Refining the changes

1 files changed, 301 insertions, 83 deletions

diff --git a/init.el b/init.el
index 6e05f1f..6f5df08 100644
--- a/init.el
+++ b/init.el
@@ -23,17 +23,43 @@
 (setq-default bidi-paragraph-direction 'left-to-right)
 (if (version<= "27.1" emacs-version)
     (setq bidi-inhibit-bpa t))
+;; Set up dictionaries
+(setq ispell-dictionary "british")
+
+(setq read-extended-command-predicate
+      #'command-completion-default-include-p)
+
+(setq enable-recursive-minibuffers t)
+
+(setq auto-mode-alist
+      (append
+       (list ;;'("\\.\\(vcf\\|gpg\\)\\'" . sensitive-minor-mode)
+        '("\\.sv\\'" . verilog-mode)
+        '("\\.mkiv\\'" . context-mode)
+        '("\\.mkii\\'" . context-mode)
+        '("\\.mkxl\\'" . context-mode))
+       auto-mode-alist))
 
 (setq face-remapping-alist '((proof-locked-face . region)))
 
 (fset 'yes-or-no-p 'y-or-n-p)
 
+;; Mac configuration
 (when (eq system-type 'darwin)
-  (setq mac-right-option-modifier 'none
-        mac-option-key-is-meta nil
-        mac-command-key-is-meta t
-        mac-command-modifier 'meta
-        mac-option-modifier nil))
+  (progn (setq mac-right-option-modifier 'none
+               mac-command-modifier 'meta
+               mac-option-modifier nil)
+
+         (defun ymhg/apply-theme (appearance)
+           "Load theme, taking current system APPEARANCE into consideration."
+           (mapc #'disable-theme custom-enabled-themes)
+           (pcase appearance
+             ;;('light (load-theme 'modus-operandi t))
+             ;;('dark (load-theme 'modus-vivendi t))
+             ('light (load-theme 'ef-spring t))
+             ('dark (load-theme 'ef-autumn t))))
+
+         (add-hook 'ns-system-appearance-change-functions #'ymhg/apply-theme)))
 
 (defun prev-window ()
   (interactive)
@@ -50,6 +76,10 @@
   (switch-to-buffer "*response*")
   (other-frame 1))
 
+(defun ymhg/pass (query)
+  "Return the password as a string from QUERY."
+  (s-trim (shell-command-to-string (concat "pass show " query))))
+
 (global-set-key (kbd "M-u")   #'upcase-dwim)
 (global-set-key (kbd "M-l")   #'downcase-dwim)
 (global-set-key (kbd "M-c")   #'capitalize-dwim)
@@ -92,6 +122,11 @@
 (define-prefix-command 'ymh-map)
 (global-set-key (kbd "C-c y") 'ymh-map)
 (define-key ymh-map (kbd "o") #'ymhg/reset-coq-windows)
+(define-key ymh-map (kbd "c") #'calendar)
+(define-key ymh-map (kbd "C-l") #'org-agenda-open-link)
+(define-key ymh-map (kbd "C-p") #'org-previous-link)
+(define-key ymh-map (kbd "C-n") #'org-next-link)
+;;(define-key y-map (kbd "C-g") #'org-zettelkasten-goto-id)
 
 (setq browse-url-handlers
       '(("wikipedia\\.org"                . eww-browse-url)
@@ -115,12 +150,6 @@
 (setq message-send-mail-function 'message-send-mail-with-sendmail)
 (setq message-fill-column 80)
 
-(use-package sendmail
-  :config
-  (if (eq system-type 'darwin)
-      (setq sendmail-program "/usr/local/bin/msmtp")
-    (setq sendmail-program "/usr/bin/msmtp")))
-
 (setq message-signature "Yann Herklotz
 Imperial College London
 https://yannherklotz.com")
@@ -174,9 +203,93 @@ https://yannherklotz.com")
 
 (straight-use-package 'use-package)
 
