Modifying radian color

.bash_aliases

@@ -1 +1,4 @@
 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'

.bash_logout

@@ -0,0 +1,7 @@
+# ~/.bash_logout: executed by bash(1) when login shell exits.
+
+# when leaving the console clear the screen to increase privacy
+
+if [ "$SHLVL" = 1 ]; then
+    [ -x /usr/bin/clear_console ] && /usr/bin/clear_console -q
+fi

.bash_profile

@@ -3,3 +3,46 @@
     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-argcomplete conda)"
+
+# Set browser
+BROWSER=$(which firefox)
+
+# Autocompletion
+bind 'set show-all-if-ambiguous on'
+#bind 'TAB:menu-complete'
+bind 'set colored-completion-prefix on'
+
+# Add paths
+# set PATH so it includes user's private bin if it exists
+if [ -d "$HOME/bin" ] ; then
+    PATH="$HOME/bin:$PATH"
+fi
+
+# set PATH so it includes user's private bin if it exists
+if [ -d "$HOME/.local/bin" ] ; then
+    PATH="$HOME/.local/bin:$PATH"
+fi
+
+if [ -d "$HOME/.emacs.d/bin" ] ; then
+    PATH="$HOME/.emacs.d/bin:$PATH"
+fi
+
+if [ -d "/usr/local/go" ]; then
+    PATH="$PATH:/usr/local/go/bin"
+fi
+
+if [ -d "$HOME/.cargo"  ]; then
+    . "$HOME/.cargo/env"
+fi
+
+if [ -e /home/polarolouis/.nix-profile/etc/profile.d/nix.sh ]; then 
+    . /home/polarolouis/.nix-profile/etc/profile.d/nix.sh;
+    export XDG_DATA_DIRS=$HOME/.nix-profile/share:$HOME/.share:"${XDG_DATA_DIRS:-/usr/local/share/:/usr/share/}" 
+fi # added by Nix installer
+

.bashrc

@@ -43,7 +43,7 @@ esac
 # uncomment for a colored prompt, if the terminal has the capability; turned
 # off by default to not distract the user: the focus in a terminal window
 # should be on the output of commands, not on the prompt
-#force_color_prompt=yes
+# force_color_prompt=yes
 
 if [ -n "$force_color_prompt" ]; then
     if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
@@ -116,3 +116,27 @@ if ! shopt -oq posix; then
   fi
 fi
 
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('/home/polarolouis/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "/home/polarolouis/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "/home/polarolouis/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="/home/polarolouis/miniconda3/bin:$PATH"
+	. "$HOME/.bash_profile"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+
+export PYENV_ROOT="$HOME/.pyenv"
+command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"
+eval "$(pyenv init -)"
+
+
+# Fix to emacs not starting in Conda environment
+export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libc_malloc_debug.so
+. "$HOME/.cargo/env"

.config/fish/config.fish

@@ -0,0 +1,16 @@
+if status is-interactive
+    # Commands to run in interactive sessions can go here
+end
+
+# Color fix
+set -x fish_color_user --bold green
+
+# For informative git prompt
+set -x __fish_git_prompt_show_informative_status 1
+set -x __fish_git_prompt_showuntrackedfiles 1
+set -x __fish_git_prompt_color_untrackedfiles --bold red
+set -x __fish_git_prompt_showdirtystate 1
+set -x __fish_git_prompt_showcolorhints 1
+
+# Aliases
+abbr --add dotfiles git --git-dir=$HOME/.dotfiles --work-tree=$HOME

