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scimax-org.el
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;;; scimax-org.el --- org-mode configuration for scimax -*- lexical-binding:t ; -*-
;;; Commentary:
;;; Code:
(require 'org)
(require 'ox-latex)
(require 'org-inlinetask)
(require 'org-mouse)
(require 'org-ref)
(require 'org-agenda)
(require 'dash)
;; * Configuration of org-mode
;; Make editing invisible regions smart
(setq org-catch-invisible-edits 'smart)
;; allow lists with letters in them.
(setq org-list-allow-alphabetical t)
;; setup archive location in archive directory in current folder
(setq org-archive-location "archive/%s_archive::")
(defcustom scimax-use-org-bullets nil
"Whether to use org-bullets-mode or not."
:group 'scimax)
(when scimax-use-org-bullets
(add-hook 'org-mode-hook (lambda () (org-bullets-mode))))
(setq org-src-tab-acts-natively t)
;; * Speed commands
;; (setq org-todo-keywords
;; '((sequence "TODO(t)" " """ "|" "DONE(d)")))
;; * My own org setup , add on Jun/08/2018;; org-capture
(setq org-todo-keywords
(quote ((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d!)")
(sequence "WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c@/!)" "PHONE" "MEETING"))))
(setq org-todo-keyword-faces
(quote (("TODO" :foreground "red" :weight bold)
("NEXT" :foreground "blue" :weight bold)
("DONE" :foreground "forest green" :weight bold)
("WAITING" :foreground "orange" :weight bold)
("HOLD" :foreground "magenta" :weight bold)
("CANCELLED" :foreground "yellow" :weight bold)
("MEETING" :foreground "oliva" :weight bold)
("PHONE" :foreground "pink" :weight bold))))
(setq org-use-fast-todo-selection t)
(setq org-directory "~/myrepo/org")
;; (let ((org-agenda-directory "~/myrepo/org/"))
; (normal-top-level-add-subdirs-to-load-path))
;; ** refile setup
(setq org-default-notes-file (concat org-directory "/gtd/refile.org"))
;; ** org-journal
;; (setq org-journal-dir "~/myrepo/org/journal/")
;; (setq org-journal-enable-agenda-integration t)
;; ** org-agenda-files, add on Jun/10/2018
(load-library "find-lisp")
(setq org-agenda-files
(find-lisp-find-files "~/myrepo/org/" "\.org$"))
;; targets include this file and any file contributing to the agenda, up to 9 levels deep
(setq org-refile-targets (quote (("~/myrepo/org/gtd/refile.org" :maxlevel . 1)
("~/myrepo/org/gtd/definition.org" :maxlevel . 1)
("~/myrepo/org/gtd/idea.org" :maxlevel . 1)
("~/myrepo/org/gtd/les.org" :maxlevel . 1)
)))
;; ** org-capture
(setq org-capture-templates
(quote (("n" "Notes" entry (file "~/myrepo/org/gtd/notes.org")
"* %?%^G\n :PROPERTIES:\n :ENTERED_ON: %T\n :END:\n%i\n")
("i" "Ideas" entry (file "~/myrepo/org/gtd/ideas.org")
"* %?%^G\n :PROPERTIES:\n :ENTERED_ON: %T\n :END:\n%i\n")
("c" "Courses" entry (file "~/myrepo/org/gtd/courses.org")
"* %?%^G\n :PROPERTIES:\n :ENTERED_ON: %T\n :END:\n%i\n")
("t" "Todo" entry (file org-default-notes-file)
"* %?%^G\n :PROPERTIES:\n :ENTERED_ON: %T\n :END:\n%i\n")
("p" "Projects" entry (file org-default-notes-file)
"* %?%^G\n :PROPERTIES:\n :ENTERED_ON: %T\n :END:\n%i\n")
;; ("j" "Journal" entry (file
;; (expand-file-name (concat (format-time-string "%Y%m%d") ".org") org-journal-dir))
;; "* Tasks%?\n* Exercise\n* Meal plan"))
)
)
)
;; (setq org-remember-templates
;; '(
