diff --git a/dotfiles/doom.org b/dotfiles/doom.org
index f9231c6..16484da 100644
--- a/dotfiles/doom.org
+++ b/dotfiles/doom.org
@@ -1,7 +1,5 @@
#+TITLE: Doom Emacs Configuration
:DRAWER:
-#+STARTUP: overview
-
#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas
@@ -29,9 +27,13 @@ https://github.com/nmartin84/.doom.d/blob/master/config.org
Documentation:
- https://github.com/hlissner/doom-emacs/blob/develop/docs/index.org
+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 [[https://github.com/junegunn/vim-easy-align][vim-easy-align]]. Very useful to align tables and stuff
+** General Bindings
| =spc := | Execute command |
| =spc <= | Switch to buffer |
| =spc X= | org-capture |
@@ -58,29 +60,38 @@ Documentation:
| =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 |
-| 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
@@ -188,6 +199,36 @@ Turn off auto-fill mode that add line breaks.
(setq magit-diff-refine-hunk 'all)
#+end_src
+** Dired
+- =C-c C-e= Writable Dired mode, when changes are done =C-c C-c=.
+ This works also with =C-x C-q=
+- =C-c C-r= use =rsync= to copy file in the background
+
+- =+= Create a directory
+- =R= Rename / move
+- =C= Copy
+- =d= Delete
+- =m= Mark
+- =U= unmark all marked
+- =t= invert the selection
+- =u= unmark / undelete
+- =x= actually delete files/directories marked for deletion
+- =!= Execute shell command on this file, or currently marked files
+- =%m= mark by pattern
+- =o= sort by time/name
+
+- =(= Hide details
+- =)= Show git infos
+
+
+#+begin_src emacs-lisp
+ (use-package! dired-narrow
+ :config
+ (map! :map dired-mode-map
+ :n "f"
+ 'dired-narrow-fuzzy))
+#+end_src
+
** PDF-Tools
#+begin_src emacs-lisp
(use-package! pdf-tools
@@ -202,6 +243,21 @@ Turn off auto-fill mode that add line breaks.
(yas-global-mode 1)
#+end_src
+** Ox-Hugo
+#+begin_src emacs-lisp
+ (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))))
+#+end_src
+
* Org Mode
- http://cachestocaches.com/2016/9/my-workflow-org-agenda/
- http://doc.norang.ca/org-mode.html#TodoKeywords
@@ -209,6 +265,7 @@ Turn off auto-fill mode that add line breaks.
** Org General Config
#+begin_src emacs-lisp
+ (setq org-directory "~/Cloud/org/")
(after! org
(setq org-directory "~/Cloud/org/")
@@ -225,6 +282,7 @@ Turn off auto-fill mode that add line breaks.
;; 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)
@@ -250,10 +308,8 @@ Display the real size of images and not the one set with =attr_latex: :width \li
** Org Links
#+begin_src emacs-lisp
(after! org
- (map! :map org-mode-map "C-c l" 'org-store-link)
-
(setq org-link-abbrev-alist
- '(("bib" . "~/Cloud/brain/references.bib::%s")
+ '(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
("notes" . "~/Cloud/brain/%s.org")
("papers" . "~/Cloud/pdfs/%s.pdf")))
)
@@ -365,8 +421,6 @@ Archive subtrees under the same hierarchy as original in the archive files
General configuration
#+begin_src emacs-lisp
(after! org
- (map! :map org-mode-map "C-c a" 'org-agenda)
-
;; File to save todo items
(setq org-agenda-files (list "~/Cloud/org/"))
@@ -544,11 +598,6 @@ Documentation:
- Template expansion: https://orgmode.org/manual/Template-expansion.html#Template-expansion
- Capture protocol: https://orgmode.org/manual/capture-protocol.html
-#+begin_src emacs-lisp
- (after! org
- (map! :map org-mode-map "C-c c" 'org-capture))
-#+end_src
-
#+begin_src emacs-lisp
(after! org
(setq org-capture-templates
@@ -657,7 +706,7 @@ Do not export headline with the =:ignore:= tag:
(setq org-html-wrap-src-lines nil)
;; Export with css class instead of inline css
- (setq org-html-htmlize-output-type 'css)
+ (setq org-html-htmlize-output-type 'nil)
)
#+end_src
