Remove <LAB Template

Disabled prof perf'ing

.gitignore

@@ -1,8 +1,7 @@
 /auto-save-list/
 /backups/
 /etc/
-/straight/*
-!/straight/versions
+/straight/
 /tutorial/
 /var/
 tramp
@@ -15,8 +14,3 @@ tramp
 /result
 /transient/
 /BROWSE
-org-roam.db
-bookmarks
-.org-id-locations
-.lsp-session-v1
-.dap-breakpoints

custom.el

@@ -3,10 +3,169 @@
  ;; 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.
+ '(conda-anaconda-home "~/opt/anaconda3")
  '(custom-safe-themes
    '("5f79df6b4c56021d173c178d90b5a600c678a192d78cc639553915985b67c4ea" "8cda1cfae8e393bfb23f1d448d4be10720835d086f7db080908a7c8d01566516" "a27f7b52fe66bacaec9059f8afd04d055a4ac3c2fba9eb9128c81e10152fc566" "1ba7196d8e7b883272ea8818a5163aec21b57023368febf55255816226f7b370" "8256e7e03444834d34915a226dc24933b0d680a0a1da568ec03f852be776f168" "4ac2f45e6b46e5bb50826d4250df71a57124169b82cc0ad75e436de6e70a9690" "29addd67feb95ca1179e60d476bb92c1f11835548e2efaec15c9ac6af2a8e6a8" "9b7a425c38c4894e161887c26381c2a6fc1de3c1407158507caaf469d76eb27b" "bce055e1681dd343659957710af77f7a6ad106677d42c61f86ebeedf637c4493" "f62c69472d3f506179d797131c014fe4095d9609dddf14542c50e0388f1e8d6d" "cf143bf23fa8160f87331893cdadc40b876556634621dfa373fcf93c4c97c444" "f459dfd377e9cb98d90e53383dcca7d73396cc0a22b31d39af24fb1cf3548fb5" "fcc14e1a22c99d77f7b1455b0c8a320f8afd0c1f4a9c5c50b45f676eb0c54ba2" "a6bae299481c3c0058e611d2c32ca169fa27203345a880806a5a8554cdd2e588" "feb9556e03558588e29e6659c8e01ea3d2a17a1e7a13e9bf9fc9e59cacba4b72" default))
+ '(delete-selection-mode nil)
+ '(dired-listing-switches "-alh")
+ '(elpy-rpc-python-command "python3")
+ '(lsp-dart-flutter-sdk-dir "~/flutter")
+ '(lsp-file-watch-ignored-directories
+   '("[/\\\\]\\.git\\'" "[/\\\\]\\.github\\'" "[/\\\\]\\.circleci\\'" "[/\\\\]\\.hg\\'" "[/\\\\]\\.bzr\\'" "[/\\\\]_darcs\\'" "[/\\\\]\\.svn\\'" "[/\\\\]_FOSSIL_\\'" "[/\\\\]\\.idea\\'" "[/\\\\]\\.ensime_cache\\'" "[/\\\\]\\.eunit\\'" "[/\\\\]node_modules" "[/\\\\]\\.yarn\\'" "[/\\\\]\\.fslckout\\'" "[/\\\\]\\.tox\\'" "[/\\\\]dist\\'" "[/\\\\]dist-newstyle\\'" "[/\\\\]\\.stack-work\\'" "[/\\\\]\\.bloop\\'" "[/\\\\]\\.metals\\'" "[/\\\\]target\\'" "[/\\\\]\\.ccls-cache\\'" "[/\\\\]\\.vscode\\'" "[/\\\\]\\.venv\\'" "[/\\\\]\\.mypy_cache\\'" "[/\\\\]\\.deps\\'" "[/\\\\]build-aux\\'" "[/\\\\]autom4te.cache\\'" "[/\\\\]\\.reference\\'" "[/\\\\]\\.lsp\\'" "[/\\\\]\\.clj-kondo\\'" "[/\\\\]\\.shadow-cljs\\'" "[/\\\\]\\.babel_cache\\'" "[/\\\\]\\.cpcache\\'" "[/\\\\]\\checkouts\\'" "[/\\\\]\\.m2\\'" "[/\\\\]bin/Debug\\'" "[/\\\\]obj\\'" "[/\\\\]_opam\\'" "[/\\\\]_build\\'" "[/\\\\]\\.elixir_ls\\'" "[/\\\\]\\.direnv\\'" "[/\\\\]\\.tmp\\'"))
+ '(lsp-java-format-on-type-enabled nil)
+ '(lsp-java-format-settings-profile nil)
+ '(lsp-pylsp-plugins-jedi-use-pyenv-environment t)
+ '(org-agenda-files
+   '("~/Documents/research/DBS/TechnicalEvaluation/technicaldraft.org" "/Users/universelaptop/Documents/research/CommitteeMeetings/First/Report/David_Crompton_Masters_Supervisory_Committee_Meeting_Report.org" "/Users/universelaptop/Documents/research/thesis/Ideas/ModelDetails.org" "/Users/universelaptop/Documents/uoft/JPB1071/WrittenAssignment/Crompton_David_1004162434_JPB1071_Written_Assignment.org"))
+ '(org-export-backends '(ascii beamer html icalendar latex odt))
+ '(org-latex-classes
+   '(("labtemplate" "\\documentclass{labtemplate}"
+      ("\\section{%s}" . "\\section*{%s}")
+      ("\\subsection{%s}" . "\\subsection*{%s}")
+      ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+      ("\\paragraph{%s}" . "\\paragraph*{%s}")
+      ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+     ("beamer" "\\documentclass[presentation]{beamer}"
+      ("\\section{%s}" . "\\section*{%s}")
+      ("\\subsection{%s}" . "\\subsection*{%s}")
+      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
+     ("article" "\\documentclass[11pt]{article}"
+      ("\\section{%s}" . "\\section*{%s}")
+      ("\\subsection{%s}" . "\\subsection*{%s}")
+      ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+      ("\\paragraph{%s}" . "\\paragraph*{%s}")
+      ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+     ("report" "\\documentclass[11pt]{report}"
+      ("\\part{%s}" . "\\part*{%s}")
+      ("\\chapter{%s}" . "\\chapter*{%s}")
+      ("\\section{%s}" . "\\section*{%s}")
+      ("\\subsection{%s}" . "\\subsection*{%s}")
+      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
+     ("book" "\\documentclass[11pt]{book}"
+      ("\\part{%s}" . "\\part*{%s}")
+      ("\\chapter{%s}" . "\\chapter*{%s}")
+      ("\\section{%s}" . "\\section*{%s}")
+      ("\\subsection{%s}" . "\\subsection*{%s}")
+      ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
+     ("letter" "\\documentclass{letter}"
+      ("" . ""))))
+ '(org-preview-latex-process-alist
+   '((dvipng :programs
+	     ("latex" "dvipng")
+	     :description "dvi > png" :message "you need to install the programs: latex and dvipng." :image-input-type "dvi" :image-output-type "png" :image-size-adjust
+	     (2.0 . 2.0)
+	     :latex-compiler
+	     ("latex -interaction nonstopmode -output-directory %o %f")
+	     :image-converter
+	     ("dvipng -D %D -T tight -o %O %f")
+	     :transparent-image-converter
+	     ("dvipng -D %D -T tight -bg Transparent -o %O %f"))
+     (dvisvgm :programs
+	      ("latex" "dvisvgm")
+	      :description "dvi > svg" :message "you need to install the programs: latex and dvisvgm." :image-input-type "dvi" :image-output-type "svg" :image-size-adjust
+	      (1.7 . 1.5)
+	      :latex-compiler
+	      ("latex -interaction nonstopmode -output-directory %o %f")
+	      :image-converter
+	      ("dvisvgm %f -n -b min -c %S -o %O"))
+     (imagemagick :programs
+		  ("latex" "convert")
+		  :description "pdf > png" :message "you need to install the programs: latex and imagemagick." :image-input-type "pdf" :image-output-type "png" :image-size-adjust
+		  (1.0 . 1.0)
+		  :latex-compiler
+		  ("pdflatex -interaction nonstopmode -output-directory %o %f")
+		  :image-converter
+		  ("convert -density %D -trim -antialias %f -quality 100 %O"))))
  '(package-selected-packages
-   '(sage-shell-mode ess lsp-dart dart-mode org-roam-bibtex org-roam-ui org-roam gnuplot auctex ox-reveal ox-pandoc pdf-tools helm-bibtex org-ref org geiser-racket rainbow-delimiters slint-mode rust-mode company-ghci lsp-haskell haskell-mode poetry python-mode yaml-mode d2-mode php-mode web-mode dap-mode flycheck lsp-ui lsp-mode company which-key nix-mode direnv magit exec-path-from-shell esup gcmh transient-dwim leaf-convert leaf-tree blackout hydra el-get leaf-keywords)))
+   '(lsp-dart dart-mode gnuplot auctex ox-pandoc pdf-tools org-ref helm-bibtex ivy-bibtex geiser-racket rainbow-delimiters rust-mode company-ghci lsp-haskell haskell-mode meson-mode company-c-headers company-ctags poetry python-mode which-key dap-mode helm-lsp lsp-treemacs flycheck lsp-ui lsp-mode company yaml-mode d2-mode php-mode web-mode nix-mode direnv magit esup ligature exec-path-from-shell transient-dwim leaf-convert leaf-tree blackout hydra el-get leaf-keywords leaf))
+ '(python-shell-completion-native-enable nil)
+ '(sql-sqlite-program "sqlite3")
+ '(warning-suppress-types '((comp) (comp) (comp) (comp) (comp))))
+'(org-latex-classes
+  '(("thesis" "\\documentclass{ut-thesis}"
+     ("\\chapter{%s}" . "\\chapter*{%s}")
+     ("\\section{%s}" . "\\section*{%}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+    ("labtemplate" "\\documentclass{labtemplate}"
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+    ("beamer" "\\documentclass[presentation]{beamer}"
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
+    ("article" "\\documentclass[11pt]{article}"
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+     ("\\paragraph{%s}" . "\\paragraph*{%s}")
+     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+    ("report" "\\documentclass[11pt]{report}"
+     ("\\part{%s}" . "\\part*{%s}")
+     ("\\chapter{%s}" . "\\chapter*{%s}")
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
+    ("letter" "\\documentclass{letter}"
+     ("" . ""))
+    ("book" "\\documentclass[11pt]{book}"
+     ("\\part{%s}" . "\\part*{%s}")
+     ("\\chapter{%s}" . "\\chapter*{%s}")
+     ("\\section{%s}" . "\\section*{%s}")
+     ("\\subsection{%s}" . "\\subsection*{%s}")
+     ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))))
+'(org-latex-default-packages-alist
+  '(("AUTO" "inputenc" t
+     ("pdflatex"))
+    ("T1" "fontenc" t
+     ("pdflatex"))
+    ("" "graphicx" t nil)
+    ("" "grffile" t nil)
+    ("" "longtable" nil nil)
+    ("" "wrapfig" nil nil)
+    ("" "rotating" nil nil)
+    ("normalem" "ulem" t nil)
+    ("" "amsmath" t nil)
+    ("" "textcomp" t nil)
+    ("" "amssymb" t nil)
+    ("" "capt-of" nil nil)
+    ("" "hyperref" nil nil)))
+'(org-pandoc-menu-entry
+  '((61 "to ms-pdf and open." org-pandoc-export-to-ms-pdf-and-open)
+    (45 "to ms-pdf." org-pandoc-export-to-ms-pdf)
+    (106 "to json and open." org-pandoc-export-to-json-and-open)
+    (74 "as json." org-pandoc-export-as-json)
+    (80 "to pptx." org-pandoc-export-to-pptx)
+    (120 "to docx and open." org-pandoc-export-to-docx-and-open)
+    (88 "to docx." org-pandoc-export-to-docx)))
+'(python-shell-completion-native-enable nil)
+'(warning-suppress-log-types
+  '((direnv)
+    (lsp-mode)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)))
+'(warning-suppress-types
+  '((lsp-mode)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)
+    (comp)))
+
 (custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.

