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dotemacs.el
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(when window-system
(blink-cursor-mode 0) ; Disable the cursor blinking
(scroll-bar-mode 0) ; Disable the scroll bar
(tool-bar-mode 0) ; Disable the tool bar
(tooltip-mode 0)) ; Disable the tooltips
(setq-default
ad-redefinition-action 'accept ; Silence warnings for redefinition
auto-window-vscroll nil ; Lighten vertical scroll
confirm-kill-emacs 'yes-or-no-p ; Confirm before exiting Emacs
cursor-in-non-selected-windows nil ; Hide the cursor in inactive windows
delete-by-moving-to-trash t ; Delete files to trash
display-time-default-load-average nil ; Don't display load average
display-time-format "%H:%M" ; Format the time string
fill-column 90 ; Set width for automatic line breaks
help-window-select t ; Focus new help windows when opened
indent-tabs-mode nil ; Stop using tabs to indent
inhibit-startup-screen t ; Disable start-up screen
initial-scratch-message "" ; Empty the initial *scratch* buffer
mouse-yank-at-point t ; Yank at point rather than pointer
ns-use-srgb-colorspace nil ; Don't use sRGB colors
recenter-positions '(5 top bottom) ; Set re-centering positions
scroll-conservatively most-positive-fixnum ; Always scroll by one line
scroll-margin 10 ; Add a margin when scrolling vertically
select-enable-clipboard t ; Merge system's and Emacs' clipboard
sentence-end-double-space nil ; End a sentence after a dot and a space
show-trailing-whitespace nil ; Display trailing whitespaces
split-height-threshold nil ; Disable vertical window splitting
split-width-threshold nil ; Disable horizontal window splitting
tab-width 4 ; Set width for tabs
uniquify-buffer-name-style 'forward ; Uniquify buffer names
window-combination-resize t ; Resize windows proportionally
x-stretch-cursor t) ; Stretch cursor to the glyph width
(cd "~/") ; Move to the user directory
(delete-selection-mode 1) ; Replace region when inserting text
(display-time-mode 1) ; Enable time in the mode-line
(fringe-mode 0) ; Disable fringes
(fset 'yes-or-no-p 'y-or-n-p) ; Replace yes/no prompts with y/n
(global-subword-mode 1) ; Iterate through CamelCase words
(menu-bar-mode 0) ; Disable the menu bar
(mouse-avoidance-mode 'banish) ; Avoid collision of mouse with point
(put 'downcase-region 'disabled nil) ; Enable downcase-region
(put 'upcase-region 'disabled nil) ; Enable upcase-region
(set-default-coding-systems 'utf-8) ; Default to utf-8 encoding
(setq visible-bell 1)
(setq backup-directory-alist `(("." . "~/.saves")))
(setq shift-select-mode nil)
(set-cursor-color "#00bfff")
(if (eq window-system 'ns)
(toggle-frame-maximized)
(toggle-frame-maximized))
(add-hook 'focus-out-hook #'garbage-collect)
(setq-default custom-file (expand-file-name ".custom.el" user-emacs-directory))
(when (file-exists-p custom-file)
(load custom-file))
(defvar me/erc-nick nil "The ERC nick to use.")
(defvar me/erc-password nil "The ERC password to use.")
(defvar me/erc-port nil "The ERC port to use.")
(defvar me/erc-server nil "The ERC server to use.")
(defvar me/font-family "Source Code Pro" "The font to use.")
(defvar me/font-size-default 130 "The font size to use for default text.")
(defvar me/font-size-header-line 130 "The font size to use for the header-line.")
(defvar me/font-size-mode-line 130 "The font size to use for the mode-line.")
(defvar me/font-size-small 100 "The font size to use for smaller text.")
(defvar me/font-size-title 130 "The font size to use for titles.")
