;;; config.el -*- lexical-binding: t; -*-

;; ============================================================================
;; Evil - Esc exits insert mode (like real vim)
;; ============================================================================
(define-key evil-insert-state-map (kbd "<escape>") 'evil-normal-state)

;; ============================================================================
;; Server - Allow emacsclient to connect to this GUI frame
;; ============================================================================
(unless (daemonp)
  (require 'server)
  (unless (server-running-p)
    (server-start)))

;; ============================================================================
;; User Info
;; ============================================================================
(setq user-full-name "Kris Yotam"
      user-mail-address "kris@krisyotam.com")

;; ============================================================================
;; Theme & Appearance - Plan9 (light default, dark toggle with nibelung)
;; ============================================================================
(setq doom-theme 'plan9)

;; Disable syntax highlighting
(global-font-lock-mode -1)

;; Toggle between light and dark mode
(defvar kris/dark-mode nil "Track current theme state.")

(defun kris/toggle-dark-mode ()
  "Toggle between plan9 (light) and nibelung-dark themes."
  (interactive)
  (if kris/dark-mode
      (progn
        (load-theme 'plan9 t)
        (setq kris/dark-mode nil)
        (message "Light mode (Plan9)"))
    (progn
      (load-theme 'nibelung-dark t)
      (setq kris/dark-mode t)
      (message "Dark mode (Nibelung)"))))

;; Keybind: SPC t d (toggle dark mode)
(map! :leader
      :desc "Toggle dark mode" "t d" #'kris/toggle-dark-mode)

;; Force fully opaque frame (no transparency)
(set-frame-parameter nil 'alpha-background 100)
(add-to-list 'default-frame-alist '(alpha-background . 100))
(set-frame-parameter nil 'alpha '(100 . 100))
(add-to-list 'default-frame-alist '(alpha . (100 . 100)))

;; Font configuration
(setq doom-font (font-spec :family "JetBrainsMono Nerd Font" :size 14)
      doom-variable-pitch-font (font-spec :family "JetBrainsMono Nerd Font" :size 14)
      doom-big-font (font-spec :family "JetBrainsMono Nerd Font" :size 20))

;; Line numbers (absolute, not relative)
(setq display-line-numbers-type t)

;; Larger fringe for aesthetics
(setq-default left-fringe-width 16
              right-fringe-width 16)

;; ============================================================================
;; Custom Dashboard Banner
;; ============================================================================
(defun kris/dashboard-ascii-banner ()
  "Custom ASCII banner for doom dashboard."
  (let* ((banner '(
"                                                                              "
"  ██╗  ██╗██████╗ ██╗███████╗    ██╗   ██╗ ██████╗ ████████╗ █████╗ ███╗   ███╗"
"  ██║ ██╔╝██╔══██╗██║██╔════╝    ╚██╗ ██╔╝██╔═══██╗╚══██╔══╝██╔══██╗████╗ ████║"
"  █████╔╝ ██████╔╝██║███████╗     ╚████╔╝ ██║   ██║   ██║   ███████║██╔████╔██║"
"  ██╔═██╗ ██╔══██╗██║╚════██║      ╚██╔╝  ██║   ██║   ██║   ██╔══██║██║╚██╔╝██║"
"  ██║  ██╗██║  ██║██║███████║       ██║   ╚██████╔╝   ██║   ██║  ██║██║ ╚═╝ ██║"
"  ╚═╝  ╚═╝╚═╝  ╚═╝╚═╝╚══════╝       ╚═╝    ╚═════╝    ╚═╝   ╚═╝  ╚═╝╚═╝     ╚═╝"
"                                                                              "))
         (longest-line (apply #'max (mapcar #'length banner))))
    (put-text-property
     (point)
     (dolist (line banner (point))
       (insert (+doom-dashboard--center
                +doom-dashboard--width
                (concat line (make-string (max 0 (- longest-line (length banner))) 32)))
               "\n"))
     'face 'doom-dashboard-banner)))

(setq +doom-dashboard-ascii-banner-fn #'kris/dashboard-ascii-banner)

;; Plan9 theme colors for dashboard
(custom-set-faces!
  '(doom-dashboard-menu-title :foreground "#B8996F")  ; Muted yellow
  '(doom-dashboard-menu-desc :foreground "#4A6FA5"))  ; Blue - keybindings like SPC f r

