.gitignore

@@ -1 +0,0 @@
-*.el

config.el

@@ -0,0 +1,902 @@
+(setq tab-always-indent t)
+(setq org-roam-directory "~/org/")
+
+
+(setq user-full-name "Judah Sotomayor"
+      user-mail-address "")
+
+(setq doom-theme 'doom-dark+)
+(setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 16 :weight 'medium))
+(setq auto-save-default nil) ;I don't like autosaving. Let me do it myself.
+
+(remove-hook '+doom-dashboard-functions #'doom-dashboard-widget-shortmenu)
+(remove-hook '+doom-dashboard-functions #'doom-dashboard-widget-footer)
+
+(setq fancy-splash-image (concat doom-private-dir "emacs.png"))
+
+(map! :desc "Switch to normal mode" :i "C-c" #'evil-normal-state)
+
+(defun bash ()
+  (interactive)
+  (term "/bin/bash"))
+(map!
+      :desc "Start a bash shell"
+      "<f6>" #'bash)
+
+(add-hook 'term-mode-hook 'hide-mode-line-mode)
+
+(use-package! sage-shell-mode
+  :defer)
+
+;; Ob-sagemath supports only evaluating with a session.
+(setq org-babel-default-header-args:sage '((:session . t)
+                                           (:results . "output")))
+
+;; C-c c for asynchronous evaluating (only for SageMath code blocks).
+(with-eval-after-load "org"
+  (define-key org-mode-map (kbd "C-c c") 'ob-sagemath-execute-async))
+
+(map! :leader
+      :desc "The Emacs Calculator"
+      "C" #'calc)
+
+(defun fava ()
+  (interactive)
+  (async-shell-command "flatpak run org.gnome.gitlab.johannesjh.favagtk"))
+(map! :leader
+ :desc "Start favagtk"
+ "r b" #'fava)
+
+(use-package! ob-mermaid)
+
+(use-package! ob-svgbob)
+(setq org-svgbob-executable "svgbob_cli")
+
+(setq org-babel-svgbob--parameters
+  '(:background transparent
+    ))
+
+(defun current-date () (interactive)
+    (shell-command-to-string " bash -c 'echo -n $(date +%Y-%m-%d)'"))
+ (defun insert-current-date () (interactive)
+    (insert (current-date)))
+
+(map! :leader
+      :desc "Insert the current date into the buffer"
+      "i d" #'insert-current-date)
+
+(use-package! age
+  :ensure t
+  :demand t
+  :custom
+  (age-program "age")
+  (age-default-identity "~/.age/personal")
+  (age-default-recipient "~/.age/personal.pub")
+  :config
+  (age-file-enable))
+
+(setq org-confirm-babel-evaluate t)
+(setq org-link-shell-confirm-function t)
+(setq org-link-elisp-confirm-function t)
+(setq enable-local-variables t)
+(setq enable-local-eval 'maybe)
+
+(after! org-roam
+(defun vulpea-project-p ()
+  "Return non-nil if current buffer has any todo entry.
+TODO entries marked as done are ignored, meaning the this
+function returns nil if current buffer contains only completed
+tasks."
+  (seq-find                                 ; (3)
+   (lambda (type)
+     (eq type 'todo))
+   (org-element-map                         ; (2)
+       (org-element-parse-buffer 'headline) ; (1)
+       'headline
+     (lambda (h)
+       (org-element-property :todo-type h)))))
+
+(defun vulpea-project-update-tag ()
+    "Update PROJECT tag in the current buffer."
+    (when (and (not (active-minibuffer-window))
+               (vulpea-buffer-p))
+      (save-excursion
+        (goto-char (point-min))
+        (let* ((tags (vulpea-buffer-tags-get))
+               (original-tags tags))
+          (if (vulpea-project-p)
+              (setq tags (cons "hastodos" tags))
+            (setq tags (remove "hastodos" tags)))
+
+          ;; cleanup duplicates
+          (setq tags (seq-uniq tags))
+
+          ;; update tags if changed
+          (when (or (seq-difference tags original-tags)
+                    (seq-difference original-tags tags))
+            (apply #'vulpea-buffer-tags-set tags))))))
+
+(defun vulpea-buffer-p ()
+  "Return non-nil if the currently visited buffer is a note."
+  (and buffer-file-name
+       (string-prefix-p
+        (expand-file-name (file-name-as-directory org-roam-directory))
+        (file-name-directory buffer-file-name))))
+
+(defun vulpea-project-files ()
+    "Return a list of note files containing 'hastodos' tag." ;
+    (seq-uniq
+     (seq-map
+      #'car
+      (org-roam-db-query
+       [:select [nodes:file]
+        :from tags
+        :left-join nodes
+        :on (= tags:node-id nodes:id)
+        :where (like tag (quote "%\"hastodos\"%"))]))))
+
+(defun vulpea-agenda-files-update (&rest _)
+  "Update the value of `org-agenda-files'."
+  (setq org-agenda-files (vulpea-project-files)))
+
+(add-hook 'find-file-hook #'vulpea-project-update-tag)
+(add-hook 'before-save-hook #'vulpea-project-update-tag)
+
+(advice-add 'org-agenda :before #'vulpea-agenda-files-update)
+(advice-add 'org-todo-list :before #'vulpea-agenda-files-update)
+
+;; functions borrowed from `vulpea' library
+;; https://github.com/d12frosted/vulpea/blob/6a735c34f1f64e1f70da77989e9ce8da7864e5ff/vulpea-buffer.el
+
+(defun vulpea-buffer-tags-get ()
+  "Return filetags value in current buffer."
+  (vulpea-buffer-prop-get-list "filetags" "[ :]"))
+
+(defun vulpea-buffer-tags-set (&rest tags)
+  "Set TAGS in current buffer.
+If filetags value is already set, replace it."
+  (if tags
+      (vulpea-buffer-prop-set
+       "filetags" (concat ":" (string-join tags ":") ":"))
+    (vulpea-buffer-prop-remove "filetags")))
+
+(defun vulpea-buffer-tags-add (tag)
+  "Add a TAG to filetags in current buffer."
