User:Timothee Flutre/Notebook/Postdoc/2012/07/25: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(→‎About Emacs: add default loading of ESS)
(8 intermediate revisions by the same user not shown)
Line 8: Line 8:
==About Emacs==
==About Emacs==


* '''Motivation''': when analyzing data for any research project, it's essential to know well a good text editor. Indeed, it's very efficient to be able to program in several languages (eg. Python, C/C++, R), interact with the shell like in a terminal, manipulate data and plot exploratory analyzes in R, ''all this within the same editor''! One such editor is [http://en.wikipedia.org/wiki/Emacs Emacs], and is available on Linux, Mac OS and Windows.
* '''Motivation''': when analyzing data for any research project, it's essential to know well a good text editor. Indeed, it's very efficient to be able to program in several languages (eg. Python, C/C++, R), interact with the shell like in a terminal, manipulate data and plot exploratory analyzes in R, ''all this within the same editor''! One such editor is [http://en.wikipedia.org/wiki/Emacs Emacs], and is available on Linux, Mac OS and Windows. For Mac OS X users, I recommend [http://vgoulet.act.ulaval.ca/en/emacs/mac/ this distribution].


* '''Configuration''': my own file <nowiki>.emacs</nowiki>
* '''Documentation''':
** official [https://www.gnu.org/software/emacs/manual/html_node/emacs/index.html manual]
** I haven't found yet any good tutorial, outside of the official [https://www.gnu.org/software/emacs/tour/ tour]
** [http://www.emacswiki.org/ wiki] (with many tips)
** [https://github.com/emacsmirror/p code] (mirrors packages)
 
* '''Important packages''':
** [http://orgmode.org/) org-mode] (already included in emacs v >= 22.1)
** [http://cx4a.org/software/auto-complete/ Auto-Complete]
** [http://ess.r-project.org/ ESS]
** [http://www.gnu.org/software/auctex/ AUCTeX]
 
* '''Configuration''': my own file <nowiki>~/.emacs</nowiki> (I try to avoid customizing it too much)


  <nowiki>
  <nowiki>
Line 53: Line 65:
;; START config Auto-Complete
;; START config Auto-Complete
(require 'auto-complete-config)
(require 'auto-complete-config)
(add-to-list 'ac-dictionary-directories "~/.emacs.d//ac-dict")
(add-to-list 'ac-dictionary-directories "~/.emacs.d/ac-dict")
(ac-config-default)
(ac-config-default)
;; END config Auto-Complete
;; END config Auto-Complete
Line 61: Line 73:
;; START config ESS
;; START config ESS
(require 'ess-site)
(require 'ess-site)
;;(load "~/src_ext_nb/ESS/ess-12.04-4/lisp/ess-site")
;;(load "~/src_ext_nb/ESS/ess-12.09-2/lisp/ess-site")


;; tips from http://emacswiki.org/emacs/EmacsSpeaksStatistics
;; tips from http://emacswiki.org/emacs/EmacsSpeaksStatistics
(setq ess-eval-visibly-p nil) ;otherwise C-c C-r (eval region) takes forever
(setq ess-eval-visibly-p nil) ;otherwise C-c C-r (eval region) takes forever
(setq ess-ask-for-ess-directory nil) ;otherwise you are prompted each time you start an interactive R session
(setq ess-ask-for-ess-directory nil) ;otherwise you are prompted each time you start an interactive R session
;; tips source: http://www.emacswiki.org/emacs/ESSAuto-complete
(setq ess-use-auto-complete t)
;; END config ESS
;; END config ESS
;; clear R console (http://stackoverflow.com/a/3450038/597069)
(defun clear-shell ()
  (interactive)
  (let ((old-max comint-buffer-maximum-size))
    (setq comint-buffer-maximum-size 0)
    (comint-truncate-buffer)
    (setq comint-buffer-maximum-size old-max)))


;;--------------------------------------------------------------------
;;--------------------------------------------------------------------