(let ((secret.el (expand-file-name ".secret.el" user-emacs-directory)))
(when (file-exists-p secret.el)
(load secret.el)))
(use-package doom-themes
:demand t
:custom
(doom-themes-enable-bold nil)
:config
(load-theme 'doom-dracula t)
(with-eval-after-load 'flycheck
(set-face-attribute 'flycheck-error nil :underline `(:color ,(doom-color 'error) :style line))
(set-face-attribute 'flycheck-info nil :underline `(:color ,(doom-color 'highlight) :style line))
(set-face-attribute 'flycheck-warning nil :underline `(:color ,(doom-color 'warning) :style line)))
(with-eval-after-load 'helm-buffers
(set-face-attribute 'helm-buffer-directory nil
:background 'unspecified
:foreground 'unspecified
:inherit 'dired-directory)
(set-face-attribute 'helm-buffer-file nil :inherit 'unspecified)
(set-face-attribute 'helm-buffer-modified nil :foreground (doom-color 'orange) :inherit 'unspecified)
(set-face-attribute 'helm-buffer-not-saved nil :foreground (doom-color 'red) :inherit 'unspecified)
(set-face-attribute 'helm-non-file-buffer nil :inherit 'font-lock-comment-face))
(with-eval-after-load 'helm-command
(set-face-attribute 'helm-M-x-key nil :foreground (doom-color 'yellow) :underline 'unspecified))
(with-eval-after-load 'helm-files
(set-face-attribute 'helm-ff-directory nil
:background 'unspecified
:foreground 'unspecified
:inherit 'dired-directory))
(with-eval-after-load 'isearch
(set-face-attribute 'isearch nil :background (doom-color 'blue) :foreground (doom-color 'dark-blue))
(set-face-attribute 'lazy-highlight nil :foreground (doom-color 'blue)))
(with-eval-after-load 'faces
(set-face-attribute 'default nil :font me/font-family :height me/font-size-default)
(set-face-attribute 'header-line nil :box `(:color ,(doom-color 'modeline-bg) :line-width 7))
(set-face-attribute 'help-argument-name nil :foreground (doom-color 'yellow))
(set-face-attribute 'mode-line nil :height me/font-size-mode-line)
(set-face-attribute 'variable-pitch nil :family 'unspecified))
(with-eval-after-load 'font-lock
(set-face-attribute 'font-lock-doc-face nil :italic t))
(with-eval-after-load 'helm
(set-face-attribute 'helm-source-header nil :background 'unspecified))
(with-eval-after-load 'markdown
(set-face-attribute 'markdown-table-face nil :height me/font-size-small))
(with-eval-after-load 'outline
(set-face-attribute 'outline-1 nil :background 'unspecified))
(with-eval-after-load 'magit-diff
(set-face-attribute 'magit-diff-added nil :background 'unspecified)
(set-face-attribute 'magit-diff-hunk-region nil :inherit 'region)
(set-face-attribute 'magit-diff-removed nil :background 'unspecified)))
;; (use-package spacemacs-theme
;; :ensure t
;; :init
;; (load-theme 'spacemacs-dark t)
;; (setq spacemacs-theme-org-agenda-height nil)
;; (setq spacemacs-theme-org-height nil))
(use-package spaceline
:demand t
:init
(setq powerline-default-separator 'arrow-fade)
:config
(require 'spaceline-config)
(spaceline-emacs-theme)
(spaceline-toggle-major-mode-on)
(spaceline-toggle-minor-modes-off)
(fancy-battery-mode 1)
(setq fancy-battery-show-percentage t)
(setq spaceline-highlight-face-func 'spaceline-highlight-face-modified)
;(setq spaceline-highlight-face-func 'spaceline-highlight-face-evil-state)
)
(custom-set-faces
'(spaceline-modified ((t (:background "OrangeRed" :foreground "#3E3D31"
:inherit (quote mode-line))))))
(when (version<= "26.0.50" emacs-version )
(global-display-line-numbers-mode))
(use-package dashboard
:ensure t
:config
(dashboard-setup-startup-hook))
(dashboard-setup-startup-hook)
(setq show-week-agenda-p t)
(setq initial-buffer-choice (lambda () (get-buffer "*dashboard*")))
(setq dashboard-items '((recents . 8)
(bookmarks . 8)
(projects . 5)
(agenda . 5)
(registers . 5)))
(setq dashboard-set-heading-icons t)
(setq dashboard-set-file-icons t)
(use-package hl-line
:ensure nil
:preface (defun me/hl-line-mode-off () (setq-local global-hl-line-mode nil))
:hook (after-init . global-hl-line-mode))
(use-package paradox
:custom
(paradox-column-width-package 27)
(paradox-column-width-version 13)
(paradox-execute-asynchronously t)
(paradox-github-token t)
(paradox-hide-wiki-packages t)
:config
(remove-hook 'paradox-after-execute-functions #'paradox--report-buffer-print))
(use-package prog-mode
:ensure nil
:preface
(defun me/prettify-symbols-compose-predicate (&rest arguments)
(when (not (eq system-type 'windows-nt))
(apply #'prettify-symbols-default-compose-p arguments)))
:custom
(prettify-symbols-compose-predicate #'me/prettify-symbols-compose-predicate)
(prettify-symbols-unprettify-at-point 'right-edge))
(use-package rainbow-mode
:hook prog-mode
:custom (rainbow-x-colors-major-mode-list '()))
(use-package simple
:ensure nil
:hook
((prog-mode . turn-on-auto-fill)
(text-mode . turn-on-auto-fill)))
(use-package fancy-battery)
(add-hook 'after-init-hook #'fancy-battery-mode)
(use-package all-the-icons)
(defun latex-word-count ()
(interactive)
(shell-command (concat "/home/gogo/Software/texcount.pl "
"-v0 "
(buffer-file-name))))
(use-package auctex
:defer t
:ensure t
:custom
(TeX-auto-save t)
(TeX-parse-self t)
(font-latex-fontify-script nil)
:config
(add-to-list 'auto-mode-alist '("\\.tex$" . LaTeX-mode)))
(use-package org
:ensure nil
:preface
(defun me/org-src-buffer-name (org-buffer-name language)
"Construct the buffer name for a source editing buffer. See `org-src--construct-edit-buffer-name'."
