Fix Cross References

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)

.gitignore

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

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",

flake.nix

@@ -1,23 +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 }:
-    flake-utils.lib.eachDefaultSystem (system: let
+  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 = {
-        emacs = pkgs.emacsWithPackagesFromUsePackage {
-          config = ./main.org;
-          package = if pkgs.stdenv.isDarwin then pkgs.emacs29-macport else pkgs.emacs29;
-        };
+        me-emacs = pkgs.emacs;
+        me-emacs-wayland = pkgs.emacs-pgtk;
       };
-    });
+    })) // {
+      overlays.default = final: prev: ({
+        me-emacs = final.emacs;
+        me-emacs-wayland = final.emacs-pgtk;
+      });
+    };
 }

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$"))

src/nmodl.el

@@ -0,0 +1,79 @@
+(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

@@ -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