;;; My basic configuration Gerardo Marx 15/Jul/2020
;;--------
;; Melpa repository:
(require 'package)
(add-to-list 'package-archives
	     '("melpa" . "https://melpa.org/packages/")t)
(package-initialize)
;; use-package
(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))
;; frame size
(setq initial-frame-alist '((top . 10)(left . 20)
			    (width . 90)(height . 50)))
;; which-key:
(use-package which-key
  :ensure t
  :config (which-key-mode))
;; doom-themes
(use-package doom-themes
  :ensure t
  :config
  (setq doom-themes-enable-bold t    ; if nil, bold is universally disabled
        doom-themes-enable-italic t) ; if nil, italics is universally disabled  
  (load-theme ;'doom-one
              'doom-tomorrow-day t)
  ;; Enable flashing mode-line on errors
  (doom-themes-visual-bell-config)
  ;; Enable custom neotree theme (all-the-icons must be installed!)
  (doom-themes-neotree-config)
  ;; or for treemacs users
 
  (setq doom-themes-treemacs-theme "doom-colors") ; use the colorful treemacs theme
  (doom-themes-treemacs-config)
    ;; Corrects (and improves) org-mode's native fontification.
  (doom-themes-org-config))
;; modeline
(use-package doom-modeline
  :ensure t
  :init (doom-modeline-mode 1))
;; icons:
(use-package all-the-icons
  :ensure t) ;; --> you need this M-x all-the-icons-install-fonts
;; startup config
(setq inhibit-startup-message t) ;;inhibit startup
(tool-bar-mode -1)
(menu-bar-mode -1)
(global-hl-line-mode +1) ;; highlith current line
(delete-selection-mode +1) ;; deletes selected text and replace it
(scroll-bar-mode -1)
(setq ns-right-alternate-modifier nil) ;; right option macos key enable
(setq backup-directory-alist '(("." . "~/.saves"))) ;; a backup dir to store no saved files
(fset 'yes-or-no-p 'y-or-n-p) ;; Ask y/n instead of yes/no
(add-hook 'prog-mode-hook 'display-line-numbers-mode) ;; display line number when programming
(show-paren-mode +1) ;; show matching parentheses
;; helm package:
(use-package helm
  :ensure t
  :demand t
  :bind (("M-x" . helm-M-x)
	 ("C-c h x" . helm-register)    ; C-x r SPC and C-x r j
	 ("C-c h g" . helm-google-suggest)
	 ("C-c h M-:" . helm-eval-expression-with-eldoc)
	 ("C-x C-f" . helm-find-files))
  :config
 (require 'helm-config)
  (helm-mode t))
;; projectile:
(use-package projectile
  :ensure t
  :config
  (define-key projectile-mode-map (kbd "C-c p") 'projectile-command-map)
  (projectile-mode t))
;; helm-projectile:
(use-package helm-projectile
  :after projectile
  :ensure t
  :init
  (require 'tramp)
  :config
  (helm-projectile-on))
;; temp:
(setq ido-enable-flex-matching t)
;; dash-board:
(use-package dashboard
  :ensure t
  :init
  (progn
    (setq recentf-exclude '("/Users/gmarx/beorg/"))
    (setq dashboard-items '(
			    ;;(recents . 5)
			    (bookmarks . 5)
			    (projects . 5)
			    (agenda . 5)))
    (setq dashboard-banner-logo-title "Welcome gMarx")
    (setq dashboard-set-file-icons t)
    (setq dashboard-set-init-info t)
    (setq dashboard-startup-banner 'logo)
    )
  :config
  (dashboard-setup-startup-hook))
;; treemacs
(use-package treemacs
  :ensure t
  :init
  (with-eval-after-load 'winum
    (define-key winum-keymap (kbd "M-0") #'treemacs-select-window))
  :config
  (progn
    (setq treemacs-is-never-other-window t)
    (setq treemacs-width 35))
  :bind
  (:map global-map
        ("M-0"       . treemacs-select-window)
	("C-x t t"   . treemacs)))
;; treemacs-projectile
(use-package treemacs-projectile
  :after treemacs projectile
  :ensure t)
;; magit
(use-package magit
  :ensure t)
;; latex
(use-package tex
  :defer t
  :ensure auctex
  :init
  (progn
    (setq-default TeX-master nil) ; Query for master file.
    (setq TeX-auto-save t) ; Enable parse on save.
    (setq TeX-save-query nil)
    (custom-set-variables '(LaTeX-command "latex -synctex=1"))
    ;;(setq TeX-command-force "LaTex")
    ;;(setq latex-run-command "pdflatex")
    (setq TeX-parse-self t) ; Enable parse on load.
    (setenv "PATH" (concat (getenv "PATH") ":/Library/TeX/texbin/"))
    (setq exec-path (append exec-path '("/Library/TeX/texbin/")))
    ;; pdf-tools configuration
    (setq TeX-PDF-mode t)
      (add-hook 'TeX-after-compilation-finished-functions
	    #'TeX-revert-document-buffer)
    (setq TeX-view-program-selection '((output-pdf "PDF Tools"))
	 TeX-source-correlate-start-server t)
    (setq pdf-info-epdfinfo-program "/usr/local/bin/epdfinfo")
    (add-to-list 'auto-mode-alist '("\\.pdf\\'" . pdf-view-mode))
    (add-hook 'pdf-view-mode-hook
	      (lambda () (pdf-tools-enable-minor-modes))) 
    )
  )
;; pdf-tools
(use-package pdf-tools
  :ensure t
  :pin melpa
