Add config for scientific project report

config.org

@@ -12,6 +12,14 @@
       doom-serif-font (font-spec :family "Fira Code Nerd Font" :size 12 :weight 'light))
 #+end_src
 * UI
+#+begin_src emacs-lisp :tangle yes
+(setq confirm-kill-emacs nil)
+#+end_src
+** Expand initial Frame
+
+#+begin_src emacs-lisp :tangle yes
+(add-hook 'window-setup-hook 'toggle-frame-maximized t)
+#+end_src
 
 * Edition modes
 
@@ -50,9 +58,30 @@ Add custom LaTeX classes to ox-latex class.
                   ("\\subsection{%s}" . "\\subsection*{%s}")
                   ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                   ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+  (add-to-list 'org-latex-classes
+               '("scrreprt" "\\documentclass{scrreprt}"
+                  ("\\part{%s}" . "\\part*{%s}")
+                  ("\\chapter{%s}" . "\\chapter*{%s}")
+                  ("\\section{%s}" . "\\section*{%s}")
+                  ("\\subsection{%s}" . "\\subsection*{%s}")
+                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+  (add-to-list 'org-latex-classes
+               '("lamme2024" "\\documentclass{scrartcl}
+                [NO-DEFAULT-PACKAGES]
+                [NO-PACKAGES]
+                [EXTRA]
+                        "
+                  ("\\part{%s}" . "\\part*{%s}")
+                  ("\\section{%s}" . "\\section*{%s}")
+                  ("\\subsection{%s}" . "\\subsection*{%s}")
+                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                  ("\\subsubsubsection{%s}" . "\\subsubsubsection*{%s}")
+                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                   ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))))
 
-
 (eval-after-load "ox-latex"
   #'custom-latex-classes)
 #+end_src
@@ -82,17 +111,19 @@ Disable LateX preview in Org-mode by default
 *** Syntax highlighting in Org-mode
 
 #+begin_src emacs-lisp :tangle yes
-(setq org-highlight-latex-and-related '(latex script entities))
+; (setq org-highlight-latex-and-related '(latex script entities))
+(setq org-highlight-latex-and-related '(native))
+;; (add-hook 'org-mode-hook #'turn-on-org-cdlatex)
+
 #+end_src
 
 \(i \in \mathbf{N}\)
 
-** Expand initial Frame
+*** Proper indentation in algorithmic
-
 #+begin_src emacs-lisp :tangle yes
-(add-hook 'window-setup-hook 'toggle-frame-maximized t)
+(with-eval-after-load 'latex
+    (add-to-list 'LaTeX-indent-environment-list '("algorithmic" current-indentation)))
 #+end_src
-
 ** Enable conda environment in a Org-mode
 
 #+begin_src emacs-lisp :tangle no
@@ -102,7 +133,14 @@ Disable LateX preview in Org-mode by default
 ** Org-roam
 Set the roam directory
 #+begin_src emacs-lisp
-(setq org-roam-directory "~/sync/Documents/org/roam/")
+(setq org-roam-directory "~/Documents/org/roam/")
+#+end_src
+
+** =typst=
+#+begin_src emacs-lisp :tangle no
+(add-to-list 'treesit-language-source-alist
+             '(typst "https://github.com/uben0/tree-sitter-typst"))
+(treesit-install-language-grammar 'typst)
 #+end_src
 