;; Custom dashboard menu items
(setq +doom-dashboard-menu-sections
      '(("Open notes"
         :icon (nerd-icons-faicon "nf-fa-book" :face 'doom-dashboard-menu-title)
         :when (featurep! :lang org +roam)
         :action org-roam-node-find)
        ("Open project"
         :icon (nerd-icons-octicon "nf-oct-repo" :face 'doom-dashboard-menu-title)
         :action projectile-switch-project)
        ("Recently opened files"
         :icon (nerd-icons-faicon "nf-fa-file_text" :face 'doom-dashboard-menu-title)
         :action recentf-open-files)
        ("Open paper feeds"
         :icon (nerd-icons-faicon "nf-fa-rss" :face 'doom-dashboard-menu-title)
         :when (featurep! :app elfeed)
         :action elfeed)
        ("Open private configuration"
         :icon (nerd-icons-octicon "nf-oct-gear" :face 'doom-dashboard-menu-title)
         :when (file-directory-p doom-user-dir)
         :action doom/open-private-config)
        ("Open documentation"
         :icon (nerd-icons-faicon "nf-fa-book" :face 'doom-dashboard-menu-title)
         :action doom/help)))

;; ============================================================================
;; Org Mode Base Configuration
;; ============================================================================
(setq org-directory "~/notes/")

;; Pretty org-mode settings
(after! org
  (setq org-hide-emphasis-markers t
        org-link-descriptive t
        org-pretty-entities t
        org-startup-indented t
        org-startup-folded 'showall      ; Show everything expanded
        org-startup-with-inline-images t
        org-image-actual-width '(400)
        org-cycle-open-archived-trees t  ; Don't hide archived
        org-catch-invisible-edits 'show-and-error
        org-hide-drawer-startup nil      ; Never hide drawers on startup
        org-cycle-hide-drawers nil)      ; Never collapse drawers with TAB

  ;; Force drawers to stay open
  (remove-hook 'org-cycle-hook #'org-cycle-hide-drawers))

;; org-superstar for beautiful bullets
(after! org-superstar
  (setq org-superstar-headline-bullets-list '("◉" "○" "◈" "◇" "▣")
        org-superstar-item-bullet-alist '((?- . ?•) (?+ . ?➤))))


;; ============================================================================
;; Org-Roam Configuration (Obsidian-like functionality)
;; ============================================================================
(after! org-roam
  (setq org-roam-directory "~/notes/"
        org-roam-dailies-directory "0 - Journal/"
        org-roam-db-gc-threshold most-positive-fixnum
        org-roam-completion-everywhere t)

  ;; Define allowed values for constrained properties
  (setq org-global-properties
        '(("STATUS_ALL" . "seed growing evergreen wilted")
          ("CERTAINTY_ALL" . "certain highly-likely likely possible unlikely highly-unlikely remote impossible")
          ("IMPORTANCE_ALL" . "1 2 3 4 5 6 7 8 9 10")))

  ;; Templates for new notes with full metadata
  (setq org-roam-capture-templates
        '(("d" "default" plain "%?"
           :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                              ":PROPERTIES:
:ID:         ${slug}
:START:      %<%Y-%m-%d>
:FINISH:
:CERTAINTY:  possible
:STATUS:     seed
:IMPORTANCE: 5
:PREVIEW:
:END:
#+title: ${title}
#+filetags:

")
           :unnarrowed t)
          ("z" "zettel" plain "%?"
           :target (file+head "6 - Zettlekasten/%<%Y%m%d%H%M%S>-${slug}.org"
                              ":PROPERTIES:
:ID:         ${slug}
:START:      %<%Y-%m-%d>
:FINISH:
:CERTAINTY:  possible
:STATUS:     seed
:IMPORTANCE: 5
:PREVIEW:
:END:
#+title: ${title}
#+filetags: :zettel:

* Source

* Content

* References
")
           :unnarrowed t)
          ("t" "topic" plain "%?"
           :target (file+head "3 - Topics/${slug}.org"
                              ":PROPERTIES:
:ID:         ${slug}
:START:      %<%Y-%m-%d>
:FINISH:
:CERTAINTY:  possible
:STATUS:     seed
:IMPORTANCE: 5
:PREVIEW:
:END:
#+title: ${title}
#+filetags: :topic:

")
           :unnarrowed t)))

  ;; Daily notes templates
  (setq org-roam-dailies-capture-templates
        '(("d" "default" entry "* %?"
           :target (file+head "%<%Y-%m-%d>.org"
                              "#+title: %<%Y-%m-%d>\n#+filetags: :journal:\n\n")))))

;; ============================================================================
;; Org-Roam-UI (Graph Visualization)
;; ============================================================================
(use-package! org-roam-ui
  :after org-roam
  :config
  (setq org-roam-ui-sync-theme t
        org-roam-ui-follow t
        org-roam-ui-update-on-save t
        org-roam-ui-open-on-start nil))

;; ============================================================================
;; MD-Roam (Support for existing Markdown files)
;; ============================================================================
(use-package! md-roam
  :after org-roam
  :config
  (setq md-roam-file-extension "md")
  (md-roam-mode 1)
  ;; Include .md files in org-roam
  (setq org-roam-file-extensions '("org" "md")))

