config_emacs/config.org

#+TITLE: Emacs Configuration
#+AUTHOR: Marc Pohling

Needs debian package ess
#+begin_src R :results output graphics :file test.png
library(ggplot2)

df <- data.frame(dose=c("D0.5", "D1", "D2"),
                len=c(4.2, 10, 29.5))
# Basic line plot with points
ggplot(data=df, aes(x=dose, y=len, group=1)) +
  geom_line()+
  geom_point()
# Change the line type
ggplot(data=df, aes(x=dose, y=len, group=1)) +
  geom_line(linetype = "dashed")+
  geom_point()
# Change the color
ggplot(data=df, aes(x=dose, y=len, group=1)) +
  geom_line(color="red")+
  geom_point()
#+end_src

#+RESULTS:
[[file:test.png]]

* Personal Information

#+begin_src emacs-lisp
 (setq user-full-name "Marc Pohling"
       user-mail-address "marc.pohling@googlemail.com")
#+end_src


* Update config in a running config
Two options:
  - reload the open file: M-x load-file, then press twice to accept
    the default filename, which is the currently opened
  - Point at the end of any sexp and press C-x C-e


* Customize settings

Move the customize settings to its own file, instead of saving
customize settings in [[file:init.el][init.el]].

#+begin_src emacs-lisp
 (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
 (load custom-file)
#+end_src


* Theme
** Font

#+begin_src emacs-lisp
 (set-face-attribute 'default nil :font "Hack-12")
#+end_src

** Material Theme
The [[https://github.com/cpaulik/emacs-material-theme][Material Theme]] comes in a dark and a light variant. Not too dark
to be strenious though.

#+begin_src emacs-lisp
 (use-package material-theme
     :if (window-system)
     :defer t
     :ensure t
;;     :init
;;     (load-theme 'material t)
 )
#+end_src
** Apropospriate Theme
Variants dark and light

#+begin_src emacs-lisp
 (use-package apropospriate-theme
     :if (window-system)
     :defer t
     :ensure t
     :init
     (load-theme 'apropospriate-dark t)
 )
#+end_src


* Sane defaults
Sources for this section include [[https://github.com/magnars/.emacs.d/blob/master/settings/sane-defaults.el][Magnars Sveen]] and [[http://pages.sachachua.com/.emacs.d/Sacha.html][Sacha Chua]]

These functions are useful. Activate them.
#+begin_src emacs-lisp
 (put 'downcase-region 'disabled nil)
 (put 'upcase-region 'disabled nil)
 (put 'narrow-to-region 'disabled nil)
 (put 'dired-find-alternate-file 'disabled nil)
#+end_src

Answering just 'y' or 'n' should be enough.
#+begin_src emacs-lisp
 (defalias 'yes-or-no-p 'y-or-n-p)
#+end_src

Keep all backup and auto-save files in one directory
#+begin_src emacs-lisp
 (setq backup-directory-alist '(("." . "~/.emacs.d/backups")))
 (setq auto-save-file-name-transforms '((".*" "~/.emacs.d/auto-save-list/" t)))
#+end_src

UTF-8 please
#+begin_src emacs-lisp
 (setq locale-coding-system 'utf-8)
 (set-terminal-coding-system 'utf-8)
 (set-keyboard-coding-system 'utf-8)
 (set-selection-coding-system 'utf-8)
 (prefer-coding-system 'utf-8)
#+end_src

Avoid tabs in place of multiple spaces (they look bad in TeX)
and show empty lines
#+begin_src emacs-lisp
 (setq-default indent-tabs-mode nil)
 (setq-default indicate-empty-lines t)
#+end_src

Turn off blinking cursor
#+begin_src emacs-lisp
 (blink-cursor-mode -1)
#+end_src

Don't count two spaces after a period as the end of a sentence.
Just one space is needed
#+begin_src emacs-lisp
 (setq sentence-end-double-space nil)
#+end_src

Delete the region when typing, just like as we expect nowadays.
#+begin_src emacs-lisp
 (delete-selection-mode t)
#+end_src

Auto-indent when pressing RET, just new-line when C-j
#+begin_src emacs-lisp
 (define-key global-map (kbd "RET") 'newline-and-indent)
 (define-key global-map (kbd "C-j") 'newline)

#+end_src

Various stuff
#+begin_src emacs-lisp
 (show-paren-mode t)
 (column-number-mode t)

 (global-visual-line-mode)
 (diminish 'visual-line-mode)