@@ -959,18 +1008,18 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
#+begin_src emacs-lisp
(after! org
- (defun org/get-headline-string-element (headline backend info)
+ (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 org/ensure-latex-clearpage (headline backend info)
+ (defun tdh-ensure-latex-clearpage (headline backend info)
(when (org-export-derived-backend-p backend 'latex)
- (let ((elmnt (org/get-headline-string-element headline backend info)))
+ (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
- 'org/ensure-latex-clearpage)
+ 'tdh-ensure-latex-clearpage)
)
#+end_src
@@ -991,7 +1040,7 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
(after! org
;; Setup default option for image size when exporting to LaTeX
(setq org-latex-image-default-scale "")
- (setq org-latex-image-default-width "")
+ (setq org-latex-image-default-width "\\linewidth")
(setq org-latex-image-default-height "")
(setq org-latex-image-default-option "")
@@ -1004,6 +1053,9 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
;; 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"))
@@ -1092,24 +1144,12 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
(insert (format "\\page{%s}\n" page)))
#+end_src
-#+begin_src emacs-lisp :tangle no
- (defun org-latex-format-headline-default-function (todo _todo-type priority text tags _info)
- "Default format function for a headline.
- See `org-latex-format-headline-function' for details."
- (concat
- (and todo (format "{\\bfseries\\sffamily %s} " todo))
- (and priority (format "\\framebox{\\#%c} " priority))
- text
- (and tags
- (format "\\hfill{}\\textsc{%s}"
- (mapconcat #'org-latex--protect-text tags ":")))
- (and todo (format "{\n\\page{%s} " todo)))
-#+end_src
-
*** Number Equations
+https://kitchingroup.cheme.cmu.edu/blog/2016/11/07/Better-equation-numbering-in-LaTeX-fragments-in-org-mode/
+
#+begin_src emacs-lisp
(after! org
- (defun org-renumber-environment (orig-func &rest args)
+ (defun tdh-org-renumber-environment (orig-func &rest args)
"A function to inject numbers in LaTeX fragment previews."
(let ((results '())
(counter -1)
@@ -1150,7 +1190,7 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
(apply orig-func args))
- (advice-add 'org-create-formula-image :around #'org-renumber-environment)
+ (advice-add 'org-create-formula-image :around #'tdh-org-renumber-environment)
)
#+end_src
@@ -1173,15 +1213,15 @@ https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_f
(defun org-babel-execute:latex-macros (body _params)
(concat
- "\n#+HTML_HEAD_EXTRA: \\(\n"
- (prefix-all-lines "#+HTML_HEAD_EXTRA: " body)
- "\n#+HTML_HEAD_EXTRA: \\)
\n"))
+ "\n#+begin_export html\n \\(\n"
+ body
+ "\n\\)
\n#+end_export\n"))
)
#+end_src
-** TODO Org Projects
-#+begin_src emacs-lisp :tangle no
+** Org Projects
+#+begin_src emacs-lisp
(setq org-publish-project-alist
'(("config"
:base-directory "~/.config/literate-dotfiles/dotfiles/"
@@ -1239,7 +1279,7 @@ https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_f
#+end_src
** TODO Org big org-project
-#+begin_src emacs-lisp
+#+begin_src emacs-lisp :tangle no
(setq org-publish-project-alist
'(("website"
:components ("nass-simscape" "nass-simscape-images"))
@@ -1418,7 +1458,50 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
)
#+end_src
-** Custom Keybindings - =,= leader key
+** 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 |
+
+#+begin_src emacs-lisp
+ (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)
+ ))
+#+end_src
+
*** Insert Elements =,i=
Insert Link to paper
#+begin_src emacs-lisp
@@ -1494,12 +1577,17 @@ Take Screenshot and insert a link:
#+begin_src emacs-lisp
(defun tdh-insert-screenshot-org-link ()
- "Capture screenshot and insert the resulting file.