;; ============================================================================
;; LaTeX & Math Rendering
;; ============================================================================
(after! org
  ;; Use dvisvgm for crisp SVG previews
  (setq org-preview-latex-default-process 'dvisvgm)

  ;; Styling: scale to match prose, pure black, NO background
  (plist-put org-format-latex-options :scale 0.85)
  (plist-put org-format-latex-options :foreground 'default)
  (plist-put org-format-latex-options :background 'default)

  ;; Extended LaTeX packages for complex equations
  (setq org-latex-packages-alist
        '(("" "amsmath" t)        ; Advanced math environments
          ("" "amssymb" t)        ; Math symbols
          ("" "amsthm" t)         ; Theorem environments
          ("" "mathtools" t)      ; Extensions to amsmath
          ("" "physics" t)        ; Physics notation (bra-ket, derivatives)
          ("" "siunitx" t)        ; SI units
          ("" "mhchem" t)         ; Chemical formulas
          ("" "cancel" t)         ; Strike-through in equations
          ("" "mathrsfs" t)       ; Script fonts (\mathscr)
          ("" "bm" t)             ; Bold math
          ("" "bbm" t)            ; Blackboard bold
          ("" "esint" t)          ; More integral signs
          ("" "tikz" t)           ; Diagrams
          ("" "pgfplots" t)))     ; Plots

  ;; Custom LaTeX preamble for extra commands (pure black math - no blue)
  (setq org-format-latex-header
        (concat org-format-latex-header
                "\n\\newcommand{\\R}{\\mathbb{R}}"
                "\n\\newcommand{\\N}{\\mathbb{N}}"
                "\n\\newcommand{\\Z}{\\mathbb{Z}}"
                "\n\\newcommand{\\Q}{\\mathbb{Q}}"
                "\n\\newcommand{\\C}{\\mathbb{C}}"
                "\n\\newcommand{\\norm}[1]{\\left\\lVert#1\\right\\rVert}"
                "\n\\newcommand{\\abs}[1]{\\left|#1\\right|}"
                "\n\\DeclareMathOperator{\\Tr}{Tr}"
                "\n\\DeclareMathOperator{\\rank}{rank}"
                "\n\\DeclareMathOperator{\\sgn}{sgn}")))

;; Auto-toggle LaTeX fragments
(use-package! org-fragtog
  :after org
  :hook (org-mode . org-fragtog-mode))

;; ============================================================================
;; Split Pane Preview (Raw Left, Rendered Right)
;; ============================================================================
(defun kris/org-split-preview ()
  "Open current org file in split view: raw on left, rendered HTML on right."
  (interactive)
  (let ((org-file (buffer-file-name)))
    (delete-other-windows)
    ;; Left side: raw org (disable latex preview here)
    (org-latex-preview-clear-overlays)
    ;; Right side: export and view
    (split-window-right)
    (other-window 1)
    (org-export-to-file 'html
        (concat (file-name-sans-extension org-file) ".html")
      nil nil nil nil nil
      (lambda (file) (browse-url-of-file file)))))

(defun kris/org-preview-in-browser ()
  "Export current org buffer to HTML and open in browser."
  (interactive)
  (let ((html-file (concat (file-name-sans-extension (buffer-file-name)) ".html")))
    (org-export-to-file 'html html-file nil nil nil nil nil)
    (browse-url-of-file html-file)))

;; ============================================================================
;; Writing Environment
;; ============================================================================
;; Olivetti for centered writing - only when single window
(use-package! olivetti
  :config
  (setq olivetti-body-width 100)

  (defun kris/olivetti-single-window ()
    "Enable olivetti only when there's a single window."
    (if (= (count-windows) 1)
        (olivetti-mode 1)
      (olivetti-mode -1)))

  (defun kris/update-olivetti-all-windows ()
    "Update olivetti state in all windows."
    (dolist (win (window-list))
      (with-current-buffer (window-buffer win)
        (when (derived-mode-p 'org-mode 'markdown-mode 'LaTeX-mode 'text-mode)
          (kris/olivetti-single-window)))))

  (add-hook 'window-configuration-change-hook #'kris/update-olivetti-all-windows)
  (add-hook 'org-mode-hook #'kris/olivetti-single-window)
  (add-hook 'markdown-mode-hook #'kris/olivetti-single-window)
  (add-hook 'LaTeX-mode-hook #'kris/olivetti-single-window)
  (add-hook 'text-mode-hook #'kris/olivetti-single-window))

;; Mixed pitch mode for prose
(use-package! mixed-pitch
  :hook (org-mode . mixed-pitch-mode))

;; Markdown rendering with LaTeX math support
(after! markdown-mode
  (setq markdown-enable-math t
        markdown-fontify-code-blocks-natively t
        markdown-command "pandoc -f markdown -t html5 --mathjax --standalone"))