.emacs.d/init.el

@@ -0,0 +1,461 @@
+;; I fixed custom variables here
+(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.
+ '(custom-safe-themes
+   '("a27c00821ccfd5a78b01e4f35dc056706dd9ede09a8b90c6955ae6a390eb1c1e" default)))
+
+;; 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)))
+
+(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)))
+
+;(require 'cl)
+(let* ((required-packages
+        '(dash
+          htmlize
+          ess
+          auctex
+	    magit))
+       (missing-packages (cl-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))))
+
+(require 'org)
+
+(require 'ess-site)
+
+(setq inhibit-splash-screen t)
+
+(setq frame-title-format
+  '("Emacs - " (buffer-file-name "%f"
+    (dired-directory dired-directory "%b"))))
+
+(global-font-lock-mode t)
+(custom-set-faces
+  '(flyspell-incorrect ((t (:inverse-video t)))))
+
+(line-number-mode 1)
+(column-number-mode 1)
+
+(load-library "paren")
+(show-paren-mode 1)
+(transient-mark-mode t)
+(require 'paren)
+
+(defalias 'yes-or-no-p 'y-or-n-p)
+
+(add-hook 'org-mode-hook 'display-line-numbers-mode)
+
+(set-terminal-coding-system 'utf-8)
+(set-keyboard-coding-system 'utf-8)
+(prefer-coding-system 'utf-8)
+
+(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
+     )
+
+;; (cua-mode t) to activate
+
+(global-set-key "\M-g" 'goto-line)
+
+(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
+
+;; 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)
+
+(global-set-key [f5] '(lambda () (interactive) (revert-buffer nil t nil)))
+
+(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)
+
+(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)
+
+(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)
+
+(setq org-directory "~/org/")
+
+(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
+
+(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"))))
+
+(setq org-agenda-include-all-todo t)
+(setq org-agenda-include-diary t)
+;; Adding the ~/org directory to the list of directories to scan
+(setq org-agenda-files '("~/org"))
+
+(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))))
+
+(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))))
+
+(global-set-key (kbd "C-c l") 'org-store-link)
+
+(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)
+
+(defun org-toggle-emphasis ()
+  "Toggle hiding/showing of org emphasize markers."
+  (interactive)
+  (if org-hide-emphasis-markers
+      (set-variable 'org-hide-emphasis-markers nil)
+    (set-variable 'org-hide-emphasis-markers t))
+  (org-mode-restart))
+(define-key org-mode-map (kbd "C-c e") 'org-toggle-emphasis)
+
+;; 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!!
+
+(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)
+
+(setq rrmooc/new-org-templates (version<= "9.2" (org-version)))
+(when  rrmooc/new-org-templates
+  (require 'org-tempo))
+
+(require 'subr-x)
+(defun rrmooc/add-org-template (old-style-template)
+  (add-to-list 'org-structure-template-alist
+	       (if rrmooc/new-org-templates
+		   (cons
+		    (cl-first old-style-template)
+		    (string-trim-right (substring (cl-second old-style-template) 8 -9)))
+		 old-style-template)))
+
+(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>")))
+
+(rrmooc/add-org-template
+ '("m" "#+begin_src emacs-lisp\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
+
+(rrmooc/add-org-template
+ '("r" "#+begin_src R :results output :session *R* :exports both\n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
+
+(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>"))
+
+(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>"))
+
+(rrmooc/add-org-template
+ '("p" "#+begin_src python :results output :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
+
+(rrmooc/add-org-template
+ '("P" "#+begin_src python :results output :session :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
+
+(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>"))
+
+(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>")))
+
+(rrmooc/add-org-template
+ '("B" "#+begin_src shell :session *shell* :results output :exports both \n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