+ "Capture screenshot and insert the resulting file.
The screenshot tool is determined by `org-download-screenshot-method'."
(interactive)
- (setq filename (concat "./figs/" (read-string "Enter file name:") ".png"))
- (shell-command (concat "maim -s " filename))
- (insert (format "[[file:%s]]" filename))
+ (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)
)
#+end_src
@@ -1513,6 +1601,16 @@ Insert link to next figure:
)
#+end_src
+Insert link to previous figure:
+#+begin_src emacs-lisp
+ (defun tdh-insert-link-to-previous-figure ()
+ (interactive)
+ (save-excursion
+ (re-search-backward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
+ (insert (concat "[[" (match-string 1) "]]"))
+ )
+#+end_src
+
Map Keys
#+begin_src emacs-lisp
(after! org
@@ -1524,6 +1622,7 @@ Map Keys
: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)))
#+end_src
@@ -1581,7 +1680,7 @@ Map Keys
(:prefix (",r" . "References")
:n "b" 'helm-bibtex
:n "B" 'helm-bibtex-with-local-bibliography
- :n "f" 'helm-bibtex-favorites
+ :n "f" 'tdh-helm-bibtex-favorites
:n "r" 'helm-resume)))
#+end_src
@@ -1635,6 +1734,12 @@ Don't ask for confirmation when evaluating following blocs
(setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))
#+end_src
+Default header arguments.
+#+begin_src emacs-lisp
+ (after! org
+ (setq org-babel-default-header-args '((:eval . "no-export"))))
+#+end_src
+
Use the current window for C-c ' source editing
#+begin_src emacs-lisp
(after! org
@@ -1788,11 +1893,11 @@ when inside a source block. Otherwise, keep the normal behavior for =ctrl-ret=.
#+begin_src emacs-lisp
(defun tdh-ctrl-ret ()
(interactive)
- (defun in-src-block-p ()
+ (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 (in-src-block-p)
+ (if (tdh-in-src-block-p)
(progn
(org-babel-execute-src-block)
(org-babel-next-src-block))
@@ -1889,11 +1994,11 @@ This function:
#+begin_src emacs-lisp
(defun tdh-ctrl-shift-ret ()
(interactive)
- (defun in-src-block-p ()
+ (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 (in-src-block-p)
+ (if (tdh-in-src-block-p)
(let ((lang (nth 0 (org-babel-get-src-block-info))))
(if (string= lang "matlab")
(if (region-active-p)
@@ -1916,11 +2021,11 @@ This function:
#+begin_src emacs-lisp
(defun tdh-align-src-block ()
(interactive)
- (defun in-src-block-p ()
+ (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 (in-src-block-p)
+ (if (tdh-in-src-block-p)
(progn
(org-edit-special)
(evil-indent (point-min) (point-max))
@@ -1928,12 +2033,6 @@ This function:
(org-table-eval-formula)))
#+end_src
-#+begin_src emacs-lisp
- (map! :after evil-org
- :map evil-org-mode-map
- :n "C-c =" #'tdh-align-src-block)
-#+end_src
-
** Helping Functions - Tangling =,b=
Org-Babel Tangle Sub-tree
#+begin_src emacs-lisp
@@ -1999,8 +2098,8 @@ Nice Functions:
(setq org-ref-bibliography-notes "~/Cloud/brain")
;; Bibliography File
- (setq reftex-default-bibliography '("~/Cloud/brain/references.bib"))
- (setq org-ref-default-bibliography '("~/Cloud/brain/references.bib"))
+ (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")
@@ -2032,10 +2131,12 @@ Nice Functions:
".pdf"))))
t)
- (map!
- :map org-mode-map
- (:desc "Insert Link"
- :ni "C-c i" #'org-ref-insert-ref-link))
+ ;; 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))))
)
#+end_src
@@ -2099,16 +2200,32 @@ Nice Functions:
"%?"