+(use-package flyspell
+  :straight nil
+  :config
+  (unbind-key "C-." flyspell-mode-map)
+  (unbind-key "C-," flyspell-mode-map)
+  (setq flyspell-mouse-map (make-sparse-keymap)))
+
+(use-package calc-forms
+  :straight nil
+  :config
+  (add-to-list 'math-tzone-names '("AOE" 12 0))
+  (add-to-list 'math-tzone-names '("IST" (float -55 -1) 0)))
+
+(use-package calendar
+  :straight nil
+  :config
+  (setq calendar-mark-diary-entries-flag t)
+  (setq calendar-mark-holidays-flag t)
+  (setq calendar-mode-line-format nil)
+  (setq calendar-time-display-form
+        '(24-hours ":" minutes
+                   (when time-zone
+                     (format "(%s)" time-zone))))
+  (setq calendar-week-start-day 1)      ; Monday
+  (setq calendar-date-style 'iso)
+  (setq calendar-date-display-form calendar-iso-date-display-form)
+  (setq calendar-time-zone-style 'numeric) ; Emacs 28.1
+  (add-hook 'calendar-today-visible-hook #'calendar-mark-today)
+  (remove-hook 'calendar-mode-hook #'org--setup-calendar-bindings)
+  (let ((map calendar-mode-map))
+    (define-key map (kbd "s") #'calendar-sunrise-sunset)
+    (define-key map (kbd "l") #'lunar-phases)
+    (define-key map (kbd "i") nil) ; Org sets this, much to my chagrin (see `remove-hook' above)
+    (define-key map (kbd "i a") #'diary-insert-anniversary-entry)
+    (define-key map (kbd "i c") #'diary-insert-cyclic-entry)
+    (define-key map (kbd "i d") #'diary-insert-entry) ; for current "day"
+    (define-key map (kbd "i m") #'diary-insert-monthly-entry)
+    (define-key map (kbd "i w") #'diary-insert-weekly-entry)
+    (define-key map (kbd "i y") #'diary-insert-yearly-entry)
+    (define-key map (kbd "M-n") #'calendar-forward-month)
+    (define-key map (kbd "M-p") #'calendar-backward-month)))
+
+(use-package cal-dst
+  :straight nil
+  :config
+  (setq calendar-standard-time-zone-name "+0000")
+  (setq calendar-daylight-time-zone-name "+0100"))
+
+(use-package diary-lib
+  :straight nil
+  :config
+  (setq diary-file "~/Dropbox/org/diary")
+  (setq diary-date-forms diary-iso-date-forms)
+  (setq diary-comment-start ";;")
+  (setq diary-comment-end "")
+  (setq diary-nonmarking-symbol "!")
+  (setq diary-show-holidays-flag t)
+  (setq diary-display-function #'diary-fancy-display) ; better than its alternative
+  (setq diary-header-line-format nil)
+  (setq diary-list-include-blanks nil)
+  (setq diary-number-of-entries 2)
+  (setq diary-mail-days 2)
+  (setq diary-abbreviated-year-flag nil)
+  ;;(add-hook 'diary-list-entries-hook #'diary-fix-timezone t)
+  (add-hook 'diary-list-entries-hook #'diary-sort-entries t)
+  (add-hook 'diary-list-entries-hook 'diary-include-other-diary-files)
+  (add-hook 'diary-mark-entries-hook 'diary-mark-included-diary-files))
+
+(use-package appt
+  :straight nil
+  :config
+  (setq appt-display-diary nil)
+  (setq appt-disp-window-function #'appt-disp-window)
+  (setq appt-display-mode-line t)
+  (setq appt-display-interval 3)
+  (setq appt-audible nil)
+  (setq appt-warning-time-regexp "appt \\([0-9]+\\)")
+  (setq appt-message-warning-time 15)
+  (run-at-time 10 nil #'appt-activate 1))
+
+(use-package savehist
+  :straight nil
+  :init
+  (savehist-mode))
+
 (use-package ef-themes
   :config
-  
   (load-theme 'ef-autumn t))
 
 (use-package pass
@@ -317,61 +430,6 @@ https://yannherklotz.com")
   :straight nil
   :after org)
 