flake.lock

@@ -1,15 +1,55 @@
 {
   "nodes": {
+    "emacs-overlay": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "nixpkgs-stable": "nixpkgs-stable"
+      },
+      "locked": {
+        "lastModified": 1692037570,
+        "narHash": "sha256-bvj/wfLLFTc8cWAwhN8tgShiy8ekPWt1+gWlEH7W4zY=",
+        "owner": "nix-community",
+        "repo": "emacs-overlay",
+        "rev": "7a4b5bbc06182e2f704630cd77a614ab0d9c2f2e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "emacs-overlay",
+        "type": "github"
+      }
+    },
     "flake-utils": {
       "inputs": {
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1731533236,
-        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
+        "lastModified": 1689068808,
+        "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "rev": "919d646de7be200f3bf08cb76ae1f09402b6f9b4",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1689068808,
+        "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "919d646de7be200f3bf08cb76ae1f09402b6f9b4",
         "type": "github"
       },
       "original": {
@@ -20,11 +60,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1737746512,
-        "narHash": "sha256-nU6AezEX4EuahTO1YopzueAXfjFfmCHylYEFCagduHU=",
+        "lastModified": 1691990649,
+        "narHash": "sha256-gMbKOiX1HwClRP9lADaaV/lnZr93NEaOFe4ApDx/zd8=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "825479c345a7f806485b7f00dbe3abb50641b083",
+        "rev": "6e287913f7b1ef537c97aa301b67c34ea46b640f",
         "type": "github"
       },
       "original": {
@@ -34,9 +74,26 @@
         "type": "github"
       }
     },
+    "nixpkgs-stable": {
+      "locked": {
+        "lastModified": 1691950488,
+        "narHash": "sha256-iUNEeudc4dGjx+HsHccnGiuZUVE/nhjXuQ1DVCsHIUY=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "720e61ed8de116eec48d6baea1d54469b536b985",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-23.05",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
-        "flake-utils": "flake-utils",
+        "emacs-overlay": "emacs-overlay",
+        "flake-utils": "flake-utils_2",
         "nixpkgs": "nixpkgs"
       }
     },
@@ -54,6 +111,21 @@
         "repo": "default",
         "type": "github"
       }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
     }
   },
   "root": "root",

flake.nix

@@ -1,21 +1,23 @@
 {
   inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+  inputs.emacs-overlay.url = "github:nix-community/emacs-overlay";
+  inputs.emacs-overlay.inputs.nixpkgs.follows = "nixpkgs";
   inputs.flake-utils.url = "github:numtide/flake-utils";
 
-  outputs = { self, nixpkgs, flake-utils }: let
-  in (flake-utils.lib.eachDefaultSystem (system: let
+  outputs = { self, nixpkgs, flake-utils, emacs-overlay }:
+    flake-utils.lib.eachDefaultSystem (system: let
       pkgs = import nixpkgs {
         inherit system;
+        overlays = [
+          emacs-overlay.overlays.default
+        ];
       };
     in {
       packages = {
-        me-emacs = pkgs.emacs;
-        me-emacs-wayland = pkgs.emacs-pgtk;
+        emacs = pkgs.emacsWithPackagesFromUsePackage {
+          config = ./main.org;
+          package = pkgs.emacs29;
+        };
       };
-    })) // {
-      overlays.default = final: prev: ({
-        me-emacs = final.emacs;
-        me-emacs-wayland = final.emacs-pgtk;
     });
-    };
 }

init.el

@@ -3,32 +3,23 @@
 ;; This file loads Org and then loads the rest of our Emacs initialization from Emacs lisp
 ;; embedded in literate Org files.
 
