115 KiB
115 KiB
Doom Emacs Configuration
- Introduction and Resources
- Useful Bindings
- Basic Configuration
- Org Mode
- Org General Config
- Org Inline Images
- Org Links
- Org Tagging
- Org Refile
- Org TODO
- Org Archive
- Org Agenda
- Org Fancy Priority
- Org Notification based on calendar event
- Org Structure Template
- Org Capture
- Org Export
- HTML Export
- Org LaTeX
- LaTeX macro both for LaTeX and HTML export
- Org Projects
- Org big org-project
- Automatically run
startblockwhen opening org-mode files - Insert ScreenShot or Picture from Phone
- Render Tables
- Org Gcal
- Citeproc-Org
- Org Wild Notifier
- Orch
- Custom Keybindings -
,leader key andC-c
- Org Babel
- Main configuration
- Appearance of source blocks
- Indentation
- Library of Babel
- Org-Babel Matlab
- Some functions for using Matlab with Org Babel
,m - Remap
ctrl-retused to execute the src block and go to the next one - Remap
ctrl-shift-retused to execute the (matlab) src block in the background and go to the next one - Align Source Blocks
- Helping Functions - Tangling
,b
- Bibliography Management
- LaTeX
- Matlab
- Mu4e
- Doom
init.el - Doom
packages.el
Introduction and Resources ignore
https://medium.com/urbint-engineering/emacs-doom-for-newbies-1f8038604e3b https://noelwelsh.com/posts/2019-01-10-doom-emacs.html https://dotdoom.netlify.com/config.html https://emacs.christianbaeuerlein.com/ https://github.com/nmartin84/.doom.d/blob/master/config.org
Documentation:
When changing init.el or package.el, tangle the files and then run doom sync.
After that, restart Emacs with spc q r.
Useful Bindings
align-regexp: equivalent of vim-easy-align. Very useful to align tables and stuff
General Bindings
spc : |
Execute command |
spc < |
Switch to buffer |
spc X |
org-capture |
spc s s |
Search in buffer with swiper |
spc s p |
Search in project |
spc p p |
Switch project |
spc p t |
TODOs in project |
spc o f |
Create frame |
spc o e |
Toggle Eshell |
spc n l |
Store link |
spc g g |
Magit status |
spc f r |
Open recent file |
spc b B |
Switch to buffer |
spc b d |
Kill current buffer |
spc b i |
ibuffer |
spc tab . |
Switch to workspace |
spc tab n |
New workspace |
spc tab r |
Rename workspace |
spc m A |
org-archive-subtree |
spc m I |
org-toggle-inline-images |
spc m d |
org-deadline |
spc m e |
org-export-dispatch |
spc m o |
org-set-property |
spc m s |
org-schedule |
spc m t |
org-todo |
Org-Babel Bindings
C-c C-v p |
org-babel-previous-src-block |
C-c C-v n |
org-babel-next-src-block |
C-c C-v e |
org-babel-execute-maybe |
C-c C-v o |
org-babel-open-src-block-result |
C-c C-v v |
org-babel-expand-src-block |
C-c C-v u |
org-babel-goto-src-block-head |
C-c C-v g |
org-babel-goto-named-src-block |
C-c C-v r |
org-babel-goto-named-result |
C-c C-v b |
org-babel-execute-buffer |
C-c C-v s |
org-babel-execute-subtree |
C-c C-v d |
org-babel-demarcate-block |
C-c C-v t |
org-babel-tangle |
C-c C-v f |
org-babel-tangle-file |
C-c C-v c |
org-babel-check-src-block |
C-c C-v j |
org-babel-insert-header-arg |
C-c C-v l |
org-babel-load-in-session |
C-c C-v i |
org-babel-lob-ingest |
C-c C-v I |
org-babel-view-src-block-info |
C-c C-v z |
org-babel-switch-to-session-with-code |
C-c C-v a |
org-babel-sha1-hash |
C-c C-v h |
org-babel-describe-bindings |
C-c C-v x |
org-babel-do-key-sequence-in-edit-buffer |
Evil bindings
gv |
Selects the previous visual |
o in visual mode |
go to the `Other` end of the selection |
g= and g- |
Increase/decrement number |
t followed by any char |
goes "till" next character (not included) |
f followed by any char |
"find" next character (included) |
yt. |
yank until next . |
Basic Configuration
Personal Information
;; These are used for a number of things, particularly for GPG configuration,
;; some email clients, file templates and snippets.
(setq user-full-name "Dehaeze Thomas"
user-mail-address "dehaeze.thomas@gmail.com")Doom Config
(setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 12 :weight 'semi-light)
doom-variable-pitch-font (font-spec :family "Hack Nerd Font Mono")
doom-unicode-font (font-spec :family "Hack Nerd Font Mono" :size 12)
doom-big-font (font-spec :family "Hack Nerd Font Mono" :size 19)) (setq doom-theme 'doom-gruvbox) (setq display-line-numbers-type t) (use-package doom-modeline
:hook (after-init . doom-modeline-mode)
:custom
(doom-modeline-height 25)
(doom-modeline-bar-width 1)
(doom-modeline-icon t)
(doom-modeline-major-mode-icon t)
(doom-modeline-major-mode-color-icon t)
(doom-modeline-buffer-file-name-style 'truncate-upto-project)
(doom-modeline-buffer-state-icon t)
(doom-modeline-buffer-modification-icon t)
(doom-modeline-minor-modes nil)
(doom-modeline-enable-word-count nil)
(doom-modeline-buffer-encoding t)
(doom-modeline-indent-info nil)
(doom-modeline-checker-simple-format t)
(doom-modeline-vcs-max-length 12)
(doom-modeline-env-version t)
(doom-modeline-irc-stylize 'identity)
(doom-modeline-github-timer nil)
(doom-modeline-gnus-timer nil))Evil
(after! evil
(map! :m "-" #'dired-jump))Make movement keys work like they should
(define-key evil-normal-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-normal-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)Make horizontal movement cross lines
(setq-default evil-cross-lines t)Which Key
(after! which-key
(setq which-key-idle-delay 0.5
which-key-idle-secondary-delay 0.01
which-key-sort-order 'which-key-key-order-alpha))Visual
Automatic line wrap.
(global-visual-line-mode nil)Turn off auto-fill mode that add line breaks.
(auto-fill-mode -1)
(remove-hook 'text-mode-hook 'turn-on-auto-fill)
;; turn on auto-fill for text-mode
(add-hook 'text-mode-hook 'turn-on-auto-fill)
(after! org
;; turn off auto-fill for org-mode
(add-hook 'org-mode-hook 'turn-off-auto-fill))Useful General Functions
(defun tdh-matlab-work ()
"Setup Matlab Work Windows"
(interactive)
(delete-other-windows)
(evil-window-vsplit)
(evil-window-right 1)
(switch-to-buffer "*MATLAB*")
(evil-window-left 1)
)Change default alert backend
(setq alert-default-style 'libnotify)Lockfiles
(setq create-lockfiles nil)Disable highlight of current line
(global-hl-line-mode -1)
(after! org
(add-hook 'org-mode-hook
(lambda()
(hl-line-mode -1)
(global-hl-line-mode -1))
't
))
Remap jump-forward key binding
(with-eval-after-load 'better-jumper
(map!
:desc "Jump Forward"
"C-i" #'better-jumper-jump-forward))Magit
(setenv "GIT_ASKPASS" "git-gui--askpass")
(after! magit
(setq magit-diff-refine-hunk 'all)
(setq magit-repository-directories `(("~/Cloud/thesis/matlab/" . 1)
("~/Cloud/thesis/papers/" . 1)))
(setq magit-repolist-columns '(("Name" 25 magit-repolist-column-ident nil)
("Status" 7 magit-repolist-column-flag)
("B<U" 3 magit-repolist-column-unpulled-from-upstream
((:right-align t)
(:help-echo "Upstream changes not in branch")))
("B>U" 3 magit-repolist-column-unpushed-to-upstream
((:right-align t)
(:help-echo "Local changes not in upstream")))
("Path" 99 magit-repolist-column-path nil)))
)Dired
C-c C-eWritable Dired mode, when changes are doneC-c C-c. This works also withC-x C-qC-c C-rusersyncto copy file in the background+Create a directoryRRename / moveCCopydDeletemMarkUunmark all markedtinvert the selectionuunmark / undeletexactually delete files/directories marked for deletion!Execute shell command on this file, or currently marked files%mmark by patternosort by time/name(Hide details)Show git infos
(use-package! dired-narrow
:config
(map! :map dired-mode-map
:n "f"
'dired-narrow-fuzzy))PDF-Tools
(use-package! pdf-tools
:config
(add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
)Yassnippets
(push "~/.config/doom/snippets" yas-snippet-dirs)
(yas-global-mode 1)Ox-Hugo
(defun tdh-export-everything-to-hugo ()
"Export all the .org files in the specified directory to markdown using Hugo"
(interactive)
(setq org-files (directory-files (read-directory-name "Directory:" "/home/thomas/Cloud/brain/") t "org$" t))
(while org-files
(setq current-org-file (car org-files))
(message "Exporting %s" current-org-file)
(find-file current-org-file)
(org-hugo-export-to-md)
(setq org-files (cdr org-files))))Org Mode
- http://cachestocaches.com/2016/9/my-workflow-org-agenda/
- http://doc.norang.ca/org-mode.html#TodoKeywords
- https://emacs.cafe/emacs/orgmode/gtd/2017/06/30/orgmode-gtd.html
Org General Config
(setq org-directory "~/Cloud/org/")
(after! org
(setq org-directory "~/Cloud/org/")
;; Replace the content marker, “⋯”, with a nice unicode arrow.
(setq org-ellipsis " ⤵")
(setq org-default-notes-file "~/Cloud/org/refile.org")
;; Avoid accidentally editing folded regions, say by adding text after an Org “⋯”.
(setq org-catch-invisible-edits 'show)
;; The following setting hides blank lines between headings which keeps folded view nice and compact.
(setq org-cycle-separator-lines 0)
;; Indent according to the outline structure
(setq org-startup-indented t)
(setq org-startup-folded t)
;; Record the information of when the task was marked as DONE
(setq org-log-done 'time)
;; begining of line on heading behavior
(setq org-special-ctrl-a/e nil)
)TAB was changed to toggle only the visibility state of the current subtree, rather than cycle through it recursively. This can be reversed with:
(after! evil-org
(remove-hook 'org-tab-first-hook #'+org-cycle-only-current-subtree-h))Org Inline Images
Display the real size of images and not the one set with attr_latex: :width \linewidth for instance.
(after! org
(setq org-image-actual-width t))Org Links
(after! org
(setq org-link-abbrev-alist
'(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
("notes" . "~/Cloud/brain/%s.org")
("papers" . "~/Cloud/pdfs/%s.pdf")))
)Org Tagging
(after! org
;; Align Tags and flush right
(setq org-tags-column -78)
;; Tags with fast selection keys
(setq org-tag-alist (quote (("@home" . ?h)
("@work" . ?w)
("@christophe" . ?c)
("@veijo" . ?v))))
)Org Refile
(after! org
(setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
)Org TODO
(after! org
;; Tags with fast selection keys
(setq org-todo-keywords '(
(sequence "TODO(t)" "NEXT(n)" "MAIL(m)" "|" "DONE(d)")
(sequence "READ(r)" "BKMK(b)" "EXER(x)" "|" "DONE(d)")
(sequence "WAIT(w@/!)" "SDAY(s)" "|" "CANC(c@/!)")
