KineticPreProcessor · yantosca · May 8, 2026 · Apr 30, 2026 · May 3, 2026 · May 3, 2026
diff --git a/.gitignore b/.gitignore
@@ -31,6 +31,9 @@
 /ci-tests/**/*results*
 /ci-tests/**/*.csv
 
+# Ignore byte-compiled emacs lisp files
+/site-lisp/*.elc
+
 # Ignore files generated by KPP (everywhere)
 **/*_Function*
 **/*_Global*
@@ -73,4 +76,4 @@ docs/build/*
 !/util/Makefile*
 
 # ReadTheDocs
-docs/_build/*
+docs/_build/*
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [Unreleased] - TBD
+### Fixed
+- Fixed several emacs font-lock issues in `site-lisp/kpp.el`
+
 ## [3.4.0] - 2026-04-29
 ### Added
 - Added `Rodas3_1` integration method (with updated coefficents by @msl3v) to `rosenbrock_autoreduce.f90`, `rosenbrock.{c,f90,m}`, `rosenbrock_adj.{c,f90}`, `rosenbrock_tlm.f90`

diff --git a/site-lisp/kpp.el b/site-lisp/kpp.el
@@ -1,130 +1,257 @@
-;; kpp.el --- kpp mode for GNU Emacs
-;; (c) Rolf Sander <rolf.sander@mpic.de>
+;;; kpp.el --- Major mode for KPP (Kinetic PreProcessor) files  -*- lexical-binding: t; -*-
 
-;; To activate it, copy kpp.el to a place where emacs can find it and
-;; then add "(require 'kpp)" to your .emacs startup file.
-
-;; Known problem:
-;; ":" inside comments between reaction products confuses font-lock
+;; Authors:    Rolf Sander <rolf.sander@mpic.de>
+;;             Bob Yantosca (used AI to "lint")
+;; Version:    1.2
+;; Keywords:   languages, kpp, chemistry
 
 ;; This program is free software; you can redistribute it and/or modify
 ;; it under the terms of the GNU General Public License as published by
 ;; the Free Software Foundation; either version 2 of the License, or
 ;; (at your option) any later version.
+;;
 ;; This program is distributed in the hope that it will be useful,
 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 ;; GNU General Public License for more details.
 