-(setq straight-check-for-modifications '(check-on-save find-when-checking))
-      
-(defvar bootstrap-version)
-(let ((bootstrap-file
-       (expand-file-name
-        "straight/repos/straight.el/bootstrap.el"
-        (or (bound-and-true-p straight-base-dir)
-            user-emacs-directory)))
-      (bootstrap-version 7))
-  (unless (file-exists-p bootstrap-file)
-    (with-current-buffer
-        (url-retrieve-synchronously
-         "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
-         'silent 'inhibit-cookies)
-      (goto-char (point-max))
-      (eval-print-last-sexp)))
-  (load bootstrap-file nil 'nomessage))
-
-(setq straight-vc-git-default-clone-depth '(1 single-branch))  ;; instead of the default 'full
-
-;; prebuild is broken in org-mode (TODO: FIX)
-;; (straight-override-recipe '(org :local-repo "/Users/universelaptop/tmp/org"))
-(straight-use-package 'org)
-
+;; Load up Org Mode and (now included) Org Babel for elisp embedded in Org Mode files
 (setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))
 
+(let* ((org-dir (expand-file-name
+                 "lisp" (expand-file-name
+                         "org" (expand-file-name
+                                "src" dotfiles-dir))))
+       (org-contrib-dir (expand-file-name
+                         "lisp" (expand-file-name
+                                 "contrib" (expand-file-name
+                                            ".." org-dir))))
+       (load-path (append (list org-dir org-contrib-dir)
+                          (or load-path nil))))
+  ;; load up Org and Org-babel
+  (require 'org)
+  (require 'ob-tangle))
+
 ;; load up all literate org-mode files in this directory
 (mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))
 

main.org

@@ -7,137 +7,62 @@
 #+author:
 #+language: en
 
-* Initialization
-
-** Straight.el
-
-Package management to be a little more fien/precise and work outside
-of Nix (as much as it would be nice to work inside of Nix too). This
-is actually contained within =init.el=
-
-#+begin_src elisp :tangle no :exports code
-(defvar bootstrap-version)
-(let ((bootstrap-file
-       (expand-file-name
-        "straight/repos/straight.el/bootstrap.el"
-        (or (bound-and-true-p straight-base-dir)
-            user-emacs-directory)))
-      (bootstrap-version 7))
-  (unless (file-exists-p bootstrap-file)
-    (with-current-buffer
-        (url-retrieve-synchronously
-         "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
-         'silent 'inhibit-cookies)
-      (goto-char (point-max))
-      (eval-print-last-sexp)))
-  (load bootstrap-file nil 'nomessage))
-#+end_src
-
-This code block actually resides in init.el (so that we can perform
-some necessary pre-configuration)
-
-** Leaf.el
+* Intialization
 
 We must initialize =leaf.el=, which we use as a use-package
-replacement for defining configs and relations between packages etc.
+replacement for defining configs for different things.
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
+  ;; <leaf-install-code>
   (eval-and-compile
-    (straight-use-package 'leaf)
+    (customize-set-variable
+     'package-archives '(("org" . "https://orgmode.org/elpa/")
+			 ("melpa" . "https://melpa.org/packages/")
+			 ("gnu" . "https://elpa.gnu.org/packages/")))
+    (package-initialize)
+    (unless (package-installed-p 'leaf)
+      (package-refresh-contents)
+      (package-install 'leaf))
 
     (leaf leaf-keywords
+      :ensure t
       :init
-      (straight-use-package 'leaf-keywords)
-      :custom
-      (leaf-alias-keyword-alist .'((:ensure . :straight)))
+      (leaf el-get :ensure t)
+      (leaf hydra :ensure t)
+      (leaf blackout :ensure t)
+
       :config
       ;; initialize leaf-keywords.el
       (leaf-keywords-init)))
+  ;; </leaf-install-code>
 
   (leaf leaf-tree :ensure t)
   (leaf leaf-convert :ensure t)
-  (leaf transient-dwim :ensure t
-    :require t ;; Needed so that org-roam may unobstructively depend on this
+  (leaf transient-dwim
+    :ensure t
     :bind (("M-=" . transient-dwim-dispatch)))
 #+end_src
 
-** MacOS Specific
-
-#+begin_src elisp :tangle yes :exports code
-(leaf macos
-  :hook (after-init hook)
-  :when (eq system-type 'darwin)
-  :init
-  (setq mac-option-modifier 'meta))
-#+end_src
-
-** Performance
-
-*** Garbage Collection
-
-This makes the garbage collection thresholds variable based on emacs
-usage. I don't know how well this plays with LSPs or similarly RAM hungry
-features. This was useful when I used a very restricted netbook w/ ~2GiB of
-RAM.
-
-Disabled for now. (May add flags to enable on specific systems)
-
-#+begin_src elisp :tangle yes :exports code
-; (leaf gcmh :ensure t
-;  :hook (after-init-hook))
-#+end_src
-
-*** Profiling
-#+begin_src elisp :tangle yes :exports code
-(leaf esup :disabled nil :ensure t)
-#+end_src
-
-** Emacs Paths
-
-*** Custom.el
-
-Ensure that the =custom.el= resides in the users' emacs directory.
-
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf custom-el
-  :leaf-defer nil
 	:config
 	;; Ensure custom writes to specific file
 	(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
 	(load custom-file 'noerror 'nomessage))
 #+end_src
 
-*** Backups
-
-Set the backups directory to reside in the users' emacs directory.
-
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf backup
-  :leaf-defer nil
 	:config
 	;; Change the location of file backups/locks into the emacs.d/backups/
 	(setq backup-directory-alist
 	      `(("." . ,(concat user-emacs-directory "backups")))))
 #+end_src
 
-** Shell Path Preservation
-
-Exec-path-from-shell ensures that path variable is preserved from
-shell.
-
-#+begin_src elisp :tangle yes :exports code
-(leaf exec-path-from-shell :ensure t
-  :config
-  (exec-path-from-shell-initialize))
-#+end_src
-
 * Visual Customization
 
-Visual Theme of Emacs config: defined in the =themes= directory.
-
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
 (leaf visual
-  :leaf-defer nil
   :doc "Visual Changes to Emacs"
   :tag "builtin" "internal"
   :custom ((menu-bar-mode . nil)
@@ -146,161 +71,93 @@ Visual Theme of Emacs config: defined in the =themes= directory.
   :custom-face ((default . '((t (:family "JuliaMono"
 					 :height 150
 					 :weight normal)))))
-  :config
+  :config (prog1 'visual
 	   ;; Set location of custom theme dir
 	   (setq custom-theme-directory (concat user-emacs-directory "themes"))
-  (load-theme 'UniverseHighContrast))
+	   (load-theme 'UniverseHighContrast)))
 #+end_src
 
-* Version Control
-#+begin_src elisp :tangle yes :exports code
-(leaf magit
-  :leaf-defer nil
-  :ensure t :require t)
+* Package Configuration
+
+** Path Preservation
+
+Exec-path-from-shell ensures that path variable is preserved from
+shell.
+
+#+begin_src elisp :tangle yes
+  (leaf exec-path-from-shell :ensure t
+    :config
+    (exec-path-from-shell-initialize))
 #+end_src
 