  :magic ("%PDF" . pdf-view-mode)
  :config
   (custom-set-variables
     '(pdf-tools-handle-upgrades nil)) 
  )
;;--------
;; latex-preview
(use-package latex-preview-pane
  :ensure t)
;; latexmk
(use-package auctex-latexmk
  :ensure t
  :init
  (auctex-latexmk-setup)
  :config
  (setq auctex-latexmk-inherit-TeX-PDF-mode t))
;;----------------------
;; flycheck
(use-package flycheck
  :ensure t
  :init (global-flycheck-mode))
;; expand region
(use-package expand-region
  :ensure t
  :bind
  ("C-=" . er/expand-region)
  ("C--" . er/contract-region))
;; org-bullets
(use-package org-bullets
  :ensure t
  :init
  (setq org-support-shift-select t))
;;  :hook
;;  (org-mode . org-bullets-mode))
;;------pomodoro
(use-package org-pomodoro
  :ensure t
  :after org 
  :bind ("C-x p" . org-pomodoro))
;; org configuration:
(add-hook 'org-mode-hook
	  (lambda()
	    ;; dictionary
	    (org-bullets-mode 1)
	    (ispell-change-dictionary "en")
	    (setq org-image-actual-width nil)
	    (setq org-tags-column 5)
	    (setq org-format-latex-options (plist-put org-format-latex-options :scale 1.5))
	    (setq org-latex-create-formula-image-program 'imagemagick)
	    (setq org-startup-indented t) ; Enable `org-indent-mode' by default
	    (visual-line-mode 1)
	    ))
;; Company-mode
(use-package company
  :ensure t
  :init
  (add-hook 'after-init-hook 'global-company-mode))
;; ispell
(dolist (hook '(org-mode-hook latex-mode-hook tex-mode-hook git-commit-mode-hook))
	(add-hook hook (lambda () (flyspell-mode 1))))
;;(setq ispell-dictionary "en")
(setq ispell-program-name "/usr/local/bin/aspell")
;; Set default font:
(add-to-list 'default-frame-alist
	     '(font . "Source Code Pro-20"))
;; Activation org-agenda and capture
(global-set-key (kbd "C-c l") 'org-store-link)
(global-set-key (kbd "C-c a") 'org-agenda)
(global-set-key (kbd "C-c c") 'org-capture)
;;++++++++++
;; sentence one space  definition 
(setq sentence-end-double-space nil)
;;---------
;; Todo states for ORG:
(setq org-todo-keywords
          (quote
           ((sequence "TODO(t)" "PROGRESS(g)" "PAUSE(p)" "CHECK(k)" "|" "DONE(d)" "CANCELED(c)"))))
(setq org-todo-keyword-faces
          '(("PROGRESS" . "orange") ("PAUSE" . "magenta") ("CHECK" . "purple") ("CANCELED" . "red") ("DONE" . "green")))
;; capture:
    (setq org-capture-templates
      (quote (
              ("a"         ; hotkey
               "Academia Todo" ; name
               entry       ; type
               (file+headline "/Users/gmarx/beorg/academia.org" "Tasks") ;target
               "* TODO [#B] %^{Task}" ; template
               )
              ("t"
               "Task PhD"
               entry
               (file+datetree "~/beorg/phd.org")
               "* TODO [#A] %^{Task}")
              ("d"
               "Students"
               item
               (file+datetree "~/beorg/students.org")
               "- %U - %^{Activity}")
              ("r"
               "to Read"
               entry
               (file+headline "~/beorg/inbox.org" "to read")
               "* TODO %^{topic to read}\n%^{Why to read this?}"
               )
              ("s"
               "Schedule an event"
               entry
               (file+headline "~/beorg/inbox.org" "Scheduled events")
               "* %^{Event}\nSCHEDULED: %^t"
               )
              ("k"
               "Task inbox"
               entry
               (file+headline "~/beorg/inbox.org" "Tasks")
               "* TODO %^{Task} -> %^{move to}"
               )
              ("c"
               "Cheat-Sheet"
               entry
               (file+headline "~/beorg/cheatsheets.org" "Notes")
               "* %^{what solves}\n%^{the commands are}"
               )
              )))
;;-------end capture
;;=======
;;python
(use-package virtualenvwrapper
  :ensure t
  :config
  (setq python-shell-interpreter "python3")
  (setq venv-location "~/.virtualenvs"))
;; org-alert
(use-package org-alert
  :ensure t
  :config
  (setq alert-default-style 'osx-notifier))
;; reftex
(use-package reftex
  :ensure t
  :defer t
  :config
  (setq reftex-cite-prompt-optional-args t)); Prompt for empty optional arguments in cite
;; org-exporter:
(use-package ox-twbs
  :ensure t)
;;multiple coursors:
(use-package ace-mc
  :ensure t
  :config
  (global-set-key (kbd "C-)") 'ace-mc-add-multiple-cursors)
  (global-set-key (kbd "C-M-)") 'ace-mc-add-single-cursor))
;;ace-jump:
(use-package ace-jump-mode
  :ensure t
  :bind ("C-x j" . ace-jump-mode))
;; pyenv:
(use-package pyvenv
  :ensure t
  :config
  (pyvenv-mode 1))
;; org-configuration:
(org-babel-do-load-languages
 'org-babel-load-languages
 '((python . t)))