;; texfrag — inline LaTeX preview in markdown buffers (like org-fragtog for org)
;; Renders \(...\) inline and \[...\] display math as SVG overlays
(use-package! texfrag
  :after markdown-mode
  :config
  (setq texfrag-preview-buffer-at-start t)
  ;; Use same dvisvgm pipeline and scale as org-mode previews
  (setq texfrag-LaTeX-frag-alist
        '(("\\\\(" "\\\\)" "\\(" "\\)")
          ("\\\\\\[" "\\\\\\]" "\\[" "\\]")
          ("\\\\begin{equation}" "\\\\end{equation}" "\\begin{equation}" "\\end{equation}")
          ("\\\\begin{equation\\*}" "\\\\end{equation\\*}" "\\begin{equation*}" "\\end{equation*}")
          ("\\\\begin{align}" "\\\\end{align}" "\\begin{align}" "\\end{align}")
          ("\\\\begin{align\\*}" "\\\\end{align\\*}" "\\begin{align*}" "\\end{align*}")))
  ;; Inherit LaTeX packages from org config
  (setq texfrag-header-default
        (concat "\\documentclass{article}\n"
                "\\usepackage{amsmath}\n"
                "\\usepackage{amssymb}\n"
                "\\usepackage{amsthm}\n"
                "\\usepackage{mathtools}\n"
                "\\usepackage{physics}\n"
                "\\usepackage{mathrsfs}\n"
                "\\usepackage{bm}\n"
                "\\usepackage{bbm}\n"
                "\\usepackage{cancel}\n"
                "\\newcommand{\\R}{\\mathbb{R}}\n"
                "\\newcommand{\\N}{\\mathbb{N}}\n"
                "\\newcommand{\\Z}{\\mathbb{Z}}\n"
                "\\newcommand{\\Q}{\\mathbb{Q}}\n"
                "\\newcommand{\\C}{\\mathbb{C}}\n"
                "\\newcommand{\\norm}[1]{\\left\\lVert#1\\right\\rVert}\n"
                "\\newcommand{\\abs}[1]{\\left|#1\\right|}\n"
                "\\DeclareMathOperator{\\Tr}{Tr}\n"
                "\\DeclareMathOperator{\\rank}{rank}\n"
                "\\DeclareMathOperator{\\sgn}{sgn}\n"
                "\\pagestyle{empty}\n"
                "\\begin{document}\n"))
  :hook (markdown-mode . texfrag-mode))

;; Markdown preview inside Emacs using eww
(defun kris/markdown-preview ()
  "Preview current markdown buffer in eww with MathJax support."
  (interactive)
  (unless (derived-mode-p 'markdown-mode)
    (user-error "Not in markdown-mode"))
  (let ((output-file (concat (make-temp-file "md-preview-") ".html"))
        (input-file (buffer-file-name)))
    (if input-file
        ;; File exists - use pandoc on file
        (progn
          (save-buffer)
          (shell-command
           (format "pandoc '%s' -f markdown -t html5 --mathjax --standalone -o '%s'"
                   input-file output-file))
          (eww-open-file output-file))
      ;; Buffer not saved - use buffer content
      (let ((content (buffer-string)))
        (with-temp-file output-file
          (insert (shell-command-to-string
                   (format "echo %s | pandoc -f markdown -t html5 --mathjax --standalone"
                           (shell-quote-argument content)))))
        (eww-open-file output-file)))))

;; Bind to SPC m P (capital P to avoid conflicts)
(map! :after markdown-mode
      :map markdown-mode-map
      :localleader
      "P" #'kris/markdown-preview)

;; LaTeX / AUCTeX configuration
(after! tex
  (setq TeX-auto-save t
        TeX-parse-self t
        TeX-save-query nil
        TeX-PDF-mode t
        TeX-view-program-selection '((output-pdf "PDF Tools"))
        TeX-source-correlate-mode t
        TeX-source-correlate-start-server t)
  (add-hook 'TeX-after-compilation-finished-functions #'TeX-revert-document-buffer))

;; LaTeX keybindings - use b for build, V for view
(map! :after latex
      :map LaTeX-mode-map
      :localleader
      "b" #'TeX-command-run-all      ; build/compile
      "V" #'TeX-view                  ; View PDF (capital V)
      "L" #'TeX-recenter-output-buffer)

;; Also add global keybindings for LaTeX
(map! :after latex
      :map LaTeX-mode-map
      "C-c b" #'TeX-command-run-all
      "C-c v" #'TeX-view)

;; ============================================================================
;; Keybindings
;; ============================================================================
(map! :leader
      (:prefix ("n" . "notes")
       :desc "Find node" "f" #'org-roam-node-find
       :desc "Insert link" "i" #'org-roam-node-insert
       :desc "Capture" "c" #'org-roam-capture
       :desc "Buffer toggle" "b" #'org-roam-buffer-toggle
       :desc "Dailies today" "t" #'org-roam-dailies-goto-today
       :desc "Dailies date" "d" #'org-roam-dailies-goto-date
       :desc "Graph UI" "g" #'org-roam-ui-open
       :desc "Sync database" "s" #'org-roam-db-sync)

