configuration orgs

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+* General configuration
+  #+BEGIN_SRC emacs-lisp
+    (use-package org
+      :ensure t
+      :init
+      (setq org-catch-invisible-edits 'smart
+            org-complete-tags-always-offer-all-agenda-tags t
+            org-completion-use-ido nil
+            org-cycle-separator-lines 0 ;; no blank lines when all colapsed
+            org-deadline-warning-days 14
+            org-directory jao-notes-dir
+            org-default-notes-file (expand-file-name "inbox.org" org-directory)
+            org-ellipsis " .." ;; ↴
+            org-email-link-description-format "Email %c: %s"
+            org-enforce-todo-dependencies t
+            org-extend-today-until 0
+            org-fast-tag-selection-single-key 'expert
+            org-hide-emphasis-markers t
+            org-hide-leading-stars t
+            ;; org-list-demote-modify-bullet '(("+" . "-") ("-" . "+") ("*" . "+"))
+            org-link-frame-setup
+            '((gnus . (lambda (&optional x) (jao-open-gnus-frame)))
+              (file . find-file-other-window))
+            org-log-done nil
+            org-modules '(bbdb bibtex gnus info w3m)
+            org-odd-levels-only t
+            org-outline-path-complete-in-steps nil
+            org-refile-allow-creating-parent-nodes 'confirm
+            org-refile-targets '((nil :maxlevel . 5)
+                                 (org-agenda-files :maxlevel . 5))
+            org-refile-use-outline-path 'file
+            org-return-follows-link t
+            org-reverse-note-order t
+            org-special-ctrl-a/e t
+            org-src-fontify-natively t
+            org-startup-folded t
+            org-tag-alist nil
+            org-tags-column -75
+            org-todo-keywords
+            '((sequence "TODO(t)" "STARTED(s!)" "|" "DONE(d!)")
+              (sequence "REPLY(r)" "WAITING(w!)" "|" "DONE(d!)")
+              (sequence "TOREAD(T)" "READING(R!)" "|" "READ(a!)")
+              (sequence "|" "CANCELLED(x!)" "SOMEDAY(o!)" "DONE(d!)"))
+            org-use-fast-todo-selection t
+            org-use-speed-commands t
+            org-gnus-prefer-web-links nil))
+    (require 'org)
+  #+END_SRC
+* Agenda
+  #+begin_src emacs-lisp
+    (setq org-agenda-custom-commands
+          '(("w" todo "WAITING" nil)
+            ("W" agenda "" ((org-agenda-ndays 21))))
+          org-agenda-files (list jao-notes-dir)
+          org-agenda-include-diary t
+          org-agenda-include-inactive-timestamps t
+          org-agenda-inhibit-startup nil
+          org-agenda-restore-windows-after-quit t
+          org-agenda-show-all-dates t
+          org-agenda-skip-deadline-if-done t
+          org-agenda-skip-scheduled-if-done nil
+          org-agenda-span 7
+          org-agenda-start-on-weekday nil
+          org-agenda-window-setup 'current-window)
+  #+end_src
+* Capture templates
+  #+BEGIN_SRC emacs-lisp
+    (setq  org-capture-templates
+           '(("t" "TODO" entry
+              (file+headline "inbox.org" "Todo")
+              "* TODO %?\n  %i%a" :prepend t)
+             ("r" "REPLY" entry
+              (file+headline "inbox.org" "Todo")
+              "* REPLY %:subject%?\n  %t\n %i%a" :prepend t)
+             ("a" "Appointment" entry
+              (file+olp "inbox.org" "Appointments")
+              "* %^T %?\n  %a" :time-prompt t)
+             ("w" "Wintermute TODO" entry
+              (file+olp "bigml.org" "Wintermute" "Tasks")
+              "* TODO %?\n  %i%a" :prepend t)
+             ("i" "Inbox note" entry (file+headline "inbox.org" "Notes")
+              "* %a\n  %i%?(added on: %u)" :prepend t)
+             ("x" "Clipboard" entry (file+headline "inbox.org" "Notes")
+              "* %?\n  %a\n  %x\n (added: %u)" :prepend t)))
+    ;; (org-capture-upgrade-templates org-capture-templates)
+  #+END_SRC
+* MIME and file apps
+  #+BEGIN_SRC emacs-lisp
+    (setq org-file-apps
+          '((system . mailcap)
+            (".*\\.djvu" . system)
+            (t . emacs)))
+  #+END_SRC
+* Calendar
+  #+BEGIN_SRC emacs-lisp
+    (setq gnus-icalendar-org-capture-file
+          (expand-file-name "inbox.org" org-directory)
+          gnus-icalendar-org-capture-headline '("Appointments"))
+    (eval-after-load "gnus"
+     '(progn (require 'org-agenda)
+             (require 'gnus-icalendar)
+             (gnus-icalendar-org-setup)))
+  #+END_SRC
+* LaTeX
+  #+begin_src emacs-lisp
+    (use-package org-fragtog
