init.el

(add-to-list 'load-path "~/.emacs.d/site-lisp/go-mode.el/")
(add-to-list 'load-path "~/.emacs.d/site-lisp/ox-ipynb/")
(autoload 'go-mode "go-mode" nil t)
(add-to-list 'auto-mode-alist '("\\.go\\'" . go-mode))

(let ((default-directory  "/usr/local/share/emacs/site-lisp"))
  (normal-top-level-add-subdirs-to-load-path))
(setq tramp-default-method "ssh")

(global-hl-line-mode 1)
(menu-bar-mode -1)
(if (display-graphic-p)
    (tool-bar-mode -1))

(require 'package)
(ido-mode t)

(setq ido-enable-flex-matching t)
(setq ido-use-filename-at-point nil)
(setq ido-use-virtual-buffers t)

(setq recentf-save-file (concat user-emacs-directory ".recentf"))
(require 'recentf)
(recentf-mode 1)

(prettify-symbols-mode 1)

;; (defun my-add-pretty-lambda ()
;;   "make some word or string show as pretty Unicode symbols"
;;   (setq prettify-symbols-alist
;;         '(
;;           ("lambda" . 955) λ
;;           ("fn", . 955)
;;           ("->" . 8594)    →
;;           ("=>" . 8658)    ⇒
;;           ("map" . 8614)    ↦
;;           ))
;;   )
;; (add-hook 'clojure-mode-hook 'my-add-pretty-lambda)

(require 'uniquify)
(setq uniquify-buffer-name-style 'forward)

;; package config
(setq package-archives '(("gnu"   . "http://elpa.emacs-china.org/gnu/")
                         ("melpa" . "http://elpa.emacs-china.org/melpa/")
                         ;; ("melpa" . "http://melpa.milkbox.net/packages/")
                           ("org" . "http://orgmode.org/elpa/")
                           ))
(package-initialize)
;; (package-refresh-contents)

(set-frame-parameter (selected-frame) 'alpha '(90 . 90))

;; some aux functions
(defun comment-or-uncomment-region-or-line ()
    "Comments or uncomments the region or the current line if there's no active region."
    (interactive)
    (let (beg end)

        (if (region-active-p)
            (setq beg (region-beginning) end (region-end))
            (setq beg (line-beginning-position) end (line-end-position)))
        (comment-or-uncomment-region beg end)))

(defun select-current-line ()
  "Select the current line"
  (interactive)
 (beginning-of-line) ; move to end of line
  (set-mark (line-end-position)))

(defun my-kill-ring-save ()
  (interactive)
  (if (not (use-region-p))
      (select-current-line))
  (kill-ring-save (region-beginning)  (region-end)))

;; use 2 spaces for tabs
(defun die-tabs ()
  (interactive)
  (set-variable 'tab-width 2)
  (mark-whole-buffer)
  (untabify (region-beginning) (region-end))
  (keyboard-quit))

;; fix weird os x kill error
(defun ns-get-pasteboard ()
  "Returns the value of the pasteboard, or nil for unsupported formats."
  (condition-case nil
      (ns-get-selection-internal 'CLIPBOARD)
    (quit nil)))

(setq electric-indent-mode nil)

(global-set-key (kbd "M-/") 'comment-or-uncomment-region-or-line)
(global-set-key (kbd "s-1") 'shell-command)

(defun open-in-vim()
  (interactive)
  (shell-command (concat "osascript -e 'tell application \"Terminal\" to activate' -e 'tell application \"System Events\" to tell process \"Terminal\" to keystroke \"t\" using command down' -e 'tell application \"Terminal\" to do script \"vim " (buffer-file-name)  "\" in selected tab of the front window'")))

(global-set-key (kbd "M-g v") 'open-in-vim)

(global-set-key (kbd "s-z") 'undo-tree-undo)

(add-to-list 'load-path "~/.emacs.d/evil")
(require 'evil)

(add-to-list 'load-path "~/.emacs.d/site-lisp")
(add-to-list 'load-path "~/.emacs.d/site-lisp/dash.el")
(add-to-list 'load-path "~/.emacs.d/site-lisp/f.el")
(add-to-list 'load-path "~/.emacs.d/site-lisp/s.el")

(defun toggle-evil-mode ()
  (interactive)
  (if (eq evil-mode t)
      (evil-mode 0)
    (evil-mode t)))

(global-set-key (kbd "s-i") 'toggle-evil-mode)

(global-unset-key (kbd "C-M-SPC"))
(global-set-key (kbd "M-x") 'helm-M-x)
(global-set-key (kbd "s-j") 'helm-M-x)
(global-set-key (kbd "s-x") 'kill-region)