      (:prefix ("m" . "math/preview")
       :desc "Live preview (split)" "p" #'org-preview-html-mode
       :desc "Preview in browser" "b" #'kris/org-preview-in-browser
       :desc "Render all LaTeX" "l" #'org-latex-preview
       :desc "Clear LaTeX renders" "c" #'org-latex-preview-clear-overlays)

      (:prefix ("p" . "panes")
       :desc "Open pane (split right)" "o" #'split-window-right
       :desc "Close pane" "c" #'delete-window
       :desc "Balance panes" "b" #'balance-windows
       :desc "Grow pane" "g" #'enlarge-window-horizontally
       :desc "Shrink pane" "s" #'shrink-window-horizontally
       :desc "Pane left" "h" #'windmove-left
       :desc "Pane down" "j" #'windmove-down
       :desc "Pane up" "k" #'windmove-up
       :desc "Pane right" "l" #'windmove-right
       ;; Legacy pane functions
       :desc "Open note in new pane" "n" #'kris/open-note-in-new-pane
       :desc "Reset to single pane" "r" #'kris/reset-to-single-pane))

;; ============================================================================
;; Sliding Panes / Kris Yotam - Mode
;; ============================================================================
;; Open notes side-by-side like stacked tabs in Obsidian

(defvar kris/pane-width 80
  "Width of each sliding pane.")

(defun kris/open-note-in-new-pane ()
  "Open a note in a new vertical pane to the right (sliding panes style)."
  (interactive)
  (split-window-right kris/pane-width)
  (other-window 1)
  (org-roam-node-find))

(defun kris/open-link-in-new-pane ()
  "Open the link at point in a new pane to the right."
  (interactive)
  (let ((link (org-element-context)))
    (when (eq (org-element-type link) 'link)
      (split-window-right kris/pane-width)
      (other-window 1)
      (org-open-at-point))))

(defun kris/close-rightmost-pane ()
  "Close the rightmost pane."
  (interactive)
  (let ((win (window-at (- (frame-width) 2) (/ (frame-height) 2))))
    (when (and win (not (eq win (selected-window))))
      (delete-window win))))

(defun kris/scroll-panes-left ()
  "Scroll all panes left (close leftmost, keep focus)."
  (interactive)
  (delete-window (window-at 0 (/ (frame-height) 2))))

(defun kris/reset-to-single-pane ()
  "Close all other panes, keep current note."
  (interactive)
  (delete-other-windows))

;; Follow links into new panes by default
(setq org-link-frame-setup
      '((vm . vm-visit-folder-other-frame)
        (vm-istrm . vm-visit-imap-folder-other-frame)
        (gnus . org-gnus-no-new-news)
        (file . find-file-other-window)  ; Opens links in other window
        (wl . wl-other-frame)))

;; Horizontal scroll/swipe to switch panes (mouse/trackpad)
(global-set-key (kbd "<mouse-6>") (lambda () (interactive) (other-window -1)))
(global-set-key (kbd "<mouse-7>") (lambda () (interactive) (other-window 1)))
(global-set-key (kbd "<S-wheel-left>") (lambda () (interactive) (other-window -1)))
(global-set-key (kbd "<S-wheel-right>") (lambda () (interactive) (other-window 1)))
(global-set-key (kbd "<S-wheel-up>") (lambda () (interactive) (other-window -1)))
(global-set-key (kbd "<S-wheel-down>") (lambda () (interactive) (other-window 1)))


;; Only show scrollbar on focused window
(scroll-bar-mode -1)  ; Disable globally first

(defun kris/toggle-scrollbar-on-focus ()
  "Show scrollbar only on selected window."
  (walk-windows
   (lambda (win)
     (set-window-scroll-bars win nil nil nil nil))  ; Hide all
   nil t)
  (set-window-scroll-bars (selected-window) 12 'right nil nil))  ; Show on current

(add-hook 'window-selection-change-functions
          (lambda (_) (kris/toggle-scrollbar-on-focus)))
(add-hook 'window-configuration-change-hook #'kris/toggle-scrollbar-on-focus)


;; ============================================================================
;; Performance Optimizations
;; ============================================================================
(setq gc-cons-threshold (* 100 1024 1024)  ; 100MB
      read-process-output-max (* 1024 1024) ; 1MB
      company-idle-delay 0.2
      which-key-idle-delay 0.3)

;; ============================================================================
;; Treemacs (Sidebar file tree)
;; ============================================================================
(after! treemacs
  (setq treemacs-width 30
        treemacs-position 'left))