(format "*%s*" org-buffer-name))
(defun me/org-set-ongoing-hydra-body ()
(setq me/ongoing-hydra-body #'hydra-org/body))
:bind
(:map org-mode-map
([remap backward-paragraph] . me/backward-paragraph-dwim)
([remap forward-paragraph] . me/forward-paragraph-dwim)
("<C-return>" . nil)
("<C-S-down>" . nil)
("<C-S-up>" . nil))
:hook
((org-mode . me/org-set-ongoing-hydra-body)
(org-mode . org-sticky-header-mode)
(org-mode . toc-org-enable))
:custom
(org-descriptive-links nil)
(org-edit-src-content-indentation 0)
(org-edit-src-persistent-message nil)
(org-fontify-done-headline t)
(org-fontify-quote-and-verse-blocks t)
(org-src-window-setup 'current-window)
(org-startup-folded 'content)
(org-startup-truncated nil)
(org-support-shift-select 0)
:config
(advice-add 'org-src--construct-edit-buffer-name :override #'me/org-src-buffer-name)
;; Prettify Org headings
(let* ((variable-tuple
(cond ((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
;((x-family-fonts "Sans Serif") '(:family "Sans Serif"))
(nil (warn "Cannot find a Sans Serif Font. Install Source Sans Pro."))))
(base-font-color (face-foreground 'default nil 'default))
(headline `(:inherit default :weight bold :foreground ,base-font-color)))
(custom-theme-set-faces
'user
`(org-level-8 ((t (,@headline ,@variable-tuple))))
`(org-level-7 ((t (,@headline ,@variable-tuple))))
`(org-level-6 ((t (,@headline ,@variable-tuple))))
`(org-level-5 ((t (,@headline ,@variable-tuple))))
`(org-level-4 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#8470ff"))))
`(org-level-3 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#228b22"))))
`(org-level-2 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#5f9ea0"))))
`(org-level-1 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#6a5acd"))))
`(org-document-title ((t (,@headline ,@variable-tuple :height 1.2 :foreground "#6a5acd"))))))
;; Agenda customization
(setq org-agenda-files (list "~/Dropbox/orgfiles/work.org" "~/Dropbox/orgfiles/Life.org" "~/Dropbox/orgfiles/newgtd.org"))
(setq org-capture-templates
'(("a" "Appointment" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Appointments:" ) "*** %?\n:SCHEDULED: %^T\n:PROPERTIES:\n:END:\n")
("f" "Follow up Later" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Follow up Later:" ) "** %?\n")
("F" "Follow up Later (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Follow up Later:" ) "** %?\n")
("l" "Important Link (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Important Links") "* %? %^L %^g \n%T" :prepend t)
("L" "Read/Watch later" entry (file+headline "~/Dropbox/orgfiles/Life.org" "Links") "** %? %^L %^g \n%T" :prepend t)
("s" "Shopping list" checkitem (file+headline "~/Dropbox/orgfiles/newgtd.org" "Shopping List:") "- [ ] %?\n" :prepend t)
("t" "Work TODO" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Work") "*** TODO %?%^g\n:CREATED: %u\n:SCHEDULED: %^T\n:DEADLINE: %^T" :prepend t)
("T" "Personal TODO" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Life") "*** TODO %?%^g\n:CREATED: %u\n:SCHEDULED: %^T\n:DEADLINE: %^T" :prepend t)
("n" "Note (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Note space:") "** %?\n%u" :prepend t)
("N" "Note (personal)" entry (file+headline "~/Dropbox/orgfiles/Life.org" "Note space:") "** %?\n%u" :prepend t)
("j" "Journal" entry (file+datetree "~/Dropbox/journal.org") "* %?\nEntered on %U\n %i\n %a")))
(defadvice org-agenda (around split-vertically activate)
(let ((split-width-threshold 80)) ; or whatever width makes sense for you
ad-do-it))
(defadvice org-capture (around split-vertically activate)
(let ((split-width-threshold 80)) ; or whatever width makes sense for you
ad-do-it))
;; Org refile
(setq org-refile-targets '((org-agenda-files :maxlevel . 3)))
(setq org-refile-use-outline-path 'file)
(setq org-outline-path-complete-in-steps nil)
(setq org-refile-allow-creating-parent-nodes 'confirm)
;; Org todo
(setq org-todo-keywords'((sequence "TODO(t)" "ONGOING(o)" "ALMOST(a)" "VERIFY(v)" "|" "DONE(d)" "DELEGATED(D)" "CANCELED(c)")))
(setq org-todo-keyword-faces
'(("TODO" . "#ff6347")
("ONGOING" . "#ffd700")
("ALMOST" . "#228b22")
("VERIFY" . "#bc8f87")
("CANCELED" . (:foreground "white" :background "#ff6347" :weight bold))
("DELEGATED" . (:foreground "white" :background "#bc8f87" :weight bold))
("DONE" . (:foreground "white" :background "#228b22" :weight bold))))
;; Org-latex output
(setq org-latex-pdf-process
'("latexmk -pdflatex='pdflatex -interaction nonstopmode' -pdf -bibtex -f %f"))
(require 'ox-beamer)
(setq org-highlight-latex-and-related '(latex script entities))
;; Org babel language load
(org-babel-do-load-languages
'org-babel-load-languages '((python . t)))
(setq org-babel-python-command "/home/gogo/Software/anaconda3/bin/python")
;; Fill Paragraph in org-mode latex block
(defun org-fill-paragraph--latex-environment (&rest args)
"Use default fill-paragraph in latex environments."
