.emacs

;; Add my emacs libs to load path
(setq load-path (cons (substitute-in-file-name "$HOME/dot/emacs") load-path))

(require 'palette)
(require 'doremi-frm)

;; default colors
;;(set-background-color "gray95")
;;(set-background-color "#fffce5")   ;;light yellow
;;(set-background-color "#e5fcff") ;;light blue
;;(set-background-color "#CC6AEEEECC6A")   ;;light green
(set-background-color "#404552C54045")   ;;dark gray-green

;(set-foreground-color "gray20")
(set-foreground-color "snow")
(set-cursor-color "orange")
;(load-theme 'solarized-light-theme t)

;;codesearch
(require 'codesearch)
(setq codesearch-csearchindex (getenv "CSEARCHINDEX"))

;;cmake mode
(require 'cmake-mode)

;;markdown-mode (see https://jblevins.org/projects/markdown-mode/)
(require 'package)
(add-to-list 'package-archives
             '("melpa-stable" . "https://stable.melpa.org/packages/"))
(package-initialize)
(autoload 'markdown-mode "markdown-mode"
   "Major mode for editing Markdown files" t)
(add-to-list 'auto-mode-alist '("\\.markdown\\'" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.md\\'" . markdown-mode))
(autoload 'gfm-mode "markdown-mode"
   "Major mode for editing GitHub Flavored Markdown files" t)
(add-to-list 'auto-mode-alist '("README\\.md\\'" . gfm-mode))

;; don't ignore (ViSUS) .idx files for completion
(setq completion-ignored-extensions (delete ".idx" completion-ignored-extensions))

;; MATLAB (OSX)
;; check OS type
(cond
 ((string-equal system-type "windows-nt") ; Microsoft Windows
  (progn
    (message "Microsoft Windows")))
 ((string-equal system-type "darwin") ; Mac OS X
  (progn
    (message "Mac OS X")
    (setq load-path (cons (substitute-in-file-name "$HOME/dot/emacs/matlab") load-path))
    (load-library "matlab-load")
    (matlab-cedet-setup)
    ;;(setq matlab-shell-command-switches '("-nojvm"))
    ;;(setq matlab-shell-command-switches '("-nosplash"))
    (global-set-key "\M-`" 'other-frame)
    ))
 ((string-equal system-type "gnu/linux") ; linux
  (progn
    (message "Linux"))))

;; fix drag-and-drop in osx
(define-key global-map [ns-drag-file] 'my-ns-open-files)
(defun my-ns-open-files ()
  "Open files in the list `ns-input-file'."
  (interactive)
  (mapc 'find-file ns-input-file)
  (setq ns-input-file nil))

(add-hook 'shell-mode-hook 'ansi-color-for-comint-mode-on)

(setq tab-stop-list (number-sequence 2 200 2))

(setq default-tab-width 2)

(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.
 '(c-offsets-alist
   (quote
    ((arglist-intro . +)
     (arglist-cont c-lineup-gcc-asm-reg 0))))
 '(cc-search-directories
   (quote
    ("." "/usr/include" "/usr/local/include/*" "../../src" "../include/*")))
 '(compilation-skip-threshold 2)
 '(css-indent-offset 2)
 '(desktop-path (quote ("." "~/.emacs.d/" "~")))
 '(desktop-restore-eager 7)
 '(desktop-save-mode t)
 '(display-time-mode t)
 '(ediff-split-window-function (quote split-window-horizontally))
 '(fill-column 80)
 '(gud-gdb-command-name "gdb --annotate=1")
 '(gud-tooltip-mode t)
 '(icomplete-mode t)
 '(indent-tabs-mode nil)
 '(inhibit-startup-screen t)
 '(initial-buffer-choice t)
 '(initial-scratch-message nil)
 '(js-indent-level 2)
 '(large-file-warning-threshold nil)
 '(line-move-visual nil)
 '(list-command-history-max nil)
 '(msb-mode t)
 '(ns-alternate-modifier (quote alt))
 '(ns-command-modifier (quote meta))
 '(ns-right-alternate-modifier (quote super))
 '(nxml-sexp-element-flag t)
 '(package-selected-packages (quote (xref-js2 js2-refactor s markdown-mode)))
 '(partial-completion-mode nil)
 '(safe-local-variable-values
   (quote
    ((TeX-master . "proposal")
     (TeX-master . "paper")
     (TeX-master . "dynamic_remote_analysis"))))
 '(savehist-mode t nil (savehist))
 '(scroll-down-aggressively 0.1)
 '(scroll-up-aggressively 0.1)
 '(set-mark-command-repeat-pop t)
 '(show-paren-mode t)
 '(standard-indent 2)
 '(tab-always-indent (quote complete))
 '(tab-width 2)
 '(tool-bar-mode nil)
 '(tramp-auto-save-directory "~/.emacs.d/autosave")
 '(x-alt-keysym (quote ctrl) t)
 '(x-ctrl-keysym (quote alt))
 '(x-hyper-keysym (quote meta) t)
 '(x-meta-keysym (quote ctrl) t)
 '(x-super-keysym (quote meta) t))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(font-lock-builtin-face ((t (:background "purple" :foreground "white" :weight bold))))
 '(font-lock-comment-delimiter-face ((t (:inherit font-lock-comment-face :weight bold))))
 '(font-lock-comment-face ((t (:foreground "light cyan"))))
 '(font-lock-constant-face ((t (:foreground "cyan1" :weight bold))))
 '(font-lock-function-name-face ((t (:foreground "green" :weight bold))))
 '(font-lock-preprocessor-face ((t (:inherit font-lock-builtin-face :foreground "white"))))
 '(font-lock-string-face ((t (:foreground "light goldenrod"))))
 '(font-lock-variable-name-face ((t (:foreground "yellow"))))
 '(rst-level-1 ((t nil))))
(put 'scroll-left 'disabled nil)