 (setq uniquify-buffer-name-style 'forward)
#+end_src


* List buffers
Ibuffer is the improved version of list-buffers.
Make ibuffer the default buffer lister. [[http://ergoemacs.org/emacs/emacs_buffer_management.html][Source]]
#+begin_src emacs-lisp
 (defalias 'list-buffers 'ibuffer)
#+end_src

Also auto refresh dired, but be quiet about it. [[http://whattheemacsd.com/sane-defaults.el-01.html][Source]]
#+begin_src emacs-lisp
 (add-hook 'dired-mode-hook 'auto-revert-mode)
 (setq global-auto-revert-non-file-buffers t)
 (setq auto-revert-verbose nil)
#+end_src


* Org Mode
** Installation
Although org mode ships with Emacs, the latest version can be installed externally. The configuration here follows the [[http://orgmode.org/elpa.html][Org mode ELPA Installation instructions.]]
Added a hook to complete org functions, company-capf is necessary for this

#+begin_src emacs-lisp
 (use-package org
     :ensure org-plus-contrib
     :init
     (add-hook 'org-mode-hook
               (lambda ()
                 (add-to-list 'company-backends 'company-capf)
                 (add-hook 'completion-at-point-functions 'pcomplete-completions-at-point nil t)
                 (company-mode t)))
 )
#+end_src

To avoid problems executing source blocks out of the box. [[https://emacs.stackexchange.com/a/28604][Others have the same problem, too]]. The solution is to remove the .elc files form the package directory:

#+begin_src sh:
 var ORG_DIR=(let* ((org-v (cadr (split-string (org-version nil t) "@"))) (len (length org-v))) (substring org-v 1 (- len 2)))
 rm ${ORG_DIR}/*.elc
#+end_src

*** Org key bindings
Set up some global key bindings that integrate with Org mode features

#+begin_src emacs-lisp
 (bind-key "C-c l" 'org-store-link)
 (bind-key "C-c c" 'org-capture)
 (bind-key "C-c a" 'org-agenda)
#+end_src

Org overwrites RET and C-j, so I need to disable the rebinds
#+begin_src emacs-lisp
 (define-key org-mode-map (kbd "RET") nil) ;;org-return
 (define-key org-mode-map (kbd "C-j") nil) ;;org-return-indent
#+end_src

*** Org agenda
For a more detailed example [[https://github.com/sachac/.emacs.d/blob/83d21e473368adb1f63e582a6595450fcd0e787c/Sacha.org#org-agenda][see here]].

#+begin_src emacs-lisp
 (setq org-agenda-files
     (delq nil
         (mapcar (lambda (x) (and (file-exists-p x) x))
                 '("~/Archiv/Dokumente/Agenda"))
     )
 )
#+end_src

*** Org capture
#+begin_src emacs-lisp
 (bind-key "C-c c" 'org-capture)
 (setq org-default-notes-file "~/Archiv/Dokumente/Notizen/notes.org")
#+end_src


** Org Setup
Speed commands are a nice and quick way to perform certain actions while at the beginning of a heading. It's not activated by default.

See the doc for speed keys by checking out the documentation for speed keys in Org mode.

#+begin_src emacs-lisp
 (setq org-use-speed-commands t)
 (setq org-image-actual-width 550)
 (setq org-highlight-latex-and-related '(latex script entities))
#+end_src


** Org tags
The default value is -77, which is weird for smaller width windows. I'd rather have the tags align horizontally with the header.
45 is a good column number to do that.

#+begin_src emacs-lisp
 (setq org-tags-column 45)
#+end_src


** Org babel languages

#+begin_src emacs-lisp
 (org-babel-do-load-languages
'org-babel-load-languages
  '((python . t)
    (C . t)
    (calc . t)
    (latex . t)
    (java . t)
    (ruby . t)
    (lisp . t)
    (R . t)
    (scheme . t)
    (shell . t)
    (sqlite . t)
    (js . t)))

 (defun my-org-confirm-babel-evaluate (lang body)
     "Do not confirm evaluation for these languages."
     (not (or (string= lang "C")
              (string= lang "java")
              (string= lang "python")
              (string= lang "R")
              (string= lang "emacs-lisp")
              (string= lang "sqlite"))))
 (setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)
#+end_src

I want plots!
#+begin_src emacs-lisp
 (use-package ess
   :ensure t
 )
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)
(add-hook 'org-mode-hook 'org-display-inline-images)
#+end_src


** Org babel/source blocks
I like to have source blocks properly syntax highlighted and with the editing popup window staying within the same window so all the windows don't jump around. Also, having the top and bottom trailing lines in the block is a waste of space, so we can remove them