(sequence "QUES(q)" "|" "ANSW(a)")
(sequence "EXAM(e)" "IDEA(i)" "|")
))
;; Display of the keywords
(setq org-todo-keyword-faces
'(("TODO" . (:foreground "#cc241d" :weight bold)) ;; red
("EXER" . (:foreground "#cc241d" :weight bold)) ;; red
("NEXT" . (:foreground "#cc241d" :weight bold)) ;; red
("MAIL" . (:foreground "#cc241d" :weight bold)) ;; red
("READ" . (:foreground "#cc241d" :weight bold)) ;; red
("ANSW" . (:foreground "#689d6a" :weight bold)) ;; aqua
("DONE" . (:foreground "#689d6a" :weight bold)) ;; aqua
("WAIT" . (:foreground "#d65d0e" :weight bold)) ;; orange
("QUES" . (:foreground "#d79921" :weight bold)) ;; yellow
("CANC" . (:foreground "#a89984" :weight bold)) ;; grey
("SDAY" . (:foreground "#98971a" :weight bold)) ;; green
("BKMK" . (:foreground "#98971a" :weight bold)) ;; green
("IDEA" . (:foreground "#98971a" :weight bold)) ;; green
("EXAM" . (:foreground "#98971a" :weight bold)))) ;; green
)Org Archive
https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb Archive subtrees under the same hierarchy as original in the archive files
(after! org
(defadvice org-archive-subtree (around fix-hierarchy activate)
(let* ((fix-archive-p (and (not current-prefix-arg)
(not (use-region-p))))
(location (org-archive--compute-location org-archive-location))
(afile (car location))
(offset (if (= 0 (length (cdr location)))
1
(1+ (string-match "[^*]" (cdr location)))))
(buffer (or (find-buffer-visiting afile) (find-file-noselect afile))))
ad-do-it
(when fix-archive-p
(with-current-buffer buffer
(goto-char (point-max))
(while (> (org-current-level) offset) (org-up-heading-safe))
(let* ((olpath (org-entry-get (point) "ARCHIVE_OLPATH"))
(path (and olpath (split-string olpath "/")))
(level offset)
tree-text)
(when olpath
(org-mark-subtree)
(setq tree-text (buffer-substring (region-beginning) (region-end)))
(let (this-command) (org-cut-subtree))
(goto-char (point-min))
(save-restriction
(widen)
(-each path
(lambda (heading)
(if (re-search-forward
(rx-to-string
`(: bol (repeat ,level "*") (1+ " ") ,heading)) nil t)
(org-narrow-to-subtree)
(goto-char (point-max))
(unless (looking-at "^")
(insert "\n"))
(insert (make-string level ?*)
" "
heading
"\n"))
(cl-incf level)))
(widen)
(org-end-of-subtree t t)
(org-paste-subtree level tree-text))))))))
)Org Agenda
General configuration
(after! org
;; File to save todo items
(setq org-agenda-files (list "~/Cloud/org/"))
;; Include archived files
(setq org-agenda-archives-mode t)
;; Set priority range from A to C with default A
(setq org-highest-priority ?A)
(setq org-lowest-priority ?C)
(setq org-default-priority ?C)
;; Set colours for priorities
(setq org-priority-faces '((?A . (:foreground "#FB4934"))
(?B . (:foreground "#FABD2F"))
(?C . (:foreground "#98971A"))))
;; Open agenda in current window
(setq org-agenda-window-setup 'current-window)
(setq org-agenda-prefix-format
'((agenda . " %?-12t% s")
(todo . "") ;; Don't show the filename for reading agenda
(tags . " %-12:c")
(search . " %-12:c"))
)
)Org Agenda Custom Views
(after! org-agenda
(defun tdh-org-agenda-skip-scheduled ()
(org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))
(setq org-agenda-custom-commands
'(("w" "Work"
((org-ql-block '(and (tags "@work")
(todo "TODO")
(priority "A"))
((org-ql-block-header "Important TODOs")))
(org-ql-block '(and (tags "@work")
(todo "TODO")
(priority "B"))
((org-ql-block-header "TODOs")))
(org-ql-block '(and (tags "@work")
(todo "TODO")
(priority "C"))
((org-ql-block-header "Not important TODOs")))))
("h" "Home"
((org-ql-block '(and (tags "@home")
(todo "TODO")
(priority "A"))
((org-ql-block-header "Things to do")))
(org-ql-block '(and (tags "@home")
(todo "TODO")
(priority "B"))
((org-ql-block-header "Things to do")))
(org-ql-block '(and (tags "@home")
(todo "TODO")
(priority "C"))
((org-ql-block-header "Things to do")))))
("q" "Questions to ask"
((org-ql-block '(and (todo "QUES")
(tags "@christophe"))
((org-ql-block-header "Questions to Christophe")))
(org-ql-block '(and (todo "QUES")
(tags "@veijo"))
((org-ql-block-header "Questions to Veijo")))
(org-ql-block '(and (todo "QUES")
(not (tags "@veijo" "@christophe")))
((org-ql-block-header "Other Questions")))))
("R" "Already read Articles and Books"
((org-ql-block '(and (todo "DONE")
(level 1)
(tags "article" "inproceedings" "techreport" "inbook"))
((org-ql-block-header "Articles")))
(org-ql-block '(and (todo "DONE")
(level 1)
(tags "book"))
((org-ql-block-header "Books")))
(org-ql-block '(and (todo "DONE")
(level 1)
(tags "phdthesis"))
((org-ql-block-header "Phd Thesis")))
(org-ql-block '(and (todo "DONE")
(level 1)
(not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
((org-ql-block-header "Other Things"))))
((org-agenda-files '("~/Cloud/brain/"))))
("r" "Articles and Books to read"
((org-ql-block '(and (todo "READ")
(level 1)
(tags "article" "inproceedings" "techreport" "inbook"))
((org-ql-block-header "Article to Read")))
(org-ql-block '(and (todo "READ")
(level 1)
(tags "book"))
((org-ql-block-header "Books to Read")))
(org-ql-block '(and (todo "READ")
(level 1)
(tags "phdthesis"))
((org-ql-block-header "Phd Thesis to Read")))
(org-ql-block '(and (todo "READ")
(level 1)
(not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
((org-ql-block-header "Other Things to Read"))))
((org-agenda-files '("~/Cloud/brain/")))))
)
)Org Fancy Priority
(use-package! org-fancy-priorities ; priority icons
:hook (org-mode . org-fancy-priorities-mode)
:config (setq org-fancy-priorities-list '("■" "■" "■")))Org Notification based on calendar event
(after! org-agenda
(setq appt-message-warning-time 5)
(defun tdh-org-agenda-to-appt ()
(interactive)
(setq appt-time-msg-list nil)
(org-agenda-to-appt))
(tdh-org-agenda-to-appt)
; Display appointments as a window manager notification
(setq appt-disp-window-function 'tdh-appt-display)
(setq appt-delete-window-function (lambda () t))
(setq tdh-appt-notification-app (concat (getenv "HOME") "/bin/appt-notification"))
(defun tdh-appt-display (min-to-app new-time msg)
(if (atom min-to-app)
(start-process "tdh-appt-notification-app" nil tdh-appt-notification-app min-to-app msg)
(dolist (i (number-sequence 0 (1- (length min-to-app))))
(start-process "tdh-appt-notification-app" nil tdh-appt-notification-app (nth i min-to-app) (nth i msg)))))
)appt-notification script
TIME="$1"TODO
MSG="$2"
dunstify --replace=85401 "Event in $TIME minutes" "$MSG"Org Structure Template
(after! org
(setq org-structure-template-alist
'(("c" . "center")
("C" . "comment")
("m" . "src matlab\n")
("l" . "src emacs-lisp\n")
("i" . "important")
("e" . "example")
("q" . "quote")
("s" . "src")))
)Org Capture
Documentation:
- Template elements: https://orgmode.org/manual/Template-elements.html#Template-elements
- Template expansion: https://orgmode.org/manual/Template-expansion.html#Template-expansion
- Capture protocol: https://orgmode.org/manual/capture-protocol.html
(after! org
(setq org-capture-templates
(quote (("t" ; key
"Todo" ; name
entry ; type
(file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
"** TODO %?\n%U\n" ; template
)
("M" ; key
"Meeting" ; name
entry ; type
(file+headline "~/Cloud/org/work-notebook.org" "Meetings") ; target
"** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
)
("m" ; key
"Mail" ; name
entry ; type
(file+headline "~/Cloud/org/work-notebook.org" "Mails") ; target
"** TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%a\n" ; template
)
("r" ; key
"Reference" ; name
entry ; type
(file+headline "~/Cloud/org/inbox-ereader.org" "Things to Read") ; target
"** TODO [#B] %?\n" ; template
)
("pm"
"Org-Protocol Mail"
entry
(file+headline "~/Cloud/org/work-notebook.org" "Mails")
"* MAIL %:description [[message:%:link][link]]\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n\n"
:immediate-finish t
)
("pu"
"Org-Protocol Url"
entry
(file+headline "~/Cloud/org/work-notebook.org" "Inbox")
"* [[%:link][%:description]]\nCaptured On: %U\n\n"
:immediate-finish t
)
("pt"
"Org-Protocol text"
entry
(file+headline "~/Cloud/org/work-notebook.org" "Inbox")
"* %:description\nSource: %:link\nCaptured On: %U\n\n#+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n"
:immediate-finish t
)
)))
)Org Export
Basic configuration:
(after! org
;; How many levels of headline to export
(setq org-export-headline-levels 4)
;; Authorize BIND to set local variables
(setq org-export-allow-bind-keywords t)
;; Use doc instead of odt
(setq org-odt-preferred-output-format "doc")
)Some defaults:
(after! org
(setq org-export-with-author t)
(setq org-export-with-creator nil)
(setq org-export-with-date t)
(setq org-export-with-toc t)
(setq org-export-with-drawers nil)
(setq org-export-with-sub-superscripts nil)
(setq org-export-with-todo-keywords nil)
)
Do not export headline with the :ignore: tag:
;; Used to not export headings with :ignore: tag
(after! org
(require 'ox-extra)
(ox-extras-activate '(ignore-headlines)))HTML Export
HTML Defaults
(after! org
;; (setq org-html-head-extra (concat
;; "<link rel='stylesheet' href='../css/htmlize.css'>\n"
;; "<link rel='stylesheet' href='../css/readtheorg.css'>\n"
;; "<link rel='stylesheet' href='../css/zenburn.css'>\n"
;; "<link rel='text/javascript' href='../js/bootstrap.min.js'>\n"
;; "<link rel='text/javascript' href='../js/jquery.min.js'>\n"
;; "<link rel='text/javascript' href='../js/jquery.stickytableheaders.min.js'>\n"
;; "<link rel='text/javascript' href='../js/readtheorg.js'>\n"))
;; cleans up anything that would have been in there.
