[Emacs] Better org-mode config, add org-ref

Better exporters, better support of org-babel

Exporters added:
- ox-ssh
- ox-epub
- ox-gfm

Better HTML and LaTeX export

org live HTML preview

Add org-ref

org/config/emacs.org

@@ -2782,34 +2782,13 @@ extended however we like!
                    :type built-in)
     :defer t
     :commands (orgtbl-mode)
-    :hook (org-mode . visual-line-mode)
+    :hook ((org-mode . visual-line-mode)
-    :hook (org-mode . org-num-mode)
+           (org-mode . org-num-mode))
     :init
     (auto-fill-mode -1)
     :config
     <<org-hydra-babel>>
-    :general
+    (require 'ox-beamer)
-    (:states 'normal
-     :keymaps 'org-mode-map
-     "RET" 'org-open-at-point)
-    (:states 'normal
-     :prefix ","
-     :keymaps 'org-mode-map
-     <<general-keybindings-gen(table=org-keybinds-various)>>
-     <<general-keybindings-gen(table=org-keybinds-babel)>>
-     <<general-keybindings-gen(table=org-keybinds-dates)>>
-     <<general-keybindings-gen(table=org-keybinds-insert)>>
-     <<general-keybindings-gen(table=org-keybinds-jump)>>
-     <<general-keybindings-gen(table=org-keybinds-tables)>>
-     <<general-keybindings-gen(table=org-keybinds-toggles)>>)
-
-    (:states 'normal
-     :keymaps 'org-src-mode-map
-     :prefix ","
-     "'" #'org-edit-src-exit
-     "k" #'org-edit-src-abort))
-
-  (after! org
     (setq org-hide-leading-stars             nil
             org-hide-macro-markers             t
             org-ellipsis                       " ⤵"
@@ -2834,6 +2813,7 @@ extended however we like!
             org-default-notes-file             (expand-file-name "notes.org" org-directory))
     <<org-agenda-files>>
     <<org-behavior-electric>>
+    <<org-babel-load-languages>>
     <<org-use-sub-superscripts>>
     <<org-latex-compiler>>
     <<org-latex-listings>>
@@ -2843,7 +2823,27 @@ extended however we like!
     <<org-re-reveal-root>>
     <<org-html-validation>>
     <<org-latex-classes>>
-      <<org-publish-projects>>)
+    <<org-publish-projects>>
+    :general
+    (:states 'normal
+     :keymaps 'org-mode-map
+     "RET" 'org-open-at-point)
+    (:states 'normal
+     :prefix ","
+     :keymaps 'org-mode-map
+     <<general-keybindings-gen(table=org-keybinds-various)>>
+     <<general-keybindings-gen(table=org-keybinds-babel)>>
+     <<general-keybindings-gen(table=org-keybinds-dates)>>
+     <<general-keybindings-gen(table=org-keybinds-insert)>>
+     <<general-keybindings-gen(table=org-keybinds-jump)>>
+     <<general-keybindings-gen(table=org-keybinds-tables)>>
+     <<general-keybindings-gen(table=org-keybinds-toggles)>>)
+
+    (:states 'normal
+     :keymaps 'org-src-mode-map
+     :prefix ","
+     "'" #'org-edit-src-exit
+     "k" #'org-edit-src-abort))
 #+end_src
 
 The main feature from ~evil-org~ that I love is how easy it is to modify
@@ -2959,10 +2959,67 @@ to easily convert a LaTeX snippet into a PNG, regardless of the
 exporter I use afterwards. Its installation is pretty simple:
 #+begin_src emacs-lisp
   (use-package ob-latex-as-png
-    :defer t
+    :straight (:build t)
-    :straight (:build t))
+    :defer t)
 #+end_src
 