-(use-package calendar
-  :straight nil
-  :config
-  (setq calendar-mark-diary-entries-flag t)
-  (setq calendar-mark-holidays-flag t)
-  (setq calendar-mode-line-format nil)
-  (setq calendar-time-display-form
-        '(24-hours ":" minutes
-                   (when time-zone
-                     (format "(%s)" time-zone))))
-  (setq calendar-week-start-day 1)      ; Monday
-  (setq calendar-date-style 'iso)
-  (setq calendar-date-display-form calendar-iso-date-display-form)
-  (setq calendar-time-zone-style 'numeric) ; Emacs 28.1
-  (add-hook 'calendar-today-visible-hook #'calendar-mark-today)
-  (remove-hook 'calendar-mode-hook #'org--setup-calendar-bindings)
-  (let ((map calendar-mode-map))
-    (define-key map (kbd "s") #'calendar-sunrise-sunset)
-    (define-key map (kbd "l") #'lunar-phases)
-    (define-key map (kbd "i") nil) ; Org sets this, much to my chagrin (see `remove-hook' above)
-    (define-key map (kbd "i a") #'diary-insert-anniversary-entry)
-    (define-key map (kbd "i c") #'diary-insert-cyclic-entry)
-    (define-key map (kbd "i d") #'diary-insert-entry) ; for current "day"
-    (define-key map (kbd "i m") #'diary-insert-monthly-entry)
-    (define-key map (kbd "i w") #'diary-insert-weekly-entry)
-    (define-key map (kbd "i y") #'diary-insert-yearly-entry)
-    (define-key map (kbd "M-n") #'calendar-forward-month)
-    (define-key map (kbd "M-p") #'calendar-backward-month)))
-
-(use-package cal-dst
-  :straight nil
-  :config
-  (setq calendar-standard-time-zone-name "+0000")
-  (setq calendar-daylight-time-zone-name "+0100"))
-
-(use-package diary-lib
-  :straight nil
-  :config
-  (setq diary-file "~/Dropbox/org/diary")
-  (setq diary-date-forms diary-iso-date-forms)
-  (setq diary-comment-start ";;")
-  (setq diary-comment-end "")
-  (setq diary-nonmarking-symbol "!")
-  (setq diary-show-holidays-flag t)
-  (setq diary-display-function #'diary-fancy-display) ; better than its alternative
-  (setq diary-header-line-format nil)
-  (setq diary-list-include-blanks nil)
-  (setq diary-number-of-entries 2)
-  (setq diary-mail-days 2)
-  (setq diary-abbreviated-year-flag nil)
-  ;;(add-hook 'diary-list-entries-hook #'diary-fix-timezone t)
-  (add-hook 'diary-list-entries-hook #'diary-sort-entries t)
-  (add-hook 'diary-list-entries-hook 'diary-include-other-diary-files)
-  (add-hook 'diary-mark-entries-hook 'diary-mark-included-diary-files))
-
 (use-package org-crypt
   :straight nil
   :after org
@@ -387,18 +445,6 @@ https://yannherklotz.com")
   (setq org-id-link-to-org-use-id 'use-existing)
   (setq org-id-track-globally t))
 
-(use-package appt
-  :straight nil
-  :config
-  (setq appt-display-diary nil)
-  (setq appt-disp-window-function #'appt-disp-window)
-  (setq appt-display-mode-line t)
-  (setq appt-display-interval 3)
-  (setq appt-audible nil)
-  (setq appt-warning-time-regexp "appt \\([0-9]+\\)")
-  (setq appt-message-warning-time 15)
-  (run-at-time 10 nil #'appt-activate 1))
-
 (use-package org-transclusion
   :after org
   :config
@@ -444,6 +490,25 @@ https://yannherklotz.com")
   ;;(define-key coq-mode-map (kbd "C-c TAB") #'smie-indent-line)
   )
 
+(use-package alectryon
+  :hook (coq-mode . alectryon-mode)
+  :config
+  (when (eq system-type 'darwin)
+    (setq alectryon-executable "/nix/store/bvlk3hyrjdgl0sg93rrdr2z71hgza0m9-python3.9-alectryon-1.4.0/bin/alectryon"))
+  (map! :map alectryon-mode-map
+        "C-c u t" #'alectryon-toggle
+        "C-c u p" #'ymhg/alectryon-preview)
+  (defun ymhg/alectryon-preview ()
+    "Display an HTML preview of the current buffer."
+    (interactive)
+    (let* ((html-fname (make-temp-file "alectryon" nil ".html"))
+           (args `("-r" "5" "-" ,html-fname)))
+      (apply #'call-process-region nil nil "rst2html5" nil nil nil args)
+      (message "Compilation complete")
+      (browse-url html-fname))))
+
+(use-package rst)
+
 (use-package boogie-friends
   :config
   (setq flycheck-dafny-executable (executable-find "dafny"))
@@ -460,10 +525,11 @@ https://yannherklotz.com")
   :init
   (vertico-mode))
 