(setq org-html-head nil)
(setq org-html-head-include-default-style nil)
(setq org-html-head-include-scripts nil)
(setq org-html-viewport nil)
(setq org-html-html5-fancy t)
(setq org-html-doctype "xhtml-strict")
(setq org-html-wrap-src-lines nil)
;; Export with css class instead of inline css
(setq org-html-htmlize-output-type 'css)
)MathJax
(after! org
(setq org-html-mathjax-template
"<script>MathJax = {
tex: {
tags: 'ams',
macros: {bm: [\"\\\\boldsymbol{#1}\",1],}
}
};
</script>
<script type=\"text/javascript\" src=\"%PATH\"></script>")
(setq org-html-mathjax-options
'((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js")
(scale "100")
(align "center")
(font "TeX")
(linebreaks "false")
(autonumber "AMS")
(indent "0em")
(multlinewidth "85%")
(tagindent ".8em")
(tagside "right")))
)TODO Ensuring useful HTML Anchors
- https://github.com/alhassy/emacs.d
- https://github.com/alphapapa/unpackaged.el#export-to-html-with-useful-anchors
This is not working
(define-minor-mode unpackaged/org-export-html-with-useful-ids-mode
"Attempt to export Org as HTML with useful link IDs.
Instead of random IDs like \"#orga1b2c3\", use heading titles,
made unique when necessary."
:global t
(if unpackaged/org-export-html-with-useful-ids-mode
(advice-add #'org-export-get-reference :override #'unpackaged/org-export-get-reference)
(advice-remove #'org-export-get-reference #'unpackaged/org-export-get-reference)))
(defun unpackaged/org-export-get-reference (datum info)
"Like `org-export-get-reference', except uses heading titles instead of random numbers."
(let ((cache (plist-get info :internal-references)))
(or (car (rassq datum cache))
(let* ((crossrefs (plist-get info :crossrefs))
(cells (org-export-search-cells datum))
;; Preserve any pre-existing association between
;; a search cell and a reference, i.e., when some
;; previously published document referenced a location
;; within current file (see
;; `org-publish-resolve-external-link').
;;
;; However, there is no guarantee that search cells are
;; unique, e.g., there might be duplicate custom ID or
;; two headings with the same title in the file.
;;
;; As a consequence, before re-using any reference to
;; an element or object, we check that it doesn't refer
;; to a previous element or object.
(new (or (cl-some
(lambda (cell)
(let ((stored (cdr (assoc cell crossrefs))))
(when stored
(let ((old (org-export-format-reference stored)))
(and (not (assoc old cache)) stored)))))
cells)
(when (org-element-property :raw-value datum)
;; Heading with a title
(unpackaged/org-export-new-title-reference datum cache))
;; NOTE: This probably breaks some Org Export
;; feature, but if it does what I need, fine.
(org-export-format-reference
(org-export-new-reference cache))))
(reference-string new))
;; Cache contains both data already associated to
;; a reference and in-use internal references, so as to make
;; unique references.
(dolist (cell cells) (push (cons cell new) cache))
;; Retain a direct association between reference string and
;; DATUM since (1) not every object or element can be given
;; a search cell (2) it permits quick lookup.
(push (cons reference-string datum) cache)
(plist-put info :internal-references cache)
reference-string))))
(defun unpackaged/org-export-new-title-reference (datum cache)
"Return new reference for DATUM that is unique in CACHE."
(cl-macrolet ((inc-suffixf (place)
`(progn
(string-match (rx bos
(minimal-match (group (1+ anything)))
(optional "--" (group (1+ digit)))
eos)
,place)
;; HACK: `s1' instead of a gensym.
(-let* (((s1 suffix) (list (match-string 1 ,place)
(match-string 2 ,place)))
(suffix (if suffix
(string-to-number suffix)
0)))
(setf ,place (format "%s--%s" s1 (cl-incf suffix)))))))
(let* ((title (org-element-property :raw-value datum))
(ref (url-hexify-string (substring-no-properties title)))
(parent (org-element-property :parent datum)))
(while (--any (equal ref (car it))
cache)
;; Title not unique: make it so.
(if parent
;; Append ancestor title.
(setf title (concat (org-element-property :raw-value parent)
"--" title)
ref (url-hexify-string (substring-no-properties title))
parent (org-element-property :parent parent))
;; No more ancestors: add and increment a number.
(inc-suffixf ref)))
ref)))TODO Folded Drawers
Adapt this from https://github.com/alhassy/emacs.d to do something similar for source blocks.
(defun my/org-drawer-format (name contents)
"Export to HTML the drawers named with prefix ‘fold_’, ignoring case.
The resulting drawer is a ‘code-details’ and so appears folded;
the user clicks it to see the information therein.
Henceforth, these are called ‘fold drawers’.
Drawers without such a prefix may be nonetheless exported if their
body contains ‘:export: t’ ---this switch does not appear in the output.
Thus, we are biased to generally not exporting non-fold drawers.
One may suspend export of fold drawers by having ‘:export: nil’
in their body definition.
Fold drawers naturally come with a title.
Either it is specfied in the drawer body by ‘:title: ⋯’,
or otherwise the drawer's name is used with all underscores replaced
by spaces.
"
(let* ((contents′ (replace-regexp-in-string ":export:.*\n?" "" contents))
(fold? (s-prefix? "fold_" name 'ignore-case))
(export? (string-match ":export:\s+t" contents))
(not-export? (string-match ":export:\s+nil" contents))
(title′ (and (string-match ":title:\\(.*\\)\n" contents)
(match-string 1 contents))))
;; Ensure we have a title.
(unless title′ (setq title′ (s-join " " (cdr (s-split "_" name)))))
;; Output
(cond
((and export? (not fold?)) contents′)
(not-export? nil)
(fold?
(thread-last contents′
(replace-regexp-in-string ":title:.*\n" "")
(format "<details class=\"code-details\"> <summary> <strong>
<font face=\"Courier\" size=\"3\" color=\"green\"> %s
</font> </strong> </summary> %s </details>" title′))))))
(setq org-html-format-drawer-function 'my/org-drawer-format)Org LaTeX
LaTeX Fragments
(after! org
;; Highligh latex parts in org mode
(setq org-highlight-latex-and-related '(latex script entities))
;; Use F9 to globally generate all the latex fragments
(map! :map org-mode-map
:n "<f9>"
(lambda () (interactive) (org-preview-latex-fragment 16)))
;; Put all the preview images in some directory
(setq org-preview-latex-image-directory "~/.ltximg/")
;; Define backends to preview LaTeX fragments
(setq org-preview-latex-process-alist '((imagemagick
:programs ("pdflatex" "convert")
:description "pdf > png"
:message "you need to install the programs: pdflatex and imagemagick."
:image-input-type "pdf"
:image-output-type "png"
:image-size-adjust (1.0 . 1.0)
:latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
:image-converter ("convert -density %D -trim -antialias %f -quality 100 %O"))
(dvipng
:programs ("latex" "dvipng")
:description "dvi > png"
:message "you need to install the programs: latex and dvipng."
:image-input-type "dvi"
:image-output-type "png"
:image-size-adjust (0.4 . 0.4)
:latex-compiler ("latex -interaction nonstopmode -output-directory %o %f")
:image-converter ("dvipng -D %D -T tight -o %O %f"))
(dvisvgm
:programs ("pdflatex" "dvisvgm")
:description "dvi > svg"
:message "you need to install the programs: latex and dvisvgm."
:image-input-type "dvi"
:image-output-type "svg"
:image-size-adjust (0.6 . 0.6)
:latex-compiler ("latex -interaction nonstopmode -output-directory %o %f")
:image-converter ("dvisvgm %f -n -b min -c %S -o %O"))
))
;; Use imagemagick/dvisvgm to generate png from pdf
(setq org-preview-latex-default-process 'dvisvgm)
;; Don't change the font size for subscripts and superscripts in latex fragments.
;; This cause the orgmode tables not to be well aligned.
(setq font-latex-fontify-script nil)
;; Colors of latex fragments
(setq org-format-latex-options (plist-put org-format-latex-options :foreground 'default))
(setq org-format-latex-options (plist-put org-format-latex-options :background 'default))
)LaTeX Classes
(after! org
;; Custom classes to use when exporting to latex
(add-to-list 'org-latex-classes
'("beamer"
,(concat "\\documentclass[presentation]{beamer}\n"
"[DEFAULT-PACKAGES]"
"[PACKAGES]"
"[EXTRA]\n")
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
(add-to-list 'org-latex-classes
'("clean-cheatsheet"
"\\documentclass{clean-cheatsheet}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("clean-beamer"
"\\documentclass{clean-beamer}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("cleanreport"
"\\documentclass{cleanreport}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("scrartcl"
"\\documentclass{scrartcl}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("scrreprt"
"\\documentclass{scrreprt}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("biblioreport"
"\\documentclass{biblioreport}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
(add-to-list 'org-latex-classes
'("moderncv"
"\\documentclass{moderncv}"
("\\section{%s}" . "\\section*{%s}")
("\\subsection{%s}" . "\\subsection*{%s}")
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
)
)Ox Latex Subfigure package
;; (use-package! ox-latex-subfigure
;; :after org
;; :config (require 'ox-latex-subfigure)) (use-package! ox-latex-subfigure
:load-path "~/.config/doom/packages/ox-latex-subfigure/"
:config (require 'ox-latex-subfigure))Clear page before heading
https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-heading/30892
(after! org
(defun tdh-get-headline-string-element (headline backend info)
(let ((prop-point (next-property-change 0 headline)))
(if prop-point (plist-get (text-properties-at prop-point headline) :parent))))
(defun tdh-ensure-latex-clearpage (headline backend info)
(when (org-export-derived-backend-p backend 'latex)
(let ((elmnt (tdh-get-headline-string-element headline backend info)))
(when (and elmnt (org-element-property :CLEARPAGE elmnt))
(concat "\\clearpage\n" headline)))))
(add-to-list 'org-export-filter-headline-functions
'tdh-ensure-latex-clearpage)
)Default added packages
(after! org
(add-to-list 'org-latex-packages-alist '("" "siunitx" t))
(add-to-list 'org-latex-packages-alist '("" "array" t))
(add-to-list 'org-latex-packages-alist '("" "tabularx" t))
(add-to-list 'org-latex-packages-alist '("" "booktabs" t))
(add-to-list 'org-latex-packages-alist '("" "bm" t))
(add-to-list 'org-latex-packages-alist '("most" "tcolorbox" t))
)Some configurations
(after! org
;; Setup default option for image size when exporting to LaTeX
(setq org-latex-image-default-scale "")
(setq org-latex-image-default-width "\\linewidth")
(setq org-latex-image-default-height "")
(setq org-latex-image-default-option "")
;; Use define labels instead of automatic generated ones
(setq org-latex-prefer-user-labels t)
;; Captions above the table
(setq org-latex-caption-above '(table))
;; Settings to export code with `minted' instead of `verbatim'.
(setq org-latex-listings 'minted)
;; Set the following as images
(setq org-latex-inline-image-rules '(("file" . "\\.\\(pdf\\|jpeg\\|jpg\\|png\\|ps\\|eps\\|tikz\\|pgf\\|svg\\|gif\\)\\'")))
;; Command used when exporting to pdf
(setq org-latex-pdf-process
'("latexmk -cd -pdflatex=\"pdflatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory %o\" -pdf -bibtex -f %f"))
)Beamer
Bold Text
(after! org
(defun tdh-my-beamer-bold (contents backend info)
(when (eq backend 'beamer)
(replace-regexp-in-string
(concat "\\`\\\\" "[A-Za-z0-9]+") ;; If not, orgmode is crazy...