+
+(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>"))
+
+(global-set-key (kbd "C-c S-t") 'org-babel-execute-subtree)
+
+(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)
+
+(setq python-shell-completion-native-enable nil)
+
+;;; Beginning of my customisations
+
+(let* ((wanted-packages
+        '(flycheck ; grammar
+flycheck-grammalecte ; grammar
+          company ; auto-complete
+	   org-appear ; org emphasis appear
+	   org-fragtog ; see latex fragment in org
+	   org-bullets ; Nicer bullets
+	   use-package
+	   eglot ; LSP client
+	   counsel ; ivy autocomplete for M-x
+	   eldoc-box ; adding popup for eldoc
+	   powerline ; A cool powerline
+	   rainbow-delimiters ; To color parenthesis, brackets
+	   focus ; A package to dim surrounding text to focus on the current text
+	   aggressive-indent ; A package to force indentation and tidy code
+))
+       (missing-wanted-packages (cl-remove-if #'package-installed-p wanted-packages)))
+  (when missing-wanted-packages
+    (message "Missing wanted packages: %s" missing-wanted-packages)
+    (package-refresh-contents)
+    (dolist (pkg missing-wanted-packages)
+      (package-install pkg)
+      (message "Wanted package %s has been installed" pkg))))
+
+(use-package smart-mode-line
+:ensure t
+:init
+(setq sml/theme 'automatic) ; To prevent the popup for loading custom theme
+:config 
+(sml/setup))
+
+;; Below we modify Org Mode behavior
+
+;; When loading org-mode turns off auto-fill-mode
+(add-hook 'org-mode-hook 'turn-off-auto-fill)
+
+;; Emphasis markers now appear when hovering
+(add-hook 'org-mode-hook 'org-appear-mode)
+
+;; Nicer org bullets
+(add-hook 'org-mode-hook (lambda () (org-bullets-mode 1)))
+
+;; Auto-toggle LaTeX fragments
+(add-hook 'org-mode-hook 'org-fragtog-mode)
+
+(global-linum-mode 1)
+(global-visual-line-mode 1) ; 1 for on & 0 for off
+
+(global-company-mode)
+
+(ivy-mode 1)
+
+(setq ivy-use-virtual-buffers t)
+(setq ivy-count-format "(%d/%d) ")
+
+;;; LSP features
+;; Enables LSP for the provided languages
+(require 'use-package)
+
+(use-package eglot
+  :defer t
+  :commands (eglot eglot-ensure)
+  :hook
+  ((ess-mode . eglot-ensure)
+   (python-mode . eglot-ensure))
+  :config
+  ;(setq eglot-stay-out-of '(company))
+  (add-to-list 'eglot-server-programs '((c-mode c++-mode) "clangd-10")
+	             )
+  )
+
+;; Forcing the ESS mode to work
+
+(with-eval-after-load 'eglot
+  (add-to-list 'eglot-server-programs
+	           '(ess-mode . ("R" "--slave" "-e" "languageserver::run()"))))
+
+;; Activating eldoc-box to have a popup with the doc
+(require 'eldoc-box)
+(add-hook 'eglot-managed-mode-hook #'eldoc-box-hover-mode t)
+
+;; Workaround to disable the popup when we open the buffer
+(defun quit-eldoc-box-frame-before-doc-buffer (orig-fun &rest _arg)
+  (eldoc-box-quit-frame)
+  (funcall orig-fun t))
+
+(advice-add 'eldoc-doc-buffer
+            :around 'quit-eldoc-box-frame-before-doc-buffer)
+
+(add-hook 'prog-mode-hook 'rainbow-delimiters-mode)
+
+(global-aggressive-indent-mode 1)
+(add-to-list 'aggressive-indent-excluded-modes 'html-mode)
+
+(use-package numpydoc
+  :ensure t
+  :bind (:map python-mode-map
+              ("C-c C-n" . numpydoc-generate)))
+
+(use-package projectile
+:ensure t
+:config 
+(projectile-mode +1)
+;(setq projectile-switch-project-action #'magit-status)
+;(setq projectile-switch-project-action #'treemacs)
+;; Recommended keymap prefix on Windows/Linux
+:bind (:map projectile-mode-map 
+	          ("C-c p" . projectile-command-map)))
+
+;; The YASnippet package
+(use-package yasnippet
+:ensure t
+:config
+(yas-global-mode 1))
+
+;; The snippets for YASnippet
+(use-package yasnippet-snippets
+:ensure t)
+
+;; Perspective
+(use-package perspective
+  :ensure t
+  :bind
+  ("C-x C-b" . persp-list-buffers)         ; or use a nicer switcher, see below
+  :custom
+  (persp-mode-prefix-key (kbd "C-c M-p"))  ; pick your own prefix key here
+  :init
+  (persp-mode))
+
+(use-package solo-jazz-theme
+  :ensure t
+  :config
+  (load-theme 'solo-jazz t nil)) ;; t nil supposed to enable NO-CONFIRM disable NO-ENABLE