+  (let* ((tags (vulpea-buffer-tags-get))
+         (tags (append tags (list tag))))
+    (apply #'vulpea-buffer-tags-set tags)))
+
+(defun vulpea-buffer-tags-remove (tag)
+  "Remove a TAG from filetags in current buffer."
+  (let* ((tags (vulpea-buffer-tags-get))
+         (tags (delete tag tags)))
+    (apply #'vulpea-buffer-tags-set tags)))
+
+(defun vulpea-buffer-prop-set (name value)
+  "Set a file property called NAME to VALUE in buffer file.
+If the property is already set, replace its value."
+  (setq name (downcase name))
+  (org-with-point-at 1
+    (let ((case-fold-search t))
+      (if (re-search-forward (concat "^#\\+" name ":\\(.*\\)")
+                             (point-max) t)
+          (replace-match (concat "#+" name ": " value) 'fixedcase)
+        (while (and (not (eobp))
+                    (looking-at "^[#:]"))
+          (if (save-excursion (end-of-line) (eobp))
+              (progn
+                (end-of-line)
+                (insert "\n"))
+            (forward-line)
+            (beginning-of-line)))
+        (insert "#+" name ": " value "\n")))))
+
+(defun vulpea-buffer-prop-set-list (name values &optional separators)
+  "Set a file property called NAME to VALUES in current buffer.
+VALUES are quoted and combined into single string using
+`combine-and-quote-strings'.
+If SEPARATORS is non-nil, it should be a regular expression
+matching text that separates, but is not part of, the substrings.
+If nil it defaults to `split-string-default-separators', normally
+\"[ \f\t\n\r\v]+\", and OMIT-NULLS is forced to t.
+If the property is already set, replace its value."
+  (vulpea-buffer-prop-set
+   name (combine-and-quote-strings values separators)))
+
+(defun vulpea-buffer-prop-get (name)
+  "Get a buffer property called NAME as a string."
+  (org-with-point-at 1
+    (when (re-search-forward (concat "^#\\+" name ": \\(.*\\)")
+                             (point-max) t)
+      (buffer-substring-no-properties
+       (match-beginning 1)
+       (match-end 1)))))
+
+(defun vulpea-buffer-prop-get-list (name &optional separators)
+  "Get a buffer property NAME as a list using SEPARATORS.
+If SEPARATORS is non-nil, it should be a regular expression
+matching text that separates, but is not part of, the substrings.
+If nil it defaults to `split-string-default-separators', normally
+\"[ \f\t\n\r\v]+\", and OMIT-NULLS is forced to t."
+  (let ((value (vulpea-buffer-prop-get name)))
+    (when (and value (not (string-empty-p value)))
+      (split-string-and-unquote value separators))))
+
+(defun vulpea-buffer-prop-remove (name)
+  "Remove a buffer property called NAME."
+  (org-with-point-at 1
+    (when (re-search-forward (concat "\\(^#\\+" name ":.*\n?\\)")
+                             (point-max) t)
+      (replace-match ""))))
+
+    (setq org-agenda-files (vulpea-project-files)))
+
+(setq org-log-done 'time)
+(after! org-mode
+    (setq org-log-done 'time)
+    (add-to-list 'org-tags-exclude-from-inheritance "hastodos")
+    (setq org-hide-emphasis-markers nil))
+
+(setq org-directory "~/org/")
+(setq org-roam-directory org-directory)
+
+(setq org-startup-with-inline-images t)
+
+;; Show images after evaluating code blocks.
+(add-hook 'org-babel-after-execute-hook 'org-display-inline-images)
+
+(use-package! org-drill
+  :defer nil
+  )
+
+  (map! :leader
+        :desc "Start org-drill"
+        "d d" #'org-drill-directory)
+
+  (map! :leader
+        :desc "Start org-drill in cram mode"
+        "d c" #'org-drill-cram)
+
+(use-package! ob-lilypond)
+(setq ly-arrange-mode t)
+
+(use-package! org-edna)
+(org-edna-mode)
+
+(use-package org-habit
+	:custom
+	(org-habit-graph-column 1)
+	(org-habit-preceding-days 10)
+	(org-habit-following-days 1)
+	(org-habit-show-habits-only-for-today nil))
+
+(use-package! org-heatmap
+	:after (org)
+	:config
+	(org-heatmap-mode))
+
+(map! :leader
+      :desc "Export to html and diplay with eww"
+      :n "m A" #'org-archive-subtree-default)
+
+(require 'org-archive)
+
+; Set the function to use for org-archive-default  (C-c C-x C-a)
+; (setq org-archive-location (concat org-directory "/archive/%s_archive::"))
+; (setq org-archive-location "archive/archived_%s::")
+
+(setq org-archive-location "~/org/archive.org")
+(setq org-archive-location (concat org-directory "/archive.org::"))
+; unmap org-archive-subtree
+
+; select command to execute via org-archive-subtree-default (C-c C-x C-a)
+(setq org-archive-default-command 'org-archive-subtree-hierarchical)
+
+(defun line-content-as-string ()
+  "Returns the content of the current line as a string"
+  (save-excursion
+    (beginning-of-line)
+    (buffer-substring-no-properties
+     (line-beginning-position) (line-end-position))))
+
+(defun org-child-list (&optional top-level)
+  "This function returns all children of a heading as a list. "
+  (interactive)
+  (save-excursion
+    ;; this only works with org-version > 8.0, since in previous
+    ;; org-mode versions the function (org-outline-level) returns
+    ;; gargabe when the point is not on a heading.
+    (unless top-level
+        (if (= (org-outline-level) 0)
+            (outline-next-visible-heading 1)
+        (org-goto-first-child)))
+    (let ((child-list (list (line-content-as-string))))
+      (while (org-goto-sibling)
+        (setq child-list (cons (line-content-as-string) child-list)))
+      child-list)))
+
+(defun fa/org-struct-subtree ()
+  "This function returns the tree structure in which a subtree belongs as a list."