"\\\\textbf"
contents)))
(add-to-list 'org-export-filter-bold-functions 'tdh-my-beamer-bold)
)Special Environments
- Make some comment those special environments
(after! org
(add-to-list 'org-beamer-environments-extra
'("cbox" ;; Name of environment
"m" ;; Selection key
"\\onslide%a{\\begin{cbox}[%h]%O"
"\\end{cbox}}\\vspace{0.5em}"))
(add-to-list 'org-beamer-environments-extra
'("csubbox" ;; Name of environment
"M" ;; Selection key
"\\onslide%a{\\tcbsubtitle{%h}"
"}"))
)TODO Custom Export - Add Page and Label for LaTeX export
(defcustom tdh-org-property-mapping
'((latex ("CUSTOM_PAGE" . tdh-insert-org-page-latex)
("CUSTOM_LABEL" . tdh-insert-org-label-latex)))
"List of mappings from org property to arbitrary strings.
Each element is a list:
(BACKEND (PROPERTY1 . FUNCTION1) (PROPERTY2 . FUNCTION2) ...)
FUNCTION are functions which get called with a single
argument (the value of PROPERTY) and are responsible for doing
whatever should be done."
:type '(repeat (cons symbol (repeat (cons string string))))) (defun tdh-replace-org-property (backend)
"Convert org properties using `tdh-org-property-mapping'.
Lookup BACKEND in `tdh-org-property-mapping' for a list of
(PROPERTY REPLACEMENT). For each healine being exported, if it has a
PROPERTY listed insert a string immediately after the healine given by
(format REPLACEMENT PROPERTY-VALUE)"
(let ((map (cdr (assoc backend tdh-org-property-mapping)))
value replacement)
(when map
(org-map-entries
(lambda ()
(dolist (it map)
(save-excursion
(when (setq value (org-entry-get (point) (car it)))
(funcall (cdr it) value)))))))))
(add-hook 'org-export-before-processing-hook #'tdh-replace-org-property) (defun tdh-insert-org-label-latex (label)
"Insert \"\\\\label{LABEL}\\n\" after the :PROPERTY: drawer."
(search-forward-regexp org-property-end-re)
(forward-char 1)
(insert (format "\\label{%s}\n" label)))
(defun tdh-insert-org-page-latex (page)
"Insert \"\\\\page{PAGE}\\n\" after the :PROPERTY: drawer."
(search-forward-regexp org-property-end-re)
(forward-char 1)
(insert (format "\\page{%s}\n" page)))Number Equations
(after! org
(defun tdh-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 #'tdh-org-renumber-environment)
)LaTeX macro both for LaTeX and HTML export
https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_for_use_in_both/
(after! org
(add-to-list 'org-src-lang-modes '("latex-macros" . latex))
(defvar org-babel-default-header-args:latex-macros
'((:results . "raw")
(:exports . "results")))
(defun prefix-all-lines (pre body)
(with-temp-buffer
(insert body)
(string-insert-rectangle (point-min) (point-max) pre)
(buffer-string)))
(defun org-babel-execute:latex-macros (body _params)
(concat
"\n#+begin_export html\n<div style=\"display: none\"> \\(\n"
body
"\n\\)</div>\n#+end_export\n"))
)Org Projects
(setq org-publish-project-alist
'(("config"
:base-directory "~/.config/literate-dotfiles/dotfiles/"
:publishing-directory "~/.config/literate-dotfiles/docs/"
:recursive nil
:publishing-function org-html-publish-to-html
:auto-sitemap nil
:section-numbers nil
:table-of-contents nil)
("stewart-simscape"
:base-directory "~/Cloud/thesis/matlab/stewart-simscape/org/"
:base-extension "org"
:publishing-directory "~/Cloud/thesis/matlab/stewart-simscape/docs/"
:author "Dehaeze Thomas"
:email "dehaeze.thomas@gmail.com/"
:recursive nil
:publishing-function org-html-publish-to-html
:auto-preamble t
:auto-sitemap nil
:html-link-up "index.html"
:html-link-home "index.html"
:with-todo-keywords nil
:html-wrap-src-lines nil
:table-of-contents nil)
("nass-simscape"
:base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
:base-extension "org"
:publishing-directory "~/Cloud/thesis/matlab/nass-simscape/docs/"
:author "Dehaeze Thomas"
:email "dehaeze.thomas@gmail.com/"
:recursive nil
:publishing-function org-html-publish-to-html
:auto-preamble t
:auto-sitemap nil
:html-link-up "index.html"
:html-link-home "index.html"
:with-todo-keywords nil
:html-wrap-src-lines nil
:table-of-contents nil)
("tikz-maker"
:base-directory "~/Cloud/tikz/org/"
:base-extension "org"
:publishing-directory "~/Cloud/tikz/docs/"
:author "Dehaeze Thomas"
:email "dehaeze.thomas@gmail.com/"
:recursive nil
:publishing-function org-html-publish-to-html
:auto-preamble t
:auto-sitemap nil
:html-link-up "index.html"
:html-link-home "index.html"
:with-todo-keywords nil
:html-wrap-src-lines nil
:table-of-contents nil)))TODO Org big org-project
(setq org-publish-project-alist
'(("website"
:components ("nass-simscape" "nass-simscape-images"))
("nass-simscape"
:base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
:base-extension "org"
:publishing-directory "~/Cloud/website/nass-simscape/"
:publishing-function org-html-publish-to-html
:html-link-up "./index.html"
:html-link-home "~/Cloud/website/index.html"
:html-footnotes-section "<div id='footnotes'><!--%s-->%s</div>"
:recursive nil
:auto-sitemap nil
:language en)
("nass-simscape-images"
:base-directory "~/Cloud/thesis/matlab/nass-simscape/docs/figs/"
:base-extension "png"
:publishing-directory "~/Cloud/website/nass-simscape/figs/"
:publishing-function org-publish-attachment)
))
Automatically run startblock when opening org-mode files
(after! org
(defun tdh-eval-startblock ()
(if (member "startblock" (org-babel-src-block-names))
(save-excursion
(org-babel-goto-named-src-block "startblock")
(org-babel-execute-src-block))
nil
)
)
(add-hook 'org-mode-hook 'tdh-eval-startblock)
)TODO Insert ScreenShot or Picture from Phone
http://pragmaticemacs.com/emacs/a-workflow-to-quickly-add-photos-to-org-mode-notes/
- One function to move file from
~/Picture/folder (where the screenshots are taken) to current directory and then insert and org link to the picture. Maybe ask if it should be copied in a sub directory (figs folder for instance). - One function to copy file from
~/Cloud/Photos/folder (where the pictures from phone are taken) to current directory (and ask for the new name of the picture) and insert org link.
;; required libraries
(require 'dash)
;; (require 'swiper)
(require 's)
;; start directory
(defvar tdh-image-dir (expand-file-name "/home/thomas/Pictures"))
(defun tdh-insert-conference-image ()
"Insert image from conference directory, rename and add link in current file.
The file is taken from a start directory set by `tdh-image-dir' and moved to the current directory, renamed and embedded at the point as an org-mode link. The user is presented with a list of files in the start directory, from which to select the file to move, sorted by most recent first."
(interactive)
(let (file-list target-dir file-list-sorted start-file start-file-full file-ext end-file end-file-base end-file-full file-number)
;; Clean directories from list but keep times
(setq file-list
(-remove (lambda (x) (nth 1 x))
(directory-files-and-attributes tdh-image-dir)))
;; Get target directory
(setq target-dir (file-name-directory (buffer-file-name)))
;; Sort list by most recent
(setq file-list-sorted
(mapcar #'car
(sort file-list
#'(lambda (x y) (time-less-p (nth 6 y) (nth 6 x))))))
;; Use ivy to select start-file
(setq start-file (ivy-read
(concat "Move selected file to " target-dir ":")
file-list-sorted
:re-builder #'ivy--regex
:sort nil
:initial-input nil))
;; add full path to start file and end-file
(setq start-file-full
(expand-file-name start-file tdh-image-dir))
;; final file name including path
(setq end-file-full
(expand-file-name start-file target-dir))
;; rename file
(rename-file start-file-full end-file-full)
(message "moved %s to %s" start-file-full start-file)
;; insert link
(insert (org-make-link-string (format "file:%s" start-file)))
;; display image
(org-display-inline-images t t)))Render Tables
https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_chapter_2_it/
(after! org
(defun tdh-render-org-table-at-point ()
(interactive)
(save-excursion
(beginning-of-line)
;; removes the overlay is already there
(if (overlays-at (point))
(delete-overlay (car (overlays-at (point))))
(let* ((element-type (org-element-type (org-element-at-point))))
(if (and (not (eq element-type 'table))
(not (eq element-type 'table-row)))
(error "not at an org table")
(while (not (eq 'table (org-element-type (org-element-at-point))))
(forward-line -1))
(tdh-render-org-table (org-element-at-point))
)))))
(defun tdh-render-org-table (table)
(interactive)
(let* ((begin (org-element-property :begin table))
(end (let ((pos (org-element-property :end table)))
(goto-char pos)
(beginning-of-line)
;; skip possible space after table
(while (not (looking-at " *[|#]"))
(setq pos (point))
(forward-line -1))
pos))
(tabletxt (buffer-substring-no-properties begin end))
(img (with-temp-buffer
(insert tabletxt)
(mark-whole-buffer)
(org-latex-convert-region-to-latex)
(org-latex-preview)
(goto-char (point-min))
(overlay-get (car (overlays-at (point))) 'display)))
(overlay (make-overlay begin end)))
(overlay-put overlay 'display img)
(forward-line -1))
)
(defun tdh-render-org-tables-in-buffer ()
(save-excursion
(org-element-map (org-element-parse-buffer) 'table 'tdh-render-org-table)))
;; Use F9 to globally generate tables
(map! :map org-mode-map :n "<f8>" (lambda () (interactive) (tdh-render-org-table-at-point)))
)Org Gcal
(use-package! org-gcal
:after org
:init
:config
(setq org-gcal-client-id "396102378658-dcmbcmrnthbe925519otsjbd921otq0v.apps.googleusercontent.com"
org-gcal-client-secret "4M5PWrbhQjwYEMXGK85lDYX9"
org-gcal-file-alist '(("dehaeze.thomas@gmail.com" . "~/Cloud/org/gcal.org")
("8kjmhe2ar0abnm054ill1fb0gc@group.calendar.google.com" . "~/Cloud/org/gcal_phd.org")))
;; Automatic fetch of the new events
;; (add-hook 'org-agenda-mode-hook (lambda () (org-gcal-fetch) ))
)Citeproc-Org
(use-package! citeproc-org
:ensure t
:after ox-hugo
:config
(citeproc-org-setup))Org Wild Notifier
(use-package! org-wild-notifier
:after org
:init
(setq alert-default-style 'libnotify)
:config
)TODO Orch
(use-package! web-server
:init
:config
) (add-to-list 'load-path "~/.config/doom/packages/orch/")
(autoload 'orch-toggle "orch" nil t)
TODO
[A]
Custom Keybindings - , leader key and C-c
C-c a |
Org Agenda |
C-c n |
Narrow to Subtree |
C-c l |
Org Link |
(after! org
(map! :map org-mode-map
(:desc "Org Agenda"
:ni "C-c a" 'org-agenda)
(:desc "Archive"
:n "C-c A" 'org-archive-subtree)
(:desc "Org Capture"
:ni "C-c c" 'org-capture)
(:desc "Store Link"
:ni "C-c l" 'org-store-link)
(:desc "Narrow Subtree"
:ni "C-c n" 'org-toggle-narrow-to-subtree)
(:desc "Org Noter"
:ni "C-c N" 'org-noter)
(:desc "Align Block"
:ni "C-c =" 'tdh-align-src-block)
(:desc "Insert Reference"
:ni "C-c r" 'org-ref-insert-ref-link)
(:desc "Insert Image"
:ni "C-c i" 'tdh-insert-image-org-link)
(:desc "Insert Image SXIV"
:ni "C-c I" 'tdh-insert-image-org-link-sxiv)
(:desc "Link to next Figure"
:ni "C-c f" 'tdh-insert-link-to-next-figure)
(:desc "Link to previous Figure"
:ni "C-c F" 'tdh-insert-link-to-previous-figure)
(:desc "Insert Screenshot"
:ni "C-c s" 'tdh-insert-screenshot-org-link)
(:desc "Find Roam"
:ni "C-c r" 'orb-find-non-ref-file)
(:desc "Insert Roam"
:ni "C-c R" 'orb-insert-non-ref)
))
Insert Elements ,i
Insert Link to paper
(defun tdh-insert-paper-org-link (paper)
"Insert an org link to some paper, choosing the file with completion"
(interactive
(list (read-file-name "Paper: " "~/Cloud/pdfs/" nil t)))
(insert (format "[[papers:%s]]" (file-name-base paper))))Insert Link to notes
(defun tdh-insert-note-org-link (note)
"Insert an org link to some note, choosing the file with completion"
(interactive
(list (read-file-name "Note: " "~/Cloud/pdfs/" nil t)))
(insert (format "[[notes:%s]]" (file-name-base note))))Insert Image that is in the figs folder
(defun tdh-insert-image-org-link (img)
"Insert an org image link, choosing the file with completion
and starting from `my-default-image-directory'."