;;ess:
(use-package ess
  :ensure t
  :init (require 'ess-site))

;; markdown:
(use-package markdown-mode
  :ensure t
  :commands (markdown-mode gfm-mode)
  :mode (("README\\.md\\'" . gfm-mode)
         ("\\.md\\'" . markdown-mode)
         ("\\.markdown\\'" . markdown-mode))
  :init
  (setq markdown-command "multimarkdown")
  (add-hook 'markdown-mode-hook
	    (lambda()
	      (ispell-change-dictionary "en")
	      (flyspell-mode 1)))
  (setq markdown-css-paths '(
			     "./assets/stylesheets/style.css"
			     "./assets/stylesheets/pilcrow.css"
			     "./assets/stylesheets/hljs-github.min.css"
			     ))
  )

;;criticMarkup
(use-package cm-mode
  :ensure t)

;;org-trello
(require 'org-trello)
(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.
 '(LaTeX-command "latex -synctex=1")
 '(custom-safe-themes
   (quote
    ("7a994c16aa550678846e82edc8c9d6a7d39cc6564baaaacc305a3fdc0bd8725f" "5b809c3eae60da2af8a8cfba4e9e04b4d608cb49584cb5998f6e4a1c87c057c4" "d74c5485d42ca4b7f3092e50db687600d0e16006d8fa335c69cf4f379dbd0eee" "2f1518e906a8b60fac943d02ad415f1d8b3933a5a7f75e307e6e9a26ef5bf570" "71e5acf6053215f553036482f3340a5445aee364fb2e292c70d9175fb0cc8af7" "99ea831ca79a916f1bd789de366b639d09811501e8c092c85b2cb7d697777f93" "bf387180109d222aee6bb089db48ed38403a1e330c9ec69fe1f52460a8936b66" default)))
 '(markdown-command "/usr/local/bin/pandoc" t)
 '(org-agenda-files
   (quote
    ("~/beorg/kinetics-estimation.org" "~/lwc/projects/dynamicSystems/trello-jason.org" "~/beorg/inbox.org" "~/beorg/academia.org" "~/beorg/water-quality.org" "~/beorg/phd.org" "~/lwc/projects/dynamicSystems/dynamic-systems.org")))
 '(org-trello-current-prefix-keybinding "C-c o" nil (org-trello))
 '(org-trello-files (quote ("~/beorg/trello-org.org")) nil (org-trello))
 '(package-selected-packages
   (quote
    (ace-jump cm-mode org-trello markdown-mode pyvenv ess ace-mc ox-twbs org-alert latex-preview-pane org-pomodoro which-key virtualenvwrapper use-package treemacs-projectile pdf-tools org-bullets mu4e-maildirs-extension mu4e-alert magit helm-projectile helm-mu flycheck expand-region doom-themes doom-modeline dashboard company auctex)))
 '(pdf-tools-handle-upgrades nil)
 '(safe-local-variable-values
   (quote
    ((markdown-css-paths . "./assets/stylesheets/main.css")
     (markdown-css-path . "./assets/stylesheets/main.css")
     (column-width . 5000)
     (fill-column . 5000:)
     (ispell-local-dictionary . castellano)
     (ispell-local-directory . castellano)
     (LaTeX-includegraphics-read-file . LaTeX-includegraphics-read-file-relative)
     (set-fill-column . 5000)
     (set-fill-column . 2000)
     (TeX-auto-save . t)
     (TeX-parse-self . t)
     (org-attach-directory . "students/")
     (org-attach-use-inheritance . t)
     (org-attach-preferred-new-method . ask))))
 '(send-mail-function (quote smtpmail-send-it)))