-* Nix Related
+** Font Related
 
-** Direnv
+*** Ligature
+
+Font related ligatures, combining multiple characters into "one".
+
+#+begin_src elisp :tangle yes
+  (leaf ligature
+	:ensure t
+	:config
+	;; Enable the "www" ligature in every possible major mode
+	(ligature-set-ligatures 't '("www"))
+	;; Enable traditional ligature support in eww-mode, if the
+	;; `variable-pitch' face supports it
+	(ligature-set-ligatures 'eww-mode '("ff" "fi" "ffi"))
+	;; Enable all Cascadia Code ligatures in programming modes
+	(ligature-set-ligatures 'prog-mode '("|||>" "<|||" "<==>" "<!--" "####" "~~>" "***" "||=" "||>"
+					     ":::" "::=" "=:=" "===" "==>" "=!=" "=>>" "=<<" "=/=" "!=="
+					     "!!." ">=>" ">>=" ">>>" ">>-" ">->" "->>" "-->" "---" "-<<"
+					     "<~~" "<~>" "<*>" "<||" "<|>" "<$>" "<==" "<=>" "<=<" "<->"
+					     "<--" "<-<" "<<=" "<<-" "<<<" "<+>" "</>" "###" "#_(" "..<"
+					     "..." "+++" "/==" "///" "_|_" "www" "&&" "^=" "~~" "~@" "~="
+					     "~>" "~-" "**" "*>" "*/" "||" "|}" "|]" "|=" "|>" "|-" "{|"
+					     "[|" "]#" "::" ":=" ":>" ":<" "$>" "==" "=>" "!=" "!!" ">:"
+					     ">=" ">>" ">-" "-~" "-|" "->" "--" "-<" "<~" "<*" "<|" "<:"
+					     "<$" "<=" "<>" "<-" "<<" "<+" "</" "#{" "#[" "#:" "#=" "#!"
+					     "##" "#(" "#?" "#_" "%%" ".=" ".-" ".." ".?" "+>" "++" "?:"
+					     "?=" "?." "??" ";;" "/*" "/=" "/>" "//" "__" "~~" "(*" "*)"
+					     "\\\\" "://"))
+	;; Enables ligature checks globally in all buffers. You can also do it
+	;; per mode with `ligature-mode'.
+	(global-ligature-mode t))
+#+end_src
+
+** Profiling
+#+begin_src elisp :tangle yes
+  (leaf esup :disabled nil :ensure t)
+#+end_src
+
+** Version Control
+#+begin_src elisp :tangle yes
+  (leaf magit :ensure t :require t)
+#+end_src
+
+** Nix Related
+
+*** Direnv
 
 In order to support direnv (loading =nix-shell= / =nix develop=)
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf direnv
 	:ensure t
-  :global-minor-mode direnv-mode)
+	:hook
+	(direnv-mode))
 #+end_src
 
-** Nix-mode
+*** Nix-mode
 
 =.nix= file mode
-#+begin_src elisp :tangle yes :exports code
-(leaf nix-mode
-  :ensure t
-  :mode "\\.nix\\'")
+#+begin_src elisp :tangle yes
+  (leaf nix-mode :ensure t)
 #+end_src
 
-* IDE Like Things
-
-** Which Key Again?
-
-#+begin_src elisp :tangle yes :exports code
-(leaf which-key
-  :ensure t
-  :global-minor-mode which-key-mode)
-#+end_src
-
-** Company Completion!
-
-We like autocomplete, it... is nice, okay?
-
-#+begin_src elisp :tangle yes :exports code
-(leaf company :ensure t
-  :bind
-  (("C-<tab>" . company-complete))
-  :hook after-init-hook
-  :global-minor-mode global-company-mode)
-#+end_src
-
-** Language Server Protocol
-
-We love language features that make languages nice
-
-#+begin_src elisp :tangle yes :exports code
-(leaf lsp-mode
-  :ensure t
-  :init
-  (setq lsp-keymap-prefix "C-c l")
-  :commands lsp lsp-deferred
-  :hook (
-  ;; which key support v v v
-  (lsp-mode-hook . lsp-enable-which-key-integration)
-#+end_src
-
-*** IDE Languages
-
-**** Dart/Flutter
-
-#+begin_src elisp :tangle yes :exports code
-(dart-mode . lsp-deferred)
-#+end_src
-
-**** Python
-
-#+begin_src elisp :tangle yes :exports code
-(python-mode . lsp-deferred)
-#+end_src
-
-**** C/C++
-
-#+begin_src elisp :tangle yes :exports code
-(c-mode-hook . lsp-deferred)
-(c++-mode-hook . lsp-deferred)
-#+end_src
-
-**** Haskell
-
-#+begin_src elisp :tangle yes :exports code
-(haskell-mode-hook . lsp-deferred)
-#+end_src
-
-**** Java
-
-#+begin_src elisp :tangle yes :exports code
-(java-mode-hook . lsp-deferred)
-#+end_src
-
-**** Rust
-
-#+begin_src elisp :tangle yes :exports code
-(rust-mode-hook . lsp-deferred)
-#+end_src
-
-#+begin_src elisp :tangle yes :exports code
-)
-#+end_src
-
-*** LSP Plugins:
-
-We do want some nice to haves of course
-
-#+begin_src elisp :tangle yes :exports code
-:init
-#+end_src
-
-- A pretty UI:
-#+begin_src elisp :tangle yes :exports code
-(leaf lsp-ui :ensure t
-  :commands lsp-ui-mode)
-#+end_src
-- Flycheck compat:
-#+begin_src elisp :tangle yes :exports code
-(leaf flycheck :ensure t)
-#+end_src
-- Debugger Compatibility
-#+begin_src elisp :tangle yes :exports code
-(leaf dap-mode :ensure t)
-#+end_src
-
-*** Projectile (Projects)
-
-#+begin_src elisp :tangle yes :exports code
-(leaf projectile
-  :commands projectile-mode
-  :config
-  (projectile-mode +1))
-#+end_src
-
-END LSP CONFIG
-
-#+begin_src elisp :tangle yes :exports code
-)
-#+end_src
-
-* WEB
+** WEB
 
 We all know the web is the future, obviously, of course.
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf web-mode
 	:ensure t
 	:mode
@@ -309,104 +166,128 @@ We all know the web is the future, obviously, of course.
 	"\\.jsx?\\'"
 	"\\.tsx?\\'")
   (leaf php-mode
-  :mode "\\.php\\'"
-  :ensure t)
-(leaf rainbow-mode
-  :leaf-defer nil
 	:ensure t)
 #+end_src
 
-* D2
+** D2
 
-#+begin_src elisp :tangle yes :exports code
-(leaf d2-mode
-  :ensure t
-  :mode "\\.d2\\'"
-  )
+#+begin_src elisp :tangle yes
+  (leaf d2-mode :ensure t)
 #+end_src
 
-* YAML
+** YAML
 
-#+begin_src elisp :tangle yes :exports code
-(leaf yaml-mode
-  :ensure t
-  :mode "\\.yaml\\'"
-  )
+#+begin_src elisp :tangle yes
+  (leaf yaml-mode :ensure t)
 #+end_src
 
-* Python Things
+** IDE Like Things
+*** Company Completion!
 
-** Python-mode
+We like autocomplete, it... is nice, okay?
+
+#+begin_src elisp :tangle yes
+  (leaf company :ensure t
+    :bind
+    (("C-<tab>" . company-complete))
+    :hook after-init-hook
+    :config (global-company-mode))
+#+end_src
+*** Language Server Protocol
+
+We love language features that make languages nice
+
+#+begin_src elisp :tangle yes
+  (leaf lsp-mode
+    :ensure t
+    :init
+    (setq lsp-keymap-prefix "C-c l")
+    :hook
+    ((dart-mode-hook . lsp)
+     (python-mode-hook . lsp)
+     (c-mode-hook . lsp)
+     (c++-mode-hook . lsp)
+     (haskell-mode-hook . lsp)
+     (java-mode-hook . lsp)
+     (rust-mode-hook . lsp)
+     ;; which key support v v v
+     (lsp-mode-hook . lsp-enable-which-key-integration))
+    :commands lsp
+    :config
+    (leaf lsp-ui :ensure t
+	  :commands lsp-ui-mode)
+    (leaf flycheck :ensure t)
+    (leaf lsp-treemacs :ensure t
+	  :commands lsp-treemacs-errors-list)
+    (leaf helm-lsp :ensure t
+	  :commands helm-lsp-workspace-symbol)
+    (leaf dap-mode :ensure t)
+    (leaf which-key :ensure t
+	  :config (which-key-mode)))
+#+end_src
+**** Projectile (Projects)
+#+begin_src elisp :tangle yes
+  (leaf projectile
+    :commands projectile-mode
+    :config
+    (projectile-mode +1))
+#+end_src
+** Python Things
+*** Python-mode
 
 Using python-mode is to have more up to date features (and
 highlighting) compared to builtin python-mode.
 