-;; auto-start kpp-mode when loading a *.def, *.eqn, *.kpp, or *.spc file
-(setq auto-mode-alist
-  (cons '("\\.def\\'" . kpp-mode) auto-mode-alist))
-(setq auto-mode-alist
-  (cons '("\\.eqn\\'" . kpp-mode) auto-mode-alist))
-(setq auto-mode-alist
-  (cons '("\\.kpp\\'" . kpp-mode) auto-mode-alist))
-(setq auto-mode-alist
-  (cons '("\\.spc\\'" . kpp-mode) auto-mode-alist))
-
-;; Turn on font-lock-mode for KPP
-(add-hook 'kpp-mode-hook 'font-lock-mode)
-
-(setq kpp-font-lock-keywords
- (list
-  '("^\\([^=\n]*=[^:\n]*\\):[^;\n]*;" 1 font-lock-constant-face) ; reaction
-  ;; alternatively, use another color for rate constant:
-  ;; '("^\\([^=\n]*=[^:\n]*\\):\\([^;\n]*\\);"
-  ;;     (1 font-lock-constant-face) (2 font-lock-keyword-face))
-  '("<[A-z0-9_#]+>" 0 font-lock-variable-name-face t) ; equation tag
-  '("{[^}\n]*}"     0 font-lock-comment-face t)       ; comment
-  '("!.*"           0 font-lock-comment-face t)       ; f90 comment
-  '("{@[^}]+}"      0 font-lock-doc-face t)           ; alternative LaTeX text
-  '("{$[^}]+}"      0 font-lock-string-face t)        ; alternative LaTeX text
-  '("{&[^}]+}"      0 font-lock-builtin-face t)       ; BibTeX reference
-  '("{%[A-z0-9#]+}" 0 font-lock-type-face t)          ; marker
-  ;; KPP sections (Tab. 3 in thesis), commands (Tab. 13 in thesis), and
-  ;; fragments (Tab. 17 in thesis)
-  (cons (concat
-         "\\(#ATOMS\\|#AUTOREDUCE\\|#CHECKALL\\|#CHECK\\|#DECLARE"
-         "\\|#DEFFIX\\|#DEFVAR\\|#DOUBLE\\|#DRIVER\\|#DUMMYINDEX"
-         "\\|#ENDINLINE\\|#EQNTAGS\\|#EQUATIONS\\|#FAMILIES\\|#FUNCTION"
-         "\\|#GRAPH\\|#HESSIAN\\|#INCLUDE\\|#INITVALUES\\|#INLINE\\|#INTEGRATOR"
-         "\\|#INTFILE\\|#JACOBIAN\\|#LANGUAGE\\|#LOOKATALL\\|#LOOKAT"
-         "\\|#MEX\\|#MINVERSION\\|#MODEL\\|#MONITOR\\|#REORDER"
-         "\\|#SETFIX\\|#SETVAR\\|#STOCHASTIC\\|#STOICMAT\\|#UPPERCASEF90"
-         "\\|#WRITE_ATM\\|#WRITE_MAT\\|#WRITE_SPC"
-         ) 'font-lock-keyword-face)
-  '("^//.*"         0 font-lock-comment-face t) ; comment
-  )
-)
-
-; comment a region (adopted from wave-comment-region)
-
-(defvar kpp-comment-region "// "
-  "*String inserted by \\[kpp-comment-region] at start of each line in region.")
+;;; Commentary:
+;;
+;; This package provides a major mode for editing KPP (Kinetic PreProcessor)
+;; files.  KPP is a software tool that assists in developing and solving
+;; chemical kinetics problems.
+;;
+;; Installation:
+;;   Copy kpp.el to a directory in `load-path' and add
+;;     (require 'kpp)
+;;   to your Emacs init file (~/.emacs or ~/.emacs.d/init.el).
+;;
+;; File extensions automatically associated with kpp-mode:
+;;   .def, .eqn, .kpp, .spc
+
+;;; Code:
+
+;; ---------------------------------------------------------------------------
+;; Customization group
+;; ---------------------------------------------------------------------------
+
+(defgroup kpp nil
+  "Major mode for editing KPP (Kinetic PreProcessor) files."
+  :group  'languages
+  :prefix "kpp-")
+
+;; ---------------------------------------------------------------------------
+;; User-configurable variables
+;; ---------------------------------------------------------------------------
+
+(defcustom kpp-comment-prefix "// "
+  ;; Fix #10: renamed from `kpp-comment-region' to avoid collision with the
+  ;; function of the same name.
+  ;; Fix #13: changed from `defvar' with leading `*' to `defcustom'.
+  "String inserted by \\[kpp-comment-region] at the start of each line."
+  :type  'string
+  :group 'kpp)
+
+;; ---------------------------------------------------------------------------
+;; Syntax table  (defined once at load time; shared by all kpp buffers)
+;; ---------------------------------------------------------------------------
+
+(defvar kpp-mode-syntax-table
+  ;; Fix #11: was recreated (and re-allocated) inside `kpp-mode' on every
+  ;; buffer visit.
+  (let ((st (copy-syntax-table)))
+    (modify-syntax-entry ?_ "w" st)  ; underscore is part of a word
+    st)
+  "Syntax table for `kpp-mode'.")
+
+;; ---------------------------------------------------------------------------
+;; Font-lock keyword specification
+;; ---------------------------------------------------------------------------
+
+(defconst kpp-font-lock-keywords
+  ;; Fix #9: was a bare `setq' on an unbound symbol; `defconst' documents
+  ;; intent and prevents inadvertent modification.
+  (list
+   ;; Reaction: "species = products : rate_constant ;"
+   ;; Highlight the LHS + products (group 1) as a constant.
+   '("^\\([^=\n]*=[^:\n]*\\):[^;\n]*;" 1 font-lock-constant-face)
+
+   ;; Equation tag, e.g. <R001> or <j_NO2>
+   ;; Fix #2: [A-z] spans ASCII 65-122 and accidentally includes the
+   ;; characters [\]^_` (91-96).  Use [A-Za-z] instead.
+   '("<[A-Za-z0-9_#]+>"  0 font-lock-variable-name-face t)
+
+   ;; Curly-brace block comment: {comment text}
+   '("{[^}\n]*}"          0 font-lock-comment-face t)
+
+   ;; Fortran-90 / KPP inline comment: ! comment to end of line
+   '("!.*"                0 font-lock-comment-face t)
+
+   ;; {@...} – alternative LaTeX text
+   ;; '("{@[^}]+}"           0 font-lock-doc-face t)
+
+   ;; uncertainty of rate coefficient
+   ;; '("{§[^}]*}"           0 font-lock-builtin-face t)
+
+   ;; {$...} – alternative LaTeX text
+   ;; '("{\\$[^}]+}"         0 font-lock-doc-face t)
+
+   ;; {&...} – BibTeX reference
+   ;; '("{&[^}]+}"           0 font-lock-function-name-face t)
+
+   ;; {%...} – marker tag, e.g. {%TrG}
+   ;; Fix #2: same [A-z] → [A-Za-z] correction as above.
+   ;; '("{%[A-Za-z0-9#]+}"   0 font-lock-type-face t)
+
+   ;; KPP sections and commands
+   ;;
+   ;; ORDERING RULE: in Emacs regex alternation (\|) the leftmost match
+   ;; wins.  Any keyword that is a strict prefix of another must therefore
+   ;; appear AFTER the longer form.
+   ;;
+   ;; \> (end-of-word boundary) prevents a short keyword from matching
+   ;; as a prefix of an unknown longer token.
+   (cons (concat
+          "\\("
+          "#ATOMS\\|#AUTOREDUCE"
+          "\\|#CHECKALL\\|#CHECK" ; CHECKALL before CHECK
+          "\\|#DEFFIX\\|#DEFVAR\\|#DOUBLE\\|#DRIVER\\|#DUMMYINDEX"
+          "\\|#ENDINLINE\\|#EQNTAGS\\|#EQUATIONS"
+          "\\|#FAMILIES\\|#FUNCTION"
+          "\\|#GRAPH"
+          "\\|#HESSIAN"
+          "\\|#INCLUDE\\|#INITVALUES\\|#INLINE\\|#INTEGRATOR\\|#INTFILE"
+          "\\|#JACOBIAN"
+          "\\|#LANGUAGE\\|#LOOKATALL\\|#LOOKAT" ; LOOKATALL before LOOKAT
+          "\\|#MEX\\|#MINVERSION\\|#MODEL\\|#MONITOR"
+          "\\|#REORDER"
+          "\\|#SETFIX\\|#SETVAR\\|#STOCHASTIC\\|#STOICMAT"
+          "\\|#UPPERCASEF90"
+          "\\)\\>")
+         'font-lock-keyword-face)
+
+   ;; LaTeX note
+   ;; '("//.*"               0 font-lock-string-face t)
+
+   ;; C++-style line comment: // comment
+   '("^//.*"              0 font-lock-comment-face t)
+
+   ;; Fixme
+   ;; '("qqq"                0 font-lock-warning-face t)       
+
+   )
+  "Font-lock keyword specification for `kpp-mode'.")
+
+;; ---------------------------------------------------------------------------
+;; Keymap
+;; (defined before `define-derived-mode'; the macro detects and reuses it)
+;; ---------------------------------------------------------------------------
+
+(defvar kpp-mode-map
+  (let ((map (make-sparse-keymap)))
+    ;; C-c ; → comment / uncomment region
+    (define-key map "\C-c;" #'kpp-comment-region)
+    ;; Fix #14: original hard-coded 8 spaces and had no docstring.
+    ;; Using `tab-width' respects the user/project preference and updates
+    ;; automatically when `tab-width' is changed locally.
+    (define-key map (kbd "TAB")
+      (lambda ()
+        "Insert `tab-width' spaces (never a literal TAB character)."
+        (interactive)
+        (insert-char ?\s tab-width)))
+    map)
+  "Keymap for `kpp-mode'.")
+
+;; ---------------------------------------------------------------------------
+;; Comment / uncomment a region   (adapted from wave-comment-region)
+;; ---------------------------------------------------------------------------
 