;; org-trello:
(use-package org-trello
  :ensure t)

;; ace-window
(use-package ace-window
  :ensure t
  :bind
  ("M-o" . 'ace-window)
  :config
  (setq aw-keys '(?a ?s ?d ?f ?g ?h ?j ?k ?l)))

;; ace-jump
(use-package ace-jump-mode
  :ensure t
  :bind
  ("C-c SPC" . 'ace-jump-mode)
  ("C-c C-j l" . 'ace-jump-line-mode)
  ("C-c C-j c" . 'ace-jump-char-mode))
;;-0-0-0-0-0-0-0
;; my functions:

;; show in finder
(defun show-in-finder ()
  (interactive)
  (shell-command (concat "open -R " buffer-file-name)))
(global-set-key (kbd "C-x x f") 'show-in-finder)
;; visit real files (symbolic link)
(setq find-file-visit-truename t)

;;-=-=-=-=-=-=-
;; mu4e
;; (use-package mu4e
;;   :commands (mu4e)
;;   :init
;;   ;;(progn (require 'helm-mu))
;;   :config
;;   (add-to-list 'load-path "/usr/local/share/emacs/site-lisp/mu/mu4e")
;;   (setq mu4e-mu-binary "/usr/local/bin/mu"))
;; ;;-+-+-+-+-+-+-+-+-+-+-+-+
;; ;; "default" parameters from Gmail
;; (setq user-full-name  "Gerardo Marx Chávez-Campos") ;;user
;; (setq mu4e-compose-signature t) ;; signature in file ~/.signature
;; (add-hook 'mu4e-compose-mode-hook 'flyspell-mode(setq ispell-local-dictionary "castellano")) ;; spell check
;; ;; attempt to show images when viewing messages
;; (setq mu4e-view-show-images t)
;; (setq mu4e-sent-folder "/Gmail/sent"
;;       ;; mu4e-sent-messages-behavior 'delete ;; Unsure how this should be configured
;;       mu4e-drafts-folder "/Gmail/drafts"
;;       user-mail-address "gmarx_cc@itmorelia.edu.mx"
;;       smtpmail-local-domain "gmail.com"
;;       smtpmail-default-smtp-server "smtp.gmail.com"
;;       smtpmail-stream-type 'starttls
;;       smtpmail-smtp-server "smtp.gmail.com"
;;       smtpmail-smtp-service 587)
;; ;;  ---
;; ;; Now I set a list of 
;; (defvar my-mu4e-account-alist
;;   '(("Gmail"
;;      (mu4e-sent-folder "/Gmail/sent")
;;      (mu4e-drafts-folder "/Gmail/drafts")
;;      (user-mail-address "gmarx_cc@itmorelia.edu.mx")
;;      (smtpmail-smtp-user "gmarx_cc@itmorelia.edu.mx")
;;      (smtpmail-local-domain "gmail.com")
;;      (smtpmail-default-smtp-server "smtp.gmail.com")
;;      (smtpmail-stream-type starttls)
;;      (smtpmail-smtp-server "smtp.gmail.com")
;;      (smtpmail-smtp-service 587)
;;      )
;;     ;; Include any other accounts here ...
;;    ("Exchange"
;;     (mu4e-sent-folder "/Exchange/sent")
;;     (mu4e-drafts-folder "/Exchange/drafts")
;;     (user-mail-address "gerardo.cc@morelia.tecnm.mx")
;;     (smtpmail-smtp-user "gerardo.cc@morelia.tecnm.mx")
;;     (smtpmail-local-domain "office365.com")
;;     (smtpmail-default-smtp-server "smtp.office365.com")
;;     (smtpmail-stream-type starttls)
;;     (smtpmail-smtp-server "smtp.office365.com")
;;     (smtpmail-smtp-service 587)
;;      )
;;    ;;
;;     ;; hotmail
;;    ("Hotmail"
;;     (mu4e-sent-folder "/Hotmail/sent")
;;     (mu4e-drafts-folder "/Hotmail/drafts")
;;     (user-mail-address "gmarx_cc@hotmail.com")
;;     (smtpmail-smtp-user "gmarx_cc@hotmail.com")
;;     (smtpmail-local-domain "office365.com")
;;     (smtpmail-default-smtp-server "smtp.office365.com")
;;     (smtpmail-stream-type starttls)
;;     (smtpmail-smtp-server "smtp.office365.com")
;;     (smtpmail-smtp-service 25)
;;      )
;;      ))
;; ;;  ---
;; (defun my-mu4e-set-account ()
;;   "Set the account for composing a message.
;;    This function is taken from: 
;;      https://www.djcbsoftware.nl/code/mu/mu4e/Multiple-accounts.html"
;;   (let* ((account
;;     (if mu4e-compose-parent-message
;;         (let ((maildir (mu4e-message-field mu4e-compose-parent-message :maildir)))
;;     (string-match "/\\(.*?\\)/" maildir)
;;     (match-string 1 maildir))
;;       (completing-read (format "Compose with account: (%s) "
;;              (mapconcat #'(lambda (var) (car var))
;;             my-mu4e-account-alist "/"))
;;            (mapcar #'(lambda (var) (car var)) my-mu4e-account-alist)
;;            nil t nil nil (caar my-mu4e-account-alist))))
;;    (account-vars (cdr (assoc account my-mu4e-account-alist))))
;;     (if account-vars
;;   (mapc #'(lambda (var)
;;       (set (car var) (cadr var)))
;;         account-vars)
;;       (error "No email account found"))))
;; (add-hook 'mu4e-compose-pre-hook 'my-mu4e-set-account)
;; ;;-+-+-+-+-+-+-+-+-+-+-+-+
;; ;;---------
;; ;; mu4e-maildirs-extension
;; (use-package mu4e-maildirs-extension
;;   :ensure t
;;   :init
;;   (mu4e-maildirs-extension)
;;   :custom
;;   (mu4e-maildirs-extension-custom-list '("/Gmail/INBOX" "/Exchange/INBOX" "/Hotmail/INBOX"))
;;   )