-(use-package savehist
-  :straight nil
-  :init
-  (savehist-mode))
+(use-package sendmail
+  :config
+  (if (eq system-type 'darwin)
+      (setq sendmail-program "/usr/local/bin/msmtp")
+    (setq sendmail-program "/usr/bin/msmtp")))
 
 (use-package notmuch
   :config
@@ -517,6 +583,158 @@ https://yannherklotz.com")
 
 (use-package ol-notmuch)
 
+(use-package ebib
+  :bind (("C-c y b" . ebib))
+  :init
+  (defun ymhg/ebib-create-identifier (key _) key)
+  (setq ebib-preload-bib-files '("~/Dropbox/bibliography/references.bib")
+        ebib-notes-default-file "~/Dropbox/bibliography/notes.org"
+        ebib-notes-template "* %T\n:PROPERTIES:\n%K\n:NOTER_DOCUMENT: papers/%k.pdf\n:END:\n%%?\n"
+        ebib-keywords (expand-file-name "~/Dropbox/bibliography/keywords.txt")
+        ebib-reading-list-file "~/Dropbox/bibliography/reading_list.org"
+        ebib-notes-storage 'multiple-notes-per-file)
+  :config
+  (add-to-list 'ebib-notes-template-specifiers '(?k . ymhg/ebib-create-identifier))
+  (add-to-list 'ebib-file-search-dirs "~/Dropbox/bibliography/papers")
+  (if (eq system-type 'darwin)
+      (add-to-list 'ebib-file-associations '("pdf" . "open"))
+    (add-to-list 'ebib-file-associations '("pdf" . nil)))
+  (add-to-list 'ebib-citation-commands '(org-mode (("ref" "[cite:@%(%K%,)]"))))
+  (add-to-list 'ebib-citation-commands '(context-mode (("cite" "\\cite[%(%K%,)]")
+                                                       ("authoryear" "\\cite[authoryear][%(%K%,)]")
+                                                       ("authoryears" "\\cite[authoryears][%(%K%,)]")
+                                                       ("entry" "\\cite[entry][%(%K%,)]")
+                                                       ("author" "\\cite[author][%(%K%,)]"))))
+
+  (advice-add 'bibtex-generate-autokey :around
+              (lambda (orig-func &rest args)
+                (replace-regexp-in-string ":" "" (apply orig-func args))))
+  (remove-hook 'ebib-notes-new-note-hook #'org-narrow-to-subtree)
+
+  (define-key ebib-index-mode-map "D" #'ebib-download-pdf-from-doi)
+
+  (defun sci-hub-pdf-url (doi)
+  "Get url to the pdf from SCI-HUB using DOI."
+  (setq *doi-utils-pdf-url* (concat "https://sci-hub.hkvisa.net/" doi) ;captcha
+        ,*doi-utils-waiting* t
+        )
+  ;; try to find PDF url (if it exists)
+  (url-retrieve (concat "https://sci-hub.hkvisa.net/" doi)
+                (lambda (_)
+                  (goto-char (point-min))
+                  (while (search-forward-regexp
+                          "\\(https:\\|sci-hub.hkvisa.net/downloads\\).+download=true'" nil t)
+                    (let ((foundurl (match-string 0)))
+                      (message foundurl)
+                      (if (string-match "https:" foundurl)
+                          (setq *doi-utils-pdf-url* foundurl)
+                        (setq *doi-utils-pdf-url* (concat "https:" foundurl))))
+                    (setq *doi-utils-waiting* nil))))
+  (while *doi-utils-waiting* (sleep-for 0.1))
+  (replace-regexp-in-string "\\\\" "" *doi-utils-pdf-url*))
+
+(defun acm-pdf-url (doi)
+  "Retrieve a DOI pdf from the ACM."
+  (concat "https://dl.acm.org/doi/pdf/" doi))
+
+(defun ieee-pdf-url (doi)
+  "Retrieve a DOI pdf from the IEEE."
+  (when (string-match "\\.\\([0-9]*\\)$" doi)
+    (let ((doi-bit (match-string 1 doi)))
+      (concat "https://ieeexplore.ieee.org/stampPDF/getPDF.jsp?tp=&arnumber=" doi-bit "&ref="))))
+
+(defun springer-pdf-url (doi)
+  "Retrieve a DOI pdf from the Springer."
+  (concat "https://link.springer.com/content/pdf/" doi ".pdf"))
+
+(defun arxiv-pdf-url (epr)
+  (concat "https://arxiv.org/pdf/" epr ".pdf"))
+
+(defun download-pdf-from-doi (key &optional doi publisher eprint journal organization url)
+  "Download pdf from doi with KEY name."
+  (let ((pub  (or publisher ""))
