Fix Cross References

Fix indents
TODO: Fix overrides for local-repo/emacs (for nix derivation)
2025-09-04 15:42:37 -04:00 · 2025-09-03 17:04:23 -04:00 · 2025-09-03 17:00:24 -04:00 · 2025-09-02 11:56:17 -04:00 · 2025-09-02 11:16:25 -04:00 · 2025-08-28 11:16:27 -04:00
7 changed files with 323 additions and 194 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,8 @@
 /auto-save-list/
 /backups/
 /etc/
-/straight/
+/straight/*
+!/straight/versions
 /tutorial/
 /var/
 tramp
--- a/custom.el
+++ b/custom.el
@@ -4,7 +4,9 @@
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(custom-safe-themes
-   '("5f79df6b4c56021d173c178d90b5a600c678a192d78cc639553915985b67c4ea" "8cda1cfae8e393bfb23f1d448d4be10720835d086f7db080908a7c8d01566516" "a27f7b52fe66bacaec9059f8afd04d055a4ac3c2fba9eb9128c81e10152fc566" "1ba7196d8e7b883272ea8818a5163aec21b57023368febf55255816226f7b370" "8256e7e03444834d34915a226dc24933b0d680a0a1da568ec03f852be776f168" "4ac2f45e6b46e5bb50826d4250df71a57124169b82cc0ad75e436de6e70a9690" "29addd67feb95ca1179e60d476bb92c1f11835548e2efaec15c9ac6af2a8e6a8" "9b7a425c38c4894e161887c26381c2a6fc1de3c1407158507caaf469d76eb27b" "bce055e1681dd343659957710af77f7a6ad106677d42c61f86ebeedf637c4493" "f62c69472d3f506179d797131c014fe4095d9609dddf14542c50e0388f1e8d6d" "cf143bf23fa8160f87331893cdadc40b876556634621dfa373fcf93c4c97c444" "f459dfd377e9cb98d90e53383dcca7d73396cc0a22b31d39af24fb1cf3548fb5" "fcc14e1a22c99d77f7b1455b0c8a320f8afd0c1f4a9c5c50b45f676eb0c54ba2" "a6bae299481c3c0058e611d2c32ca169fa27203345a880806a5a8554cdd2e588" "feb9556e03558588e29e6659c8e01ea3d2a17a1e7a13e9bf9fc9e59cacba4b72" default)))
+   '("5f79df6b4c56021d173c178d90b5a600c678a192d78cc639553915985b67c4ea" "8cda1cfae8e393bfb23f1d448d4be10720835d086f7db080908a7c8d01566516" "a27f7b52fe66bacaec9059f8afd04d055a4ac3c2fba9eb9128c81e10152fc566" "1ba7196d8e7b883272ea8818a5163aec21b57023368febf55255816226f7b370" "8256e7e03444834d34915a226dc24933b0d680a0a1da568ec03f852be776f168" "4ac2f45e6b46e5bb50826d4250df71a57124169b82cc0ad75e436de6e70a9690" "29addd67feb95ca1179e60d476bb92c1f11835548e2efaec15c9ac6af2a8e6a8" "9b7a425c38c4894e161887c26381c2a6fc1de3c1407158507caaf469d76eb27b" "bce055e1681dd343659957710af77f7a6ad106677d42c61f86ebeedf637c4493" "f62c69472d3f506179d797131c014fe4095d9609dddf14542c50e0388f1e8d6d" "cf143bf23fa8160f87331893cdadc40b876556634621dfa373fcf93c4c97c444" "f459dfd377e9cb98d90e53383dcca7d73396cc0a22b31d39af24fb1cf3548fb5" "fcc14e1a22c99d77f7b1455b0c8a320f8afd0c1f4a9c5c50b45f676eb0c54ba2" "a6bae299481c3c0058e611d2c32ca169fa27203345a880806a5a8554cdd2e588" "feb9556e03558588e29e6659c8e01ea3d2a17a1e7a13e9bf9fc9e59cacba4b72" default))
+ '(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)))
 (custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
--- a/flake.lock
+++ b/flake.lock
@@ -1,55 +1,15 @@
 {
  "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": 1689068808,
-        "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=",
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
        "owner": "numtide",
        "repo": "flake-utils",
-        "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",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
        "type": "github"
      },
      "original": {
@@ -60,11 +20,11 @@
    },
    "nixpkgs": {
      "locked": {
-        "lastModified": 1691990649,
-        "narHash": "sha256-gMbKOiX1HwClRP9lADaaV/lnZr93NEaOFe4ApDx/zd8=",
+        "lastModified": 1737746512,
+        "narHash": "sha256-nU6AezEX4EuahTO1YopzueAXfjFfmCHylYEFCagduHU=",
        "owner": "NixOS",
        "repo": "nixpkgs",
-        "rev": "6e287913f7b1ef537c97aa301b67c34ea46b640f",
+        "rev": "825479c345a7f806485b7f00dbe3abb50641b083",
        "type": "github"
      },
      "original": {
@@ -74,26 +34,9 @@
        "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": {
-        "emacs-overlay": "emacs-overlay",
-        "flake-utils": "flake-utils_2",
+        "flake-utils": "flake-utils",
        "nixpkgs": "nixpkgs"
      }
    },
@@ -111,21 +54,6 @@
        "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",
--- a/flake.nix
+++ b/flake.nix
@@ -1,28 +1,21 @@
 {
  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, emacs-overlay }: let
-    mkEmacs = pkgs: v: pkgs.emacsWithPackagesFromUsePackage {
-      config = ./main.org;
-      package = pkgs."${v}${if pkgs.stdenv.isDarwin then "-macport" else "-pgtk"}";
-    };    
+  outputs = { self, nixpkgs, flake-utils }: let
  in (flake-utils.lib.eachDefaultSystem (system: let
      pkgs = import nixpkgs {
        inherit system;
-        overlays = [
-          emacs-overlay.overlays.default
-        ];
      };
    in {
      packages = {
-        me-emacs = mkEmacs pkgs "emacs29";
+        me-emacs = pkgs.emacs;
+        me-emacs-wayland = pkgs.emacs-pgtk;
      };
    })) // {
-      overlays.default = final: prev: (emacs-overlay.overlays.default final prev) // {
-        me-emacs = mkEmacs final "emacs29";
-      };      
+      overlays.default = final: prev: ({
+        me-emacs = final.emacs;
+        me-emacs-wayland = final.emacs-pgtk;
+      });
    };
 }
--- a/init.el
+++ b/init.el
@@ -3,22 +3,31 @@
 ;; This file loads Org and then loads the rest of our Emacs initialization from Emacs lisp
 ;; embedded in literate Org files.

