From 764fd0e0dc069e219f7f0d8eeaff481cf9228ee6 Mon Sep 17 00:00:00 2001
From: Thomas Dehaeze <dehaeze.thomas@gmail.com>
Date: Sun, 6 Feb 2022 21:49:32 +0100
Subject: [PATCH] Update emacs config

---
 doom.org           | 188 +++++++++++++++++++++++++--------------------
 emacs-snippets.org | 108 +++++++++++++++++---------
 2 files changed, 178 insertions(+), 118 deletions(-)

diff --git a/doom.org b/doom.org
index ff3ddc9..52b8822 100644
--- a/doom.org
+++ b/doom.org
@@ -12,11 +12,6 @@
 #+html_head: <script type="text/javascript" src="./dist/script.js"></script>
 #+property: header-args:emacs-lisp :tangle ~/.config/doom/config.el :results none :padline no
 
-* Installation
-#+begin_src bash :tangle no
-yay -Ss aspell aspell-fr aspell-en
-#+end_src
-
 * Introduction and Resources
 https://medium.com/urbint-engineering/emacs-doom-for-newbies-1f8038604e3b
 https://noelwelsh.com/posts/2019-01-10-doom-emacs.html
@@ -241,7 +236,7 @@ Turn off auto-fill mode that add line breaks.
 ** Spell Check
 Switch from one language to an other ([[https://stackoverflow.com/questions/42159012/emacs-spell-check-on-fly-for-2-languages][link]]).
 #+begin_src emacs-lisp
-(setq ispell-dictionary "en_US")
+(setq ispell-dictionary "en")
 (setq ispell-program-name "aspell")
 #+end_src
 
@@ -290,8 +285,6 @@ Switch from one language to an other ([[https://stackoverflow.com/questions/4215
 
 (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
@@ -396,17 +389,25 @@ Disable flycheck for now with orgmode buffers:
 
 ** 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$" t))
+;; (defun tdh-export-everything-to-hugo ()
+;;   "Export all the .org files in the specified directory to markdown using Hugo"
+;;   (interactive)
+;;   (setq org-files (directory-files (read-directory-name "Directory:" "/home/thomas/Cloud/brain/") t "org$" 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))))
+;;   (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
+
+** Tramp
+#+begin_src emacs-lisp
+(add-to-list 'tramp-remote-process-environment "GIT_AUTHOR_EMAIL=thomas.dehaeze@esrf.fr")
+(add-to-list 'tramp-remote-process-environment "GIT_AUTHOR_NAME='Thomas Dehaeze'")
+(add-to-list 'tramp-remote-process-environment "GIT_COMMITTER_EMAIL=thomas.dehaeze@esrf.fr")
+(add-to-list 'tramp-remote-process-environment "GIT_COMMITTER_EMAIL='Thomas Dehaeze'")
 #+end_src
 
 ** Others
@@ -721,10 +722,12 @@ This idea comes from [[https://blog.lambda.cx/posts/org-agenda-new-tab/][here]].
   :config (setq org-fancy-priorities-list '("■" "■" "■")))
 #+end_src
 
-** Org Notification based on calendar event
+** TODO [#B] Org Notification based on calendar event
 https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarms-audio-visual-triggered-by-org-mode-events
 
-#+begin_src emacs-lisp
+- [ ] Issue with this part on ubuntu
+
+#+begin_src emacs-lisp :tangle no
 (after! org-agenda
   (setq appt-message-warning-time 5)
   (defun tdh-org-agenda-to-appt ()
@@ -737,7 +740,7 @@ https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarm
   (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"))
+  (setq tdh-appt-notification-app (concat (getenv "HOME") "/.local/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)
@@ -747,11 +750,11 @@ https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarm
 #+end_src
 
 *** appt-notification script
-#+begin_src bash :tangle ~/.config/doom/bin/appt-notification :shebang "#!/usr/bin/env bash" :comments none :mkdirp yes
+#+begin_src bash :tangle ~/.local/bin/appt-notification :shebang "#!/usr/bin/env bash" :comments none :mkdirp yes
 TIME="$1"TODO
 MSG="$2"
 
-dunstify --replace=85401 "Event in $TIME minutes" "$MSG"
+notify-send "Event in $TIME minutes" "$MSG"
 #+end_src
 