+        (epr  (or eprint ""))
+        (jour (or journal ""))
+        (org  (or organization ""))
+        (link (or url "")))
+    (url-copy-file (cond
+                    ((not doi) link)
+                    ((or (string-match "ACM" (s-upcase pub))
+                         (string-match "association for computing machinery" (s-downcase pub)))
+                     (acm-pdf-url doi))
+                    ((string-match "arxiv" (s-downcase pub))
+                     (arxiv-pdf-url epr))
+                    ((or (string-match "IEEE" (s-upcase pub))
+                         (string-match "IEEE" (s-upcase jour))
+                         (string-match "IEEE" (s-upcase org)))
+                     (ieee-pdf-url doi))
+                    ((string-match "springer" (s-downcase pub))
+                     (springer-pdf-url doi))
+                    (t (sci-hub-pdf-url doi)))
+                   (concat (car ebib-file-search-dirs) "/" key ".pdf"))))
+
+(defun download-pdf-from-link (link key)
+  (url-copy-file link
+                 (concat (car ebib-file-search-dirs) "/" key ".pdf")))
+
+(defun download-pdf-from-downloads (key)
+  (copy-file (concat "~/Downloads/" key ".pdf")
+             (concat (car ebib-file-search-dirs) "/" key ".pdf") t))
+
+(defun get-bib-from-doi (doi)
+  "Get the bibtex from DOI."
+  (shell-command (concat "curl -L -H \"Accept: application/x-bibtex; charset=utf-8\" "
+                         "https://doi.org/" doi)))
+
+(defun ebib-download-pdf-from-doi ()
+  "Download a PDF for the current entry."
+  (interactive)
+  (let* ((key (ebib--get-key-at-point))
+         (doi (ebib-get-field-value "doi" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (publisher (ebib-get-field-value "publisher" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (eprinttype (ebib-get-field-value "eprinttype" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (eprint (ebib-get-field-value "eprint" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (journal (ebib-get-field-value "journal" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (journaltitle (ebib-get-field-value "journaltitle" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (organization (ebib-get-field-value "organization" key ebib--cur-db 'noerror 'unbraced 'xref))
+         (url (ebib-get-field-value "url" key ebib--cur-db 'noerror 'unbraced 'xref)))
+    (unless key
+      (error "[Ebib] No key assigned to entry"))
+    (download-pdf-from-doi key doi (or publisher eprinttype) eprint (or journal journaltitle) organization url)))
+
+(defun ebib-check-file ()
+  "Download a PDF for the current entry."
+  (interactive)
+  (let ((key (ebib--get-key-at-point)))
+    (unless (file-exists-p (concat (car ebib-file-search-dirs) "/" key ".pdf"))
+      (error "[Ebib] No PDF found."))
+    t)))
+
+(use-package spell-fu
+  :config
+  (add-hook 'spell-fu-mode-hook
+            (lambda ()
+              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "en_GB"))
+              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "de_DE"))
+              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "fr_FR"))
+              (spell-fu-dictionary-add
+               (spell-fu-get-personal-dictionary "fr-personal" "~/.aspell.en_GB.pws"))
+              (spell-fu-dictionary-add
+               (spell-fu-get-personal-dictionary "de-personal" "~/.aspell.de_DE.pws"))
+              (spell-fu-dictionary-add
+               (spell-fu-get-personal-dictionary "fr-personal" "~/.aspell.fr_FR.pws")))))
+
+(use-package ledger-mode)
+
+(use-package geiser
+  :config
+  ;;(unbind-key "C-." geiser-mode-map)
+  (unbind-key "C-." geiser-repl-mode-map))
+
+(use-package geiser-chicken
+  :config
+  (setq geiser-chicken-binary "chicken-csi"))
+
 (setq gc-cons-threshold (* 1024 1024 10))
 
 (custom-set-variables