(interactive
(list (file-relative-name (read-file-name "Image: " (concat default-directory "figs/")) default-directory)))
(insert (format "[[file:%s]]" img)))
Insert Image that is in the figs folder using SXIV
(defun tdh-insert-image-org-link-sxiv ()
"Insert an org image link, choosing the file with completion
and starting from `my-default-image-directory'."
(interactive)
(setq img (shell-command-to-string "ls figs/*.{jpg,jpeg,bmp,png,gif} 2> /dev/null | sxiv -i -t -o | tail -1 | tr -d '\n'"))
(unless (equal "" img)
(insert (format "[[file:%s]]" img)))
)Copy picture from phone folder using SXIV and insert it
(defun tdh-insert-phone-picture ()
(interactive)
(setq img (shell-command-to-string "~/.config/doom/bin/copy-phone-picture.sh"))
(unless (equal "" img)
(insert (format "[[file:%s]]" img)))
)Bash script for copying pictures taken by phone.
if [ -z "$1" ]; then
oldpath=$(ls -t ~/Cloud/photos/phone/*.jpg | sxiv -i -t -o | tail -1);
else
oldpath=$(ls -t $1 | sxiv -i -t -o | tail -1);
fi
if [ -n "$oldpath" ]; then
newfilename=$(basename $oldpath .jpg | rofi -i -dmenu -p "Filename")
if [ -n "$newfilename" ]; then
cp $oldpath "figs/$newfilename.jpg"
printf "figs/$newfilename.jpg"
fi
fiTake Screenshot and insert a link:
- Ask for a name
screenshot_name - use
maim -s figs/screenshot_name.pngto take a screenshot with selection - Then insert the following to the buffer
(defun tdh-insert-screenshot-org-link ()
"Capture screenshot and insert the resulting file.
The screenshot tool is determined by `org-download-screenshot-method'."
(interactive)
(if (string-match "_" (file-name-base buffer-file-name))
(setq filename (read-string "Enter file name:" (car (split-string (file-name-base buffer-file-name) "_"))))
(setq filename (read-string "Enter file name:")))
(setq filepath (concat "./figs/" filename ".png"))
(shell-command (concat "maim -s " filepath))
(insert (format "#+name: fig:%s\n#+caption:\n[[file:%s]]" filename filepath))
(search-backward "caption")
(end-of-line)
)Insert link to next figure:
(defun tdh-insert-link-to-next-figure ()
(interactive)
(save-excursion
(re-search-forward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
(insert (concat "[[" (match-string 1) "]]"))
)Insert link to previous figure:
(defun tdh-insert-link-to-previous-figure ()
(interactive)
(save-excursion
(re-search-backward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
(insert (concat "[[" (match-string 1) "]]"))
)Map Keys
(after! org
(map! :map org-mode-map
(:prefix (",i" . "Insert")
:n "p" 'tdh-insert-paper-org-link
:n "n" 'tdh-insert-note-org-link
:n "f" 'tdh-insert-image-org-link
:n "F" 'tdh-insert-image-org-link-sxiv
:n "i" 'tdh-insert-phone-picture
:n "l" 'tdh-insert-link-to-next-figure
:n "L" 'tdh-insert-link-to-previous-figure
:n "s" 'tdh-insert-screenshot-org-link)))
LaTeX ,l
(defun tdh-latex-watch ()
"Watch LaTeX file using latexmk"
(interactive)
(start-process-shell-command "latexmk-watch" "*latexmk-watch-output*"
"latexmk" (format "-pdflatex=\"xelatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory='%s'\" -pdf -pvc -bibtex -f %s.tex"
(file-name-directory buffer-file-name)
(file-name-base buffer-file-name)))) (defun tdh-latex-watch-kill ()
"Kill the currently running TeX job."
(interactive)
(delete-process "latexmk-watch")
) (after! org
(map! :map org-mode-map
(:prefix (",l" . "LaTeX")
:n "w" 'tdh-latex-watch
:n "k" 'tdh-latex-watch-kill
:n "l" 'org-latex-export-to-latex)))Org LaTeX Automatic fragment
(defun tdh-automatic-latex-fragment-activate ()
(interactive)
(add-hook 'org-mode-hook 'org-fragtog-mode))
(defun tdh-automatic-latex-fragment-deactivate ()
(interactive)
(remove-hook 'org-mode-hook 'org-fragtog-mode)) (after! org
(map! :map org-mode-map
(:prefix (",l" . "LaTeX")
:n "f" 'tdh-automatic-latex-fragment-activate
:n "F" 'tdh-automatic-latex-fragment-deactivate)))
Bibtex ,r
(after! org
(map! :map org-mode-map
(:prefix (",r" . "References")
:n "b" 'helm-bibtex
:n "B" 'helm-bibtex-with-local-bibliography
:n "f" 'tdh-helm-bibtex-favorites
:n "r" 'helm-resume)))
Open ranger in current directory ,o
(defun tdh-open-ranger-in-workdir ()
(interactive)
(call-process-shell-command
(concat "termite --directory=" default-directory " --exec=ranger") nil 0)) (after! org
(map! :map org-mode-map
:n ",o" 'tdh-open-ranger-in-workdir))
View in External programs ,v
Open PDF output with zathura
(defun tdh-open-org-pdf-externally ()
(interactive)
(call-process "zathura" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".pdf"))
)Open HTML output externally
(defun tdh-open-org-html-externally ()
(interactive)
(call-process "xdg-open" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".html"))
) (after! org
(map! :map org-mode-map
(:prefix (",v" . "View")
:n "p" 'tdh-open-org-pdf-externally
:n "h" 'tdh-open-org-html-externally)))Org Babel
Main configuration
Don't ask for confirmation when evaluating following blocs
(defun tdh-org-confirm-babel-evaluate (lang body)
(not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python"))))
(after! org
(setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))Default header arguments.
(after! org
(setq org-babel-default-header-args '((:eval . "no-export"))))Use the current window for C-c ' source editing
(after! org
(setq org-src-window-setup 'current-window))Appearance of source blocks
(defun tdh-org-prettify-symbols ()
(mapc (apply-partially 'add-to-list 'prettify-symbols-alist)
(cl-reduce 'append
(mapcar (lambda (x) (list x (cons (upcase (car x)) (cdr x))))
`(("#+begin_src" . ?✎)
("#+end_src" . ?□)
("#+begin_quote" . ?«)
("#+end_quote" . ?»)))))
(turn-on-prettify-symbols-mode))
(add-hook 'org-mode-hook #'tdh-org-prettify-symbols)Indentation
(after! org
(setq org-edit-src-content-indentation 2
org-src-tab-acts-natively nil
org-src-preserve-indentation nil)
)Library of Babel
Add all named source blocks to org-babel-library-of-babel (link).
(after! org
(org-babel-lob-ingest "~/.config/literate-dotfiles/dotfiles/emacs-library-babel.org"))Org-Babel Matlab
(after! org
(setq org-babel-matlab-shell-command "/home/thomas/.local/bin/matlab -softwareopengl -nodesktop -nosplash")
)Default options for Matlab code
(after! org
(setq org-babel-default-header-args:matlab
'((:results . "none")
(:session . "*MATLAB*")
(:comments . "org")
(:exports . "both")
(:cache . "no")
(:noweb . "no")
(:hlines . "no")
(:tangle . "yes")
(:mkdir . "yes")
(:eval . "no-export")))
)Better format the output results for Matlab (link).
(after! org
(defun org-babel-octave-evaluate-session
(session body result-type &optional matlabp)
"Evaluate BODY in SESSION."
(let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
(wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
(full-body
(pcase result-type
(`output
(mapconcat
#'org-babel-chomp
(list (if matlabp
(multi-replace-regexp-in-string
'(("%.*$" . "") ;Remove comments
(";\\s-*\n+" . "; ") ;Concatenate lines
("\\(\\.\\)\\{3\\}\\s-*\n+" . " ") ;Handle continuations
(",*\\s-*\n+" . ", ")) ;Concatenate lines
body)
body)
org-babel-octave-eoe-indicator) "\n"))
(`value
(if (and matlabp org-babel-matlab-with-emacs-link)
(concat
(format org-babel-matlab-emacs-link-wrapper-method
body
(org-babel-process-file-name tmp-file 'noquote)
(org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
(mapconcat
#'org-babel-chomp
(list (format org-babel-octave-wrapper-method
body
(org-babel-process-file-name tmp-file 'noquote)
(org-babel-process-file-name tmp-file 'noquote))
org-babel-octave-eoe-indicator) "\n")))))
(raw (if (and matlabp org-babel-matlab-with-emacs-link)
(save-window-excursion
(with-temp-buffer
(insert full-body)
(write-region "" 'ignored wait-file nil nil nil 'excl)
(matlab-shell-run-region (point-min) (point-max))
(message "Waiting for Matlab Emacs Link")
(while (file-exists-p wait-file) (sit-for 0.01))
"")) ;; matlab-shell-run-region doesn't seem to
;; make *matlab* buffer contents easily
;; available, so :results output currently
;; won't work
(org-babel-comint-with-output
(session
(if matlabp
org-babel-octave-eoe-indicator
org-babel-octave-eoe-output)
t full-body)
(insert full-body) (comint-send-input nil t)))) results)
(pcase result-type
(`value
(org-babel-octave-import-elisp-from-file tmp-file))
(`output
(setq results
(if matlabp
(cdr (reverse (delete "" (mapcar #'org-strip-quotes
(mapcar #'org-trim (remove-car-upto-newline raw))))))
(cdr (member org-babel-octave-eoe-output
(reverse (mapcar #'org-strip-quotes
(mapcar #'org-trim raw)))))))
(mapconcat #'identity (reverse results) "\n")))))
(defun remove-car-upto-newline (raw)
"Truncate each string in a list of strings up to the first newline"
(cons (mapconcat #'identity
(cdr (split-string-and-unquote (car raw) "\n"))
"\n") (cdr raw)))
(defun multi-replace-regexp-in-string (replacements-list string &optional rest)
(interactive)
"Replace multiple regexps in a string. Order matters."