;; ("Todo" ?t "* TODO %^{Brief Description} %^g\n%?\nAdded: %U\n" "~/org/gtd/newgtd.org" "Tasks" :clock-in t :clock-resume t)
;; ("Idea" ?i "\n* %^{topic} %T %^g\n%?\nAdded: %U\n" "~/org/gtd/journal.org" "Idea")
;; ("Concept" ?c "\n* %T %^{topic} %^g\n%?\nAdded: %U\n" "~/org/gtd/concept.org" "Concpet")
;; ("Diary" ?d "\n* %T %^{topic} %^g\n%?\n#+BEGIN_COMMENT \nEntered on: %U \n#+END_COMMENT" "~/org/gtd/journal.org" "Diary")
;; ("Project" ?p "* TODO %^{Brief Description} %^g\n%?\nAdded: %U\n" "~/org/gtd/newgtd.org" "Project" :clock-in t :clock-resume t)
;; ("Summary today" ?s "\n* %T %^{topic} %^g\n%?\nAdded: %U\n" "~/org/gtd/journal.org" "Summary")
;; ("Journal" ?j "\n* %^{topic} %^g\n%?\nAdded: %U\n" "~/org/gtd/journal.org" "Journal")
;; ("Notes" ?n "\n* %^{topic} %^g\n%?\nAdded: %U\n" "~/org/gtd/journal.org" "Notes")
;; ))
;; (setq org-todo-keyword-faces
;; (quote (("TODO" :foreground "red" :weight bold)
;; ("NEXT" :foreground "blue" :weight bold)
;; ("DONE" :foreground "forest green" :weight bold)
;; ("WAITIN fsG" :foreground "orange" :weight bold)
;; ("HOLD" :foreground "magenta" :weight bold)
;; ("CANCELLED" :foreground "yellow" :weight bold)
;; ("MEETING" :foreground "oliva" :weight bold)
;; ("PHONE" :foreground "pink" :weight bold))))
;; (setq org-todo-state-tags-triggers
;; (quote (("CANCELLED" ("CANCELLED" . t))
;; ("WAITING" ("WAITING" . t))
;; ("HOLD" ("WAITING") ("HOLD" . t))
;; (done ("WAITING") ("HOLD"))
;; ("TODO" ("WAITING") ("CANCELLED") ("HOLD"))
;; ("NEXT" ("WAITING") ("CANCELLED") ("HOLD"))
;; ("DONE" ("WAITING") ("CANCELLED") ("HOLD")))))
(setq org-agenda-exporter-settings
'((ps-number-of-columns 1)
(ps-landscape-mode t)
(htmlize-output-type 'css)))
;; Do not dim blocked tasks
(setq org-agenda-dim-blocked-tasks nil)
;; Compact the block agenda view
(setq org-agenda-compact-blocks t)
(setq org-agenda-custom-commands
'(
("P" "Projects"
((agenda)
(tags-todo "PROJECT")
(tags-todo "READING")
(tags-todo "MANUSCRIPT")
(tags-todo "EXPERIMENT")
(tags-todo "ANALYSIS")))
("H" "Office and Home Lists"
((agenda)
(tags-todo "OFFICE")
(tags-todo "COURSES")
(tags-todo "PROJECT")
(tags-todo "READING")
(tags-todo "HOME")))
("D" "Daily Action List"
(
(agenda "" ((org-agenda-ndays 1)
(org-agenda-sorting-strategy
(quote ((agenda time-up priority-down tag-up) )))
(org-deadline-warning-days 7)
))))
)
)
(defun gtd ()
(interactive)
(find-file "~/myrepo/org/gtd/refile.org")
)
;; (defun journal_ljl ()
;; (interactive)
;; (find-file "~/org/gtd/journal.org")
;; )
;; (defun exp_record ()
;; (interactive)
;; (find-file "~/org/gtd/exp_record.org")
;; )
(defun idea ()
(interactive)
(find-file "~/myrepo/org/gtd/idea.org")
)
;; (defun manu1 ()
;; (interactive)
;; (find-file "~/ljl_article/Effect_of_planetary_rotation_on_oceanic_surface_boundary_layer_turbulence.tex"))
(defun les ()
(interactive)
(find-file "~/myrepo/org/gtd/les.org")
)
;; ** My shortcut in org-mode
;; Standard key bindings
;; (define-key global-map "\C-c c" 'org-capture)
;; (global-set-key (kbd "C-c l") 'org-store-link)
;; (define-key global-map "\C-ca" 'org-agenda)
;; (global-set-key (kbd "C-c b") 'org-iswitchb)
(global-set-key (kbd "C-c g") 'gtd)
;; (global-set-key (kbd "C-c j") 'journal_ljl)
;; (global-set-key (kbd "C-c e") 'exp_record)
;; (global-set-key (kbd "C-c m") 'manu1)