;;; Insert current date (from http://www.emacswiki.org/emacs/InsertDate)
(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.%H%M")
                   ((equal prefix '(4)) "%d.%m.%Y")
                   ((equal prefix '(16)) "%A, %B %d, %Y"))))
      (insert (format-time-string format))))

(defun insert-standard-date ()
    "Inserts standard date time string." 
    (interactive)
    (insert (format-time-string "%c")))

;;; Revert the current buffer without asking first.
(defun fast-revert-buffer ()
"Revert the buffer from the original file without asking."
  (interactive)
  (revert-buffer t t))

;;; increase/decrease text scale in all buffers
;; (defadvice text-scale-increase (around all-buffers (arg) activate)
;;     (dolist (buffer (buffer-list))
;;       (with-current-buffer buffer
;;         ad-do-it)))

;;; Assign shortcuts
(global-set-key (kbd "C-}") '(lambda() (interactive) (text-scale-increase 1)))
(global-set-key (kbd "C-{") '(lambda() (interactive) (text-scale-increase -1)))
(global-set-key "\C-ce" 'ediff-buffers)
(global-set-key (kbd "C-c l") 'insert-date)
(global-set-key (kbd "C-S-p") '(lambda() (interactive) (scroll-down 1)))
(global-set-key (kbd "C-S-n") '(lambda() (interactive) (scroll-up 1)))
(global-set-key "\C-x\C-b" 'electric-buffer-list)
(global-set-key "\C-cr" 'fast-revert-buffer)
(global-set-key "\C-ct" 'toggle-truncate-lines)
(global-set-key "\C-cd" 'hide-subtree)
(global-set-key "\C-cs" 'show-subtree)
(global-set-key "\C-x\M-\." 'tags-search)
(global-set-key "\C-x\M-\," 'tags-loop-continue)
(global-set-key "\C-x\M->" 'tags-query-replace)
(global-set-key "\C-c\M-q" 'align-regexp)
(global-set-key "\C-c\C-v" 'codesearch-search-at-point)
(global-set-key "\C-c\C-f" 'codesearch-search)
(global-set-key "\C-c\C-c" 'comment-region)
(global-set-key "\C-c\C-k" 'compile)
(global-set-key (kbd "C-;") 'indent-relative)

(c-add-style "VisIt" '("gnu" 
                       (c-basic-offset . 4)
                       (c-offsets-alist . ((innamespace . 0)
                                           (substatement-open 0)
                                           (brace-list-open 0)
                                           (access-label . -)
                                           (case-label . 0)
                                           (member-init-intro . +)
                                           (topmost-intro . 0)))))

(c-add-style "ir-tools" '("gnu" 
                          (c-basic-offset . 4)
                          (c-offsets-alist . ((innamespace . 0)
                                              (substatement-open 0)
                                              (brace-list-open 0)
                                              (access-label . -)
                                              (case-label . 0)
                                              (member-init-intro . +)
                                              (topmost-intro . 0)))))