 ** Org Structure Template
@@ -924,6 +927,17 @@ Do not export headline with the =:ignore:= tag:
   )
 #+end_src
 
+** Open Files
+#+begin_src emacs-lisp
+(after! org
+  (setq org-file-apps
+        '((auto-mode . emacs)
+          ("\\.x?html?\\'" . "firefox %s")
+          ("\\.pdf\\'" . "zathura \"%s\"")
+          ("\\.pdf::\\([0-9]+\\)\\'" . "zathura \"%s\" -p %1")))
+  )
+#+end_src
+
 ** HTML Export
 *** HTML Defaults
 #+begin_src emacs-lisp
@@ -1854,14 +1868,6 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
   )
 #+end_src
 
-** Citeproc-Org
-#+begin_src emacs-lisp
-(use-package! citeproc-org
-  :after ox-hugo
-  :config
-  (citeproc-org-setup))
-#+end_src
-
 ** Org Wild Notifier
 #+begin_src emacs-lisp
 (use-package! org-wild-notifier
@@ -1925,8 +1931,6 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
      :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)
    ))
@@ -2109,6 +2113,17 @@ Map Keys
         :n "F" 'tdh-automatic-latex-fragment-deactivate)))
 #+end_src
 
+*** Org-Appear
+#+begin_src emacs-lisp
+(use-package! org-appear
+  :after org
+  :hook (org-mode . org-appear-mode)
+  :config (setq
+           org-appear-autolinks t
+           org-appear-autoentities t
+           org-appear-autosubmarkers t ))
+#+end_src
+
 *** Bibtex =,r=
 #+begin_src emacs-lisp
 (after! org
@@ -2164,7 +2179,7 @@ Open HTML output externally
 Don't ask for confirmation when evaluating following blocs
 #+begin_src emacs-lisp
 (defun tdh-org-confirm-babel-evaluate (lang body)
-  (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python"))))
+  (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python" "ipython" "jupyter-python" "dot"))))
 
 (after! org
   (setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))
@@ -2212,7 +2227,6 @@ Add all named source blocks to =org-babel-library-of-babel= ([[file:emacs-librar
   (org-babel-lob-ingest "~/.config/literate-dotfiles/emacs-library-babel.org"))
 #+end_src
 
-
 ** Org-Babel Matlab
 #+begin_src emacs-lisp
 (after! org
@@ -2333,7 +2347,7 @@ yay -S mermaid-cli
 (use-package! ob-mermaid
   :after org
   :config
-  (setq ob-mermaid-cli-path "/usr/bin/mmdc")
+  (setq ob-mermaid-cli-path "/home/thomas/.npm-global/bin/mmdc")
   )
 #+end_src
 
@@ -2541,8 +2555,10 @@ This function:
         (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)))
+              (progn (tdh-org-babel-execute-matlab-background)))
+          (org-babel-next-src-block))
+        (if (string= lang "jupyter-python")
+            (org-babel-execute-maybe)
           (org-babel-next-src-block))
         )
     (org-babel-next-src-block)
@@ -2602,12 +2618,21 @@ Org-Tangle and Org-Babel Jump to Tangle File
         (error "Cannot open tangle file %S" file)))))
 #+end_src
 
+#+begin_src emacs-lisp
+(defun tdh-org-babel-tangle-block ()
+  (interactive)
+  (let ((current-prefix-arg '(4)))
+    (call-interactively 'org-babel-tangle)
+    ))
+#+end_src
+
 Map Functions
 #+begin_src emacs-lisp
 (after! org
   (map! :map org-mode-map
         (:prefix (",b" . "Tangle")
         :n  "F" 'tdh-org-babel-jump-to-tangle-file
+        :n  "b" 'tdh-org-babel-tangle-block
         :n  "T" 'tdh-org-babel-tangle-subtree)))
 #+end_src
 
@@ -2633,15 +2658,13 @@ Nice Functions:
   :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")
+  (setq bibtex-completion-notes-path "~/Cloud/brain/")
 
   ;; Bibliography File
-  (setq reftex-default-bibliography  '("~/Cloud/brain/biblio/references.bib"))
-  (setq org-ref-default-bibliography '("~/Cloud/brain/biblio/references.bib"))
+  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"))
 
   ;; Folder where all the pdf are located
-  (setq org-ref-pdf-directory "~/Cloud/pdfs")
+  (setq bibtex-completion-library-path '("~/Cloud/pdfs/"))
 