;; ;; mu4e-alert
;; (use-package mu4e-alert
;;   :ensure t
;;   :after mu4e
;;   :init
;;   (setq mu4e-alert-interesting-mail-query
;;     (concat
;;      "flag:unread maildir:/Exchange/INBOX "
;;      "OR "
;;      "flag:unread maildir:/Gmail/INBOX"
;;      ))
;;   (mu4e-alert-enable-mode-line-display)
;;   (defun gjstein-refresh-mu4e-alert-mode-line ()
;;     (interactive)
;;     (mu4e~proc-kill)
;;     (mu4e-alert-enable-mode-line-display)
;;     )
;;   (run-with-timer 0 60 'gjstein-refresh-mu4e-alert-mode-line))
;; ;; helm
;; (use-package helm-mu
;;   :ensure t
;;   :config
;;   ;;(define-key mu4e-main-mode-map "s" 'helm-mu)
;;   ;;(define-key mu4e-headers-mode-map "s" 'helm-mu)
;;   ;;(define-key mu4e-view-mode-map "s" 'helm-mu)
;;   )


;;=-=-=-=-=-=-=-=-=-=-=-=
;;agenda files
;;(setq org-agenda-files '("~/beorg/phd.org" "~/beorg/students.org" "~/beorg/inbox.org" "~/beorg/academia.org"))
(setq recentf-exclude (org-agenda-files))
  


(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.
 '(org-document-title ((t (\,@headline (\,@ variable-tuple) :height 1.5 :underline nil))))
 '(org-level-1 ((t (\,@headline (\,@ variable-tuple) :height 1.25))))
 '(org-level-2 ((t (\,@headline (\,@ variable-tuple) :height 1.15))))
 '(org-level-3 ((t (\,@headline (\,@ variable-tuple) :height 1.12))))
 '(org-level-4 ((t (\,@headline (\,@ variable-tuple) :height 1.1))))
 '(org-level-5 ((t (\,@headline (\,@ variable-tuple)))))
 '(org-level-6 ((t (\,@headline (\,@ variable-tuple)))))
 '(org-level-7 ((t (\,@headline (\,@ variable-tuple)))))
 '(org-level-8 ((t (\,@headline (\,@ variable-tuple))))))