.emacs

;; absolute path of ~/.emacs.d
(setq emacs-home (expand-file-name (concat (getenv "HOME") "/.emacs.d/")))

;; disable welcome screen
(setq inhibit-startup-screen t)

;; =============================================================================
;; =========================== melpa package manager ===========================
;; =============================================================================

;; melpa package repository for extra packages
(require 'package)
;; run 'M-x package-refresh-contents RET' to get the melpa packages
(add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/"))
(add-to-list 'package-archives '("melpa-stable" . "https://stable.melpa.org/packages/") t)

;; =============================================================================
;; ============================== auto generated ===============================
;; =============================================================================

;; Added by Package.el.  This must come before configurations of
;; installed packages.  Don't delete this line.  If you don't want it,
;; just comment it out by adding a semicolon to the start of the line.
;; You may delete these explanatory comments.
(package-initialize)

(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.
 '(ansi-color-faces-vector
   [default default default italic underline success warning error])
 '(ansi-color-names-vector
   ["#242424" "#e5786d" "#95e454" "#cae682" "#8ac6f2" "#333366" "#ccaa8f" "#f6f3e8"])
 '(custom-enabled-themes '(tsdh-dark))
 '(package-selected-packages
   '(yasnippet company-rtags company-quickhelp use-package grip-mode cmake-ide undo-fu highlight-indent-guides conda blacken company-web web-mode impatient-mode clang-format multi-term company-irony-c-headers helm-rtags flycheck-rtags rtags ein diff-hl neotree flycheck-irony flycheck-mypy pylint flycheck magit helm-projectile ggtags company-irony irony projectile yaml-mode s dash dictcc helm-gtags helm-themes helm cmake-mode company company-jedi jedi epc markdown-mode flyspell-popup xclip)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(ediff-current-diff-A ((t (:foreground "White" :background "brown"))))
 '(ediff-even-diff-A ((t (:background "blue"))))
 '(ediff-even-diff-Ancestor ((t (:background "blue"))))
 '(ediff-even-diff-B ((t (:background "blue"))))
 '(ediff-even-diff-C ((t (:background "blue"))))
 '(ediff-odd-diff-A ((t (:background "blue"))))
 '(ediff-odd-diff-Ancestor ((t (:background "blue"))))
 '(ediff-odd-diff-B ((t (:background "blue"))))
 '(ediff-odd-diff-C ((t (:background "blue"))))
 '(term-color-blue ((t (:background "deep sky blue" :foreground "deep sky blue")))))

;; =============================================================================
;; =================== install packages via package manager ====================
;; =============================================================================

;; all packages, which have to installed via emacs package manager
(setq my-package-list '(blacken clang-format cmake-ide cmake-mode company company-irony company-irony-c-headers company-jedi
				     company-rtags company-quickhelp company-web conda dictcc diff-hl dash ein epc ggtags grip-mode
				     flycheck flycheck-irony flycheck-mypy flycheck-rtags
				     flymake-shellcheck
				     flyspell-popup helm helm-gtags helm-rtags helm-projectile
				     helm-themes highlight-indent-guides
				     impatient-mode irony yasnippet jedi magit markdown-mode
				     multi-term neotree projectile
				     rtags s undo-fu use-package web-mode yaml-mode xclip))

;; The file run_melpa contains the variable run-melpa. If the variable is true,
;; new packages must be installed.
;; The var is set by the setup.py script.
(load (concat emacs-home "run_melpa.el"))
(when run-melpa
  (progn
      (unless package-archive-contents
	(package-refresh-contents))
      (dolist (my-package my-package-list)
	(unless (package-installed-p my-package)
	  (progn
	    (package-install my-package)
	    (message "install package: %s" my-package)
	    )))
      ;; Set the variable to nil, otherwise all packages will be checked at
      ;; every start, which unnecessarily increases the start time.
      (write-region "(setq run-melpa nil)\n" nil (concat emacs-home "run_melpa.el")
		    )))


;; =============================================================================
;; ================ load emacs lisp functions from extra files  ================
;; =============================================================================

;; the directory contains packages which are not available at the package manager
(setq load-path (cons (concat emacs-home "lisp") load-path))
;; self-defined general functions
(load-file (concat emacs-home "lisp/help_function/autoload.el"))
;; configuration for different modes
(dolist (config (directory-files (concat emacs-home "modes") t ".el"))
  (load-file config))
;; loads host-dependent configurations, which are generated by the setup.py script
(load-file (concat emacs-home "setup_generated.el"))
;; loads host-dependent configurations, e.g. paths to executables
(if (file-exists-p (concat emacs-home "local-vars.el"))
    (load-file (concat emacs-home "local-vars.el")))