+  (interactive)
+  (let ((archive-tree nil))
+    (save-excursion
+      (while (org-up-heading-safe)
+        (let ((heading
+               (buffer-substring-no-properties
+                (line-beginning-position) (line-end-position))))
+          (if (eq archive-tree nil)
+              (setq archive-tree (list heading))
+            (setq archive-tree (cons heading archive-tree))))))
+    archive-tree))
+
+(defun org-archive-subtree-hierarchical ()
+  "This function archives a subtree hierarchical"
+  (interactive)
+  (let ((org-tree (fa/org-struct-subtree))
+        (source-buffer (current-buffer))
+        (file (abbreviate-file-name
+                   (or (buffer-file-name (buffer-base-buffer))
+                       (error "No file associated to buffer")))))
+    (save-excursion
+      (setq location (org-archive--compute-location
+                (or (org-entry-get nil "ARCHIVE" 'inherit)
+                    org-archive-location))
+            afile (car location)
+            heading (cdr location)
+            infile-p (equal file (abbreviate-file-name (or afile ""))))
+      (unless afile
+        (error "Invalid `org-archive-location'"))
+      (if (not (equal heading ""))
+          (progn
+            (setq org-tree (cons heading
+                               (mapcar (lambda (s) (concat "*" s)) org-tree)))
+            (org-demote-subtree)))
+      (if (> (length afile) 0)
+        (progn
+          (setq newfile-p (not (file-exists-p afile))
+                visiting (find-buffer-visiting afile)
+                target-buffer (or visiting (find-file-noselect afile))))
+        (progn
+          (setq target-buffer (current-buffer))))
+      (unless target-buffer
+        (error "Cannot access file \"%s\"" afile))
+      (org-cut-subtree)
+      (set-buffer target-buffer)
+      (setq ind-target-buffer (clone-indirect-buffer nil nil))
+      (set-buffer ind-target-buffer)
+      (org-mode)
+      (goto-char (point-min))
+
+      ; simplified version of org-complex-heading-regexp-format
+	  (setq my-org-complex-heading-regexp-format
+	      (concat "^"
+		      "\\(%s\\)"
+		      "\\(?: *\\[[0-9%%/]+\\]\\)*"
+		      "\\(?:[ \t]+\\(:[[:alnum:]_@#%%:]+:\\)\\)?"
+		      "[ \t]*$"))
+      (setq top-level-p t)
+      (while (not (equal org-tree nil))
+        (let ((child-list (org-child-list top-level-p))
+              (re (format my-org-complex-heading-regexp-format (regexp-quote (car org-tree))))
+             )
+          (if (member "______FOUND_MATCH" (mapcar (lambda (s) (replace-regexp-in-string re "______FOUND_MATCH" s)) child-list))
+              (progn
+                (re-search-forward re nil t)
+                (setq org-tree (cdr org-tree)))
+            (progn
+              (if (not top-level-p) (newline))
+              (org-insert-struct org-tree)
+              (setq org-tree nil))))
+        (setq top-level-p nil))
+      (end-of-buffer)
+      (newline)
+      (org-yank)
+      ;; Kill the indirect buffer, returning the current buffer to the direct target buffer
+      (kill-buffer ind-target-buffer)
+      ;; Save and kill the target buffer, if it is not the source buffer.
+      (when (not (eq source-buffer target-buffer))
+            (save-buffer target-buffer)
+            (kill-buffer target-buffer))
+      ;; ensure font-lock and indentation are normal
+      (set-buffer source-buffer)
+      (org-restart-font-lock)
+      (org-indent-mode t)
+      (message "Subtree archived %s"
+               (concat "in file: " (abbreviate-file-name afile))))))
+
+(defun org-insert-struct (struct)
+  "TODO"
+  (interactive)
+  (when struct
+    (insert (car struct))
+    (if  (not (equal (length struct) 1))
+        (newline))
+    (org-insert-struct (cdr struct))))
+
+(setq templates/post-capture-props "#+date: [%<%Y-%m-%d %a>]\n#+lastmod:\n#+categories[]:\n#+tags[]:\n#+images[]: ")
+(setq templates/post-capture-title "#+TITLE: ${title}\n")
+(setq templates/post-capture-template (concat templates/post-capture-title templates/post-capture-props))
+
+(setq org-preview-latex-image-directory (concat org-directory (file-name-as-directory "images/latexsnip")))
+
+(setq org-hugo-base-dir (concat org-directory (file-name-as-directory "website")))
+(setq org-hugo-default-section-directory "posts")
+
+(after! org
+  ;; Import ox-latex to get org-latex-classes and other funcitonality
+  ;; for exporting to LaTeX from org
+  (use-package! ox-latex
+    :init
+    :config
+
+    (setq org-latex-with-hyperref nil) ;; stop org adding hypersetup{author..} to latex export
+    ;; (setq org-latex-prefer-user-labels t)
+    (setq org-latex-logfiles-extensions
+          (quote ("lof" "lot" "tex~" "aux" "idx" "log" "out" "toc" "nav" "snm" "vrb" "dvi" "fdb_latexmk" "blg" "brf" "fls" "entoc" "ps" "spl" "bbl" "xmpi" "run.xml" "bcf" "acn" "acr" "alg" "glg" "gls" "ist")))
+
+    (unless (boundp 'org-latex-classes)
+      (setq org-latex-classes nil))))
+
+(after! ox-latex
+  (setq org-latex-pdf-process
+  '("lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f"
+    "lualatex --output-directory=/home/user/Documents -shell-escape -interaction nonstopmode %f"))
+  )
+
+(setq-default org-html-with-latex `dvisvgm)
+
+
+
+(unless (boundp 'org-latex-classes)
+  (setq org-latex-classes nil))
+
+(add-to-list 'org-latex-classes