(require 'expand-region)
(global-set-key (kbd "C-j") 'er/pand-region)
(setq make-backup-files nil)

;;(load "~/.emacs.d/org-mind-map/org-mind-map.el")

(require 'org)
(require 'ob-ipython)
(require 'ox-ipynb)
(require 'ob-mathematica)

;; don't prompt me to confirm everytime I want to evaluate a block
(setq org-confirm-babel-evaluate nil)
(setq org-display-inlineimages t)

;;; display/update images in the buffer after I evaluate
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)
(setq org-babel-python-command "python3")

(org-babel-do-load-languages
 'org-babel-load-languages
 '(
   (emacs-lisp . t)
   (ipython . t)
   (python . t)
   (js . t)
   (ruby . t)
   (C .t)
   (shell .t)
   (mathematica .t)
   (clojure .t)
   (R .t)
   (ein . t)
   ;; other languages..
   ))

(setq shell-file-name "bash")
(setq shell-command-switch "-ic")

;; (add-to-list 'org-latex-minted-langs '(ipython "python"))

;; (add-to-list 'load-path
;;               "~/.emacs.d/plugins/yasnippet")
;; (require 'yasnippet)
;; (yas-global-mode 0)

(add-to-list 'load-path "~/.emacs.d/site-lisp/writegood-mode")
(require 'writegood-mode)

(add-to-list 'load-path "~/.emacs.d/site-lisp/fountain-mode")
(require 'fountain-mode)

(setq org-src-fontify-natively t)

(load "auctex.el" nil t t)

(require 'ox)
(visual-line-mode t)
(add-hook 'org-mode-hook #'(lambda ()
                             ;; make the lines in the buffer wrap around the edges of the screen.
                             ;; to press C-c q  or fill-paragraph ever again!
                             (visual-line-mode)
                             (org-indent-mode)))
(require 'ob-mathematica)
(require 'ob-clojure)

(setq package-check-signature nil)

(setq ispell-program-name "/usr/local/bin/aspell")

(global-set-key (kbd "s-/") 'comment-or-uncomment-region)

;; disable scroll bar in gui mode
(when (display-graphic-p)
    ()
    (scroll-bar-mode -1))

(defun get-selected-text (start end)
  (interactive "r")
    (if (use-region-p)
        (let ((regionp (buffer-substring start end)))
          (message "%d" start)
          (message "%d" end)
            (message regionp))))

(defun universal-copy(start end)
  "copy the whole line if no region selected, or copy the region"
  (interactive "r")
  (if (use-region-p)
  (kill-ring-save start end)
  (kill-ring-save (line-beginning-position) (line-end-position))))

(global-set-key (kbd "s-c") 'universal-copy)

;; socks proxy settings for emacs url package.
;; (setq socks-noproxy '("127.0.0.1"))
;; (setq socks-server '("Default server" "127.0.0.1" 1080 5))
;; (setq url-gateway-method 'socks)
                           
;; (setq url-gateway-method 'native)

;; define default bibliography doc
(setq reftex-default-bibliography '("~/Dropbox/bibliography/references.bib"))

;; see org-ref for use of these variables
(setq org-ref-bibliography-notes "~/Dropbox/bibliography/notes.org"
      org-ref-default-bibliography '("~/Dropbox/bibliography/references.bib")
      org-ref-pdf-directory "~/Dropbox/bibliography/bibtex-pdfs/")

(setq bibtex-completion-bibliography "~/Dropbox/bibliography/references.bib"
      bibtex-completion-library-path "~/Dropbox/bibliography/bibtex-pdfs"
      bibtex-completion-notes-path "~/Dropbox/bibliography/helm-bibtex-notes")

;; open pdf with system pdf viewer (works on mac)
(setq bibtex-completion-pdf-open-function
  (lambda (fpath)
    (start-process "open" "*open*" "open" fpath)))

;; alternative
(setq bibtex-completion-pdf-open-function 'org-open-file)

(require 'org-ref)

(require 'ox-latex)
(unless (boundp 'org-latex-classes)
  (setq org-latex-classes nil))

(add-to-list 'org-latex-classes
'("IEEEtran"
"\documentclass[10pt,journal]{IEEEtran}"
("\section{%s}" . "\section_{%s}")
("\subsection{%s}" . "\subsection_{%s}")
("\subsubsection{%s}" . "\subsubsection*{%s}")))

(require 'org-ref-citeproc)

(defun org-ref-open-bibtex-pdf ()
  (interactive)
  (save-excursion
    (bibtex-beginning-of-entry)
    (let* ((bibtex-expand-strings t)
           (entry (bibtex-parse-entry t))
           (key (reftex-get-bib-field "=key=" entry))
           (pdf (org-ref-get-mendeley-filename key)))
      (message "opening pdf %s" pdf)
      (if (file-exists-p pdf)
          (org-open-link-from-string (format "[[file:%s]]" pdf))
        (ding)))))