 * Emacs Server & Emacs Client
@@ -154,7 +192,7 @@ systemctl --user enable --now emacs
   ;; (setq plantuml-default-exec-mode 'jar)
   (setq plantuml-executable-path "/usr/bin/plantuml")
   ;; setup plantuml for org-babel
-  (add-to-list 'org-src-lang-modes '("plantuml" . plantuml))
+  ;; (add-to-list 'org-src-lang-modes '("plantuml" . plantuml))
   (setq org-plantuml-exec-mode 'executable)
   (setq org-plantuml-executable-path plantuml-executable-path)
   ;; (require 'ob-plantuml) ; OBSOLETED
@@ -164,3 +202,43 @@ systemctl --user enable --now emacs
   (add-to-list 'auto-mode-alist '("\\.puml\\'" . plantuml-mode))
   (add-to-list 'auto-mode-alist '("\\.plantuml\\'" . plantuml-mode))
 #+end_src
+
+
+* Org-ref-acronyms
+
+#+begin_src emacs-lisp :tangle yes
+(after! org
+  (require 'org-ref)
+ (add-to-list 'org-latex-classes
+          '("scientific-project"
+             "\\documentclass{scrreprt}
+             [NO-DEFAULT-PACKAGES]
+             [EXTRA]
+                \\makeindex
+                \\makeglossaries          "
+
+;             ("\\part{%s}" . "\\part*{%s}")
+             ("\\chapter{%s}" . "\\chapter{%s}")
+             ("\\section{%s}" . "\\section*{%s}")
+             ("\\subsection{%s}" . "\\subsection*{%s}")
+             ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+             ("\\paragraph{%s}" . "\\paragraph*{%s}")
+             ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+                (add-hook 'org-export-before-parsing-hook #'org-ref-acronyms-before-parsing)
+                (add-hook 'org-export-before-parsing-hook #'org-ref-glossary-before-parsing))
+#+end_src
+
+#+RESULTS:
+| org-ref-glossary-before-parsing | org-ref-acronyms-before-parsing | org-attach-expand-links |
+| org-ref-glossary-before-parsing | org-ref-acronyms-before-parsing | org-attach-expand-links |
+
+#+begin_src emacs-lisp :tangle yes
+(after! org (org-add-link-type
+ "latex" nil
+ (lambda (path desc format)
+   (cond
+    ((eq format 'html)
+     (format "<span class=\"%s\">%s</span>" path desc))
+    ((eq format 'latex)
+     (format "\\%s{%s}" path desc))))))
+#+end_src

init.el

@@ -31,21 +31,21 @@
        ;;deft              ; notational velocity for Emacs
        doom              ; what makes DOOM look the way it does
        doom-dashboard    ; a nifty splash screen for Emacs
-       doom-quit         ; DOOM quit-message prompts when you quit Emacs
+       ;;doom-quit         ; DOOM quit-message prompts when you quit Emacs
        (emoji +unicode)  ; 🙂
        hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
        ;;hydra
        indent-guides     ; highlighted indent columns
-       ligatures         ; ligatures and symbols to make your code pretty again
+       ;;ligatures         ; ligatures and symbols to make your code pretty again
        ;;minimap           ; show a map of the code on the side
        modeline          ; snazzy, Atom-inspired modeline, plus API
        ;;nav-flash         ; blink cursor line after big motions
        ;;neotree           ; a project drawer, like NERDTree for vim
        ophints           ; highlight the region an operation acts on
        (popup +defaults)   ; tame sudden yet inevitable temporary windows
-       tabs              ; a tab bar for Emacs
+       ;;tabs              ; a tab bar for Emacs
        treemacs          ; a project drawer, like neotree but cooler
-       ;;unicode           ; extended unicode support for various languages
+       unicode           ; extended unicode support for various languages
        (vc-gutter +pretty) ; vcs diff in the fringe
        vi-tilde-fringe   ; fringe tildes to mark beyond EOB
        ;;window-select     ; visually switch windows
@@ -68,8 +68,8 @@
 
        :emacs
        dired             ; making dired pretty [functional]
-       electric          ; smarter, keyword-based electric-indent
+       ;;electric          ; smarter, keyword-based electric-indent
-       ibuffer         ; interactive buffer management
+       ;;ibuffer         ; interactive buffer management
        undo              ; persistent, smarter undo for your inevitable mistakes
        vc                ; version-control and Emacs, sitting in a tree
 
@@ -82,7 +82,7 @@
        :checkers
        syntax              ; tasing you for every semicolon you forget
        (spell +flyspell) ; tasing you for misspelling mispelling
-       grammar           ; tasing grammar mistake every you make
+       ;;grammar           ; tasing grammar mistake every you make
 