-#+begin_src elisp :tangle yes :exports code
-(leaf python-mode
-  :ensure t
-  :mode "\\.py\\'"
+#+begin_src elisp :tangle yes
+  (leaf python-mode :ensure t
 	:config
 	(setq python-shell-interpreter "ipython"
 	      python-shell-interpreter-args "-i --simple-prompt --InteractiveShell.display_page=True"))
 #+end_src
-
-** Poetry
+*** Poetry
 
 For when we aren't nix'ing things, and want some nice poetry.
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf poetry :ensure t)
 #+end_src
+** Java
 
-* C
+LSP for java is /nice/.
 
-Who even needs C++, not me, no way, no how.
-
-#+begin_src elisp :tangle no :exports code
-(leaf c-config
-  :config
-;  (leaf company-ctags :ensure t
-;      :hook c-mode-hook c++-mode-hook)
-;  (leaf company-c-headers :ensure t
-;      :hook c-mode-hook c++-mode-hook)
-;  (leaf meson-mode :ensure t
-;      :hook c-mode-hook c++-mode-hook)
-  )
+#+begin_src elisp :tangle yes
+  (leaf lsp-java
+	:hook (java-mode-hook . lsp))
 #+end_src
-
-* Haskell
-
-#+begin_src elisp :tangle yes :exports code
-(leaf haskell-mode
-  :ensure t
-  :mode "\\.hs\\'"
-  :init
+** C
+Who even needs C++, not me, no way, no how.
+#+begin_src elisp :tangle yes
+  (leaf company-ctags :ensure t)
+  (leaf company-c-headers :ensure t)
+  (leaf meson-mode :ensure t)
+#+end_src
+** Haskell
+#+begin_src elisp :tangle yes
+  (leaf haskell-mode :ensure t
+	:config
 	(leaf lsp-haskell :ensure t)
 	(leaf company-ghci :ensure t))
 #+end_src
-
-* Rust
-
-#+begin_src elisp :tangle yes :exports code
-(leaf rust-mode :ensure t
-  :mode "\\.rs\\'"
-  :init
-  (leaf slint-mode :ensure t))
+** Rust
+#+begin_src elisp :tangle yes
+  (leaf rust-mode :ensure t)
 #+end_src
-
-* Minecraft??
-
+** Minecraft??
 Minecraft =mcfunction= support, because, it can be annoying to type
 this stuff otherwise.
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf mcf-mode
-  :straight (mcf-mode :type git :host github :repo "rasensuihei/mcf"))
+	:el-get rasensuihei/mcf)
 #+end_src
-
-* Lisps
+** Lisps
 
 Gonna need to have pretty brackets
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf rainbow-delimiters
 	:ensure t
 	:commands rainbow-delimiters-mode
@@ -415,179 +296,37 @@ Gonna need to have pretty brackets
 	      :hook (emacs-lisp-mode-hook . rainbow-delimiters-mode)
 	      (geiser-mode-hook . rainbow-delimiters-mode)))
 #+end_src
-
-** Racket
+*** Racket
 Makes using racket so much nicer
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf geiser-racket :ensure t)
 #+end_src
-
-** Clojure
-
-For using clojure, we use both [[https://github.com/clojure-emacs/clojure-mode][clojure-mode]] and for REPL we use [[https://github.com/clojure-emacs/cider][CIDER]].
-
-#+begin_src elisp :tangle yes :exports code
-(leaf clojure-mode :ensure t cider)
-#+end_src
-
-* Org
-
-We ensure that org is available (though it is builtin)
-
-For Version compatibility we actually install org in init.el (to not
-conflict with the builtin version of Org)
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org
-  :require t org-tempo
-  :hook
-  (org-mode-hook . auto-fill-mode)
-  :config
-  (setq document-dir (expand-file-name (if (eq system-type 'darwin) "~/Nextcloud" "~/Documents")))
-  (setq org-directory (concat document-dir "/org"))
-  (when (not (file-exists-p org-directory)) (mkdir org-directory))
-  (set-fill-column 100)
-  (setq org-src-fontify-natively t
-  	org-confirm-babel-evaluate nil
-  	org-src-preserve-indentation t))
-;; (tempo-define-template "Fig. Caption"
-;; 			   '("" (P "Image: " image t)
-;; 			     (P "Caption: " caption t)
-;; 			     (P "Figure Name: " name t)
-;; 			     "#+CAPTION: " (s caption) > n >
-;; 			     "#+NAME: fig:" (s name) > n >
-;; 			     "#+ATTR_LaTeX: :placement [H]" > n >
-;; 			     "[[" (s image) "]]" > n > p >)
-;; 			   "<fig" "Inserts Figure with Caption"))
-#+end_src
-
-We also want to set our document directory (which as it stands is OS
-dependent)
-
-** Citations/References
+** Org
 
 We use org-ref because it provides some niceties, like doi-utils for
 updating our bibliography.
 
-#+begin_src elisp :tangle yes :exports code
-(leaf org-ref :ensure t helm-bibtex pdf-tools
+#+begin_src elisp :tangle yes
+  (leaf ivy-bibtex :ensure t)
+  (leaf helm-bibtex :ensure t)
+  (leaf org-ref :ensure t
 	:after org
-  :bind*
-  ("C-c ]" . org-ref-insert-link)
+	:init
+	(leaf pdf-tools :ensure t)
 	:config
-  (setq org-bib-dir (concat document-dir "/Bibliography"))
-  (setq org-bib-file (concat org-bib-dir "/references.bib"))
-  ;; Where should PDFs be stored
-  (setq bibtex-completion-library-path `(,(concat org-bib-dir "/bibtex-pdfs/"))
-	;; Where is the bibliography expected (org-ref & org-cite)
-	bibtex-completion-bibliography (list org-bib-file)
-	org-cite-global-bibliography (list org-bib-file)
-
-	bibtex-completion-notes-path (concat org-bib-dir "/notes")
-	bibtex-completion-notes-template-multiple-files "* ${author-or-editor}, ${title}, ${journal}, (${year}) :${=type=}: \n\nSee [[cite:&${=key=}]]\n"
-
-	bibtex-completion-additional-search-fields '(keywords)
-	bibtex-completion-display-formats
-	'((article       . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${journal:40}")
-	  (inbook        . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} Chapter ${chapter:32}")
-	  (incollection  . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
-	  (inproceedings . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
-	  (t             . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*}"))
-	bibtex-completion-pdf-open-function
-	(lambda (fpath)
-	  (call-process "open" nil 0 nil fpath)))
-  ;; For bibtex generated keys (in-org citation format)
-  (setq bibtex-autokey-year-length 4
-	bibtex-autokey-name-year-separator "-"
-	bibtex-autokey-year-title-separator "-"
-	bibtex-autokey-titleword-separator "-"
-	bibtex-autokey-titlewords 2
-	bibtex-autokey-titlewords-stretch 1
-	bibtex-autokey-titleword-length 5)
-  (add-to-list 'org-export-before-parsing-functions 'org-ref-csl-preprocess-buffer)
-  (add-to-list 'org-export-before-parsing-functions 'org-ref-refproc)
-  :require org-ref org-ref-helm oc-bibtex oc-bibtex oc-csl oc-natbib org-ref-refproc)
+	:require org-ref org-ref-ivy org-ref-helm doi-utils)
 #+end_src
 