(not (eql (org-element-type (org-element-context)) 'latex-environment)))
(advice-add 'org-fill-paragraph :before-while #'org-fill-paragraph--latex-environment))
(global-set-key (kbd "\C-c c") 'org-capture)
(global-set-key (kbd "\C-c a") 'org-agenda)
(use-package org-sticky-header
:custom
(org-sticky-header-full-path 'full)
(org-sticky-header-outline-path-separator " / ")
:config
(setq-default
org-sticky-header-header-line-format
'(:eval (setq org-sticky-header-stickyline (concat " " (org-sticky-header--fetch-stickyline))))))
(use-package toc-org :after org)
;(add-hook 'org-mode-hook 'org-indent-mode)
;(use-package org-bullets
; :config
; (add-hook 'org-mode-hook (lambda () (org-bullets-mode t))))
(use-package org-bullets
:hook (org-mode . org-bullets-mode)
:config
(setq org-bullets-bullet-list '("◉" "○" "□" "◉" "○" "□" "✸")))
(set-language-environment 'utf-8)
(setq locale-coding-system 'utf-8)
;; set the default encoding system
(prefer-coding-system 'utf-8)
(setq default-file-name-coding-system 'utf-8)
(set-default-coding-systems 'utf-8)
(set-terminal-coding-system 'utf-8)
(set-keyboard-coding-system 'utf-8)
;; Treat clipboard input as UTF-8 string first; compound text next, etc.
(setq x-select-request-type '(UTF8_STRING COMPOUND_TEXT TEXT STRING))
;; (let* ((variable-tuple
;; (cond ((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
;; ((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
;; ((x-list-fonts "Source Sans Pro") '(:font "Source Sans Pro"))
;; ;((x-family-fonts "Sans Serif") '(:family "Sans Serif"))
;; (nil (warn "Cannot find a Sans Serif Font. Install Source Sans Pro."))))
;; (base-font-color (face-foreground 'default nil 'default))
;; (headline `(:inherit default :weight bold :foreground ,base-font-color)))
;;
;; (custom-theme-set-faces
;; 'user
;; `(org-level-8 ((t (,@headline ,@variable-tuple))))
;; `(org-level-7 ((t (,@headline ,@variable-tuple))))
;; `(org-level-6 ((t (,@headline ,@variable-tuple))))
;; `(org-level-5 ((t (,@headline ,@variable-tuple))))
;; `(org-level-4 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#8470ff"))))
;; `(org-level-3 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#228b22"))))
;; `(org-level-2 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#5f9ea0"))))
;; `(org-level-1 ((t (,@headline ,@variable-tuple :height 1.0 :foreground "#6a5acd"))))
;; `(org-document-title ((t (,@headline ,@variable-tuple :height 1.2 :foreground "#6a5acd"))))))
(use-package org-ref
;; :init
; code to run before loading-org-ref
:config
(setq
org-ref-completion-library 'org-ref-helm-bibtex
org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename-helm-bibtex
;org-ref-bibliography-notes "~/Dropbox/orgfiles/bibnotes.org"
org-ref-default-bibliography (list "/home/gogo/Dropbox/Bibliography/references.bib")
org-ref-pdf-directory '("/home/gogo/Dropbox/Research_papers")
org-ref-notes-directory "/home/gogo/wiki/refs/"
org-ref-notes-function 'orb-edit-notes)
(defun my/org-ref-open-pdf-at-point ()
"Open the pdf for bibtex key under point if it exists."
(interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(pdf-file (concat org-ref-pdf-directory
(org-ref-get-pdf-filename
(org-ref-get-mendeley-filename key)))))
(if (file-exists-p pdf-file)
(find-file pdf-file)
(message "no pdf found for %s" pdf-file))))
; default keybindings
:bind
(:map org-mode-map
("\C-c(" . org-ref-helm-insert-ref-link)
("\C-c)" . org-ref-helm-insert-cite-link)))
;; (global-set-key (kbd "\C-c c") 'org-capture)
;; (global-set-key (kbd "\C-c a") 'org-agenda)
;; (setq org-agenda-files (list "~/Dropbox/orgfiles/work.org" "~/Dropbox/orgfiles/Life.org" "~/Dropbox/orgfiles/newgtd.org"))
;; (setq org-capture-templates
;; '(("a" "Appointment" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Appointments:" ) "*** %?\n:SCHEDULED: %^T\n:PROPERTIES:\n:END:\n")
;; ("f" "Follow up Later" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Follow up Later:" ) "** %?\n")
;; ("F" "Follow up Later (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Follow up Later:" ) "** %?\n")
;; ("l" "Important Link (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Important Links") "* %? %^L %^g \n%T" :prepend t)
;; ("L" "Read/Watch later" entry (file+headline "~/Dropbox/orgfiles/Life.org" "Links") "** %? %^L %^g \n%T" :prepend t)
;; ("s" "Shopping list" checkitem (file+headline "~/Dropbox/orgfiles/newgtd.org" "Shopping List:") "- [ ] %?\n" :prepend t)