 (defun kpp-comment-region (beg-region end-region arg)
-  "Comments every line in the region.
-Puts kpp-comment-region at the beginning of every line in the region.
-BEG-REGION and END-REGION are args which specify the region boundaries.
-With non-nil ARG, uncomments the region."
+  ;; Fix #10: the variable formerly named `kpp-comment-region' clashed with
+  ;; this function name.  The variable is now `kpp-comment-prefix'.
+  "Comment every line in the region.
+Inserts `kpp-comment-prefix' at the start of every line between
+BEG-REGION and END-REGION.  With non-nil ARG, uncomment instead."
   (interactive "*r\nP")
-  (let ((end-region-mark (make-marker)) (save-point (point-marker)))
+  (let ((end-region-mark (make-marker))
+        (save-point      (point-marker)))
     (set-marker end-region-mark end-region)
     (goto-char beg-region)
     (beginning-of-line)
-    (if (not arg)			;comment the region
-	(progn (insert kpp-comment-region)
-	       (while (and  (= (forward-line 1) 0)
-			    (< (point) end-region-mark))
-		 (insert kpp-comment-region)))
-      (let ((com (regexp-quote kpp-comment-region))) ;uncomment the region
-	(if (looking-at com)
-	    (delete-region (point) (match-end 0)))
-	(while (and  (= (forward-line 1) 0)
-		     (< (point) end-region-mark))
-	  (if (looking-at com)
-	      (delete-region (point) (match-end 0))))))
+    (if (not arg)
+        ;; --- comment the region ---
+        (progn
+          (insert kpp-comment-prefix)
+          (while (and (= (forward-line 1) 0)
+                      (< (point) end-region-mark))
+            (insert kpp-comment-prefix)))
+      ;; --- uncomment the region ---
+      (let ((com (regexp-quote kpp-comment-prefix)))
+        (when (looking-at com)
+          (delete-region (point) (match-end 0)))
+        (while (and (= (forward-line 1) 0)
+                    (< (point) end-region-mark))
+          (when (looking-at com)
+            (delete-region (point) (match-end 0))))))
     (goto-char save-point)
     (set-marker end-region-mark nil)
     (set-marker save-point nil)))
 