-** Extra Export Options
-
-*** LaTeX (Obviously)
-
-We really do require latex
-
-#+begin_src elisp :tangle yes :exports code
-(leaf ox-latex :require t
-  :after org
-  :config
-  (add-to-list 'org-latex-packages-alist '("" "minted"))
-  (setq org-latex-listings 'minted) 
-  (setq org-latex-prefer-user-labels t)
-  (add-to-list 'org-latex-classes
-  	       '("labtemplate" "\\documentclass{labtemplate}"
-  		 ("\\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
-  	       '("thesis" "\\documentclass[11pt]{ut-thesis}"
-  		 ("\\part{%s}" . "\\part*{%s}")
-  		 ("\\chapter{%s}" . "\\chapter*{%s}")
-  		 ("\\section{%s}" . "\\section*{%s}")
-  		 ("\\subsection{%s}" . "\\subsection*{%s}")
-  		 ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))))
-#+end_src
-
-*** HTML Export
-
-#+begin_src elisp :tangle yes :exports code
-(leaf ox-html
-  :after org
-  :config
-  (setq org-html-head "
-<style type=\"text/css\">
-  pre.src {
-      background-color: #000;
-      color: #ccc;
-      border-radius: 2ch;
-  }
-  pre.src:before {
-      background-color: #ccc;
-      color: #000;
-      border-radius: 0.5ch;
-  }
-</style>
-"))
-#+end_src
-
-*** Pandoc the Panacea of Exports
-
 For more export formats we use pandoc:
-#+begin_src elisp :tangle yes :exports code
-(leaf ox-pandoc :ensure t :require t
+#+begin_src elisp :tangle yes
+  (leaf ox-pandoc :ensure t
 	:after org)
 #+end_src
 
-*** Slideshows
-
-**** Web based (reveal)
-
-Writing mockup presentations can be quicker when you focus on the text
-of the presentation first, and prettifying later. Reveal.js is a nice
-in between of these.
-
-#+begin_src elisp :tangle yes :exports code
-(leaf ox-reveal :ensure t :require t
-  :config
-  (setq org-reveal-root "https://cdn.jsdelivr.net/npm/reveal.js"))
-#+end_src
-
-** LaTeX: with AuCTeX
-
 Nicer LaTeX editing (AuCTeX):
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf auctex :ensure t
 	:after org)
 #+end_src
@@ -595,149 +334,81 @@ Nicer LaTeX editing (AuCTeX):
 We also ma(k|d)e use of org-tempo for templating things, which can be
 nice. Should use the export based templating probably. Eventually.
 
+#+begin_src elisp :tangle yes
+  (leaf org-cfg
+	:after org
+	:require org-ref oc-csl org-tempo ox-latex ox-pandoc
+	:init
+	:bind
+	("C-c ]" . org-ref-insert-link)
+	("s-[" . org-ref-insert-link-hydra/body)
+	:hook
+	(org-mode-hook . auto-fill-mode)
+	:config
+	(set-fill-column 100)
+	(setq org-src-fontify-natively t
+	      org-confirm-babel-evaluate nil
+	      org-src-preserve-indentation t)
+
+	(setq bibtex-completion-bibliography
+	      (list (expand-file-name "~/Documents/Bibliography/references.bib")))
+
+	(setq org-ref-bibliography-notes "~/Documents/Bibliography/notes.org"
+	      org-ref-default-bibliography '("~/Documents/Bibliography/references.bib")
+	      org-ref-pdf-directory "~/Documents/Bibliography/bibtex-pdfs/")
+
+	(setq org-ref-insert-link-function 'org-ref-insert-link-hydra/body
+	      org-ref-insert-cite-function 'org-ref-cite-insert-helm
+	      org-ref-insert-label-function 'org-ref-insert-label-link
+	      org-ref-insert-ref-function 'org-ref-insert-ref-link
+	      org-ref-cite-onclick-function (lambda (_) (org-ref-citation-hydra/body)))
+	(tempo-define-template "Fig. Caption"
+			       '("" (P "Image: " image t)
+				 (P "Caption: " caption t)
+				 (P "Figure Name: " name t)
+				 "#+CAPTION: " (s caption) > n >
+				 "#+NAME: fig:" (s name) > n >
+				 "#+ATTR_LaTeX: :placement [H]" > n >
+				 "[[" (s image) "]]" > n > p >)
+			       "<fig" "Inserts Figure with Caption")
+	(add-to-list 'org-latex-packages-alist '("" "minted"))
+	(setq org-latex-listings 'minted) 
+
+	(add-to-list 'org-latex-classes
+		     '("labtemplate" "\\documentclass{labtemplate}"
+		       ("\\section{%s}" . "\\section*{%s}")
+		       ("\\subsection{%s}" . "\\subsection*{%s}")
+		       ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+		       ("\\paragraph{%s}" . "\\paragraph*{%s}")
+		       ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+		     )
+
+	(setq org-latex-pdf-process
+	      '("%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+		"bibtex %b"
+		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
+		"%latex -shell-escape -interaction nonstopmode -output-directory %o %f")))
+#+end_src
+
 And in case we want to make some (GNU)?plots?
 
-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle yes
   (leaf gnuplot
 	:ensure t)
 #+end_src
-
-** Org Mode Agenda/Calendar Things
-
-*** Agenda Location
-
-Make it so that all files in the " src_elisp{org-agenda-files} " variable (e.g. "=~/Documents=") will be
-included in the tablutation and collation of all the dates and todos
-etc.
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-agenda
-  :after org
-  :config
-  (setq org-agenda-files `(,(concat org-directory))))
-#+end_src
-
-*** Capture Things
-
-Unless specified otherwise, any captured note, date, meeting, idea,
-should be put into the src_elisp{org-directory}.
-
-Similarly, we have a default file for notes that we capture, in there
-=note.org=, which is where all captured things go when they aren't
-told to go elsewhere.
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-capture
-  :after org
-  :config
-  (setq org-default-notes-file (concat org-directory "/notes.org")))
-#+end_src
-
-We also want to configure what type of things we want to capture,
-e.g. meetings, deadlines and whatever else:
-
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-capture
-  :after org-capture
-  :config
-  (add-hook 'org-capture-mode-hook #'org-id-get-create)
-  (setq org-capture-templates
-	'(("t" "Todo" entry (file+headline "todos.org" "Tasks")
-	   "* TODO %^{Todo?} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:ADDED: %U\n:END:\n  %i\n  %a \n%?\n")
-	  ("h" "Habit" entry (file+headline "todos.org" "Habits")
-	   "* TODO %^{Habit} %^G\nSCHEDULED: %^T\n:PROPERTIES:\n:STYLE: habit\n:ADDED: %U\n:END:\n%?\n")
-	  ("j" "Journal" entry (file+datetree "journal.org")
-	   "* %^{Journal Entry:} %^G\nEntered on %U\n  %i\n:PROPERTIES:\n:ADDED: %U\n:END:\n  %a\n%?\n")
-	  ("m" "Meeting" entry (file+headline "dates.org" "Meetings")
-	   "* %^{Meeting Title:} %^G\nSCHEDULED: %^t\n:PROPERTIES:\n:CATEGORY: Meeting\n:LOCATION: %^{LOCATION}\n:ADDED: %U\n:END:\n%?\n"))))
-#+end_src
-
-*** Habits
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-habit
-  :after org
-  :require t
-  :config
-  (add-to-list 'org-modules 'org-habit t)
-  (setq org-habit-graph-column 80))
-#+end_src
-
-*** Org Mobile
-
-So that we can edit and view things on the go. We could use the proper =org-mobile= module of org,
-instead we synchronize w/ Nextcloud, as to have it be the format we like when using =Orgzly Revived=
-
-** Org Notes (Roam)
-
-Let alone being able to maintain dates and times and journal entries: having notes for consolidating
-a personal wiki (separately) is also rather useful. For this we use Org-roam, a slip-note style note
-taking package.
-
-*** Org Roam
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-roam :ensure t
-  :after org transient-dwim
-  :require t
-  :config
-  (setq org-roam-directory (file-truename org-directory))
-  (org-roam-db-autosync-mode)
-  (transient-define-prefix transient--org-roam ()
-    ["Org Roam"
-     ("M-c" "Capture Note" org-roam-capture)
-     ("M-i" "Insert Note" org-roam-node-insert)
-     ("M-f" "Find Note" org-roam-node-find)])
-  (transient-append-suffix 'transient-dwim-org "M-o" '("M-n" "roam" transient--org-roam))
-  (setq org-roam-capture-templates
-	'(("d" "default" plain "%?"
-	   :target (file+head "notes/%<%Y%m%d%H%M%S>-${slug}.org"
-			      "#+title: ${title}\n")
-	   :unnarrowed t))))
-#+end_src
-
-**** Org Roam UI
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-roam-ui :ensure t
-  :after org-roam)
-#+end_src
-
-**** Org Roam Bibtex (ORB)
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-roam-bibtex :ensure t
-  :after org-roam org-ref
-  :require t
-  :hook (after-init-hook . org-roam-bibtex-mode))
-#+end_src
-
-** Org Babel
-
-#+begin_src elisp :tangle yes :exports code
-(leaf org-babel
-  :after org
-  :config
-  (org-babel-do-load-languages
-   'org-babel-load-languages
-   '((emacs-lisp . t)
-     (python . t)
-     (shell . t))))
-#+end_src
-
-* Flutter
-
-#+begin_src elisp :tangle yes :exports code
+** Flutter
+#+begin_src elisp :tangle yes
   (leaf dart-mode :ensure t)
   (leaf lsp-dart :ensure t)
 #+end_src
-
-* BQN
-
-#+begin_src elisp :tangle yes :exports code
+** BQN
+#+begin_src elisp :tangle yes
   (leaf bqn-mode
-  :ensure (bqn-mode :type git :host github :repo "museoa/bqn-mode")
-  :defer-config
-  (set-face-attribute 'bqn-default nil :family 'unspecified))
+    :el-get "museoa/bqn-mode"
+    :config
+    (leaf bqn-font
+	  :after bqn-mode
+	  :config
+	  (set-face-attribute 'bqn-default nil :family 'unspecified)))
 #+end_src