-;; 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)))
+(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))

-(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))
+(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)
+
+(setq dotfiles-dir (file-name-directory (or (buffer-file-name) load-file-name)))  

 ;; load up all literate org-mode files in this directory
 (mapc #'org-babel-load-file (directory-files dotfiles-dir t "\\.org$"))
--- a/main.org
+++ b/main.org
@@ -9,42 +9,58 @@

 * 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

 We must initialize =leaf.el=, which we use as a use-package
 replacement for defining configs and relations between packages etc.

 #+begin_src elisp :tangle yes :exports code
-(eval-and-compile
-  (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))
+  (eval-and-compile
+    (straight-use-package 'leaf)

-  (leaf leaf-keywords
-    :ensure t
-    :init
-    (leaf el-get :ensure t)
-    (leaf hydra :ensure t)
-    (leaf blackout :ensure t)
+    (leaf leaf-keywords
+      :init
+      (straight-use-package 'leaf-keywords)
+      :custom
+      (leaf-alias-keyword-alist .'((:ensure . :straight)))
+      :config
+      ;; initialize leaf-keywords.el
+      (leaf-keywords-init)))

-    :config
-    ;; initialize leaf-keywords.el
-    (leaf-keywords-init)))
-
-(leaf leaf-tree :ensure t)
-(leaf leaf-convert :ensure t)
-(leaf transient-dwim :ensure t
-  :bind (("M-=" . transient-dwim-dispatch)))
+  (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
+    :bind (("M-=" . transient-dwim-dispatch)))
 #+end_src

-#+RESULTS:
-: transient-dwim
-
 ** MacOS Specific

 #+begin_src elisp :tangle yes :exports code
@@ -59,9 +75,16 @@ replacement for defining configs and relations between packages etc.

 *** 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))
+; (leaf gcmh :ensure t
+;  :hook (after-init-hook))
 #+end_src

 *** Profiling
@@ -77,6 +100,7 @@ Ensure that the =custom.el= resides in the users' emacs directory.

 #+begin_src elisp :tangle yes :exports code
 (leaf custom-el
+  :leaf-defer nil
  :config
  ;; Ensure custom writes to specific file
  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
@@ -89,6 +113,7 @@ Set the backups directory to reside in the users' emacs directory.