;; ============================================================================
;; Elfeed - Academic Research Feed Reader
;; ============================================================================
(after! elfeed
  (setq elfeed-feeds
        '(
          ;; ========================================
          ;; LLMs & AI (PRIMARY FOCUS)
          ;; Training methods, alignment, advances
          ;; ========================================
          ("http://export.arxiv.org/rss/cs.LG" llm ml arxiv)      ; Machine Learning
          ("http://export.arxiv.org/rss/cs.CL" llm nlp arxiv)     ; Computation & Language
          ("http://export.arxiv.org/rss/cs.AI" llm ai arxiv)      ; Artificial Intelligence
          ("http://export.arxiv.org/rss/cs.NE" llm neural arxiv)  ; Neural & Evolutionary
          ("http://export.arxiv.org/rss/stat.ML" llm stats arxiv) ; Statistical ML

          ;; ========================================
          ;; Marine Biology
          ;; Cetaceans, orcas, migration, acoustics
          ;; ========================================
          ;; bioRxiv feeds
          ("http://connect.biorxiv.org/biorxiv_xml.php?subject=zoology" marine bio biorxiv)
          ("http://connect.biorxiv.org/biorxiv_xml.php?subject=animal_behavior_and_cognition" marine bio biorxiv)
          ("http://connect.biorxiv.org/biorxiv_xml.php?subject=ecology" marine bio biorxiv)
          ;; PubMed custom searches (cetaceans, orcas, marine acoustics)
          ("https://pubmed.ncbi.nlm.nih.gov/rss/search/1234567/?limit=50&utm_campaign=pubmed-2&fc=20231201000000" marine cetacean pubmed)
          ;; PLOS ONE Marine Mammals
          ("https://journals.plos.org/plosone/feed/atom?filterSubjects=Marine+mammals" marine plos)
          ;; Nature Marine Biology
          ("http://feeds.nature.com/subjects/marine-biology.rss" marine nature)

          ;; ========================================
          ;; Pedagogy & Education
          ;; STEAM and mathematics education
          ;; ========================================
          ("http://export.arxiv.org/rss/physics.ed-ph" pedagogy physics-ed arxiv)  ; Physics Education
          ("http://export.arxiv.org/rss/math.HO" pedagogy math-ed arxiv)           ; Math History/Overview
          ;; Education journals
          ("https://www.tandfonline.com/feed/rss/ujme20" pedagogy math-ed journal)  ; Journal of Math Ed
          ("https://stemeducationjournal.springeropen.com/articles/most-recent/rss.xml" pedagogy stem journal)))

  ;; Default filter - show all unread
  (setq elfeed-search-filter "@2-weeks-ago +unread")

  ;; ========================================
  ;; Quick filters for each research area
  ;; ========================================
  (defun kris/elfeed-llm ()
    "Show only LLM/AI papers."
    (interactive)
    (elfeed-search-set-filter "@6-months-ago +unread +llm"))

  (defun kris/elfeed-marine ()
    "Show only marine biology papers."
    (interactive)
    (elfeed-search-set-filter "@6-months-ago +unread +marine"))

  (defun kris/elfeed-pedagogy ()
    "Show only pedagogy/education papers."
    (interactive)
    (elfeed-search-set-filter "@6-months-ago +unread +pedagogy"))

  (defun kris/elfeed-all ()
    "Show all unread papers."
    (interactive)
    (elfeed-search-set-filter "@2-weeks-ago +unread"))

  ;; Keybindings for filters (in elfeed search mode)
  (map! :map elfeed-search-mode-map
        :n "L" #'kris/elfeed-llm
        :n "M" #'kris/elfeed-marine
        :n "P" #'kris/elfeed-pedagogy
        :n "A" #'kris/elfeed-all
        ;; Fetch/update feeds
        :n "g r" #'elfeed-search-fetch
        :n "g R" #'elfeed-search-update--force
        :n "R" #'elfeed-update)

  ;; Entry display settings
  (setq elfeed-show-entry-switch #'pop-to-buffer
        elfeed-show-entry-delete #'elfeed-kill-buffer)

  ;; Larger entry display for reading abstracts
  (add-hook 'elfeed-show-mode-hook
            (lambda ()
              (setq-local shr-max-width 80)
              (visual-line-mode 1))))

;; ============================================================================
;; Elfeed-Score - Numerical scoring for entries
;; ============================================================================
(use-package! elfeed-score
  :after elfeed
  :config
  (elfeed-score-enable)
  (setq elfeed-score-serde-score-file "~/.config/doom/elfeed-score.el")

  ;; Sort by score in search view
  (setq elfeed-search-sort-function #'elfeed-score-sort)

  ;; Show score in search format
  (setq elfeed-search-print-entry-function #'elfeed-score-print-entry)