        :tools
        ;;ansible
@@ -92,7 +92,7 @@
        ;;direnv
        ;;docker
        editorconfig      ; let someone else argue about tabs vs spaces
-       ein               ; tame Jupyter notebooks with emacs
+       ;;ein               ; tame Jupyter notebooks with emacs
        (eval +overlay)     ; run code, run (also, repls)
        ;;gist              ; interacting with github gists
        lookup              ; navigate your code and its documentation
@@ -100,7 +100,7 @@
        magit             ; a git porcelain for Emacs
        ;;make              ; run make tasks from Emacs
        ;;pass              ; password manager for nerds
-       pdf               ; pdf enhancements
+       ;;pdf               ; pdf enhancements
        ;;prodigy           ; FIXME managing external services & code builders
        rgb               ; creating color strings
        ;;taskrunner        ; taskrunner for all your projects
@@ -116,7 +116,7 @@
        :lang
        ;;agda              ; types of types of types of types...
        ;;beancount         ; mind the GAAP
-       (cc +lsp)         ; C > C++ == 1
+       cc         ; C > C++ == 1
        ;;clojure           ; java with a lisp
        common-lisp       ; if you've seen one lisp, you've seen them all
        coq               ; proofs-as-programs
@@ -132,12 +132,12 @@
        ess               ; emacs speaks statistics
        ;;factor
        ;;faust             ; dsp, but you get to keep your soul
-       ;;fortran           ; in FORTRAN, GOD is REAL (unless declared INTEGER)
+       fortran           ; in FORTRAN, GOD is REAL (unless declared INTEGER)
        ;;fsharp            ; ML stands for Microsoft's Language
        ;;fstar             ; (dependent) types and (monadic) effects and Z3
        ;;gdscript          ; the language you waited for
        ;;(go +lsp)         ; the hipster dialect
-       ;;(graphql +lsp)    ; Give queries a REST
+       (graphql +lsp)    ; Give queries a REST
        (haskell +lsp)    ; a language that's lazier than I am
        ;;hy                ; readability of scheme w/ speed of python
        ;;idris             ; a language you can depend on
@@ -145,9 +145,9 @@
        (java +lsp)       ; the poster child for carpal tunnel syndrome
        javascript        ; all(hope(abandon(ye(who(enter(here))))))
        julia             ; a better, faster MATLAB
-       kotlin            ; a better, slicker Java(Script)
+       ;;kotlin            ; a better, slicker Java(Script)
        latex             ; writing papers in Emacs has never been so fun
-       lean              ; for folks with too much to prove
+       ;;lean              ; for folks with too much to prove
        ;;ledger            ; be audit you can be
        lua               ; one-based indices? one-based indices
        markdown          ; writing docs for people to ignore
@@ -156,7 +156,7 @@
        (ocaml +lsp)             ; an objective camel
        (org +roam2 +hugo +pandoc +brain)               ; organize your plain life in plain text
        php               ; perl's insecure younger brother
-       ;;plantuml          ; diagrams for confusing people more
+       plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
        python            ; beautiful is better than ugly
        ;;qt                ; the 'cutest' gui framework ever
@@ -164,7 +164,7 @@
        raku              ; the artist formerly known as perl6
        ;;rest              ; Emacs as a REST client
        rst               ; ReST in peace
-       ;;(ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
+       (ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
        (rust +lsp)       ; Fe2O3.unwrap().unwrap().unwrap().unwrap()
        scala             ; java, but good
        (scheme +guile)   ; a fully conniving family of lisps

packages.el

@@ -48,20 +48,24 @@
                                         ;(unpin! pinned-package another-pinned-package)
 ;; ...Or *all* packages (NOT RECOMMENDED; will likely break things)
                                         ;(unpin! t)
-
 ; (package! conda)
 
 (package! quarto-mode)
 
-(package! org-elp)
+;; (package! org-elp)
-
 
 (package! pasp-mode)
 
 (package! ob-pasp
-  :recipe (:host github :repo "UncleSamulus/ob-pasp"))
+  :recipe (:host github :repo "samuelortion/ob-pasp"))
 
-(package! ox-hugo)
+;; (package! ox-hugo)
 
 (package! groovy-mode)
 (package! nextflow-mode :recipe (:host github :repo "emiller88/nextflow-mode"))
+
+;; typst
+;;(package! typst-ts-mode :recipe
+;;  (:host sourcehut :repo "meow_king/typst-ts-mode"))
+
+(package! org-ref)