+#+begin_src emacs-lisp
+  (use-package ob-restclient
+    :straight (:build t)
+    :defer t)
+#+end_src
+
+One of the amazing features of org-mode is its literary programming capacities
+by running code blocks from within Org-mode itself. But for that, only a couple
+of languages are supported directly by Org-mode itself, and they need to be
+activated. Here are the languages I activated in my Org-mode configuration:
+#+NAME: org-babel-languages-table
+| C          |
+| dot        |
+| emacs-lisp |
+| gnuplot    |
+| latex      |
+| makefile   |
+| plantuml   |
+| python     |
+| sass       |
+| shell      |
+
+#+NAME: org-babel-languages-gen
+#+header: :cache yes :results replace
+#+header: :var languages=org-babel-languages-table[,0]
+#+BEGIN_SRC emacs-lisp :exports none
+  (format "'(%s)"
+          (mapconcat (lambda ($language)
+                       (format "(%s . t)" $language))
+                     languages
+                     "\n  "))
+#+END_SRC
+
+#+RESULTS[52f5db378c4060c5ce47e6228e95feefba4fe24d]: org-babel-languages-gen
+#+begin_example
+'((C . t)
+  (dot . t)
+  (emacs-lisp . t)
+  (gnuplot . t)
+  (latex . t)
+  (latex-as-png . t)
+  (makefile . t)
+  (plantuml . t)
+  (python . t)
+  (restclient . t)
+  (sass . t)
+  (shell . t))
+#+end_example
+
+The corresponding code is as follows:
+#+NAME: org-babel-load-languages
+#+BEGIN_SRC emacs-lisp :noweb yes :tangle no
+  (org-babel-do-load-languages
+   'org-babel-load-languages
+   <<org-babel-languages-gen()>>)
+#+END_SRC
+
 *** File export
 :PROPERTIES:
 :CUSTOM_ID: Packages-Configuration-Org-mode-File-exportik95fl6184j0
@@ -2977,38 +3034,64 @@ describing phonetics evolution. So, let’s disable it:
   (setq org-use-sub-superscripts (quote {}))
 #+END_SRC
 
-#+begin_src emacs-lisp
-  (use-package htmlize
-    :defer t)
-#+end_src
 
-There’s not really any unified Markdown specification, meaning
+**** Epub
-everyone can pretty much do whatever they want with the syntax and
+:PROPERTIES:
-still call it Markdown. Great… But something I appreciate is Github
+:CUSTOM_ID: Packages-Configuration-Org-mode-File-export-Epub-w5ycfuz095j0
-supports some extra HTML to make our files extra spicy! And lucky me,
+:END:
-there’s a package for exporting my org files to Github-flavored
+A backend for exporting files through org I like is ~ox-epub~ which, as
-Markdown!
+you can guess, exports org files to the [[https://www.w3.org/publishing/epub32/][Epub format]].
-#+begin_src emacs-lisp
-  (use-package ox-gfm
-    :after ox
-    :straight (:build t))
-#+end_src
-
-Another backend for exporting files through org I like is ~ox-epub~
-which, as you can guess, exports org files to the [[https://www.w3.org/publishing/epub32/][Epub format]].
 #+begin_src emacs-lisp
   (use-package ox-epub
     :after ox
     :straight (:build t))
 #+end_src
 
-Yet another exporter I enjoy is [[https://github.com/dantecatalfamo/ox-ssh][~ox-ssh~]] with which I manage my
+**** HTML
-~$HOME/.ssh/config~ file. You won’t find my org file for managing my
+:PROPERTIES:
-servers on my repos though.
+:CUSTOM_ID: Packages-Configuration-Org-mode-File-export-HTMLxjc5fl6184j0
+:END:
+For Reveal.JS exports, I need to set where to find the framework by
+default:
+#+NAME: org-re-reveal-root
+#+BEGIN_SRC emacs-lisp
+  (setq org-re-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js")
+#+END_SRC
+
+On HTML exports, Org-mode tries to include a validation link for the
+exported HTML. Let’s disable that since I never use it.
+#+NAME: org-html-validation
+#+BEGIN_SRC emacs-lisp
+  (setq org-html-validation-link nil)
+#+END_SRC
+
 #+begin_src emacs-lisp
-  (use-package ox-ssh
+  (use-package htmlize
-    :after ox
+    :defer t)
-    :straight (:build t))
+#+end_src
+
+This package allows for live-previewing the HTML export of an org
+buffer in an XWidget Webkit browser window. But when testing it, it’s
+not great for large org files, I should keep its usage for smaller org
+files.
+#+begin_src emacs-lisp
+  (use-package preview-org-html-mode
+    :defer t
+    :after org
+    :straight (preview-org-html-mode :build t
+                                     :type git
+                                     :host github
+                                     :repo "jakebox/preview-org-html-mode")
+    :general
+    (:keymaps '(org-mode-map)
+     :states 'normal
+     :prefix ","
+     "P"  '(:ignore :which-key "preview")
+     "Ph" #'preview-org-html-mode
+     "Pr" #'preview-org-html-refresh
+     "Pp" #'preview-org-html-pop-window-to-frame)
+    :config
+    (setq preview-org-html-refresh-configuration 'save))
 #+end_src
 