+             '("ethz"
+               "\\documentclass[a4paper,11pt,titlepage]{memoir}
+    \\usepackage[utf8]{inputenc}
+    \\usepackage[T1]{fontenc}
+    \\usepackage{fixltx2e}
+    \\usepackage{graphicx}
+    \\usepackage{longtable}
+    \\usepackage{float}
+    \\usepackage{wrapfig}
+    \\usepackage{rotating}
+    \\usepackage[normalem]{ulem}
+    \\usepackage{amsmath}
+    \\usepackage{textcomp}
+    \\usepackage{marvosym}
+    \\usepackage{wasysym}
+    \\usepackage{amssymb}
+    \\usepackage[hidelinks]{hyperref}
+    \\usepackage{mathpazo}
+    \\usepackage{color}
+    \\usepackage{enumerate}
+    \\definecolor{bg}{rgb}{0.95,0.95,0.95}
+    \\tolerance=1000
+          [NO-DEFAULT-PACKAGES]
+          [PACKAGES]
+          [EXTRA]
+    \\linespread{1.1}
+    \\hypersetup{pdfborder=0 0 0}"
+               ("\\chapter{%s}" . "\\chapter*{%s}")
+               ("\\section{%s}" . "\\section*{%s}")
+               ("\\subsection{%s}" . "\\subsection*{%s}")
+               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+               ("\\paragraph{%s}" . "\\paragraph*{%s}")
+               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+
+(add-to-list 'org-latex-classes
+             '("article"
+               "\\documentclass[11pt,a4paper]{article}
+    \\usepackage[utf8]{inputenc}
+    \\usepackage[T1]{fontenc}
+    \\usepackage{fixltx2e}
+    \\usepackage{graphicx}
+    \\usepackage{longtable}
+    \\usepackage{float}
+    \\usepackage{wrapfig}
+    \\usepackage{rotating}
+    \\usepackage[normalem]{ulem}
+    \\usepackage{amsmath}
+    \\usepackage{textcomp}
+    \\usepackage{marvosym}
+    \\usepackage{wasysym}
+    \\usepackage{amssymb}
+    \\usepackage[hidelinks]{hyperref}
+    \\usepackage{mathpazo}
+    \\usepackage{color}
+    \\usepackage{enumerate}
+    \\definecolor{bg}{rgb}{0.95,0.95,0.95}
+    \\tolerance=1000
+          [NO-DEFAULT-PACKAGES]
+          [PACKAGES]
+          [EXTRA]
+    \\linespread{1.1}
+    \\hypersetup{pdfborder=0 0 0}"
+               ("\\section{%s}" . "\\section*{%s}")
+               ("\\subsection{%s}" . "\\subsection*{%s}")
+               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+               ("\\paragraph{%s}" . "\\paragraph*{%s}")))
+
+
+(add-to-list 'org-latex-classes '("ebook"
+                                  "\\documentclass[11pt, oneside]{memoir}
+    \\setstocksize{9in}{6in}
+    \\settrimmedsize{\\stockheight}{\\stockwidth}{*}
+    \\setlrmarginsandblock{2cm}{2cm}{*} % Left and right margin
+    \\setulmarginsandblock{2cm}{2cm}{*} % Upper and lower margin
+    \\checkandfixthelayout
+    % Much more laTeX code omitted
+    "
+                                  ("\\chapter{%s}" . "\\chapter*{%s}")
+                                  ("\\section{%s}" . "\\section*{%s}")
+                                  ("\\subsection{%s}" . "\\subsection*{%s}")))
+
+(defun +org-refresh-latex-images-previews-h ()
+  (dolist (buffer (doom-buffers-in-mode 'org-mode (buffer-list)))
+    (with-current-buffer buffer
+      (+org--toggle-inline-images-in-subtree (point-min) (point-max) 'refresh)
+      (unless (eq org-latex-preview-default-process 'dvisvgm)
+        (org-clear-latex-preview (point-min) (point-max))
+        (org--latex-preview-region (point-min) (point-max))))))
+
+(add-hook 'doom-load-theme-hook #'+org-refresh-latex-images-previews-h)
+
+(defun eww-open-this-file ()
+       (set 'directory (file-name-directory buffer-file-name))
+       (set 'filename (file-name-sans-extension buffer-file-name))
+       (set 'extension ".html")
+       (set 'filename (format "%s%s" filename extension))
+       (eww-open-file filename)
+       (evil-window-left)
+)
+
+(defun org-export-and-open-eww ()
+    "Export current file to html and open in eww"
+    (interactive)
+
+    (org-html-export-to-html)
+    (if (equal (file-name-extension buffer-file-name) "org")
+         (eww-open-this-file)
+      (message "Failed")
+    )
+)
+
+(map! :leader
+        :desc "Export to html and diplay with eww"
+        "r E" #'org-export-and-open-eww)
+
+(use-package! citar
+  :ensure t
+  :demand t
+  :custom
+  (citar-bibliography "~/org/references.bib")
+  (citar-file-note-extensions '(".org"))
+  (org-cite-global-bibliography '("~/org/references.bib"))
+
+  (org-cite-csl-styles-dir
+   (expand-file-name "~/Zotero/styles/"))
+  (org-cite-export-processors
+    '((t . (csl "apa.csl")) ))
+
+  :hook
+  (LaTeX-mode . citar-capf-setup)
+  (org-mode . citar-capf-setup))
+(citar-org-roam-mode)
+
+(after! citar
+    (setq citar-indicator-files-icons
+      (citar-indicator-create
+       :symbol (nerd-icons-faicon
+                "nf-fa-file_o"
+                :face 'nerd-icons-green
+                :v-adjust -0.1)
+       :function #'citar-has-files
+       :padding "  " ; need this because the default padding is too low for these icons
+       :tag "has:files"))
+
+    (setq citar-indicator-links-icons
+      (citar-indicator-create
+       :symbol (nerd-icons-faicon
+                "nf-fa-link"
+                :face 'nerd-icons-orange
+                :v-adjust 0.01)
+       :function #'citar-has-links
+       :padding "  "
+       :tag "has:links"))
+
+    (setq citar-indicator-notes-icons
+      (citar-indicator-create
+       :symbol (nerd-icons-codicon
+                "nf-cod-note"
+                :face 'nerd-icons-blue