:file-name "${slug}"
:head ,(concat "#+TITLE: ${title}\n"
- "#+SETUPFILE ./org-roam-setup-file.org\n"
+ "#+SETUPFILE: ./setup/org-setup-file.org\n"
+ "#+HUGO_SECTION: zettels\n"
"\n"
"- Tags ::\n"
- "\n")
+ "\n"
+ "* Bibliography :ignore:\n"
+ "bibliography:./biblio/references.bib"
+ )
+ :unnarrowed t)))
+ (setq org-roam-capture-ref-templates
+ `(("r" "ref" plain (function org-roam--capture-get-point)
+ "%?"
+ :file-name "${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)))
)
#+end_src
#+begin_src emacs-lisp
- (defun my/org-roam--backlinks-list (file)
+ (defun tdh-org-roam--backlinks-list (file)
(if (org-roam--org-roam-file-p file)
(--reduce-from
(concat acc (format "- [[file:%s][%s]]\n"
@@ -2117,23 +2234,24 @@ Nice Functions:
"" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
""))
- (defun my/org-export-preprocessor (backend)
- (let ((links (my/org-roam--backlinks-list (buffer-file-name))))
+ (defun tdh-org-export-preprocessor (backend)
+ (let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
(unless (string= links "")
(save-excursion
(goto-char (point-max))
(insert (concat "\n* Backlinks\n") links)))))
- (add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
+ (add-hook 'org-export-before-processing-hook 'tdh-org-export-preprocessor)
#+end_src
** Helm-Bibtex ([[https://github.com/tmalsburg/helm-bibtex][link]])
#+begin_src emacs-lisp
(use-package! helm-bibtex
+ :after-call helm-bibtex
:init
:config
;; Bibliography file
- (setq bibtex-completion-bibliography "~/Cloud/brain/references.bib")
+ (setq bibtex-completion-bibliography "~/Cloud/brain/biblio/references.bib")
;; Directory with all the pdfs
(setq bibtex-completion-library-path "~/Cloud/pdfs")
@@ -2160,32 +2278,57 @@ Nice Functions:
;; Template used when creating new Note file
(setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
- "#+NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
- "#+ROAM_KEY: cite:${=key=}\n"
+ "#+SETUPFILE: ./setup/org-setup-file.org\n"
+ "#+HUGO_SECTION: ${=type=}\n"
+ "#+ROAM_KEY: ${=key=}\n"
"\n"
- "- Author :: ${author}\n"
+ "- Tags ::\n"
+ "- Reference :: cite:${=key=}\n"
+ "- Author(s) :: ${author}\n"
"- Year :: ${year}\n"
- "- DOI :: ${DOI}\n"
- "\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" 'tdehaeze/open-pdf-externally helm-source-bibtex 1)
+ (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)
)
#+end_src
+#+begin_src emacs-lisp
+ (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-relative-name path) "][Notes]]"))
+ (message "No note file associated"))
+ )))
+#+end_src
+
Open pdf externally
#+begin_src emacs-lisp
- (defun tdehaeze/open-pdf-externally (key)
+ (defun tdh-open-pdf-externally (key)
(call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))
#+end_src
Special Commands
#+begin_src emacs-lisp
- (defun helm-bibtex-favorites (&optional arg)
+ (defun tdh-helm-bibtex-favorites (&optional arg)
"Search Favorite BibTeX entries"
(interactive "P")
(helm-bibtex arg nil "favorite "))
@@ -2213,33 +2356,82 @@ List all element of the bibliography without pdf associated
)
#+end_src
-** Org-Roam-Bibtex ([[https://github.com/Zaeph/org-roam-bibtex][link]])
+** Deft
#+begin_src emacs-lisp
- (use-package! org-roam-bibtex
- :load-path "~/.config/doom/packages/org-roam-bibtex/"
+ (use-package! deft
+ :custom
+ (deft-directory "~/Cloud/brain/"))
+#+end_src
+
+** Org-Roam-Bibtex ([[https://github.com/Zaeph/org-roam-bibtex][link]])
+Provides nice functions such as:
+- =orb-find-non-ref-file=
+- =orb-insert-non-ref=
+- =orb-note-action=
+
+#+begin_src emacs-lisp
+ (use-package! org-roam-bibtex
+ :hook (org-roam-mode . org-roam-bibtex-mode)
+ :config
+ (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))
+
+ (setq org-roam-bibtex-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/${=key=}.pdf\n"
+ ":END:\n"
+ "\n"
+ "* Bibliography :ignore:\n"
+ "bibliography:./biblio/references.bib"
+ )
+ :unnarrowed t)))
+
+ (setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
+ )
+#+end_src
+
+#+begin_src emacs-lisp
+ (defun tdh-open-bib-with-zathura (key)
+ "Open the pdf corresponding to the reference KEY with Zathura"
+ (if (listp key)
+ (setq key (car key)))
+ (call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))
+#+end_src
+
+** Org-Ref-Ox-Hugo ([[https://github.com/jethrokuan/org-ref-ox-hugo][link]])
+This package is used to correctly format the bibliography and links when exporting to hugo.