+      :after org
+      :ensure t
+      :hook ((org-mode . org-fragtog-mode)))
+
+    (require 'org-fragtog)
+
+    (setq org-format-latex-options
+          `(:foreground default
+                        :background
+                        ,(if (jao-colors-scheme-dark-p) "black" "white")
+                        :scale 1.25
+                        :html-foreground "black"
+                        :html-background "Transparent"
+                        :html-scale 1.0
+                        :matchers ("begin" "$1" "$" "$$" "\\(" "\\["))
+          org-preview-latex-image-directory
+          (expand-file-name "~/.emacs.d/cache/ltximg/")
+          org-latex-hyperref-template nil
+          org-highlight-latex-and-related '(latex script entities))
+
+    (require 'ox-latex)
+    (add-to-list 'org-latex-classes
+                 '("bmlarticle"
+                   "\\documentclass{bmlarticle}\n[NO-DEFAULT-PACKAGES]\n[EXTRA]"
+                   ("\\section{%s}" . "\\section*{%s}")
+                   ("\\subsection{%s}" . "\\subsection*{%s}")
+                   ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                   ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                   ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+    (use-package cdlatex
+      :ensure t
+      :hook ((org-mode . org-cdlatex-mode))
+      :diminish ((cdlatex-mode . " £")
+                 (org-cdlatex-mode . " £")))
+
+  #+end_src
+
+* Export (minted)
+
+  #+begin_src emacs-lisp
+    (setq org-latex-listings 'minted
+          org-latex-packages-alist '(("" "minted"))
+          org-latex-pdf-process
+          '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+            "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))
+  #+end_src
+
+* Babel
+  - [[http://cachestocaches.com/2018/6/org-literate-programming][Literate Programming with Org-mode]]
+  - [[http://howardism.org/Technical/Emacs/literate-devops.html][Literate DevOps]]
+
+  #+begin_src emacs-lisp
+    (setq org-src-window-setup 'other-window) ;; current-window
+    (require 'org-tempo nil t) ;; <s TAB for 9.2 and later
+
+    ;; (use-package ob-elixir
+    ;;   :ensure t
+    ;;   :after org)
+
+    (use-package ob-prolog
+      :ensure t
+      :after org)
+
+    (org-babel-do-load-languages
+     'org-babel-load-languages
+     '((calc . t)
+       (clojure . t)
+       ;; (elixir . t)
+       (emacs-lisp .t)
+       (gnuplot .t)
+       (haskell . t)
+       (makefile . t)
+       (ocaml . t)
+       (org . t)
+       (python . t)
+       (scheme .t)
+       (shell . t)
+       (prolog . t)))
+  #+end_src
+
+* Org cliplink (link from clipboard)
+  [[https://github.com/rexim/org-cliplink][GitHub - rexim/org-cliplink: Insert org-mode links from clipboard]]
+
+  #+BEGIN_SRC emacs-lisp
+    (use-package org-cliplink
+      :ensure t
+      :bind (:map org-mode-map ("C-c C-f" . org-cliplink))
+      :config
+      (add-to-list 'org-capture-templates
+                   '("k" "Cliplink capture task" entry
+                     (file+headline "inbox.org" "Todo")
+                     "* TODO %(org-cliplink-capture) %?" :prepend t)
+                   t))
+  #+END_SRC
+
+* Org download
+
+  #+begin_src emacs-lisp
+    (use-package org-download
+      :ensure t
+      :after org
+      :init (setq org-download-screenshot-method "import %s")
+      :bind
+      (:map org-mode-map
+            (("C-c S" . org-download-screenshot)
+             ("C-c I" . org-download-yank))))
+  #+end_src
+
+* Org roam
+  #+begin_src emacs-lisp
+    (use-package org-roam
+      :ensure t
+      :init
+      (defun jao-roam--slug (slug) (replace-regexp-in-string "_" "-" slug))
+
+      (defun jao-roam--cat ()
+        (let* ((cats (seq-difference (directory-files org-roam-directory)
+                                     '("." ".." "attic")))
+               (cat (completing-read "Top level cat: " cats)))
+          (cond ((file-exists-p (expand-file-name cat org-roam-directory)) cat)
+                ((yes-or-no-p "New category, create?") cat)
+                (t (jao-roam--cat)))))
+
+      (setq org-roam-capture-templates
+            `(("d" "default" plain #'org-roam-capture--get-point
+               "%a %i"
+               :file-name "%(jao-roam--cat)/%(jao-roam--slug \"${slug}\")"
+               :head ,(concat "#+title: ${title}"
+                              "\n#+created: %T"
+                              "\n#+roam_tags: %?"
