polarolouis/dotfiles
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Compare commits

base: polarolouis:66c1940a80b4393da46a1501100c6a50b0dbbbca
Branches Tags
polarolouis:main
polarolouis:anna
polarolouis:poste-stage-inrae
polarolouis:sacha
..
compare: polarolouis:75cfb0a46b363f30e5023b2b802a5834e9d8703b
Branches Tags
polarolouis:anna
polarolouis:poste-stage-inrae
polarolouis:sacha
polarolouis:main

No commits in common. "66c1940a80b4393da46a1501100c6a50b0dbbbca" and "75cfb0a46b363f30e5023b2b802a5834e9d8703b" have entirely different histories.
66c1940a80 ... 75cfb0a46b

4 changed files with 0 additions and 520 deletions
Show stats Expand all files Collapse all files

3
.bash_aliases
View file

@ -1,5 +1,2 @@
alias dc="docker compose"
alias dotfiles='/usr/bin/git --git-dir=$HOME/.dotfiles/ --work-tree=$HOME'
# Creating an alias to have git graph
git config --global alias.graph 'log --oneline --graph'

11
.bash_profile
View file

@ -3,14 +3,3 @@
source ~/.bashrc
PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]$(__git_ps1 " (%s)")\$ '
fi
# Thefuck to have 'fuck' alias to correct last command
eval $(thefuck --alias fuck)
# To enable conda auto-completion
eval "$(register-python-argcomplete3 conda)"
# Autocompletion
bind 'set show-all-if-ambiguous on'
#bind 'TAB:menu-complete'
bind 'set colored-completion-prefix on'

7
.emacs.d/init.el
View file

@ -300,10 +300,3 @@ A->B
(add-hook 'org-mode-hook 'org-babel-result-hide-all)
(setq python-shell-completion-native-enable nil)
(when (require 'company-mode nil 'noerror)
package-install 'company-mode)
(global-company-mode)
(load-theme 'leuven t)

499
.emacs.d/init.org
View file

@ -1,499 +0,0 @@
# -*- mode: org -*-
#+TITLE: Emacs init file written in org-mode
#+AUTHOR: Arnaud Legrand, Konrad Hinsen
#+STARTUP: indent
#+LANGUAGE: en
This is a "minimal" =.emacs= configuration file. For this configuration
to work, you'll need one of:
- Emacs 26 (preferred)
- Emacs 25 plus Org-Mode 9
* 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 (preferred) and melpa in addition to the default GNU archive
#+BEGIN_SRC emacs-lisp :tangle init.el
(package-initialize)
(add-to-list 'package-archives
'("gnu" . "https://elpa.gnu.org/packages/"))
(add-to-list 'package-archives
'("melpa-stable" . "https://stable.melpa.org/packages/"))
(add-to-list 'package-archives
'("melpa" . "https://melpa.org/packages/"))
(setq package-archive-priorities '(("melpa-stable" . 100)
("melpa" . 50)
("gnu" . 10)))
#+END_SRC
* Install packages
#+begin_src emacs-lisp :tangle init.el
(require 'cl)
(let* ((required-packages
'(dash
htmlize
ess
auctex))
(missing-packages (remove-if #'package-installed-p required-packages)))
(when missing-packages
(message "Missing packages: %s" missing-packages)
(package-refresh-contents)
(dolist (pkg missing-packages)
(package-install pkg)
(message "Package %s has been installed" pkg))))
#+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
'(
(emacs-lisp . t)
(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:
*** Enable the old template system with Orgmode 9.2 and later
#+begin_src emacs-lisp :tangle init.el
(setq rrmooc/new-org-templates (version<= "9.2" (org-version)))
(when rrmooc/new-org-templates
(require 'org-tempo))
#+end_src
*** Template definitions that work with the old and new templating systems
#+begin_src emacs-lisp :tangle init.el
(require 'subr-x)
(defun rrmooc/add-org-template (old-style-template)
(add-to-list 'org-structure-template-alist
(if rrmooc/new-org-templates
(cons
(first old-style-template)
(string-trim-right (substring (second old-style-template) 8 -9)))
old-style-template)))
#+end_src
*** With capital letters:
To use this type <s and then TAB
#+begin_src emacs-lisp :tangle init.el
(unless rrmooc/new-org-templates
;; this template is predefined in the new templating system
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("m" "#+begin_src emacs-lisp\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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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.
(rrmooc/add-org-template
'("b" "#+begin_src shell :session session :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
(rrmooc/add-org-template
'("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
* Company-mode :LOUIS:Completion:
** Installing Company-mode
#+begin_src emacs-lisp :tangle init.el
(when (require 'company-mode nil 'noerror)
package-install 'company-mode)
#+end_src
** Global enable Company-mode
#+begin_src emacs-lisp :tangle init.el
(global-company-mode)
#+end_src
* Thème
** Activation du thème
#+begin_src emacs-lisp :tangle init.el
(load-theme 'leuven t)
#+end_src