.emacs.d/init.org

@@ -0,0 +1,848 @@
+# -*- 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
+;; I fixed custom variables here
+(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.
+ '(custom-safe-themes
+   '("a27c00821ccfd5a78b01e4f35dc056706dd9ede09a8b90c6955ae6a390eb1c1e" default)))
+
+;; 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
+	    magit))
+       (missing-packages (cl-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
+** Add the line numbers on the left                                  :LOUIS:
+Add the number lines on the left side when Org mode is active
+#+begin_src emacs-lisp :tangle init.el
+(add-hook 'org-mode-hook 'display-line-numbers-mode)
+#+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) to activate 
+#+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)
+;; Adding the ~/org directory to the list of directories to scan
+(setq org-agenda-files '("~/org"))
+
+#+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
+** Toggling the visibility of emphasis markers                       :LOUIS:
+Sourced from [[https://stackoverflow.com/questions/10969617/hiding-markup-elements-in-org-mode]["Hiding markup Elements" on StackOverflow]]
+#+begin_src emacs-lisp :tangle init.el
+(defun org-toggle-emphasis ()
+  "Toggle hiding/showing of org emphasize markers."
+  (interactive)
+  (if org-hide-emphasis-markers
+      (set-variable 'org-hide-emphasis-markers nil)
+    (set-variable 'org-hide-emphasis-markers t))
+  (org-mode-restart))
+(define-key org-mode-map (kbd "C-c e") 'org-toggle-emphasis)
+#+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
+		    (cl-first old-style-template)
+		    (string-trim-right (substring (cl-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
+* Custom Louis                                                        :LOUIS:
+#+begin_src emacs-lisp :tangle init.el
+;;; Beginning of my customisations
+#+end_src
+** TODO Change to use package for clarity ! Installing wanted packages
+#+begin_src emacs-lisp :tangle init.el
+(let* ((wanted-packages
+        '(flycheck ; grammar
+flycheck-grammalecte ; grammar
+          company ; auto-complete
+	   org-appear ; org emphasis appear
+	   org-fragtog ; see latex fragment in org
+	   org-bullets ; Nicer bullets
+	   use-package
+	   eglot ; LSP client
+	   counsel ; ivy autocomplete for M-x
+	   eldoc-box ; adding popup for eldoc
+	   powerline ; A cool powerline
+	   rainbow-delimiters ; To color parenthesis, brackets
+	   focus ; A package to dim surrounding text to focus on the current text
+	   aggressive-indent ; A package to force indentation and tidy code
+))
+       (missing-wanted-packages (cl-remove-if #'package-installed-p wanted-packages)))
+  (when missing-wanted-packages
+    (message "Missing wanted packages: %s" missing-wanted-packages)
+    (package-refresh-contents)
+    (dolist (pkg missing-wanted-packages)
+      (package-install pkg)
+      (message "Wanted package %s has been installed" pkg))))
+#+end_src
+
+#+begin_src emacs-lisp
+; :tangle init.el
+;; Install straight.el
+(defvar bootstrap-version)
+(let ((bootstrap-file
+       (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
+      (bootstrap-version 5))
+  (unless (file-exists-p bootstrap-file)
+    (with-current-buffer
+        (url-retrieve-synchronously
+         "https://raw.githubusercontent.com/raxod502/straight.el/develop/install.el"
+         'silent 'inhibit-cookies)
+      (goto-char (point-max))
+      (eval-print-last-sexp)))
+  (load bootstrap-file nil 'nomessage))
+#+end_src