;; =============================================================================
;; =============================== enable modes ================================
;; =============================================================================

(require 'use-package)

;; the ido mode improve the path navigation in the mini buffer
(require 'ido)
(ido-mode t)
;; add llvm ir highlighting
;; from offical repo: https://github.com/llvm-mirror/llvm/tree/e74acf4ba7bb2df0b2a04548061b4c886efc368a/utils/emacs
(require 'llvm-mode)
;; symon is a hardware monitor, which display cpu, memory usage and more in the mini-buffer
;; https://github.com/zk-phi/symon
(require 'symon)

;; helm is a framework, which improve the UI of emacs
;; https://github.com/emacs-helm/helm
(require 'helm)
(helm-mode t)

;; company is a backend for auto completion in different modes (https://company-mode.github.io/)
(require 'company)
(add-hook 'after-init-hook 'global-company-mode)

;; register different company backends
(let ((company-backends-to-enable
       '(company-cmake
	 ;; add new backend
	 )))
  (dolist (backend company-backends-to-enable)
    (add-to-list 'company-backends backend))
  (eval-after-load 'company 'company-backends)
  )
;; this package enables a function to display the function documentation during running company completion
;; run `M-x company-show-doc-buffer` to verify if your company backend supports this
(company-quickhelp-mode)

;; library to managing projects, e.g a git repo is a project
(require 'projectile)
(setq projectile-indexing-method 'hybrid)
(setq projectile-sort-order 'recentf)

;; enable helm extension for projectile
(require 'helm-projectile)
(helm-projectile-on)

;; flycheck allows to highlight warnings and errors in the source code using external tools
(require 'flycheck)
(add-hook 'after-init-hook #'global-flycheck-mode)

;; diff-hl is a plugin which show git diff inside the buffer
;; highlight works just in GUI mode, navigation also in terminal
(require 'diff-hl)
(global-diff-hl-mode)
;; use flycheck to update highlight without saving file
(diff-hl-flydiff-mode)
(add-hook 'magit-post-refresh-hook 'diff-hl-magit-post-refresh)

;; emacs ipython notebook (ein)
;; the polymode allows to display markdown cells in notebooks
(setq ein:polymode t)

(add-hook 'rst-mode-hook 'sphinx-build-mode)

(require 'conda)

;; add indentation highlighting in buffers
(require 'highlight-indent-guides)
;; configure style
(set-face-background 'highlight-indent-guides-odd-face "darkgray")
(set-face-background 'highlight-indent-guides-even-face "dimgray")
(set-face-foreground 'highlight-indent-guides-character-face "dimgray")
(setq highlight-indent-guides-method 'character)
;; setup modes with indentation highlighting
(add-hook 'yaml-mode-hook 'highlight-indent-guides-mode)
(add-hook 'python-mode-hook 'highlight-indent-guides-mode)

;; enable yasnippet
(require 'yasnippet)
(yas-global-mode 1)

;; =============================================================================
;; =========================== configure main usage ============================
;; =============================================================================

;; enable c++-mode at cuda cu.files
(add-to-list 'auto-mode-alist '("\\.cu\\'" . c++-mode))

;; enable sh-mode at singularity .def recipe
(add-to-list 'auto-mode-alist '("\\.def\\'" . sh-mode))

;; enable copy/paste between emacs and x11
;; to install use following command in emcas (RET means key enter): M-x package-install RET xclip RET
;; the enable_xclip variable is generated by the setup.py script and located in setup_generated.el
(if (= enable_xclip 1)
    (progn
      (xclip-mode 1)
      (setq select-enable-clipboard t)
      )
  ()
  )

;; show cursor position within line
(column-number-mode 1)

(if (= flyspell-enable 1)
    (progn
     ;; enable on the fly spellcheck
     ;; spellcheck for the complete text
     (add-hook 'text-mode-hook 'flyspell-mode)
     ;;  spellcheck just for comments and strings (depends on the prog language)
     (add-hook 'prog-mode-hook 'flyspell-prog-mode)
     ;; when this mode is enabled, the spellchecker pop menu opens if the cursor stays on the wrong word for more than one second
     (add-hook 'flyspell-mode-hook #'flyspell-popup-auto-correct-mode)
     ))

(setq ediff-split-window-function 'split-window-horizontally)

;; disable scroll bar in GUI mode
(scroll-bar-mode -1)