 (setq org-ref-pdf-directory "/Users/toeinriver/Dropbox/bibliography/bibtex-pdfs"
        bibtex-completion-pdf-field "file"
        org-ref-get-pdf-filename-function 'org-ref-get-zotero-pdf-filename)

(defun org-ref-get-zotero-pdf-filename (key)
  "Return the pdf filename indicated by zotero file field.
Argument KEY is the bibtex key."
  (let* ((results (org-ref-get-bibtex-key-and-file key))
   (bibfile (cdr results))
   entry)
    (with-temp-buffer
      (insert-file-contents bibfile)
      (bibtex-set-dialect (parsebib-find-bibtex-dialect) t)
      (bibtex-search-entry key nil 0)
      (setq entry (bibtex-parse-entry))
      (let ((e (org-ref-reftex-get-bib-field "file" entry)))
  (if (> (length e) 4)
      (let ((clean-field (replace-regexp-in-string "/+" "/" e)))
        (let ((first-file (car (split-string clean-field ";" t))))
    (concat org-ref-pdf-directory first-file)))
    (message "PDF filename not found.")
    )))))

;; Override this function.
(defun org-ref-open-bibtex-pdf ()
  "Open pdf for a bibtex entry, if it exists.
assumes point is in
the entry of interest in the bibfile.  but does not check that."
  (interactive)
  (save-excursion
    (bibtex-beginning-of-entry)
    (let* ((bibtex-expand-strings t)
     (entry (bibtex-parse-entry t))
     (key (reftex-get-bib-field "=key=" entry))
     (pdf (org-ref-get-zotero-pdf-filename key)))
      (message "%s" pdf )
      (if (file-exists-p pdf)
    (org-open-link-from-string (format "[[file:%s]]" pdf))
  (ding)))))

(require 'guide-key)
(setq guide-key/guide-key-sequence '("C-x r"))
(setq guide-key/recursive-key-sequence-flag t)
(guide-key-mode 1)  ; Enable guide-key-mode
(setq guide-key/idle-delay 0.1)

(defun guide-key/my-hook-function-for-org-mode ()
  (guide-key/add-local-guide-key-sequence "C-c")
  (guide-key/add-local-guide-key-sequence "C-c C-x")
  (guide-key/add-local-highlight-command-regexp "org-"))
(add-hook 'org-mode-hook 'guide-key/my-hook-function-for-org-mode)

;; (require 'evil-surround)
;; (global-evil-surround-mode 1)
;; (global-set-key (kbd "TAB") 'hippie-expand)

(require 'expand-region)

(defun smart-tab ()
  "This smart tab is minibuffer compliant: it acts as usual in
    the minibuffer. Else, if mark is active, indents region. Else if
    point is at the end of a symbol, expands it. Else indents the
    current line."
  (interactive)
  (if (minibufferp)
      (unless (minibuffer-complete)
        (hippie-expand nil))
    (if mark-active
        (indent-region (region-beginning)
                       (region-end))
      (if (looking-at "\\_>")
         (hippie-expand nil)
        (indent-for-tab-command)))))
(global-set-key (kbd "TAB") 'smart-tab)

(setq hippie-expand-try-functions-list
      '(
        try-expand-dabbrev
  try-expand-dabbrev-from-kill
  try-expand-dabbrev-all-buffers
  try-expand-line
  try-complete-file-name-partially
  try-complete-file-name
  try-complete-lisp-symbol
  try-complete-lisp-symbol-partially
  ))

(setq org-latex-pdf-process '("latexmk -pdflatex='%latex -shell-escape -interaction nonstopmode' -pdf -output-directory=%o -f %f"))

(add-to-list 'org-latex-classes
             '("acm"
               "\\documentclass[]{hitec}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))

(put 'upcase-region 'disabled nil)

(setq org-agenda-files '("~/Dropbox/orgfiles/i.org"))
(setq org-agenda-include-diary t)
(put 'erase-buffer 'disabled nil)

(show-paren-mode 1)

(setq cider-repl-pop-to-buffer-on-connect nil)
(require 'cider-eldoc)

;; (require 'ob-clojure)

(setq cider-lein-parameters "repl :headless :host localhost")
(put 'downcase-region 'disabled nil)

(require 'ggtags)
(add-hook 'c-mode-common-hook
          (lambda ()
            (when (derived-mode-p 'c-mode 'c++-mode 'java-mode 'asm-mode)
              (ggtags-mode 1))))