(global-set-key (kbd "C-c i") 'idea)
(global-set-key (kbd "C-c l") 'les)
;; (global-set-key (kbd "<f12>") 'org-agenda)
;; (global-set-key (kbd "C-M-r") 'org-capture)
(global-set-key (kbd "<f5>") 'org-todo)
(add-hook 'org-agenda-mode-hook 'hl-line-mode)
(setq org-blank-before-new-entry '((heading . t) (plain-list-item . nil)))
;----------------------------------------------
(setq org-icalendar-include-todo t)
(setq org-icalendar-store-UID t)
(setq org-icalendar-use-scheduled '(todo-start event-if-todo event-if-not-todo))
(setq org-icalendar-use-deadline '(todo-due event-if-todo event-if-not-todo))
;;==================================================================
(setq org-use-speed-commands t)
(add-to-list 'org-speed-commands-user (cons "P" 'org-set-property))
(add-to-list 'org-speed-commands-user (cons "d" 'org-deadline))
;; Mark a subtree
(add-to-list 'org-speed-commands-user (cons "m" 'org-mark-subtree))
;; Widen
(add-to-list 'org-speed-commands-user (cons "S" 'widen))
;; kill a subtree
(add-to-list 'org-speed-commands-user (cons "k" (lambda ()
(org-mark-subtree)
(kill-region
(region-beginning)
(region-end)))))
;; Jump to headline
(add-to-list 'org-speed-commands-user
(cons "q" (lambda ()
(avy-with avy-goto-line
(avy--generic-jump "^\\*+" nil avy-style)))))
(defun org-teleport (&optional arg)
"Teleport the current heading to after a headline selected with avy.
With a prefix ARG move the headline to before the selected
headline. With a numeric prefix, set the headline level. If ARG
is positive, move after, and if negative, move before."
(interactive "P")
;; Kill current headline
(org-mark-subtree)
(kill-region (region-beginning) (region-end))
;; Jump to a visible headline
(avy-with avy-goto-line (avy--generic-jump "^\\*+" nil avy-style))
(cond
;; Move before and change headline level
((and (numberp arg) (> 0 arg))
(save-excursion
(yank))
;; arg is what we want, second is what we have
;; if n is positive, we need to demote (increase level)
(let ((n (- (abs arg) (car (org-heading-components)))))
(cl-loop for i from 1 to (abs n)
do
(if (> 0 n)
(org-promote-subtree)
(org-demote-subtree)))))
;; Move after and change level
((and (numberp arg) (< 0 arg))
(org-mark-subtree)
(goto-char (region-end))
(when (eobp) (insert "\n"))
(save-excursion
(yank))
;; n is what we want and second is what we have
;; if n is positive, we need to demote
(let ((n (- (abs arg) (car (org-heading-components)))))
(cl-loop for i from 1 to (abs n)
do
(if (> 0 n) (org-promote-subtree)
(org-demote-subtree)))))
;; move to before selection
((equal arg '(4))
(save-excursion
(yank)))
;; move to after selection
(t
(org-mark-subtree)
(goto-char (region-end))
(when (eobp) (insert "\n"))
(save-excursion
(yank))))
(outline-hide-leaves))
(add-to-list 'org-speed-commands-user (cons "T" 'org-teleport))
;; * Org-id
(setq org-id-link-to-org-use-id 'create-if-interactive)
(setq org-link-search-must-match-exact-headline 'query-to-create)
(setq org-id-locations-file
(expand-file-name "user/.org-id-locations" scimax-dir))
(require 'org-id)
;; * Agenda setup
;; record time I finished a task when I change it to DONE
;;---------------------------------------------
(setq org-log-done 'time)
;; I don't want to see things that are done. turn that off here.
