactive "P")
    (let ((format (cond
                   ((not prefix) "** %Y-%m-%d")
                   ((equal prefix '(4)) "[%Y-%m-%d]"))))
      (insert (format-time-string format))))
#+end_src
[16:34:01; 24.04.2013]

** Adding date with command "C-c t":				       :LUKA:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-c t") 'insert-time-date)
(defun insert-time-date (prefix)
    "Insert the current date. With prefix-argument, use ISO format. With
   two prefix arguments, write out the day and month name."
    (interactive "P")
    (let ((format (cond
                   ((not prefix) "[%H:%M:%S; %d.%m.%Y]")
                   ((equal prefix '(4)) "[%H:%M:%S; %Y-%m-%d]"))))
      (insert (format-time-string format))))
#+end_src
[16:34:15; 24.04.2013]
** Org-store-link:                                                  :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-c l") 'org-store-link)
#+end_src
** Navigating through org-mode:
Additional shortcuts for navigating through org-mode documents:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-c <up>") 'outline-up-heading)
(global-set-key (kbd "C-c <left>") 'outline-previous-visible-heading)
(global-set-key (kbd "C-c <right>") 'outline-next-visible-heading)
#+end_src
* Org-mode + babel:
** Seamless use of babel (no confirmation, lazy export)              :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
;; In org-mode 9 you need to have #+PROPERTY: header-args :eval never-export 
;; in the beginning or your document to tell org-mode not to evaluate every 
;; code block every time you export.
(setq org-confirm-babel-evaluate nil) ;; Do not ask for confirmation all the time!!
#+end_src
** Some initial languages we want org-babel to support:             :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
  (org-babel-do-load-languages
   'org-babel-load-languages
   '(
     (shell . t)
     (python . t)
     (R . t)
     (ruby . t)
     (ocaml . t)
     (ditaa . t)
     (dot . t)
     (octave . t)
     (sqlite . t)
     (perl . t)
     (screen . t)
     (plantuml . t)
     (lilypond . t)
     (org . t)
     (makefile . t)
     ))
  (setq org-src-preserve-indentation t)
#+end_src

** Adding source code blocks: 					       :LUKA:
*** With capital letters:
To use this type <s and then TAB
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>"))
#+end_src
*** Emacs-elisp code:
To use this type <m and then TAB
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("m" "#+begin_src emacs-lisp :tangle init.el\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
#+end_src

*** R code:
To use this type <r and then TAB. This creates an R block for textual output.
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("r" "#+begin_src R :results output :session *R* :exports both\n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
#+end_src

To use this type <R and then TAB. This creates an R block for graphics
that are stored in the =/tmp/=.
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("R" "#+begin_src R :results output graphics :file (org-babel-temp-file \"figure\" \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
#+end_src

To use this type <RR and then TAB. This creates an R block for
graphics that are stored in the directory of the current file.

#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("RR" "#+begin_src R :results output graphics :file  (org-babel-temp-file (concat (file-name-directory (or load-file-name buffer-file-name)) \"figure-\") \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
#+end_src
*** Python code
To use this type <p and then TAB
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("p" "#+begin_src python :results output :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
#+end_src

#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("P" "#+begin_src python :results output :session :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
#+end_src

#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("PP" "#+begin_src python :results file :session :var matplot_lib_filename=(org-babel-temp-file \"figure\" \".png\") :exports both\nimport matplotlib.pyplot as plt\n\nimport numpy\nx=numpy.linspace(-15,15)\nplt.figure(figsize=(10,5))\nplt.plot(x,numpy.cos(x)/x)\nplt.tight_layout()\n\nplt.savefig(matplot_lib_filename)\nmatplot_lib_filename\n#+end_src" "<src lang=\"python\">\n\n</src>"))
#+end_src
*** Bash "sh" code:
To use this type <b and then TAB
#+begin_src emacs-lisp :tangle init.el
(if (memq system-type '(windows-nt ms-dos))
    ;; Non-session shell execution does not seem to work under Windows, so we use
    ;; a named session just like for B.
    (add-to-list 'org-structure-template-alist
                 '("b" "#+begin_src shell :session session :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
  (add-to-list 'org-structure-template-alist
               '("b" "#+begin_src shell :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>")))
#+end_src

To use this type <B and then TAB. This comes with a session argument
(e.g., in case you want to keep ssh connexions open).
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("B" "#+begin_src shell :session *shell* :results output :exports both \n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
#+end_src
*** Graphviz
#+begin_src emacs-lisp :tangle init.el
(add-to-list 'org-structure-template-alist
        '("g" "#+begin_src dot :results output graphics :file \"/tmp/graph.pdf\" :exports both
   digraph G {
      node [color=black,fillcolor=white,shape=rectangle,style=filled,fontname=\"Helvetica\"];
      A[label=\"A\"]
      B[label=\"B\"]
      A->B
   }\n#+end_src" "<src lang=\"dot\">\n\n</src>"))
#+end_src
** Evaluating whole subtree:                                          :LUKA:
#+begin_src emacs-lisp :tangle init.el
(global-set-key (kbd "C-c S-t") 'org-babel-execute-subtree)
#+end_src
** Display images                                                   :ARNAUD:
#+begin_src emacs-lisp :tangle init.el
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images) 
(add-hook 'org-mode-hook 'org-display-inline-images)
(add-hook 'org-mode-hook 'org-babel-result-hide-all)
#+end_src
** Optimizing Python execution
*** Don't use readline completion
This often fails, yielding an ugly warning, and isn't of any use in Org-mode anyway
#+begin_src emacs-lisp :tangle init.el
(setq python-shell-completion-native-enable nil)
#+end_src