;; START config AUCTeX
;; START config AUCTeX
(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/auctex.el" nil t t)
;;(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/auctex.el" nil t t)
(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/preview-latex.el" nil t t)
;;(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/preview-latex.el" nil t t)
(add-to-list 'load-path "/home/tflutre/src/LATEX_PKGS/AUCTEX")
;;(add-to-list 'load-path "/home/tflutre/src/LATEX_PKGS/AUCTEX")
(setq TeX-auto-save t)
(setq TeX-auto-save t)
(setq TeX-parse-self t)
(setq TeX-parse-self t)
Line 84: Line 107:


;; START config org-mode
;; START config org-mode
(setq load-path (cons "/home/tflutre/src/ORG-MODE/org-7.8.03/lisp" load-path))
(setq load-path (cons "/home/tflutre/src/ORG-MODE/org-7.8.03/contrib/lisp" load-path))
(require 'org-install)
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-cc" 'org-capture)
(global-set-key "\C-cc" 'org-capture)
Line 105: Line 124:
       '(("breaklines")))
       '(("breaklines")))
(setq org-log-done 'time)
(setq org-log-done 'time)
(setq org-startup-truncated nil) ;so that lines longer than the screen are not truncated
;; END config org-mode
;; END config org-mode
;;--------------------------------------------------------------------                                                                 
;; START config python-mode
(setq
python-shell-interpreter "ipython"
python-shell-interpreter-args ""
python-shell-prompt-regexp "In \\[[0-9]+\\]: "
python-shell-prompt-output-regexp "Out\\[[0-9]+\\]: "
python-shell-completion-setup-code
  "from IPython.core.completerlib import module_completion"
python-shell-completion-module-string-code
  "';'.join(module_completion('''%s'''))\n"
python-shell-completion-string-code
  "';'.join(get_ipython().Completer.all_completions('''%s'''))\n")
;; END config python-mode
</nowiki>
</nowiki>
* '''Important packages''':
** [http://ess.r-project.org/ ESS]
** [http://cx4a.org/software/auto-complete/ Auto-Complete]
** [http://orgmode.org/) org-mode]
** [http://www.gnu.org/software/auctex/ AUCTeX]


* '''Tips''':
* '''Tips''':
** from the office computer, log interactively to a cluster node, launch <code>emacs --daemon</code> and keep the terminal open indefinitely; then access this session from any computer, e.g. a laptop, with <code>emacsclient -t</code>
** from the office computer (desktop), log interactively to a cluster node, launch <code>emacs --daemon</code> and keep the terminal open indefinitely; then access this session from any computer, e.g. a laptop, with <code>emacsclient -t</code>
** especially useful with [http://en.wikipedia.org/wiki/PuTTY PuTTY] on Windows, launch emacs so that its window is the terminal itself, via <code>emacs -nw</code>
** especially useful with [http://en.wikipedia.org/wiki/PuTTY PuTTY] on Windows, launch emacs so that its window is the terminal itself, via <code>emacs -nw</code>


Revision as of 07:41, 20 January 2014

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

About Emacs

  • Motivation: when analyzing data for any research project, it's essential to know well a good text editor. Indeed, it's very efficient to be able to program in several languages (eg. Python, C/C++, R), interact with the shell like in a terminal, manipulate data and plot exploratory analyzes in R, all this within the same editor! One such editor is Emacs, and is available on Linux, Mac OS and Windows. For Mac OS X users, I recommend this distribution.
  • Documentation:
    • official manual
    • I haven't found yet any good tutorial, outside of the official tour
    • wiki (with many tips)
    • code (mirrors packages)
  • Configuration: my own file ~/.emacs (I try to avoid customizing it too much)
;; .emacs