;; http://orgmode.org/manual/Global-TODO-list.html#Global-TODO-list
;(setq org-agenda-skip-scheduled-if-done t)
;(setq org-agenda-skip-deadline-if-done t)
;(setq org-agenda-skip-timestamp-if-done t)
;(setq org-agenda-todo-ignore-scheduled t)
;(setq org-agenda-todo-ignore-deadlines t)
;(setq org-agenda-todo-ignore-timestamp t)
;(setq org-agenda-todo-ignore-with-date t)
;(setq org-agenda-start-on-weekday nil) ;; start on current day
(setq org-upcoming-deadline '(:foreground "blue" :weight bold))
;; use timestamps in date-trees. for the journal
(setq org-datetree-add-timestamp 'active)
(add-to-list
'org-agenda-custom-commands
'("w" "Weekly Review"
( ;; deadlines
(tags-todo "+DEADLINE<=\"<today>\""
((org-agenda-overriding-header "Late Deadlines")))
;; scheduled past due
(tags-todo "+SCHEDULED<=\"<today>\""
((org-agenda-overriding-header "Late Scheduled")))
;; now the agenda
(agenda ""
((org-agenda-overriding-header "weekly agenda")
(org-agenda-ndays 7)
(org-agenda-tags-todo-honor-ignore-options t)
(org-agenda-todo-ignore-scheduled nil)
(org-agenda-todo-ignore-deadlines nil)
(org-deadline-warning-days 0)))
;; and last a global todo list
(todo "TODO"))))
;; * Block templates
;; add <p for python expansion
(add-to-list 'org-structure-template-alist
'("p" "#+BEGIN_SRC python :results output org drawer\n?\n#+END_SRC"
"<src lang=\"python\">\n?\n</src>"))
;; add <por for python expansion with raw output
(add-to-list 'org-structure-template-alist
'("por" "#+BEGIN_SRC python :results output raw\n?\n#+END_SRC"
"<src lang=\"python\">\n?\n</src>"))
;; add <pv for python expansion with value
(add-to-list 'org-structure-template-alist
'("pv" "#+BEGIN_SRC python :results value\n?\n#+END_SRC"
"<src lang=\"python\">\n?\n</src>"))
;; add <el for emacs-lisp expansion
(add-to-list 'org-structure-template-alist
'("el" "#+BEGIN_SRC emacs-lisp\n?\n#+END_SRC"
"<src lang=\"emacs-lisp\">\n?\n</src>"))
(add-to-list 'org-structure-template-alist
'("ell" "#+BEGIN_SRC emacs-lisp :lexical t\n?\n#+END_SRC"
"<src lang=\"emacs-lisp\">\n?\n</src>"))
;; add <sh for shell
(add-to-list 'org-structure-template-alist
'("sh" "#+BEGIN_SRC sh\n?\n#+END_SRC"
"<src lang=\"shell\">\n?\n</src>"))
(add-to-list 'org-structure-template-alist
'("lh" "#+latex_header: " ""))
(add-to-list 'org-structure-template-alist
'("lc" "#+latex_class: " ""))
(add-to-list 'org-structure-template-alist
'("lco" "#+latex_class_options: " ""))
(add-to-list 'org-structure-template-alist
'("ao" "#+attr_org: " ""))
(add-to-list 'org-structure-template-alist
'("al" "#+attr_latex: " ""))
(add-to-list 'org-structure-template-alist
'("ca" "#+caption: " ""))
(add-to-list 'org-structure-template-alist
'("tn" "#+tblname: " ""))
(add-to-list 'org-structure-template-alist
'("n" "#+name: " ""))
(add-to-list 'org-structure-template-alist
'("o" "#+options: " ""))
(add-to-list 'org-structure-template-alist
'("ti" "#+title: " ""))
;; table expansions
(loop for i from 1 to 6
do
(let ((template (make-string i ?t))
(expansion (concat "|"
(mapconcat
'identity
(loop for j to i collect " ")
"|"))))
(setf (substring expansion 2 3) "?")
(add-to-list 'org-structure-template-alist
`(,template ,expansion ""))))
;; * Babel settings
;; enable prompt-free code running
(setq org-confirm-babel-evaluate nil
org-confirm-elisp-link-function nil
org-confirm-shell-link-function nil)
;; register languages in org-mode
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(latex . t)
(python . t)
(shell . t)
(matlab . t)
(sqlite . t)
(ruby . t)
(perl . t)
(org . t)
(dot . t)
(plantuml . t)
(R . t)
(fortran . t)
(C . t)))
;; no extra indentation in the source blocks
(setq org-src-preserve-indentation t)
;; use syntax highlighting in org-file code blocks
(setq org-src-fontify-natively t)
(setq org-babel-default-header-args:python
'((:results . "output replace")
(:session . "none")
(:exports . "both")
(:cache . "no")
(:noweb . "no")
(:hlines . "no")
(:tangle . "no")
(:eval . "never-export")))
;; ** jupyter ipython blocks
(require 'scimax-org-babel-ipython-upstream)
;; ** jupyter-hy blocks
;; make src blocks open in the right mode
(add-to-list 'org-src-lang-modes '("jupyter-hy" . hy))
(add-to-list 'org-latex-minted-langs '(jupyter-hy "hylang"))
;; set default headers for convenience
(setq org-babel-default-header-args:jupyter-hy
'((:results . "output replace")
(:session . "hy")
(:kernel . "calysto_hy")
(:exports . "both")
(:eval . "never-export")
(:cache . "no")
(:noweb . "no")
(:hlines . "no")
(:tangle . "no")))
(defalias 'org-babel-execute:jupyter-hy 'org-babel-execute:ipython)
(defalias 'org-babel-prep-session:jupyter-hy 'org-babel-prep-session:ipython)
(defalias 'org-babel-jupyter-hy-initiate-session 'org-babel-ipython-initiate-session)
(add-to-list 'org-structure-template-alist
'("hy" "#+BEGIN_SRC jupyter-hy\n?\n#+END_SRC"
"<src lang=\"hy\">\n?\n</src>"))
;; * Images in org-mode
;; default with images open
(setq org-startup-with-inline-images "inlineimages")
;; default width
(setq org-image-actual-width nil)
(add-hook 'org-babel-after-execute-hook
'org-display-inline-images)
(defun scimax-align-result-table ()
"Align tables in the subtree."