(add-hook 'fountain-mode-hook
          (lambda ()
            (global-set-key (kbd "TAB") 'smart-tab)))
(define-key ggtags-mode-map (kbd "C-c g s") 'ggtags-find-other-symbol)
(define-key ggtags-mode-map (kbd "C-c g h") 'ggtags-view-tag-history)
(define-key ggtags-mode-map (kbd "C-c g r") 'ggtags-find-reference)
(define-key ggtags-mode-map (kbd "C-c g f") 'ggtags-find-file)
(define-key ggtags-mode-map (kbd "C-c g c") 'ggtags-create-tags)
(define-key ggtags-mode-map (kbd "C-c g u") 'ggtags-update-tags)

(define-key ggtags-mode-map (kbd "M-,") 'pop-tag-mark)

(setq
 helm-gtags-ignore-case t
 helm-gtags-auto-update t
 helm-gtags-use-input-at-cursor t
 helm-gtags-pulse-at-cursor t
 helm-gtags-prefix-key "\C-cg"
 helm-gtags-suggested-key-mapping t
 )

(require 'helm-gtags)
;; Enable helm-gtags-mode
(add-hook 'dired-mode-hook 'helm-gtags-mode)
(add-hook 'eshell-mode-hook 'helm-gtags-mode)
(add-hook 'c-mode-hook 'helm-gtags-mode)
(add-hook 'c++-mode-hook 'helm-gtags-mode)
(add-hook 'asm-mode-hook 'helm-gtags-mode)

(define-key helm-gtags-mode-map (kbd "C-c g a") 'helm-gtags-tags-in-this-function)
(define-key helm-gtags-mode-map (kbd "C-j") 'helm-gtags-select)
(define-key helm-gtags-mode-map (kbd "M-.") 'helm-gtags-dwim)
(define-key helm-gtags-mode-map (kbd "M-,") 'helm-gtags-pop-stack)
(define-key helm-gtags-mode-map (kbd "C-c <") 'helm-gtags-previous-history)
(define-key helm-gtags-mode-map (kbd "C-c >") 'helm-gtags-next-history)

(fa-config-default)
(add-to-list 'auto-mode-alist '("\\.h\\'" . c++-mode))
(set-default 'semantic-case-fold t)

;;If your includes aren't located in default dirs e.g. /usr/include/ etc, then you have to do something like this:
;;(semantic-add-system-include "~/Software/deal.II/include/" 'c++-mode)
;;(semantic-add-system-include "/usr/local/boost_1_54_0/" 'c++-mode)

(require 'semantic/bovine/c)
(add-to-list 'semantic-lex-c-preprocessor-symbol-file
       "/usr/lib/gcc/x86_64-linux-gnu/4.8/include/stddef.h")

(require 'sr-speedbar)
(defalias 'speedbar 'sr-speedbar-toggle)
(setq speedbar-initial-expansion-list-name "quick buffers")

(require 'company)
(add-hook 'after-init-hook 'global-company-mode)

(setq company-backends (delete 'company-semantic company-backends))
(define-key c-mode-map  [(tab)] 'company-complete)
(define-key c++-mode-map  [(tab)] 'company-complete)
(add-to-list 'company-backends 'company-c-headers)

(load-theme 'leuven t)

(require 'cc-mode)
(require 'semantic)

(global-semanticdb-minor-mode 1)
(global-semantic-idle-scheduler-mode 1)

(semantic-mode 1)

(projectile-mode +1)

(setq
 ;; use gdb-many-windows by default
 gdb-many-windows t
 ;; Non-nil means display source file containing the main routine at startup
 gdb-show-main t
 )

(setq org-latex-pdf-process
  '("xelatex -interaction nonstopmode %f"
     "xelatex -interaction nonstopmode %f")) ;; for multiple passes

(setq company-idle-delay nil)

(setq gofmt-command "goimports")
;; UPDATE: gofmt-before-save is more convenient then having a command
;; for running gofmt manually. In practice, you want to
;; gofmt/goimports every time you save anyways.
(add-hook 'before-save-hook 'gofmt-before-save)

(global-set-key (kbd "C-c M-n") 'company-complete)
(global-set-key (kbd "C-c C-n") 'company-complete)

(defun my-go-mode-hook ()
  ;; UPDATE: I commented the next line out because it isn't needed
  ;; with the gofmt-before-save hook above.
  ;; (local-set-key (kbd "C-c m") 'gofmt)
  (local-set-key (kbd "M-.") 'godef-jump)
  (set (make-local-variable 'company-backends) '(company-go)))