(c-add-style "ViSUS" '("gnu" 
                       (c-basic-offset . 2)
                       (tab-width . 2)
                       (c-require-final-newline . 'nil)
                       (fill-column . 95)
                       (c-offsets-alist . ((innamespace . 0)
                                           (substatement-open 0)
                                           (statement-cont 0)
                                           (brace-list-open 0)
                                           (access-label . -)
                                           (case-label . 0)
                                           (member-init-intro . +)
                                           (case-label . +)
                                           (statement-case-open . 0)
                                           (inextern-lang . 0)
                                           (topmost-intro . 0)))))

(c-add-style "SCHOOL" '("ViSUS" 
                       (c-basic-offset . 2)))

(c-add-style "PIDX" '("ViSUS" 
                       (c-basic-offset . 2)))

(c-add-style "UINTAH" '("ViSUS" 
                       (c-basic-offset . 2)))

;; pick default style based on environment var 'MYPROJECT'
(setq CurrentProject (getenv "MYPROJECT"))
(setq my-c-style "ViSUS")
;;TODO: use (cond instead
(if (equal CurrentProject "VISUS")
    (setq my-c-style "ViSUS")
  (if (equal CurrentProject "VISIT")
      (setq my-c-style "VisIt")
    (if (equal CurrentProject "PIDX")
        (setq my-c-style "PIDX")
      (if (equal CurrentProject "UINTAH")
          (setq my-c-style "UINTAH")
        (if (equal CurrentProject "SCHOOL")
            (setq my-c-style "SCHOOL")
          (if (equal CurrentProject "RT")
              (setq my-c-style "SCHOOL")
            (if (equal CurrentProject "HWRT")
                (setq my-c-style "SCHOOL")
              (if (equal CurrentProject "IRTOOLS")
                  (setq my-c-style "ir-tools")
                (setq my-c-style "ViSUS")))))))))

;;
;;C++ mode
;;
(add-to-list 'auto-mode-alist '("\\.h$" . c++-mode))
(add-to-list 'auto-mode-alist '("\\.hxx" . c++-mode))
(add-to-list 'auto-mode-alist '("\\.cxx" . c++-mode))
(add-to-list 'auto-mode-alist '("\\.cu" . c++-mode))
(add-to-list 'auto-mode-alist '("\\.vert" . c++-mode))
(add-to-list 'auto-mode-alist '("\\.frag" . c++-mode))

;;C++ mode hooks
;; <ctc> still need:
;;        X no indent after namespace and in switch/case
;;        X drag and drop should open new file, not copy contents of file into current buffer
;;        o y_or_n instead of requiring yes_or_no
;;        X a way to set c-basic-offset to 4 for some projects (VisIt)
;;        

;;; Save c-basic-offset and c-offsets-alist in .emacs.desktop
(add-to-list 'desktop-globals-to-save 'c-basic-offset)
(add-to-list 'desktop-globals-to-save 'c-offsets-alist)

;; Discovered macros to use with:
;; (read-kbd-macro "C-c <left>")
;; You can use view-lossage to see what to put in the quotes.
(defun hs-mode-set-keys ()
	(progn
    (message "running hs-mode-set-keys hook...")
		(local-set-key [3 right] 'hs-show-block)
		(local-set-key [3 left] 'hs-hide-block)
		(local-set-key [3 up] 'hs-hide-level)
		(local-set-key [3 down] 'hs-show-all)
))
(add-hook 'hs-minor-mode-hook 'hs-mode-set-keys)

(add-hook 'c-mode-common-hook 'hs-minor-mode)
;;(add-hook 'c-mode-common-hook 'outline-minor-mode)

;;Find other file
(defun ff-find-other-file-set-keys()
  (progn
    (message "running ff-find-other-file-set-keys hook...")
    (local-set-key (kbd "C-c a") 'ff-find-other-file)))
(add-hook 'c-mode-common-hook 'ff-find-other-file-set-keys)
	    
(add-hook 'c-mode-common-hook (lambda() (local-set-key "\M-j" 'indent-for-comment)))

;; Customizations for all modes in CC Mode.
(defun my-c-mode-common-hook ()
  ;; set my personal style for the current buffer
  (message "running my-c-mode-common-hook...")
  (c-set-style my-c-style))
(add-hook 'c-mode-common-hook 'my-c-mode-common-hook)

;; Python Hook
(add-hook 'python-mode-hook
          'my-python-customizations)
(defun my-python-customizations ()
  "set up my personal customizations for python mode"
  (message "setting my python customizations...")
  (setq python-indent 4)
  (local-unset-key (kbd "C-c C-c"))
  (local-set-key "\C-c\C-c" 'comment-region)
  (setq tab-width 4)
  (setq indent-tabs-mode 1))