(save-restriction
(save-excursion
(unless (org-before-first-heading-p) (org-narrow-to-subtree))
(org-element-map (org-element-parse-buffer) 'table
(lambda (tbl)
(goto-char (org-element-property :post-affiliated tbl))
(org-table-align))))))
(add-hook 'org-babel-after-execute-hook
'scimax-align-result-table)
;; * Colored src blocks
;; based on patches from Rasmus <[email protected]>
;; This function overwrites the org-src function to make src blocks be colored again.
(defun org-src-font-lock-fontify-block (lang start end)
"Fontify code block.
LANG is the language of the block. START and END are positions of
the block. This function is called by Emacs automatic
fontification, as long as `org-src-fontify-natively' is non-nil."
(let ((lang-mode (org-src--get-lang-mode lang)))
(when (fboundp lang-mode)
(let ((string (buffer-substring-no-properties start end))
(modified (buffer-modified-p))
(org-buffer (current-buffer))
(block-faces (let ((face-name (intern (format "org-block-%s" lang))))
(append (and (facep face-name) (list face-name))
'(org-block)))))
(remove-text-properties start end '(face nil))
(with-current-buffer
(get-buffer-create
(format " *org-src-fontification:%s*" lang-mode))
(erase-buffer)
(insert string " ") ;; so there's a final property change
(unless (eq major-mode lang-mode) (funcall lang-mode))
(org-font-lock-ensure)
(let ((pos (point-min)) next)
(while (setq next (next-single-property-change pos 'face))
(let ((new-face (get-text-property pos 'face)))
(put-text-property
(+ start (1- pos)) (1- (+ start next)) 'face
(list :inherit (append (and new-face (list new-face))
block-faces))
org-buffer))
(setq pos next))
;; Add the face to the remaining part of the font.
(put-text-property (1- (+ start pos))
end 'face
(list :inherit block-faces) org-buffer)))
(add-text-properties
start end
'(font-lock-fontified t fontified t font-lock-multiline t))
(set-buffer-modified-p modified)))))
(defun org-fontify-meta-lines-and-blocks-1 (limit)
"Fontify #+ lines and blocks."
(let ((case-fold-search t))
(if (re-search-forward
"^\\([ \t]*#\\(\\(\\+[a-zA-Z]+:?\\| \\|$\\)\\(_\\([a-zA-Z]+\\)\\)?\\)[ \t]*\\(\\([^ \t\n]*\\)[ \t]*\\(.*\\)\\)\\)"
limit t)
(let ((beg (match-beginning 0))
(block-start (match-end 0))
(block-end nil)
(lang (match-string 7))
(beg1 (line-beginning-position 2))
(dc1 (downcase (match-string 2)))
(dc3 (downcase (match-string 3)))
end end1 quoting block-type ovl)
(cond
((and (match-end 4) (equal dc3 "+begin"))
;; Truly a block
(setq block-type (downcase (match-string 5))
quoting (member block-type org-protecting-blocks))
(when (re-search-forward
(concat "^[ \t]*#\\+end" (match-string 4) "\\>.*")
nil t) ;; on purpose, we look further than LIMIT
(setq end (min (point-max) (match-end 0))
end1 (min (point-max) (1- (match-beginning 0))))
(setq block-end (match-beginning 0))
(when quoting
(org-remove-flyspell-overlays-in beg1 end1)
(remove-text-properties beg end
'(display t invisible t intangible t)))
(add-text-properties
beg end '(font-lock-fontified t font-lock-multiline t))
(add-text-properties beg beg1 '(face org-meta-line))
(org-remove-flyspell-overlays-in beg beg1)
(add-text-properties ; For end_src
end1 (min (point-max) (1+ end)) '(face org-meta-line))
(org-remove-flyspell-overlays-in end1 end)
(cond
((and lang (not (string= lang "")) org-src-fontify-natively)
(org-src-font-lock-fontify-block lang block-start block-end)