 #+begin_src elisp :tangle yes :exports code
 (leaf backup
+  :leaf-defer nil
  :config
  ;; Change the location of file backups/locks into the emacs.d/backups/
  (setq backup-directory-alist
@@ -112,6 +137,7 @@ Visual Theme of Emacs config: defined in the =themes= directory.

 #+begin_src elisp :tangle yes :exports code
 (leaf visual
+  :leaf-defer nil
  :doc "Visual Changes to Emacs"
  :tag "builtin" "internal"
  :custom ((menu-bar-mode . nil)
@@ -128,7 +154,9 @@ Visual Theme of Emacs config: defined in the =themes= directory.

 * Version Control
 #+begin_src elisp :tangle yes :exports code
-(leaf magit :ensure t :require t)
+(leaf magit
+  :leaf-defer nil
+  :ensure t :require t)
 #+end_src

 * Nix Related
@@ -139,15 +167,16 @@ In order to support direnv (loading =nix-shell= / =nix develop=)
 #+begin_src elisp :tangle yes :exports code
 (leaf direnv
  :ensure t
-  :config
-  (direnv-mode))
+  :global-minor-mode direnv-mode)
 #+end_src

 ** Nix-mode

 =.nix= file mode
 #+begin_src elisp :tangle yes :exports code
-(leaf nix-mode :ensure t)
+(leaf nix-mode
+  :ensure t
+  :mode "\\.nix\\'")
 #+end_src

 * IDE Like Things
@@ -155,8 +184,9 @@ In order to support direnv (loading =nix-shell= / =nix develop=)
 ** Which Key Again?

 #+begin_src elisp :tangle yes :exports code
-(leaf which-key :ensure t
-  :config (which-key-mode))
+(leaf which-key
+  :ensure t
+  :global-minor-mode which-key-mode)
 #+end_src

 ** Company Completion!
@@ -168,7 +198,7 @@ We like autocomplete, it... is nice, okay?
  :bind
  (("C-<tab>" . company-complete))
  :hook after-init-hook
-  :config (global-company-mode))
+  :global-minor-mode global-company-mode)
 #+end_src

 ** Language Server Protocol
@@ -181,9 +211,9 @@ We love language features that make languages nice
  :init
  (setq lsp-keymap-prefix "C-c l")
  :commands lsp lsp-deferred
-  :hook
+  :hook (
  ;; which key support v v v
-  ((lsp-mode-hook . lsp-enable-which-key-integration)
+  (lsp-mode-hook . lsp-enable-which-key-integration)
 #+end_src

 *** IDE Languages
@@ -222,7 +252,7 @@ We love language features that make languages nice
 **** Rust

 #+begin_src elisp :tangle yes :exports code
-(rust-mode-hook . lsp-deferred))
+(rust-mode-hook . lsp-deferred)
 #+end_src

 #+begin_src elisp :tangle yes :exports code
@@ -233,6 +263,10 @@ We love language features that make languages nice

 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
@@ -256,6 +290,12 @@ We do want some nice to haves of course
  (projectile-mode +1))
 #+end_src

+END LSP CONFIG
+
+#+begin_src elisp :tangle yes :exports code
+)
+#+end_src
+
 * WEB

 We all know the web is the future, obviously, of course.
@@ -269,19 +309,29 @@ 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

 #+begin_src elisp :tangle yes :exports code
-(leaf d2-mode :ensure t)
+(leaf d2-mode
+  :ensure t
+  :mode "\\.d2\\'"
+  )
 #+end_src

 * YAML

 #+begin_src elisp :tangle yes :exports code
-(leaf yaml-mode :ensure t)
+(leaf yaml-mode
+  :ensure t
+  :mode "\\.yaml\\'"
+  )
 #+end_src

 * Python Things
@@ -292,7 +342,9 @@ 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
+(leaf python-mode
+  :ensure t
+  :mode "\\.py\\'"
  :config
  (setq python-shell-interpreter "ipython"
 	python-shell-interpreter-args "-i --simple-prompt --InteractiveShell.display_page=True"))
@@ -310,27 +362,34 @@ For when we aren't nix'ing things, and want some nice poetry.