(add-hook 'go-mode-hook 'my-go-mode-hook)
(add-hook 'go-mode-hook 'go-eldoc-setup)
(add-hook 'go-mode-hook 'company-mode)
(setq-default indent-tabs-mode nil)
(setq default-tab-width 4)


;; Set to the location of your Org files on your local system
;; (setq org-directory "/Users/toeinriver/Dropbox/Apps/MobileOrg")
;; Set to the name of the file where new notes will be stored
;; (setq org-mobile-inbox-for-pull "/Users/toeinriver/Dropbox/Apps/MobileOrg/flagged.org")
;; Set to <your Dropbox root directory>/MobileOrg.
;; (setq org-mobile-directory "/Users/toeinriver/Dropbox/Apps/MobileOrg")
(defun org-summary-todo (n-done n-not-done)
  "Switch entry to DONE when all subentries are done, to TODO otherwise."
  (let (org-log-done org-log-states)   ; turn off logging
    (org-todo (if (= n-not-done 0) "DONE" "TODO"))))

(add-hook 'org-after-todo-statistics-hook 'org-summary-todo)

(require 'ag)
(require 'helm-ag)
(global-set-key (kbd "s-F") 'ag)
(setq ag-highlight-search t)


(setenv "PATH" (concat (getenv "PATH") ":/usr/local/bin"))
(setq exec-path (append exec-path '("/usr/local/bin")))

(setq org-babel-clojure-backend 'cider)

(require 'virtualenvwrapper)
(venv-initialize-interactive-shells) ;; if you want interactive shell support
;; (venv-initialize-eshell) ;; if you want eshell support
;; note that setting `venv-location` is not necessary if you
;; use the default location (`~/.virtualenvs`), or if the
;; the environment variable `WORKON_HOME` points to the right place
;; (setq venv-location "/path/to/your/virtualenvs/")

(require 'neotree)
(global-set-key [f8] 'neotree-toggle)

;; (setq explicit-shell-file-name "/bin/bash")
(let ((path (shell-command-to-string ". ~/.bash_profile; echo -n $PATH")))
  (setenv "PATH" path)
  (setq exec-path
        (append
         (split-string-and-unquote path ":")
         exec-path)))
(push '(font . "ubuntu mono 11") default-frame-alist)

(setq org-startup-indented t)
(setq org-hide-leading-stars t)

(persp-mode t)

(defun hide-org-bullets ()
  (font-lock-add-keywords
   'org-mode `(("\\(?:^\\(?1:\\*+\\)[[:blank:]]\\)"
              (0 (progn (compose-region
                         (match-beginning 1) (match-end 1)
                         (pcase (length (match-string 1))
                           (1 ?\u2219)
                           (2 ?\u2022)
                           (3 ?\u25c9)
                           (_ ?\u25CB)))
                        nil))))))

(blink-cursor-mode 0)
(setq ring-bell-function 'ignore)
(global-set-key (kbd "C-c h") 'helm-command-prefix)
(global-unset-key (kbd "C-x c"))

(defun my/goto-same-spot-in-other-buffer ()
  "Go to the same location in the other buffer. Useful for when you have cloned indirect buffers"
  (interactive)
  (org-tree-to-indirect-buffer)
)

(global-set-key (kbd "<s-mouse-1>") 'my/goto-same-spot-in-other-buffer)
(global-set-key (kbd "s-m") 'my/goto-same-spot-in-other-buffer)
;; (global-set-key (kbd "<C-s-mouse-1>") 'my/jump-to-point-and-show)
;; (global-set-key (kbd "C-s-m") 'my/jump-to-point-and-show)

(add-to-list 'load-path "~/.emacs.d/site-lisp/helm-fzf")
(require 'helm-fzf)
(global-set-key (kbd "s-t") (lambda () (interactive)(helm-fzf default-directory)))


;; (add-hook 'LaTeX-mode-hook 'flyspell-mode)
;; (add-hook 'org-mode-hook 'flyspell-mode)

(setq org-indirect-buffer-display 'new-frame)
(setq tramp-default-method "ssh")

;; (require 'org-brain)
;; (use-package org-brain :ensure t
;;   :init
;;   (setq org-brain-path "~/Document/org")
;;   ;; For Evil users
;;   (with-eval-after-load 'evil
;;     (evil-set-initial-state 'org-brain-visualize-mode 'emacs))
;;   :config
;;   (setq org-id-track-globally t)
;;   (setq org-id-locations-file "~/.emacs.d/.org-id-locations")
;;   (push '("b" "Brain" plain (function org-brain-goto-end)
;;           "* %i%?" :empty-lines 1)
;;         org-capture-templates)
;;   (setq org-brain-visualize-default-choices 'all)
;;   (setq org-brain-title-max-length 12))