(add-text-properties beg1 block-end (list 'src-block t 'lang (substring-no-properties lang))))
(quoting
(add-text-properties beg1 (min (point-max) (1+ end1))
(let ((face-name (intern (format "org-block-%s" lang))))
(append (and (facep face-name) (list face-name))
'(face org-block))))) ; end of source block
((not org-fontify-quote-and-verse-blocks))
((string= block-type "quote")
(add-text-properties beg1 (min (point-max) (1+ end1)) '(face org-quote)))
((string= block-type "verse")
(add-text-properties beg1 (min (point-max) (1+ end1)) '(face org-verse))))
(add-text-properties beg beg1 '(face org-block-begin-line))
(add-text-properties (min (point-max) (1+ end)) (min (point-max) (1+ end1))
'(face org-block-end-line))
t))
((member dc1 '("+title:" "+author:" "+email:" "+date:"))
(org-remove-flyspell-overlays-in
(match-beginning 0)
(if (equal "+title:" dc1) (match-end 2) (match-end 0)))
(add-text-properties
beg (match-end 3)
(if (member (intern (substring dc1 1 -1)) org-hidden-keywords)
'(font-lock-fontified t invisible t)
'(font-lock-fontified t face org-document-info-keyword)))
(add-text-properties
(match-beginning 6) (min (point-max) (1+ (match-end 6)))
(if (string-equal dc1 "+title:")
'(font-lock-fontified t face org-document-title)
'(font-lock-fontified t face org-document-info))))
((equal dc1 "+caption:")
(org-remove-flyspell-overlays-in (match-end 2) (match-end 0))
(remove-text-properties (match-beginning 0) (match-end 0)
'(display t invisible t intangible t))
(add-text-properties (match-beginning 1) (match-end 3)
'(font-lock-fontified t face org-meta-line))
(add-text-properties (match-beginning 6) (+ (match-end 6) 1)
'(font-lock-fontified t face org-block))
t)
((member dc3 '(" " ""))
(org-remove-flyspell-overlays-in beg (match-end 0))
(add-text-properties
beg (match-end 0)
'(font-lock-fontified t face font-lock-comment-face)))
(t ;; just any other in-buffer setting, but not indented
(org-remove-flyspell-overlays-in (match-beginning 0) (match-end 0))
(remove-text-properties (match-beginning 0) (match-end 0)
'(display t invisible t intangible t))
(add-text-properties beg (match-end 0)
'(font-lock-fontified t face org-meta-line))
t))))))
(defface org-block-emacs-lisp
`((t (:background "LightCyan1")))
"Face for elisp src blocks")
(defface org-block-python
`((t (:background "DarkSeaGreen1")))
"Face for python blocks")
(defface org-block-ipython
`((t (:background "thistle1")))
"Face for python blocks")
(defface org-block-jupyter-hy
`((t (:background "light goldenrod yellow")))
"Face for hylang blocks")
(defface org-block-sh
`((t (:background "gray90")))
"Face for python blocks")
;; * Latex Export settings
;; Interpret "_" and "^" for export when braces are used.
(setq org-export-with-sub-superscripts '{})
(setq org-latex-default-packages-alist
'(("AUTO" "inputenc" t)
("" "lmodern" nil)
("T1" "fontenc" t)
("" "fixltx2e" nil)
("" "graphicx" t)
("" "longtable" nil)
("" "float" nil)
("" "wrapfig" nil)
("" "rotating" nil)
("normalem" "ulem" t)
("" "amsmath" t)
("" "textcomp" t)
("" "marvosym" t)
("" "wasysym" t)
("" "amssymb" t)
("" "amsmath" t)
("version=3" "mhchem" t)
("numbers,super,sort&compress" "natbib" nil)
("" "natmove" nil)
("" "url" nil)
("" "minted" nil)
("" "underscore" nil)
("linktocpage,pdfstartview=FitH,colorlinks,
linkcolor=blue,anchorcolor=blue,
citecolor=blue,filecolor=blue,menucolor=blue,urlcolor=blue"
"hyperref" nil)
("" "attachfile" nil)))
;; do not put in \hypersetup. Use your own if you want it e.g.