;; ("t" "Work TODO" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Work") "*** TODO %?%^g\n:CREATED: %u\n:SCHEDULED: %^T\n:DEADLINE: %^T" :prepend t)
;; ("T" "Personal TODO" entry (file+headline "~/Dropbox/orgfiles/newgtd.org" "Life") "*** TODO %?%^g\n:CREATED: %u\n:SCHEDULED: %^T\n:DEADLINE: %^T" :prepend t)
;; ("n" "Note (work)" entry (file+headline "~/Dropbox/orgfiles/work.org" "Note space:") "** %?\n%u" :prepend t)
;; ("N" "Note (personal)" entry (file+headline "~/Dropbox/orgfiles/Life.org" "Note space:") "** %?\n%u" :prepend t)
;; ("j" "Journal" entry (file+datetree "~/Dropbox/journal.org") "* %?\nEntered on %U\n %i\n %a")))
;;
;; (defadvice org-agenda (around split-vertically activate)
;; (let ((split-width-threshold 80)) ; or whatever width makes sense for you
;; ad-do-it))
;; (defadvice org-capture (around split-vertically activate)
;; (let ((split-width-threshold 80)) ; or whatever width makes sense for you
;; ad-do-it))
;; (global-set-key (kbd "\C-c \C-w") 'org-refile)
;; ;(global-set-key (kbd "S-c") "C")
;; (setq org-refile-targets '((org-agenda-files :maxlevel . 3)))
;; (setq org-refile-use-outline-path 'file)
;; (setq org-outline-path-complete-in-steps nil)
;; (setq org-refile-allow-creating-parent-nodes 'confirm)
;; (setq org-todo-keywords'((sequence "TODO(t)" "ONGOING(o)" "ALMOST(a)" "ORDERED(O)" "FEEDBACK(f)" "VERIFY(v)" "|" "DONE(d)" "DELEGATED" "RECIEVED(r)" "CANCELED(c)")))
;;
;; (setq org-todo-keyword-faces
;; '(("TODO" . org-warning) ("ONGOING" . "orange")
;; ("CANCELED" . "red") ("DONE" . "#00ff7f") ("RECIEVED" . "green") ("ALMOST". "blue")))
;; (setq org-latex-pdf-process
;; '("latexmk -pdflatex='pdflatex -interaction nonstopmode' -pdf -bibtex -f %f"))
;; (require 'ox-beamer)
;; (setq org-highlight-latex-and-related '(latex script entities))
(use-package org-autolist
:hook (org-mode . org-autolist-mode))
;(add-hook 'org-mode-hook (lambda () (org-autolist-mode)))
(use-package pdf-tools
:ensure t
:config
(pdf-tools-install))
;; (org-babel-do-load-languages
;; 'org-babel-load-languages '((python . t)))
;; (setq org-babel-python-command "/home/gogo/anaconda3/bin/python")
;; (defun org-fill-paragraph--latex-environment (&rest args)
;; "Use default fill-paragraph in latex environments."
;; (not (eql (org-element-type (org-element-context)) 'latex-environment)))
;; (advice-add 'org-fill-paragraph :before-while #'org-fill-paragraph--latex-environment)
(use-package org-roam
:ensure t
:init
(setq org-roam-v2-ack t)
:custom
(org-roam-directory "~/wiki")
(setq org-roam-complete-link-at-point t)
:bind (("C-c n l" . org-roam-buffer-toggle)
("C-c n f" . org-roam-node-find)
("C-c n i" . org-roam-node-insert)
:map org-mode-map
("C-M-i" . completion-at-point))
:config
(org-roam-setup)
(add-to-list 'display-buffer-alist
'("\\*org-roam\\*"
(display-buffer-in-direction)
(direction . right)
(window-width . 0.33)
(window-height . fit-window-to-buffer))))
(use-package org-roam-bibtex
:after org-roam
:hook (org-roam-mode . org-roam-bibtex-mode)
:config
(require 'org-ref)
:bind
(:map org-roam-bibtex-mode-map
(("C-c m f" . orb-find-non-ref-file))
:map org-mode-map
(("C-c m t" . orb-insert-non-ref)
("C-c m a" . orb-note-actions)))
:custom
(orb-autokey-format "%a%y")
(setq orb-note-actions-interface 'helm))
(setq orb-preformat-keywords
'("citekey" "title" "url" "author-or-editor" "keywords" "file")
orb-process-file-keyword t
orb-file-field-extensions '("pdf"))
(setq org-roam-capture-templates
'(("d" "default" plain "%?"
:if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
"#+title: ${title}\n")
:unnarrowed t)
("r" "bibliography reference" plain
(file "/home/gogo/.emacs.d/template/orb-org-noter-integration-template")
:if-new
(file+head "refs/${citekey}.org" "#+title: ${title}\n"))))
;; (use-package org-roam
;; ;; :init
;; :hook (after-init . org-roam-mode)
;; :config
;; (setq
;; org-roam-directory "~/wiki"
;; org-roam-tag-sources '(prop all-directories)
;; org-roam-capture-templates
;; '(("d" "default" plain (function org-roam--capture-get-point)
;; "%?"
;; :file-name "%<%Y-%m-%d-%H%M%S>-${slug}"
;; :head "#+TITLE: ${title} "
;; :unnarrowed t)
;; ("r" "reference" plain (function org-roam--capture-get-point)
;; "User input: %^{PROMPT}"
;; :file-name "references/%<%Y-%m-%d-%H%M%S>-${slug}"
;; :head "#+TITLE: ${title}"
;; :unnarrowed t))))
;; (defvar orb-title-format "${author-or-editor-abbrev} (${date}). ${title}."