   (setq org-ref-bibliography-entry-format
         '(("article" . "%a, %t, %j, v(%n), %p (%y).")
@@ -2663,20 +2686,20 @@ Nice Functions:
   ;; 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
+  ;;              '("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)
+  ;; (add-to-list 'org-ref-helm-user-candidates
+  ;;              '("Drag and Drop" . (lambda () (call-process "/bin/bash" nil 0 nil "-c" (concat
+  ;;                                                                                       "dragon "
+  ;;                                                                                       (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)
@@ -2687,6 +2710,11 @@ Nice Functions:
   )
 #+end_src
 
+#+begin_src emacs-lisp
+(after! org
+  (require 'org-ref))
+#+end_src
+
 #+begin_src emacs-lisp
 (defun tdh-org-ref-open-pdf-at-point ()
   "Open the pdf in external program for bibtex key under point if it exists."
@@ -2826,12 +2854,10 @@ Re-Export all roam files.
   :init
   :config
   ;; Bibliography file
-  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"
-    "~/Cloud/acoustic/resources/acoustics.bib"))
+  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"))
 
   ;; Directory with all the pdfs
-  (setq bibtex-completion-library-path '("~/Cloud/pdfs/"
-                                         "~/Cloud/acoustic/resources/pdfs/"))
+  (setq bibtex-completion-library-path '("~/Cloud/pdfs/"))
 
   ;; Directory with notes files
   (setq bibtex-completion-notes-path "~/Cloud/brain/")
@@ -2947,13 +2973,6 @@ List all element of the bibliography without pdf associated
   )
 #+end_src
 
-** Deft ([[https://github.com/jrblevin/deft][link]])
-#+begin_src emacs-lisp :tangle no
-(use-package! deft
-  :custom
-  (deft-directory "~/Cloud/brain/"))
-#+end_src
-
 ** Org-Roam-Bibtex ([[https://github.com/org-roam/org-roam-bibtex][link]])
 Provides nice functions such as:
 - =orb-find-non-ref-file=
@@ -2977,15 +2996,6 @@ Provides nice functions such as:
   (call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))
 #+end_src
 
-** Citeproc-org ([[https://github.com/andras-simonyi/citeproc-org][link]])
-#+begin_src emacs-lisp
-(use-package! citeproc-org
-  :after org
-  :config
-  (citeproc-org-setup)
-  (setq citeproc-org-html-backends '(html)))
-#+end_src
-
 ** Bibtex-Mode
 #+begin_src emacs-lisp
 (after! bibtex
@@ -2993,6 +3003,18 @@ Provides nice functions such as:
         :n "C-c c" 'org-ref-clean-bibtex-entry))
 #+end_src
 
+** Citar
+#+begin_src emacs-lisp
+;; (use-package! citar
+;;   :custom
+;;   (org-cite-global-bibliography '("~/Cloud/brain/biblio/references.bib"))
+;;   (setq citar-library-paths '("~/Cloud/pdfs/"))
+;;   (setq citar-open-note-function 'orb-citar-edit-note)
+;;   (org-cite-insert-processor 'citar)
+;;   (org-cite-follow-processor 'citar)
+;;   (org-cite-activate-processor 'citar))
+#+end_src
+
 * 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
@@ -3115,6 +3137,9 @@ Provides nice functions such as:
 #+end_src
 
 * Mu4e
+:PROPERTIES:
+:header-args:emacs-lisp: :tangle no
+:END:
 ** Resources
 Documentation:
 - [ ] Mu4e documentation: http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
@@ -3367,7 +3392,9 @@ Choose account label to feed msmtp -a option based on From header in Message buf
 
        :checkers
        syntax          ; tasing you for every semicolon you forget
-       (spell +aspell)          ; tasing you for misspelling mispelling
+       (spell
+        +aspell
+        +everywhere)          ; tasing you for misspelling mispelling
 
        :lang
        data              ; config/data formats
@@ -3383,6 +3410,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
         +hugo            ; use Emacs for hugo blogging
         +roam2         ;
         +gnuplot
+        +jupyter
         +present)        ; using org-mode for presentations
        python            ; beautiful is better than ugly
        (sh                ; she sells {ba,z,fi}sh shells on the C xor
@@ -3440,6 +3468,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
 #+begin_src emacs-lisp
 ;; Automatic toggling of LaTeX fragments
 (package! org-fragtog)
+(package! org-appear)
 #+end_src
 