 Who even needs C++, not me, no way, no how.

-#+begin_src elisp :tangle yes :exports code
+#+begin_src elisp :tangle no :exports code
 (leaf c-config
-  :hook c-mode-hook c++-mode-hook
  :config
-  (leaf company-ctags :ensure t)
-  (leaf company-c-headers :ensure t)
-  (leaf meson-mode :ensure t))
+;  (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)
+  )
 #+end_src

 * Haskell

 #+begin_src elisp :tangle yes :exports code
-(leaf haskell-mode :ensure t)
-(leaf lsp-haskell :ensure t)
-(leaf company-ghci :ensure t)
+(leaf haskell-mode
+  :ensure t
+  :mode "\\.hs\\'"
+  :init
+  (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))
 #+end_src
@@ -341,7 +400,7 @@ Minecraft =mcfunction= support, because, it can be annoying to type
 this stuff otherwise.
 #+begin_src elisp :tangle yes :exports code
 (leaf mcf-mode
-  :el-get rasensuihei/mcf)
+  :straight (mcf-mode :type git :host github :repo "rasensuihei/mcf"))
 #+end_src

 * Lisps
@@ -364,22 +423,34 @@ Makes using racket so much nicer
 (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 :ensure t
+(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))
+  	org-confirm-babel-evaluate nil
+  	org-src-preserve-indentation t))
 ;; (tempo-define-template "Fig. Caption"
 ;; 			   '("" (P "Image: " image t)
 ;; 			     (P "Caption: " caption t)
@@ -434,7 +505,9 @@ updating our bibliography.
 	bibtex-autokey-titlewords 2
 	bibtex-autokey-titlewords-stretch 1
 	bibtex-autokey-titleword-length 5)
-  :require org-ref org-ref-helm oc-bibtex oc-bibtex oc-csl oc-natbib)
+  (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)
 #+end_src

 ** Extra Export Options
@@ -449,28 +522,21 @@ We really do require latex
  :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}")))
+  	       '("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}")))
-
-  (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")))
+  	       '("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
@@ -540,9 +606,9 @@ And in case we want to make some (GNU)?plots?

 *** 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.
+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
@@ -577,9 +643,9 @@ e.g. meetings, deadlines and whatever else:
  :config
  (add-hook 'org-capture-mode-hook #'org-id-get-create)
  (setq org-capture-templates
-	'(("t" "Todo" entry (file+headline "todo.org" "Tasks")
+	'(("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 "todo.org" "Habits")
+	  ("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")
@@ -613,14 +679,39 @@ taking package.

 #+begin_src elisp :tangle yes :exports code
 (leaf org-roam :ensure t
-  :after org
+  :after org transient-dwim
  :require t
  :config
  (setq org-roam-directory (file-truename org-directory))
-  (org-roam-db-autosync-mode))
+  (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 Babel (ORB)
+**** 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

@@ -631,7 +722,8 @@ taking package.
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((emacs-lisp . t)
-     (python . t))))
+     (python . t)
+     (shell . t))))
 #+end_src

 * Flutter
@@ -645,7 +737,7 @@ taking package.