+
+#+begin_src emacs-lisp
+ (use-package! org-ref-ox-hugo
+ :load-path "~/.config/doom/packages/org-ref-ox-hugo/"
:config
- (org-roam-bibtex-mode)
- (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))
-
-
-
- (setq org-roam-bibtex-template
- `(("r" "ref" plain (function org-roam-capture--get-point) ""
- :file-name "${=key=}"
- :head ,(concat "#+TITLE: ${title}\n"
- "#+SETUPFILE ./org-notes-setup-file.org\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/${=key=}.pdf\n"
- ":END:\n")
- :unnarrowed t)))
+ (add-to-list 'org-ref-formatted-citation-formats
+ '("md"
+ ("article" . "${author}, *${title}*, ${journal}, *${volume}(${number})*, ${pages} (${year}). ${doi}")
+ ("inproceedings" . "${author}, *${title}*, In ${editor}, ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
+ ("book" . "${author}, *${title}* (${year}), ${address}: ${publisher}.")
+ ("phdthesis" . "${author}, *${title}* (${year}). ${school}.")
+ ("inbook" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
+ ("incollection" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
+ ("proceedings" . "${editor} (Eds.), _${booktitle}_ (${year}). ${address}: ${publisher}.")
+ ("unpublished" . "${author}, *${title}* (${year}). Unpublished manuscript.")
+ ("misc" . "${author} (${year}). *${title}*. Retrieved from [${howpublished}](${howpublished}). ${note}.")
+ (nil . "${author}, *${title}* (${year}).")))
+
+ (setq reference-link-class "reference-link")
+ (setq bibtex-entry-class "bibtex-entry")
)
#+end_src
@@ -2254,7 +2446,7 @@ List all element of the bibliography without pdf associated
** Clean Output Files
#+begin_src emacs-lisp
- (defun latex/clean ()
+ (defun tdh-latex-clean ()
"Clean LaTeX output using latexmk"
(interactive)
(async-shell-command
@@ -2265,7 +2457,7 @@ List all element of the bibliography without pdf associated
))
(map! :map LaTeX-mode-map
- :n ",C" 'latex/clean)
+ :n ",C" 'tdh-latex-clean)
(add-hook 'TeX-mode-hook #'TeX-fold-mode)
#+end_src
@@ -2338,34 +2530,34 @@ List all element of the bibliography without pdf associated
** Key Bindings
#+begin_src emacs-lisp
- (defun matlab-add-breakpoint ()
+ (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 matlab-remove-breakpoint ()
+ (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 matlab-list-breakpoints ()
+ (defun tdh-matlab-list-breakpoints ()
(interactive)
(matlab-shell-run-command (concat "dbstatus " (buffer-name))))
- (defun matlab-clear-breakpoints ()
+ (defun tdh-matlab-clear-breakpoints ()
(interactive)
(matlab-shell-run-command (concat "dbclear in " (buffer-name))))
- (defun matlab-go-to-file-directory ()
+ (defun tdh-matlab-go-to-file-directory ()
(interactive)
(matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))
#+end_src
#+begin_src emacs-lisp
(map! :map matlab-mode-map
- :n ",g" 'matlab-go-to-file-directory
- :n ",da" 'matlab-add-breakpoint
- :n ",dr" 'matlab-remove-breakpoint
- :n ",dL" 'matlab-list-breakpoints
- :n ",dc" 'matlab-clear-breakpoints
+ :n ",g" 'tdh-matlab-go-to-file-directory
+ :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
@@ -2397,7 +2589,7 @@ Send math and source code:
| =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.