;; \hypersetup{pdfkeywords={%s},\n pdfsubject={%s},\n pdfcreator={%}}
(setq org-latex-with-hyperref nil)
;; this is for code syntax highlighting in export. you need to use
;; -shell-escape with latex, and install pygments.
(setq org-latex-listings 'minted)
(setq org-latex-minted-options
'(("frame" "lines")
("fontsize" "\\scriptsize")
("linenos" "")))
;; avoid getting \maketitle right after begin{document}
;; you should put \maketitle if and where you want it.
;;;(setq org-latex-title-command "") ; ljl, Oct/14/2019
(setq org-latex-prefer-user-labels t)
;; ** Custom new classes
;; customized article. better margins
(add-to-list 'org-latex-classes
'("article-1" ;class-name
"\\documentclass{article}
\\usepackage[top=1in, bottom=1.in, left=1in, right=1in]{geometry}
[PACKAGES]
[EXTRA]" ;;header-string
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*a{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
;; This is for when you don't want any default packages, and you want
;; to declare them all yourself.
(add-to-list 'org-latex-classes
'("article-no-defaults" ;class-name
"\\documentclass{article}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]" ;;header-string
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*a{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
;; * Fragment overlays
(defun org-latex-fragment-tooltip (beg end image imagetype)
"Add the fragment tooltip to the overlay and set click function to toggle it."
(overlay-put (ov-at) 'help-echo
(concat (buffer-substring beg end)
"\nmouse-1 to toggle."))
(overlay-put (ov-at) 'local-map (let ((map (make-sparse-keymap)))
(define-key map [mouse-1]
`(lambda ()
(interactive)
(org-remove-latex-fragment-image-overlays ,beg ,end)))
map)))
(advice-add 'org--format-latex-make-overlay :after 'org-latex-fragment-tooltip)
(defun org-latex-fragment-justify (justification)
"Justify the latex fragment at point with JUSTIFICATION.
JUSTIFICATION is a symbol for 'left, 'center or 'right."
(interactive
(list (intern-soft
(completing-read "Justification (left): " '(left center right)
nil t nil nil 'left))))
(let* ((ov (ov-at))
(beg (ov-beg ov))
(end (ov-end ov))
(shift (- beg (line-beginning-position)))
(img (overlay-get ov 'display))
(img (and (and img (consp img) (eq (car img) 'image)
(image-type-available-p (plist-get (cdr img) :type)))
img))
space-left offset)
(when (and img (= beg (line-beginning-position)))
(setq space-left (- (window-max-chars-per-line) (car (image-display-size img)))
offset (floor (cond
((eq justification 'center)
(- (/ space-left 2) shift))
((eq justification 'right)
(- space-left shift))
(t
0))))
(when (>= offset 0)
(overlay-put ov 'before-string (make-string offset ?\ ))))))
(defun org-latex-fragment-justify-advice (beg end image imagetype)
"After advice function to justify fragments."
(org-latex-fragment-justify (or (plist-get org-format-latex-options :justify) 'left)))
(advice-add 'org--format-latex-make-overlay :after 'org-latex-fragment-justify-advice)
;; ** numbering latex equations
(defun org-renumber-environment (orig-func &rest args)
"A function to inject numbers in LaTeX fragment previews."
(let ((results '())
(counter -1)
(numberp))
(setq results (loop for (begin . env) in
(org-element-map (org-element-parse-buffer) 'latex-environment
(lambda (env)
(cons
(org-element-property :begin env)
(org-element-property :value env))))
collect
(cond
((and (string-match "\\\\begin{equation}" env)
(not (string-match "\\\\tag{" env)))
(incf counter)
(cons begin counter))
((string-match "\\\\begin{align}" env)
(prog2
(incf counter)
(cons begin counter)
(with-temp-buffer
(insert env)
(goto-char (point-min))
;; \\ is used for a new line. Each one leads to a number
(incf counter (count-matches "\\\\$"))
;; unless there are nonumbers.