+                              "\n#+roam_ref: %:url\n\n"))))
+
+      :custom ((org-roam-directory (expand-file-name "~/org/notes"))
+               (org-roam-encrypt-files nil)
+               (org-roam-buffer-position nil)
+               (org-roam-buffer-height nil)
+               (org-roam-buffer-window-parameters nil)
+               (org-roam-link-use-custom-faces t)
+               (org-roam-link-auto-replace t)
+               (org-roam-tag-sources '(prop vanilla all-directories))
+               (org-roam-file-exclude-regexp ".+/code\\|attic/.*"))
+
+      :config
+      (defvar org-roam-consult-flags
+        '("--null" "--ignore-case" "--type=org" "--line-buffered"
+          "--color=always" "--max-columns=250" "--no-heading" "--line-number"))
+
+      (defun consult-org-roam ()
+        "Search org-roam directory using consult-ripgrep. With live-preview."
+        (interactive)
+        (let ((consult-ripgrep-command
+               (format "rg %s . -e ARG OPTS"
+                       (mapconcat 'identity org-roam-consult-flags " "))))
+          (consult-ripgrep org-roam-directory)))
+
+      (major-mode-hydra-define+ org-mode ()
+        ("Roam"
+         (("i" org-roam-insert "insert")
+          ("f" org-roam-find-file "find-file")
+          ("o" consult-org-roam "consult")
+          ("v" org-roam-buffer-toggle-display "toggle backlinks"))))
+
+      (jao-define-attached-buffer (regexp-quote org-roam-buffer) 0.33)
+
+      :hook ((after-init . org-roam-mode))
+      :bind (("C-c n" . org-roam-capture)
+             ("C-c N" . org-roam-find-file))
+      :diminish)
+  #+end_src
+* Links
+  #+begin_src emacs-lisp
+    (require 'org-gnus nil t)
+    (require 'ol-gnus nil t)
+    (require 'ol-w3m nil t)
+    (require 'ol-eshell nil t)
+    (require 'ol-bbdb nil t)
+    (require 'ol-docview nil t)
+    (require 'ol-info nil t)
+
+    (setq org-link-abbrev-alist
+          '(("jao.io" "https://jao.io/")))
+  #+end_src
+* jao-org
+  #+begin_src emacs-lisp
+    (use-package jao-org-utils)
+
+    (use-package jao-org-links
+      :commands jao-org-links-setup
+      :bind (("C-c T" . jao-org-insert-doc)))
+
+    (jao-org-utils-setup)
+    (jao-org-utils-eldoc-setup)
+    (jao-org-links-setup jao-sink-dir)
+
+    (with-eval-after-load "pdf-view"
+      (define-key pdf-view-mode-map (kbd "C-c o") #'jao-org-pdf-goto-org)
+      (define-key pdf-view-mode-map (kbd "C-c O") #'jao-org-pdf-goto-org*))
+  #+end_src
+* Geiser and org
+  #+begin_src emacs-lisp
+    (defun jao-org--set-geiser-impl () (setq-local geiser-repl--impl 'guile))
+    (add-hook 'org-mode-hook #'jao-org--set-geiser-impl)
+  #+end_src
+* Keybindings
+    #+begin_src emacs-lisp
+      (define-key mode-specific-map [?a] 'org-agenda)
+      (define-key org-mode-map "\C-cv" 'jao-org-copy-link-at-point)
+      (define-key org-mode-map [(control ?c) tab] 'org-force-cycle-archived)
+      (define-key org-mode-map [(f7)] 'org-archive-to-archive-sibling)
+      (define-key org-mode-map "\C-cW" 'jao-insert-w3m-link)
+      (define-key org-mode-map "\C-c'" 'org-edit-src-code)
+      (define-key org-mode-map "\C-co" 'outline-hide-other)
+      (global-set-key "\C-cr" 'org-capture)
+      (global-set-key "\C-c\C-l" 'org-store-link)
+      (global-set-key "\C-cL" 'org-insert-link-global)
+      (global-set-key "\C-cO" 'org-open-at-point-global)
+      (global-set-key "\C-ca" 'org-agenda)
+      (global-set-key [(f3)] #'org-capture-goto-last-stored)
+     #+end_src