+                :v-adjust -0.3)
+       :function #'citar-has-notes
+       :padding "    "
+       :tag "has:notes"))
+
+    (setq citar-indicator-cited-icons
+      (citar-indicator-create
+       :symbol (nerd-icons-faicon
+                "nf-fa-circle_o"
+                :face 'nerd-icon-green)
+       :function #'citar-is-cited
+       :padding "  "
+       :tag "is:cited"))
+
+(setq citar-indicators
+  (list citar-indicator-files-icons
+        citar-indicator-links-icons
+        citar-indicator-notes-icons
+        citar-indicator-cited-icons)))
+
+(add-to-list 'org-latex-classes
+    '("student-apa7"
+      "\\documentclass[stu]{apa7}
+\\hypersetup{hidelinks}
+\\usepackage{times}
+[NO-DEFAULT-PACKAGES]
+[NO-PACKAGES]"
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+(add-to-list 'org-latex-classes
+    '("student-turabian"
+      "\\documentclass{turabian-researchpaper}
+[NO-DEFAULT-PACKAGES]
+[NO-PACKAGES]"
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}")
+     ("\\usepackage{biblatex-chicago}")))
+
+(add-to-list 'org-latex-classes
+    '("student-mla"
+      "\\documentclass[stu]{mla}
+\\hypersetup{hidelinks}
+\\usepackage{times} "
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+       ;; org-latex-compilers = ("pdflatex" "xelatex" "lualatex"), which are the possible values for %latex
+
+(use-package! engrave-faces)
+(setq org-latex-listings 'engraved)
+
+(use-package! org-roam
+  :after md-roam
+  :init (setq org-roam-directory "~/org/"))      :custom
+
+(after! org-roam
+  :ensure t
+  :custom
+  (setq org-roam-capture-templates
+       `(
+         ("d" "default" plain "%?"
+          :target (file+head "%<%Y%m%d-%H%M%S>.org"
+                             "#+TITLE: ${title}\n#+HTML_HEAD: <link rel=\"stylesheet\" type=\"text/css\" href=\"css/retro.css\" />\n")
+          :unnarrowed t)
+
+        ("s" "school" plain "%?"
+          :target (file+head "%<%Y%m%d-%H%M%S>.org"
+"#+TITLE: ${title}
+#+LATEX_CLASS: student-apa7
+#+LATEX_OPTIONS: stu,hidelinks
+#+LATEX_HEADER: \\course{}
+#+LATEX_HEADER:\\authorsnames{Judah Sotomayor}
+#+LATEX_HEADER: \\authorsaffiliations{}
+#+LATEX_HEADER: \\professor{}
+#+LATEX_HEADER: \\usepackage{times}
+#+LATEX_HEADER: \\duedate{}
+#+OPTIONS: toc:nil\n")
+          :unnarrowed t)
+
+         ("c" "encrypted" plain "%?"
+          :target (file+head "%<%Y%m%d-%H%M%S>.sec.org.age"
+                             "#+TITLE: ${title}\n#+FILETAGS: :secure:noexport:\n#+HTML_HEAD: <link rel=\"stylesheet\" type=\"text/css\" href=\"css/retro.css\" />\n\n\n* No Export Below This Line")
+          :unnarrowed t))))
+
+(after! org-roam (map! :leader (:prefix ("r" . "roam")
+
+                :desc "Search for a node in org-roam files"
+                "f" #'org-roam-node-find
+
+                :desc "Insert the link to a node from org-roam"
+                "i" #'org-roam-node-insert
+
+                :desc "Rescan org-roam files and add new nodes to database"
+                "s" #'org-roam-db-sync
+
+                :desc "Jump to a random node"
+                "r" #'org-roam-node-random
+
+                :desc "Capture inside an existing or new node"
+                "c" #'org-roam-capture
+
+                :desc "Go to or create a daily note"
+                "d" #'org-roam-dailies-goto-today
+
+                :desc "Seek a daily note"
+                "D" #'org-roam-dailies-goto-date
+
+                :desc "Extract a subtree to a new file"
+                "e" #'org-roam-extract-subtree))
+
+            (map!
+                :desc "Alternative keybind to insert a roam link while in insert mode"
+                :i "M-[" #'org-roam-node-insert))
+
+(use-package! websocket
+    :after org-roam)
+
+(use-package! org-roam-ui
+    :after org-roam ;; or :after org
+;;         normally we'd recommend hooking orui after org-roam, but since org-roam does not have
+;;         a hookable mode anymore, you're advised to pick something yourself
+;;         if you don't care about startup time, use
+;;  :hook (after-init . org-roam-ui-mode)
+    :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 t))
+
+(after! org-roam-ui (map! :leader (:prefix ("r" . "roam") (:prefix ("u" . "roam-ui")
+
+                :desc "Focus the current node in org-roam-ui view"
+                "f" #'org-roam-ui-node-zoom
+
+                :desc "Focus the current node's local graph in org-roam-ui view"
+                "l" #'org-roam-ui-node-local
+
+                :desc "Begin org-roam ui mode"
+                "u" #'open-org-roam-ui
+
+                ))))
+
+(defun open-org-roam-ui ()
+  (interactive)
+  (org-roam-ui-mode)
+  (async-shell-command "surf http://localhost:35901/"))
+
+(setq browse-url-browser-function 'browse-url-generic
+      browse-url-generic-program "surf")
+
+ '(org-file-apps
+    (quote
+      ((auto-mode . emacs)
+      ("\\.mm\\'" . default)
+      ("\\.x?html?\\'" . "surf %s")
+      ("\\.pdf\\'" . default))))
+
+(after! org-roam
+(setq org-roam-dailies-capture-templates
+  `(("d" "default" entry
+     "* %?"
+     :target (file+head "%<%Y-%m-%d>.sec.org.age"
+                        "#+title: %<%Y-%m-%d>\n")))))
+
+(require 'cl-lib)
+
+(defun org-global-props-key-re (key)
+  "Construct a regular expression matching key and an optional plus and eating the spaces behind.