-(defvar kpp-mode-map ()
-  "Keymap used in kpp mode.")
+;; ---------------------------------------------------------------------------
+;; Major mode definition
+;; ---------------------------------------------------------------------------
+
+;;;###autoload
+(define-derived-mode kpp-mode fundamental-mode "KPP"
+  ;; Fix #8:  `define-derived-mode' replaces the manual boilerplate that
+  ;;          was in the original:
+  ;;            • calls `kill-all-local-variables'         (Fix #4)
+  ;;            • sets `major-mode' and `mode-name'
+  ;;            • calls `use-local-map' with kpp-mode-map
+  ;;            • calls `run-mode-hooks'
+  ;;            • installs :syntax-table automatically
+  "Major mode for editing KPP (Kinetic PreProcessor) files.
 
-(if kpp-mode-map
-    ()
-  (setq kpp-mode-map (make-sparse-keymap))
-  (define-key kpp-mode-map "\C-c;"    'kpp-comment-region)
-  ;; TAB inserts 8 spaces, not the TAB character
-  (define-key kpp-mode-map (kbd "TAB")
-    (lambda () (interactive) (insert "        ")))
-)
+Turning on `kpp-mode' runs the hook `kpp-mode-hook'.
 
-(defun kpp-mode ()
-  "Major mode for editing kpp code.
-Turning on kpp mode calls the value of the variable `kpp-mode-hook'
-with no args, if that value is non-nil.
+Known issue: `:' inside KPP inline comments (between reaction products
+and the rate constant) may confuse font-lock.
 
-Command Table:
 \\{kpp-mode-map}"
-  (interactive)
-  (make-local-variable 'font-lock-defaults)
-  (setq font-lock-defaults '((kpp-font-lock-keywords) t t))
-  (make-local-variable 'comment-start)
-  (setq comment-start "{")
-  (make-local-variable 'comment-end)
-  (setq comment-end "}")
-  (use-local-map kpp-mode-map)
-  (setq mode-name "kpp")
-  (setq major-mode 'kpp-mode)
-  (turn-on-font-lock)
-  (set-syntax-table (copy-syntax-table))
-  (modify-syntax-entry ?_ "w") ; the underscore can be part of a word
-  (auto-fill-mode 0)           ; no automatic line breaks
-  (run-hooks 'kpp-mode-hook)
-)
+  :syntax-table kpp-mode-syntax-table  ; Fix #11: reuse pre-built table
+  ;; Fix #12: `setq-local' replaces the two-step
+  ;;          `(make-local-variable ...) (setq ...)' pattern.
+  (setq-local font-lock-defaults '((kpp-font-lock-keywords) t t))
+  ;; KPP uses { } as block-comment delimiters.
+  (setq-local comment-start      "{ ")
+  (setq-local comment-end        " }")
+  (setq-local comment-start-skip "{+\\s-*")   ; added: needed by comment cmds
+  ;; Disable automatic line wrapping.
+  (auto-fill-mode 0)
+  ;; Fix #1 + #5: the original called `(turn-on-font-lock)' (deprecated)
+  ;; and also registered `font-lock-mode' (a toggle!) on `kpp-mode-hook'.
+  ;; With the hook in place, `turn-on-font-lock' ran first (enabling it),
+  ;; then the hook ran `font-lock-mode' with no argument (toggling it OFF).
+  ;; Net result: font-lock ended up disabled.  Fix: call `font-lock-mode'
+  ;; with explicit argument 1 here; do NOT add it to `kpp-mode-hook'.
+  (font-lock-mode 1))
+
+;; ---------------------------------------------------------------------------
+;; Auto-mode associations
+;; ---------------------------------------------------------------------------
+
+;; Fix #7: `add-to-list' is idempotent; the original `(setq … (cons …))'
+;; pattern appended duplicate entries every time the file was reloaded.
+
+;;;###autoload
+(add-to-list 'auto-mode-alist '("\\.def\\'" . kpp-mode))
+;;;###autoload
+(add-to-list 'auto-mode-alist '("\\.eqn\\'" . kpp-mode))
+;;;###autoload
+(add-to-list 'auto-mode-alist '("\\.kpp\\'" . kpp-mode))
+;;;###autoload
+(add-to-list 'auto-mode-alist '("\\.spc\\'" . kpp-mode))
 
 (provide 'kpp)
 
-;; kpp.el ends here
+;;; kpp.el ends here