+** Smart mode line (Powerline)
+#+begin_src emacs-lisp :tangle init.el
+(use-package smart-mode-line
+:ensure t
+:init
+(setq sml/theme 'automatic) ; To prevent the popup for loading custom theme
+:config 
+(sml/setup))
+#+end_src
+** Org modifications
+#+begin_src emacs-lisp :tangle init.el
+;; Below we modify Org Mode behavior
+#+end_src
+*** Disabling auto-fill-mode when using org
+This snippet disables the auto-fill-mode which wraps the line when it exceeds a certain length
+#+begin_src emacs-lisp :tangle init.el
+;; When loading org-mode turns off auto-fill-mode
+(add-hook 'org-mode-hook 'turn-off-auto-fill)
+#+end_src
+*** Activating org-appear minor mode
+This mode makes the emphasis markers appear when the cursor is on it
+#+begin_src emacs-lisp :tangle init.el
+;; Emphasis markers now appear when hovering
+(add-hook 'org-mode-hook 'org-appear-mode)
+#+end_src
+*** Nicer Org bullets
+#+begin_src emacs-lisp :tangle init.el
+;; Nicer org bullets
+(add-hook 'org-mode-hook (lambda () (org-bullets-mode 1)))
+#+end_src
+*** Auto toggle the preview of LaTeX fragments
+#+begin_src emacs-lisp :tangle init.el
+;; Auto-toggle LaTeX fragments
+(add-hook 'org-mode-hook 'org-fragtog-mode)
+#+end_src
+** Visual line mode activated on startup
+#+begin_src emacs-lisp :tangle init.el
+(global-linum-mode 1)
+(global-visual-line-mode 1) ; 1 for on & 0 for off
+#+end_src
+** Remote image display                                           :disabled:
+This code was taken from https://emacs.stackexchange.com/questions/42281/org-mode-is-it-possible-to-display-online-images and makes use of the =org-yt= package.
+
+#+begin_src emacs-lisp 
+(require 'org-yt)
+
+(defun org-image-link (protocol link _description)
+  "Interpret LINK as base64-encoded image data."
+  (cl-assert (string-match "\\`img" protocol) nil
+             "Expected protocol type starting with img")
+  (let ((buf (url-retrieve-synchronously (concat (substring protocol 3) ":" link))))
+    (cl-assert buf nil
+               "Download of image \"%s\" failed." link)
+    (with-current-buffer buf
+      (goto-char (point-min))
+      (re-search-forward "\r?\n\r?\n")
+      (buffer-substring-no-properties (point) (point-max)))))
+
+(org-link-set-parameters
+ "imghttp"
+ :image-data-fun #'org-image-link)
+
+(org-link-set-parameters
+ "imghttps"
+ :image-data-fun #'org-image-link)
+#+end_src
+** Global enable Company-mode                                   :completion:
+#+begin_src emacs-lisp :tangle init.el
+(global-company-mode)
+#+end_src
+** Ivy for Emacs command completion
+#+begin_src emacs-lisp :tangle init.el
+(ivy-mode 1)
+
+(setq ivy-use-virtual-buffers t)
+(setq ivy-count-format "(%d/%d) ")
+#+end_src
+** LSP, programming and other IDE features
+*** Enabling eglot and adding ess-mode lsp
+Language Server Protocol (LSP) provides intellisense completion and other nice features of VS Code.
+#+begin_src emacs-lisp :tangle init.el
+;;; LSP features
+;; Enables LSP for the provided languages
+(require 'use-package)
+
+(use-package eglot
+  :defer t
+  :commands (eglot eglot-ensure)
+  :hook
+  ((ess-mode . eglot-ensure)
+   (python-mode . eglot-ensure))
+  :config
+  ;(setq eglot-stay-out-of '(company))
+  (add-to-list 'eglot-server-programs '((c-mode c++-mode) "clangd-10")
+	             )
+  )
+
+;; Forcing the ESS mode to work
+
+(with-eval-after-load 'eglot
+  (add-to-list 'eglot-server-programs
+	           '(ess-mode . ("R" "--slave" "-e" "languageserver::run()"))))
+
+#+end_src
+*** Floating pop-up for eldoc
+#+begin_src emacs-lisp :tangle init.el