 **** LaTeX
@@ -3032,30 +3115,44 @@ syntax highlights:
 
 The default packages break my LaTeX exports: for some reasons, images
 are not loaded and exported in PDFs, so I needed to redifine the
-default packages excluding the one that broke my exports. I also added
+default packages excluding the one that broke my exports; namely, I
-a default package, ~minted~ for syntax highlighting.
+need to remove ~inputenc~, ~fontenc~ and ~grffile~. I also added some default
+packages:
+- ~minted~ for syntax highlighting
+- ~cleveref~ for better references to various elements.
+- ~svg~ for inserting SVG files in PDF outputs
+- ~booktabs~ for nicer tables
+- and ~tabularx~ for tabulars with adjustable columns
 #+NAME: org-latex-default-packages
 #+BEGIN_SRC emacs-lisp
-  (setq org-latex-default-packages-alist '((""         "graphicx"  t)
+  (dolist (package '(("AUTO" "inputenc" t ("pdflatex"))
-                                           ("T1"       "fontspec"  t ("pdflatex"))
+                     ("T1"   "fontenc"  t ("pdflatex"))
-                                           (""         "longtable" nil)
+                     (""     "grffile"  t)))
-                                           (""         "wrapfig"   nil)
+    (delete package org-latex-default-packages-alist))
-                                           (""         "rotating"  nil)
+
-                                           ("normalem" "ulem"      t)
+  (dolist (package '((""           "minted")
-                                           (""         "amsmath"   t)
+                     ("capitalize" "cleveref")
-                                           (""         "textcomp"  t)
+                     (""           "svg")
-                                           (""         "amssymb"   t)
+                     (""           "booktabs")
-                                           (""         "capt-of"   nil)
+                     (""           "tabularx")))
-                                           (""         "minted"    nil)
+    (add-to-list 'org-latex-default-packages-alist package t))
-                                           (""         "hyperref"  nil)))
+
+  (setq org-latex-reference-command "\\cref{%s}")
 #+END_SRC
 
-By the way, reference links in LaTeX should be written in this format:
+By the way, reference links in LaTeX should be written in this format,
+since we are using ~cleveref~:
 #+NAME: org-export-latex-hyperref-format
 #+BEGIN_SRC emacs-lisp
   (setq org-export-latex-hyperref-format "\\ref{%s}")
 #+END_SRC
 
+And Minted should be default break lines if a line is too long:
+#+name: org-export-latex-minted-options
+#+begin_src emacs-lisp
+  (setq org-latex-minted-options '(("breaklines") ("tabsize" "2")))
+#+end_src
+
 When it comes to the export itself, the latex file needs to be
 processed several times through XeLaTeX in order to get some
 references right. Don’t forget to also run bibtex!
@@ -3076,23 +3173,34 @@ add their extension like so:
     (add-to-list 'org-latex-logfiles-extensions ext t))
 #+end_src
 
-**** HTML
+**** Markdown
 :PROPERTIES:
-:CUSTOM_ID: Packages-Configuration-Org-mode-File-export-HTMLxjc5fl6184j0
+:CUSTOM_ID: Packages-Configuration-Org-mode-File-export-Markdown-g2vh5vz095j0
 :END:
-For Reveal.JS exports, I need to set where to find the framework by
+There’s not really any unified Markdown specification, meaning
-default:
+everyone can pretty much do whatever they want with the syntax and
-#+NAME: org-re-reveal-root
+still call it Markdown. Great… But something I appreciate is Github
-#+BEGIN_SRC emacs-lisp
+supports some extra HTML to make our files extra spicy! And lucky me,
-  (setq org-re-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js")
+there’s a package for exporting my org files to Github-flavored
-#+END_SRC
+Markdown!
+#+begin_src emacs-lisp
+  (use-package ox-gfm
+    :after ox
+    :straight (:build t))
+#+end_src
 
-On HTML exports, Org-mode tries to include a validation link for the
+**** SSH Config
-exported HTML. Let’s disable that since I never use it.
+:PROPERTIES:
-#+NAME: org-html-validation
+:CUSTOM_ID: Packages-Configuration-Org-mode-File-export-SSH-Config-tatextz095j0
-#+BEGIN_SRC emacs-lisp
+:END:
-  (setq org-html-validation-link nil)
+Yet another exporter I enjoy is [[https://github.com/dantecatalfamo/ox-ssh][~ox-ssh~]] with which I manage my
-#+END_SRC
+~$HOME/.ssh/config~ file. You won’t find my org file for managing my
+servers on my repos though.
+#+begin_src emacs-lisp
+  (use-package ox-ssh
+    :after ox
+    :straight (:build t))
+#+end_src
 