I noticed that fontification doesn't work with markdown mode when the block is indented after editing it in the org src buffer - the leading #s for headers don't get fontified properly because they apppear as Org comments. Setting ~org-src-preserve-identation~ makes things consistent as it doesn't pad source blocks with leading spaces

#+begin_src emacs-lisp
 (setq org-src-fontify-natively t
       org-src-window-setup 'current-window
       org-src-strip-leading-and-trailing-blank-lines t
       org-src-preserve-indentation t
       org-src-tab-acts-natively t)
#+end_src



* which-key
Greatly increases discovery of functions!
Click [[https://github.com/justbur/emacs-which-key][here]] for source and more info.
Info in Emacs: M-x customize-group which-key

#+begin_src emacs-lisp
 (use-package which-key
     :ensure t
     :diminish which-key-mode
     :config
     (which-key-mode)
     (which-key-setup-side-window-right-bottom)
     (which-key-setup-minibuffer)
     (setq which-key-idle-delay 0.5)
 )
#+end_src


* Ido (currently inactive)
better completion

begin_src emacs-lisp
 (use-package ido
     :init
     (setq ido-enable-flex-matching t)
     (setq ido-everywhere t)
     (ido-mode t)
     (use-package ido-vertical-mode
         :ensure t
         :defer t
         :init
         (ido-vertical-mode 1)
         (setq ido-vertical-define-keys 'C-n-and-C-p-only)
     )
 )
end_src


* ivy / counsel / swiper

Flx is required for fuzzy-matching
Is it really necessary?
begin_src emacs-lisp
 (use-package flx)
end_src

Ivy displays a window with suggestions for hotkeys and M-x

#+begin_src emacs-lisp
 (use-package ivy
     :ensure t
     :diminish
     (ivy-mode . "")                   ;; does not display ivy in the mode line
     :init
     (ivy-mode 1)
     :bind
     ("C-c C-r" . ivy-resume)
     :config
     (setq ivy-use-virtual-buffers t)  ;; recent files and bookmarks in ivy-switch-buffer
     (setq ivy-height 20)              ;; height of ivy window
     (setq ivy-count-format "%d/%d")   ;; current and total number
     (setq ivy-re-builders-alist       ;; regex replaces spaces with *
           '((t . ivy--regex-plus)))
 )
#+end_src

Counsel replaces:
- M-x
- C-x C-f find-file
- C-c h f describe-function
- C-c h v describe-variable
- M-i     imenu

The find-file replacement is nicer to navigate

#+begin_src emacs-lisp
 (use-package counsel
     :ensure t
     :bind*                           ;; load counsel when pressed
     (("M-x"     . counsel-M-x)
      ("C-x C-f" . counsel-find-file)
      ("C-c h f" . counsel-describe-function)
      ("C-c h v" . counsel-describe-variable)
      ("M-i"     . counsel-imenu)
     )
 )
#+end_src

Swiper ivy-enhances isearch

#+begin_src emacs-lisp
 (use-package swiper
     :ensure t
     :bind
     (("C-s"     . swiper)
      ("C-c C-r" . ivy-resume)
     )
 )
#+end_src
 

* Recentf
Requires counsel
#+begin_src emacs-lisp
 (use-package recentf
     :bind ("C-x C-r" . counsel-recentf)
     :config
     (recentf-mode t)
     (setq recentf-max-saved-items 200)
 )
#+end_src


* Programming
** Common things
List of plugins and settings which are shared between the language plugins


Highlight whitespaces, tabs, empty lines.

#+begin_src emacs-lisp
 (use-package whitespace
   :demand t
   :ensure nil
   :init
   (dolist (hook '(prog-mode-hook
                   text-mode-hook
                   conf-mode-hook))
    (add-hook hook #'whitespace-mode))
;;   :hook ;;not working in use-package 2.3
;;   ((prog-mode . whitespace-turn-on)
;;    (text-mode . whitespace-turn-on))
   :config
   (setq-default whitespace-style '(face empty tab trailing))
 )
#+end_src

Disable Eldoc, it interferes with flycheck

#+begin_src emacs-lisp
 (use-package eldoc
   :ensure nil
   :config
   (global-eldoc-mode -1)
 )
#+end_src

Colorize colors as text with their value
#+begin_src emacs-lisp
 (use-package rainbow-mode
   :ensure t
   :init
   (add-hook 'prog-mode-hook 'rainbow-mode t)
;;   :hook prog-mode ;; not working in use-package 2.3
   :config
   (setq-default rainbow-x-colors-major-mode-list '())
 )
#+end_src