(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(column-number-mode t) ;; in the mode line
 '(size-indication-mode t) ;; in the mode line
 '(display-time-mode 1) ;; in the mode line
 '(display-time-day-and-date t) ;; in the mode line
 '(display-time-24hr-format t) ;; in the mode line
 '(case-fold-search t)
 '(current-language-environment "UTF-8")
 '(default-input-method "rfc1345")
 '(global-font-lock-mode t nil (font-lock))
 '(show-paren-mode t))
(custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 )

(setq inhibit-startup-message t)

(add-to-list 'load-path "~/.emacs.d/")

(setq latex-run-command "pdflatex")

;; config for C/C++ code
(setq c-default-style "bsd"
          c-basic-offset 2
          tab-width 2
          indent-tabs-mode t)

;;--------------------------------------------------------------------

;; START config Auto-Complete
(require 'auto-complete-config)
(add-to-list 'ac-dictionary-directories "~/.emacs.d/ac-dict")
(ac-config-default)
;; END config Auto-Complete

;;--------------------------------------------------------------------

;; START config ESS
(require 'ess-site)
;;(load "~/src_ext_nb/ESS/ess-12.09-2/lisp/ess-site")

;; tips from http://emacswiki.org/emacs/EmacsSpeaksStatistics
(setq ess-eval-visibly-p nil) ;otherwise C-c C-r (eval region) takes forever
(setq ess-ask-for-ess-directory nil) ;otherwise you are prompted each time you start an interactive R session

;; tips source: http://www.emacswiki.org/emacs/ESSAuto-complete
(setq ess-use-auto-complete t)
;; END config ESS

;; clear R console (http://stackoverflow.com/a/3450038/597069)
(defun clear-shell ()
   (interactive)
   (let ((old-max comint-buffer-maximum-size))
     (setq comint-buffer-maximum-size 0)
     (comint-truncate-buffer)
     (setq comint-buffer-maximum-size old-max)))

;;--------------------------------------------------------------------

;; START config AUCTeX
;;(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/auctex.el" nil t t)
;;(load "/home/tflutre/src/LATEX_PKGS/AUCTEX/preview-latex.el" nil t t)
;;(add-to-list 'load-path "/home/tflutre/src/LATEX_PKGS/AUCTEX")
(setq TeX-auto-save t)
(setq TeX-parse-self t)
(setq-default TeX-master nil)
(setq TeX-save-query nil)
(setq TeX-PDF-mode t) ;; to have a pdf output for all LaTeX documents
;; END config AUCTeX

;;--------------------------------------------------------------------

;; START config org-mode
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-cc" 'org-capture)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (sh . t)
   (python . t)
   ))
(setq org-confirm-babel-evaluate nil)
(require 'org-latex)
(add-to-list 'org-export-latex-packages-alist '("" "listings"))
(setq org-export-latex-listings t)
(setq org-export-latex-listings-options
      '(("breaklines")))
(setq org-log-done 'time)
(setq org-startup-truncated nil) ;so that lines longer than the screen are not truncated
;; END config org-mode

;;--------------------------------------------------------------------                                                                  

;; START config python-mode
(setq
 python-shell-interpreter "ipython"
 python-shell-interpreter-args ""
 python-shell-prompt-regexp "In \\[[0-9]+\\]: "
 python-shell-prompt-output-regexp "Out\\[[0-9]+\\]: "
 python-shell-completion-setup-code
   "from IPython.core.completerlib import module_completion"
 python-shell-completion-module-string-code
   "';'.join(module_completion('''%s'''))\n"
 python-shell-completion-string-code
   "';'.join(get_ipython().Completer.all_completions('''%s'''))\n")
;; END config python-mode
  • Tips:
    • from the office computer (desktop), log interactively to a cluster node, launch emacs --daemon and keep the terminal open indefinitely; then access this session from any computer, e.g. a laptop, with emacsclient -t
    • especially useful with PuTTY on Windows, launch emacs so that its window is the terminal itself, via emacs -nw


Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Timothee_Flutre/Notebook/Postdoc/2012/07/25&oldid=765151"