 *** Keybindings
 :PROPERTIES:
@@ -3448,6 +3556,90 @@ The project is then defined like so:
                 "langue-phundrak-com-pdf"))
 #+END_SRC
 
+*** Org-ref and Bibtex configuration
+:PROPERTIES:
+:CUSTOM_ID: Packages-Configuration-Org-mode-org-ref-1h586cd085j0
+:END:
+#+begin_src emacs-lisp
+  (use-package reftex
+    :commands turn-on-reftex
+    :init (setq reftex-default-bibliography "~/org/bibliography/references.bib"
+                reftex-plug-into-AUCTeX     t))
+#+end_src
+
+#+begin_src emacs-lisp
+  (use-package org-ref
+    :straight (:build t)
+    :after (org ox-bibtex)
+    :demand t
+    :custom-face
+    (org-ref-cite-face ((t (:weight bold))))
+    :init
+    (setq org-ref-completion-library    'org-ref-ivy-cite
+          org-ref-bibliography-notes    "~/org/bibliography/notes.org"
+          org-ref-default-bibliography  "~/org/bibliography/references.bib"
+          org-ref-pdf-directory         "~/org/bibliography/bibtex-pdfs/"
+          org-latex-logfiles-extensions '("lof" "lot" "aux" "idx" "out" "log" "fbd_latexmk"
+                                          "toc" "nav" "snm" "vrb" "dvi" "blg" "brf" "bflsb"
+                                          "entoc" "ps" "spl" "bbl" "pygtex" "pygstyle"))
+    (add-hook 'org-mode-hook (lambda () (require 'org-ref)))
+    :config
+    (setq bibtex-completion-pdf-field "file")
+    (general-define-key
+     :keymaps '(bibtex-mode-map)
+     :states 'normal
+     "C-t" #'org-ref-bibtex-next-entry
+     "C-s" #'org-ref-bibtex-previous-entry
+     "gt"  #'org-ref-bibtex-next-entry
+     "gs"  #'org-ref-bibtex-previous-entry)
+    (general-define-key
+     :keymaps '(bibtex-mode-map)
+     :states 'normal
+     :prefix ","
+     ;; Navigation
+     "t" #'org-ref-bibtex-next-entry
+     "s" #'org-ref-bibtex-previous-entry
+
+     ;; Open
+     "b" #'org-ref-open-in-browser
+     "n" #'org-ref-open-bibtex-notes
+     "p" #'org-ref-open-bibtex-pdf
+
+     ;; Misc
+     "h" #'org-ref-bibtex-hydra/body
+     "i" #'org-ref-bibtex-hydra/org-ref-bibtex-new-entry/body-and-exit
+     "s" #'org-ref-sort-bibtex-entry
+
+     "l" '(:ignore :which-key "lookup")
+     "la" #'arxiv-add-bibtex-entry
+     "lA" #'arxiv-get-pdf-add-bibtex-entry
+     "ld" #'doi-utils-add-bibtex-entry-from-doi
+     "li" #'isbn-to-bibtex
+     "lp" #'pubmed-insert-bibtex-from-pmid)
+    (general-define-key
+     :keymaps '(org-mode-map)
+     :states 'normal
+     :prefix ","
+     "ic" #'org-ref-insert-link))
+#+end_src
+
+#+begin_src emacs-lisp
+  (use-package ivy-bibtex
+    :defer t
+    :straight (:build t)
+    :config
+    (setq org-ref-bibliography-notes   "~/org/bibliography/notes.org"
+          org-ref-default-bibliography "~/org/bibliography/references.bib"
+          org-ref-pdf-directory        "~/org/bibliography/bibtex-pdfs/"
+          bibtex-completion-pdf-open-function #'find-file)
+
+    (general-define-key
+       :keymaps '(bibtex-mode-map)
+       :states 'normal
+       :prefix "SPC"
+       "m" #'ivy-bibtex))
+#+end_src
+
 *** Visual Configuration
 :PROPERTIES:
 :CUSTOM_ID: Packages-Configuration-Org-mode-Visual-Configurationrol5fl6184j0