;; Latex Hook
(add-hook 'latex-mode-hook
          'my-latex-customizations)
(defun my-latex-customizations ()
  "set up my personal customizations for latex mode"
  (local-unset-key (kbd "C-c C-c"))
  (local-set-key "\C-c\C-c" 'comment-region))

;; Xml Hook
;; ...
;; xml mode sucks, nxml mode is much better
(add-to-list 'auto-mode-alist '("\\.xml\\'" . nxml-mode))
(add-to-list 'auto-mode-alist '("\\.svgz?\\'" . nxml-mode))
(add-to-list 'auto-mode-alist '("\\.config" . nxml-mode))
(add-to-list 'auto-mode-alist '("\\.[mg]idx\\'" . nxml-mode))

;;Shell scripts
(defun cam-setup-sh-mode ()
  "My own personal preferences for `sh-mode'.

This is a custom function that sets up the parameters I usually
prefer for `sh-mode'.  It is automatically added to
`sh-mode-hook', but is can also be called interactively."
  (interactive)
  (setq sh-basic-offset 2
        sh-indentation 2
        sh-indent-after-function 2))
(add-hook 'sh-mode-hook 'cam-setup-sh-mode)

;; vc-ediff
(require 'vc-ediff)

(defun my-vc-dir-hide-up-to-date ()
  (interactive)
  (vc-dir-hide-up-to-date)
  (vc-dir-hide-unregistered))

(defun vc-dir-hide-unregistered ()
  "Hide unregistered items from display."
  (interactive)
  (let ((crt (ewoc-nth vc-ewoc -1))
        (first (ewoc-nth vc-ewoc 0)))
    ;; Go over from the last item to the first and remove the
    ;; unregistered files and directories with no child files.
    (while (not (eq crt first))
      (let* ((data (ewoc-data crt))
             (dir (vc-dir-fileinfo->directory data))
             (next (ewoc-next vc-ewoc crt))
             (prev (ewoc-prev vc-ewoc crt))
             ;; ewoc-delete does not work without this...
             (inhibit-read-only t))
        (when (or
               ;; Remove directories with no child files.
               (and dir
                    (or
                     ;; Nothing follows this directory.
                     (not next)
                     ;; Next item is a directory.
                     (vc-dir-fileinfo->directory (ewoc-data next))))
               ;; Remove files in the unregistered state.
               (eq (vc-dir-fileinfo->state data) 'unregistered))
          (ewoc-delete vc-ewoc crt))
        (setq crt prev)))))


(defun my-ediff-revision (file rev1 &optional rev2)
  "Run Ediff by comparing 'master' against the 'current'."
  (find-file file)
  (if (and (buffer-modified-p)
           (y-or-n-p (format "Buffer %s is modified. Save buffer? "
                             (buffer-name))))
      (save-buffer (current-buffer)))

  (ediff-load-version-control)
  (ediff-vc-internal rev1 rev2 nil))

(defun my-vc-diff (&optional arg)
  (interactive "P")
  (call-interactively
   (cond (arg (lambda nil (interactive) (vc-diff nil)))
         (t (lambda nil (interactive)
              (my-ediff-revision (buffer-file-name)
                                 (read-string "revision? " "HEAD" nil "HEAD")
                                 ""))))))

(add-hook  'vc-dir-mode-hook
           (lambda nil
             (define-key vc-dir-mode-map "x" 'my-vc-dir-hide-up-to-date)
             (define-key vc-dir-mode-map "E" 'my-vc-diff)))


;;; Remove ^Ms from the entire buffer.
(defun strip-control-ms ()
  "Delete all ^Ms."
  (interactive)
  (save-excursion
    (beginning-of-buffer)
    (while (and (not (eobp))
		(re-search-forward "\C-m" nil t))
      (delete-region (match-beginning 0) (match-end 0)))))


;;ctc - get machine name, 11 for desktop, 10 for laptop
(when (or (string-prefix-p "jupiter" (system-name)) (string-prefix-p "mercury" (system-name)))
    (set-face-attribute 'default nil :font "-apple-Monaco-medium-normal-normal-*-11-*-*-*-m-0-iso10646-1")
  (if (string= (system-name) "mercury.local") 
    (set-face-attribute 'default nil :font "-apple-Monaco-medium-normal-normal-*-12-*-*-*-m-0-iso10646-1")
    (if (string= (system-name) "atlanta.sci.utah.edu") 
        (message "can't set system font")
                                        ;(set-face-attribute 'default nil :font "-unknown-DejaVu Sans Mono-normal-normal-normal-*-12-*-*-*-m-0-fontset-auto2")
      (set-face-attribute 'default nil :font "-apple-Monaco-medium-normal-normal-*-14-*-*-*-m-0-iso10646-1"))))