(if (null replacements-list)
string
(let ((regex (caar replacements-list))
(replacement (cdar replacements-list)))
(multi-replace-regexp-in-string (cdr replacements-list)
(replace-regexp-in-string regex replacement
string rest)))))
)
Some functions for using Matlab with Org Babel ,m
whos matlab function
(defun tdh-matlab-whos (&optional start end)
"Get what is in the Matlab workspace"
(interactive)
(if (use-region-p)
(let ((regionp (buffer-substring (region-beginning) (region-end))))
(process-send-string "*MATLAB*" (concat "whosEmacs " regionp "\n")))
(process-send-string "*MATLAB*" (concat "whosEmacs" "\n"))))
help matlab function
(defun tdh-matlab-help (&optional start end)
"Get help on the selected function"
(interactive)
(if (use-region-p)
(let ((regionp (buffer-substring (region-beginning) (region-end))))
(process-send-string "*MATLAB*" (concat "help " regionp "\n")))
(process-send-string "*MATLAB*" (concat "help " (read-string "Matlab help:") "\n")))
)Specify a Matlab command to run
(defun tdh-matlab-run-command ()
"Prompt user to enter a matlab command"
(interactive)
(process-send-string "*MATLAB*" (concat (read-string "Matlab Command: ") "\n")))Specify a Matlab command to run and show output in mini-buffer
(defun tdh-matlab-run-command-show-output ()
"Prompt user to enter a matlab command"
(interactive)
(process-send-string "*MATLAB*" (concat "evalEmacs('" (read-string "Matlab Command: ") "')\n")))Org-Babel Tangle File and Execute with Matlab
(defun tdh-matlab-tangle-and-execute ()
"Jump to tangle file for the source block at point."
(interactive)
(let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
(cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
(setq file filename)))
((symbol-function 'delete-file) #'ignore))
(org-babel-tangle '(4)))
(when file
(setq file (expand-file-name file))
(if (file-readable-p file)
(process-send-string "*MATLAB*" (concat "run " file "\n"))
(error "Cannot open tangle file %S" file)))))Map Functions
(after! org
(map! :map org-mode-map
(:prefix (",m" . "Matlab")
:n "e" 'tdh-matlab-run-command
:n "E" 'tdh-matlab-run-command-show-output
:n "T" 'tdh-matlab-tangle-and-execute
:nv "h" 'tdh-matlab-help
:nv "w" 'tdh-matlab-whos)))
Remap ctrl-ret used to execute the src block and go to the next one
Remap ctrl-ret to execute the source block and go to the next source block
when inside a source block. Otherwise, keep the normal behavior for ctrl-ret.
(defun tdh-ctrl-ret ()
(interactive)
(defun tdh-in-src-block-p ()
"Returns t when the point is inside a source code block"
(string= "src" (org-in-block-p '("src"))))
(if (tdh-in-src-block-p)
(progn
(org-babel-execute-src-block)
(org-babel-next-src-block))
(+org--insert-item 'below))) (map! :after evil-org
:map evil-org-mode-map
:n "<C-return>" #'tdh-ctrl-ret)
Remap ctrl-shift-ret used to execute the (matlab) src block in the background and go to the next one
tdh-org-babel-execute-matlab-background
(defun tdh-org-babel-execute-matlab-background (&optional arg info params)
(interactive)
(let* ((org-babel-current-src-block-location
(or org-babel-current-src-block-location
(nth 5 info)
(org-babel-where-is-src-block-head)))
(info (if info (copy-tree info) (org-babel-get-src-block-info))))
;; Merge PARAMS with INFO before considering source block
;; evaluation since both could disagree.
(cl-callf org-babel-merge-params (nth 2 info) params)
(when (org-babel-check-evaluate info)
(cl-callf org-babel-process-params (nth 2 info))
(let* ((params (nth 2 info))
(cache (let ((c (cdr (assq :cache params))))
(and (not arg) c (string= "yes" c))))
(new-hash (and cache (org-babel-sha1-hash info :eval)))
(old-hash (and cache (org-babel-current-result-hash)))
(current-cache (and new-hash (equal new-hash old-hash))))
(cond
(current-cache
(save-excursion ;Return cached result.
(goto-char (org-babel-where-is-src-block-result nil info))
(forward-line)
(skip-chars-forward " \t")
(let ((result (org-babel-read-result)))
(message (replace-regexp-in-string "%" "%%" (format "%S" result)))
result)))
((org-babel-confirm-evaluate info)
(let* ((lang (nth 0 info))
(result-params (cdr (assq :result-params params)))
;; Expand noweb references in BODY and remove any
;; coderef.
(body
(let ((coderef (nth 6 info))
(expand
(if (org-babel-noweb-p params :eval)
(org-babel-expand-noweb-references info)
(nth 1 info))))
(if (not coderef) expand
(replace-regexp-in-string
(org-src-coderef-regexp coderef) "" expand nil nil 1))))
(dir (cdr (assq :dir params)))
(mkdirp (cdr (assq :mkdirp params)))
(default-directory
(cond
((not dir) default-directory)
((member mkdirp '("no" "nil" nil))
(file-name-as-directory (expand-file-name dir)))
(t
(let ((d (file-name-as-directory (expand-file-name dir))))
(make-directory d 'parents)
d))))
(cmd (intern (concat "org-babel-execute:" lang)))
result)
(process-send-string "*MATLAB*" (concat body "\n"))
result))
)))
)
)
tdh-matlab-execute-selected
(defun tdh-matlab-execute-selected (start end)
"Execute selected text in the *MATLAB* buffer"
(interactive "r")
(let ((regionp (buffer-substring start end)))
(process-send-string "*MATLAB*" (concat regionp "\n"))))
Remap ctrl-shift-ref
This function:
- first check if inside a source block, if not does nothing
-
when check if the language is
matlab- if it is not, it just runs the code and go to the next source block
- if it is in a
matlabblock, it first check if a region if selected, if so it just runs the selected region. if no region is selected, it runs all the code blocks and goes to the next block
(defun tdh-ctrl-shift-ret ()
(interactive)
(defun tdh-in-src-block-p ()
"Returns t when the point is inside a source code block"
(string= "src" (org-in-block-p '("src"))))
(if (tdh-in-src-block-p)
(let ((lang (nth 0 (org-babel-get-src-block-info))))
(if (string= lang "matlab")
(if (region-active-p)
(tdh-matlab-execute-selected (region-beginning) (region-end))
(progn (tdh-org-babel-execute-matlab-background)
(org-babel-next-src-block)))
(tdh-ctrl-ret))
)
)
) (map! :after evil-org
:map evil-org-mode-map
:n "<C-S-return>" #'tdh-ctrl-shift-ret)Align Source Blocks
(defun tdh-align-src-block ()
(interactive)
(defun tdh-in-src-block-p ()
"Returns t when the point is inside a source code block"
(string= "src" (org-in-block-p '("src"))))
(if (tdh-in-src-block-p)
(progn
(org-edit-special)
(evil-indent (point-min) (point-max))
(org-edit-src-exit))
(org-table-eval-formula)))
Helping Functions - Tangling ,b
Org-Babel Tangle Sub-tree
(defun tdh-org-babel-tangle-subtree ()
"Tangle the current subtree"
(interactive)
(progn
(org-narrow-to-subtree)
(org-babel-tangle)
(widen))
)Org-Tangle and Org-Babel Jump to Tangle File
(defun tdh-org-babel-jump-to-tangle-file ()
"Jump to tangle file for the source block at point."
(interactive)
(let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
(cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
(setq file filename)))
((symbol-function 'delete-file) #'ignore))
(org-babel-tangle '(4)))
(when file
(setq file (expand-file-name file))
(if (file-readable-p file)
(find-file file)
(error "Cannot open tangle file %S" file)))))Map Functions
(after! org
(map! :map org-mode-map
(:prefix (",b" . "Tangle")
:n "F" 'tdh-org-babel-jump-to-tangle-file
:n "T" 'tdh-org-babel-tangle-subtree)))Bibliography Management
My bibliography management is mainly based on the following packages:
org-reffor nice citationsorg-noterto annotate documentsorg-roamto manage and links all my noteshelm-bibtexas an interface to easily find referencesorg-roam-bibtexthat connects all the above packages
Org Ref (link)
Nice Functions:
org-ref-insert-ref-linkorg-ref-helm-insert-cite-linkorg-ref-list-of-figuresorg-ref-find-bad-citationsorg-ref-clean-bibtex-entry
(use-package! org-ref
:after org
:init
:config
;; Folder where the notes files are located (or file if just one Note file)
(setq org-ref-notes-directory "~/Cloud/brain")
(setq org-ref-bibliography-notes "~/Cloud/brain")
;; Bibliography File
(setq reftex-default-bibliography '("~/Cloud/brain/biblio/references.bib"))
(setq org-ref-default-bibliography '("~/Cloud/brain/biblio/references.bib"))
;; Folder where all the pdf are located
(setq org-ref-pdf-directory "~/Cloud/pdfs")
(setq org-ref-bibliography-entry-format
'(("article" . "%a, %t, %j, v(%n), %p (%y).")
("book" . "%a, %t, %u (%y).")
("techreport" . "%a, %t, %i, %u (%y).")
("phdthesis" . "%a, %t (%y).")
("proceedings" . "%e, %t in %S, %u (%y).")
("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)")))
;; Tell org-ref to let helm-bibtex find notes for it
(setq org-ref-notes-function
(lambda (thekey)
(let ((bibtex-completion-bibliography (org-ref-find-bibliography)))
(bibtex-completion-edit-notes
(list (car (org-ref-get-bibtex-key-and-file thekey)))))))
;; Problem with speed: don't display broken links
(setq org-ref-show-broken-links t)
;; Display information on the citation
(setq org-ref-show-citation-on-enter t)
(add-to-list 'org-ref-helm-user-candidates
'("Open pdf in Zathura" . (lambda () (call-process "zathura" nil 0 nil (concat
(file-name-as-directory org-ref-pdf-directory)
(car (org-ref-get-bibtex-key-and-file))
".pdf"))))
t)
(add-to-list 'org-ref-helm-user-candidates
'("Drag and Drop" . (lambda () (call-process "/bin/bash" nil 0 nil "-c" (concat
"dragon-drag-and-drop "
(file-name-as-directory org-ref-pdf-directory)
(car (org-ref-get-bibtex-key-and-file))
".pdf"))))
t)
;; Let Mathjax deals with equation reference
(defun org-ref-eqref-export (keyword desc format)
(cond
((eq format 'latex) (format "\\eqref{%s}" keyword))
((eq format 'html) (format "\\eqref{%s}" keyword))
((eq format 'md) (format "\\eqref{%s}" keyword))))
) (defun tdh-org-ref-open-pdf-at-point ()
"Open the pdf in external program for bibtex key under point if it exists."
(interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(pdf-file (funcall org-ref-get-pdf-filename-function key)))
(if (file-exists-p pdf-file)
(call-process "zathura" nil 0 nil pdf-file)
(message "no pdf found for %s" key))))Org Noter (link)
(use-package! org-noter
:defer t
:after (:any org pdf-view)
:config
(setq org-noter-always-create-frame nil)
(setq org-noter-kill-frame-at-session-end nil)
;; Fraction of the frame that the document window will occupy when split
(setq org-noter-doc-split-fraction '(0.6 . 0.6))
;; Save the last visited location automatically; when starting a new session, go to that location
(setq org-noter-auto-save-last-location nil)
;; Add an empty line between each note's heading and content
(setq org-noter-separate-notes-from-heading t)
;; List of paths to check (non recursively) when searching for a notes file
(setq org-noter-notes-search-path "~/Cloud/brain")
(defun org-noter-init-pdf-view ()
(pdf-view-fit-page-to-window)
(pdf-view-auto-slice-minor-mode)
(run-at-time "0.5 sec" nil #'org-noter))
(add-hook 'pdf-view-mode-hook 'org-noter-init-pdf-view)
(map!
:map pdf-view-mode-map
(:desc "Insert Note"
:n "i" #'org-noter-insert-note))
)Org Roam (link)
(use-package! org-roam
:custom-face
(org-roam-link ((t (:inherit org-link :foreground "#cc241d"))))
:config
(setq org-roam-directory "~/Cloud/brain/")
(setq org-roam-completion-system 'helm)
(setq org-roam-tag-sources '(prop last-directory))
(setq org-roam-capture-templates
`(("d" "default" plain (function org-roam--capture-get-point)
"%?"
:file-name "${slug}"
:head ,(concat "#+TITLE: ${title}\n"
"#+SETUPFILE: ./setup/org-setup-file.org\n"
"#+HUGO_SECTION: zettels\n"
"\n"
"- Tags ::\n"
"\n"
"* Bibliography :ignore:\n"
"bibliography:./biblio/references.bib"
)
:unnarrowed t)))
(setq org-roam-capture-ref-templates
`(("r" "ref" plain (function org-roam--capture-get-point)
"%?"
:file-name "${slug}"
:head ,(concat "#+TITLE: ${title}\n"
"#+SETUPFILE: ./setup/org-setup-file.org\n"
"#+HUGO_SECTION: websites\n"
"#+ROAM_KEY: ${ref}\n"
"\n"
"- Tags ::\n"
)
:unnarrowed t)))
)Automatic export of backlinks
(after! (org org-roam)
(defun tdh-org-roam--backlinks-list (file)
(when (org-roam--org-roam-file-p file)
(mapcar #'car (org-roam-db-query [:select :distinct [from]
:from links
:where (= to $s1)
:and from :not :like $s2] file "%private%"))))
(defun tdh-org-export-preprocessor (_backend)
(when-let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
(insert "\nBacklinks:\n")
(dolist (link links)
(insert (format "- [[file:%s][%s]]\n"
(file-relative-name link org-roam-directory)
(org-roam--get-title-or-slug link))))))
(add-hook 'org-export-before-processing-hook #'tdh-org-export-preprocessor)
(defun tdh-org-roam-export-all ()
"Re-exports all Org-roam files to Hugo markdown."
(interactive)
(dolist (f (org-roam--list-all-files))
(with-current-buffer (find-file f)
(when (s-contains? "SETUPFILE" (buffer-string))
(org-hugo-export-wim-to-md)))))
)Helm-Bibtex (link)
(use-package! helm-bibtex
:after-call helm-bibtex
:init
:config
;; Bibliography file
(setq bibtex-completion-bibliography "~/Cloud/brain/biblio/references.bib")
;; Directory with all the pdfs
(setq bibtex-completion-library-path "~/Cloud/pdfs/")
;; Directory with notes files
(setq bibtex-completion-notes-path "~/Cloud/brain/")
(setq bibtex-completion-notes-extension ".org")
(setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))
;; Use "tags" field when looking for bib entries
(setq helm-bibtex-additional-search-fields '(tags))
(setq helm-bibtex-full-frame nil)
;; Display of bibtex entries with helm
(setq bibtex-completion-display-formats
'((t . "${author:36} ${title:*} ${year:4} ${=type=:7} ${=has-note=:1}")))
;; Special symbols for notes and pdf
(setq bibtex-completion-pdf-symbol "⌘")
(setq bibtex-completion-notes-symbol "✎")
;; Template used when creating new Note file
(setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
"#+SETUPFILE: ./setup/org-setup-file.org\n"
"#+HUGO_SECTION: ${=type=}\n"
"#+ROAM_KEY: ${=key=}\n"
"\n"
"- Tags ::\n"
"- Reference :: cite:${=key=}\n"
"- Author(s) :: ${author}\n"
"- Year :: ${year}\n"
"\n"
"* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
":PROPERTIES:\n"
":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
":END:\n"
"\n"
"* Bibliography :ignore:\n"
"bibliography:./biblio/references.bib"
))
;; Make "Edit notes" the default action
(helm-delete-action-from-source "Edit notes" helm-source-bibtex)
(helm-add-action-to-source "Edit notes" 'helm-bibtex-edit-notes helm-source-bibtex 0)
(helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
(helm-add-action-to-source "Open PDF Externally" 'tdh-open-pdf-externally helm-source-bibtex 1)
(helm-add-action-to-source "Insert Link to Note" 'tdh-insert-link-to-note helm-source-bibtex 2)
(helm-add-action-to-source "Insert E-Reader Link" 'tdh-insert-link-to-pdf-entry helm-source-bibtex 3)
) (defun tdh-insert-link-to-pdf-entry (key)
"Insert a link to a pdf associated with the bibtex entry."
(let*
((entry (bibtex-completion-get-entry key))
(title (bibtex-completion-get-value "title" entry)))
(insert (concat "[[file:Download/" key ".pdf][" title "]] (cite:" key ")"))
)
) (defun tdh-insert-link-to-note (key)
"Insert a link to a note associated with the bibtex entry."
(if (and bibtex-completion-notes-path
(f-directory? bibtex-completion-notes-path))
(let* ((path (f-join bibtex-completion-notes-path
(s-concat key bibtex-completion-notes-extension))))
(if (file-exists-p path)
(insert (concat "[[file:" (file-relative-name path) "][Notes]]"))
(message "No note file associated"))
)))Open pdf externally
(defun tdh-open-pdf-externally (key)
(call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))Special Commands
(defun tdh-helm-bibtex-favorites (&optional arg)
"Search Favorite BibTeX entries"
(interactive "P")
(helm-bibtex arg nil "favorite "))List all element of the bibliography without pdf associated
(defun tdh-list-bib-without-pdf-associated ()
(interactive)
(bibtex-completion-init)
(setq candidates (bibtex-completion-candidates))
(defun canditate-is-pdf-present (candidate)
(bibtex-completion-find-pdf-in-library (cdr (assoc "=key=" candidate)))
)
(setq candidates-without-pdf (remove-if #'canditate-is-pdf-present candidates))
(setq candidate-without-pdf-names (mapcar
(lambda (x) (cdr (assoc "title" x)))
candidates-without-pdf))
(with-output-to-temp-buffer "*bib-without-pdf*" (princ (string-join candidate-without-pdf-names "\n")))
(switch-to-buffer-other-window "*bib-without-pdf*")
)Deft
(use-package! deft
:custom
(deft-directory "~/Cloud/brain/"))Org-Roam-Bibtex (link)
Provides nice functions such as:
orb-find-non-ref-fileorb-insert-non-reforb-note-action
(use-package! org-roam-bibtex
:hook (org-roam-mode . org-roam-bibtex-mode)
:config
(setq orb-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))
(setq orb-templates
`(("r" "ref" plain (function org-roam-capture--get-point) ""
:file-name "${=key=}"
:head ,(concat "#+TITLE: ${title}\n"
"#+SETUPFILE: ./setup/org-setup-file.org\n"
"#+HUGO_SECTION: ${=type=}\n"
"#+ROAM_KEY: ${ref}\n"
"\n"
"- Tags ::\n"
"- Reference :: ${ref}\n"
"- Author(s) :: ${author}\n"
"- Year :: ${year}\n"
"\n"
"* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
":PROPERTIES:\n"
":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
":END:\n"
"\n"
"* Bibliography :ignore:\n"
"bibliography:./biblio/references.bib"
)
:unnarrowed t)))
(setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
) (defun tdh-open-bib-with-zathura (key)
"Open the pdf corresponding to the reference KEY with Zathura"
(if (listp key)
(setq key (car key)))
(call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))Citeproc-org (link)
(use-package! citeproc-org
:after org
:config
(citeproc-org-setup))LaTeX
- https://tex.stackexchange.com/questions/52179/what-is-your-favorite-emacs-and-or-auctex-command-trick
- https://tex.stackexchange.com/questions/20843/useful-shortcuts-or-key-bindings-or-predefined-commands-for-emacsauctex
Master file
(setq-default TeX-master nil)Clean Output Files
(defun tdh-latex-clean ()
"Clean LaTeX output using latexmk"
(interactive)
(async-shell-command
;; command and parameters
"latexmk -c "
(shell-quote-argument buffer-file-name)
" &"
))
(map! :map LaTeX-mode-map
:n ",C" 'tdh-latex-clean)
(add-hook 'TeX-mode-hook #'TeX-fold-mode)PDF Viewer
(setq TeX-view-program-selection '((output-pdf "Zathura")))
(setq TeX-source-correlate-mode t)
(setq TeX-source-correlate-start-server t)
(setq TeX-source-correlate-method 'synctex)
(setq TeX-view-program-list
'(("PDF Tools" TeX-pdf-tools-sync-view)))Bibtex
(use-package! bibtex
:config
(bibtex-set-dialect 'BibTeX))Matlab
Setup Matlab Mode
(setq matlab-shell-command "/home/thomas/.local/bin/matlab")
(setq matlab-shell-command-switches (list "-softwareopengl -nodesktop -nosplash"))
(setq matlab-indent-function t)
(setq mlint-programs '("mlint" "/home/thomas/.local/bin/mlint"))
Setup Flycheck to work with mlint
(defvar mlint-executable "/home/thomas/.local/bin/mlint")
(flycheck-define-command-checker 'matlab-mlint
"A Matlab checker based on mlint."