  ;; Keybindings for scoring
  (map! :map elfeed-search-mode-map
        :n "=" #'elfeed-score-set-score
        :n "+" #'(lambda () (interactive)
                   (elfeed-score-set-score (+ (elfeed-score-get-score (elfeed-search-selected :single)) 10)))
        :n "-" #'(lambda () (interactive)
                   (elfeed-score-set-score (- (elfeed-score-get-score (elfeed-search-selected :single)) 10)))))

;; Elfeed keybindings
(map! :leader
      (:prefix ("e" . "elfeed")
       :desc "Open Elfeed" "e" #'elfeed
       :desc "Update feeds" "u" #'elfeed-update
       :desc "Update feed" "f" #'elfeed-search-fetch
       :desc "Score explain" "s" #'elfeed-score-scoring-explain-entry))

;; ============================================================================
;; Research Workflow - Bibliography & Paper Management
;; Based on Ahmed Khaled's EmacsConf 2021 talk
;; ============================================================================

;; Library paths
(defconst kris/bib-libraries '("~/bib-lib/library.bib" "~/bib-lib/temp-lib.bib"))
(defconst kris/main-bib-library (nth 0 kris/bib-libraries))
(defconst kris/pdf-library-paths '("~/bib-lib/pdfs/" "~/bib-lib/temp-pdfs/"))
(defconst kris/main-pdf-library (nth 0 kris/pdf-library-paths))
(defconst kris/bib-notes-dir "~/bib-lib/roam/")

;; ============================================================================
;; arXiv Import Functions (defined globally, not inside use-package)
;; Uses org-ref style completing-read for library selection
;; ============================================================================

;; Custom arXiv import with library prompt (like org-ref)
(defun kris/arxiv-to-library (arxiv-id)
  "Fetch arXiv paper by ARXIV-ID, prompt for library, download PDF, add BibTeX."
  (interactive
   (list (read-string "arXiv ID: "
                      (when (car kill-ring)
                        (let ((kill (car kill-ring)))
                          (when (string-match "\\([0-9]\\{4\\}\\.[0-9]\\{4,5\\}\\)" kill)
                            (match-string 1 kill)))))))
  (let* ((bibfile (completing-read "Bibfile: " kris/bib-libraries nil t nil nil kris/main-bib-library))
         (pdfdir (if (string-match "temp" bibfile)
                     (expand-file-name "temp-pdfs/" "~/bib-lib/")
                   kris/main-pdf-library)))
    (kris/arxiv-fetch-and-add arxiv-id bibfile pdfdir)))

;; Import arXiv paper from current elfeed entry (press 'a')
(defun kris/elfeed-arxiv-to-library ()
  "Import arXiv paper from current elfeed entry to local library.
Prompts for which bibliography file to use (like org-ref)."
  (interactive)
  (let* ((link (elfeed-entry-link elfeed-show-entry))
         (match-idx (string-match "arxiv.org/abs/\\([0-9v.]+\\)" link))
         (arxiv-id (when match-idx
                     (replace-regexp-in-string "v[0-9]+$" "" (match-string 1 link)))))
    (if arxiv-id
        (let* ((bibfile (completing-read "Bibfile: " kris/bib-libraries nil t nil nil kris/main-bib-library))
               (pdfdir (if (string-match "temp" bibfile)
                           (expand-file-name "temp-pdfs/" "~/bib-lib/")
                         kris/main-pdf-library)))
          (kris/arxiv-fetch-and-add arxiv-id bibfile pdfdir))
      (message "No arXiv ID found in this entry"))))

;; Core fetch function - downloads PDF and adds BibTeX entry
(defun kris/arxiv-fetch-and-add (arxiv-id bibfile pdfdir)
  "Fetch arXiv paper ARXIV-ID, save PDF to PDFDIR, add entry to BIBFILE."
  (let* ((arxiv-id (replace-regexp-in-string "^https?://arxiv.org/abs/" "" arxiv-id))
         (url (format "http://export.arxiv.org/api/query?id_list=%s" arxiv-id))
         (pdf-url (format "https://arxiv.org/pdf/%s.pdf" arxiv-id)))
    (message "Fetching arXiv:%s..." arxiv-id)
    (url-retrieve url
                  (lambda (_status arxiv-id pdf-url bibfile pdfdir)
                    (goto-char (point-min))
                    (re-search-forward "\n\n")
                    (let* ((xml (libxml-parse-xml-region (point) (point-max)))
                           (entry (car (dom-by-tag xml 'entry)))
                           (title (string-trim (dom-text (car (dom-by-tag entry 'title)))))
                           (authors (mapcar (lambda (a) (dom-text (car (dom-by-tag a 'name))))
                                            (dom-by-tag entry 'author)))
                           (published (dom-text (car (dom-by-tag entry 'published))))
                           (year (substring published 0 4))
                           (abs-url (format "https://arxiv.org/abs/%s" arxiv-id))
                           (first-author (car (split-string (car authors))))
                           (title-word (car (split-string (downcase title))))
                           (key (format "%s%s_%s" (downcase first-author) (substring year 2) title-word))
                           (pdf-file (expand-file-name (concat key ".pdf") pdfdir))
                           (bib-entry (format "@article{%s,
  author       = {%s},
  url          = {%s},
  year         = {%s},
  journal      = {arXiv},
  title        = {%s},
}
"
                                              key
                                              (mapconcat #'identity authors " and ")
                                              abs-url
                                              year
                                              title)))
                      (message "Downloading PDF: %s" arxiv-id)
                      (url-copy-file pdf-url pdf-file t)
                      (with-temp-buffer
                        (insert bib-entry)
                        (append-to-file (point-min) (point-max) bibfile))
                      (message "Added: %s -> %s (bib: %s)" key pdf-file (file-name-nondirectory bibfile))))
                  (list arxiv-id pdf-url bibfile pdfdir))))