 #+begin_src elisp :tangle yes :exports code
 (leaf bqn-mode
-  :el-get "museoa/bqn-mode"
+  :ensure (bqn-mode :type git :host github :repo "museoa/bqn-mode")
  :defer-config
  (set-face-attribute 'bqn-default nil :family 'unspecified))
 #+end_src
--- a/straight/versions/default.el
+++ b/straight/versions/default.el
@@ -0,0 +1,104 @@
+(("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
Author	SHA1	Message	Date
david	71bb316433	Fix Cross References	2025-09-04 15:42:37 -04:00
david	72ec0bbcca	Fix indents	2025-09-03 17:04:23 -04:00
david	51149a1c62	TODO: Fix overrides for local-repo/emacs (for nix derivation)	2025-09-03 17:00:24 -04:00
david	2adc03c10d	Cleanup Straight/Org Literate Loading	2025-09-02 11:56:17 -04:00
david	abd4dbb085	Merge branch 'master' of https://git.syzygial.cc/Syzygial/EmacsConfig	2025-09-02 11:16:25 -04:00
David	2ba07d3ba9	Update packages	2025-08-28 11:16:27 -04:00
David	7601c515d7	Fix loads and defers	2025-08-28 11:16:18 -04:00
David	491d9e173b	No-defer to load pure customizations	2025-08-27 17:06:31 -04:00
David	707ae8ed9e	Add note and disable GCMH	2025-08-27 16:59:57 -04:00
David	8e573a4739	Fix: Load Leaf w/ Straight.el	2025-08-27 16:53:42 -04:00
david	5a840488b5	Todo.org -> todos.org	2025-03-24 10:29:56 -04:00
david	14454885f1	Org-ref pre-process hook & org babel for shell	2025-03-20 12:06:21 -04:00
david	db7573be44	straight/org fixup	2025-03-18 10:12:10 -04:00
David Crompton	3f9a4859a9	No longer need community overlay (for now)	2025-03-18 09:52:53 -04:00
David Crompton	2c35aebce7	Nix Package Overlay -> Straight	2025-03-18 09:48:28 -04:00
david	91e2a5430d	macport not avail for emacs-30, use regular/native	2025-03-13 11:39:50 -04:00
david	80eb9e5e07	rainbowmode	2025-03-13 11:30:26 -04:00
David Crompton	c4135ecee1	default nixpkgs emacs not 29	2025-03-11 12:43:56 -04:00
David Crompton	f840fea7c3	Update option for wayland or not	2025-02-01 11:09:51 -05:00
David Crompton	87858e66b8	flake.lock: Update Flake lock file updates: • Updated input 'emacs-overlay': 'github:nix-community/emacs-overlay/7a4b5bbc06182e2f704630cd77a614ab0d9c2f2e?narHash=sha256-bvj/wfLLFTc8cWAwhN8tgShiy8ekPWt1%2BgWlEH7W4zY%3D' (2023-08-14) → 'github:nix-community/emacs-overlay/4ebe4c890e7c8662ae31192359a56b0505cf10ba?narHash=sha256-R1p2ZXOydII%2BMT/SpeOXBjo/dgfD/gIArge2YAgSw38%3D' (2025-01-25) • Removed input 'emacs-overlay/flake-utils' • Removed input 'emacs-overlay/flake-utils/systems' • Updated input 'emacs-overlay/nixpkgs-stable': 'github:NixOS/nixpkgs/720e61ed8de116eec48d6baea1d54469b536b985?narHash=sha256-iUNEeudc4dGjx%2BHsHccnGiuZUVE/nhjXuQ1DVCsHIUY%3D' (2023-08-13) → 'github:NixOS/nixpkgs/035f8c0853c2977b24ffc4d0a42c74f00b182cd8?narHash=sha256-YnHJJ19wqmibLQdUeq9xzE6CjrMA568KN/lFPuSVs4I%3D' (2025-01-23) • Updated input 'flake-utils': 'github:numtide/flake-utils/919d646de7be200f3bf08cb76ae1f09402b6f9b4?narHash=sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0%3D' (2023-07-11) → 'github:numtide/flake-utils/11707dc2f618dd54ca8739b309ec4fc024de578b?narHash=sha256-l0KFg5HjrsfsO/JpG%2Br7fRrqm12kzFHyUHqHCVpMMbI%3D' (2024-11-13) • Updated input 'nixpkgs': 'github:NixOS/nixpkgs/6e287913f7b1ef537c97aa301b67c34ea46b640f?narHash=sha256-gMbKOiX1HwClRP9lADaaV/lnZr93NEaOFe4ApDx/zd8%3D' (2023-08-14) → 'github:NixOS/nixpkgs/825479c345a7f806485b7f00dbe3abb50641b083?narHash=sha256-nU6AezEX4EuahTO1YopzueAXfjFfmCHylYEFCagduHU%3D' (2025-01-24)	2025-01-25 19:04:07 -05:00
david	031084e3c6	;; -> ;	2024-07-14 14:19:06 -04:00
david	d3257d36e4	Override treeSitter passthrough	2024-07-14 14:18:24 -04:00
david	5433a14e49	LSP: Add tree-sitter to emacs package	2024-07-14 13:57:47 -04:00
david	d2df2d938d	Org Roam (Separate Leaf)	2024-06-27 15:27:23 -04:00
david	e575c6c432	Org Roam UI	2024-06-27 15:20:24 -04:00
david	0326ba9bdd	ORB BB	2024-06-27 13:54:50 -04:00
david	7abd4f5b71	Org-roam: transient keybinds	2024-06-27 11:23:53 -04:00