** Company Mode
Complete Anything!

Activate company and make it react nearly instantly

#+begin_src emacs-lisp
 (use-package company
     :ensure t
     :config
     (setq-default company-minimum-prefix-length 1
                   company-tooltip-align-annotation t
                   company-tooltop-flip-when-above t
                   company-show-numbers t
                   company-idle-delay 0.1)
 )
#+end_src

*** Company backend hooks

Backend configuration for python-mode

Common backends are:
- company-files:    files & directory
- company-keywords: keywords
- company-capf:     ??
- company-abbrev:   ??
- company-dabbrev:  dynamic abbreviations
- company-ispell:   ??

#+begin_src emacs-lisp
 (defun company/python-mode-hook()
   (set (make-local-variable 'company-backends)
        '((company-jedi company-dabbrev) company-capf company-files))
   (company-mode t)
 )
#+end_src

Backend configuration for lisp-mode

#+begin_src emacs-lisp
 (defun company/elisp-mode-hook()
   (set (make-local-variable 'company-backends)
        '((company-elisp company-dabbrev) company-capf company-files))
   (company-mode t)
 )
#+end_src

*** Misc Company packages

Addon to sort suggestions by usage

#+begin_src emacs-lisp
 (use-package company-statistics
     :ensure t
     :after company
     :config
     (company-statistics-mode 1)
 )
#+end_src

Get a popup with documentation of the completion candidate.
For the popups the package pos-tip.el is used and automatically installed.
[[https://github.com/expez/company-quickhelp][Company Quickhelp]]
[[https://www.emacswiki.org/emacs/PosTip][See here for Pos-Tip details]]

#+begin_src emacs-lisp
 (use-package company-quickhelp
     :ensure t
     :after company
     :config
     (company-quickhelp-mode 1)
 )
#+end_src

Maybe add [[https://github.com/hlissner/emacs-company-dict][company-dict]]? It's a dictionary based on major modes, plus it has Yasnippet integration.

** Projectile
   Brings search functions on project level

   #+begin_src emacs-lisp
(use-package projectile
  :ensure t
  :defer t
  :bind
  (("C-c p p" . projectile-switch-project)
   ("C-c p s s" . projectile-ag))
  :init
  (setq-default
   projectile-cache-file (expand-file-name ".projectile-cache" user-emacs-directory)
   projectile-known-projects-file (expand-file-name
                                   ".projectile-bookmarks" user-emacs-directory))
  :config
  (projectile-mode t)
  (setq-default
   projectile-completion-system 'ivy
   projectile-enable-caching t
   projectile-mode-line '(:eval (projectile-project-name)))
 )
   #+end_src
** Lisp

#+begin_src emacs-lisp
(add-hook 'emacs-lisp-mode-hook 'company/elisp-mode-hook)
#+end_src

** Python

Systemwide following packages need to be installed:
- venv

The virtual environments need to have following modules installed:
- jedi
- epc
- pylint

#+begin_src emacs-lisp
 (use-package flycheck
     :ensure t
     :init
     (add-hook 'after-init-hook #'global-flycheck-mode)
     (add-hook 'python-mode-hook (lambda ()
                                     (semantic-mode 1)
                                     (flycheck-select-checker 'python-pylint)))
 )
#+end_src


Automatically start python-mode when opening a .py-file.
Not sure if python.el is better than python-mode.el.
See [[https://github.com/jorgenschaefer/elpy/issues/887][here]] for info about ~python-shell-completion-native-enable~.
The custom function is to run inferiour processes (do I really need that?), see [[https://emacs.stackexchange.com/questions/16361/how-to-automatically-run-inferior-process-when-loading-major-mode][here]].

Also limit the completion backends to those which make sense in Python.
#+begin_src emacs-lisp
 (use-package python
     :mode ("\\.py\\'" . python-mode)
     :interpreter ("python" . python-mode)
     :init
     (add-hook 'python-mode-hook 'company/python-mode-hook)
     :config
     (setq python-shell-completion-native-enable nil)
 )
#+end_src


Jedi is a backend for python autocompletion and needs to be installed on the server:
- pip install jedi
Code checks need to be installed, too:
- pip install flake8

#+begin_src emacs-lisp
 (use-package company-jedi
     :defer t
;;     :after company
     :ensure t
     :config
     (setq jedi:environment-virtualenv (list (expand-file-name "~/Archiv/Programmierprojekte/Python/virtualenv/")))
     (setq jedi:python-environment-directory (list (expand-file-name "~/Archiv/Programmierprojekte/Python/virtualenv/")))
     (add-hook 'python-mode-hook 'jedi:setup)
     (setq jedi:complete-on-dot t)
     (setq jedi:use-shortcuts t)
;;     (add-hook 'python-mode-hook 'company/python-mode-hook)
 )
#+end_src

A wrapper to handle virtual environments.
I strongly recommend to install virtual environments on the terminal, not through this wrapper, but changing venvs is fine.