;; allows to load every .dir-locals.el
;; can be a secure problem
;; by default, safe (system-dependent) variables are stored in the .emacs.
(setq enable-local-variables :all)

;; =============================================================================
;; ============================ global key bindings ============================
;; =============================================================================

;; replace the default emacs functions and do the same things without kill-ring
;; bind them to emacs's default shortcut keys:
(global-set-key (kbd "C-j") 'my-delete-line-backward) ; Ctrl+Shift+k
(global-set-key (kbd "C-k") 'my-delete-line)
(global-set-key (kbd "<C-delete>") 'my-delete-word)
(global-set-key (kbd "<M-DEL>") 'my-backward-delete-word)

;; swap shortcut of move to begin and move to indentation
(global-set-key (kbd "M-m") 'move-beginning-of-line)
(global-set-key (kbd "C-a") 'back-to-indentation)

;; shortcut to open the spellcheck pop-menu
(global-set-key (kbd "M-$") 'flyspell-popup-correct)

;; open company completion popup
(global-set-key (kbd "M-#") 'company-complete)

;; windmove is a built-in function that allows you to change the window selectively
;; it improves the functionality of 'C-x o'.
(global-set-key (kbd "C-c <left>")  'windmove-left)
(global-set-key (kbd "C-c <right>") 'windmove-right)
(global-set-key (kbd "C-c <up>")    'windmove-up)
(global-set-key (kbd "C-c <down>")  'windmove-down)
;; if the C-c bindings are overwritten by another mode
(global-set-key (kbd "C-x C-<left>")  'windmove-left)
(global-set-key (kbd "C-x C-<right>") 'windmove-right)
(global-set-key (kbd "C-x C-<up>")    'windmove-up)
(global-set-key (kbd "C-x C-<down>")  'windmove-down)

;; the original shortcut is M-|
;; but some German keyboards are too cheep to execute this combination
(global-set-key (kbd "M-_")  'shell-command-on-region)

;; original shortcut is C-x z
(global-set-key (kbd "M-<f3>")  'repeat)

;; another shortcut for switching framework
(global-set-key (kbd "C-x <down>") 'other-frame)

;; another shortcut for comment-line
(global-set-key (kbd "C-x ;") 'comment-line)

;; add shortcut to the dired-mode
(add-hook
 'dired-mode-hook
 (lambda()
   (define-key dired-mode-map "J" 'ido-dired)))

;; replace default emacs functions with helm functions
(global-set-key (kbd "M-x") 'helm-M-x)
(global-set-key (kbd "C-x r b") #'helm-filtered-bookmarks)
(global-set-key (kbd "C-x C-f") #'helm-find-files)
(global-set-key (kbd "C-x b") #'helm-buffers-list)

;; run dictcc translation
(global-set-key (kbd "M-ü") 'dictcc)

;; allow smart completion with <TAB>
(define-key helm-map (kbd "TAB") 'helm-execute-persistent-action)

;; set prefix key binding for every projectile command
(define-key projectile-mode-map (kbd "C-c p") 'projectile-command-map)
(projectile-mode +1)

;; run magit status command
(global-set-key (kbd "C-x g") 'magit-status)

(global-set-key (kbd "<f8>") 'neotree-toggle)

(global-unset-key (kbd "C-_"))
(global-set-key (kbd "C-_")   'undo-fu-only-undo)
(global-set-key (kbd "C-:") 'undo-fu-only-redo)


;; =============================================================================
;; =================================== other ===================================
;; =============================================================================

;; save all backup files to a central directory
(setq backup-directory-alist '(("." . "~/.emacs.d/backup"))
  backup-by-copying t    ; Don't delink hardlinks
  version-control t      ; Use version numbers on backups
  delete-old-versions t  ; Automatically delete excess backups
  kept-new-versions 20   ; how many of the newest versions to keep
  kept-old-versions 5    ; and how many of the old
  )

;; remove trailing whitespaces in source code files
(defun nuke_traling ()
  (add-hook 'before-save-hook #'delete-trailing-whitespace nil t))
(add-hook 'prog-mode-hook #'nuke_traling)
(add-hook 'markdown-mode-hook #'nuke_traling)
(add-hook 'rst-mode-hook #'nuke_traling)

;; =============================================================================
;; ================================== Macros ===================================
;; =============================================================================

;; load macros from file and maybe bind to key
;; (load-file "~/.emacs.d/macros/gen.macs")
;; (global-company-mode "\C-x\C-kT" 'myMacro)