+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.
#+begin_src emacs-lisp
(defun mu4e-message-maildir-matches (msg rx)
(when rx
@@ -2582,10 +2774,11 @@ Choose account label to feed msmtp -a option based on From header in Message buf
:ui
doom ; what makes DOOM look the way it does
+ deft
hl-todo ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
hydra
- modeline ; snazzy, Atom-inspired modeline, plus API
- nav-flash ; blink the current line after jumping
+ (modeline
+ +light) ; snazzy, Atom-inspired modeline, plus API
ophints ; highlight the region an operation acts on
(popup ; tame sudden yet inevitable temporary windows
+all ; catch all popups that start with an asterix
@@ -2593,7 +2786,6 @@ Choose account label to feed msmtp -a option based on From header in Message buf
unicode ; extended unicode support for various languages
vc-gutter ; vcs diff in the fringe
vi-tilde-fringe ; fringe tildes to mark beyond EOB
- window-select ; visually switch windows
workspaces ; tab emulation, persistence & separate workspaces
:editor
@@ -2606,7 +2798,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
:emacs
(dired +icons) ; making dired pretty [functional]
electric ; smarter, keyword-based electric-indent
- ibuffer ; interactive buffer management
+ (ibuffer +icons) ; interactive buffer management
vc ; version-control and Emacs, sitting in a tree
:term
@@ -2676,7 +2868,9 @@ Choose account label to feed msmtp -a option based on From header in Message buf
(package! matlab-mode
:recipe (:host github :repo "matlab-mode/mirror"))
(package! org-ref)
+ (package! org-roam-bibtex)
(package! org-ql)
(package! org-fancy-priorities)
+ (package! evil-escape :disable t)
+ (package! dired-narrow)
#+end_src
-
diff --git a/dotfiles/emacs-snippets.org b/dotfiles/emacs-snippets.org
index a68eee1..0e611fc 100644
--- a/dotfiles/emacs-snippets.org
+++ b/dotfiles/emacs-snippets.org
@@ -113,6 +113,14 @@ $0
\end{$1}
#+end_src
+** Caption
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/caption
+#contributor : Thomas Dehaeze
+#name :Caption
+# --
+#+caption: $0
+#+end_src
+
** Block
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/block
#contributor : Thomas Dehaeze
@@ -147,18 +155,6 @@ $0
$0
#+end_src
-** TODO Name Caption Figure
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/name-caption-figure
-#name: name-caption-figure
-#key: ncf
-# --
-#+name: fig:${1:name}
-#+caption: ${2:Caption}
-[[${3:`(read-file-name "File: ")`}]]
-
-$0
-#+end_src
-
** Bibliography with completion
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/bib
#name: bibliography with completion
@@ -177,7 +173,7 @@ cite:${1:$$(completing-read
(let ((bibtex-files (org-ref-find-bibliography)))(bibtex-global-key-alist)))}
#+end_src
-** TODO Ref
+** Ref
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/ref
#name: org-ref ref link with completion
#key: ref
@@ -229,8 +225,7 @@ $0
# --
#+name: fig:${1:figure_name}
#+caption: ${2:Figure caption}