+;; Activating eldoc-box to have a popup with the doc
+(require 'eldoc-box)
+(add-hook 'eglot-managed-mode-hook #'eldoc-box-hover-mode t)
+
+;; Workaround to disable the popup when we open the buffer
+(defun quit-eldoc-box-frame-before-doc-buffer (orig-fun &rest _arg)
+  (eldoc-box-quit-frame)
+  (funcall orig-fun t))
+
+(advice-add 'eldoc-doc-buffer
+            :around 'quit-eldoc-box-frame-before-doc-buffer)
+
+#+end_src
+*** Rainbow delimiters
+#+begin_src emacs-lisp :tangle init.el
+(add-hook 'prog-mode-hook 'rainbow-delimiters-mode)
+#+end_src
+*** Aggressive indent
+#+begin_src emacs-lisp :tangle init.el
+(global-aggressive-indent-mode 1)
+(add-to-list 'aggressive-indent-excluded-modes 'html-mode)
+#+end_src
+*** NumpyDoc to generate python docstring
+#+begin_src emacs-lisp :tangle init.el
+(use-package numpydoc
+  :ensure t
+  :bind (:map python-mode-map
+              ("C-c C-n" . numpydoc-generate)))
+#+end_src
+*** Projectile for project management
+#+begin_src emacs-lisp :tangle init.el
+(use-package projectile
+:ensure t
+:config 
+(projectile-mode +1)
+;(setq projectile-switch-project-action #'magit-status)
+;(setq projectile-switch-project-action #'treemacs)
+;; Recommended keymap prefix on Windows/Linux
+:bind (:map projectile-mode-map 
+	          ("C-c p" . projectile-command-map)))
+#+end_src
+*** YASnippet to provided code snippets
+#+begin_src emacs-lisp :tangle init.el
+;; The YASnippet package
+(use-package yasnippet
+:ensure t
+:config
+(yas-global-mode 1))
+
+;; The snippets for YASnippet
+(use-package yasnippet-snippets
+:ensure t)
+#+end_src
+*** Treemacs                                                     :disabled:
+#+begin_src emacs-lisp 
+;:tangle init.el
+(use-package treemacs
+  :ensure t
+  :defer t
+  :init
+  (with-eval-after-load 'winum
+    (define-key winum-keymap (kbd "M-0") #'treemacs-select-window))
+  (with-eval-after-load 'treemacs
+    (define-key treemacs-mode-map [mouse-1] #'treemacs-single-click-expand-action))
+  :config
+  (add-hook 'prog-mode-hook 'treemacs)
+  (progn
+    (setq treemacs-collapse-dirs                   (if treemacs-python-executable 3 0)
+          treemacs-deferred-git-apply-delay        0.5
+          treemacs-directory-name-transformer      #'identity
+          treemacs-display-in-side-window          t
+          treemacs-eldoc-display                   'simple
+          treemacs-file-event-delay                2000
+          treemacs-file-extension-regex            treemacs-last-period-regex-value
+          treemacs-file-follow-delay               0.2
+          treemacs-file-name-transformer           #'identity
+          treemacs-follow-after-init               t
+          treemacs-expand-after-init               t
+          treemacs-find-workspace-method           'find-for-file-or-pick-first
+          treemacs-git-command-pipe                ""
+          treemacs-goto-tag-strategy               'refetch-index
+          treemacs-header-scroll-indicators        '(nil . "^^^^^^")
+          treemacs-hide-dot-git-directory          t
+          treemacs-indentation                     2
+          treemacs-indentation-string              " "
+          treemacs-is-never-other-window           nil
+          treemacs-max-git-entries                 5000
+          treemacs-missing-project-action          'ask
+          treemacs-move-forward-on-expand          nil
+          treemacs-no-png-images                   nil
+          treemacs-no-delete-other-windows         t
+          treemacs-project-follow-cleanup          nil