+Test for existence of the plus: (match-beginning 1)"
+  (concat "^" (regexp-quote key) "\\(\\+\\)?[[:space:]]+"))
+
+(defun org-global-props (&optional buffer)
+  "Get the plists of global org properties of current buffer."
+  (with-current-buffer (or buffer (current-buffer))
+    (org-element-map (org-element-parse-buffer) 'keyword (lambda (el) (when (string-equal (org-element-property :key el) "PROPERTY") (nth 1 el))))))
+
+(defun org-global-prop-value (key)
+  "Get global org property KEY of current buffer.
+Adding up values for one key is supported."
+  (let ((key-re (org-global-props-key-re key))
+    (props (org-global-props))
+    ret)
+    (cl-loop with val for prop in props
+         when (string-match key-re (setq val (plist-get prop :value))) do
+         (setq
+          val (substring val (match-end 0))
+          ret (if (match-beginning 1)
+              (concat ret " " val)
+            val)))
+    ret))
+
+(after! org
+  (use-package! ox-extra
+    :config
+    (ox-extras-activate '(latex-header-blocks ignore-headlines))))
+
+(add-to-list 'org-latex-classes
+             '("altacv" "\\documentclass[10pt,a4paper,ragged2e,withhyper]{altacv}
+\\usepackage[rm]{roboto}
+\\usepackage[defaultsans]{lato}
+\\usepackage{paracol}
+[NO-DEFAULT-PACKAGES]
+[NO-PACKAGES]
+% Change the page layout if you need to
+\\geometry{left=1.25cm,right=1.25cm,top=1.5cm,bottom=1.5cm,columnsep=1.2cm}
+
+% Use roboto and lato for fonts
+\\renewcommand{\\familydefault}{\\sfdefault}
+
+% Change the colours if you want to
+\\definecolor{SlateGrey}{HTML}{2E2E2E}
+\\definecolor{LightGrey}{HTML}{666666}
+\\definecolor{DarkPastelRed}{HTML}{450808}
+\\definecolor{PastelRed}{HTML}{8F0D0D}
+\\definecolor{GoldenEarth}{HTML}{E7D192}
+
+\\colorlet{name}{black}
+\\colorlet{tagline}{black}
+\\colorlet{heading}{black}
+\\colorlet{headingrule}{black}
+\\colorlet{subheading}{black}
+\\colorlet{accent}{black}
+\\colorlet{emphasis}{SlateGrey}
+\\colorlet{body}{LightGrey}
+
+% Change some fonts, if necessary
+\\renewcommand{\\namefont}{\\Huge\\rmfamily\\bfseries}
+\\renewcommand{\\personalinfofont}{\\footnotesize}
+\\renewcommand{\\cvsectionfont}{\\LARGE\\rmfamily\\bfseries}
+\\renewcommand{\\cvsubsectionfont}{\\large\\bfseries}
+
+% Change the bullets for itemize and rating marker
+% for \cvskill if you want to
+\\renewcommand{\\itemmarker}{{\\small\\textbullet}}
+\\renewcommand{\\ratingmarker}{\\faCircle}
+"
+
+               ("\\cvsection{%s}" . "\\cvsection*{%s}")
+               ("\\cvevent{%s}" . "\\cvevent*{%s}")))
+
+(add-to-list 'org-latex-classes
+             '("mcdowellcv"
+               "\\documentclass[]{mcdowellcv}
+                \\usepackage{amsmath}
+                \\usepackage[]{multicol}
+    [NO-DEFAULT-PACKAGES]
+    [NO-PACKAGES]"
+               ("\\section{%s}" . "\\section*{%s}")
+               ("\\subsection{%s}" . "\\subsection*{%s}")
+               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+               ("\\paragraph{%s}" . "\\paragraph*{%s}")
+               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")
+               ("\\cvsection{%s}" . "\\cvsection*{%s}")
+               ("\\cvevent{%s}" . "\\cvevent*{%s}")))
+
+(map! :n "g j" #'evil-next-visual-line)
+(map! :n "g k" #'evil-previous-visual-line)
+
+(after! company-mode
+  (setq company-idle-delay nil))
+(setq company-idle-delay nil)
+
+(use-package! exec-path-from-shell)
+(after! exec-path-from-shell
+  (dolist (var '("SSH_AUTH_SOCK" "SSH_AGENT_PID" "GPG_AGENT_INFO"))
+  (add-to-list 'exec-path-from-shell-variables var))
+  (exec-path-from-shell-initialize)
+  )
+
+;; file-truename is optional; it seems required when you use symbolic
+;; links, which Org-roam does not resolve
+(use-package! md-roam
+  :config
+  (setq org-roam-file-extensions '("org" "md")) ; enable Org-roam for a markdown extension
+  (setq md-roam-file-extension "md") ; default "md". Specify an extension such as "markdown"
+  (setq md-roam-file-extension-single "md")
+  (setq md-roam-use-org-extract-ref nil)
+
+  (org-roam-db-autosync-mode 1))

custom.el

@@ -0,0 +1,18 @@
+(put 'narrow-to-region 'disabled nil)
+(custom-set-variables
+ ;; custom-set-variables was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
+ '(magit-todos-insert-after '(bottom) nil nil "Changed by setter of obsolete option `magit-todos-insert-at'")
+ '(warning-suppress-types
+   '((org-element-cache)
+     (org-element-cache)
+     (org-element-cache)
+     (defvaralias))))
+(custom-set-faces
+ ;; custom-set-faces was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
+ )

init.el

@@ -0,0 +1,196 @@
+;;; init.el -*- lexical-binding: t; -*-
+
+;; This file controls what Doom modules are enabled and what order they load
+;; in. Remember to run 'doom sync' after modifying it!
+
+;; NOTE Press 'SPC h d h' (or 'C-h d h' for non-vim users) to access Doom's
+;;      documentation. There you'll find a link to Doom's Module Index where all
+;;      of our modules are listed, including what flags they support.