;; "Format of the title to use for `orb-templates'.")
;; (use-package org-roam-bibtex
;; :after org-roam
;; :hook (org-roam-mode . org-roam-bibtex-mode)
;; :config
;; (require 'org-ref)
;; :bind (:map org-roam-bibtex-mode-map
;; (("C-c m f" . orb-find-non-ref-file))
;; :map org-mode-map
;; (("C-c m t" . orb-insert-non-ref)
;; ("C-c m a" . orb-note-actions)))
;; :init
;; :custom
;; (orb-autokey-format "%a%y")
;; (orb-templates
;; `(("r" "ref" plain
;; (function org-roam-capture--get-point)
;; ""
;; :file-name "refs/${citekey}"
;; :head ,(s-join "\n"
;; (list
;; (concat "#+title: "
;; orb-title-format)
;; "#+roam_key: ${ref}"
;; "#+created: %U"
;; "#+last_modified: %U\n\n"))
;; :unnarrowed t)
;; ("p" "ref + physical" plain
;; (function org-roam-capture--get-point)
;; ""
;; :file-name "refs/${citekey}"
;; :head ,(s-join "\n"
;; (list
;; (concat "#+title: "
;; orb-title-format)
;; "#+roam_key: ${ref}"
;; ""
;; "* Notes :physical:")))
;; ("n" "ref + noter" plain
;; (function org-roam-capture--get-point)
;; ""
;; :file-name "refs/${citekey}"
;; :head ,(s-join "\n"
;; (list
;; (concat "#+title: "
;; orb-title-format)
;; "#+roam_key: ${ref}"
;; ""
;; "* Notes :noter:"
;; ":PROPERTIES:"
;; ":NOTER_DOCUMENT: %(orb-process-file-field \"${citekey}\")"
;; ":NOTER_PAGE:"
;; ":END:"))))))
;; ;(use-package org-roam-bibtex
;; ; :after org-roam
;; ; :hook (org-roam-mode . org-roam-bibtex-mode))
;; ;(use-package org-noter)
(use-package org-noter
:bind (:map org-mode-map
(("C-c N" . zp/org-noter-dwim))
:map org-noter-doc-mode-map
(("M-p" . zp/org-noter-insert-precise-note-dwim)))
; M-i replaces tab-to-tab-stop
:config
(setq org-noter-hide-other t
org-noter-auto-save-last-location t
org-noter-doc-split-fraction '(0.57 0.43))
(defun zp/org-noter-visual-line-mode ()
"Enable visual-line-mode in ‘org-noter’ notes.
Workaround to counter race conditions with the margins."
(let ((parent (current-buffer))
(refresh (lambda (parent)
(with-current-buffer parent
(visual-line-mode 'toggle)
(visual-line-mode 'toggle)))))
(run-at-time "1 sec" nil refresh parent)
(run-at-time "5 sec" nil refresh parent)))
(add-hook 'org-noter-notes-mode-hook #'zp/org-noter-visual-line-mode)
;; Fix for hiding truncation
(defun org-noter--set-notes-scroll (_window &rest _ignored)
nil)
;; Fix for visual-line-mode with PDF files
(defun org-noter--note-after-tipping-point (_point _note-property _view)
nil)
(defun zp/org-noter-indirect (arg)
"Ensure that org-noter starts in an indirect buffer.
Without this wrapper, org-noter creates a direct buffer
restricted to the notes, but this causes problems with the refile
system. Namely, the notes buffer gets identified as an
agenda-files buffer.
This wrapper addresses it by having org-noter act on an indirect
buffer, thereby propagating the indirectness."
(interactive "P")
(if (org-entry-get nil org-noter-property-doc-file)
(with-selected-window (org-tree-to-indirect-buffer nil t)
;; (with-selected-window (zp/org-tree-to-indirect-buffer-folded nil t)
(org-noter arg)
(kill-buffer))
(org-noter arg)))
(defun zp/org-noter-dwim (arg)
"Run org-noter on the current tree, even if we’re in the agenda."
(interactive "P")
(let ((in-agenda (derived-mode-p 'org-agenda-mode))
(marker))
(cond (in-agenda
(setq marker (get-text-property (point) 'org-marker))
(with-current-buffer (marker-buffer marker)
(goto-char marker)
(unless (org-entry-get nil org-noter-property-doc-file)
(user-error "No org-noter info on this tree"))
(zp/org-noter-indirect arg)))
(t
(zp/org-noter-indirect arg)
(setq marker (point-marker))))
(org-with-point-at marker
(let ((tags (org-get-tags)))
(when (and (org-entry-get nil org-noter-property-doc-file)
(not (member "noter" tags)))
(org-set-tags (push "noter" tags)))))
(unless in-agenda
(set-marker marker nil))))
(defun zp/org-noter-insert-precise-note-dwim (force-mouse)
"Insert note associated with a specific location.
If in nov-mode, use point rather than the mouse to target the
position."