+          treemacs-persist-file                    (expand-file-name ".cache/treemacs-persist" user-emacs-directory)
+          treemacs-position                        'left
+          treemacs-read-string-input               'from-child-frame
+          treemacs-recenter-distance               0.1
+          treemacs-recenter-after-file-follow      nil
+          treemacs-recenter-after-tag-follow       nil
+          treemacs-recenter-after-project-jump     'always
+          treemacs-recenter-after-project-expand   'on-distance
+          treemacs-litter-directories              '("/node_modules" "/.venv" "/.cask")
+          treemacs-project-follow-into-home        nil
+          treemacs-show-cursor                     nil
+          treemacs-show-hidden-files               t
+          treemacs-silent-filewatch                nil
+          treemacs-silent-refresh                  nil
+          treemacs-sorting                         'alphabetic-asc
+          treemacs-select-when-already-in-treemacs 'move-back
+          treemacs-space-between-root-nodes        t
+          treemacs-tag-follow-cleanup              t
+          treemacs-tag-follow-delay                1.5
+          treemacs-text-scale                      nil
+          treemacs-user-mode-line-format           nil
+          treemacs-user-header-line-format         nil
+          treemacs-wide-toggle-width               70
+          treemacs-width                           35
+          treemacs-width-increment                 1
+          treemacs-width-is-initially-locked       t
+          treemacs-workspace-switch-cleanup        nil)
+
+    ;; The default width and height of the icons is 22 pixels. If you are
+    ;; using a Hi-DPI display, uncomment this to double the icon size.
+    ;;(treemacs-resize-icons 44)
+
+    (treemacs-follow-mode t)
+    (treemacs-filewatch-mode t)
+    (treemacs-fringe-indicator-mode 'always)
+    (when treemacs-python-executable
+      (treemacs-git-commit-diff-mode t))
+
+    (pcase (cons (not (null (executable-find "git")))
+                 (not (null treemacs-python-executable)))
+      (`(t . t)
+       (treemacs-git-mode 'deferred))
+      (`(t . _)
+       (treemacs-git-mode 'simple)))
+
+    (treemacs-hide-gitignored-files-mode nil))
+  :bind
+  (:map global-map
+        ("M-0"       . treemacs-select-window)
+        ("C-x t 1"   . treemacs-delete-other-windows)
+        ("C-x t t"   . treemacs)
+        ("C-x t d"   . treemacs-select-directory)
+        ("C-x t B"   . treemacs-bookmark)
+        ("C-x t C-t" . treemacs-find-file)
+        ("C-x t M-t" . treemacs-find-tag)))
+
+(use-package treemacs-projectile
+  :after (treemacs projectile)
+  :ensure t)
+
+(use-package treemacs-icons-dired
+  :hook (dired-mode . treemacs-icons-dired-enable-once)
+  :ensure t)
+
+(use-package treemacs-magit
+  :after (treemacs magit)
+  :ensure t)
+#+end_src
+** Perspective to handle multiple workspaces
+#+begin_src emacs-lisp :tangle init.el
+;; Perspective
+(use-package perspective
+  :ensure t
+  :bind
+  ("C-x C-b" . persp-list-buffers)         ; or use a nicer switcher, see below
+  :custom
+  (persp-mode-prefix-key (kbd "C-c M-p"))  ; pick your own prefix key here
+  :init
+  (persp-mode))
+#+end_src
+* Theme
+** Activation du thème
+#+begin_src emacs-lisp :tangle init.el
+(use-package solo-jazz-theme
+  :ensure t
+  :config
+  (load-theme 'solo-jazz t nil)) ;; t nil supposed to enable NO-CONFIRM disable NO-ENABLE
+#+end_src

.radian_profile

@@ -0,0 +1 @@
+options(radian.color_scheme = "manni")