+
+;; NOTE Move your cursor over a module's name (or its flags) and press 'K' (or
+;;      'C-c c k' for non-vim users) to view its documentation. This works on
+;;      flags as well (those symbols that start with a plus).
+;;
+;;      Alternatively, press 'gd' (or 'C-c c d') on a module to browse its
+;;      directory (for easy access to its source code).
+
+(doom! :input
+       ;;bidi              ; (tfel ot) thgir etirw uoy gnipleh
+       ;;chinese
+       ;;japanese
+       ;;layout            ; auie,ctsrnm is the superior home row
+
+       :completion
+       company           ; the ultimate code completion backend
+       ;;helm
+       ;;ido
+       ;;ivy
+       vertico           ; the search engine of the future
+
+       :ui
+       ;;deft              ; notational velocity for Emacs
+       doom              ; what makes DOOM look the way it does
+       doom-dashboard    ; a nifty splash screen for Emacs
+       ;;doom-quit         ; DOOM quit-message prompts when you quit Emacs
+       ;;(emoji +unicode)  ; 🙂
+       hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
+       ;;hydra
+       indent-guides     ; highlighted indent columns
+       ;;ligatures         ; ligatures and symbols to make your code pretty again
+       ;;minimap           ; show a map of the code on the side
+       modeline          ; snazzy, Atom-inspired modeline, plus API
+       nav-flash         ; blink cursor line after big motions
+       ;;neotree           ; a project drawer, like NERDTree for vim
+       ophints           ; highlight the region an operation acts on
+       (popup +defaults)   ; tame sudden yet inevitable temporary windows
+       ;;tabs              ; a tab bar for Emacs
+       treemacs          ; a project drawer, like neotree but cooler
+       ;;unicode           ; extended unicode support for various languages
+       (vc-gutter +pretty) ; vcs diff in the fringe
+       vi-tilde-fringe   ; fringe tildes to mark beyond EOB
+       window-select     ; visually switch windows
+       ;;workspaces        ; tab emulation, persistence & separate workspaces
+       zen               ; distraction-free coding or writing
+
+       :editor
+       (evil +everywhere); come to the dark side, we have cookies
+       file-templates    ; auto-snippets for empty files
+       fold              ; (nigh) universal code folding
+       (format )  ; automated prettiness
+       ;;god               ; run Emacs commands without modifier keys
+       ;;lispy             ; vim for lisp, for people who don't like vim
+       ;;multiple-cursors  ; editing in many places at once
+       ;;objed             ; text object editing for the innocent
+       ;;parinfer          ; turn lisp into python, sort of
+       ;;rotate-text       ; cycle region at point between text candidates
+       snippets          ; my elves. They type so I don't have to
+       word-wrap         ; soft wrapping with language-aware indent
+
+       :emacs
+       dired             ; making dired pretty [functional]
+       electric          ; smarter, keyword-based electric-indent
+       ibuffer         ; interactive buffer management
+       undo              ; persistent, smarter undo for your inevitable mistakes
+       vc                ; version-control and Emacs, sitting in a tree
+
+       :term
+       ;;eshell            ; the elisp shell that works everywhere
+       ;;shell             ; simple shell REPL for Emacs
+       term              ; basic terminal emulator for Emacs
+       ;;vterm             ; the best terminal emulation in Emacs
+
+       :checkers
+       (syntax +flymake +childframe)              ; tasing you for every semicolon you forget
+       (spell +flyspell +everywhere) ; tasing you for misspelling mispelling
+       grammar           ; tasing grammar mistake every you make
+
+       :tools
+       ;;ansible
+       (biblio +icons)            ; Writes a PhD for you (citation needed)
+       ;;debugger          ; FIXME stepping through code, to help you add bugs
+       ;;direnv
+       ;;docker
+       editorconfig      ; let someone else argue about tabs vs spaces
+       ;;ein               ; tame Jupyter notebooks with emacs
+       (eval +overlay)     ; run code, run (also, repls)
+       ;;gist              ; interacting with github gists
+       (lookup +dictionary +offline)              ; navigate your code and its documentation
+       lsp               ; M-x vscode
+       magit             ; a git porcelain for Emacs
+       ;;make              ; run make tasks from Emacs
+       ;;pass              ; password manager for nerds
+       pdf               ; pdf enhancements
+       ;;prodigy           ; FIXME managing external services & code builders
+       ;;rgb               ; creating color strings
+       ;;taskrunner        ; taskrunner for all your projects
+       ;;terraform         ; infrastructure as code
+       ;;tmux              ; an API for interacting with tmux
+       ;;tree-sitter       ; syntax and parsing, sitting in a tree...
+       ;;upload            ; map local to remote projects via ssh/ftp
+
+       :os
+       ;;(:if IS-MAC macos)  ; improve compatibility with macOS
+       ;;tty               ; improve the terminal Emacs experience
+
+       :lang
+       ;;agda              ; types of types of types of types...
+       (beancount +lsp)         ; mind the GAAP
+       (cc +lsp)         ; C > C++ == 1
+       ;;clojure           ; java with a lisp
+       ;;common-lisp       ; if you've seen one lisp, you've seen them all
+       ;;coq               ; proofs-as-programs
+       ;;crystal           ; ruby at the speed of c
+       ;;csharp            ; unity, .NET, and mono shenanigans
+       data              ; config/data formats
+       ;;(dart +flutter)   ; paint ui and not much else
+       ;;dhall
+       ;;elixir            ; erlang done right
+       ;;elm               ; care for a cup of TEA?