(interactive "P")
(if (and (derived-mode-p 'nov-mode)
(not force-mouse))
(let ((pos (if (region-active-p)
(min (region-beginning) (point))
(point))))
(org-noter-insert-note pos))
(org-noter-insert-precise-note)))
(define-key org-noter-doc-mode-map (kbd "j") 'pdf-view-next-line-or-next-page)
(define-key org-noter-doc-mode-map (kbd "k") 'pdf-view-previous-line-or-previous-page))
(use-package projectile
:hook
(after-init . projectile-global-mode)
:init
(setq-default
projectile-cache-file (expand-file-name ".projectile-cache" user-emacs-directory)
projectile-known-projects-file (expand-file-name ".projectile-bookmarks" user-emacs-directory))
:custom
(projectile-completion-system 'helm)
(projectile-enable-caching t))
(use-package yaml-mode :mode "\\.yml\\'")
(use-package python
:ensure nil
:hook (python-mode . turn-on-prettify-symbols-mode)
:config
(when (executable-find "ipython")
(setq-default
python-shell-interpreter "ipython"
python-shell-interpreter-args "--colors=Linux --profile=default --simple-prompt"
python-shell-prompt-output-regexp "Out\\[[0-9]+\\]: "
python-shell-prompt-regexp "In \\[[0-9]+\\]: "
python-shell-completion-setup-code
"from IPython.core.completerlib import module_completion"
python-shell-completion-module-string-code
"';'.join(module_completion('''%s'''))\n"
python-shell-completion-string-code
"';'.join(get_ipython().Completer.all_completions('''%s'''))\n")))
(use-package anaconda-mode
:hook ((python-mode . anaconda-mode)
(python-mode . anaconda-eldoc-mode)))
;(add-hook 'python-mode-hook 'anaconda-mode)
;(add-hook 'python-mode-hook 'anaconda-eldoc-mode)
(use-package conda
:ensure t
:init
(setq conda-anaconda-home (expand-file-name "~/Software/anaconda3"))
(setq conda-env-home-directory (expand-file-name "~/Software/anaconda3")))
(use-package company-anaconda
:after company
:config
(add-to-list 'company-backends 'company-anaconda))
;(eval-after-load "company"
; '(add-to-list 'company-backends 'company-anaconda))
;(use-package pyvenv)
;(setenv "WORKON_HOME" (concat (getenv "CONDA_PREFIX") "/envs"))
;(pyvenv-mode 1)
(use-package em-hist
:ensure nil
:custom (eshell-hist-ignoredups t))
(use-package esh-mode
:ensure nil
:preface
(defun me/eshell-bol-shifted ()
"See `eshell-bol'. Support shift."
(interactive "^")
(eshell-bol))
:bind
(:map eshell-mode-map
([remap eshell-bol] . me/eshell-bol-shifted))
:hook
((eshell-mode . me/hl-line-mode-off)
(eshell-mode . (lambda () (setq-local scroll-margin 0))))
:custom
(eshell-scroll-to-bottom-on-input t))
(setq eshell-prompt-regexp "^[^#$\n]*[#$] "
eshell-prompt-function
(lambda nil
(concat
"[" (user-login-name) "@" (system-name) " "
(if (string= (eshell/pwd) (getenv "HOME"))
"~" (eshell/basename (eshell/pwd)))
"]"
(if (= (user-uid) 0) "# " "$ "))))
(use-package term
:ensure nil
:hook
((term-mode . me/hl-line-mode-off)
(term-mode . (lambda () (setq-local scroll-margin 0)))))
(use-package git-commit
:preface
(defun me/git-commit-auto-fill-everywhere ()
(setq fill-column 72)
(setq-local comment-auto-fill-only-comments nil))
:hook
(git-commit-mode . me/git-commit-auto-fill-everywhere)
:custom
(git-commit-summary-max-length 50))
(use-package magit
:bind
(:map magit-hunk-section-map
("RET" . magit-diff-visit-file-other-window)
([return] . magit-diff-visit-file-other-window))
:custom
(magit-display-buffer-function 'magit-display-buffer-same-window-except-diff-v1)
(magit-diff-highlight-hunk-body nil)
(magit-diff-highlight-hunk-region-functions
'(magit-diff-highlight-hunk-region-dim-outside magit-diff-highlight-hunk-region-using-face))
(magit-popup-display-buffer-action '((display-buffer-same-window)))
(magit-refs-show-commit-count 'all)
(magit-section-show-child-count t)
:config
(remove-hook 'magit-section-highlight-hook #'magit-section-highlight))
(use-package gitattributes-mode)
(use-package gitconfig-mode)
(use-package gitignore-mode)
;; (use-package company
;; :bind
;; (:map company-active-map
;; ("RET" . nil)
;; ([return] . nil)
;; ("TAB" . company-complete-selection)
;; ([tab] . company-complete-selection)
;; ("<C-tab>" . company-complete-common))
;; :hook
;; (after-init . global-company-mode)
;; :custom
;; (company-dabbrev-downcase nil)
;; (company-idle-delay .2)
;; (company-minimum-prefix-length 1)
;; (company-require-match nil)
;; (company-tooltip-align-annotations t)
;; :config
;; (add-to-list 'company-backends 'company-capf)