 #+begin_src emacs-lisp
@@ -3460,11 +3489,6 @@ Choose account label to feed msmtp -a option based on From header in Message buf
            :files ("*.el" "filters" "preprocessors")))
 #+end_src
 
-#+begin_src emacs-lisp
-;; Renders Org-mode citations in CSL styles
-(package! citeproc-org)
-#+end_src
-
 #+begin_src emacs-lisp
 ;; Connector between Org-roam, BibTeX-completion, and Org-ref
 (package! org-roam-bibtex
diff --git a/emacs-snippets.org b/emacs-snippets.org
index 2692ff8..006ab17 100644
--- a/emacs-snippets.org
+++ b/emacs-snippets.org
@@ -330,7 +330,7 @@ $0
 #+name: tab:${1:table_name}
 #+caption: ${2:Table caption}
 #+attr_latex: :environment tabularx :width ${3:\linewidth} :align ${4:lXX}
-#+attr_latex: :center t :booktabs t :float t
+#+attr_latex: :center t :booktabs t
 | $0  |   |   |
 |---+---+---|
 |   |   |   |
@@ -418,6 +418,25 @@ $1
 $0
 #+end_src
 
+** Python Specific
+*** Pfigure
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/pfigure
+#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
+#name :Python-Figure
+# --
+,#+begin_src jupyter-python :file ${2:filename}.png :results none
+# Figure - ${1:description}
+plt.figure(figsize=(${3:1200}/150, ${4:800}/150), dpi=150)
+plt.clf
+$0
+plt.savefig('figs/$2.pdf', transparent=True, bbox_inches='tight', pad_inches=0)
+,#+end_src
+
+,#+name: fig:$2
+,#+caption: $1
+[[file:figs/$2.png]]
+#+end_src
+
 ** Matlab Specific
 *** Mconfig
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mconfig
@@ -436,49 +455,25 @@ $0
 $0
 #+end_src
 
-*** Mdescription
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
-#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
-#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              |
-
-$0
-#+end_src
-
 *** Mfigure
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
 #contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
 #name :Matlab-Figure
 # --
-,#+begin_src matlab :tangle no :exports results :results file replace
-   exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}');
+,#+begin_src matlab :exports none :results none
+%% ${1:description}
+figure;
+$0
 ,#+end_src
 
-,#+name: fig:$1
-,#+caption: $0
+,#+begin_src matlab :tangle no :exports results :results file replace
+exportFig('figs/${2:filename}.pdf', 'width', '${3:full}', 'height', '${4:full}');
+,#+end_src
+
+,#+name: fig:$2
+,#+caption: $1
 ,#+RESULTS:
-[[file:figs/$1.png]]
+[[file:figs/$2.png]]
 #+end_src
 
 *** Mfunction
@@ -594,3 +589,44 @@ $0
 $0
 ,#+end_src
 #+end_src
+
+* Python
+** Function
+#+begin_src conf :tangle ~/.config/doom/snippets/python/de
+# -*- coding: utf-8 -*-
+# name: de
+# contributor: Orestis Markou
+# contributor: Yasser González Fernández <yglez@uh.cu>
+# contributor: Tibor Simko <tibor.simko@cern.ch>
+# --
+def ${1:name}($2):
+    """
+    $3
+    ${2:$
+    (let* ((indent
+            (concat "\n" (make-string (current-column) 32)))
+           (args
+            (mapconcat
+             '(lambda (x)
+                (if (not (string= (nth 0 x) ""))
+                    (concat "@param " (nth 0 x) ": " indent
+                            "@type " (nth 0 x) ": ")))
+             (mapcar
+              '(lambda (x)
+                 (mapcar
+                  '(lambda (x)
+                     (replace-regexp-in-string "[[:blank:]]*$" ""
+                      (replace-regexp-in-string "^[[:blank:]]*" "" x)))
+                  x))
+              (mapcar '(lambda (x) (split-string x "="))
+                      (split-string text ",")))
+             indent)))
+      (if (string= args "")
+          (concat indent "@return: " indent "@rtype: " indent (make-string 3 34))
+        (mapconcat
+         'identity
+         (list "" args "@return: " "@rtype: " (make-string 3 34))
+         indent)))
+    }
+    $0
+#+end_src