;; Function to reformat bibliography using biber & rebiber
(defun kris/reformat-bib-library (&optional filename)
  "Format bibliography using biber & rebiber, update with conference versions."
  (interactive)
  (or filename (setq filename kris/main-bib-library))
  (let ((cmnd (concat
               (format "rebiber -i %s ; " filename)
               (format "biber --tool --output_align --output_indent=2 --output_fieldcase=lower --output_file=%s %s"
                       filename filename))))
    (async-shell-command cmnd "*bib-reformat*")))

;; Keybinding for elfeed - press 'a' to add arXiv paper
(map! :after elfeed
      :map elfeed-show-mode-map
      :n "a" #'kris/elfeed-arxiv-to-library)

;; ============================================================================
;; org-ref - Bibliography management
;; ============================================================================
(use-package! org-ref
  :after org
  :config
  (setq bibtex-completion-bibliography kris/bib-libraries
        bibtex-completion-library-path kris/pdf-library-paths
        bibtex-completion-notes-path kris/bib-notes-dir
        bibtex-dialect 'biblatex))

;; ============================================================================
;; org-roam-bibtex - Link notes to bibliography entries
;; ============================================================================
(use-package! org-roam-bibtex
  :after org-roam
  :config
  (require 'org-ref)
  (org-roam-bibtex-mode 1)

  (setq orb-preformat-keywords '("citekey" "title" "url" "author-or-editor" "keywords" "file")
        orb-process-file-keyword t
        orb-file-field-extensions '("pdf"))

  ;; Capture template for bibliography notes
  ;; Stored in ~/notes/references/ (symlinked to ~/bib-lib/roam/references/)
  (add-to-list 'org-roam-capture-templates
               '("r" "bibliography reference" plain "%?"
                 :target (file+head "references/${citekey}.org"
                                    ":PROPERTIES:
:ROAM_REFS: cite:${citekey}
:END:
#+title: Notes on ${title}
#+filetags: :reference:

* Summary

* Key Points

* Quotes

* My Thoughts

")
                 :unnarrowed t)))

;; ============================================================================
;; Citar - Enhanced citation management
;; ============================================================================
(after! citar
  (setq citar-bibliography kris/bib-libraries
        citar-library-paths kris/pdf-library-paths
        citar-notes-paths (list kris/bib-notes-dir)
        citar-file-extensions '("pdf" "org" "md"))

  ;; Use with org-roam-bibtex
  (setq citar-open-note-function 'orb-citar-edit-note)

  ;; Open PDFs externally with zathura by default
  (setq citar-file-open-functions
        '(("pdf" . (lambda (file) (start-process "zathura" nil "zathura" file)))
          (t . find-file))))

;; Function to open PDF inside Emacs with pdf-tools
(defun kris/citar-open-pdf-in-emacs ()
  "Open a PDF from the bibliography inside Emacs using pdf-tools."
  (interactive)
  (let ((citar-file-open-functions '(("pdf" . find-file) (t . find-file))))
    (citar-open-files)))

;; ============================================================================
;; Zotero Integration via zotxt
;; ============================================================================
(use-package! zotxt
  :after org
  :config
  ;; Enable in org-mode
  (add-hook 'org-mode-hook #'org-zotxt-mode))

;; ============================================================================
;; Research Keybindings
;; ============================================================================
(map! :leader
      (:prefix ("r" . "research")
       :desc "Import arXiv paper" "a" #'kris/arxiv-to-library
       :desc "Open Zotero item" "z" #'org-zotxt-insert-reference-link
       :desc "Insert citation" "c" #'citar-insert-citation
       :desc "Open PDF (zathura)" "p" #'citar-open-files
       :desc "Open PDF (emacs)" "P" #'kris/citar-open-pdf-in-emacs
       :desc "Open notes" "n" #'citar-open-notes
       :desc "Reformat bibliography" "r" #'kris/reformat-bib-library
       :desc "Search bibliography" "s" #'citar-open))