(goto-char (point-min))
(decf counter (count-matches "\\nonumber")))))
(t
(cons begin nil)))))
(when (setq numberp (cdr (assoc (point) results)))
(setf (car args)
(concat
(format "\\setcounter{equation}{%s}\n" numberp)
(car args)))))
(apply orig-func args))
(advice-add 'org-create-formula-image :around #'org-renumber-environment)
;; * Markup commands for org-mode
(loop for (type beginning-marker end-marker)
in '((subscript "_{" "}")
(superscript "^{" "}")
(italics "/" "/")
(bold "*" "*")
(verbatim "=" "=")
(code "~" "~")
(underline "_" "_")
(strikethrough "+" "+"))
do
(eval `(defun ,(intern (format "org-%s-region-or-point" type)) ()
,(format "%s the region, word or character at point"
(upcase (symbol-name type)))
(interactive)
(cond
;; We have an active region we want to apply
((region-active-p)
(let* ((bounds (list (region-beginning) (region-end)))
(start (apply 'min bounds))
(end (apply 'max bounds))
(lines))
(unless (memq ',type '(subscript superscript))
(save-excursion
(goto-char start)
(unless (looking-at " \\|\\<")
(backward-word)
(setq start (point)))
(goto-char end)
(unless (looking-at " \\|\>")
(forward-word)
(setq end (point)))))
(setq lines
(s-join "\n" (mapcar
(lambda (s)
(if (not (string= (s-trim s) ""))
(concat ,beginning-marker
(s-trim s)
,end-marker)
s))
(split-string
(buffer-substring start end) "\n"))))
(setf (buffer-substring start end) lines)
(forward-char (length lines))))
;; We are on a word with no region selected
((thing-at-point 'word)
(cond
;; beginning of a word
((looking-back " " 1)
(insert ,beginning-marker)
(re-search-forward "\\>")
(insert ,end-marker))
;; end of a word
((looking-back "\\>" 1)
(insert ,(concat beginning-marker end-marker))
(backward-char ,(length end-marker)))
;; not at start or end, so we just sub/sup the character at point
((memq ',type '(subscript superscript))
(insert ,beginning-marker)
(forward-char ,(- (length beginning-marker) 1))
(insert ,end-marker))
;; somewhere else in a word, and handled sub/sup. mark up the
;; whole word.
(t
(re-search-backward "\\<")
(insert ,beginning-marker)
(re-search-forward "\\>")
(insert ,end-marker))))
;; not at a word or region, insert markers and put point between
;; them.
(t
(insert ,(concat beginning-marker end-marker))
(backward-char ,(length end-marker)))))))
(defun org-latex-math-region-or-point (&optional arg)
"Wrap the selected region in latex math markup.
\(\) or $$ (with prefix ARG) or @@latex:@@ with double prefix.
Or insert those and put point in the middle to add an equation."
(interactive "P")
(let ((chars
(cond
((null arg)
'("\\(" . "\\)"))
((equal arg '(4))
'("$" . "$"))
((equal arg '(16))
'("@@latex:" . "@@")))))
(if (region-active-p)
(progn
(goto-char (region-end))
(insert (cdr chars))
(goto-char (region-beginning))
(insert (car chars)))
(insert (concat (car chars) (cdr chars)))
(backward-char (length (cdr chars))))))
(defun helm-insert-org-entity ()
"Helm interface to insert an entity from `org-entities'.
F1 inserts utf-8 character
F2 inserts entity code
F3 inserts LaTeX code (does not wrap in math-mode)
F4 inserts HTML code
F5 inserts the entity code."
(interactive)
(helm :sources
(reverse
(let ((sources '())
toplevel
secondlevel)
(dolist (element (append
'("* User" "** User entities")
org-entities-user org-entities))
(when (and (stringp element)
(s-starts-with? "* " element))
(setq toplevel element))
(when (and (stringp element)
(s-starts-with? "** " element))
(setq secondlevel element)
(add-to-list
'sources
`((name . ,(concat
toplevel
(replace-regexp-in-string
"\\*\\*" " - " secondlevel)))
(candidates . nil)
(action . (("insert utf-8 char" . (lambda (x)
(mapc (lambda (candidate)
(insert (nth 6 candidate)))
(helm-marked-candidates))))
("insert org entity" . (lambda (x)
(mapc (lambda (candidate)
(insert
(concat "\\" (car candidate))))
(helm-marked-candidates))))
("insert latex" . (lambda (x)
(mapc (lambda (candidate)
(insert (nth 1 candidate)))
(helm-marked-candidates))))
("insert html" . (lambda (x)
(mapc (lambda (candidate)
(insert (nth 3 candidate)))
(helm-marked-candidates))))
("insert code" . (lambda (x)
(mapc (lambda (candidate)
(insert (format "%S" candidate)))
(helm-marked-candidates)))))))))
(when (and element (listp element))
(setf (cdr (assoc 'candidates (car sources)))
(append
(cdr (assoc 'candidates (car sources)))
(list (cons
(format "%10s %s" (nth 6 element) element)
element))))))
sources))))
(defun ivy-insert-org-entity ()