(global-visual-line-mode t)
(setq markdown-command "/usr/local/bin/pandoc")

(require 'highlight-symbol)
(global-set-key [(f3)] 'highlight-symbol)
(global-set-key (kbd "s-g") 'highlight-symbol-next)
(global-set-key (kbd "s-G") 'highlight-symbol-prev)
(global-set-key (kbd "s-@") 'highlight-symbol-query-replace)
(setq inferior-lisp-program "/usr/local/bin/sbcl")
;; (setq slime-contribs '(slime-fancy helm-slime))
;; (require 'hippie-expand-slime)
;; (add-hook 'slime-mode-hook 'set-up-slime-hippie-expand)
;; (add-hook 'slime-repl-mode-hook 'set-up-slime-hippie-expand)

(global-set-key (kbd "s-<f3>") 'highlight-symbol-remove-all)

(setq python-shell-interpreter "python3")

(global-set-key (kbd "s-Z") 'undo-tree-redo)

(setq tramp-default-method "ssh")
(global-flycheck-mode)
(package-install 'exec-path-from-shell)
(exec-path-from-shell-initialize)
(linum-mode t)

(provide 'init)
;;; init.el ends here
(set-variable 'markdown-command "pandoc -s --mathjax")

(use-package evil-surround
  :ensure t
  :config
  (global-evil-surround-mode 1))


(setq org-image-actual-width nil)
(setq org-src-fontify-natively t)

(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.
 '(ob-ein-languages
   (quote
    (("ein" . python)
     ("ein-python" . python)
     ("ein-R" . R)
     ("ein-r" . R)
     ("ein-julia" . julia)
     ("ein-hy" . hy)
     ("ein-Cpp17" . C++))))
 '(org-agenda-files
   (quote
    ("~/Dropbox/read-notes/journals/journal-20191208.org" "~/Dropbox/orgfiles/i.org")))
 '(org-directory "~/Dropbox/orgfiles")
 '(package-selected-packages
   (quote
    (gist simple-call-tree call-graph google-translate el-get cask px yasnippet-classic-snippets slime helm-projectile wolfram-mode ein xkcd edit-server-htmlize edit-server posframe pyim multiple-cursors helm-describe-modes ox-pandoc ob-ipython org jupyter ox-epub writeroom-mode zenburn-theme yasnippet-snippets writegood-mode virtualenvwrapper use-package typescript-mode tramp-theme sr-speedbar solidity-flycheck solaire-mode smex smartparens sly request-deferred pyvenv pyenv-mode projectile persp-mode origami org-ref org-brain ob-async nimbus-theme neotree multi markdown-mode magit macrostep iedit hippie-expand-slime highlight-symbol hideshow-org helm-gtags helm-ag guide-key go-errcheck go-eldoc go ggtags function-args fountain-mode fold-dwim-org flymake-python-pyflakes expand-region exec-path-from-shell evil-surround dumb-jump company-solidity company-c-headers cider auctex alert ag))))
(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.
 )
;; (require 'poetry)
(global-set-key (kbd "M-c") 'capitaLize-word)

(require 'paredit)
(paredit-mode 1)
(setq tramp-default-method "ssh")

(use-package company
  :ensure t
  :config
  (progn
    (add-hook 'after-init-hook 'global-company-mode)))

(require 'multiple-cursors)
(global-unset-key (kbd "M-<down-mouse-1>"))
(global-set-key (kbd "M-<mouse-1>") 'mc/add-cursor-on-click)

(global-set-key (kbd "s-d") 'mc/mark-next-like-this)
(global-set-key (kbd "s-D") 'mc/mark-previous-like-this)

(if (> emacs-major-version 25)
    (require 'posframe)
  nil)

(require 'pyim)
(require 'pyim-basedict) ; 拼音词库设置，五笔用户 *不需要* 此行设置

(pyim-basedict-enable)   ; 拼音词库，五笔用户 *不需要* 此行设置
(setq default-input-method "pyim")
(global-set-key (kbd "C-\\") 'toggle-input-method)

(use-package pyim
  :ensure nil
  :demand t
  :config
  ;; 激活 basedict 拼音词库，五笔用户请继续阅读 README
  (use-package pyim-basedict
    :ensure nil
    :config (pyim-basedict-enable))

  (setq default-input-method "pyim")

  ;; 我使用全拼
  (setq pyim-default-scheme 'quanpin)

  ;; 设置 pyim 探针设置，这是 pyim 高级功能设置，可以实现 *无痛* 中英文切换 :-)
  ;; 我自己使用的中英文动态切换规则是：
  ;; 1. 光标只有在注释里面时，才可以输入中文。
  ;; 2. 光标前是汉字字符时，才能输入中文。
  ;; 3. 使用 M-j 快捷键，强制将光标前的拼音字符串转换为中文。
  (setq-default pyim-english-input-switch-functions
                '(pyim-probe-dynamic-english
                  pyim-probe-isearch-mode
                  pyim-probe-program-mode
                  pyim-probe-org-structure-template))