(when (string-prefix-p "gunship" (system-name))
    (message "configuring for gunship (swapping meta and alt keys)...")
    ;; with TweakUI Ctrl key "swap left alt with left ctrl" on SUSE, this has changed (first set of swaps takes care of it)
    ;; I GIVE UP: can't remap ctrl on linux (though you can on OSX), so I'm just undoing swap-alt-ctrl setting
    (if 0
        (custom-set-variables
         '(x-ctrl-keysym (quote alt))
         '(x-alt-keysym (quote ctrl))
         '(x-super-keysym (quote meta))
         '(x-meta-keysym (quote ctrl) t)
         '(x-hyper-keysym (quote meta) t)
         )
      (custom-set-variables
       '(x-meta-keysym (quote alt))
       '(x-super-keysym (quote meta))
       ))
  ;;for mercury: mac-control-modifier
  ;;example here: http://ergoemacs.org/emacs/emacs_hyper_super_keys.html
)


(put 'upcase-region 'disabled nil)

(defun find-duplicate-lines (&optional insertp interp)
  (interactive "i\np")
  (let ((max-pon (line-number-at-pos (point-max)))
        (gather-dups))
    (while (< (line-number-at-pos) max-pon) (= (forward-line) 0)
           (let ((this-line (buffer-substring-no-properties (line-beginning-position 1) (line-end-position 1)))
                 (next-line (buffer-substring-no-properties (line-beginning-position 2) (line-end-position 2))))
             (when  (equal this-line next-line)  (setq gather-dups (cons this-line gather-dups)))))
    (if (or insertp interp)
        (save-excursion (newline) (princ gather-dups (current-buffer)))
      gather-dups)))

;;dired
(defun file-info ()
  (interactive)
  (let ((dired-listing-switches "-alh"))
    (dired-other-window buffer-file-name)))
(global-set-key (kbd "C-c i") 'file-info)

(add-hook 'dired-mode-hook
          (lambda nil
            (define-key dired-do-query-replace-regexp "Q" 'dired-do-query-replace-regexp)))

(require 'package)
(let* ((no-ssl (and (memq system-type '(windows-nt ms-dos))
                    (not (gnutls-available-p))))
       (url (concat (if no-ssl "http" "https") "://melpa.org/packages/")))
  (add-to-list 'package-archives (cons "melpa" url) t))
(when (< emacs-major-version 24)
  ;; For important compatibility libraries like cl-lib
  (add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/")))
(package-initialize)

; insert date and a line underneath (since I do it all the time)
; TODO: get the text of the C-c l command, add the line to it, and insert as a single action. That way, undo will remove all of it
(fset 'dateline
   [?\C-u ?\C-u ?\C-c ?l return ?\M-2 ?\M-9 ?- return])
(global-set-key (kbd "C-c k") 'dateline)

; s.el (required by dockerfile-mode)
(add-to-list 'load-path "~/emacs/s.el")

; dockerfile mode
(add-to-list 'load-path "~/emacs/dockerfile-mode/")
(require 'dockerfile-mode)
(add-to-list 'auto-mode-alist '("Dockerfile\\'" . dockerfile-mode))


; --- javascript --- (see https://emacs.cafe/emacs/javascript/setup/2017/04/23/emacs-setup-javascript.html)
; (need to install js2-mode, js2-refactor, xref-js2 using M-x package-install RET <name>)
; also: conda install -c anaconda the-silver-searcher 
(require 'js2-mode)
(add-to-list 'auto-mode-alist '("\\.js\\'" . js2-mode))

;; Better imenu
(add-hook 'js2-mode-hook #'js2-imenu-extras-mode)

;; js "tags"
(require 'js2-refactor)
(require 'xref-js2)

(add-hook 'js2-mode-hook #'js2-refactor-mode)
(js2r-add-keybindings-with-prefix "C-c C-r")
(define-key js2-mode-map (kbd "C-k") #'js2r-kill)

;; js-mode (which js2 is based on) binds "M-." which conflicts with xref, so
;; unbind it.
(define-key js-mode-map (kbd "M-.") nil)

(add-hook 'js2-mode-hook
          (lambda ()
            (add-hook 'xref-backend-functions #'xref-js2-xref-backend nil t)))

; --- /javascript ---