-#+attr_latex: :${3:scale 1}
-[[file:${4:figs/}$1.${5:pdf}]]
+[[file:${3:figs/}$1.${4:pdf}]]
$0
#+end_src
@@ -250,128 +245,6 @@ $0
\left$1 $0 \right$2
#+end_src
-** Mconfig
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mconfig
-#contributor : Thomas Dehaeze
-#name :Matlab-Configuration-Header
-# --
-#+PROPERTY: header-args:matlab :session *MATLAB*
-#+PROPERTY: header-args:matlab+ :tangle ${1:filename}.m
-#+PROPERTY: header-args:matlab+ :comments org
-#+PROPERTY: header-args:matlab+ :exports both
-#+PROPERTY: header-args:matlab+ :results none
-#+PROPERTY: header-args:matlab+ :eval no-export
-#+PROPERTY: header-args:matlab+ :noweb yes
-#+PROPERTY: header-args:matlab+ :mkdirp yes
-#+PROPERTY: header-args:matlab+ :output-dir ${2:figs}
-$0
-#+end_src
-
-** Mdescription
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
-#contributor : Thomas Dehaeze
-#name :Measurement-Description
-# --
-,* Measurement description
-,** Setup :ignore:
-*Setup*:
-
-,** Goal :ignore:
-*Goal*:
-
-,** Measurements :ignore:
-*Measurements*:
-
-Three measurements are done:
-| Measurement File | Description |
-|-------------------------+------------------------------|
-| =mat/data_${1:001}.mat= | $2 |
-
-Each of the measurement =mat= file contains one =data= array with 3 columns:
-| Column number | Description |
-|---------------+-------------------|
-| 1 | $3 |
-| 2 | $4 |
-| 3 | Time |
-
-$0
-#+end_src
-
-** Mfigure
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
-#contributor : Thomas Dehaeze
-#name :Matlab-Figure
-# --
-,#+begin_src matlab :tangle no :exports results :results file replace
- exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}')
-,#+end_src
-
-,#+name: fig:$1
-,#+caption: $0
-,#+RESULTS:
-[[file:figs/$1.png]]
-#+end_src
-
-** Mfunction
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfunction
-#contributor : Thomas Dehaeze
-#name :Matlab-Function
-# --
-,* ${1:Function Name}
-:PROPERTIES:
-:header-args:matlab+: :tangle src/${2:matlab_file_name}.m
-:header-args:matlab+: :comments none :mkdirp yes :eval no
-:END:
-<>
-
-This Matlab function is accessible [[file:src/$2.m][here]].
-
-,#+begin_src matlab
- function [${4:in_data}] = $2(${3:in_data})
- % $2 - $0
- %
- % Syntax: [$4] = $2($3)
- %
- % Inputs:
- % - $3 -
- %
- % Outputs:
- % - $4 -
-
- end
-,#+end_src
-#+end_src
-
-** Mheader
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mheader
-#contributor : Thomas Dehaeze
-#name :Matlab-Header
-# --
-,* ${1:Heading Name}
-:PROPERTIES:
-:header-args:matlab+: :tangle matlab/${2:matlab_file_name}.m
-:header-args:matlab+: :comments org :mkdirp yes
-:END:
-<>
-
-,** ZIP file containing the data and matlab files :ignore:
-,#+begin_src bash :exports none :results none
- if [ matlab/$2.m -nt data/$2.zip ]; then
- cp matlab/$2.m $2.m;
- zip data/$2 \
- mat/data.mat \
- $2.m
- rm $2.m;
- fi
-,#+end_src
-
-,#+begin_note
- All the files (data and Matlab scripts) are accessible [[file:data/$2.zip][here]].