src/nmodl.el

@@ -1,79 +0,0 @@
-(defvar nmodl-mode-hook nil)
-
-(defvar wpdl-mode-map
-  (let ((map (make-keymap)))
-    ; (define-key map "\C-j" 'newline-and-indent)
-    map)
-  "Keymap for NMODL major mode")
-
-;;;###autoload
-(add-to-list 'auto-mode-alist '("\\.mod\\'" . nmodl-mode))
-
-(setq nmodl-keywords
-      '(
-	"NEURON"
-	"UNITS"
-	"PARAMETER"
-	"ASSIGNED"
-	"STATE"
-	"INITIAL"
-	"BREAKPOINT"
-	"DERIVATIVE"
-	"PROCEDURE"
-	))
-
-(setq nmodl-neuron-keywords
-      '(
-	"TITLE"
-	"SUFFIX"
-	"POINT_PROCESS"
-	"RANGE"
-	"GLOBAL"
-	"POINTER"
-	"BBCOREPOINTER"
-	"USEION"
-	"NONSPECIFIC_CURRENT"
-	"SOLVE"
-	"METHOD"
-	))
-
-(defvar nmodl-font-lock-keywords
-  `(
-    ,(regexp-opt nmodl-keywords t) . 'font-lock-keyword-face
-   )
-  "Minimal highlighting expressions for NMODL mode")
-
-(setq nmodl-font-lock-keywords
-      `(
-	(,(regexp-opt nmodl-keywords t) . 'font-lock-keyword-face)
-	(,(regexp-opt nmodl-neuron-keywords t) . 'font-lock-constant-face)
-	("^[[:space:]]*\\([[:alpha:]][[:alnum:]_]*\\)" . 'font-lock-variable-name-face)
-	))
-
-(setq nmodl-syntax-rules
-      (syntax-propertize-rules
-       ("TITLE\\([^\n]\\)[^\n]*\\(\n\\)" (1 "|") (2 "|"))
-       ("\\<\\(COMMENT\\)\\>" (1 "<"))
-       ("\\<ENDCOMMEN\\(T\\)\\>" (1 ">"))
-       ("^[^:\n]*\\(:\\)[^\n]*\\(\n\\)" (1 "!") (2 "!"))
-       ("\\({\\)" (1 "("))
-       ("\\(}\\)" (1 ")"))
-       ))
-
-(defun nmodl-indent ()
-  (indent-relative-first-indent-point)
-  )
-
-(defun nmodl-mode ()
-  "Major mode for editing Workflow Process Description Language files"
-  (interactive)
-  (kill-all-local-variables)
-  (setq-local font-lock-defaults '(nmodl-font-lock-keywords))
-  (setq-local syntax-propertize-function nmodl-syntax-rules)
-  (setq-local c-syntactic-indentation t)
-  (setq-local indent-line-function 'nmodl-indent)
-  ;; (use-local-map wpdl-mode-map)
-  (setq major-mode 'nmodl-mode)
-  (setq mode-name "NMODL")
-  (run-hooks 'nmodl-mode-hook))
-