  (setq-default pyim-punctuation-half-width-functions
                '(pyim-probe-punctuation-line-beginning
                  pyim-probe-punctuation-after-punctuation))

  ;; 开启拼音搜索功能
  (pyim-isearch-mode 1)

  ;; 使用 popup-el 来绘制选词框, 如果用 emacs26, 建议设置
  ;; 为 'posframe, 速度很快并且菜单不会变形，不过需要用户
  ;; 手动安装 posframe 包。
  (setq pyim-page-tooltip 'posframe)
  (defun my-converter (string)
    ;; (if (equal string "二呆")
    ;;     "超级帅小伙"
    ;;   string)
    string
  )
  (setq pyim-magic-converter #'my-converter)

  ;; 选词框显示5个候选词
  (setq pyim-page-length 5)

  :bind
  (("M-j" . pyim-convert-string-at-point) ;与 pyim-probe-dynamic-english 配合
   ("C-;" . pyim-delete-word-from-personal-buffer)))

(setq org-special-ctrl-a/e t)

(add-hook 'term-mode-hook (lambda()
                            (yas-minor-mode -1)
                            (setq yas-dont-activate t)))

(setq org-cycle-include-plain-lists 'integrate)


;; org-protocol setup
;; (setq server-socket-dir (format "/tmp/emacs%d" (user-uid)))
(server-start)
(require 'org-protocol)
(setq org-capture-templates
      (quote
       (
        ;; ("w"
        ;;  "Default template"
        ;;  entry
        ;;  (file+headline "~/org/capture.org" "Notes")
        ;;  "* %^{Title}\n\n  Source: %u, %c\n\n  %i"
        ;;  :empty-lines 1)
        ;; ... more templates here ...
        ;; ("w" "Web site" entry
        ;;  (file "")
        ;;  "* %a :website:\n\n%U %?\n\n%:initial")
        ("w" "Web site" entry
         (file "")
         "* %a :website:\n\n%U %?\n\n%:initial")
        ("t" "todo" entry (file org-default-notes-file)
         "* TODO %?\n%u\n%a\n" :clock-in t :clock-resume t)
        ("m" "Meeting" entry (file org-default-notes-file)
         "* MEETING with %? :MEETING:\n%t" :clock-in t :clock-resume t)
        ("d" "Diary" entry (file+datetree "~/org/diary.org")
         "* %?\n%U\n" :clock-in t :clock-resume t)
        ("i" "Idea" entry (file org-default-notes-file)
         "* %? :IDEA: \n%t" :clock-in t :clock-resume t)
        ("n" "Next Task" entry (file+headline org-default-notes-file "Tasks")
         "** NEXT %? \nDEADLINE: %t"
         )
        ("p" "Protocol" entry (file+headline ,(concat org-directory "notes.org") "Inbox")
        "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?")
	("L" "Protocol Link" entry (file+headline ,(concat org-directory "notes.org") "Inbox")
        "* %? [[%:link][%:description]] \nCaptured On: %U")
        )))

(add-to-list 'load-path "~/.emacs.d/site-lisp/org-protocol-capture-html/")
(require 'org-protocol-capture-html)

(require 'edit-server)

(if (not (server-running-p server-name))
    (use-package edit-server
      :ensure t
      :config
      (progn
        ;; Don't pop up a new frame
        (setq edit-server-new-frame nil)
        (setq edit-server-default-major-mode 'org-mode)
        (setq edit-server-url-major-mode-alist
              '(("github\\.com" . markdown-mode)
                ("stackexchange\\.com" . markdown-mode)
                ("stackoverflow\\.com" . markdown-mode)
                ("reddit\\.com" . markdown-mode)))

        ;; Integration with Gmail
        (use-package edit-server-htmlize
          :ensure t
          :defer t
          :config
          (progn
            (add-hook 'edit-server-start-hook #'edit-server-maybe-dehtmlize-buffer)
            (add-hook 'edit-server-done-hook  #'edit-server-maybe-htmlize-buffer)))

        (edit-server-start))))

(use-package xkcd
  :defer t
  :config
  (progn
    (bind-keys
     :map xkcd-mode-map
      ("/" . xkcd-get)
      ("g" . xkcd-get-latest)
      ("c" . xkcd-get-latest-cached)
      ("p" . xkcd-prev)
      ("n" . xkcd-next)
      ("v" . xkcd-open-browser)
      ("w" . xkcd-copy-link)
      ("?" . xkcd-open-explanation-browser))))