:command `(,mlint-executable source)
:error-patterns
'((warning line-start "L " line " (C " (1+ digit) "): " (message) line-end))
:modes '(matlab-mode))
(add-to-list 'flycheck-checkers 'matlab-mlint)
;; Automatic startup of flycheck for matlab
(add-hook 'matlab-mode-hook 'flycheck-mode)Completion in the Matlab Shell
(map! :map matlab-shell-mode-map
:i "<tab>" 'matlab-shell-tab)Beautify code
(defun tdh-matlab-beautify-buffer ()
"Beautify Current Matlab Buffer"
(interactive)
;; First verifies is the current file is a Matlab file
(if (string= (file-name-extension (buffer-file-name)) "m")
(progn
(save-buffer)
(matlab-shell-run-command (concat "MBeautify.formatFileNoEditor(\"" (buffer-file-name) "\", \"" (buffer-file-name) "\")"))
(revert-buffer :ignore-auto :noconfirm))
(message "Current buffer is not a matlab file")
)
)Key Bindings
(defun tdh-matlab-add-breakpoint ()
(interactive)
(matlab-shell-run-command (concat "dbstop in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
(defun tdh-matlab-remove-breakpoint ()
(interactive)
(matlab-shell-run-command (concat "dbclear in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
(defun tdh-matlab-list-breakpoints ()
(interactive)
(matlab-shell-run-command (concat "dbstatus " (buffer-name))))
(defun tdh-matlab-clear-breakpoints ()
(interactive)
(matlab-shell-run-command (concat "dbclear in " (buffer-name))))
(defun tdh-matlab-no-debug-on-error ()
(interactive)
(matlab-shell-run-command (concat "dbclear if error")))
(defun tdh-matlab-debug-on-error ()
(interactive)
(matlab-shell-run-command (concat "dbstop if error")))
(defun tdh-matlab-go-to-file-directory ()
(interactive)
(matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name)))) (map! :map matlab-mode-map
(:prefix ("," . "prefix")
:n "g" 'tdh-matlab-go-to-file-directory
(:prefix ("d" . "Debug")
:n "de" 'tdh-matlab-debug-on-error
:n "dE" 'tdh-matlab-no-debug-on-error
:n "da" 'tdh-matlab-add-breakpoint
:n "dr" 'tdh-matlab-remove-breakpoint
:n "dL" 'tdh-matlab-list-breakpoints
:n "dc" 'tdh-matlab-clear-breakpoints
:n "dl" 'gud-cont
:n "ds" 'gud-step
:n "dn" 'gud-next
:n "dq" 'gud-finish)))Mu4e
Resources
Documentation:
- Mu4e documentation: http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
- https://github.com/djcb/mu
Use contexts for multiple accounts:
- https://vxlabs.com/2017/02/07/mu4e-0-9-18-e-mailing-with-emacs-now-even-better/
- http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
- https://notanumber.io/2016-10-03/better-email-with-mu4e/
Send math and source code:
Cheatsheet
| Command | Usage |
|---|---|
C-j |
Next mail |
C-k |
Previous mail |
R/C/F |
Reply/Compose/Forward |
t |
Move to Archive |
d |
Move to Trash |
Helping function
This is a helper to help determine which account context I am in based on the folder in my maildir the email (eg. ~/.mail/nine27) is located in.
(defun mu4e-message-maildir-matches (msg rx)
(when rx
(if (listp rx)
;; If rx is a list, try each one for a match
(or (mu4e-message-maildir-matches msg (car rx))
(mu4e-message-maildir-matches msg (cdr rx)))
;; Not a list, check rx
(string-match rx (mu4e-message-field msg :maildir)))))Choose account label to feed msmtp -a option based on From header in Message buffer; This function must be added to message-send-mail-hook for on-the-fly change of From address before sending message since message-send-mail-hook is processed right before sending message.
(defun choose-msmtp-account ()
(if (message-mail-p)
(save-excursion
(let*
((from (save-restriction
(message-narrow-to-headers)
(message-fetch-field "from")))
(account
(cond
((string-match "dehaeze.thomas@gmail.com" from) "gmail")
((string-match "thomas.dehaeze@esrf.fr" from) "esrf"))))
(setq message-sendmail-extra-arguments (list '"-a" account))))))Basic Config
(use-package! mu4e
:config
(setq mail-user-agent 'mu4e-user-agent
mu4e-mu-binary "/usr/bin/mu"
mu4e-maildir "~/.mail"
mu4e-compose-format-flowed t
mu4e-compose-in-new-frame nil
mu4e-view-show-images t
mu4e-html2text-command "w3m -dump -T text/html"
mu4e-use-fancy-chars t
mu4e-headers-include-related t
mu4e-attachment-dir "~/Downloads"
message-kill-buffer-on-exit t
mu4e-compose-signature-auto-include t
mu4e-view-show-images t
mu4e-view-show-addresses t)
)Additional config
(use-package! mu4e
:config
;; Use imagemagick, if available.
(when (fboundp 'imagemagick-register-types)
(imagemagick-register-types))
;; Sometimes html email is just not readable in a text based client, this lets me open the
;; email in my browser.
(add-to-list 'mu4e-view-actions '("View in browser" . mu4e-action-view-in-browser) t)
;; Spell checking ftw.
(add-hook 'mu4e-compose-mode-hook 'flyspell-mode)
;; Use Helm to select mailboxes
(setq mu4e-completing-read-function 'completing-read)
;; Don't ask for a 'context' upon opening mu4e
(setq mu4e-context-policy 'pick-first)
;; Don't ask to quit... why is this the default?
(setq mu4e-confirm-quit nil)
)Provide Information
(use-package! mu4e
:config
(setq mu4e-user-mail-address-list '("dehaeze.thomas@gmail.com" "thomas.dehaeze@esrf.fr")
mu4e-compose-signature "Thomas Dehaeze\n"
user-mail-address "dehaeze.thomas@gmail.com")
;; Default Folders
(setq mu4e-sent-folder "/gmail/Sent"
mu4e-drafts-folder "/gmail/Drafts"
mu4e-trash-folder "/gmail/Trash"
mu4e-refile-folder "/gmail/Archive")
)Receiving emails using mbsync
(use-package! mu4e
:config
(setq mu4e-get-mail-command "checkmail"
mu4e-update-interval nil
mu4e-change-filenames-when-moving t) ;; Fix for mbsync
)Contexts
(use-package! mu4e
:config
(setq mu4e-contexts
`( ,(make-mu4e-context
:name "gmail"
:enter-func (lambda () (mu4e-message "Switch to the gmail context"))
:match-func (lambda (msg) (when msg
(string-prefix-p "/gmail" (mu4e-message-field msg :maildir))))
:leave-func (lambda () (mu4e-clear-caches))
:vars '(
(user-mail-address . "dehaeze.thomas@gmail.com")
(user-full-name . "Thomas Dehaeze")
(mu4e-sent-folder . "/gmail/Sent")
(mu4e-trash-folder . "/gmail/Trash")
(mu4e-drafts-folder . "/gmail/Drafts")
(mu4e-refile-folder . "/gmail/Archive")
(mu4e-compose-signature . "Thomas Dehaeze\n")
))
,(make-mu4e-context
:name "esrf"
:enter-func (lambda () (mu4e-message "Switch to the esrf context"))
:match-func (lambda (msg) (when msg
(string-prefix-p "/esrf" (mu4e-message-field msg :maildir))))
:leave-func (lambda () (mu4e-clear-caches))
:vars '(
(user-mail-address . "thomas.dehaeze@esrf.fr")
(user-full-name . "Thomas Dehaeze")
(mu4e-sent-folder . "/esrf/Sent")
(mu4e-trash-folder . "/esrf/Trash")
(mu4e-drafts-folder . "/esrf/Drafts")
(mu4e-refile-folder . "/esrf/Archive")
(mu4e-compose-signature . "Thomas Dehaeze\n")
))
))
)Sending mails
(use-package! mu4e
:config
(setq message-send-mail-function 'message-send-mail-with-sendmail
sendmail-program "/usr/bin/msmtp"
user-full-name "Thomas Dehaeze")
;; This prevents saving the email to the Sent folder since gmail will do this for us on their end.
(setq mu4e-sent-messages-behavior 'delete)
;; Use the correct account context when sending mail based on the from header.
(setq message-sendmail-envelope-from 'header)
(add-hook 'message-send-mail-hook 'choose-msmtp-account)
)Bookmarks
(use-package! mu4e
:config
(setq mu4e-bookmarks `(,(make-mu4e-bookmark
:name "All Inboxes"
:query "maildir:/gmail/Inbox OR maildir:/esrf/Inbox"
:key ?i)
("flag:unread" "Unread messages" ?u)
("date:today..now" "Today's messages" ?t)
("date:7d..now" "Last 7 days" ?w)))
)
Doom init.el
(when noninteractive
(after! undo-tree
(global-undo-tree-mode -1)))
(doom! :completion
company ; the ultimate code completion backend
helm ; the *other* search engine for love and life
ivy ; a search engine for love and life
:ui
doom ; what makes DOOM look the way it does
deft
hl-todo ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
hydra
modeline
ophints ; highlight the region an operation acts on
(popup ; tame sudden yet inevitable temporary windows
+all ; catch all popups that start with an asterix
+defaults) ; default popup rules
unicode ; extended unicode support for various languages
vc-gutter ; vcs diff in the fringe
vi-tilde-fringe ; fringe tildes to mark beyond EOB
workspaces ; tab emulation, persistence & separate workspaces
(emoji +unicode)
:editor
(evil +everywhere); come to the dark side, we have cookies
fold ; (nigh) universal code folding
rotate-text ; cycle region at point between text candidates
snippets ; my elves. They type so I don't have to
word-wrap ; soft wrapping with language-aware indent
:emacs
(dired +icons) ; making dired pretty [functional]
electric ; smarter, keyword-based electric-indent
(ibuffer +icons) ; interactive buffer management
vc ; version-control and Emacs, sitting in a tree
undo
:term
eshell ; a consistent, cross-platform shell (WIP)
vterm
:tools
debugger ; Stepping through code, to help you add bugs
(eval +overlay) ; run code, run (also, repls)
(lookup ; helps you navigate your code and documentation
+docsets) ; ...or in Dash docsets locally
lsp
magit ; a git porcelain for Emacs
docker
;;pass ; password manager for nerds
pdf ; pdf enhancements
eval
biblio
(lookup +dictionary)
:checkers
syntax ; tasing you for every semicolon you forget
spell ; tasing you for misspelling mispelling
:lang
data ; config/data formats
emacs-lisp ; drown in parentheses
go
(javascript
+lsp)
latex ; writing papers in Emacs has never been so fun
;; markdown ; writing docs for people to ignore
(org ; organize your plain life in plain text
+dragndrop ; drag & drop files/images into org buffers
+hugo ; use Emacs for hugo blogging
+roam ;
+present) ; using org-mode for presentations
python ; beautiful is better than ugly
(sh ; she sells {ba,z,fi}sh shells on the C xor
+lsp)
(web
+lsp)
yaml
:email
(mu4e +gmail)
:app
calendar
;;(rss +org) ; emacs as an RSS reader
;;write ; emacs for writers (fiction, notes, papers, etc.)
:config
literate
(default +bindings)
)
Doom packages.el
(package! poet-theme)
(package! spice-mode)
(package! org-pandoc-import
:recipe (:host github
:repo "tecosaur/org-pandoc-import"
:files ("*.el" "filters" "preprocessors")))
(package! citeproc-org)
(package! org-wild-notifier)
(package! org-gcal)
;; (package! ox-latex-subfigure
;; :recipe (:host github :repo "linktohack/ox-latex-subfigure"))
;; (package! matlab-mode)
(package! matlab-mode
:recipe (:host github :repo "matlab-mode/mirror"))
(package! org-ref)
(package! citeproc-org)
(package! org-ql)
(package! org-fancy-priorities)
(package! evil-escape :disable t)
(package! dired-narrow)
(package! web-server)