+       emacs-lisp        ; drown in parentheses
+       ;;erlang            ; an elegant language for a more civilized age
+       ;;ess               ; emacs speaks statistics
+       ;;factor
+       ;;faust             ; dsp, but you get to keep your soul
+       ;;fortran           ; in FORTRAN, GOD is REAL (unless declared INTEGER)
+       ;;fsharp            ; ML stands for Microsoft's Language
+       ;;fstar             ; (dependent) types and (monadic) effects and Z3
+       ;;gdscript          ; the language you waited for
+       ;;(go +lsp)         ; the hipster dialect
+       ;;(graphql +lsp)    ; Give queries a REST
+       ;;(haskell +lsp)    ; a language that's lazier than I am
+       ;;hy                ; readability of scheme w/ speed of python
+       ;;idris             ; a language you can depend on
+       ;;json              ; At least it ain't XML
+       ;;(java +lsp)       ; the poster child for carpal tunnel syndrome
+       ;;javascript        ; all(hope(abandon(ye(who(enter(here))))))
+       ;;julia             ; a better, faster MATLAB
+       ;;kotlin            ; a better, slicker Java(Script)
+       (latex +lsp +cdlatex +fold)            ; writing papers in Emacs has never been so fun
+       ;;lean              ; for folks with too much to prove
+       ;;ledger            ; be audit you can be
+       lua               ; one-based indices? one-based indices
+       markdown          ; writing docs for people to ignore
+       ;;nim               ; python + lisp at the speed of c
+       ;;nix               ; I hereby declare "nix geht mehr!"
+       ;;ocaml             ; an objective camel
+       (org +roam2 +gnuplot +hugo +pomodoro +noter +present +pretty)               ; organize your plain life in plain text
+       ;;php               ; perl's insecure younger brother
+       ;;plantuml          ; diagrams for confusing people more
+       ;;purescript        ; javascript, but functional
+       python            ; beautiful is better than ugly
+       ;;qt                ; the 'cutest' gui framework ever
+       ;;racket            ; a DSL for DSLs
+       ;;raku              ; the artist formerly known as perl6
+       ;;rest              ; Emacs as a REST client
+       ;;rst               ; ReST in peace
+       ;;(ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
+       (rust +lsp)       ; Fe2O3.unwrap().unwrap().unwrap().unwrap()
+       ;;scala             ; java, but good
+       ;;(scheme +guile)   ; a fully conniving family of lisps
+       sh                ; she sells {ba,z,fi}sh shells on the C xor
+       ;;sml
+       ;;solidity          ; do you need a blockchain? No.
+       ;;swift             ; who asked for emoji variables?
+       ;;terra             ; Earth and Moon in alignment for performance.
+       web               ; the tubes
+       ;;yaml              ; JSON, but readable
+       ;zig               ; C, but simpler
+
+       :email
+       ;;(mu4e +org +gmail)
+       ;;notmuch
+       ;;(wanderlust +gmail)
+
+       :app
+       calendar
+       ;;emmgs
+       ;;everywhere        ; *leave* Emacs!? You must be joking
+       ;;irc               ; how neckbeards socialize
+       ;;(rss +org)        ; emacs as an RSS reader
+       ;;twitter           ; twitter client https://twitter.com/vnought
+
+       :config
+       literate
+       (default +bindings +smartparens)
+
+)

packages.el

@@ -0,0 +1,87 @@
+;; -*- no-byte-compile: t; -*-
+;;; $DOOMDIR/packages.el
+
+;; To install a package with Doom you must declare them here and run 'doom sync'
+;; on the command line, then restart Emacs for the changes to take effect -- or
+;; use 'M-x doom/reload'.
+
+
+;; To install SOME-PACKAGE from MELPA, ELPA or emacsmirror:
+;(package! some-package)
+
+;; To install a package directly from a remote git repo, you must specify a
+;; `:recipe'. You'll find documentation on what `:recipe' accepts here:
+;; https://github.com/radian-software/straight.el#the-recipe-format
+;(package! another-package
+;  :recipe (:host github :repo "username/repo"))
+
+;; If the package you are trying to install does not contain a PACKAGENAME.el
+;; file, or is located in a subdirectory of the repo, you'll need to specify
+;; `:files' in the `:recipe':
+;(package! this-package
+;  :recipe (:host github :repo "username/repo"
+;           :files ("some-file.el" "src/lisp/*.el")))
+
+;; If you'd like to disable a package included with Doom, you can do so here
+;; with the `:disable' property:
+;(package! builtin-package :disable t)
+
+;; You can override the recipe of a built in package without having to specify
+;; all the properties for `:recipe'. These will inherit the rest of its recipe
+;; from Doom or MELPA/ELPA/Emacsmirror:
+;(package! builtin-package :recipe (:nonrecursive t))
+;(package! builtin-package-2 :recipe (:repo "myfork/package"))
+
+;; Specify a `:branch' to install a package from a particular branch or tag.
+;; This is required for some packages whose default branch isn't 'master' (which
+;; our package manager can't deal with; see radian-software/straight.el#279)
+;(package! builtin-package :recipe (:branch "develop"))
+
+;; Use `:pin' to specify a particular commit to install.
+;(package! builtin-package :pin "1a2b3c4d5e")
+
+
+;; Doom's packages are pinned to a specific commit and updated from release to
+;; release. The `unpin!' macro allows you to unpin single packages...
+;(unpin! pinned-package)
+;; ...or multiple packages
+;(unpin! pinned-package another-pg-ql)
+;; Org-mode
+
+;;(package! org-habit-plus
+ ; ; :recipe (:host github :type git :repo "myshevchuk/org-habit-plus"))
+
+(package! org-roam-ui)
+
+
+(package! ob-lilypond
+  :recipe (:host github :type git :repo "mjago/ob-lilypond"))
+
+
+;; Sagemath-related
+;(package! sage-shell-mode)
+;(package! ob-sagemath)
+
+(package! engrave-faces)
+;; Graphing
+(package! ob-mermaid)
+(package! ob-svgbob
+  :recipe (:host nil :type git :repo "https://git.tecosaur.net/tec/ob-svgbob"))
+
+; Security-related
+(package! age)
+
+(package! org-edna)
+
+(package! org-heatmap
+  :recipe (:host github :type git :repo "aspiers/org-heatmap"))
+
+(package! exec-path-from-shell)
+(package! anki-editor)
+(package! calfw)
+
+(package! noCtrlC
+  :recipe (:host nil :type git :repo "https://git.freedomland.xyz/judahsotomayor/noctrlc"))
+
+(package! md-roam
+  :recipe (:host github :repo "nobiot/md-roam"))