(provide 'setup-xkcd)

;; (server-mode 1)
(setenv "EDITOR" "emacsclient")

;; add save-as function
(defun save-as (filename)
  (interactive "F")
  (write-region (point-min) (point-max) filename))

(global-set-key (kbd "s-S") 'save-as)

(global-set-key (kbd "s-b") 'helm-buffers-list)
(global-set-key (kbd "C-x C-f") 'helm-find-files)
(global-set-key (kbd "s-o") 'helm-find-files)

(setq helm-locate-command
      "glocate %s %s"
      helm-locate-create-db-command
      "gupdatedb --output='%s' --localpaths='%s'")

(setq helm-locate-project-list
      (list "/Users/yongguo/.emacs.d/"))

;; Set common-lisp system and, optionally, some contribs
;; (setq slime-lisp-implementations
;;       '(
;;         (clisp ("/opt/local/bin/clisp" "-q -I"))
;;         (sbcl  ("/usr/local/bin/sbcl") :coding-system utf-8-unix)))
(setq inferior-lisp-program "/usr/local/bin/sbcl --noinform --no-linedit")
(setq slime-contribs '(slime-fancy))

(require 'px)

(global-set-key (kbd "s-w") 'ido-kill-buffer)
(global-set-key (kbd "s-p") 'apropos)
(global-set-key (kbd "C-e") 'end-of-visual-line)
;; define keys in evil mode command mode
(eval-after-load 'evil-ex
  '(evil-ex-define-cmd "bl" 'gud-break))

(with-eval-after-load 'evil-maps
  (define-key evil-normal-state-map (kbd "C-e") 'end-of-visual-line)
  (define-key evil-normal-state-map (kbd "C-a") 'evil-first-non-blank-of-visual-line)
  (define-key evil-insert-state-map (kbd "C-e") 'end-of-visual-line)
  (define-key evil-normal-state-map (kbd "C-e") 'end-of-visual-line)
  (define-key evil-visual-state-map (kbd "C-e") 'end-of-visual-line)
  (define-key evil-insert-state-map (kbd "C-a") 'evil-first-non-blank-of-visual-line)
  (define-key evil-normal-state-map (kbd "C-n") 'evil-next-line)
  (define-key evil-normal-state-map (kbd "C-p") 'evil-previous-line)
  (define-key evil-insert-state-map (kbd "C-n") 'evil-next-line)
  (define-key evil-insert-state-map (kbd "C-p") 'evil-previous-line)
  (define-key evil-normal-state-map (kbd "C-k") 'evil-delete-line)
  (define-key evil-insert-state-map (kbd "C-k") 'evil-delete-line)
  )

(defun get-lang-from-src-block-mode (mode-name)
  (message mode-name)
     (if
      (equalp mode-name "ipython")
      "python"
      mode-name)
     )

(defun open-src-block-region-in-sublime()
  (interactive)
  (let ((lang (get-lang-from-src-block-mode (nth 0 (org-babel-get-src-block-info)))))
    (shell-command (format "subl -n -w --command \"set_file_type {\\\"syntax\\\":\\\"Packages/%s/%s.sublime-syntax\\\"}\"" (capitalize lang) lang))))

(global-set-key (kbd "M-g s") 'open-src-block-region-in-sublime)

;; (defvar current-src-block-lang nil)
;; (defadvice org-edit-special (before org-edit-src-code activate)
;;   (let ((lang (nth 0 (org-babel-get-src-block-info))))
;;     (setq current-src-block-lang lang)
;;   ))

(setq org-columns-default-format "%50ITEM(Task) %10CLOCKSUM %16TIMESTAMP_IA")
(setq org-refile-targets (quote ((nil :maxlevel . 9)
                                 (org-agenda-files :maxlevel . 9))))

;; (defconst org-protocol-capture-html-pandoc-no-wrap-option "--wrap=auto")


(message "This is the end of init.el")

(defun copy-from-osx ()
  (shell-command-to-string "pbpaste"))

(defun paste-to-osx (text &optional push)
  (let ((process-connection-type nil))
    (let ((proc (start-process "pbcopy" "*Messages*" "pbcopy")))
      (process-send-string proc text)
      (process-send-eof proc))))

(setq interprogram-cut-function 'paste-to-osx)
(setq interprogram-paste-function 'copy-from-osx)

(global-set-key (kbd "C-c a") 'org-agenda)

(org-agenda nil "a")

;; archive all the DONE tasks using a single command
(defun my-org-archive-done-tasks ()
  (interactive)
  (org-map-entries 'org-archive-subtree "/DONE" 'file))