;; (setq company-dabbrev-char-regexp "[A-z:-]"))
;;
;;
;; (use-package yasnippet
;; :bind
;; (:map yas-minor-mode-map
;; ("TAB" . nil)
;; ([tab] . nil)
;; ("<C-tab>" . yas-expand))
;; :hook
;; ((emacs-lisp-mode . yas-minor-mode)
;; (html-mode . yas-minor-mode)
;; (js-mode . yas-minor-mode)
;; (org-mode . yas-minor-mode)
;; (python-mode . yas-minor-mode)
;; (LaTeX-mode . yas-minor-mode))
;; :custom
;; (yas-snippet-dirs `(,(expand-file-name "snippets/" user-emacs-directory)))
;; (yas-verbosity 2)
;; :config
;; (yas-reload-all))
;; (use-package yasnippet-snippets)
(global-set-key [remap kill-buffer] #'kill-this-buffer)
(use-package edit-server
:hook (after-init . edit-server-start))
(use-package server
:ensure nil
:hook (after-init . server-start))
;; (use-package newcomment
;; :ensure nil
;; :bind
;; ("<M-return>" . comment-indent-new-line)
;; :custom
;; (comment-auto-fill-only-comments t)
;; (comment-multi-line t))
(use-package ediff-wind
:ensure nil
:custom
(ediff-split-window-function #'split-window-horizontally)
(ediff-window-setup-function #'ediff-setup-windows-plain))
(use-package helm
:preface
(defun me/helm-focus-follow ()
;; (let ((point (point)))
;; (when (and (pulse-available-p) (> point 1))
;; (pulse-momentary-highlight-one-line point)))
(recenter-top-bottom (car recenter-positions)))
(defun me/helm-grab-candidates (beg end)
(interactive "r")
(if (region-active-p)
(kill-ring-save beg end)
(with-helm-buffer (kill-ring-save (point-min) (point-max)))))
:bind
(([remap execute-extended-command] . helm-M-x)
([remap find-file] . helm-find-files)
([remap isearch-forward] . helm-occur)
([remap switch-to-buffer] . helm-buffers-list)
:map helm-map
("<left>" . backward-char)
("<right>" . forward-char)
("M-w" . me/helm-grab-candidates))
:hook
(after-init . helm-mode)
;; (helm-after-action . me/helm-focus-follow)
:custom
(helm-M-x-fuzzy-match t)
(helm-always-two-windows t)
(helm-buffer-max-length nil)
(helm-buffers-fuzzy-matching t)
(helm-completion-in-region-fuzzy-match t)
(helm-display-header-line nil)
(helm-ff-no-preselect t)
(helm-ff-skip-boring-files t)
(helm-find-file-ignore-thing-at-point t)
(helm-help-full-frame nil)
(helm-mode-fuzzy-match t)
(helm-net-prefer-curl (if (executable-find "curl") t nil))
(helm-org-headings-fontify t)
(helm-scroll-amount 5)
(helm-split-window-default-side 'left)
(helm-truncate-lines t))
(use-package helm-imenu
:ensure nil
:bind
(:map helm-imenu-map
("<left>" . backward-char)
("<right>" . forward-char)))
(add-to-list 'display-buffer-alist
`(,(rx bos "*helm" (* not-newline) "*" eos)
(display-buffer-in-side-window)
(inhibit-same-window . t)
(window-height . 0.4)))
(global-set-key (kbd "M-x") 'helm-M-x)
(with-eval-after-load 'helm
(define-key helm-map (kbd "C-c p") 'ignore)
(define-key helm-map (kbd "<tab>") 'helm-execute-persistent-action) ; rebind tab to run persistent action
(define-key helm-map (kbd "C-i") 'helm-execute-persistent-action) ; make TAB works in terminal
(define-key helm-map (kbd "C-z") 'helm-select-action))
(use-package helm-ag
:bind
(:map helm-ag-map
("<left>" . backward-char)
("<right>" . forward-char))
:custom
(helm-ag-show-status-function nil))
(use-package helm-descbinds
:bind
([remap describe-bindings] . helm-descbinds)
:custom
(helm-descbinds-window-style 'split-window))
(use-package helm-describe-modes
:bind ([remap describe-mode] . helm-describe-modes))
(use-package helm-org
:commands helm-org-in-buffer-headings)
(use-package helm-projectile
:defer nil
:bind
(:map helm-projectile-find-file-map
("<left>" . backward-char)
("<right>" . forward-char))
:config
(helm-projectile-toggle 1))
(use-package helm-bibtex
:ensure t
:config
(setq bibtex-completion-pdf-field "file")
(setq bibtex-completion-bibliography '("/home/gogo/Dropbox/Bibliography/references.bib")) ; my master.bib
(setq bibtex-completion-library-path '("/home/gogo/Dropbox/Research_papers")) ; pdf folder
(setq bibtex-completion-notes-path "/home/gogo/Dropbox/Notes/"))
;(autoload 'helm-bibtex "helm-bibtex" "" t)
;(setq bibtex-completion-bibliography
; '("/home/gogo/Dropbox/Bibliography/references.bib"))
;(setq bibtex-completion-library-path '("/home/gogo/Dropbox/Research_papers"))
;(setq bibtex-completion-notes-path "/home/gogo/Dropbox/Notes/")
(use-package help-mode
:ensure nil
:bind
(:map help-mode-map
("<" . help-go-back)
(">" . help-go-forward)))
(use-package aggressive-indent