TODO: automatically start an inferior python process or switch to it if already created

#+begin_src emacs-lisp
 (use-package pyvenv
     :ensure t
     :init
     (setenv "WORKON_HOME" (expand-file-name "~/Archiv/Programmierprojekte/Python/virtualenv/"))
     :config
     (pyvenv-mode t)
     (defun my/post-activate-hook()
         (setq jedi:environment-root pyvenv-virtual-env)
         (setq jedi:environment-virtualenv pyvenv-virtual-env)
         (setq jedi:tooltip-method '(nil)) ;; variants: nil or pos-tip and/or popup
         (setq python-shell-virtualenv-root pyvenv-virtual-env)
         ;; default traceback, other option M-x jedi:toggle-log-traceback
         ;; traceback is in  jedi:pop-to-epc-buffer
         (jedi:setup)
         (company/python-mode-hook)
         (setq jedi:server-args '("--log-traceback")))
;;         (add-to-list 'company-backends 'company-jedi)
;;         (add-to-list 'company-backends 'company-anaconda)
;;         (lambda ()
;;           (set (make-local-variable 'company-backends)
;;                '((company-jedi company-dabbrev) company-capf company-files)))
;;         (setq flycheck-checker 'python-pylint))
;;         (flycheck-select-checker 'python-pylint))
;;         (setq flycheck-checker 'python-flake8)
     (add-hook 'pyvenv-post-activate-hooks 'my/post-activate-hook)
 )
#+end_src


I want Emacs to automatically start the proper virtual environment.
Required is a .python-version file with, content in the first line being /path/to/virtualenv/
[[https://github.com/marcwebbie/auto-virtualenv][Github source]]

Depends on pyvenv

#+begin_src emacs-lisp
 (use-package auto-virtualenv
     :ensure t
;;     :after pyvenv
;;     :defer t
     :init
     (add-hook 'python-mode-hook 'auto-virtualenv-set-virtualenv)
     ;; activate on changing buffers
     ;; (add-hook 'window-configuration-change-hook 'auto-virtualenv-set-virtualenv)
     ;; activate on focus in
     ;; (add-hook 'focus-in-hook 'auto-virtualenv-set-virtualenv)
 )
#+end_src

Anaconda test

begin_src emacs-lisp
 (use-package anaconda-mode
     :ensure t
     :defer t
     :init
     (add-hook 'python-mode-hook 'anaconda-mode)
;;     (add-hook 'python-mode-hook 'anaconda-eldoc-mode)
     :config
     (setq anaconda-eldoc-mode 1)
 )
end_src

begin_src emacs-lisp
 (use-package company-anaconda
     :ensure t
     :defer t
     :init
     (defun my/company-anaconda-hook()
         (add-to-list 'company-backends 'company-anaconda))
     (add-hook 'python-mode-hook 'my/company-anaconda-hook)
 )
end_src



* Hydra
Hydra allows grouping of commands

#+begin_src emacs-lisp
 (use-package hydra
     :ensure t
     :bind
     ("C-c f" . hydra-flycheck/body)
     :config
     (setq-default hydra-default-hint nil)
 )
#+end_src

** Hydra Flycheck
Flycheck is necessary, obviously

#+begin_src emacs-lisp
 (defhydra hydra-flycheck (:color blue)

  "
^
^Flycheck^          ^Errors^            ^Checker^
^────────^──────────^──────^────────────^───────^───────────
_q_ quit _<_ previous _?_ describe
_m_ manual _>_ next _d_ disable
_v_ verify setup _f_ check _s_ select
^^                  ^^                  ^^
"
     ("q" nil)
     ("<" flycheck-previous-error :color red)
     (">" flycheck-next-error :color red)
     ("?" flycheck-describe-checker)
     ("d" flycheck-disable-checker)
     ("f" flycheck-buffer)
     ("m" flycheck-manual)
     ("s" flycheck-select-checker)
     ("v" flycheck-verify-setup)
 )
#+end_src


* Quality of Life