-,#+end_note
-
-$0
-#+end_src
-
** Minipage
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minipage
#contributor : Thomas Dehaeze
@@ -397,34 +270,6 @@ $0
#+END_EXPORT
#+end_src
-** Minit
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minit
-#contributor : Thomas Dehaeze
-#name :Matlab-Init
-# --
-,** Matlab Init :noexport:ignore:
-,#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
- <>
-,#+end_src
-
-,#+begin_src matlab :exports none :results silent :noweb yes
- <>
-,#+end_src
-
-$0
-#+end_src
-
-** Mtable
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mtable
-#contributor : Thomas Dehaeze
-#name :Matlab-Table
-# --
-,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
- data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
-,#+end_src
-$0
-#+end_src
-
** Multicolumn
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/multicolumn
#contributor : Thomas Dehaeze
@@ -532,7 +377,7 @@ $1
,#+begin_src emacs-lisp :tangle user-init.el
$1
,#+end_src
-#+end_src
+#+end_Sec
** Wrap
#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/wrap
@@ -542,3 +387,154 @@ $1
#+attr_latex: :float wrap
$0
#+end_src
+
+** Matlab Specific
+*** Mconfig
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mconfig
+#contributor : Thomas Dehaeze
+#name :Matlab-Configuration-Header
+# --
+#+PROPERTY: header-args:matlab :session *MATLAB*
+#+PROPERTY: header-args:matlab+ :tangle ${1:filename}.m
+#+PROPERTY: header-args:matlab+ :comments org
+#+PROPERTY: header-args:matlab+ :exports both
+#+PROPERTY: header-args:matlab+ :results none
+#+PROPERTY: header-args:matlab+ :eval no-export
+#+PROPERTY: header-args:matlab+ :noweb yes
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+#+PROPERTY: header-args:matlab+ :output-dir ${2:figs}
+$0
+#+end_src
+
+*** Mdescription
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
+#contributor : Thomas Dehaeze
+#name :Measurement-Description
+# --
+,* Measurement description
+,** Setup :ignore:
+*Setup*:
+
+,** Goal :ignore:
+*Goal*:
+
+,** Measurements :ignore:
+*Measurements*:
+
+Three measurements are done:
+| Measurement File | Description |
+|-------------------------+------------------------------|
+| =mat/data_${1:001}.mat= | $2 |
+
+Each of the measurement =mat= file contains one =data= array with 3 columns:
+| Column number | Description |
+|---------------+-------------------|
+| 1 | $3 |
+| 2 | $4 |
+| 3 | Time |
+
+$0
+#+end_src
+
+*** Mfigure
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
+#contributor : Thomas Dehaeze
+#name :Matlab-Figure
+# --
+,#+begin_src matlab :tangle no :exports results :results file replace
+ exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}');
+,#+end_src
+
+,#+name: fig:$1
+,#+caption: $0
+,#+RESULTS:
+[[file:figs/$1.png]]
+#+end_src
+
+*** Mfunction
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfunction
+#contributor : Thomas Dehaeze
+#name :Matlab-Function
+# --
+,* ${1:Function Name}
+:PROPERTIES:
+:header-args:matlab+: :tangle src/${2:matlab_file_name}.m
+:header-args:matlab+: :comments none :mkdirp yes :eval no
+:END:
+<>
+
+This Matlab function is accessible [[file:src/$2.m][here]].
+
+,#+begin_src matlab
+ function [${4:in_data}] = $2(${3:in_data})
+ % $2 - $0
+ %
+ % Syntax: [$4] = $2($3)
+ %
+ % Inputs:
+ % - $3 -
+ %
+ % Outputs:
+ % - $4 -
+
+ end
+,#+end_src
+#+end_src
+
+*** Mheader
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mheader
+#contributor : Thomas Dehaeze
+#name :Matlab-Header
+# --
+,* ${1:Heading Name}
+:PROPERTIES:
+:header-args:matlab+: :tangle matlab/${2:matlab_file_name}.m
+:header-args:matlab+: :comments org :mkdirp yes
+:END:
+<>
+
+,** ZIP file containing the data and matlab files :ignore:
+,#+begin_src bash :exports none :results none
+ if [ matlab/$2.m -nt data/$2.zip ]; then
+ cp matlab/$2.m $2.m;
+ zip data/$2 \
+ mat/data.mat \
+ $2.m
+ rm $2.m;
+ fi
+,#+end_src
+
+,#+begin_note
+ All the files (data and Matlab scripts) are accessible [[file:data/$2.zip][here]].
+,#+end_note
+
+$0
+#+end_src
+
+*** Minit
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minit
+#contributor : Thomas Dehaeze
+#name :Matlab-Init
+# --
+,** Matlab Init :noexport:ignore:
+,#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
+ <>
+,#+end_src
+
+,#+begin_src matlab :exports none :results silent :noweb yes
+ <>
+,#+end_src
+
+$0
+#+end_src
+
+*** Mtable
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mtable
+#contributor : Thomas Dehaeze
+#name :Matlab-Table
+# --
+,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
+ data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
+,#+end_src
+$0
+#+end_src