straight/versions/default.el

@@ -1,104 +0,0 @@
-(("ace-window" . "77115afc1b0b9f633084cf7479c767988106c196")
- ("auctex" . "a2809e4d7068aaa7fa9cbd51214606393d4ab9eb")
- ("avy" . "933d1f36cca0f71e4acb5fac707e9ae26c536264")
- ("biblio.el" . "bb9d6b4b962fb2a4e965d27888268b66d868766b")
- ("bqn-mode" . "a253194d880e762a2886feac4745ae9cf967567b")
- ("bui.el" . "f3a137628e112a91910fd33c0cff0948fa58d470")
- ("cfrs" . "981bddb3fb9fd9c58aed182e352975bd10ad74c8")
- ("cider" . "8a4405ca0d8dd02d1f35e287131838feec2a81c6")
- ("citeproc-el" . "f5217b9fdbcb41a0381ecf92108390fc843090dd")
- ("clojure-mode" . "28dc02114ae70db6bb68d537ea77985f272120bc")
- ("company-ghci" . "a1d25652583ab4666c5a78cac18cd8039776b50d")
- ("company-mode" . "ca045bc54411f274779057d94a1807efe7f8d2a6")
- ("compat" . "97f24af413a38a7f1aaedb29f5aaaa333796a5b4")
- ("d2-mode" . "e1fc7d6c1915acaf476060c0f79b8bdef6bd1952")
- ("dap-mode" . "c81014ccc390e8994b061bd2d9f8b5dd84498a3d")
- ("dart-mode" . "edb45cb7095b1e4f62eaae33e56fe9af5b010213")
- ("dash.el" . "af5ea5d8a13735fa27d2c3e6f756d065639a7b45")
- ("el-get" . "8d3edab760ff84baf4ce36c0b33bfb8668c6d212")
- ("eldoc" . "5cba6bcbd3b3d3f1ae9668cf6a1f9e2d3ebb10df")
- ("emacs-async" . "59f6ee68eb9bed8de12d71ca78a11dd8effbc2aa")
- ("emacs-direnv" . "c0bf3b81c7a97e2a0d06d05495e86848254fcc1f")
- ("emacs-htmlize" . "c9a8196a59973fabb3763b28069af9a4822a5260")
- ("emacs-request" . "c22e3c23a6dd90f64be536e176ea0ed6113a5ba6")
- ("emacs-web-server" . "3982c55e9061475038a3ccd61aecb2de3d407cec")
- ("emacs-websocket" . "40c208eaab99999d7c1e4bea883648da24c03be3")
- ("emacs-which-key" . "38d4308d1143b61e4004b6e7a940686784e51500")
- ("emacsmirror-mirror" . "dc1c32049771890965c0d498be5cced13a65296a")
- ("emacsql" . "bc6713fb763388f43111ba1488df9263d5dc505b")
- ("eros" . "a9a92bdc6be0521a6a06eb464be55ed61946639c")
- ("esup" . "4b49c8d599d4cc0fbf994e9e54a9c78e5ab62a5f")
- ("exec-path-from-shell" . "4896a797252fbfdac32fb77508500ac7d220f717")
- ("f.el" . "931b6d0667fe03e7bf1c6c282d6d8d7006143c52")
- ("flycheck" . "8c0dbfaa463e69efb41ef2cda9c4e89b99e266a0")
- ("geiser" . "c8b862f00e208f2c09bf2a2b2436af0a466a2531")
- ("gnu-elpa-mirror" . "4809077cd69544e81d946c7bb64c3d7e33e24ff1")
- ("gnuplot" . "43e9674b869475b1c2a32f045c167673eb2faae0")
- ("haskell-mode" . "e5d32021ea30438fb957976760b94af66a55b53b")
- ("helm" . "c8d147be4d89cb3355b89a645ba3703a46bad15d")
- ("helm-bibtex" . "6064e8625b2958f34d6d40312903a85c173b5261")
- ("ht.el" . "1c49aad1c820c86f7ee35bf9fff8429502f60fef")
- ("hydra" . "59a2a45a35027948476d1d7751b0f0215b1e61aa")
- ("imenu-list" . "76f2335ee6f2f066d87fe4e4729219d70c9bc70d")
- ("jsonrpc" . "444cafedd091815e674b6c93458ba97a55a76928")
- ("leaf-convert.el" . "da86654f1021445cc42c1a5a9195f15097352209")
- ("leaf-keywords.el" . "82ec27e3441900daedeaaebca509181f964da81f")
- ("leaf-tree.el" . "89c3b8842df067bba67663d309f43aa311acdccd")
- ("leaf.el" . "69c9b057cdeee560450c1d04a9a058235ecff0f7")
- ("let-alist" . "35a1dae3c540705433a510c13c8af80206b29b5f")
- ("llama" . "5990ae7b5cba3425252f64b9377352c9a01690d5")
- ("lsp-dart" . "34e2a1191f723792d5f366b314cd6b07de4f1566")
- ("lsp-docker" . "ff41f4a76b640d39dc238bacba7f654c297827fa")
- ("lsp-haskell" . "aa9b5bce355790de1fbdbe239650d704f46a19a0")
- ("lsp-mode" . "c0cafd07ea7e0a2d82fcd0680eb36da10356d700")
- ("lsp-treemacs" . "3e5550f278db74f15ebe34add0138b138207ec08")
- ("lsp-ui" . "030d36960338fd633a98b332bc3734c412c25ca6")
- ("magit" . "7de46ddeb30e095645d93d73bbbc5fe3e8565ac5")
- ("map" . "6ac89e5dd1084afdc1d8fdd717de11c572212428")
- ("markdown-mode" . "d51c469133d220823cc6ab50ff8e8743ed6e42fb")
- ("mcf" . "4e44b6e24d9fe7a4ce7249df79f4473c0b473232")
- ("melpa" . "06f8868ff6e2966b8482cd100271e1d1afc2ce79")
- ("nix-mode" . "719feb7868fb567ecfe5578f6119892c771ac5e5")
- ("nongnu-elpa" . "cdbf329f7dae98bbd39a3bf090bd01793f6d5947")
- ("org" . "526a7d1cc65409d5546b009f54fed28726a9457d")
- ("org-ref" . "6a22c20f863b997497b618507adbcc8cb10a9f86")
- ("org-reveal" . "f55c851bf6aeb1bb2a7f6cf0f2b7bd0e79c4a5a0")
- ("org-roam" . "89dfaef38b6caa3027f20f96a551dc8f194ac533")
- ("org-roam-bibtex" . "b065198f2c3bc2a47ae520acd2b1e00e7b0171e6")
- ("org-roam-ui" . "5ac74960231db0bf7783c2ba7a19a60f582e91ab")
- ("ox-pandoc" . "5766c70b6db5a553829ccdcf52fcf3c6244e443d")
- ("parsebib" . "7bfde4e4679413424a9a9af099203d5c23e32cd2")
- ("parseclj" . "6af22372e0fe14df882dd300b22b12ba2d7e00b0")
- ("parseedn" . "3407e4530a367b6c2b857dae261cdbb67a440aaa")
- ("pdf-tools" . "30b50544e55b8dbf683c2d932d5c33ac73323a16")
- ("pfuture" . "19b53aebbc0f2da31de6326c495038901bffb73c")
- ("php-mode" . "40b8abed3079771e060dd99a56703520dabf5be4")
- ("poetry.el" . "1dff0d4a51ea8aff5f6ce97b154ea799902639ad")
- ("posframe" . "12f540c9ad5da09673b2bca1132b41f94c134e82")
- ("ppp.el" . "d5d854c3006dfd268e62c7f91c2aad6f86a505b5")
- ("project" . "a0ebb2e9cfda339d8ebda77447c9d822fe313c2d")
- ("python-mode" . "fcff76c308b4409007c61492e4936e7c0b7d5aee")
- ("pyvenv" . "31ea715f2164dd611e7fc77b26390ef3ca93509b")
- ("queue" . "8df1334d54d4735d2f821790422a850dfaaa08ef")
- ("racket" . "22e56ce80389544d3872cf4beb4008fb514b2218")
- ("rainbow-delimiters" . "f40ece58df8b2f0fb6c8576b527755a552a5e763")
- ("rainbow-mode" . "2e6b18609c2fdd1a2dc513937a64d276fd6cf24c")
- ("rust-mode" . "9915b3a585a7a75e9126df9e0e9d1df8057ae3cf")
- ("s.el" . "dda84d38fffdaf0c9b12837b504b402af910d01d")
- ("seq" . "da86da9bf111f68fb81efd466d76d53af5aebc00")
- ("sesman" . "7bca68dbbab0af26a6a23be1ff5fa97f9a18e022")
- ("slint-mode" . "168a6cfb90b5e36360074c83f80d5bbac2f0287e")
- ("spinner" . "fa117f0893788f3fe24673715a6b83bb34d238dd")
- ("straight.el" . "b7da472452615dc44b4ce76c64a059d6db3b7017")
- ("string-inflection" . "617df25e91351feffe6aff4d9e4724733449d608")
- ("tablist" . "fcd37147121fabdf003a70279cf86fbe08cfac6f")
- ("transient" . "07a104aa73b5d5e3168ba6e202ebfb60188af6ed")
- ("transient-dwim.el" . "cb5e0d35729fc6448553b7a17fc5c843f00e8c1d")
- ("treemacs" . "5fa84199501fd43e5573b1277a2b1699c7473cc1")
- ("web-mode" . "1eb0abb1a9bffbb33db7bbfc6efe5b48bf416d57")
- ("wfnames" . "164e4efa2a96bed201a0a5402e137ebeef15bcc6")
- ("with-editor" . "7787e19764c1089390584ac17a80129ef9afaa14")
- ("xref" . "63b5875528e9c8dba3abbc76dae1b49351273c1c")
- ("yaml-mode" . "d91f878729312a6beed77e6637c60497c5786efa")
- ("yaml.el" . "f99ef76c80e6fc3fcf650c4fe34e10726594a4c4"))
-:gamma